From 8cd63309471cb3887cdba410d3cc47436e42ea9d Mon Sep 17 00:00:00 2001
From: r614 <steradian614@gmail.com>
Date: Mon, 10 Jun 2019 15:46:12 -0700
Subject: [PATCH 01/18] Fixed Line Length bug

---
 .../java/org/biojava/nbio/structure/io/PDBFileParser.java     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
index eeac1912ab..06d2cc340a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -2002,7 +2002,7 @@ private void switchCAOnly(){
 
 	/** safes repeating a few lines ... */
 	private Integer conect_helper (String line,int start,int end) {
-		if (line.length() < end) return null;
+		if (line.length() < start || line.length() < end) return null;
 
 		String sbond = line.substring(start,end).trim();
 		int bond  = -1 ;
@@ -3651,4 +3651,4 @@ public FileParsingParameters getFileParsingParameters(){
 	}
 
 
-}
\ No newline at end of file
+}

From 312c2cb2b2c6970e4aa6f0db98650d10e6494b13 Mon Sep 17 00:00:00 2001
From: bagasfadhil <56031711+bagasfadhil@users.noreply.github.com>
Date: Tue, 1 Oct 2019 20:13:45 +0700
Subject: [PATCH 02/18] Update .gitattributes

---
 .gitattributes | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitattributes b/.gitattributes
index 196ded22fd..5228d268be 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,4 +1,5 @@
 # Set the default behavior, in case people don't have core.autocrlf set.
+# Set
 * text=auto
 
 # Explicitly declare text files you want to always be normalized and converted

From e7786fe6ea969c2590655d6b117dbd6dfccd1707 Mon Sep 17 00:00:00 2001
From: Jonathan Leitschuh <Jonathan.Leitschuh@gmail.com>
Date: Mon, 10 Feb 2020 23:15:18 -0500
Subject: [PATCH 03/18] Use HTTPS instead of HTTP to resolve dependencies

This fixes a security vulnerability in this project where the `pom.xml`
files were configuring Maven to resolve dependencies over HTTP instead of
HTTPS.

Signed-off-by: Jonathan Leitschuh <Jonathan.Leitschuh@gmail.com>
---
 biojava-genome/pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index bd67b30190..da492a3a6f 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -21,7 +21,7 @@
 		<repository>
 			<id>biojava-maven-repo</id>
 			<name>BioJava repository</name>
-			<url>http://www.biojava.org/download/maven/</url>
+			<url>https://www.biojava.org/download/maven/</url>
 			<snapshots>
 				<enabled>true</enabled>
 			</snapshots>

From e9ba77f9c57fe447292d7cbaf8ad6840d53e29ae Mon Sep 17 00:00:00 2001
From: me <seh@internet.earth>
Date: Sat, 7 Mar 2020 15:39:41 -0500
Subject: [PATCH 04/18] dependency upgrades (untested)

---
 biojava-structure-gui/pom.xml                      |  2 +-
 biojava-structure/pom.xml                          |  2 +-
 .../structure/io/mmcif/ZipChemCompProvider.java    |  5 +++--
 .../symmetry/internal/CeSymmIterative.java         |  2 +-
 .../internal/GraphComponentOrderDetector.java      |  2 +-
 .../symmetry/internal/GraphComponentRefiner.java   |  2 +-
 pom.xml                                            | 14 +++++++-------
 7 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index e6605344bc..8dfa407860 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -42,7 +42,7 @@
         <dependency>
             <groupId>net.sourceforge.jmol</groupId>
             <artifactId>jmol</artifactId>
-            <version>14.29.17</version>
+            <version>14.29.27</version>
         </dependency>
         <!-- logging dependencies (managed by parent pom, don't set versions or
             scopes here) -->
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 688984e845..78c0081f24 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.jgrapht</groupId>
   			<artifactId>jgrapht-core</artifactId>
-  			<version>1.1.0</version>
+  			<version>1.4.0</version>
 		</dependency>
 
 		<!-- JAXb explicit dependency is needed since Java 9. See https://stackoverflow.com/questions/43574426/how-to-resolve-java-lang-noclassdeffounderror-javax-xml-bind-jaxbexception-in-j
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
index ef7c984946..f06d294f78 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
@@ -33,6 +33,7 @@
 import java.nio.file.Paths;
 import java.nio.file.StandardCopyOption;
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
 import java.util.zip.GZIPInputStream;
 import java.util.zip.ZipEntry;
@@ -236,7 +237,7 @@ private synchronized ChemComp getFromZip(String recordName) {
 		final String filename = "chemcomp/" + recordName+".cif.gz";
 
 		// try with resources block to read from the filesystem.
-		try (FileSystem fs = FileSystems.newFileSystem(m_zipFile, null)) {
+		try (FileSystem fs = FileSystems.newFileSystem(m_zipFile, (ClassLoader)null)) {
 			Path cif = fs.getPath(filename);
 
 			if (Files.exists(cif)) {
@@ -293,7 +294,7 @@ private synchronized boolean addToZipFileSystem(Path zipFile, File[] files, Path
 		*/
 
 		// Copy in each file.
-		try (FileSystem zipfs = FileSystems.newFileSystem(zipFile, null)) {
+		try (FileSystem zipfs = FileSystems.newFileSystem(zipFile, (ClassLoader)null)) {
 			Files.createDirectories(pathWithinArchive);
 			for (File f : files) {
 				if (!f.isDirectory() && f.exists()) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
index c007319f6e..66df0f2658 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
@@ -45,7 +45,7 @@
 import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType;
 import org.biojava.nbio.structure.symmetry.utils.SymmetryTools;
 import org.jgrapht.Graph;
-import org.jgrapht.alg.ConnectivityInspector;
+import org.jgrapht.alg.connectivity.ConnectivityInspector;
 import org.jgrapht.graph.DefaultEdge;
 import org.jgrapht.graph.SimpleGraph;
 import org.slf4j.Logger;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java
index f6accbfb96..822e62a8c2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java
@@ -29,7 +29,7 @@
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.symmetry.utils.SymmetryTools;
 import org.jgrapht.Graph;
-import org.jgrapht.alg.ConnectivityInspector;
+import org.jgrapht.alg.connectivity.ConnectivityInspector;
 import org.jgrapht.graph.DefaultEdge;
 
 /**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java
index 375d0dd61b..6c7d44f6a7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java
@@ -35,7 +35,7 @@
 import org.biojava.nbio.structure.align.util.AlignmentTools;
 import org.biojava.nbio.structure.symmetry.utils.SymmetryTools;
 import org.jgrapht.Graph;
-import org.jgrapht.alg.ConnectivityInspector;
+import org.jgrapht.alg.connectivity.ConnectivityInspector;
 import org.jgrapht.graph.DefaultEdge;
 
 /**
diff --git a/pom.xml b/pom.xml
index 9ff4c461ee..13cecbdb8a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -39,10 +39,10 @@
 		<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
 		<!-- needed for failsafe plugin in integrationtest module - JD 2018-03-08 -->
     	<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-		<maxmem>512M</maxmem>
+		<maxmem>1024M</maxmem>
 		<mmtf.version>1.0.9</mmtf.version>
-		<slf4j.version>1.7.25</slf4j.version>
-		<log4j.version>2.6.2</log4j.version>
+		<slf4j.version>2.0.0-alpha1</slf4j.version>
+		<log4j.version>2.13.1</log4j.version>
 	</properties>
 	<scm>
 		<connection>scm:git:git://github.com/biojava/biojava.git</connection>
@@ -474,7 +474,7 @@
 			<dependency>
 				<groupId>junit</groupId>
 				<artifactId>junit</artifactId>
-				<version>4.12</version>
+				<version>4.13</version>
 				<scope>test</scope>
 			</dependency>
 			<dependency>
@@ -513,17 +513,17 @@
 			<dependency>
 			    <groupId>javax.xml.bind</groupId>
 			    <artifactId>jaxb-api</artifactId>
-			    <version>2.3.0</version>
+			    <version>2.4.0-b180830.0359</version>
 			</dependency>
 			<dependency>
 				<groupId>com.sun.xml.bind</groupId>
 				<artifactId>jaxb-core</artifactId>
-				<version>2.3.0</version>
+				<version>2.3.0.1</version>
 			</dependency>
 			<dependency>
 				<groupId>com.sun.xml.bind</groupId>
 				<artifactId>jaxb-impl</artifactId>
-				<version>2.3.0</version>
+				<version>2.3.3-b02</version>
 			</dependency>
 			<dependency>
 				<groupId>javax.activation</groupId>

From 8f22e0e84051675f41035bed4bb4bb7120b80412 Mon Sep 17 00:00:00 2001
From: me <seh@internet.earth>
Date: Sat, 7 Mar 2020 16:08:24 -0500
Subject: [PATCH 05/18] automated IDE cleanups and some possible bug fixes

---
 .../nbio/aaproperties/CommandPrompt.java      |  29 +-
 .../nbio/aaproperties/Constraints.java        |  18 +-
 .../nbio/aaproperties/IPeptideProperties.java |  36 +-
 .../nbio/aaproperties/PeptideProperties.java  |  14 +-
 .../aaproperties/PeptidePropertiesImpl.java   |  18 +-
 .../org/biojava/nbio/aaproperties/Utils.java  |   4 +-
 .../profeat/IProfeatProperties.java           |  31 +-
 .../profeat/ProfeatPropertiesImpl.java        |  15 +-
 .../profeat/convertor/Convert2Charge.java     |   2 +-
 .../convertor/Convert2Hydrophobicity.java     |   2 +-
 .../Convert2NormalizedVanDerWaalsVolume.java  |   2 +-
 .../profeat/convertor/Convert2Polarity.java   |   2 +-
 .../convertor/Convert2Polarizability.java     |   2 +-
 .../convertor/Convert2SecondaryStructure.java |   2 +-
 .../Convert2SolventAccessibility.java         |   2 +-
 .../xml/AminoAcidCompositionTable.java        |   4 +-
 .../xml/CaseFreeAminoAcidCompoundSet.java     |  22 +-
 .../nbio/aaproperties/xml/Element.java        |   2 +-
 .../nbio/aaproperties/xml/ElementTable.java   |   4 +-
 .../xml/ModifiedAminoAcidCompoundSet.java     |   4 +-
 .../aaproperties/xml/SchemaGenerator.java     |   2 +-
 .../nbio/aaproperties/CookBookTest.java       |   4 +-
 .../GenbankCommandPromptTest.java             |  12 +-
 .../PeptidePropertiesImplTest.java            |   2 +-
 .../aaproperties/profeat/CookBookTest.java    |  36 +-
 .../nbio/aaproperties/xml/AminoAcidTest.java  |  42 +-
 .../nbio/aaproperties/xml/ElementTest.java    | 166 ++---
 .../xml/GenerateJavaCodesFromTextTest.java    |   6 +-
 .../src/main/java/demo/CookbookMSA.java       |   2 +-
 .../src/main/java/demo/DemoDistanceTree.java  |  12 +-
 .../biojava/nbio/alignment/Alignments.java    |  54 +-
 .../FractionalIdentityInProfileScorer.java    |   4 +-
 .../alignment/FractionalIdentityScorer.java   |   3 +-
 .../FractionalSimilarityInProfileScorer.java  |   4 +-
 .../alignment/FractionalSimilarityScorer.java |   3 +-
 .../org/biojava/nbio/alignment/GuideTree.java |  29 +-
 .../SimpleProfileProfileAligner.java          |   2 +-
 .../biojava/nbio/alignment/SmithWaterman.java |   2 +-
 .../alignment/StandardRescoreRefiner.java     |   4 +-
 .../alignment/SubstitutionMatrixScorer.java   |   4 +-
 .../alignment/io/StockholmFileAnnotation.java |   8 +-
 .../alignment/io/StockholmFileParser.java     | 349 ++++++-----
 .../io/StockholmSequenceAnnotation.java       |   2 +-
 .../nbio/alignment/io/StockholmStructure.java |  21 +-
 .../alignment/routines/AlignerHelper.java     |  23 +-
 .../AnchoredPairwiseSequenceAligner.java      |   9 +-
 .../alignment/routines/GuanUberbacher.java    |   2 +-
 .../template/AbstractMatrixAligner.java       |   8 +-
 .../AbstractPairwiseSequenceAligner.java      |   6 +-
 .../AbstractProfileProfileAligner.java        |   6 +-
 .../CallablePairwiseSequenceAligner.java      |   2 +-
 .../CallablePairwiseSequenceScorer.java       |   2 +-
 .../CallableProfileProfileAligner.java        |   2 +-
 .../nbio/alignment/template/GapPenalty.java   |   4 +-
 .../org/biojava/nbio/phylo/Comparison.java    |   2 +-
 .../nbio/phylo/DistanceTreeEvaluator.java     |   4 +-
 .../biojava/nbio/phylo/ForesterWrapper.java   |   9 +-
 .../nbio/phylo/TreeConstructorType.java       |   2 +-
 .../java/org/biojava/nbio/phylo/TreeType.java |   2 +-
 .../alignment/CookbookAlignAllGlobal.java     |   2 +-
 .../nbio/alignment/CookbookAlignAllLocal.java |   2 +-
 .../biojava/nbio/alignment/CookbookMSA.java   |   2 +-
 .../nbio/alignment/CookbookMSAProfiler.java   |   4 +-
 .../FractionalIdentityScorerTest.java         |  12 +-
 .../FractionalSimilarityScorerTest.java       |  12 +-
 .../biojava/nbio/alignment/GuideTreeTest.java |  17 +-
 .../nbio/alignment/NeedlemanWunschTest.java   |  26 +-
 .../nbio/alignment/SimpleProfilePairTest.java |  19 +-
 .../SimpleProfileProfileAlignerTest.java      |  16 +-
 .../SimpleSubstitutionMatrixTest.java         |  12 +-
 .../nbio/alignment/SmithWatermanTest.java     |   6 +-
 .../nbio/alignment/TestDNAAlignment.java      |  13 +-
 .../nbio/alignment/TestSubOptimalMSA.java     |   2 +-
 .../alignment/aaindex/TestAAINDEXLoading.java |   2 +-
 .../alignment/io/TestStockholmParser.java     |   4 +-
 .../alignment/routines/AlignerHelperTest.java |  23 +-
 .../routines/GuanUberbacherTest.java          |  12 +-
 .../nbio/phylo/TestDistanceTreeEvaluator.java |   6 +-
 .../nbio/phylo/TestForesterWrapper.java       |  23 +-
 .../java/demo/DemoSixFrameTranslation.java    |   4 +-
 .../main/java/demo/ParseFastaFileDemo.java    |  10 +-
 .../core/alignment/SimpleAlignedSequence.java |  13 +-
 .../nbio/core/alignment/SimpleProfile.java    |  43 +-
 .../core/alignment/SimpleProfilePair.java     |   3 +-
 .../alignment/matrices/AAIndexFileParser.java |  14 +-
 .../alignment/matrices/AAIndexProvider.java   |   2 +-
 .../matrices/ScaledSubstitutionMatrix.java    |  10 +-
 .../matrices/SimpleSubstitutionMatrix.java    |  23 +-
 .../matrices/SubstitutionMatrixHelper.java    |  12 +-
 .../org/biojava/nbio/core/search/io/Hit.java  |   5 +-
 .../org/biojava/nbio/core/search/io/Hsp.java  |  52 +-
 .../biojava/nbio/core/search/io/Result.java   |  36 +-
 .../nbio/core/search/io/ResultFactory.java    |   2 +-
 .../biojava/nbio/core/search/io/SearchIO.java |   4 +-
 .../search/io/blast/BlastTabularParser.java   |  14 +-
 .../core/search/io/blast/BlastXMLParser.java  |  16 +-
 .../nbio/core/sequence/AccessionID.java       |   2 +-
 .../nbio/core/sequence/CDSSequence.java       |   2 +-
 .../core/sequence/ChromosomeSequence.java     |   2 +-
 .../nbio/core/sequence/DNASequence.java       |   6 +-
 .../nbio/core/sequence/GeneSequence.java      |  14 +-
 .../sequence/MultipleSequenceAlignment.java   |   4 +-
 .../nbio/core/sequence/ProteinSequence.java   |   8 +-
 .../nbio/core/sequence/RNASequence.java       |   6 +-
 .../sequence/SequenceOptimizationHints.java   |   8 +-
 .../core/sequence/StartCodonSequence.java     |   2 +-
 .../nbio/core/sequence/StopCodonSequence.java |   2 +-
 .../biojava/nbio/core/sequence/Strand.java    |   2 +-
 .../nbio/core/sequence/TaxonomyID.java        |   4 +-
 .../core/sequence/TranscriptSequence.java     |  18 +-
 .../compound/AminoAcidCompoundSet.java        |  23 +-
 .../sequence/compound/NucleotideCompound.java |   5 +-
 .../nbio/core/sequence/edits/Edit.java        |  20 +-
 .../sequence/features/AbstractFeature.java    |  76 +--
 .../sequence/features/DBReferenceInfo.java    |   6 +-
 .../features/DatabaseReferenceInterface.java  |   2 +-
 .../features/FeatureDbReferenceInfo.java      |   8 +-
 .../sequence/features/FeatureInterface.java   |  38 +-
 .../features/FeaturesKeyWordInterface.java    |   2 +-
 .../sequence/features/QualityFeature.java     |   2 +-
 .../sequence/features/QuantityFeature.java    |   2 +-
 .../nbio/core/sequence/io/ABITrace.java       |  64 +-
 .../sequence/io/BufferedReaderBytesRead.java  |  14 +-
 .../CasePreservingProteinSequenceCreator.java |   4 +-
 .../core/sequence/io/DNASequenceCreator.java  |   2 +-
 .../core/sequence/io/FastaGeneWriter.java     |  14 +-
 .../nbio/core/sequence/io/FastaReader.java    |  15 +-
 .../core/sequence/io/FastaReaderHelper.java   |  28 +-
 .../nbio/core/sequence/io/FastaWriter.java    |   6 +-
 .../core/sequence/io/FastaWriterHelper.java   |  26 +-
 .../io/FileProxyDNASequenceCreator.java       |   6 +-
 .../io/FileProxyProteinSequenceCreator.java   |   4 +-
 .../io/FileProxyRNASequenceCreator.java       |   6 +-
 .../nbio/core/sequence/io/GenbankReader.java  |   6 +-
 .../core/sequence/io/GenbankReaderHelper.java |  36 +-
 .../sequence/io/GenbankSequenceParser.java    | 330 +++++-----
 .../nbio/core/sequence/io/GenbankWriter.java  |   2 +-
 .../core/sequence/io/GenbankWriterHelper.java |  22 +-
 .../sequence/io/GenericFastaHeaderParser.java |  10 +-
 .../io/GenericGenbankHeaderFormat.java        |   6 +-
 .../io/GenericGenbankHeaderParser.java        |   4 +-
 .../sequence/io/GenericInsdcHeaderFormat.java |  10 +-
 .../nbio/core/sequence/io/IUPACParser.java    |  52 +-
 .../sequence/io/ProteinSequenceCreator.java   |   4 +-
 .../core/sequence/io/RNASequenceCreator.java  |   2 +-
 .../core/sequence/io/embl/EmblReader.java     |  46 +-
 .../template/FastaHeaderFormatInterface.java  |   2 +-
 .../GenbankHeaderFormatInterface.java         |   4 +-
 .../io/template/SequenceCreatorInterface.java |   6 +-
 .../SequenceHeaderParserInterface.java        |   2 +-
 .../io/template/SequenceParserInterface.java  |   2 +-
 .../nbio/core/sequence/io/util/IOUtils.java   |  21 +-
 .../loader/GenbankProxySequenceReader.java    |  28 +-
 .../loader/SequenceFileProxyLoader.java       |  13 +-
 .../loader/StringProxySequenceReader.java     |   9 +-
 .../loader/UniprotProxySequenceReader.java    |  41 +-
 .../core/sequence/location/FuzzyPoint.java    |  21 +-
 .../core/sequence/location/InsdcParser.java   |  13 +-
 .../sequence/location/LocationHelper.java     |  24 +-
 .../sequence/location/SimpleLocation.java     |   2 +-
 .../location/template/AbstractLocation.java   |  16 +-
 .../sequence/location/template/Location.java  |  28 +-
 .../sequence/location/template/Point.java     |   2 +-
 .../storage/ArrayListSequenceReader.java      |  26 +-
 .../sequence/storage/BitSequenceReader.java   |   5 +-
 .../storage/FourBitSequenceReader.java        |  29 +-
 .../storage/JoiningSequenceReader.java        |   9 +-
 .../storage/SingleCompoundSequenceReader.java |   9 +-
 .../storage/TwoBitSequenceReader.java         |   6 +-
 .../template/AbstractCompoundSet.java         |  17 +-
 .../template/AbstractCompoundTranslator.java  |  25 +-
 .../AbstractNucleotideCompoundSet.java        |  21 +-
 .../sequence/template/AbstractSequence.java   |  43 +-
 .../sequence/template/ComplementCompound.java |   2 +-
 .../nbio/core/sequence/template/Compound.java |  18 +-
 .../core/sequence/template/CompoundSet.java   |  18 +-
 .../nbio/core/sequence/template/Sequence.java |  20 +-
 .../core/sequence/template/SequenceMixin.java |  29 +-
 .../sequence/template/SequenceProxyView.java  |   7 +-
 .../sequence/template/SequenceReader.java     |   4 +-
 .../core/sequence/template/SequenceView.java  |   6 +-
 .../transcription/DNAToRNATranslator.java     |   2 +-
 .../core/sequence/transcription/Frame.java    |   4 +-
 .../RNAToAminoAcidTranslator.java             |  18 +-
 .../core/sequence/transcription/Table.java    |   6 +-
 .../transcription/TranscriptionEngine.java    |   2 +-
 .../core/sequence/views/RnaSequenceView.java  |   8 +-
 .../core/sequence/views/WindowedSequence.java |   2 +-
 .../biojava/nbio/core/util/CRC64Checksum.java |   2 +-
 .../nbio/core/util/ConcurrencyTools.java      |   2 +-
 .../nbio/core/util/FileDownloadUtils.java     |  27 +-
 .../biojava/nbio/core/util/FlatFileCache.java |   4 +-
 .../nbio/core/util/InputStreamProvider.java   |   8 +-
 .../nbio/core/util/PrettyXMLWriter.java       |  33 +-
 .../core/util/SingleLinkageClusterer.java     |  48 +-
 .../biojava/nbio/core/util/SoftHashMap.java   |   8 +-
 .../core/util/StringManipulationHelper.java   |  16 +-
 .../nbio/core/util/UncompressInputStream.java |   4 +-
 .../org/biojava/nbio/core/util/XMLHelper.java |   6 +-
 .../org/biojava/nbio/core/util/XMLWriter.java |  22 +-
 .../nbio/core/TestAmbiguityCompoundSet.java   |   1 -
 .../alignment/SimpleAlignedSequenceTest.java  |  23 +-
 .../core/alignment/SimpleProfileTest.java     |  17 +-
 .../alignment/SimpleSequencePairTest.java     |   9 +-
 .../nbio/core/fasta/TestFASTAReader.java      |  12 +-
 .../io/blast/BlastTabularParserTest.java      |   6 +-
 .../search/io/blast/BlastXMLParserTest.java   |   6 +-
 .../biojava/nbio/core/sequence/DNATest.java   |  26 +-
 .../sequence/JoiningSequenceReaderTest.java   |  26 +-
 .../MultipleSequenceAlignmentTest.java        |   8 +-
 .../core/sequence/TestSequenceEquals.java     |  12 +-
 .../nbio/core/sequence/TranslationTest.java   |  24 +-
 .../compound/AmbiguityDNACompoundTest.java    |   4 +-
 .../nbio/core/sequence/io/ABITracerTest.java  |  12 +-
 .../core/sequence/io/FastaReaderTest.java     |  32 +-
 .../core/sequence/io/GenbankCookbookTest.java |  16 +-
 .../core/sequence/io/GenbankReaderTest.java   |  12 +-
 .../core/sequence/io/GenbankWriterTest.java   |   6 +-
 .../io/GenericFastaHeaderParserTest.java      |   8 +-
 .../GenbankProxySequenceReaderTest.java       |   6 +-
 .../SimpleGenbankProxySequenceReaderTest.java |   6 +-
 .../sequence/location/InsdcParserTest.java    |   9 +-
 .../sequence/location/LocationParserTest.java |   2 +-
 .../location/TargetedLocationParserTest.java  |  10 +-
 .../core/sequence/views/WindowViewTests.java  |   6 +-
 .../core/util/TestUncompressInputStream.java  |   2 +-
 .../nbio/genome/GeneFeatureHelper.java        |  41 +-
 .../genome/homology/BlastHomologyHits.java    |   9 +-
 .../homology/GFF3FromUniprotBlastHits.java    |  22 +-
 .../genome/io/fastq/AbstractFastqReader.java  |   3 +-
 .../genome/io/fastq/AbstractFastqWriter.java  |  26 +-
 .../nbio/genome/io/fastq/FastqParser.java     |  10 +-
 .../nbio/genome/io/fastq/FastqTools.java      |   4 +-
 .../nbio/genome/io/fastq/FastqVariant.java    |   4 +-
 .../nbio/genome/io/fastq/ParseListener.java   |  15 +-
 .../genome/io/fastq/StreamingFastqParser.java |   9 +-
 .../parsers/cytoband/CytobandParser.java      |   9 +-
 .../parsers/geneid/GeneIDXMLReader.java       |   6 +-
 .../GeneChromosomePositionParser.java         |   6 +-
 .../parsers/genename/GeneNamesParser.java     |   2 +-
 .../nbio/genome/parsers/gff/Feature.java      |  22 +-
 .../genome/parsers/gff/FeatureHelper.java     |   2 +-
 .../nbio/genome/parsers/gff/FeatureI.java     |  20 +-
 .../nbio/genome/parsers/gff/FeatureList.java  |  21 +-
 .../nbio/genome/parsers/gff/GFF3Reader.java   |   4 +-
 .../nbio/genome/parsers/gff/GFF3Writer.java   |  12 +-
 .../genome/parsers/gff/GeneIDGFF2Reader.java  |  13 +-
 .../genome/parsers/gff/GeneMarkGTFReader.java |   6 +-
 .../nbio/genome/parsers/gff/LocIterator.java  |   6 +-
 .../nbio/genome/parsers/gff/Location.java     |  22 +-
 .../genome/parsers/twobit/TwoBitFacade.java   |   2 +-
 .../genome/parsers/twobit/TwoBitParser.java   |  16 +-
 .../nbio/genome/query/BlastXMLQuery.java      |  10 +-
 .../nbio/genome/uniprot/UniprotToFasta.java   |   6 +-
 .../genome/util/ChromosomeMappingTools.java   |  18 +-
 .../nbio/genome/util/ProteinMappingTools.java |   2 +-
 .../biojava/nbio/genome/util/SplitFasta.java  |   6 +-
 .../biojava/nbio/genome/FeatureListTest.java  |   3 +-
 .../nbio/genome/GeneFeatureHelperTest.java    |   4 +-
 .../nbio/genome/TestGenomeMapping.java        |  56 +-
 .../org/biojava/nbio/genome/TestLocation.java |   8 +-
 .../io/fastq/AbstractFastqReaderTest.java     |  56 +-
 .../io/fastq/AbstractFastqWriterTest.java     |  10 +-
 .../nbio/genome/io/fastq/ConvertTest.java     |   2 +-
 .../genome/io/fastq/FastqBuilderTest.java     |   4 +-
 .../nbio/genome/io/fastq/FastqTest.java       |  26 +-
 .../nbio/genome/io/fastq/FastqToolsTest.java  |   4 +-
 .../genome/io/fastq/FastqVariantTest.java     |   6 +-
 .../io/fastq/IlluminaFastqReaderTest.java     |   6 +-
 .../io/fastq/SangerFastqReaderTest.java       |   6 +-
 .../io/fastq/SolexaFastqReaderTest.java       |   6 +-
 .../io/fastq/StreamingFastqParserTest.java    |  14 +-
 .../nbio/structure/test/MMcifTest.java        |   2 +-
 .../structure/test/PDBFileParserTest.java     |  22 +-
 .../nbio/structure/test/StructureTest.java    |  26 +-
 .../biojava/nbio/structure/test/Test1a4w.java |  26 +-
 .../test/align/AlignmentToolsTest.java        |  40 +-
 .../test/align/FlipAFPChainTest.java          |   7 +-
 .../test/align/TestSimilarityCalc.java        |  12 +-
 .../test/align/ce/OptimalCECPMainTest.java    |  12 +-
 .../fatcat/AFPChainSerialisationTest.java     |  34 +-
 .../test/align/fatcat/FlipAFPChainTest.java   |   9 +-
 .../test/align/fatcat/MyTestHelper.java       |   2 +-
 .../fatcat/TestFlexibleRotationMatrices.java  |  26 +-
 .../test/align/fatcat/TestOutputStrings.java  |  64 +-
 .../test/ecod/EcodInstallationTest.java       |  20 +-
 .../structure/test/ecod/EcodParseTest.java    |  24 +-
 .../structure/test/io/LoadOldXMLfileTest.java |   2 +-
 .../structure/test/io/TestBioassemblies.java  |   4 +-
 .../test/io/TestLongPdbVsMmCifParsing.java    |  21 +-
 .../scop/BerkeleyScopInstallationTest.java    |   2 +-
 .../test/scop/RemoteScopInstallationTest.java |   2 +-
 .../structure/test/scop/ScopDatabaseTest.java |   2 +-
 .../test/scop/ScopInstallationTest.java       |   2 +-
 .../nbio/structure/test/scop/ScopTest.java    |  12 +-
 .../TestQuatSymmetryDetectorExamples.java     |   2 +-
 .../org/biojava/nbio/phosphosite/Dataset.java |   6 +-
 .../org/biojava/nbio/phosphosite/Site.java    |  16 +-
 .../org/biojava/nbio/protmod/Component.java   |   8 +-
 .../nbio/protmod/ModificationCategory.java    |   6 +-
 .../nbio/protmod/ModificationCondition.java   |   4 +-
 .../protmod/ModificationConditionImpl.java    |   2 +-
 .../protmod/ModificationOccurrenceType.java   |   6 +-
 .../nbio/protmod/ProteinModification.java     |  28 +-
 .../nbio/protmod/ProteinModificationImpl.java |   6 +-
 .../protmod/ProteinModificationRegistry.java  |  56 +-
 .../protmod/io/ComponentXMLConverter.java     |   6 +-
 .../io/ModifiedCompoundXMLConverter.java      |  56 +-
 .../io/ProteinModificationXmlReader.java      |  34 +-
 .../io/StructureGroupXMLConverter.java        |   6 +-
 .../protmod/structure/ModifiedCompound.java   |  24 +-
 .../structure/ModifiedCompoundImpl.java       |  18 +-
 .../ProteinModificationIdentifier.java        |  66 +-
 .../nbio/protmod/structure/StructureUtil.java |   8 +-
 .../protmod/phosphosite/TestAcetylation.java  |   5 +-
 .../ModifiedCompoundSerializationTest.java    |   5 +-
 .../ProteinModificationParserTest.java        |   2 +-
 .../ProteinModificationRegistryTest.java      |   2 +-
 .../src/main/java/demo/ParseGO.java           |   8 +-
 .../nbio/ontology/IntegerOntology.java        |  14 +-
 .../org/biojava/nbio/ontology/OntoTools.java  |   8 +-
 .../org/biojava/nbio/ontology/Ontology.java   |  70 +--
 .../nbio/ontology/OntologyFactory.java        |   5 +-
 .../biojava/nbio/ontology/OntologyOps.java    |   2 +-
 .../biojava/nbio/ontology/OntologyTerm.java   |   6 +-
 .../org/biojava/nbio/ontology/RemoteTerm.java |   6 +-
 .../org/biojava/nbio/ontology/Synonym.java    |   7 +-
 .../java/org/biojava/nbio/ontology/Term.java  |  18 +-
 .../org/biojava/nbio/ontology/Triple.java     |  16 +-
 .../org/biojava/nbio/ontology/Variable.java   |   2 +-
 .../biojava/nbio/ontology/io/GOParser.java    |   6 +-
 .../biojava/nbio/ontology/io/OboParser.java   |  22 +-
 .../nbio/ontology/io/TabDelimParser.java      |   2 +-
 .../ontology/obo/OboFileEventListener.java    |  12 +-
 .../nbio/ontology/obo/OboFileHandler.java     | 106 ++--
 .../nbio/ontology/obo/OboFileParser.java      | 136 ++---
 .../ontology/utils/AbstractAnnotation.java    |   2 +-
 .../nbio/ontology/utils/Annotation.java       |   4 +-
 .../ontology/utils/KeyedWeakReference.java    |   2 +-
 .../biojava/nbio/ontology/utils/SmallMap.java |   2 +-
 .../nbio/ontology/utils/WeakValueHashMap.java |  10 +-
 .../nbio/ontology/TestOboFileParsing.java     |  34 +-
 .../src/main/java/demo/PredictDisorder.java   |   2 +-
 .../nbio/data/sequence/SequenceUtil.java      |   5 +-
 .../java/org/biojava/nbio/ronn/Jronn.java     |  18 +-
 .../org/biojava/nbio/ronn/ModelLoader.java    |   9 +-
 .../biojava/nbio/ronn/NullOutputStream.java   |   2 +-
 .../java/org/biojava/nbio/ronn/ORonn.java     |  16 +-
 .../org/biojava/nbio/ronn/ORonnModel.java     |   2 +-
 .../org/biojava/nbio/ronn/RonnConstraint.java |   4 +-
 .../java/org/biojava/nbio/ronn/JronnTest.java |   2 +-
 .../ronn/NonstandardProteinCompoundTest.java  |   2 +-
 .../src/main/java/demo/AFPFromFasta.java      |   2 +-
 .../java/demo/DemoAlignmentFromFasta.java     |  17 +-
 .../src/main/java/demo/DemoCE.java            |   4 +-
 .../src/main/java/demo/DemoFATCAT.java        |   4 +-
 .../src/main/java/demo/DemoMultipleMC.java    |   6 +-
 .../src/main/java/demo/DemoRotationAxis.java  |   6 +-
 .../src/main/java/demo/DemoSW3DAligner.java   |   4 +-
 .../main/java/demo/DemoShowLargeAssembly.java |   2 +-
 .../java/demo/DemoShowValidationResults.java  |   4 +-
 .../java/demo/DemoStructureFromFasta.java     |  17 +-
 .../nbio/structure/align/gui/AboutDialog.java |  43 +-
 .../structure/align/gui/AlignmentCalcDB.java  |   2 +-
 .../gui/AlignmentCalculationRunnable.java     |   6 +-
 .../structure/align/gui/AlignmentGui.java     |  24 +-
 .../structure/align/gui/ChooseDirAction.java  |   2 +-
 .../align/gui/ConfigPDBInstallPanel.java      |  18 +-
 .../structure/align/gui/DBResultTable.java    |  12 +-
 .../nbio/structure/align/gui/DBSearchGUI.java |  60 +-
 .../nbio/structure/align/gui/DisplayAFP.java  |  26 +-
 .../structure/align/gui/DotPlotPanel.java     |   6 +-
 .../gui/GUIAlignmentProgressListener.java     |   4 +-
 .../align/gui/GUIFarmJobRunnable.java         |   7 +-
 .../nbio/structure/align/gui/HelpDialog.java  |  49 +-
 .../nbio/structure/align/gui/JPrintPanel.java |   2 +-
 .../structure/align/gui/MemoryMonitor.java    |  32 +-
 .../nbio/structure/align/gui/MenuCreator.java | 142 ++---
 .../align/gui/MultipleAlignmentCalc.java      |   2 +-
 .../align/gui/MultipleAlignmentGUI.java       |  20 +-
 .../gui/MultipleAlignmentJmolDisplay.java     |   6 +-
 .../align/gui/MyAlignmentLoadListener.java    |   2 +-
 .../align/gui/MySaveFileListener.java         |   4 +-
 .../structure/align/gui/ParameterGUI.java     |  35 +-
 .../align/gui/StructureLoaderThread.java      |  48 +-
 .../nbio/structure/align/gui/SystemInfo.java  |  47 +-
 .../align/gui/aligpanel/AligPanel.java        |  74 ++-
 .../AligPanelMouseMotionListener.java         |   2 +-
 .../gui/aligpanel/MultipleAligPanel.java      |  72 ++-
 .../MultipleAligPanelMouseMotionListener.java |   4 +-
 .../MultipleAlignmentCoordManager.java        |   4 +-
 .../gui/autosuggest/AutoSuggestProvider.java  |  10 +-
 .../DefaultAutoSuggestProvider.java           |   2 +-
 .../align/gui/autosuggest/JAutoSuggest.java   |   4 +-
 .../autosuggest/SCOPAutoSuggestProvider.java  |   6 +-
 .../structure/align/gui/jmol/AtomInfo.java    |  10 +-
 .../align/gui/jmol/AtomInfoParser.java        |   6 +-
 .../structure/align/gui/jmol/JmolPanel.java   | 184 +++---
 .../structure/align/gui/jmol/JmolTools.java   |   4 +-
 .../align/gui/jmol/MultipleAlignmentJmol.java | 190 +++---
 .../align/gui/jmol/RasmolCommandListener.java |  14 +-
 .../gui/jmol/StructureAlignmentJmol.java      | 150 +++--
 .../structure/align/webstart/JNLPProxy.java   |   8 +-
 .../align/webstart/WebStartMain.java          |  15 +-
 .../nbio/structure/gui/BiojavaJmol.java       |  30 +-
 .../nbio/structure/gui/JmolViewerImpl.java    |  20 +-
 .../structure/gui/ScaleableMatrixPanel.java   |   5 +-
 .../biojava/nbio/structure/gui/Selection.java |   6 +-
 .../nbio/structure/gui/SequenceDisplay.java   |   6 +-
 .../nbio/structure/gui/StructureViewer.java   |  18 +-
 .../gui/events/AlignmentPositionListener.java |  12 +-
 .../events/JmolAlignedPositionListener.java   |   4 +-
 .../gui/util/AlternativeAlignmentFrame.java   |  16 +-
 .../gui/util/JButtonTableCellRenderer.java    |   2 +-
 .../gui/util/JTableDataButtonModel.java       |   2 +-
 .../gui/util/JTableMouseButtonListener.java   |   2 +-
 .../nbio/structure/gui/util/MenuCreator.java  |  91 ++-
 .../nbio/structure/gui/util/PDBDirPanel.java  |   2 +-
 .../structure/gui/util/PDBUploadPanel.java    |   8 +-
 .../structure/gui/util/ScopSelectPanel.java   |   2 +-
 .../gui/util/SelectMultiplePanel.java         |   6 +-
 .../gui/util/SequenceMouseListener.java       |   2 +-
 .../gui/util/SequenceScalePanel.java          |  10 +-
 .../gui/util/StructurePairSelector.java       |   4 +-
 .../gui/util/color/ColorInterpolator.java     |   2 +-
 .../gui/util/color/ContinuousColorMapper.java |   2 +-
 .../gui/util/color/DefaultMatrixMapper.java   |   2 +-
 .../gui/util/color/GradientMapper.java        |   4 +-
 .../gui/util/color/GradientPanel.java         |   5 +-
 .../util/color/LinearColorInterpolator.java   |   4 +-
 .../gui/util/color/LogColorMapper.java        |   2 +-
 .../symmetry/gui/SymmetryDisplay.java         |   6 +-
 .../structure/symmetry/gui/SymmetryGui.java   |  27 +-
 .../symmetry/gui/SymmetryListener.java        |  59 +-
 .../JmolSymmetryScriptGeneratorH.java         |  36 +-
 ...JmolSymmetryScriptGeneratorPointGroup.java |  77 +--
 .../structure/gui/JmolViewerImplTest.java     |   4 +-
 .../nbio/structure/gui/RenderStyleTest.java   |   4 +-
 .../structure/gui/StructureViewerTest.java    |   6 +-
 .../nbio/structure/gui/TestAtomInfo.java      |   2 +-
 .../src/main/java/demo/DemoCE.java            |   6 +-
 .../src/main/java/demo/DemoFATCAT.java        |   4 +-
 .../src/main/java/demo/DemoMmtfReader.java    |   5 +-
 .../src/main/java/demo/DemoMultipleMC.java    |   6 +-
 .../org/biojava/nbio/structure/AminoAcid.java |  22 +-
 .../java/org/biojava/nbio/structure/Atom.java |  60 +-
 .../biojava/nbio/structure/AtomIterator.java  |   2 +-
 .../nbio/structure/AtomPositionMap.java       |  62 +-
 .../org/biojava/nbio/structure/Author.java    |   5 +-
 .../nbio/structure/BioAssemblyIdentifier.java |  10 +-
 .../java/org/biojava/nbio/structure/Bond.java |  10 +-
 .../org/biojava/nbio/structure/BondImpl.java  |   8 +-
 .../org/biojava/nbio/structure/BondType.java  |   2 +-
 .../java/org/biojava/nbio/structure/Calc.java |  25 +-
 .../org/biojava/nbio/structure/Chain.java     |  10 +-
 .../org/biojava/nbio/structure/ChainImpl.java |   6 +-
 .../org/biojava/nbio/structure/DBRef.java     |   4 +-
 .../org/biojava/nbio/structure/Element.java   |  34 +-
 .../biojava/nbio/structure/ElementType.java   |   4 +-
 .../biojava/nbio/structure/EntityInfo.java    |  10 +-
 .../biojava/nbio/structure/EntityType.java    |   2 +-
 .../nbio/structure/ExperimentalTechnique.java |  10 +-
 .../org/biojava/nbio/structure/Group.java     |  82 +--
 .../biojava/nbio/structure/GroupIterator.java |   2 +-
 .../org/biojava/nbio/structure/GroupType.java |   6 +-
 .../biojava/nbio/structure/HetatomImpl.java   |   2 +-
 .../nbio/structure/JournalArticle.java        |   4 +-
 .../org/biojava/nbio/structure/Model.java     |   6 +-
 .../org/biojava/nbio/structure/Mutator.java   |   6 +-
 .../org/biojava/nbio/structure/PDBHeader.java |  22 +-
 .../org/biojava/nbio/structure/PDBRecord.java |   4 +-
 .../org/biojava/nbio/structure/PDBStatus.java |  51 +-
 .../nbio/structure/PassthroughIdentifier.java |   9 +-
 .../biojava/nbio/structure/ResidueNumber.java |   2 +-
 .../biojava/nbio/structure/ResidueRange.java  |  14 +-
 .../nbio/structure/ResidueRangeAndLength.java |   4 +-
 .../biojava/nbio/structure/SeqMisMatch.java   |  30 +-
 .../nbio/structure/SeqMisMatchImpl.java       |   2 +-
 .../java/org/biojava/nbio/structure/Site.java |  11 +-
 .../nbio/structure/StandardAminoAcid.java     |   4 +-
 .../nbio/structure/StructureException.java    |   2 +-
 .../biojava/nbio/structure/StructureIO.java   |   8 +-
 .../biojava/nbio/structure/StructureImpl.java |   2 +-
 .../nbio/structure/StructureTools.java        | 135 ++---
 .../structure/SubstructureIdentifier.java     |   4 +-
 .../biojava/nbio/structure/URLIdentifier.java |   6 +-
 .../nbio/structure/align/AFPTwister.java      |  14 +-
 .../nbio/structure/align/ClusterAltAligs.java |  11 +-
 .../biojava/nbio/structure/align/FarmJob.java |  10 +-
 .../align/MultiThreadedDBSearch.java          |  20 +-
 .../align/MultipleStructureAligner.java       |  12 +-
 .../structure/align/StrucAligParameters.java  |  22 +-
 .../structure/align/StructureAlignment.java   |  12 +-
 .../align/StructureAlignmentFactory.java      |  16 +-
 .../structure/align/StructurePairAligner.java |  12 +-
 .../ce/AbstractUserArgumentProcessor.java     |  29 +-
 .../structure/align/ce/CECPParameters.java    |   6 +-
 .../nbio/structure/align/ce/CECalculator.java |  42 +-
 .../nbio/structure/align/ce/CeCPMain.java     |  14 +-
 .../align/ce/CeCPUserArgumentProcessor.java   |   4 +-
 .../align/ce/CeCalculatorEnhanced.java        |  49 +-
 .../nbio/structure/align/ce/CeMain.java       |   2 +-
 .../nbio/structure/align/ce/CeParameters.java |  14 +-
 .../structure/align/ce/CeSideChainMain.java   |   2 +-
 .../align/ce/ConfigStrucAligParams.java       |  10 +-
 .../nbio/structure/align/ce/GuiWrapper.java   |  16 +-
 .../structure/align/ce/MatrixListener.java    |   4 +-
 .../structure/align/ce/OptimalCECPMain.java   |  32 +-
 .../align/ce/UserArgumentProcessor.java       |   4 +-
 .../align/client/FarmJobParameters.java       |   2 +-
 .../align/client/FarmJobRunnable.java         |  14 +-
 .../structure/align/client/JFatCatClient.java |  24 +-
 .../structure/align/client/StructureName.java |   6 +-
 .../events/AlignmentProgressListener.java     |  12 +-
 .../nbio/structure/align/fatcat/FatCat.java   |   2 +-
 .../fatcat/FatCatUserArgumentProcessor.java   |   4 +-
 .../align/fatcat/calc/AFPCalculator.java      |  19 +-
 .../align/fatcat/calc/AFPChainer.java         |  22 +-
 .../align/fatcat/calc/AFPOptimizer.java       |   4 +-
 .../align/fatcat/calc/AFPPostProcessor.java   |   2 +-
 .../align/fatcat/calc/FatCatParameters.java   |   8 +-
 .../structure/align/fatcat/calc/SigEva.java   |   6 +-
 .../calc/StructureAlignmentOptimizer.java     |  17 +-
 .../structure/align/helper/AlignUtils.java    |   4 +-
 .../align/helper/JointFragments.java          |  16 +-
 .../nbio/structure/align/model/AFP.java       |   2 +-
 .../nbio/structure/align/model/AFPChain.java  |  14 +-
 .../structure/align/model/AfpChainWriter.java |  56 +-
 .../align/multiple/AbstractScoresCache.java   |   4 +-
 .../nbio/structure/align/multiple/Block.java  |  28 +-
 .../structure/align/multiple/BlockImpl.java   |   6 +-
 .../structure/align/multiple/BlockSet.java    |  24 +-
 .../align/multiple/BlockSetImpl.java          |   8 +-
 .../align/multiple/MultipleAlignment.java     |  34 +-
 .../multiple/MultipleAlignmentEnsemble.java   |  40 +-
 .../MultipleAlignmentEnsembleImpl.java        |  49 +-
 .../align/multiple/MultipleAlignmentImpl.java |  12 +-
 .../structure/align/multiple/ScoresCache.java |   6 +-
 .../align/multiple/mc/MultipleMcMain.java     |  27 +-
 .../multiple/mc/MultipleMcOptimizer.java      |  55 +-
 .../multiple/mc/MultipleMcParameters.java     |   8 +-
 .../align/multiple/util/CoreSuperimposer.java |  15 +-
 .../util/MultipleAlignmentDisplay.java        |   2 +-
 .../util/MultipleAlignmentScorer.java         |  10 +-
 .../multiple/util/MultipleAlignmentTools.java |  74 ++-
 .../util/MultipleAlignmentWriter.java         |  12 +-
 .../multiple/util/MultipleSuperimposer.java   |   5 +-
 .../multiple/util/ReferenceSuperimposer.java  |  15 +-
 .../structure/align/pairwise/AligNPE.java     |   2 +-
 .../structure/align/pairwise/Alignable.java   |  36 +-
 .../align/pairwise/AlignmentResult.java       |   6 +-
 .../align/pairwise/AlternativeAlignment.java  |  38 +-
 .../align/pairwise/FragmentJoiner.java        |  29 +-
 .../nbio/structure/align/pairwise/Gotoh.java  |   2 +-
 .../structure/align/quaternary/QsAlign.java   |  71 ++-
 .../align/quaternary/QsAlignResult.java       |  16 +-
 .../align/quaternary/QsRelation.java          |   2 +-
 .../align/seq/SmithWaterman3DParameters.java  |   8 +-
 .../align/seq/SmithWaterman3Daligner.java     |   4 +-
 .../align/util/AFPAlignmentDisplay.java       |  40 +-
 .../structure/align/util/AlignmentTools.java  |  64 +-
 .../nbio/structure/align/util/AtomCache.java  |  10 +-
 .../nbio/structure/align/util/CliTools.java   |  26 +-
 .../structure/align/util/CollectionTools.java |   2 +-
 .../align/util/SynchronizedOutFile.java       |   6 +-
 .../align/util/URLConnectionTools.java        |   2 +-
 .../align/util/UserConfiguration.java         |  10 +-
 .../structure/align/xml/AFPChainFlipper.java  |   2 +-
 .../align/xml/AFPChainXMLConverter.java       |  20 +-
 .../align/xml/AFPChainXMLParser.java          |  84 +--
 .../xml/MultipleAlignmentXMLConverter.java    |  10 +-
 .../align/xml/MultipleAlignmentXMLParser.java |  48 +-
 .../align/xml/PdbPairXMLConverter.java        |   2 +-
 .../structure/align/xml/PdbPairsMessage.java  |   2 +-
 .../align/xml/RepresentativeXMLConverter.java |   2 +-
 .../nbio/structure/asa/AsaCalculator.java     |  18 +-
 .../biojava/nbio/structure/asa/GroupAsa.java  |  16 +-
 .../basepairs/BasePairParameters.java         |  14 +-
 .../nbio/structure/cath/CathCategory.java     |  39 +-
 .../nbio/structure/cath/CathDatabase.java     |  26 +-
 .../nbio/structure/cath/CathDomain.java       |  24 +-
 .../nbio/structure/cath/CathFactory.java      |   2 +-
 .../nbio/structure/cath/CathInstallation.java |  83 ++-
 .../nbio/structure/cluster/Subunit.java       |   6 +-
 .../structure/cluster/SubunitCluster.java     |  11 +-
 .../structure/cluster/SubunitExtractor.java   |   6 +-
 .../structure/contact/AtomContactSet.java     |  29 +-
 .../nbio/structure/contact/BoundingBox.java   |   6 +-
 .../nbio/structure/contact/Contact.java       |   8 +-
 .../biojava/nbio/structure/contact/Grid.java  |   8 +-
 .../nbio/structure/contact/GridCell.java      |  14 +-
 .../nbio/structure/contact/GroupContact.java  |   6 +-
 .../structure/contact/GroupContactSet.java    |  20 +-
 .../biojava/nbio/structure/contact/Pair.java  |   4 +-
 .../structure/contact/StructureInterface.java |  46 +-
 .../contact/StructureInterfaceCluster.java    |   2 +-
 .../contact/StructureInterfaceList.java       |  13 +-
 .../domain/AssignmentXMLSerializer.java       |   2 +-
 .../nbio/structure/domain/DomainProvider.java |   4 +-
 .../structure/domain/PDBDomainProvider.java   |  16 +-
 .../nbio/structure/domain/PDPDomain.java      |   4 +-
 .../nbio/structure/domain/PDPProvider.java    |   6 +-
 .../domain/RemoteDomainProvider.java          |  28 +-
 .../structure/domain/RemotePDPProvider.java   |  27 +-
 .../structure/domain/SerializableCache.java   |   7 +-
 .../structure/domain/pdp/ClusterDomains.java  |   6 +-
 .../nbio/structure/domain/pdp/Cut.java        |   4 +-
 .../nbio/structure/domain/pdp/CutDomain.java  |   4 +-
 .../nbio/structure/domain/pdp/Domain.java     |   2 +-
 .../domain/pdp/GetDistanceMatrix.java         |   6 +-
 .../nbio/structure/ecod/EcodDatabase.java     |  10 +-
 .../nbio/structure/ecod/EcodDomain.java       |   4 +-
 .../nbio/structure/ecod/EcodFactory.java      |   8 +-
 .../nbio/structure/ecod/EcodInstallation.java |  20 +-
 .../structure/geometry/MomentsOfInertia.java  |  10 +-
 .../structure/geometry/SuperPosition.java     |   6 +-
 .../structure/geometry/SuperPositionQCP.java  |   6 +-
 .../biojava/nbio/structure/io/BondMaker.java  |  14 +-
 .../nbio/structure/io/CAConverter.java        |   2 +-
 .../nbio/structure/io/EntityFinder.java       |  25 +-
 .../structure/io/FastaAFPChainConverter.java  |  24 +-
 .../structure/io/FastaStructureParser.java    |   8 +-
 .../nbio/structure/io/FileConvert.java        |  14 +-
 .../biojava/nbio/structure/io/GroupToSDF.java |   6 +-
 .../nbio/structure/io/LocalPDBDirectory.java  |  16 +-
 .../structure/io/PDBBioAssemblyParser.java    |   6 +-
 .../nbio/structure/io/PDBFileParser.java      | 367 ++++++-----
 .../nbio/structure/io/PDBParseException.java  |   2 +-
 .../io/SandboxStyleStructureProvider.java     |   2 +-
 .../nbio/structure/io/SeqRes2AtomAligner.java |  28 +-
 .../nbio/structure/io/StructureIOFile.java    |   8 +-
 .../io/StructureSequenceMatcher.java          |  20 +-
 .../structure/io/cif/CifFileConsumerImpl.java |   7 +-
 .../io/mmcif/AllChemCompProvider.java         |   2 +-
 .../io/mmcif/ChemCompGroupFactory.java        |   4 +-
 .../io/mmcif/ChemicalComponentDictionary.java |  12 +-
 .../io/mmcif/DownloadChemCompProvider.java    |  20 +-
 .../structure/io/mmcif/MMCIFFileTools.java    |   2 +-
 .../structure/io/mmcif/MMcifConsumer.java     |  90 +--
 .../nbio/structure/io/mmcif/MMcifParser.java  |  10 +-
 .../structure/io/mmcif/MetalBondConsumer.java |   9 +-
 .../io/mmcif/SimpleMMcifConsumer.java         | 103 ++--
 .../structure/io/mmcif/SimpleMMcifParser.java | 569 ++++++++++--------
 .../io/mmcif/ZipChemCompProvider.java         |  16 +-
 .../io/mmcif/chem/ChemCompTools.java          |  10 +-
 .../structure/io/mmcif/chem/PolymerType.java  |  10 +-
 .../io/mmcif/model/AbstractBean.java          |  14 +-
 .../structure/io/mmcif/model/ChemComp.java    |   8 +-
 .../io/mmcif/model/ChemCompBond.java          |  27 +-
 .../io/mmcif/model/DatabasePDBrev.java        |   2 +-
 .../nbio/structure/io/mmcif/model/Entity.java |   2 +-
 .../io/mmtf/MmtfStructureReader.java          |  22 +-
 .../io/mmtf/MmtfStructureWriter.java          |  14 +-
 .../nbio/structure/io/mmtf/MmtfUtils.java     |  10 +-
 .../io/sifts/SiftsChainToUniprotMapping.java  |  10 +-
 .../nbio/structure/io/sifts/SiftsEntity.java  |   2 +-
 .../nbio/structure/io/sifts/SiftsSegment.java |   2 +-
 .../structure/io/sifts/SiftsXMLParser.java    |  12 +-
 .../io/util/PDBTemporaryStorageUtils.java     |  32 +-
 .../structure/jama/CholeskyDecomposition.java |   6 +-
 .../jama/EigenvalueDecomposition.java         |  23 +-
 .../nbio/structure/jama/LUDecomposition.java  |  14 +-
 .../biojava/nbio/structure/jama/Matrix.java   |  33 +-
 .../nbio/structure/jama/QRDecomposition.java  |   9 +-
 .../jama/SingularValueDecomposition.java      |  10 +-
 .../structure/math/SparseSquareMatrix.java    |   2 +-
 .../nbio/structure/math/SparseVector.java     |   4 +-
 .../nbio/structure/math/SymbolTable.java      |   4 +-
 .../quaternary/BioAssemblyTools.java          |  14 +-
 .../quaternary/BiologicalAssemblyBuilder.java |  27 +-
 .../BiologicalAssemblyTransformation.java     |   4 +-
 .../quaternary/CartesianProduct.java          |   8 +-
 .../structure/rcsb/GetRepresentatives.java    |  14 +-
 .../nbio/structure/rcsb/PdbIdLists.java       |   5 +-
 .../nbio/structure/rcsb/RCSBDescription.java  |   4 +-
 .../rcsb/RCSBDescriptionFactory.java          |  47 +-
 .../nbio/structure/rcsb/RCSBLigands.java      |   4 +-
 .../structure/rcsb/RCSBLigandsFactory.java    |  40 +-
 .../structure/rcsb/RCSBMacromolecule.java     |   4 +-
 .../nbio/structure/rcsb/RCSBPolymer.java      |   8 +-
 .../nbio/structure/rcsb/RCSBUpdates.java      |   8 +-
 .../nbio/structure/rcsb/ReadUtils.java        |   4 +-
 .../biojava/nbio/structure/scop/Astral.java   |  16 +-
 .../scop/BerkeleyScopInstallation.java        |   4 +-
 .../scop/CachedRemoteScopInstallation.java    |   6 +-
 .../nbio/structure/scop/ScopCategory.java     |  30 +-
 .../nbio/structure/scop/ScopDatabase.java     |  26 +-
 .../nbio/structure/scop/ScopDescription.java  |   2 +-
 .../nbio/structure/scop/ScopDomain.java       |  18 +-
 .../nbio/structure/scop/ScopFactory.java      |   5 +-
 .../nbio/structure/scop/ScopInstallation.java |  77 ++-
 .../scop/server/ListStringWrapper.java        |   4 +-
 .../scop/server/ScopDescriptions.java         |   2 +-
 .../structure/scop/server/ScopDomains.java    |   2 +-
 .../nbio/structure/scop/server/ScopNodes.java |   2 +-
 .../scop/server/TreeSetStringWrapper.java     |   4 +-
 .../nbio/structure/scop/server/XMLUtil.java   |  12 +-
 .../nbio/structure/secstruc/BridgeType.java   |   2 +-
 .../nbio/structure/secstruc/DSSPParser.java   |  14 +-
 .../nbio/structure/secstruc/SecStrucCalc.java | 111 ++--
 .../structure/secstruc/SecStrucElement.java   |   8 +-
 .../structure/secstruc/SecStrucGroup.java     |   2 +-
 .../structure/secstruc/SecStrucState.java     |   4 +-
 .../structure/secstruc/SecStrucTools.java     |  15 +-
 .../nbio/structure/secstruc/SecStrucType.java |   2 +-
 .../symmetry/axis/HelixAxisAligner.java       |  30 +-
 .../symmetry/axis/RotationAxisAligner.java    |  24 +-
 .../symmetry/core/C2RotationSolver.java       |  10 +-
 .../symmetry/core/HelicalRepeatUnit.java      |  36 +-
 .../nbio/structure/symmetry/core/Helix.java   |  12 +-
 .../symmetry/core/HelixExtender.java          |  13 +-
 .../structure/symmetry/core/HelixLayers.java  |   2 +-
 .../structure/symmetry/core/HelixSolver.java  |  18 +-
 .../symmetry/core/PermutationGroup.java       |  14 +-
 .../symmetry/core/QuatSymmetryDetector.java   |   5 +-
 .../symmetry/core/QuatSymmetryResults.java    |  12 +-
 .../symmetry/core/QuatSymmetrySubunits.java   |  25 +-
 .../symmetry/core/RotationGroup.java          |  27 +-
 .../symmetry/core/RotationSolver.java         |  20 +-
 .../core/SymmetryPerceptionMethod.java        |   2 +-
 .../symmetry/core/SystematicSolver.java       |  14 +-
 .../symmetry/geometry/DistanceBox.java        |  27 +-
 .../symmetry/geometry/IcosahedralSampler.java |   4 +-
 .../symmetry/geometry/Icosahedron.java        |  14 +-
 .../symmetry/geometry/Octahedron.java         |   9 +-
 .../symmetry/geometry/Polyhedron.java         |  12 +-
 .../structure/symmetry/geometry/Prism.java    |   6 +-
 .../symmetry/geometry/RectangularPrism.java   |  18 +-
 .../symmetry/geometry/SphereSampler.java      |  10 +-
 .../symmetry/geometry/Tetrahedron.java        |   8 +-
 .../internal/AngleOrderDetectorPlus.java      |   4 +-
 .../symmetry/internal/CESymmParameters.java   |   4 +-
 .../structure/symmetry/internal/CeSymm.java   |   8 +-
 .../symmetry/internal/CeSymmIterative.java    |  23 +-
 .../symmetry/internal/CeSymmResult.java       |   5 +-
 .../internal/GraphComponentOrderDetector.java |   7 +-
 .../internal/GraphComponentRefiner.java       |  10 +-
 .../symmetry/internal/OrderDetector.java      |   2 +-
 .../symmetry/internal/ResidueGroup.java       |   2 +-
 .../SequenceFunctionOrderDetector.java        |   2 +-
 .../internal/SequenceFunctionRefiner.java     |  26 +-
 .../symmetry/internal/SymmOptimizer.java      |  50 +-
 .../symmetry/internal/SymmetryAxes.java       |   8 +-
 .../symmetry/internal/SymmetryRefiner.java    |   2 +-
 .../symmetry/misc/ChainSignature.java         |   6 +-
 .../misc/ProteinComplexSignature.java         |  14 +-
 .../symmetry/utils/BlastClustReader.java      |  12 +-
 .../symmetry/utils/PermutationGenerator.java  |   4 +-
 .../structure/symmetry/utils/PowerSet.java    |  10 +-
 .../symmetry/utils/SymmetryTools.java         |  44 +-
 .../validation/ModelledSubgroup.java          |  12 +-
 .../nbio/structure/validation/Programs.java   |   2 +-
 .../WwPDBValidationInformation.java           |   2 +-
 .../nbio/structure/xtal/BravaisLattice.java   |  12 +-
 .../nbio/structure/xtal/CrystalBuilder.java   |  20 +-
 .../nbio/structure/xtal/CrystalCell.java      |   2 +-
 .../nbio/structure/xtal/CrystalTransform.java |   4 +-
 .../nbio/structure/xtal/SpaceGroup.java       |  32 +-
 .../nbio/structure/xtal/SymoplibParser.java   |  12 +-
 .../nbio/structure/xtal/TransformType.java    |  12 +-
 .../structure/xtal/UnitCellBoundingBox.java   |   8 +-
 .../xtal/io/SpaceGroupMapAdapter.java         |   6 +-
 .../structure/xtal/io/SpaceGroupMapRoot.java  |   4 +-
 .../xtal/io/TransfAlgebraicAdapter.java       |  10 +-
 .../xtal/io/TreeMapSpaceGroupWrapper.java     |   4 +-
 .../nbio/structure/AtomPositionMapTest.java   |  11 +-
 .../biojava/nbio/structure/ChemCompTest.java  |  18 +-
 .../biojava/nbio/structure/ElementTest.java   |   5 +-
 .../nbio/structure/HetatomImplTest.java       |  12 +-
 .../biojava/nbio/structure/PDBStatusTest.java |  36 +-
 .../nbio/structure/PdbFileFormat30Test.java   |   4 +-
 .../nbio/structure/ResidueNumberTest.java     |   6 +-
 .../nbio/structure/ResidueRangeTest.java      |  10 +-
 .../org/biojava/nbio/structure/SiteTest.java  |  12 +-
 .../org/biojava/nbio/structure/Test4hhb.java  |   4 +-
 .../biojava/nbio/structure/TestAltLocs.java   |  39 +-
 .../biojava/nbio/structure/TestAtomCache.java |   4 +-
 .../biojava/nbio/structure/TestCloning.java   |   2 +-
 .../TestDownloadChemCompProvider.java         |   3 +-
 .../nbio/structure/TestEntityHeuristics.java  |  20 +-
 .../nbio/structure/TestNucleotides.java       |   8 +-
 .../nbio/structure/TestParsingCalcium.java    |  13 +-
 .../TestStructureCrossReferences.java         |   6 +-
 .../nbio/structure/TestStructureImpl.java     |   6 +-
 .../structure/TestStructureSerialization.java |   2 +-
 .../nbio/structure/TestVeryLongFileName.java  |   1 -
 .../nbio/structure/align/ce/CeCPMainTest.java |  31 +-
 .../align/ce/TestSmallAlignment.java          |   6 +-
 .../align/ce/TestWebStartClient.java          |   4 +-
 .../align/client/TestStructureName.java       |  50 +-
 .../multiple/TestAFPChainConversion.java      |   5 +-
 .../align/multiple/TestSampleGenerator.java   |  20 +-
 .../util/TestMultipleAlignmentScorer.java     |  24 +-
 .../util/TestMultipleAlignmentTools.java      |   6 +-
 .../util/TestMultipleAlignmentWriter.java     |  16 +-
 .../structure/align/util/AtomCacheTest.java   |  10 +-
 .../align/util/RotationAxisTest.java          |   2 +-
 .../structure/contact/TestContactCalc.java    |   2 +-
 .../structure/geometry/TestSuperPosition.java |   9 +-
 .../io/FastaAFPChainConverterTest.java        |   6 +-
 .../io/StructureSequenceMatcherTest.java      |   4 +-
 .../nbio/structure/io/TestDBRefParsing.java   |   2 +-
 .../structure/io/TestDifficultMmCIFFiles.java |   2 +-
 .../nbio/structure/io/TestHardBioUnits.java   |   2 +-
 .../nbio/structure/io/TestHeaderOnly.java     |  12 +-
 .../io/TestMMcifOrganismParsing.java          |   2 +-
 .../structure/io/TestNonDepositedFiles.java   |   8 +-
 .../io/TestQuaternaryStructureProviders.java  |  14 +-
 .../io/mmcif/TestChemCompProvider.java        |   4 +-
 .../structure/io/mmtf/TestMmtfRoundTrip.java  |  60 +-
 .../io/mmtf/TestMmtfStructureReader.java      |   2 -
 .../io/mmtf/TestMmtfStructureWriter.java      |   3 +-
 .../nbio/structure/io/mmtf/TestMmtfUtils.java |  10 +-
 .../rcsb/RCSBDescriptionFactoryTest.java      |  19 +-
 .../structure/redmine/Test1DARSeqAlign.java   |   6 +-
 .../structure/secstruc/TestDSSPParser.java    |   3 +-
 .../TestSequenceFunctionOrderDetector.java    |   9 +-
 .../symmetry/internal/TestSingleRefiner.java  |  50 +-
 .../symmetry/internal/TestSymmetryAxes.java   |  25 +-
 .../symmetry/utils/TestSymmetryTools.java     |   3 +-
 .../structure/test/util/GlobalsHelper.java    |   3 +-
 .../TestValidationReportParsing.java          |   2 +-
 .../nbio/structure/xtal/TestCrystalCell.java  |   2 +-
 .../nbio/structure/xtal/TestCrystalInfo.java  |   4 +-
 .../xtal/TestInterfaceClustering.java         |   4 +-
 .../nbio/structure/xtal/TestSpaceGroup.java   |  45 +-
 .../org/biojava/nbio/survival/cox/CoxCC.java  |  27 +-
 .../nbio/survival/cox/CoxCoefficient.java     |   2 +-
 .../biojava/nbio/survival/cox/CoxHelper.java  |   4 +-
 .../biojava/nbio/survival/cox/CoxInfo.java    |  45 +-
 .../biojava/nbio/survival/cox/CoxMart.java    |   2 +-
 .../org/biojava/nbio/survival/cox/CoxR.java   |  15 +-
 .../biojava/nbio/survival/cox/CoxScore.java   |   2 +-
 .../nbio/survival/cox/CoxVariables.java       |  15 +-
 .../nbio/survival/cox/ResidualsCoxph.java     |   8 +-
 .../biojava/nbio/survival/cox/StrataInfo.java |  30 +-
 .../nbio/survival/cox/SurvFitInfo.java        |  11 +-
 .../nbio/survival/cox/SurvivalInfo.java       |  21 +-
 .../nbio/survival/cox/SurvivalInfoHelper.java |  35 +-
 .../nbio/survival/cox/SurvivalInfoIndex.java  |   6 +-
 .../biojava/nbio/survival/cox/WaldTest.java   |  12 +-
 .../comparators/CoxComparatorInterface.java   |   8 +-
 ...CoxVariablesOverallModelFitComparator.java |  10 +-
 .../CoxVariablesVariableComparator.java       |  14 +-
 .../cox/comparators/MeanModelComparator.java  |  10 +-
 .../SurvivalInfoValueComparator.java          |   9 +-
 .../nbio/survival/cox/stats/AgScore.java      |  14 +-
 .../nbio/survival/data/ChangeValue.java       |   2 +-
 .../biojava/nbio/survival/data/WorkSheet.java | 113 ++--
 .../figure/CensorStatusSelect.java            |   3 +-
 .../kaplanmeier/figure/ExpressionFigure.java  |  24 +-
 .../kaplanmeier/figure/KMFigureInfo.java      |   4 +-
 .../kaplanmeier/figure/KaplanMeierFigure.java |  47 +-
 .../figure/NumbersAtRiskPanel.java            |   6 +-
 .../kaplanmeier/figure/SurvFitKM.java         |  53 +-
 .../metadata/ClinicalMetaDataOutcome.java     |   4 +-
 .../metadata/DiscreteQuantizerInterface.java  |   2 +-
 .../kaplanmeier/metadata/MeanQuantizer.java   |   4 +-
 .../kaplanmeier/metadata/MetaDataInfo.java    |   4 +-
 biojava-ws/src/main/java/demo/HmmerDemo.java  |   2 +-
 .../main/java/demo/NCBIQBlastServiceDemo.java |   2 +-
 ...motePairwiseAlignmentOutputProperties.java |   9 +-
 .../RemotePairwiseAlignmentProperties.java    |   9 +-
 .../RemotePairwiseAlignmentService.java       |   8 +-
 .../qblast/MapToStringTransformer.java        |   7 +-
 .../qblast/NCBIQBlastAlignmentProperties.java |  14 +-
 .../qblast/NCBIQBlastOutputProperties.java    |   4 +-
 .../alignment/qblast/NCBIQBlastService.java   |   6 +-
 .../biojava/nbio/ws/hmmer/HmmerDomain.java    |   5 +-
 .../biojava/nbio/ws/hmmer/HmmerResult.java    |   5 +-
 .../org/biojava/nbio/ws/hmmer/HmmerScan.java  |   2 +-
 .../nbio/ws/hmmer/RemoteHmmerScan.java        |  13 +-
 pom.xml                                       |   8 +-
 873 files changed, 6921 insertions(+), 7680 deletions(-)

diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java
index db9d1d7b69..ae7375ad82 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java
@@ -95,8 +95,8 @@ public static void run(String[] args) throws Exception{
 		/*
 		 * Parse input arguments
 		 */
-		List<Character> propertyList = new ArrayList<Character>();
-		List<Character> specificList = new ArrayList<Character>();
+		List<Character> propertyList = new ArrayList<>();
+		List<Character> specificList = new ArrayList<>();
 		String inputLocation = null;
 		String outputLocation = null;
 		String aminoAcidCompositionLocation = null;
@@ -179,15 +179,15 @@ private static LinkedHashMap<String, ProteinSequence> readInputFile(String input
 		}
 		LinkedHashMap<String, ProteinSequence> ret;
 		if ( inputLocation.toLowerCase().contains(".gb")) {
-			GenbankReader<ProteinSequence, AminoAcidCompound> genbankReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(
-					inStream, new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
+			GenbankReader<ProteinSequence, AminoAcidCompound> genbankReader = new GenbankReader<>(
+					inStream, new GenericGenbankHeaderParser<>(),
 					new ProteinSequenceCreator(set));
 			ret = genbankReader.process();
 
 
 		} else {
-			FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
-					inStream, new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+			FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
+					inStream, new GenericFastaHeaderParser<>(),
 					new ProteinSequenceCreator(set));
 			ret = fastaReader.process();
 
@@ -198,9 +198,9 @@ private static LinkedHashMap<String, ProteinSequence> readInputFile(String input
 	public enum PropertyName{MolecularWeight, Absorbance_True, Absorbance_False, ExtinctionCoefficient_True, ExtinctionCoefficient_False,
 		InstabilityIndex, ApliphaticIndex, AverageHydropathyValue, IsoelectricPoint, NetCharge_pH_7, A, R,
 		N, D, C, E, Q, G, H, I, L,
-		K, M, F, P, S, T, W, Y, V};
+		K, M, F, P, S, T, W, Y, V}
 
-	private static void printHeader(PrintStream output, List<Character> propertyList, List<Character> specificList, String delimiter) throws IOException{
+	private static void printHeader(PrintStream output, List<Character> propertyList, List<Character> specificList, String delimiter) {
 		int specificCount = 0;
 		/*
 		 * 1 Molecular weight
@@ -214,7 +214,7 @@ private static void printHeader(PrintStream output, List<Character> propertyList
 		 * 9 Composition of the 20 standard amino acid
 		 * 0 Composition of the specific amino acid
 		 */
-		List<String> sList = new ArrayList<String>();
+		List<String> sList = new ArrayList<>();
 		sList.add("SequenceName");
 		for(Character c:propertyList){
 			switch(c){
@@ -238,7 +238,7 @@ private static void printHeader(PrintStream output, List<Character> propertyList
 				sList.add(PropertyName.T.toString()); sList.add(PropertyName.W.toString());
 				sList.add(PropertyName.Y.toString()); sList.add(PropertyName.V.toString());
 				break;
-			case '0': sList.add("" + specificList.get(specificCount++)); break;
+			case '0': sList.add(String.valueOf(specificList.get(specificCount++))); break;
 			}
 		}
 		for(int i = 0; i < sList.size(); i++){
@@ -277,14 +277,11 @@ private static void compute(PrintStream output, String header, String sequence,
 		IPeptideProperties pp = new PeptidePropertiesImpl();
 
 		int specificCount = 0;
-		List<Double> dList = new ArrayList<Double>();
+		List<Double> dList = new ArrayList<>();
 		for(Character c:propertyList){
 			switch(c){
 			case '1':
-				if(aaTable == null)
-					dList.add(pp.getMolecularWeight(pSequence));
-				else
-					dList.add(pp.getMolecularWeight(pSequence));
+				dList.add(pp.getMolecularWeight(pSequence));
 				break;
 			case '2':
 				dList.add(pp.getAbsorbance(pSequence, true));
@@ -323,7 +320,7 @@ private static void compute(PrintStream output, String header, String sequence,
 				dList.add(aaCompound2Double.get(Constraints.Y));
 				dList.add(aaCompound2Double.get(Constraints.V));
 				break;
-			case '0': dList.add(pp.getEnrichment(pSequence, aaSet.getCompoundForString("" + specificList.get(specificCount++)))); break;
+			case '0': dList.add(pp.getEnrichment(pSequence, aaSet.getCompoundForString(String.valueOf(specificList.get(specificCount++))))); break;
 			}
 		}
 		output.print(header.replace(delimiter, "_"));
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
index f223eaca23..a35ecfafa9 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
@@ -41,7 +41,7 @@
  * @see IPeptideProperties
  */
 public class Constraints {
-	private static AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
+	private static final AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
 	//A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y, V
 	public static AminoAcidCompound A = aaSet.getCompoundForString("A");
 	public static AminoAcidCompound R = aaSet.getCompoundForString("R");
@@ -64,14 +64,14 @@ public class Constraints {
 	public static AminoAcidCompound Y = aaSet.getCompoundForString("Y");
 	public static AminoAcidCompound V = aaSet.getCompoundForString("V");
 
-	public static Map<AminoAcidCompound, Double> aa2ExtinctionCoefficient = new HashMap<AminoAcidCompound, Double>();
-	public static Map<AminoAcidCompound, Double> aa2MolecularWeight = new HashMap<AminoAcidCompound, Double>();
-	public static Map<AminoAcidCompound, Double> aa2Hydrophathicity = new HashMap<AminoAcidCompound, Double>();
-	public static Map<AminoAcidCompound, Double> aa2PKa = new HashMap<AminoAcidCompound, Double>();
-	public static Map<String, Double> diAA2Instability = new HashMap<String, Double>();
+	public static Map<AminoAcidCompound, Double> aa2ExtinctionCoefficient = new HashMap<>();
+	public static Map<AminoAcidCompound, Double> aa2MolecularWeight = new HashMap<>();
+	public static Map<AminoAcidCompound, Double> aa2Hydrophathicity = new HashMap<>();
+	public static Map<AminoAcidCompound, Double> aa2PKa = new HashMap<>();
+	public static Map<String, Double> diAA2Instability = new HashMap<>();
 
-	public static Map<AminoAcidCompound, Double> aa2NTerminalPka = new HashMap<AminoAcidCompound, Double>();
-	public static Map<AminoAcidCompound, Double> aa2CTerminalPka = new HashMap<AminoAcidCompound, Double>();
+	public static Map<AminoAcidCompound, Double> aa2NTerminalPka = new HashMap<>();
+	public static Map<AminoAcidCompound, Double> aa2CTerminalPka = new HashMap<>();
 
 	static{
 		initMolecularWeight();
@@ -287,7 +287,7 @@ private static void initInstability(){
 		SingleLetterAACode[] aa = SingleLetterAACode.values();
 		for(int i = 0; i < aa.length; i++){
 			for(int j = 0; j < aa.length; j++){
-				diAA2Instability.put("" + aa[i] + aa[j], instability[i][j]);
+				diAA2Instability.put(String.valueOf(aa[i]) + aa[j], instability[i][j]);
 			}
 		}
 	}
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
index babe1e54d8..f8eacb7269 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
@@ -61,7 +61,7 @@ public interface IPeptideProperties{
 	 * @return the total molecular weight of sequence + weight of water molecule
 	 * @see ProteinSequence
 	 */
-	public double getMolecularWeight(ProteinSequence sequence);
+    double getMolecularWeight(ProteinSequence sequence);
 
 	/**
 	 * Returns the molecular weight of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters.
@@ -80,7 +80,7 @@ public interface IPeptideProperties{
 	 * @throws FileNotFoundException
 	 * 		thrown if either elementMassFile or aminoAcidCompositionFile are not found
 	 */
-	public double getMolecularWeight(ProteinSequence sequence, File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException;
+    double getMolecularWeight(ProteinSequence sequence, File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException;
 
 	/**
 	 * Returns the molecular weight of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters.
@@ -99,7 +99,7 @@ public interface IPeptideProperties{
 	 * @throws FileNotFoundException
 	 * 		thrown if either elementMassFile or aminoAcidCompositionFile are not found
 	 */
-	public double getMolecularWeight(ProteinSequence sequence, File elementMassFile, File aminoAcidCompositionFile)
+    double getMolecularWeight(ProteinSequence sequence, File elementMassFile, File aminoAcidCompositionFile)
 		throws JAXBException, FileNotFoundException;
 
 	/**
@@ -114,7 +114,7 @@ public double getMolecularWeight(ProteinSequence sequence, File elementMassFile,
 	 * 		a amino acid composition table obtained by calling IPeptideProperties.obtainAminoAcidCompositionTable
 	 * @return the total molecular weight of sequence + weight of water molecule
 	 */
-	public double getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCompositionTable aminoAcidCompositionTable);
+    double getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCompositionTable aminoAcidCompositionTable);
 
 	/**
 	 * This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to
@@ -129,7 +129,7 @@ public double getMolecularWeight(ProteinSequence sequence, File elementMassFile,
 	 * @throws FileNotFoundException
 	 * 		thrown if either elementMassFile or aminoAcidCompositionFile are not found
 	 */
-	public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile)
+    AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile)
 		throws JAXBException, FileNotFoundException;
 
 	/**
@@ -146,7 +146,7 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidC
 	 * @throws FileNotFoundException
 	 * 		thrown if either elementMassFile or aminoAcidCompositionFile are not found
 	 */
-	public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMassFile, File aminoAcidCompositionFile)
+    AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMassFile, File aminoAcidCompositionFile)
 		throws JAXBException, FileNotFoundException;
 
 	/**
@@ -166,7 +166,7 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMas
 	 * @return the extinction coefficient of sequence
 	 * @see ProteinSequence
 	 */
-	public double getExtinctionCoefficient(ProteinSequence sequence, boolean assumeCysReduced);
+    double getExtinctionCoefficient(ProteinSequence sequence, boolean assumeCysReduced);
 
 	/**
 	 * Returns the absorbance (optical density) of sequence. The sequence argument
@@ -182,7 +182,7 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMas
 	 * @return the absorbance (optical density) of sequence
 	 * @see ProteinSequence
 	 */
-	public double getAbsorbance(ProteinSequence sequence, boolean assumeCysReduced);
+    double getAbsorbance(ProteinSequence sequence, boolean assumeCysReduced);
 
 	/**
 	 * Returns the instability index of sequence. The sequence argument must be
@@ -196,7 +196,7 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMas
 	 * @return the instability index of sequence
 	 * @see ProteinSequence
 	 */
-	public double getInstabilityIndex(ProteinSequence sequence);
+    double getInstabilityIndex(ProteinSequence sequence);
 
 	/**
 	 * Returns the apliphatic index of sequence. The sequence argument must be a
@@ -213,7 +213,7 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMas
 	 * @return the aliphatic index of sequence
 	 * @see ProteinSequence
 	 */
-	public double getApliphaticIndex(ProteinSequence sequence);
+    double getApliphaticIndex(ProteinSequence sequence);
 
 	/**
 	 * Returns the average hydropathy value of sequence. The sequence argument
@@ -229,7 +229,7 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMas
 	 * @return the average hydropathy value of sequence
 	 * @see ProteinSequence
 	 */
-	public double getAvgHydropathy(ProteinSequence sequence);
+    double getAvgHydropathy(ProteinSequence sequence);
 
 	/**
 	 * Returns the isoelectric point of sequence. The sequence argument must be
@@ -250,9 +250,9 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMas
 	 * @return the isoelectric point of sequence
 	 * @see ProteinSequence
 	 */
-	public double getIsoelectricPoint(ProteinSequence sequence, boolean useExpasyValues);
+    double getIsoelectricPoint(ProteinSequence sequence, boolean useExpasyValues);
 
-	public double getIsoelectricPoint(ProteinSequence seuqence);
+	double getIsoelectricPoint(ProteinSequence seuqence);
 
 	/**
 	 * Returns the net charge of sequence at pH 7. The sequence argument must be
@@ -274,11 +274,11 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMas
 	 * @return the net charge of sequence at given pHPoint
 	 * @see ProteinSequence
 	 */
-	public double getNetCharge(ProteinSequence sequence, boolean useExpasyValues, double pHPoint);
+    double getNetCharge(ProteinSequence sequence, boolean useExpasyValues, double pHPoint);
 
-	public double getNetCharge(ProteinSequence sequence, boolean useExpasyValues);
+	double getNetCharge(ProteinSequence sequence, boolean useExpasyValues);
 
-	public double getNetCharge(ProteinSequence sequence);
+	double getNetCharge(ProteinSequence sequence);
 
 	/**
 	 * Returns the composition of specified amino acid in the sequence. The
@@ -296,7 +296,7 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMas
 	 * @see ProteinSequence
 	 * @see AminoAcidCompound
 	 */
-	public double getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode);
+    double getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode);
 
 	/**
 	 * Returns the composition of the 20 standard amino acid in the sequence.
@@ -311,5 +311,5 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMas
 	 * @see ProteinSequence
 	 * @see AminoAcidCompound
 	 */
-	public Map<AminoAcidCompound, Double> getAAComposition(ProteinSequence sequence);
+    Map<AminoAcidCompound, Double> getAAComposition(ProteinSequence sequence);
 }
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
index b0918bf559..9ee64f5a65 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
@@ -64,7 +64,7 @@ public enum SingleLetterAACode { W, C, M, H, Y, F, Q, N, I, R, D, P, T, K, E, V,
 	 * To initialize the standardAASet
 	 */
 	static{
-		standardAASet = new HashSet<Character>();
+		standardAASet = new HashSet<>();
 		for(SingleLetterAACode c:SingleLetterAACode.values()) standardAASet.add(c.toString().charAt(0));
 	}
 
@@ -529,9 +529,9 @@ public static final Map<AminoAcidCompound, Double> getAAComposition(String seque
 	 */
 	public static final Map<String, Double> getAACompositionString(String sequence){
 		Map<AminoAcidCompound, Double> aa2Composition = getAAComposition(sequence);
-		Map<String, Double> aaString2Composition = new HashMap<String, Double>();
-		for(AminoAcidCompound aaCompound:aa2Composition.keySet()){
-			aaString2Composition.put(aaCompound.getShortName(), aa2Composition.get(aaCompound));
+		Map<String, Double> aaString2Composition = new HashMap<>();
+		for(Map.Entry<AminoAcidCompound, Double> entry : aa2Composition.entrySet()){
+			aaString2Composition.put(entry.getKey().getShortName(), entry.getValue());
 		}
 		return aaString2Composition;
 	}
@@ -549,9 +549,9 @@ public static final Map<String, Double> getAACompositionString(String sequence){
 	 */
 	public static final Map<Character, Double> getAACompositionChar(String sequence){
 		Map<AminoAcidCompound, Double> aa2Composition = getAAComposition(sequence);
-		Map<Character, Double> aaChar2Composition = new HashMap<Character, Double>();
-		for(AminoAcidCompound aaCompound:aa2Composition.keySet()){
-			aaChar2Composition.put(aaCompound.getShortName().charAt(0), aa2Composition.get(aaCompound));
+		Map<Character, Double> aaChar2Composition = new HashMap<>();
+		for(Map.Entry<AminoAcidCompound, Double> entry : aa2Composition.entrySet()){
+			aaChar2Composition.put(entry.getKey().getShortName().charAt(0), entry.getValue());
 		}
 		return aaChar2Composition;
 	}
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java
index 98e14c6a83..fd45f81767 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java
@@ -210,7 +210,7 @@ private Map<AminoAcidCompound, Integer> getExtinctAACount(ProteinSequence sequen
 			}
 		}
 		AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
-		Map<AminoAcidCompound, Integer> extinctAA2Count = new HashMap<AminoAcidCompound, Integer>();
+		Map<AminoAcidCompound, Integer> extinctAA2Count = new HashMap<>();
 		//Ignore Case is always true
 		extinctAA2Count.put(aaSet.getCompoundForString("W"), numW + smallW);
 		extinctAA2Count.put(aaSet.getCompoundForString("C"), (int) (numC + smallC));
@@ -352,16 +352,16 @@ private double getIsoelectricPointInnovagen(ProteinSequence sequence){
 			{3.55, 7.50, 10.00},// Y
 			{3.55, 7.50, 0.0}}; // Z
 
-	private final double PH_MIN = 0.0; /* minimum pH value */
-	private final double PH_MAX = 14.0; /* maximum pH value */
-	private final double MAXLOOP = 2000.0; /* maximum number of iterations */
-	private final double EPSI = 0.0001; /* desired precision */
+	private static final double PH_MIN = 0.0; /* minimum pH value */
+	private static final double PH_MAX = 14.0; /* maximum pH value */
+	private static final double MAXLOOP = 2000.0; /* maximum number of iterations */
+	private static final double EPSI = 0.0001; /* desired precision */
 
 	private double exp10(double pka){
 		return Math.pow(10, pka);
 	}
 
-	private double getIsoelectricPointExpasy(String sequence){
+	private double getIsoelectricPointExpasy(CharSequence sequence){
 		//
 		// Compute the amino-acid composition.
 		//
@@ -390,7 +390,7 @@ private double getIsoelectricPointExpasy(String sequence){
 		double phMax = PH_MAX;
 
 		double phMid = 0.0;
-		double charge = 1.0;
+		double charge;
 		for (int i = 0; i < MAXLOOP && (phMax - phMin) > EPSI; i++){
 			phMid = phMin + (phMax - phMin) / 2.0;
 
@@ -532,7 +532,7 @@ private Map<AminoAcidCompound, Integer> getChargedAACount(ProteinSequence sequen
 			}
 		}
 		AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
-		Map<AminoAcidCompound, Integer> chargedAA2Count = new HashMap<AminoAcidCompound, Integer>();
+		Map<AminoAcidCompound, Integer> chargedAA2Count = new HashMap<>();
 		chargedAA2Count.put(aaSet.getCompoundForString("K"), numK);
 		chargedAA2Count.put(aaSet.getCompoundForString("R"), numR);
 		chargedAA2Count.put(aaSet.getCompoundForString("H"), numH);
@@ -558,7 +558,7 @@ public double getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAci
 	@Override
 	public Map<AminoAcidCompound, Double> getAAComposition(ProteinSequence sequence) {
 		int validLength = 0;
-		Map<AminoAcidCompound, Double> aa2Composition = new HashMap<AminoAcidCompound, Double>();
+		Map<AminoAcidCompound, Double> aa2Composition = new HashMap<>();
 		AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
 		for(AminoAcidCompound aa:aaSet.getAllCompounds()){
 			aa2Composition.put(aa, 0.0);
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java
index e69b083be7..381158d730 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java
@@ -110,7 +110,7 @@ public final static int getNumberOfInvalidChar(String sequence, Set<Character> c
 	 * 		a new sequence with all invalid characters being replaced by '-'.
 	 */
 	public final static String cleanSequence(String sequence, Set<Character> cSet){
-		Set<Character> invalidCharSet = new HashSet<Character>();
+		Set<Character> invalidCharSet = new HashSet<>();
 		StringBuilder cleanSeq = new StringBuilder();
 		if(cSet == null) cSet = PeptideProperties.standardAASet;
 		for(char c:sequence.toCharArray()){
@@ -163,7 +163,7 @@ public static final String checkSequence(String sequence){
 	 * 		a sequence with no invalid characters.
 	 */
 	public static final String checkSequence(String sequence, Set<Character> cSet){
-		boolean containInvalid = false;
+		boolean containInvalid;
 		if(cSet != null){
 			containInvalid = sequence != null && doesSequenceContainInvalidChar(sequence, cSet);
 		}else{
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
index 0fab96f94a..e0d3b3d4cb 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
@@ -45,19 +45,22 @@ public interface IProfeatProperties {
 	/**
 	 * Enumeration of the seven different attributes
 	 */
-	public enum ATTRIBUTE {HYDROPHOBICITY, VOLUME, POLARITY, POLARIZABILITY, CHARGE, SECONDARYSTRUCTURE, SOLVENTACCESSIBILITY};
+    enum ATTRIBUTE {HYDROPHOBICITY, VOLUME, POLARITY, POLARIZABILITY, CHARGE, SECONDARYSTRUCTURE, SOLVENTACCESSIBILITY}
+
 	/**
 	 * Enumeration of the three different groupings for each attributes
 	 */
-	public enum GROUPING {GROUP1, GROUP2, GROUP3};
+    enum GROUPING {GROUP1, GROUP2, GROUP3}
+
 	/**
 	 * Enumeration of the transition between groupA and groupB
 	 */
-	public enum TRANSITION {BETWEEN_11, BETWEEN_22, BETWEEN_33, BETWEEN_12, BETWEEN_13, BETWEEN_23};
+    enum TRANSITION {BETWEEN_11, BETWEEN_22, BETWEEN_33, BETWEEN_12, BETWEEN_13, BETWEEN_23}
+
 	/**
 	 * Enumeration of the distribution for the first, first 25%, first 50%, first 75% and 100% of the grouping
 	 */
-	public enum DISTRIBUTION {FIRST, FIRST25, FIRST50, FIRST75, ALL};
+    enum DISTRIBUTION {FIRST, FIRST25, FIRST50, FIRST75, ALL}
 
 	/**
 	 * Returns the composition of the specific grouping for the given attribute.
@@ -73,11 +76,11 @@ public enum DISTRIBUTION {FIRST, FIRST25, FIRST50, FIRST75, ALL};
 	 * @throws Exception
 	 * 	throws Exception if attribute or group are unknown
 	 */
-	public double getComposition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception;
+    double getComposition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception;
 
-	public Map<GROUPING, Double> getComposition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception;
+	Map<GROUPING, Double> getComposition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception;
 
-	public Map<ATTRIBUTE, Map<GROUPING, Double>> getComposition(ProteinSequence sequence) throws Exception;
+	Map<ATTRIBUTE, Map<GROUPING, Double>> getComposition(ProteinSequence sequence) throws Exception;
 
 	/**
 	 * Returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
@@ -93,11 +96,11 @@ public enum DISTRIBUTION {FIRST, FIRST25, FIRST50, FIRST75, ALL};
 	 * @throws Exception
 	 * 	throws Exception if attribute or group are unknown
 	 */
-	public double getTransition(ProteinSequence sequence, ATTRIBUTE attribute, TRANSITION transition) throws Exception;
+    double getTransition(ProteinSequence sequence, ATTRIBUTE attribute, TRANSITION transition) throws Exception;
 
-	public Map<TRANSITION, Double> getTransition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception;
+	Map<TRANSITION, Double> getTransition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception;
 
-	public Map<ATTRIBUTE, Map<TRANSITION, Double>> getTransition(ProteinSequence sequence) throws Exception;
+	Map<ATTRIBUTE, Map<TRANSITION, Double>> getTransition(ProteinSequence sequence) throws Exception;
 
 	/**
 	 * Computes and return the position with respect to the sequence where the given distribution of the grouping can be found.<br/>
@@ -120,11 +123,11 @@ public enum DISTRIBUTION {FIRST, FIRST25, FIRST50, FIRST75, ALL};
 	 * @throws Exception
 	 * 	throws Exception if attribute or group are unknown
 	 */
-	public double getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group, DISTRIBUTION distribution) throws Exception;
+    double getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group, DISTRIBUTION distribution) throws Exception;
 
-	public Map<DISTRIBUTION, Double> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception;
+	Map<DISTRIBUTION, Double> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception;
 
-	public Map<GROUPING, Map<DISTRIBUTION, Double>> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception;
+	Map<GROUPING, Map<DISTRIBUTION, Double>> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception;
 
-	public Map<ATTRIBUTE , Map<GROUPING, Map<DISTRIBUTION, Double>>> getDistributionPosition(ProteinSequence sequence) throws Exception;
+	Map<ATTRIBUTE , Map<GROUPING, Map<DISTRIBUTION, Double>>> getDistributionPosition(ProteinSequence sequence) throws Exception;
 }
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java
index 5408c127c5..1d663923d7 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java
@@ -23,6 +23,7 @@
 import org.biojava.nbio.aaproperties.profeat.convertor.*;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 
+import java.util.EnumMap;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -127,35 +128,35 @@ private Convertor getConvertor(ATTRIBUTE attribute) throws Exception{
 
 	@Override
 	public Map<GROUPING, Double> getComposition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception {
-		Map<GROUPING, Double> grouping2Composition = new HashMap<GROUPING, Double>();
+		Map<GROUPING, Double> grouping2Composition = new EnumMap<>(GROUPING.class);
 		for(GROUPING group:GROUPING.values()) grouping2Composition.put(group, getComposition(sequence, attribute, group));
 		return grouping2Composition;
 	}
 
 	@Override
 	public Map<ATTRIBUTE, Map<GROUPING, Double>> getComposition(ProteinSequence sequence) throws Exception {
-		Map<ATTRIBUTE, Map<GROUPING, Double>> attribute2Grouping2Composition = new HashMap<ATTRIBUTE, Map<GROUPING, Double>>();
+		Map<ATTRIBUTE, Map<GROUPING, Double>> attribute2Grouping2Composition = new EnumMap<>(ATTRIBUTE.class);
 		for(ATTRIBUTE attribute:ATTRIBUTE.values()) attribute2Grouping2Composition.put(attribute, getComposition(sequence, attribute));
 		return attribute2Grouping2Composition;
 	}
 
 	@Override
 	public Map<TRANSITION, Double> getTransition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception {
-		Map<TRANSITION, Double> transition2Double = new HashMap<TRANSITION, Double>();
+		Map<TRANSITION, Double> transition2Double = new EnumMap<>(TRANSITION.class);
 		for(TRANSITION transition:TRANSITION.values()) transition2Double.put(transition, getTransition(sequence, attribute, transition));
 		return transition2Double;
 	}
 
 	@Override
 	public Map<ATTRIBUTE, Map<TRANSITION, Double>> getTransition(ProteinSequence sequence) throws Exception {
-		Map<ATTRIBUTE, Map<TRANSITION, Double>> attribute2Transition2Double = new HashMap<ATTRIBUTE, Map<TRANSITION, Double>>();
+		Map<ATTRIBUTE, Map<TRANSITION, Double>> attribute2Transition2Double = new EnumMap<>(ATTRIBUTE.class);
 		for(ATTRIBUTE attribute:ATTRIBUTE.values()) attribute2Transition2Double.put(attribute, getTransition(sequence, attribute));
 		return attribute2Transition2Double;
 	}
 
 	@Override
 	public Map<DISTRIBUTION, Double> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception {
-		Map<DISTRIBUTION, Double> distribution2Double = new HashMap<DISTRIBUTION, Double>();
+		Map<DISTRIBUTION, Double> distribution2Double = new EnumMap<>(DISTRIBUTION.class);
 		for(DISTRIBUTION distribution:DISTRIBUTION.values())
 			distribution2Double.put(distribution, getDistributionPosition(sequence, attribute, group, distribution));
 		return distribution2Double;
@@ -163,7 +164,7 @@ public Map<DISTRIBUTION, Double> getDistributionPosition(ProteinSequence sequenc
 
 	@Override
 	public Map<GROUPING, Map<DISTRIBUTION, Double>> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception {
-		Map<GROUPING, Map<DISTRIBUTION, Double>> grouping2Distribution2Double = new HashMap<GROUPING, Map<DISTRIBUTION, Double>>();
+		Map<GROUPING, Map<DISTRIBUTION, Double>> grouping2Distribution2Double = new EnumMap<>(GROUPING.class);
 		for(GROUPING group:GROUPING.values())
 			grouping2Distribution2Double.put(group, getDistributionPosition(sequence, attribute, group));
 		return grouping2Distribution2Double;
@@ -172,7 +173,7 @@ public Map<GROUPING, Map<DISTRIBUTION, Double>> getDistributionPosition(ProteinS
 	@Override
 	public Map<ATTRIBUTE, Map<GROUPING, Map<DISTRIBUTION, Double>>> getDistributionPosition(ProteinSequence sequence) throws Exception {
 		Map<ATTRIBUTE, Map<GROUPING, Map<DISTRIBUTION, Double>>> attribute2Grouping2Distribution2Double =
-			new HashMap<ATTRIBUTE, Map<GROUPING, Map<DISTRIBUTION, Double>>>();
+                new EnumMap<>(ATTRIBUTE.class);
 		for(ATTRIBUTE attribute:ATTRIBUTE.values())
 			attribute2Grouping2Distribution2Double.put(attribute, getDistributionPosition(sequence, attribute));
 		return attribute2Grouping2Distribution2Double;
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Charge.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Charge.java
index 5bf4bc76f4..b2beeed2bb 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Charge.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Charge.java
@@ -39,7 +39,7 @@ public char convert(char c){
 		}
 	}
 
-	private static String[] subCategory = {"Positive", "Neutral", "Negative"};
+	private static final String[] subCategory = {"Positive", "Neutral", "Negative"};
 	@Override
 	public String[] getGrouping(){return Convert2Charge.subCategory;}
 	@Override
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Hydrophobicity.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Hydrophobicity.java
index 105fdec86f..c2810e45dd 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Hydrophobicity.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Hydrophobicity.java
@@ -38,7 +38,7 @@ public char convert(char c){
 			return unknownGroup;//Non-standard AA
 		}
 	}
-	private static String[] subCategory = {"Polar", "Neutral", "Hydrophobicity"};
+	private static final String[] subCategory = {"Polar", "Neutral", "Hydrophobicity"};
 	@Override
 	public String[] getGrouping(){return subCategory;}
 	@Override
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2NormalizedVanDerWaalsVolume.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2NormalizedVanDerWaalsVolume.java
index 4facf925b7..970a93534b 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2NormalizedVanDerWaalsVolume.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2NormalizedVanDerWaalsVolume.java
@@ -38,7 +38,7 @@ public char convert(char c){
 			return unknownGroup;//Non-standard AA
 		}
 	}
-	private static String[] subCategory = {"Range_0-2.78", "Range_2.95-4.0", "Range_4.03-8.08"};
+	private static final String[] subCategory = {"Range_0-2.78", "Range_2.95-4.0", "Range_4.03-8.08"};
 	@Override
 	public String[] getGrouping(){return subCategory;}
 	@Override
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarity.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarity.java
index 2b1f1bec61..80ecc69183 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarity.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarity.java
@@ -38,7 +38,7 @@ public char convert(char c){
 			return unknownGroup;//Non-standard AA
 		}
 	}
-	private static String[] subCategory = {"Value_4.9-6.2", "Value_8.0-9.2", "Value_10.4-13.0"};
+	private static final String[] subCategory = {"Value_4.9-6.2", "Value_8.0-9.2", "Value_10.4-13.0"};
 	@Override
 	public String[] getGrouping(){return subCategory;}
 	@Override
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarizability.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarizability.java
index 1af72b5cc9..7888cf66a5 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarizability.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarizability.java
@@ -39,7 +39,7 @@ public char convert(char c){
 		}
 	}
 
-	private static String[] subCategory = {"Value_0-0.08", "Value_0.128-0.186", "Value_0.219-0.409"};
+	private static final String[] subCategory = {"Value_0-0.08", "Value_0.128-0.186", "Value_0.219-0.409"};
 	@Override
 	public String[] getGrouping(){return subCategory;}
 	@Override
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SecondaryStructure.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SecondaryStructure.java
index 70a51daf41..b3321f659f 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SecondaryStructure.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SecondaryStructure.java
@@ -37,7 +37,7 @@ public char convert(char c){
 			return unknownGroup;//Non-standard AA
 		}
 	}
-	private static String[] subCategory = {"Helix", "Strand", "Coil"};
+	private static final String[] subCategory = {"Helix", "Strand", "Coil"};
 	@Override
 	public String[] getGrouping(){return subCategory;}
 	@Override
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SolventAccessibility.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SolventAccessibility.java
index 27c7676198..c3497e220f 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SolventAccessibility.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SolventAccessibility.java
@@ -38,7 +38,7 @@ public char convert(char c){
 		}
 	}
 
-	private static String[] subCategory = {"Buried", "Exposed", "Intermediate"};
+	private static final String[] subCategory = {"Buried", "Exposed", "Intermediate"};
 	@Override
 	public String[] getGrouping(){return subCategory;}
 	@Override
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java
index 4731e90453..5be7ee1c4f 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java
@@ -83,7 +83,7 @@ private void generatesAminoAcidCompoundSet(){
 	 * 		Stores the mass of elements and isotopes
 	 */
 	public void computeMolecularWeight(ElementTable eTable){
-		this.aaSymbol2MolecularWeight = new HashMap<Character, Double>();
+		this.aaSymbol2MolecularWeight = new HashMap<>();
 		for(AminoAcidComposition a:aminoacid){
 			//Check to ensure that the symbol is of single character
 			if(a.getSymbol().length() != 1){
@@ -91,7 +91,7 @@ public void computeMolecularWeight(ElementTable eTable){
 			}
 			//Check to ensure that the symbols are not repeated
 			char c = a.getSymbol().charAt(0);
-			if(this.aaSymbol2MolecularWeight.keySet().contains(c)){
+			if(this.aaSymbol2MolecularWeight.containsKey(c)){
 				throw new Error("Symbol " + c + " is repeated.\r\n" +
 						"Please check AminoAcidComposition XML file to ensure there are no repeated symbols. Note that this is case-insensitive.\r\n" +
 						"This means that having 'A' and 'a' would be repeating.");
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
index 9b211ab305..3b5079bcc7 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
@@ -39,9 +39,9 @@
  */
 public class CaseFreeAminoAcidCompoundSet implements CompoundSet<AminoAcidCompound> {
 
-	private final Map<String, AminoAcidCompound> aminoAcidCompoundCache = new HashMap<String, AminoAcidCompound>();
+	private final Map<String, AminoAcidCompound> aminoAcidCompoundCache = new HashMap<>();
 	private final Map<AminoAcidCompound, Set<AminoAcidCompound>> equivalentsCache =
-			new HashMap<AminoAcidCompound, Set<AminoAcidCompound>>();
+			new HashMap<>();
 
 	public CaseFreeAminoAcidCompoundSet() {
 		aminoAcidCompoundCache.put("A", new AminoAcidCompound(null, "A", "Ala", "Alanine", 71.0788f));
@@ -83,9 +83,9 @@ public CaseFreeAminoAcidCompoundSet() {
 		//which then does the actual conversion to Pyl.
 		aminoAcidCompoundCache.put("O", new AminoAcidCompound(null, "O", "Pyl", "Pyrrolysine", 255.3172f));
 
-		Map<String, AminoAcidCompound> lowerCaseSet = new HashMap<String, AminoAcidCompound>();
-		for(String s:this.aminoAcidCompoundCache.keySet()){
-			lowerCaseSet.put(s.toLowerCase(), this.aminoAcidCompoundCache.get(s));
+		Map<String, AminoAcidCompound> lowerCaseSet = new HashMap<>();
+		for(Map.Entry<String, AminoAcidCompound> entry : this.aminoAcidCompoundCache.entrySet()){
+			lowerCaseSet.put(entry.getKey().toLowerCase(), entry.getValue());
 		}
 		this.aminoAcidCompoundCache.putAll(lowerCaseSet);
 	}
@@ -144,7 +144,7 @@ public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound)
 			addAmbiguousEquivalents("I", "L", "J");
 			// ambiguous gaps
 			AminoAcidCompound gap1, gap2, gap3;
-			Set<AminoAcidCompound> gaps = new HashSet<AminoAcidCompound>();
+			Set<AminoAcidCompound> gaps = new HashSet<>();
 			gaps.add(gap1 = aminoAcidCompoundCache.get("-"));
 			gaps.add(gap2 = aminoAcidCompoundCache.get("."));
 			gaps.add(gap3 = aminoAcidCompoundCache.get("_"));
@@ -152,7 +152,7 @@ public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound)
 			equivalentsCache.put(gap2, gaps);
 			equivalentsCache.put(gap3, gaps);
 			// X is never equivalent, even to itself
-			equivalentsCache.put(aminoAcidCompoundCache.get("X"), new HashSet<AminoAcidCompound>());
+			equivalentsCache.put(aminoAcidCompoundCache.get("X"), new HashSet<>());
 		}
 		return equivalentsCache.get(compound);
 	}
@@ -162,18 +162,18 @@ private void addAmbiguousEquivalents(String one, String two, String either) {
 		Set<AminoAcidCompound> equivalents;
 		AminoAcidCompound cOne, cTwo, cEither;
 
-		equivalents = new HashSet<AminoAcidCompound>();
+		equivalents = new HashSet<>();
 		equivalents.add(cOne = aminoAcidCompoundCache.get(one));
 		equivalents.add(cTwo = aminoAcidCompoundCache.get(two));
 		equivalents.add(cEither = aminoAcidCompoundCache.get(either));
 		equivalentsCache.put(cEither, equivalents);
 
-		equivalents = new HashSet<AminoAcidCompound>();
+		equivalents = new HashSet<>();
 		equivalents.add(cOne);
 		equivalents.add(cEither);
 		equivalentsCache.put(cOne, equivalents);
 
-		equivalents = new HashSet<AminoAcidCompound>();
+		equivalents = new HashSet<>();
 		equivalents.add(cTwo);
 		equivalents.add(cEither);
 		equivalentsCache.put(cTwo, equivalents);
@@ -186,7 +186,7 @@ public boolean hasCompound(AminoAcidCompound compound) {
 
 	@Override
 	public List<AminoAcidCompound> getAllCompounds() {
-		return new ArrayList<AminoAcidCompound>(aminoAcidCompoundCache.values());
+		return new ArrayList<>(aminoAcidCompoundCache.values());
 	}
 
 
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java
index b03d15d1ac..1a9f15bb28 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java
@@ -120,7 +120,7 @@ public List<Isotope> getIsotopes() {
 
 	public void setIsotopes(List<Isotope> isotopes) {
 		this.isotope = isotopes;
-		this.name2Isotope = new HashMap<String, Isotope>();
+		this.name2Isotope = new HashMap<>();
 		if(isotopes != null){
 			for(Isotope i:isotopes){
 				name2Isotope.put(i.getName(), i);
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java
index efac678f23..05b54c7014 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java
@@ -58,8 +58,8 @@ public void setElement(List<Element> eList){
 	 * Populate the Maps for quick retrieval
 	 */
 	public void populateMaps(){
-		this.elementName2Element = new HashMap<String, Element>();
-		this.isotopeName2Isotope = new HashMap<String, Isotope>();
+		this.elementName2Element = new HashMap<>();
+		this.isotopeName2Isotope = new HashMap<>();
 		if(this.element != null){
 			for(Element e:this.element){
 				this.elementName2Element.put(e.getName(), e);
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java
index d9c11c7e66..b1c63e9655 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java
@@ -28,7 +28,7 @@
 
 public class ModifiedAminoAcidCompoundSet implements CompoundSet<AminoAcidCompound> {
 
-	private final Map<String, AminoAcidCompound> aminoAcidCompoundCache = new HashMap<String, AminoAcidCompound>();
+	private final Map<String, AminoAcidCompound> aminoAcidCompoundCache = new HashMap<>();
 
 	public ModifiedAminoAcidCompoundSet(List<AminoAcidComposition> aaList, Map<Character, Double> aaSymbol2MolecularWeight) {
 		this.aminoAcidCompoundCache.put("-", new AminoAcidCompound(null, "-", "", "", 0.0f));
@@ -84,7 +84,7 @@ public boolean hasCompound(AminoAcidCompound compound) {
 
 	@Override
 	public List<AminoAcidCompound> getAllCompounds() {
-		return new ArrayList<AminoAcidCompound>(aminoAcidCompoundCache.values());
+		return new ArrayList<>(aminoAcidCompoundCache.values());
 	}
 
 	@Override
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java
index 8005bf3bac..b5cfea39c2 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java
@@ -27,7 +27,7 @@
 import java.io.IOException;
 
 public class SchemaGenerator extends SchemaOutputResolver{
-	private String fileName;
+	private final String fileName;
 
 	public SchemaGenerator(String filename){
 		this.fileName = filename;
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java
index 25ebf3abed..78e916a377 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java
@@ -74,8 +74,8 @@ public void shortExample4(){
 
 		//Enrichment of a list of amino acid types
 		Map<String, Double> composition = PeptideProperties.getAACompositionString(sequence);
-		for(String aa:composition.keySet()){
-			logger.debug("Composition of {}: {}", aa, composition.get(aa));
+		for(Map.Entry<String, Double> entry : composition.entrySet()){
+			logger.debug("Composition of {}: {}", entry.getKey(), entry.getValue());
 		}
 	}
 
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/GenbankCommandPromptTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/GenbankCommandPromptTest.java
index d76acd34c0..846e7092f4 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/GenbankCommandPromptTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/GenbankCommandPromptTest.java
@@ -33,8 +33,8 @@ public void testAdvancedXMLExample() throws Exception{
 		//-i BondFeature.gb -a
 		String[] args = new String[11];
 		args[0] = "-i";
-		args[1] = "./src/test/resources/BondFeature.gb";;
-		args[2] = "-x";
+		args[1] = "./src/test/resources/BondFeature.gb";
+        args[2] = "-x";
 		args[3] = "./src/main/resources/AdvancedAminoAcidComposition.xml";
 		args[4] = "-0";
 		args[5] = "0";
@@ -53,8 +53,8 @@ public void testExample1() throws Exception{
 		//-i BondFeature.gb -a
 		String[] args = new String[7];
 		args[0] = "-i";
-		args[1] = "./src/test/resources/BondFeature.gb";;
-		args[2] = "-a";
+		args[1] = "./src/test/resources/BondFeature.gb";
+        args[2] = "-a";
 		args[3] = "-o";
 		args[4] = output.toString();
 		args[5] = "-f";
@@ -69,8 +69,8 @@ public void testExample1WithCSV() throws Exception{
 		//-i BondFeature.gb -a
 		String[] args = new String[7];
 		args[0] = "-i";
-		args[1] = "./src/test/resources/BondFeature.gb";;
-		args[2] = "-a";
+		args[1] = "./src/test/resources/BondFeature.gb";
+        args[2] = "-a";
 		args[3] = "-o";
 		args[4] = output.toString();
 		args[5] = "-f";
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java
index 6220ea0b28..915bc06b5c 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java
@@ -345,7 +345,7 @@ public void testNetCharge(){
 			logger.debug(p);
 			logger.debug("pH\tInnovagen\tExpasy\tdiff");
 			for ( int i = 1; i < 15; i++) {
-				double phPoint = (new Double(i)).doubleValue();
+				double phPoint = new Double(i);
 				double chrgInnovagen = PeptideProperties.getNetCharge(p,false,phPoint);
 				double chrgExpasy = PeptideProperties.getNetCharge(p,true,phPoint);
 				logger.debug(String.format("%2.1f\t%2.2f\t%2.2f\t%2.2f", phPoint, chrgInnovagen,
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/profeat/CookBookTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/profeat/CookBookTest.java
index b68370cfc9..aa98c006f7 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/profeat/CookBookTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/profeat/CookBookTest.java
@@ -43,11 +43,11 @@ public void shortExample1() throws Exception{
 		 */
 		String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
 		Map<ATTRIBUTE, Map<GROUPING, Double>> attribute2Grouping2Double = ProfeatProperties.getComposition(sequence);
-		for(ATTRIBUTE a:attribute2Grouping2Double.keySet()){
-			logger.info("======={}=======", a);
-			logger.info("GROUP1 = {}", attribute2Grouping2Double.get(a).get(GROUPING.GROUP1));
-			logger.info("GROUP2 = {}", attribute2Grouping2Double.get(a).get(GROUPING.GROUP2));
-			logger.info("GROUP3 = {}", attribute2Grouping2Double.get(a).get(GROUPING.GROUP3));
+		for(Map.Entry<ATTRIBUTE, Map<GROUPING, Double>> entry : attribute2Grouping2Double.entrySet()){
+			logger.info("======={}=======", entry.getKey());
+			logger.info("GROUP1 = {}", entry.getValue().get(GROUPING.GROUP1));
+			logger.info("GROUP2 = {}", entry.getValue().get(GROUPING.GROUP2));
+			logger.info("GROUP3 = {}", entry.getValue().get(GROUPING.GROUP3));
 		}
 	}
 
@@ -58,14 +58,14 @@ public void shortExample2() throws Exception{
 		 */
 		String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
 		Map<ATTRIBUTE, Map<TRANSITION, Double>> attribute2Transition2Double = ProfeatProperties.getTransition(sequence);
-		for(ATTRIBUTE a:attribute2Transition2Double.keySet()){
-			logger.info("======={}=======", a);
-			logger.info("1<=>1 = {}", attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_11));
-			logger.info("2<=>2 = {}", attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_22));
-			logger.info("3<=>3 = {}", attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_33));
-			logger.info("1<=>2 = {}", attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_12));
-			logger.info("1<=>3 = {}", attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_13));
-			logger.info("2<=>3 = {}", attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_23));
+		for(Map.Entry<ATTRIBUTE, Map<TRANSITION, Double>> entry : attribute2Transition2Double.entrySet()){
+			logger.info("======={}=======", entry.getKey());
+			logger.info("1<=>1 = {}", entry.getValue().get(TRANSITION.BETWEEN_11));
+			logger.info("2<=>2 = {}", entry.getValue().get(TRANSITION.BETWEEN_22));
+			logger.info("3<=>3 = {}", entry.getValue().get(TRANSITION.BETWEEN_33));
+			logger.info("1<=>2 = {}", entry.getValue().get(TRANSITION.BETWEEN_12));
+			logger.info("1<=>3 = {}", entry.getValue().get(TRANSITION.BETWEEN_13));
+			logger.info("2<=>3 = {}", entry.getValue().get(TRANSITION.BETWEEN_23));
 		}
 	}
 
@@ -76,11 +76,11 @@ public void shortExample3() throws Exception{
 		 */
 		String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
 		Map<ATTRIBUTE , Map<GROUPING, Map<DISTRIBUTION, Double>>> attribute2Grouping2Distribution2Double = ProfeatProperties.getDistributionPosition(sequence);
-		for(ATTRIBUTE a:attribute2Grouping2Distribution2Double.keySet()){
-			logger.info("======={}=======", a);
-			logger.info("GROUP1 = {}", attribute2Grouping2Distribution2Double.get(a).get(GROUPING.GROUP1));
-			logger.info("GROUP2 = {}", attribute2Grouping2Distribution2Double.get(a).get(GROUPING.GROUP2));
-			logger.info("GROUP3 = {}", attribute2Grouping2Distribution2Double.get(a).get(GROUPING.GROUP3));
+		for(Map.Entry<ATTRIBUTE, Map<GROUPING, Map<DISTRIBUTION, Double>>> entry : attribute2Grouping2Distribution2Double.entrySet()){
+			logger.info("======={}=======", entry.getKey());
+			logger.info("GROUP1 = {}", entry.getValue().get(GROUPING.GROUP1));
+			logger.info("GROUP2 = {}", entry.getValue().get(GROUPING.GROUP2));
+			logger.info("GROUP3 = {}", entry.getValue().get(GROUPING.GROUP3));
 		}
 	}
 }
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java
index 528192dcb4..e2fa5e3bea 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java
@@ -133,35 +133,35 @@ public void readXml() throws JAXBException, IOException{
 
 	@Test
 	public void generateXml() throws JAXBException, IOException{
-		List<Name2Count> elementList = new ArrayList<Name2Count>();
+		List<Name2Count> elementList = new ArrayList<>();
 		elementList.add(new Name2Count("Carbon", 3));
 		elementList.add(new Name2Count("Hydrogen", 5));
 		elementList.add(new Name2Count("Nitrogen", 1));
 		elementList.add(new Name2Count("Oxygen", 1));
 		AminoAcidComposition alanine = new AminoAcidComposition("A", "Ala", "Alanine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 		elementList.add(new Name2Count("Carbon", 6));
 		elementList.add(new Name2Count("Hydrogen", 12));
 		elementList.add(new Name2Count("Nitrogen", 4));
 		elementList.add(new Name2Count("Oxygen", 1));
 		AminoAcidComposition arginine = new AminoAcidComposition("R", "Arg", "Arginine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 		elementList.add(new Name2Count("Carbon", 4));
 		elementList.add(new Name2Count("Hydrogen", 6));
 		elementList.add(new Name2Count("Nitrogen", 2));
 		elementList.add(new Name2Count("Oxygen", 2));
 		AminoAcidComposition asparagine = new AminoAcidComposition("N", "Asn", "Asparagine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 		elementList.add(new Name2Count("Carbon", 4));
 		elementList.add(new Name2Count("Hydrogen", 5));
 		elementList.add(new Name2Count("Nitrogen", 1));
 		elementList.add(new Name2Count("Oxygen", 3));
 		AminoAcidComposition asparticAcid = new AminoAcidComposition("D", "Asp", "Aspartic Acid", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 3));
 		elementList.add(new Name2Count("Hydrogen", 5));
@@ -170,7 +170,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Sulfur", 1));
 		AminoAcidComposition cysteine = new AminoAcidComposition("C", "Cys", "Cysteine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 5));
 		elementList.add(new Name2Count("Hydrogen", 7));
@@ -178,7 +178,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Oxygen", 3));
 		AminoAcidComposition glutamicAcid = new AminoAcidComposition("E", "Glu", "Glutamic Acid", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 5));
 		elementList.add(new Name2Count("Hydrogen", 8));
@@ -186,7 +186,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Oxygen", 2));
 		AminoAcidComposition glutamine = new AminoAcidComposition("Q", "Gln", "Glutamine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 2));
 		elementList.add(new Name2Count("Hydrogen", 3));
@@ -194,7 +194,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Oxygen", 1));
 		AminoAcidComposition glycine = new AminoAcidComposition("G", "Gly", "Glycine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 6));
 		elementList.add(new Name2Count("Hydrogen", 7));
@@ -202,7 +202,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Oxygen", 1));
 		AminoAcidComposition histidine = new AminoAcidComposition("H", "His", "Histidine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 6));
 		elementList.add(new Name2Count("Hydrogen", 11));
@@ -210,7 +210,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Oxygen", 1));
 		AminoAcidComposition isoleucine = new AminoAcidComposition("I", "Ile", "Isoleucine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 6));
 		elementList.add(new Name2Count("Hydrogen", 11));
@@ -218,7 +218,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Oxygen", 1));
 		AminoAcidComposition leucine = new AminoAcidComposition("L", "Leu", "Leucine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 6));
 		elementList.add(new Name2Count("Hydrogen", 12));
@@ -226,7 +226,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Oxygen", 1));
 		AminoAcidComposition lysine = new AminoAcidComposition("K", "Lys", "Lysine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 5));
 		elementList.add(new Name2Count("Hydrogen", 9));
@@ -235,7 +235,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Sulfur", 1));
 		AminoAcidComposition methionine = new AminoAcidComposition("M", "Met", "Methionine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 9));
 		elementList.add(new Name2Count("Hydrogen", 9));
@@ -243,7 +243,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Oxygen", 1));
 		AminoAcidComposition phenylalanine = new AminoAcidComposition("F", "Phe", "Phenylalanine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 5));
 		elementList.add(new Name2Count("Hydrogen", 7));
@@ -251,7 +251,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Oxygen", 1));
 		AminoAcidComposition proline = new AminoAcidComposition("P", "Pro", "Proline", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 3));
 		elementList.add(new Name2Count("Hydrogen", 5));
@@ -259,7 +259,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Oxygen", 2));
 		AminoAcidComposition serine = new AminoAcidComposition("S", "Ser", "Serine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 4));
 		elementList.add(new Name2Count("Hydrogen", 7));
@@ -267,7 +267,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Oxygen", 2));
 		AminoAcidComposition threonine = new AminoAcidComposition("T", "Thr", "Threonine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 11));
 		elementList.add(new Name2Count("Hydrogen", 10));
@@ -275,7 +275,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Oxygen", 1));
 		AminoAcidComposition tryptophan = new AminoAcidComposition("W", "Trp", "Tryptophan", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 9));
 		elementList.add(new Name2Count("Hydrogen", 9));
@@ -283,7 +283,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Oxygen", 2));
 		AminoAcidComposition tyrosine = new AminoAcidComposition("Y", "Tyr", "Tyrosine", elementList, null);
 
-		elementList = new ArrayList<Name2Count>();
+		elementList = new ArrayList<>();
 
 		elementList.add(new Name2Count("Carbon", 5));
 		elementList.add(new Name2Count("Hydrogen", 9));
@@ -291,7 +291,7 @@ public void generateXml() throws JAXBException, IOException{
 		elementList.add(new Name2Count("Oxygen", 1));
 		AminoAcidComposition valine = new AminoAcidComposition("V", "Val", "Valine", elementList, null);
 
-		List<AminoAcidComposition> aList = new ArrayList<AminoAcidComposition>();
+		List<AminoAcidComposition> aList = new ArrayList<>();
 		aList.add(alanine);
 		aList.add(arginine);
 		aList.add(asparagine);
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java
index 37376b6bd0..07d2a76cf7 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java
@@ -62,98 +62,98 @@ public void readXml() throws JAXBException, IOException{
 
 	@Test
 	public void generateXml() throws JAXBException, IOException {
-		List<Isotope> iList = new ArrayList<Isotope>();
+		List<Isotope> iList = new ArrayList<>();
 		Element hydrogen = new Element("Hydrogen", "H", 1, null, 1.00794);
 		iList.add(new Isotope("Hydrogen", 1, 1.00782503207));
 		iList.add(new Isotope("Deuterium", 2, 2.0141017778));
 		iList.add(new Isotope("Tritium", 3, 3.0160492777));
 		hydrogen.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element helium = new Element("Helium", "He", 2, null, 4.002602);
 		iList.add(new Isotope("Helium-3", 3, 3.0160293191));
 		iList.add(new Isotope("Helium-4", 4, 4.00260325415));
 		helium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element lithium = new Element("Lithium", "Li", 3, null, 6.941);
 		iList.add(new Isotope("Lithium-6", 6, 6.015122795));
 		iList.add(new Isotope("Lithium-7", 7, 7.01600455));
 		lithium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element beryllium = new Element("Beryllium", "Be", 4, null, 9.012182);
 		iList.add(new Isotope("Beryllium-9", 9, 9.0121822));
 		beryllium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element boron = new Element("Boron", "B", 5, null, 10.811);
 		iList.add(new Isotope("Boron-10", 10, 10.012937));
 		iList.add(new Isotope("Boron-11", 11, 11.0093054));
 		boron.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element carbon = new Element("Carbon", "C", 6, null, 12.0107);
 		iList.add(new Isotope("Carbon-12", 12, 12.0));
 		iList.add(new Isotope("Carbon-13", 13, 13.0033548378));
 		iList.add(new Isotope("Carbon-14", 14, 14.003241989));
 		carbon.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element nitrogen = new Element("Nitrogen", "N", 7, null, 14.0067);
 		iList.add(new Isotope("Nitrogen-14", 14, 14.0030740048));
 		iList.add(new Isotope("Nitrogen-15", 15, 15.0001088982));
 		nitrogen.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element oxygen = new Element("Oxygen", "O", 8, null, 15.9994);
 		iList.add(new Isotope("Oxygen-16", 16, 15.99491461956));
 		iList.add(new Isotope("Oxygen-17", 17, 16.9991317));
 		iList.add(new Isotope("Oxygen-18", 18, 17.999161));
 		oxygen.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element fluorine = new Element("Fluorine", "F", 9, null, 18.9984032);
 		iList.add(new Isotope("Fluorine-19", 19, 18.99840322));
 		fluorine.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element neon = new Element("Neon", "Ne", 10, null, 20.1797);
 		iList.add(new Isotope("Neon-20", 20, 19.9924401754));
 		iList.add(new Isotope("Neon-21", 21, 20.99384668));
 		iList.add(new Isotope("Neon-22", 22, 21.991385114));
 		neon.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element sodium = new Element("Sodium", "Na", 11, null, 22.98976928);
 		iList.add(new Isotope("Sodium-23", 23, 22.9897692809));
 		sodium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element magnesium = new Element("Magnesium", "Mg", 12, null, 24.305);
 		iList.add(new Isotope("Magnesium-24", 24, 23.9850417));
 		iList.add(new Isotope("Magnesium-25", 25, 24.98583692));
 		iList.add(new Isotope("Magnesium-26", 26, 25.982592929));
 		magnesium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element aluminium = new Element("Aluminium", "Al", 13, null, 26.9815386);
 		iList.add(new Isotope("Aluminium-27", 27, 26.98153863));
 		aluminium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element silicon = new Element("Silicon", "Si", 14, null, 28.0855);
 		iList.add(new Isotope("Silicon-28", 28, 27.9769265325));
 		iList.add(new Isotope("Silicon-29", 29, 28.9764947));
 		iList.add(new Isotope("Silicon-30", 30, 29.97377017));
 		silicon.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element phosphorus = new Element("Phosphorus", "P", 15, null, 30.973762);
 		iList.add(new Isotope("Phosphorus-31", 31, 30.97376163));
 		phosphorus.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element sulfur = new Element("Sulfur", "S", 16, null, 32.065);
 		iList.add(new Isotope("Sulfur-32", 32, 31.972071));
 		iList.add(new Isotope("Sulfur-33", 33, 32.97145876));
@@ -161,27 +161,27 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Sulfur-36", 36, 35.96708076));
 		sulfur.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element chlorine = new Element("Chlorine", "Cl", 17, null, 35.453);
 		iList.add(new Isotope("Chlorine-35", 35, 34.96885268));
 		iList.add(new Isotope("Chlorine-37", 37, 36.96590259));
 		chlorine.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element argon = new Element("Argon", "Ar", 18, null, 39.948);
 		iList.add(new Isotope("Argon-36", 36, 35.967545106));
 		iList.add(new Isotope("Argon-38", 38, 37.9627324));
 		iList.add(new Isotope("Argon-40", 40, 39.9623831225));
 		argon.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element potassium = new Element("Potassium", "K", 19, null, 39.0983);
 		iList.add(new Isotope("Potassium-39", 39, 38.96370668));
 		iList.add(new Isotope("Potassium-40", 40, 39.96399848));
 		iList.add(new Isotope("Potassium-41", 41, 40.96182576));
 		potassium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element calcium = new Element("Calcium", "Ca", 20, null, 40.078);
 		iList.add(new Isotope("Calcium-40", 40, 39.96259098));
 		iList.add(new Isotope("Calcium-42", 42, 41.95861801));
@@ -191,12 +191,12 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Calcium-48", 48, 47.952534));
 		calcium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element scandium = new Element("Scandium", "Sc", 21, null, 44.955912);
 		iList.add(new Isotope("Scandium-45", 45, 44.9559119));
 		scandium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element titanium = new Element("Titanium", "Ti", 22, null, 47.867);
 		iList.add(new Isotope("Titanium-46", 46, 45.9526316));
 		iList.add(new Isotope("Titanium-47", 47, 46.9517631));
@@ -205,13 +205,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Titanium-50", 50, 49.9447912));
 		titanium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element vanadium = new Element("Vanadium", "V", 23, null, 50.9415);
 		iList.add(new Isotope("Vanadium-50", 50, 49.9471585));
 		iList.add(new Isotope("Vanadium-51", 51, 50.9439595));
 		vanadium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element chromium = new Element("Chromium", "Cr", 24, null, 51.9961);
 		iList.add(new Isotope("Chromium-50", 50, 49.9460442));
 		iList.add(new Isotope("Chromium-52", 52, 51.9405075));
@@ -219,12 +219,12 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Chromium-54", 54, 53.9388804));
 		chromium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element manganese = new Element("Manganese", "Mn", 25, null, 54.938045);
 		iList.add(new Isotope("Manganese-55", 55, 54.9380451));
 		manganese.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element iron = new Element("Iron", "Fe", 26, null, 55.845);
 		iList.add(new Isotope("Iron-54", 54, 53.9396105));
 		iList.add(new Isotope("Iron-56", 56, 55.9349375));
@@ -232,12 +232,12 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Iron-58", 58, 57.9332756));
 		iron.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element cobalt = new Element("Cobalt", "Co", 27, null, 58.933195);
 		iList.add(new Isotope("Cobalt-59", 59, 58.933195));
 		cobalt.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element nickel = new Element("Nickel", "Ni", 28, null, 58.6934);
 		iList.add(new Isotope("Nickel-58", 58, 57.9353429));
 		iList.add(new Isotope("Nickel-60", 60, 59.9307864));
@@ -246,13 +246,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Nickel-64", 64, 63.927966));
 		nickel.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element copper = new Element("Copper", "Cu", 29, null, 63.546);
 		iList.add(new Isotope("Copper-63", 63, 62.9295975));
 		iList.add(new Isotope("Copper-65", 65, 64.9277895));
 		copper.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element zinc = new Element("Zinc", "Zn", 30, null, 65.38);
 		iList.add(new Isotope("Zinc-64", 64, 63.9291422));
 		iList.add(new Isotope("Zinc-66", 66, 65.9260334));
@@ -261,13 +261,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Zinc-70", 70, 69.9253193));
 		zinc.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element gallium = new Element("Gallium", "Ga", 31, null, 69.723);
 		iList.add(new Isotope("Gallium-69", 69, 68.9255736));
 		iList.add(new Isotope("Gallium-71", 71, 70.9247013));
 		gallium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element germanium = new Element("Germanium", "Ge", 32, null, 72.64);
 		iList.add(new Isotope("Germanium-70", 70, 69.9242474));
 		iList.add(new Isotope("Germanium-72", 72, 71.9220758));
@@ -276,12 +276,12 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Germanium-76", 76, 75.9214026));
 		germanium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element arsenic = new Element("Arsenic", "As", 33, null, 74.9216);
 		iList.add(new Isotope("Arsenic-75", 75, 74.9215965));
 		arsenic.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element selenium = new Element("Selenium", "Se", 34, null, 78.96);
 		iList.add(new Isotope("Selenium-74", 74, 73.9224764));
 		iList.add(new Isotope("Selenium-76", 76, 75.9192136));
@@ -291,13 +291,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Selenium-82", 82, 81.9166994));
 		selenium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element bromine = new Element("Bromine", "Br", 35, null, 79.904);
 		iList.add(new Isotope("Bromine-79", 79, 78.9183371));
 		iList.add(new Isotope("Bromine-81", 81, 80.9162906));
 		bromine.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element krypton = new Element("Krypton", "Kr", 36, null, 83.798);
 		iList.add(new Isotope("Krypton-78", 78, 77.9203648));
 		iList.add(new Isotope("Krypton-80", 80, 79.916379));
@@ -307,13 +307,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Krypton-86", 86, 85.91061073));
 		krypton.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element rubidium = new Element("Rubidium", "Rb", 37, null, 85.4678);
 		iList.add(new Isotope("Rubidium-85", 85, 84.911789738));
 		iList.add(new Isotope("Rubidium-87", 87, 86.909180527));
 		rubidium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element strontium = new Element("Strontium", "Sr", 38, null, 87.62);
 		iList.add(new Isotope("Strontium-84", 84, 83.913425));
 		iList.add(new Isotope("Strontium-86", 86, 85.9092602));
@@ -321,12 +321,12 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Strontium-88", 88, 87.9056121));
 		strontium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element yttrium = new Element("Yttrium", "Y", 39, null, 88.90585);
 		iList.add(new Isotope("Yttrium-89", 89, 88.9058483));
 		yttrium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element zirconium = new Element("Zirconium", "Zr", 40, null, 91.224);
 		iList.add(new Isotope("Zirconium-90", 90, 89.9047044));
 		iList.add(new Isotope("Zirconium-91", 91, 90.9056458));
@@ -335,12 +335,12 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Zirconium-96", 96, 95.9082734));
 		zirconium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element niobium = new Element("Niobium", "Nb", 41, null, 92.90638);
 		iList.add(new Isotope("Niobium-93", 93, 92.9063781));
 		niobium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element molybdenum = new Element("Molybdenum", "Mo", 42, null, 95.96);
 		iList.add(new Isotope("Molybdenum-92", 92, 91.906811));
 		iList.add(new Isotope("Molybdenum-94", 94, 93.9050883));
@@ -351,14 +351,14 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Molybdenum-100", 100, 99.907477));
 		molybdenum.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element technetium = new Element("Technetium", "Tc", 43, null, 98.0);
 		iList.add(new Isotope("Technetium-97", 97, 96.906365));
 		iList.add(new Isotope("Technetium-98", 98, 97.907216));
 		iList.add(new Isotope("Technetium-99", 99, 98.9062547));
 		technetium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element ruthenium = new Element("Ruthenium", "Ru", 44, null, 101.07);
 		iList.add(new Isotope("Ruthenium-96", 96, 95.907598));
 		iList.add(new Isotope("Ruthenium-98", 98, 97.905287));
@@ -369,12 +369,12 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Ruthenium-104", 104, 103.905433));
 		ruthenium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element rhodium = new Element("Rhodium", "Rh", 45, null, 102.9055);
 		iList.add(new Isotope("Rhodium-103", 103, 102.905504));
 		rhodium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element palladium = new Element("Palladium", "Pd", 46, null, 106.42);
 		iList.add(new Isotope("Palladium-102", 102, 101.905609));
 		iList.add(new Isotope("Palladium-104", 104, 103.904036));
@@ -384,13 +384,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Palladium-110", 110, 109.905153));
 		palladium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element silver = new Element("Silver", "Ag", 47, null, 107.8682);
 		iList.add(new Isotope("Silver-107", 107, 106.905097));
 		iList.add(new Isotope("Silver-109", 109, 108.904752));
 		silver.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element cadmium = new Element("Cadmium", "Cd", 48, null, 112.411);
 		iList.add(new Isotope("Cadmium-106", 106, 105.906459));
 		iList.add(new Isotope("Cadmium-108", 108, 107.904184));
@@ -402,13 +402,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Cadmium-116", 116, 115.904756));
 		cadmium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element indium = new Element("Indium", "In", 49, null, 114.818);
 		iList.add(new Isotope("Indium-113", 113, 112.904058));
 		iList.add(new Isotope("Indium-115", 115, 114.903878));
 		indium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element tin = new Element("Tin", "Sn", 50, null, 118.71);
 		iList.add(new Isotope("Tin-112", 112, 111.904818));
 		iList.add(new Isotope("Tin-114", 114, 113.902779));
@@ -422,13 +422,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Tin-124", 124, 123.9052739));
 		tin.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element antimony = new Element("Antimony", "Sb", 51, null, 121.76);
 		iList.add(new Isotope("Antimony-121", 121, 120.9038157));
 		iList.add(new Isotope("Antimony-123", 123, 122.904214));
 		antimony.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element tellurium = new Element("Tellurium", "Te", 52, null, 127.6);
 		iList.add(new Isotope("Tellurium-120", 120, 119.90402));
 		iList.add(new Isotope("Tellurium-122", 122, 121.9030439));
@@ -440,12 +440,12 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Tellurium-130", 130, 129.9062244));
 		tellurium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element iodine = new Element("Iodine", "I", 53, null, 126.90447);
 		iList.add(new Isotope("Iodine-127", 127, 126.904473));
 		iodine.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element xenon = new Element("Xenon", "Xe", 54, null, 131.293);
 		iList.add(new Isotope("Xenon-124", 124, 123.905893));
 		iList.add(new Isotope("Xenon-126", 126, 125.904274));
@@ -458,12 +458,12 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Xenon-136", 136, 135.907219));
 		xenon.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element caesium = new Element("Caesium", "Cs", 55, null, 132.9054519);
 		iList.add(new Isotope("Caesium-133", 133, 132.905451933));
 		caesium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element barium = new Element("Barium", "Ba", 56, null, 137.327);
 		iList.add(new Isotope("Barium-130", 130, 129.9063208));
 		iList.add(new Isotope("Barium-132", 132, 131.9050613));
@@ -474,13 +474,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Barium-138", 138, 137.9052472));
 		barium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element lanthanum = new Element("Lanthanum", "La", 57, null, 138.90547);
 		iList.add(new Isotope("Lanthanum-138", 138, 137.907112));
 		iList.add(new Isotope("Lanthanum-139", 139, 138.9063533));
 		lanthanum.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element cerium = new Element("Cerium", "Ce", 58, null, 140.116);
 		iList.add(new Isotope("Cerium-136", 136, 135.907172));
 		iList.add(new Isotope("Cerium-138", 138, 137.905991));
@@ -488,12 +488,12 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Cerium-142", 142, 141.909244));
 		cerium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element praseodymium = new Element("Praseodymium", "Pr", 59, null, 140.90765);
 		iList.add(new Isotope("Praseodymium-141", 141, 140.9076528));
 		praseodymium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element neodymium = new Element("Neodymium", "Nd", 60, null, 144.242);
 		iList.add(new Isotope("Neodymium-142", 142, 141.9077233));
 		iList.add(new Isotope("Neodymium-143", 143, 142.9098143));
@@ -504,13 +504,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Neodymium-150", 150, 149.920891));
 		neodymium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element promethium = new Element("Promethium", "Pm", 61, null, 145.0);
 		iList.add(new Isotope("Promethium-145", 145, 144.912749));
 		iList.add(new Isotope("Promethium-147", 147, 146.9151385));
 		promethium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element samarium = new Element("Samarium", "Sm", 62, null, 150.36);
 		iList.add(new Isotope("Samarium-144", 144, 143.911999));
 		iList.add(new Isotope("Samarium-147", 147, 146.9148979));
@@ -521,13 +521,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Samarium-154", 154, 153.9222093));
 		samarium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element europium = new Element("Europium", "Eu", 63, null, 151.964);
 		iList.add(new Isotope("Europium-151", 151, 150.9198502));
 		iList.add(new Isotope("Europium-153", 153, 152.9212303));
 		europium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element gadolinium = new Element("Gadolinium", "Gd", 64, null, 157.25);
 		iList.add(new Isotope("Gadolinium-152", 152, 151.919791));
 		iList.add(new Isotope("Gadolinium-154", 154, 153.9208656));
@@ -538,12 +538,12 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Gadolinium-160", 160, 159.9270541));
 		gadolinium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element terbium = new Element("Terbium", "Tb", 65, null, 158.92535);
 		iList.add(new Isotope("Terbium-159", 159, 158.9253468));
 		terbium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element dysprosium = new Element("Dysprosium", "Dy", 66, null, 162.5);
 		iList.add(new Isotope("Dysprosium-156", 156, 155.924283));
 		iList.add(new Isotope("Dysprosium-158", 158, 157.924409));
@@ -554,12 +554,12 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Dysprosium-164", 164, 163.9291748));
 		dysprosium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element holmium = new Element("Holmium", "Ho", 67, null, 164.93032);
 		iList.add(new Isotope("Holmium-165", 165, 164.9303221));
 		holmium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element erbium = new Element("Erbium", "Er", 68, null, 167.259);
 		iList.add(new Isotope("Erbium-162", 162, 161.928778));
 		iList.add(new Isotope("Erbium-164", 164, 163.9292));
@@ -569,12 +569,12 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Erbium-170", 170, 169.9354643));
 		erbium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element thulium = new Element("Thulium", "Tm", 69, null, 168.93421);
 		iList.add(new Isotope("Thulium-169", 169, 168.9342133));
 		thulium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element ytterbium = new Element("Ytterbium", "Yb", 70, null, 173.054);
 		iList.add(new Isotope("Ytterbium-168", 168, 167.933897));
 		iList.add(new Isotope("Ytterbium-170", 170, 169.9347618));
@@ -585,13 +585,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Ytterbium-176", 176, 175.9425717));
 		ytterbium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element lutetium = new Element("Lutetium", "Lu", 71, null, 174.9668);
 		iList.add(new Isotope("Lutetium-175", 175, 174.9407718));
 		iList.add(new Isotope("Lutetium-176", 176, 175.9426863));
 		lutetium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element hafnium = new Element("Hafnium", "Hf", 72, null, 178.49);
 		iList.add(new Isotope("Hafnium-174", 174, 173.940046));
 		iList.add(new Isotope("Hafnium-176", 176, 175.9414086));
@@ -601,13 +601,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Hafnium-180", 180, 179.94655));
 		hafnium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element tantalum = new Element("Tantalum", "Ta", 73, null, 180.94788);
 		iList.add(new Isotope("Tantalum-180", 180, 179.9474648));
 		iList.add(new Isotope("Tantalum-181", 181, 180.9479958));
 		tantalum.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element tungsten = new Element("Tungsten", "W", 74, null, 183.84);
 		iList.add(new Isotope("Tungsten-180", 180, 179.946704));
 		iList.add(new Isotope("Tungsten-182", 182, 181.9482042));
@@ -616,13 +616,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Tungsten-186", 186, 185.9543641));
 		tungsten.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element rhenium = new Element("Rhenium", "Re", 75, null, 186.207);
 		iList.add(new Isotope("Rhenium-185", 185, 184.952955));
 		iList.add(new Isotope("Rhenium-187", 187, 186.9557531));
 		rhenium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element osmium = new Element("Osmium", "Os", 76, null, 190.23);
 		iList.add(new Isotope("Osmium-184", 184, 183.9524891));
 		iList.add(new Isotope("Osmium-186", 186, 185.9538382));
@@ -633,13 +633,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Osmium-192", 192, 191.9614807));
 		osmium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element iridium = new Element("Iridium", "Ir", 77, null, 192.217);
 		iList.add(new Isotope("Iridium-191", 191, 190.960594));
 		iList.add(new Isotope("Iridium-193", 193, 192.9629264));
 		iridium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element platinum = new Element("Platinum", "Pt", 78, null, 195.084);
 		iList.add(new Isotope("Platinum-190", 190, 189.959932));
 		iList.add(new Isotope("Platinum-192", 192, 191.961038));
@@ -649,12 +649,12 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Platinum-198", 198, 197.967893));
 		platinum.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element gold = new Element("Gold", "Au", 79, null, 196.966569);
 		iList.add(new Isotope("Gold-197", 197, 196.9665687));
 		gold.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element mercury = new Element("Mercury", "Hg", 80, null, 200.59);
 		iList.add(new Isotope("Mercury-196", 196, 195.965833));
 		iList.add(new Isotope("Mercury-198", 198, 197.966769));
@@ -665,13 +665,13 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Mercury-204", 204, 203.9734939));
 		mercury.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element thallium = new Element("Thallium", "Tl", 81, null, 204.3833);
 		iList.add(new Isotope("Thallium-203", 203, 202.9723442));
 		iList.add(new Isotope("Thallium-205", 205, 204.9744275));
 		thallium.setIsotopes(iList);
 
-		iList = new ArrayList<Isotope>();
+		iList = new ArrayList<>();
 		Element lead = new Element("Lead", "Pb", 82, null, 207.2);
 		iList.add(new Isotope("Lead-204", 204, 203.9730436));
 		iList.add(new Isotope("Lead-206", 206, 205.9744653));
@@ -679,7 +679,7 @@ public void generateXml() throws JAXBException, IOException {
 		iList.add(new Isotope("Lead-208", 208, 207.9766521));
 		lead.setIsotopes(iList);
 
-		List<Element> eList = new ArrayList<Element>();
+		List<Element> eList = new ArrayList<>();
 		eList.add(hydrogen);
 		eList.add(helium);
 		eList.add(lithium);
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/GenerateJavaCodesFromTextTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/GenerateJavaCodesFromTextTest.java
index 45515d9b11..a23c24f5e2 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/GenerateJavaCodesFromTextTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/GenerateJavaCodesFromTextTest.java
@@ -43,7 +43,7 @@ public class GenerateJavaCodesFromTextTest {
 	//@Test
 	public void generateCodes() throws IOException{
 		BufferedReader input = new BufferedReader(new FileReader("./src/test/resources/Symbol2Name.txt"));
-		Map<String, String> symbol2Name = new HashMap<String, String>();
+		Map<String, String> symbol2Name = new HashMap<>();
 		String line = input.readLine();//Header line is not required
 		while((line = input.readLine()) != null){
 			String[] sA = line.split("\t");
@@ -52,10 +52,10 @@ public void generateCodes() throws IOException{
 		input.close();
 
 		input = new BufferedReader(new FileReader("./src/test/resources/Symbol2Weight.txt"));
-		List<String> elementNameList = new ArrayList<String>();
+		List<String> elementNameList = new ArrayList<>();
 		String elementName = null;
 		String elementNameLower = null;
-		Double elementMass = null;
+		Double elementMass;
 		while((line = input.readLine()) != null){
 			String[] sA = line.split("\t");
 			if(sA[0].length() > 0){
diff --git a/biojava-alignment/src/main/java/demo/CookbookMSA.java b/biojava-alignment/src/main/java/demo/CookbookMSA.java
index d2952bbeac..c617745539 100644
--- a/biojava-alignment/src/main/java/demo/CookbookMSA.java
+++ b/biojava-alignment/src/main/java/demo/CookbookMSA.java
@@ -43,7 +43,7 @@ public static void main(String[] args) throws Exception {
 	}
 
 	private static void multipleSequenceAlignment(String[] ids) throws Exception {
-		List<ProteinSequence> lst = new ArrayList<ProteinSequence>();
+		List<ProteinSequence> lst = new ArrayList<>();
 		for (String id : ids) {
 			lst.add(getSequenceForId(id));
 		}
diff --git a/biojava-alignment/src/main/java/demo/DemoDistanceTree.java b/biojava-alignment/src/main/java/demo/DemoDistanceTree.java
index c9f82d39f7..4cf86d7cc3 100644
--- a/biojava-alignment/src/main/java/demo/DemoDistanceTree.java
+++ b/biojava-alignment/src/main/java/demo/DemoDistanceTree.java
@@ -58,11 +58,11 @@ public static void main(String[] args) throws Exception {
 				.getResourceAsStream("/PF00104_small.fasta");
 
 		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader =
-				new FastaReader<ProteinSequence, AminoAcidCompound>(
-				inStream,
-				new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
-				new ProteinSequenceCreator(AminoAcidCompoundSet
-						.getAminoAcidCompoundSet()));
+				new FastaReader<>(
+						inStream,
+						new GenericFastaHeaderParser<>(),
+						new ProteinSequenceCreator(AminoAcidCompoundSet
+								.getAminoAcidCompoundSet()));
 
 		LinkedHashMap<String, ProteinSequence> proteinSequences =
 				fastaReader.process();
@@ -70,7 +70,7 @@ public static void main(String[] args) throws Exception {
 		inStream.close();
 
 		MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> msa =
-				new MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound>();
+				new MultipleSequenceAlignment<>();
 
 		for (ProteinSequence proteinSequence : proteinSequences.values()) {
 			msa.addAlignedSequence(proteinSequence);
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
index 4ed72d0979..6584a22c0a 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
@@ -58,7 +58,7 @@ public class Alignments {
 	/**
 	 * List of implemented sequence pair in a profile scoring routines.
 	 */
-	public static enum PairInProfileScorerType {
+	public enum PairInProfileScorerType {
 		IDENTITIES,  // similar to MUSCLE
 		SIMILARITIES
 	}
@@ -66,7 +66,7 @@ public static enum PairInProfileScorerType {
 	/**
 	 * List of implemented pairwise sequence alignment routines.
 	 */
-	public static enum PairwiseSequenceAlignerType {
+	public enum PairwiseSequenceAlignerType {
 		GLOBAL,              // Needleman-Wunsch/Gotoh
 		GLOBAL_LINEAR_SPACE, // Guan-Uberbacher
 		LOCAL,               // Smith-Waterman/Gotoh
@@ -76,7 +76,7 @@ public static enum PairwiseSequenceAlignerType {
 	/**
 	 * List of implemented pairwise sequence scoring routines.
 	 */
-	public static enum PairwiseSequenceScorerType {
+	public enum PairwiseSequenceScorerType {
 		GLOBAL,
 		GLOBAL_IDENTITIES,   // similar to CLUSTALW and CLUSTALW2
 		GLOBAL_SIMILARITIES,
@@ -90,7 +90,7 @@ public static enum PairwiseSequenceScorerType {
 	/**
 	 * List of implemented profile-profile alignment routines.
 	 */
-	public static enum ProfileProfileAlignerType {
+	public enum ProfileProfileAlignerType {
 		GLOBAL,              // similar to MUSCLE and KALIGN
 		GLOBAL_LINEAR_SPACE, // similar to CLUSTALW and CLUSTALW2
 		GLOBAL_CONSENSUS,    // similar to CLUSTAL
@@ -102,7 +102,7 @@ public static enum ProfileProfileAlignerType {
 	/**
 	 * List of implemented profile refinement routines.
 	 */
-	public static enum RefinerType {
+	public enum RefinerType {
 		PARTITION_SINGLE,     // similar to CLUSTALW2
 		PARTITION_SINGLE_ALL, // similar to CLUSTALW2
 		PARTITION_TREE,       // similar to MUSCLE
@@ -189,7 +189,7 @@ public static <S extends Sequence<C>, C extends Compound> Profile<S, C> getMulti
 		runPairwiseScorers(scorers);
 
 		// stage 2: hierarchical clustering into a guide tree
-		GuideTree<S, C> tree = new GuideTree<S, C>(sequences, scorers);
+		GuideTree<S, C> tree = new GuideTree<>(sequences, scorers);
 		scorers = null;
 
 		// stage 3: progressive alignment
@@ -233,7 +233,7 @@ public static <S extends Sequence<C>, C extends Compound> SequencePair<S, C> get
 	static <S extends Sequence<C>, C extends Compound> List<PairwiseSequenceAligner<S, C>> getAllPairsAligners(
 			List<S> sequences, PairwiseSequenceAlignerType type, GapPenalty gapPenalty,
 			SubstitutionMatrix<C> subMatrix) {
-		List<PairwiseSequenceAligner<S, C>> allPairs = new ArrayList<PairwiseSequenceAligner<S, C>>();
+		List<PairwiseSequenceAligner<S, C>> allPairs = new ArrayList<>();
 		for (int i = 0; i < sequences.size(); i++) {
 			for (int j = i+1; j < sequences.size(); j++) {
 				allPairs.add(getPairwiseAligner(sequences.get(i), sequences.get(j), type, gapPenalty, subMatrix));
@@ -256,7 +256,7 @@ static <S extends Sequence<C>, C extends Compound> List<PairwiseSequenceAligner<
 	public static <S extends Sequence<C>, C extends Compound> List<PairwiseSequenceScorer<S, C>> getAllPairsScorers(
 			List<S> sequences, PairwiseSequenceScorerType type, GapPenalty gapPenalty,
 			SubstitutionMatrix<C> subMatrix) {
-		List<PairwiseSequenceScorer<S, C>> allPairs = new ArrayList<PairwiseSequenceScorer<S, C>>();
+		List<PairwiseSequenceScorer<S, C>> allPairs = new ArrayList<>();
 		for (int i = 0; i < sequences.size(); i++) {
 			for (int j = i+1; j < sequences.size(); j++) {
 				allPairs.add(getPairwiseScorer(sequences.get(i), sequences.get(j), type, gapPenalty, subMatrix));
@@ -291,7 +291,7 @@ public static <S extends Sequence<C>, C extends Compound> double[] getAllPairsSc
 	 * @return calculated elements
 	 */
 	static <E> List<E> getListFromFutures(List<Future<E>> futures) {
-		List<E> list = new ArrayList<E>();
+		List<E> list = new ArrayList<>();
 		for (Future<E> f : futures) {
 			// TODO when added to ConcurrencyTools, log completions and exceptions instead of printing stack traces
 			try {
@@ -326,9 +326,9 @@ public static <S extends Sequence<C>, C extends Compound> PairwiseSequenceAligne
 		switch (type) {
 		default:
 		case GLOBAL:
-			return new NeedlemanWunsch<S, C>(query, target, gapPenalty, subMatrix);
+			return new NeedlemanWunsch<>(query, target, gapPenalty, subMatrix);
 		case LOCAL:
-			return new SmithWaterman<S, C>(query, target, gapPenalty, subMatrix);
+			return new SmithWaterman<>(query, target, gapPenalty, subMatrix);
 		case GLOBAL_LINEAR_SPACE:
 		case LOCAL_LINEAR_SPACE:
 			// TODO other alignment options (Myers-Miller, Thompson)
@@ -374,18 +374,18 @@ static <S extends Sequence<C>, C extends Compound> PairwiseSequenceScorer<S, C>
 		case GLOBAL:
 			return getPairwiseAligner(query, target, PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix);
 		case GLOBAL_IDENTITIES:
-			return new FractionalIdentityScorer<S, C>(getPairwiseAligner(query, target,
+			return new FractionalIdentityScorer<>(getPairwiseAligner(query, target,
 					PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix));
 		case GLOBAL_SIMILARITIES:
-			return new FractionalSimilarityScorer<S, C>(getPairwiseAligner(query, target,
+			return new FractionalSimilarityScorer<>(getPairwiseAligner(query, target,
 					PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix));
 		case LOCAL:
 			return getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix);
 		case LOCAL_IDENTITIES:
-			return new FractionalIdentityScorer<S, C>(getPairwiseAligner(query, target,
+			return new FractionalIdentityScorer<>(getPairwiseAligner(query, target,
 					PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix));
 		case LOCAL_SIMILARITIES:
-			return new FractionalSimilarityScorer<S, C>(getPairwiseAligner(query, target,
+			return new FractionalSimilarityScorer<>(getPairwiseAligner(query, target,
 					PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix));
 		case KMERS:
 		case WU_MANBER:
@@ -413,7 +413,7 @@ static <S extends Sequence<C>, C extends Compound> ProfileProfileAligner<S, C> g
 		switch (type) {
 		default:
 		case GLOBAL:
-			return new SimpleProfileProfileAligner<S, C>(profile1, profile2, gapPenalty, subMatrix);
+			return new SimpleProfileProfileAligner<>(profile1, profile2, gapPenalty, subMatrix);
 		case GLOBAL_LINEAR_SPACE:
 		case GLOBAL_CONSENSUS:
 		case LOCAL:
@@ -443,7 +443,7 @@ static <S extends Sequence<C>, C extends Compound> ProfileProfileAligner<S, C> g
 		switch (type) {
 		default:
 		case GLOBAL:
-			return new SimpleProfileProfileAligner<S, C>(profile1, profile2, gapPenalty, subMatrix);
+			return new SimpleProfileProfileAligner<>(profile1, profile2, gapPenalty, subMatrix);
 		case GLOBAL_LINEAR_SPACE:
 		case GLOBAL_CONSENSUS:
 		case LOCAL:
@@ -473,7 +473,7 @@ static <S extends Sequence<C>, C extends Compound> ProfileProfileAligner<S, C> g
 		switch (type) {
 		default:
 		case GLOBAL:
-			return new SimpleProfileProfileAligner<S, C>(profile1, profile2, gapPenalty, subMatrix);
+			return new SimpleProfileProfileAligner<>(profile1, profile2, gapPenalty, subMatrix);
 		case GLOBAL_LINEAR_SPACE:
 		case GLOBAL_CONSENSUS:
 		case LOCAL:
@@ -503,7 +503,7 @@ static <S extends Sequence<C>, C extends Compound> ProfileProfileAligner<S, C> g
 		switch (type) {
 		default:
 		case GLOBAL:
-			return new SimpleProfileProfileAligner<S, C>(profile1, profile2, gapPenalty, subMatrix);
+			return new SimpleProfileProfileAligner<>(profile1, profile2, gapPenalty, subMatrix);
 		case GLOBAL_LINEAR_SPACE:
 		case GLOBAL_CONSENSUS:
 		case LOCAL:
@@ -550,7 +550,7 @@ public static <S extends Sequence<C>, C extends Compound> Profile<S, C> getProgr
 			ProfileProfileAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) {
 
 		// find inner nodes in post-order traversal of tree (each leaf node has a single sequence profile)
-		List<GuideTreeNode<S, C>> innerNodes = new ArrayList<GuideTreeNode<S, C>>();
+		List<GuideTreeNode<S, C>> innerNodes = new ArrayList<>();
 		for (GuideTreeNode<S, C> n : tree) {
 			if (n.getProfile() == null) {
 				innerNodes.add(n);
@@ -567,7 +567,7 @@ public static <S extends Sequence<C>, C extends Compound> Profile<S, C> getProgr
 							getProfileProfileAligner(p1, pf2, type, gapPenalty, subMatrix)) :
 					((p2 != null) ? getProfileProfileAligner(pf1, p2, type, gapPenalty, subMatrix) :
 							getProfileProfileAligner(pf1, pf2, type, gapPenalty, subMatrix));
-			n.setProfileFuture(ConcurrencyTools.submit(new CallableProfileProfileAligner<S, C>(aligner), String.format(
+			n.setProfileFuture(ConcurrencyTools.submit(new CallableProfileProfileAligner<>(aligner), String.format(
 					"Aligning pair %d of %d", i++, all)));
 		}
 
@@ -599,9 +599,9 @@ public static <S extends Sequence<C>, C extends Compound> Profile<S, C> getProgr
 	static <S extends Sequence<C>, C extends Compound> List<SequencePair<S, C>>
 			runPairwiseAligners(List<PairwiseSequenceAligner<S, C>> aligners) {
 		int n = 1, all = aligners.size();
-		List<Future<SequencePair<S, C>>> futures = new ArrayList<Future<SequencePair<S, C>>>();
+		List<Future<SequencePair<S, C>>> futures = new ArrayList<>();
 		for (PairwiseSequenceAligner<S, C> aligner : aligners) {
-			futures.add(ConcurrencyTools.submit(new CallablePairwiseSequenceAligner<S, C>(aligner),
+			futures.add(ConcurrencyTools.submit(new CallablePairwiseSequenceAligner<>(aligner),
 					String.format("Aligning pair %d of %d", n++, all)));
 		}
 		return getListFromFutures(futures);
@@ -619,9 +619,9 @@ public static <S extends Sequence<C>, C extends Compound> Profile<S, C> getProgr
 	public static <S extends Sequence<C>, C extends Compound> double[] runPairwiseScorers(
 			List<PairwiseSequenceScorer<S, C>> scorers) {
 		int n = 1, all = scorers.size();
-		List<Future<Double>> futures = new ArrayList<Future<Double>>();
+		List<Future<Double>> futures = new ArrayList<>();
 		for (PairwiseSequenceScorer<S, C> scorer : scorers) {
-			futures.add(ConcurrencyTools.submit(new CallablePairwiseSequenceScorer<S, C>(scorer),
+			futures.add(ConcurrencyTools.submit(new CallablePairwiseSequenceScorer<>(scorer),
 					String.format("Scoring pair %d of %d", n++, all)));
 		}
 		List<Double> results = getListFromFutures(futures);
@@ -644,9 +644,9 @@ public static <S extends Sequence<C>, C extends Compound> double[] runPairwiseSc
 	static <S extends Sequence<C>, C extends Compound> List<ProfilePair<S, C>>
 			runProfileAligners(List<ProfileProfileAligner<S, C>> aligners) {
 		int n = 1, all = aligners.size();
-		List<Future<ProfilePair<S, C>>> futures = new ArrayList<Future<ProfilePair<S, C>>>();
+		List<Future<ProfilePair<S, C>>> futures = new ArrayList<>();
 		for (ProfileProfileAligner<S, C> aligner : aligners) {
-			futures.add(ConcurrencyTools.submit(new CallableProfileProfileAligner<S, C>(aligner),
+			futures.add(ConcurrencyTools.submit(new CallableProfileProfileAligner<>(aligner),
 					String.format("Aligning pair %d of %d", n++, all)));
 		}
 		return getListFromFutures(futures);
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityInProfileScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityInProfileScorer.java
index c84ea753d9..179a4cf1ce 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityInProfileScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityInProfileScorer.java
@@ -41,7 +41,7 @@
 public class FractionalIdentityInProfileScorer<S extends Sequence<C>, C extends Compound>
 		extends FractionalIdentityScorer<S, C> implements PairInProfileScorer<S, C> {
 
-	private Profile<S, C> profile;
+	private final Profile<S, C> profile;
 
 	/**
 	 * Creates a fractional identity scorer for an aligned pair of sequences in the given alignment profile.
@@ -51,7 +51,7 @@ public class FractionalIdentityInProfileScorer<S extends Sequence<C>, C extends
 	 * @param target index in the profile of the second sequence of the pair
 	 */
 	public FractionalIdentityInProfileScorer(Profile<S, C> profile, int query, int target) {
-		super(new SimpleSequencePair<S, C>(profile.getAlignedSequence(query), profile.getAlignedSequence(target)));
+		super(new SimpleSequencePair<>(profile.getAlignedSequence(query), profile.getAlignedSequence(target)));
 		this.profile = profile;
 	}
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java
index 4b494db779..9217cfbe4d 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java
@@ -40,7 +40,8 @@ public class FractionalIdentityScorer<S extends Sequence<C>, C extends Compound>
 		implements PairwiseSequenceScorer<S, C> {
 
 	// always stored
-	private S query, target;
+	private final S query;
+    private final S target;
 	private int max, score;
 
 	// optional cached input field
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityInProfileScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityInProfileScorer.java
index ecd975d459..52292e27e3 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityInProfileScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityInProfileScorer.java
@@ -41,7 +41,7 @@
 public class FractionalSimilarityInProfileScorer<S extends Sequence<C>, C extends Compound>
 		extends FractionalSimilarityScorer<S, C> implements PairInProfileScorer<S, C> {
 
-	private Profile<S, C> profile;
+	private final Profile<S, C> profile;
 
 	/**
 	 * Creates a fractional similarity scorer for an aligned pair of sequences in the given alignment profile.
@@ -51,7 +51,7 @@ public class FractionalSimilarityInProfileScorer<S extends Sequence<C>, C extend
 	 * @param target index in the profile of the second sequence of the pair
 	 */
 	public FractionalSimilarityInProfileScorer(Profile<S, C> profile, int query, int target) {
-		super(new SimpleSequencePair<S, C>(profile.getAlignedSequence(query), profile.getAlignedSequence(target)));
+		super(new SimpleSequencePair<>(profile.getAlignedSequence(query), profile.getAlignedSequence(target)));
 		this.profile = profile;
 	}
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java
index 05911367f8..cecfb87932 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java
@@ -40,7 +40,8 @@ public class FractionalSimilarityScorer<S extends Sequence<C>, C extends Compoun
 		implements PairwiseSequenceScorer<S, C> {
 
 	// always stored
-	private S query, target;
+	private final S query;
+    private final S target;
 	private int max, score;
 
 	// optional cached input field
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java
index ecbcf66e79..5b4fd7d099 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java
@@ -54,11 +54,11 @@
  */
 public class GuideTree<S extends Sequence<C>, C extends Compound> implements Iterable<GuideTreeNode<S, C>> {
 
-	private List<S> sequences;
-	private List<PairwiseSequenceScorer<S, C>> scorers;
-	private BasicSymmetricalDistanceMatrix distances;
-	private String newick;
-	private Node root;
+	private final List<S> sequences;
+	private final List<PairwiseSequenceScorer<S, C>> scorers;
+	private final BasicSymmetricalDistanceMatrix distances;
+	private final String newick;
+	private final Node root;
 
 	/**
 	 * Creates a guide tree for use during progressive multiple sequence alignment.
@@ -170,10 +170,13 @@ public String toString() {
 	 */
 	public class Node implements GuideTreeNode<S, C> {
 
-		private GuideTreeNode<S, C> parent, child1, child2;
-		private double distance;
-		private String name;
-		private boolean isLeaf, isVisited;
+		private final GuideTreeNode<S, C> parent;
+		private GuideTreeNode<S, C> child1;
+		private GuideTreeNode<S, C> child2;
+		private final double distance;
+		private final String name;
+		private final boolean isLeaf;
+		private boolean isVisited;
 		private Profile<S, C> profile;
 		private Future<ProfilePair<S, C>> profileFuture;
 
@@ -182,7 +185,7 @@ private Node(PhylogenyNode node, Node parent) {
 			distance = node.getDistanceToParent();
 			name = node.getName();
 			if(isLeaf = node.isExternal()) {
-				profile = new SimpleProfile<S, C>(sequences.get(distances.getIndex(name)));
+				profile = new SimpleProfile<>(sequences.get(distances.getIndex(name)));
 			} else {
 				child1 = new Node(node.getChildNode1(), this);
 				child2 = new Node(node.getChildNode2(), this);
@@ -237,7 +240,7 @@ public void setProfileFuture(Future<ProfilePair<S, C>> profileFuture) {
 
 		@Override
 		public Enumeration<GuideTreeNode<S, C>> children() {
-			Vector<GuideTreeNode<S, C>> children = new Vector<GuideTreeNode<S, C>>();
+			Vector<GuideTreeNode<S, C>> children = new Vector<>();
 			children.add(getChild1());
 			children.add(getChild2());
 			return children.elements();
@@ -301,11 +304,11 @@ private void visit() {
 	// helper class that defines the default post-order (leaves to root) traversal
 	private class PostOrderIterator implements Iterator<GuideTreeNode<S, C>> {
 
-		private Stack<Node> nodes;
+		private final Stack<Node> nodes;
 
 		private PostOrderIterator() {
 			getRoot().clearVisited();
-			nodes = new Stack<Node>();
+			nodes = new Stack<>();
 			nodes.push(getRoot());
 		}
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java
index 73579ab8f4..47fb7976e0 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java
@@ -110,7 +110,7 @@ public SimpleProfileProfileAligner(Future<ProfilePair<S, C>> query, Profile<S, C
 
 	@Override
 	protected void setProfile(List<Step> sx, List<Step> sy) {
-		profile = pair = new SimpleProfilePair<S, C>(getQuery(), getTarget(), sx, sy);
+		profile = pair = new SimpleProfilePair<>(getQuery(), getTarget(), sx, sy);
 	}
 
 }
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SmithWaterman.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SmithWaterman.java
index 7d7e017694..819d8f5187 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SmithWaterman.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SmithWaterman.java
@@ -69,7 +69,7 @@ public SmithWaterman(S query, S target, GapPenalty gapPenalty, SubstitutionMatri
 
 	@Override
 	protected void setProfile(List<Step> sx, List<Step> sy) {
-		profile = pair = new SimpleSequencePair<S, C>(getQuery(), getTarget(), sx, xyStart[0],
+		profile = pair = new SimpleSequencePair<>(getQuery(), getTarget(), sx, xyStart[0],
 				getQuery().getLength() - xyMax[0], sy, xyStart[1], getTarget().getLength() - xyMax[1]);
 	}
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/StandardRescoreRefiner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/StandardRescoreRefiner.java
index 40c8dc1e76..f61670ebae 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/StandardRescoreRefiner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/StandardRescoreRefiner.java
@@ -34,8 +34,8 @@
 public class StandardRescoreRefiner<S extends Sequence<C>, C extends Compound> extends AbstractScorer
 		implements RescoreRefiner<S, C> {
 
-	private PairInProfileScorerType pips;
-	private ProfileProfileAlignerType ppa;
+	private final PairInProfileScorerType pips;
+	private final ProfileProfileAlignerType ppa;
 
 	public StandardRescoreRefiner(PairInProfileScorerType pips, ProfileProfileAlignerType ppa) {
 		this.pips = pips;
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SubstitutionMatrixScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SubstitutionMatrixScorer.java
index a903ebd1ce..a2a531c8ad 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SubstitutionMatrixScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SubstitutionMatrixScorer.java
@@ -40,8 +40,8 @@ public class SubstitutionMatrixScorer<S extends Sequence<C>, C extends Compound>
 
 	private final SubstitutionMatrix<C> matrix;
 
-	private S query;
-	private S target;
+	private final S query;
+	private final S target;
 	private double score;
 
 	public SubstitutionMatrixScorer(SequencePair<S, C> pair, SubstitutionMatrix<C> matrix) {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java
index ddeb03b451..7e5cbfa325 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java
@@ -125,7 +125,7 @@ public void setRefLocation(String refLocation) {
 	private Set<DatabaseReference> dbReferences;
 	private StringBuffer refComment;
 	/**TODO When implementing toString(), the function should loop on the vector */
-	private Vector<StockholmFileAnnotationReference> references = new Vector<StockholmFileAnnotation.StockholmFileAnnotationReference>();
+	private Vector<StockholmFileAnnotationReference> references = new Vector<>();
 	private StringBuffer keywords;
 	private CharSequence comment;
 	private StringBuffer pfamAccession;
@@ -137,7 +137,7 @@ public void setRefLocation(String refLocation) {
 	private float falseDiscoveryRate;
 
 	public StockholmFileAnnotation() {
-		embTrees = new HashMap<String, List<String>>();
+		embTrees = new HashMap<>();
 	}
 
 	public StringBuffer getDbComment() {
@@ -164,7 +164,7 @@ public void setDbReferences(Set<DatabaseReference> dbReferences) {
 	 */
 	public void addDBReference(String dbReferenceRepresentingString) {
 		if (this.dbReferences == null) {
-			this.dbReferences = new HashSet<DatabaseReference>();
+			this.dbReferences = new HashSet<>();
 		}
 		dbReferences.add(new DatabaseReference(dbReferenceRepresentingString));
 	}
@@ -492,7 +492,7 @@ public void setGFMembership(String membership) {
 	public void addGFNewHampshire(String newHampshire) {
 		List<String> hampshireTree = embTrees.get(TREE_DEFAULT_ID);
 		if (hampshireTree == null) {
-			hampshireTree = new ArrayList<String>();
+			hampshireTree = new ArrayList<>();
 		}
 		hampshireTree.add(newHampshire);
 		embTrees.put(TREE_DEFAULT_ID, hampshireTree);
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileParser.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileParser.java
index eb92301be9..5180bf1dbb 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileParser.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileParser.java
@@ -356,7 +356,7 @@ public List<StockholmStructure> parse(InputStream inStream, int max) throws IOEx
 		if (internalScanner == null) {
 			internalScanner = new Scanner(inStream);
 		}
-		ArrayList<StockholmStructure> structures = new ArrayList<StockholmStructure>();
+		ArrayList<StockholmStructure> structures = new ArrayList<>();
 		while (max != INFINITY && max-- > 0) {
 			StockholmStructure structure = parse(internalScanner);
 			if (structure != null) {
@@ -399,7 +399,7 @@ StockholmStructure parse(Scanner scanner) throws ParserException, IOException {
 				throw new IllegalArgumentException("No Scanner defined");
 			}
 		}
-		String line = null;
+		String line;
 		int linesCount = 0;
 		try {
 			while (scanner.hasNextLine()) {
@@ -507,9 +507,8 @@ StockholmStructure parse(Scanner scanner) throws ParserException, IOException {
 		if (structure != null) {
 			int length = -1;
 			Map<String, StringBuffer> sequences = structure.getSequences();
-			for (String sequencename : sequences.keySet()) {
-				StringBuffer sequence = sequences.get(sequencename);
-				if (length == -1) {
+			for (StringBuffer sequence : sequences.values()) {
+                if (length == -1) {
 					length = sequence.length();
 				} else if (length != sequence.length()) {
 					throw new RuntimeException("Sequences have different lengths");
@@ -544,79 +543,114 @@ private void handleSequenceLine(String line) throws ParserException {
 	 *            the line to be parsed
 	 */
 	private void handleFileAnnotation(String featureName, String value) {
-		if (featureName.equals(GF_ACCESSION_NUMBER)) {
-			stockholmStructure.getFileAnnotation().setGFAccessionNumber(value);
-		} else if (featureName.equals(GF_IDENTIFICATION)) {
-			stockholmStructure.getFileAnnotation().setGFIdentification(value);
-		} else if (featureName.equals(GF_DB_REFERENCE)) {
-			stockholmStructure.getFileAnnotation().addDBReference(value);
-		} else if (featureName.equals(GF_DEFINITION)) {
-			stockholmStructure.getFileAnnotation().setGFDefinition(value);
-		} else if (featureName.equals(GF_AUTHOR)) {
-			stockholmStructure.getFileAnnotation().setGFAuthors(value);
-		} else if (featureName.equals(GF_ALIGNMENT_METHOD)) {
-			stockholmStructure.getFileAnnotation().setAlignmentMethod(value);
-		} else if (featureName.equals(GF_BUILD_METHOD)) {
-			stockholmStructure.getFileAnnotation().addGFBuildMethod(value);
-		} else if (featureName.equals(GF_SEARCH_METHOD)) {
-			stockholmStructure.getFileAnnotation().setGFSearchMethod(value);
-		} else if (featureName.equals(GF_SOURCE_SEED)) {
-			stockholmStructure.getFileAnnotation().setGFSourceSeed(value);
-		} else if (featureName.equals(GF_SOURCE_STRUCTURE)) {
-			stockholmStructure.getFileAnnotation().setGFSourceStructure(value);
-		} else if (featureName.equals(GF_GATHERING_THRESHOLD)) {
-			stockholmStructure.getFileAnnotation().setGFGatheringThreshs(value);
-		} else if (featureName.equals(GF_TRUSTED_CUTOFF)) {
-			stockholmStructure.getFileAnnotation().setGFTrustedCutoffs(value);
-		} else if (featureName.equals(GF_NOISE_CUTOFF)) {
-			stockholmStructure.getFileAnnotation().setGFNoiseCutoffs(value);
-		} else if (featureName.equals(GF_TYPE_FIELD)) {
-			stockholmStructure.getFileAnnotation().setGFTypeField(value);
-		} else if (featureName.equals(GF_PREVIOUS_IDS)) {
-			stockholmStructure.getFileAnnotation().setGFPreviousIDs(value);
-		} else if (featureName.equals(GF_SEQUENCE)) {
-			// status = STATUS_IN_SEQUENCE;
-			stockholmStructure.getFileAnnotation().setGFNumSequences(value);
-		} else if (featureName.equals(GF_DB_COMMENT)) {
-			stockholmStructure.getFileAnnotation().setGFDBComment(value);
-			// } else if (featureName.equals(GF_DB_REFERENCE)) {
-			// stockholmStructure.getFileAnnotation().addDBReference(value);
-		} else if (featureName.equals(GF_REFERENCE_COMMENT)) {
-			stockholmStructure.getFileAnnotation().setGFRefComment(value);
-		} else if (featureName.equals(GF_REFERENCE_NUMBER)) {
-			StockholmFileAnnotationReference reference = new StockholmFileAnnotationReference();
-			stockholmStructure.getFileAnnotation().getReferences().add(reference);
-		} else if (featureName.equals(GF_REFERENCE_MEDLINE)) {
-			stockholmStructure.getFileAnnotation().getReferences().lastElement().setRefMedline(value);
-		} else if (featureName.equals(GF_REFERENCE_TITLE)) {
-			stockholmStructure.getFileAnnotation().getReferences().lastElement().addToRefTitle(value);
-		} else if (featureName.equals(GF_REFERENCE_AUTHOR)) {
-			stockholmStructure.getFileAnnotation().getReferences().lastElement().addToRefAuthor(value);
-		} else if (featureName.equals(GF_REFERENCE_LOCALTION)) {
-			stockholmStructure.getFileAnnotation().getReferences().lastElement().setRefLocation(value);
-		} else if (featureName.equals(GF_KEYWORDS)) {
-			stockholmStructure.getFileAnnotation().setGFKeywords(value);
-		} else if (featureName.equals(GF_COMMENT)) {
-			stockholmStructure.getFileAnnotation().addToGFComment(value);
-		} else if (featureName.equals(GF_PFAM_ACCESSION)) {
-			stockholmStructure.getFileAnnotation().setGFPfamAccession(value);
-		} else if (featureName.equals(GF_LOCATION)) {
-			stockholmStructure.getFileAnnotation().setGFLocation(value);
-		} else if (featureName.equals(GF_WIKIPEDIA_LINK)) {
-			stockholmStructure.getFileAnnotation().setGFWikipediaLink(value);
-		} else if (featureName.equals(GF_CLAN)) {
-			stockholmStructure.getFileAnnotation().setGFClan(value);
-		} else if (featureName.equals(GF_MEMBERSHIP)) {
-			stockholmStructure.getFileAnnotation().setGFMembership(value);
-		} else if (featureName.equals(GF_NEW_HAMPSHIRE)) {
-			stockholmStructure.getFileAnnotation().addGFNewHampshire(value);
-		} else if (featureName.equals(GF_TREE_ID)) {
-			stockholmStructure.getFileAnnotation().addGFTreeID(value);
-		} else if (featureName.equals(GF_FALSE_DISCOVERY_RATE)) {
-			stockholmStructure.getFileAnnotation().addGFFalseDiscoveryRate(value);
-		} else {
-			// unknown feature
-			logger.warn("Unknown File Feature [{}].\nPlease contact the Biojava team.", featureName);
+		switch (featureName) {
+			case GF_ACCESSION_NUMBER:
+				stockholmStructure.getFileAnnotation().setGFAccessionNumber(value);
+				break;
+			case GF_IDENTIFICATION:
+				stockholmStructure.getFileAnnotation().setGFIdentification(value);
+				break;
+			case GF_DB_REFERENCE:
+				stockholmStructure.getFileAnnotation().addDBReference(value);
+				break;
+			case GF_DEFINITION:
+				stockholmStructure.getFileAnnotation().setGFDefinition(value);
+				break;
+			case GF_AUTHOR:
+				stockholmStructure.getFileAnnotation().setGFAuthors(value);
+				break;
+			case GF_ALIGNMENT_METHOD:
+				stockholmStructure.getFileAnnotation().setAlignmentMethod(value);
+				break;
+			case GF_BUILD_METHOD:
+				stockholmStructure.getFileAnnotation().addGFBuildMethod(value);
+				break;
+			case GF_SEARCH_METHOD:
+				stockholmStructure.getFileAnnotation().setGFSearchMethod(value);
+				break;
+			case GF_SOURCE_SEED:
+				stockholmStructure.getFileAnnotation().setGFSourceSeed(value);
+				break;
+			case GF_SOURCE_STRUCTURE:
+				stockholmStructure.getFileAnnotation().setGFSourceStructure(value);
+				break;
+			case GF_GATHERING_THRESHOLD:
+				stockholmStructure.getFileAnnotation().setGFGatheringThreshs(value);
+				break;
+			case GF_TRUSTED_CUTOFF:
+				stockholmStructure.getFileAnnotation().setGFTrustedCutoffs(value);
+				break;
+			case GF_NOISE_CUTOFF:
+				stockholmStructure.getFileAnnotation().setGFNoiseCutoffs(value);
+				break;
+			case GF_TYPE_FIELD:
+				stockholmStructure.getFileAnnotation().setGFTypeField(value);
+				break;
+			case GF_PREVIOUS_IDS:
+				stockholmStructure.getFileAnnotation().setGFPreviousIDs(value);
+				break;
+			case GF_SEQUENCE:
+				// status = STATUS_IN_SEQUENCE;
+				stockholmStructure.getFileAnnotation().setGFNumSequences(value);
+				break;
+			case GF_DB_COMMENT:
+				stockholmStructure.getFileAnnotation().setGFDBComment(value);
+				// } else if (featureName.equals(GF_DB_REFERENCE)) {
+				// stockholmStructure.getFileAnnotation().addDBReference(value);
+				break;
+			case GF_REFERENCE_COMMENT:
+				stockholmStructure.getFileAnnotation().setGFRefComment(value);
+				break;
+			case GF_REFERENCE_NUMBER:
+				StockholmFileAnnotationReference reference = new StockholmFileAnnotationReference();
+				stockholmStructure.getFileAnnotation().getReferences().add(reference);
+				break;
+			case GF_REFERENCE_MEDLINE:
+				stockholmStructure.getFileAnnotation().getReferences().lastElement().setRefMedline(value);
+				break;
+			case GF_REFERENCE_TITLE:
+				stockholmStructure.getFileAnnotation().getReferences().lastElement().addToRefTitle(value);
+				break;
+			case GF_REFERENCE_AUTHOR:
+				stockholmStructure.getFileAnnotation().getReferences().lastElement().addToRefAuthor(value);
+				break;
+			case GF_REFERENCE_LOCALTION:
+				stockholmStructure.getFileAnnotation().getReferences().lastElement().setRefLocation(value);
+				break;
+			case GF_KEYWORDS:
+				stockholmStructure.getFileAnnotation().setGFKeywords(value);
+				break;
+			case GF_COMMENT:
+				stockholmStructure.getFileAnnotation().addToGFComment(value);
+				break;
+			case GF_PFAM_ACCESSION:
+				stockholmStructure.getFileAnnotation().setGFPfamAccession(value);
+				break;
+			case GF_LOCATION:
+				stockholmStructure.getFileAnnotation().setGFLocation(value);
+				break;
+			case GF_WIKIPEDIA_LINK:
+				stockholmStructure.getFileAnnotation().setGFWikipediaLink(value);
+				break;
+			case GF_CLAN:
+				stockholmStructure.getFileAnnotation().setGFClan(value);
+				break;
+			case GF_MEMBERSHIP:
+				stockholmStructure.getFileAnnotation().setGFMembership(value);
+				break;
+			case GF_NEW_HAMPSHIRE:
+				stockholmStructure.getFileAnnotation().addGFNewHampshire(value);
+				break;
+			case GF_TREE_ID:
+				stockholmStructure.getFileAnnotation().addGFTreeID(value);
+				break;
+			case GF_FALSE_DISCOVERY_RATE:
+				stockholmStructure.getFileAnnotation().addGFFalseDiscoveryRate(value);
+				break;
+			default:
+				// unknown feature
+				logger.warn("Unknown File Feature [{}].\nPlease contact the Biojava team.", featureName);
+				break;
 		}
 	}
 
@@ -630,33 +664,47 @@ private void handleFileAnnotation(String featureName, String value) {
 	 *            the line to be parsed.
 	 */
 	private void handleConsensusAnnotation(String featureName, String value) {
-		if (featureName.equals(GC_SECONDARY_STRUCTURE)) {
-			stockholmStructure.getConsAnnotation().setSecondaryStructure(value);
-		} else if (featureName.equals(GC_SEQUENSE_CONSENSUS)) {
-			stockholmStructure.getConsAnnotation().setSequenceConsensus(value);
-		} else if (featureName.equals(GC_SURFACE_ACCESSIBILITY)) {
-			stockholmStructure.getConsAnnotation().setSurfaceAccessibility(value);
-		} else if (featureName.equals(GC_TRANS_MEMBRANE)) {
-			stockholmStructure.getConsAnnotation().setTransMembrane(value);
-		} else if (featureName.equals(GC_POSTERIOR_PROBABILITY)) {
-			stockholmStructure.getConsAnnotation().setPosteriorProbability(value);
-		} else if (featureName.equals(GC_LIGAND_BINDING)) {
-			stockholmStructure.getConsAnnotation().setLigandBinding(value);
-		} else if (featureName.equals(GC_ACTIVE_SITE)) {
-			stockholmStructure.getConsAnnotation().setActiveSite(value);
-		} else if (featureName.equals(GC_AS_PFAM_PREDICTED)) {
-			stockholmStructure.getConsAnnotation().setAsPFamPredicted(value);
-		} else if (featureName.equals(GC_AS_SWISSPROT)) {
-			stockholmStructure.getConsAnnotation().setAsSwissProt(value);
-		} else if (featureName.equals(GC_INTRON)) {
-			stockholmStructure.getConsAnnotation().setIntron(value);
-		} else if (featureName.equals(GC_REFERENCE_ANNOTATION)) {
-			stockholmStructure.getConsAnnotation().setReferenceAnnotation(value);
-		} else if (featureName.equals(GC_MODEL_MASK)) {
-			stockholmStructure.getConsAnnotation().setModelMask(value);
-		} else {
-			// unknown feature
-			logger.warn("Unknown Consensus Feature [{}].\nPlease contact the Biojava team.", featureName);
+		switch (featureName) {
+			case GC_SECONDARY_STRUCTURE:
+				stockholmStructure.getConsAnnotation().setSecondaryStructure(value);
+				break;
+			case GC_SEQUENSE_CONSENSUS:
+				stockholmStructure.getConsAnnotation().setSequenceConsensus(value);
+				break;
+			case GC_SURFACE_ACCESSIBILITY:
+				stockholmStructure.getConsAnnotation().setSurfaceAccessibility(value);
+				break;
+			case GC_TRANS_MEMBRANE:
+				stockholmStructure.getConsAnnotation().setTransMembrane(value);
+				break;
+			case GC_POSTERIOR_PROBABILITY:
+				stockholmStructure.getConsAnnotation().setPosteriorProbability(value);
+				break;
+			case GC_LIGAND_BINDING:
+				stockholmStructure.getConsAnnotation().setLigandBinding(value);
+				break;
+			case GC_ACTIVE_SITE:
+				stockholmStructure.getConsAnnotation().setActiveSite(value);
+				break;
+			case GC_AS_PFAM_PREDICTED:
+				stockholmStructure.getConsAnnotation().setAsPFamPredicted(value);
+				break;
+			case GC_AS_SWISSPROT:
+				stockholmStructure.getConsAnnotation().setAsSwissProt(value);
+				break;
+			case GC_INTRON:
+				stockholmStructure.getConsAnnotation().setIntron(value);
+				break;
+			case GC_REFERENCE_ANNOTATION:
+				stockholmStructure.getConsAnnotation().setReferenceAnnotation(value);
+				break;
+			case GC_MODEL_MASK:
+				stockholmStructure.getConsAnnotation().setModelMask(value);
+				break;
+			default:
+				// unknown feature
+				logger.warn("Unknown Consensus Feature [{}].\nPlease contact the Biojava team.", featureName);
+				break;
 		}
 	}
 
@@ -667,21 +715,29 @@ private void handleConsensusAnnotation(String featureName, String value) {
 	 *            the line to be parsed
 	 */
 	private void handleSequenceAnnotation(String seqName, String featureName, String value) {
-		if (featureName.equals(GS_ACCESSION_NUMBER)) {
-			stockholmStructure.addGSAccessionNumber(seqName, value);
-		} else if (featureName.equals(GS_DESCRIPTION)) {
-			stockholmStructure.addGSDescription(seqName, value);
-		} else if (featureName.equals(GS_DATABASE_REFERENCE)) {
-			stockholmStructure.addGSdbReference(seqName, value);
-		} else if (featureName.equals(GS_ORGANISM_SPECIES)) {
-			stockholmStructure.addGSOrganismSpecies(seqName, value);
-		} else if (featureName.equals(GS_ORGANISM_CLASSIFICATION)) {
-			stockholmStructure.addGSOrganismClassification(seqName, value);
-		} else if (featureName.equals(GS_LOOK)) {
-			stockholmStructure.addGSLook(seqName, value);
-		} else {
-			// unknown feature
-			logger.warn("Unknown Sequence Feature [{}].\nPlease contact the Biojava team.", featureName);
+		switch (featureName) {
+			case GS_ACCESSION_NUMBER:
+				stockholmStructure.addGSAccessionNumber(seqName, value);
+				break;
+			case GS_DESCRIPTION:
+				stockholmStructure.addGSDescription(seqName, value);
+				break;
+			case GS_DATABASE_REFERENCE:
+				stockholmStructure.addGSdbReference(seqName, value);
+				break;
+			case GS_ORGANISM_SPECIES:
+				stockholmStructure.addGSOrganismSpecies(seqName, value);
+				break;
+			case GS_ORGANISM_CLASSIFICATION:
+				stockholmStructure.addGSOrganismClassification(seqName, value);
+				break;
+			case GS_LOOK:
+				stockholmStructure.addGSLook(seqName, value);
+				break;
+			default:
+				// unknown feature
+				logger.warn("Unknown Sequence Feature [{}].\nPlease contact the Biojava team.", featureName);
+				break;
 		}
 	}
 
@@ -693,27 +749,38 @@ private void handleSequenceAnnotation(String seqName, String featureName, String
 	 */
 	private void handleResidueAnnotation(String seqName, String featureName, String value) {
 
-		if (featureName.equals(GR_SURFACE_ACCESSIBILITY)) {
-			stockholmStructure.addSurfaceAccessibility(seqName, value);
-		} else if (featureName.equals(GR_TRANS_MEMBRANE)) {
-			stockholmStructure.addTransMembrane(seqName, value);
-		} else if (featureName.equals(GR_POSTERIOR_PROBABILITY)) {
-			stockholmStructure.addPosteriorProbability(seqName, value);
-		} else if (featureName.equals(GR_LIGAND_BINDING)) {
-			stockholmStructure.addLigandBinding(seqName, value);
-		} else if (featureName.equals(GR_ACTIVE_SITE)) {
-			stockholmStructure.addActiveSite(seqName, value);
-		} else if (featureName.equals(GR_AS_PFAM_PREDICTED)) {
-			stockholmStructure.addASPFamPredicted(seqName, value);
-		} else if (featureName.equals(GR_AS_SWISSPROT)) {
-			stockholmStructure.addASSwissProt(seqName, value);
-		} else if (featureName.equals(GR_INTRON)) {
-			stockholmStructure.addIntron(seqName, value);
-		} else if (featureName.equals(GR_SECONDARY_STRUCTURE)) {
-			stockholmStructure.addSecondaryStructure(seqName, value);
-		} else {
-			// unknown feature
-			logger.warn("Unknown Residue Feature [{}].\nPlease contact the Biojava team.", featureName);
+		switch (featureName) {
+			case GR_SURFACE_ACCESSIBILITY:
+				stockholmStructure.addSurfaceAccessibility(seqName, value);
+				break;
+			case GR_TRANS_MEMBRANE:
+				stockholmStructure.addTransMembrane(seqName, value);
+				break;
+			case GR_POSTERIOR_PROBABILITY:
+				stockholmStructure.addPosteriorProbability(seqName, value);
+				break;
+			case GR_LIGAND_BINDING:
+				stockholmStructure.addLigandBinding(seqName, value);
+				break;
+			case GR_ACTIVE_SITE:
+				stockholmStructure.addActiveSite(seqName, value);
+				break;
+			case GR_AS_PFAM_PREDICTED:
+				stockholmStructure.addASPFamPredicted(seqName, value);
+				break;
+			case GR_AS_SWISSPROT:
+				stockholmStructure.addASSwissProt(seqName, value);
+				break;
+			case GR_INTRON:
+				stockholmStructure.addIntron(seqName, value);
+				break;
+			case GR_SECONDARY_STRUCTURE:
+				stockholmStructure.addSecondaryStructure(seqName, value);
+				break;
+			default:
+				// unknown feature
+				logger.warn("Unknown Residue Feature [{}].\nPlease contact the Biojava team.", featureName);
+				break;
 		}
 	}
 }
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmSequenceAnnotation.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmSequenceAnnotation.java
index 9044c3a34c..0bf25c1a4a 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmSequenceAnnotation.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmSequenceAnnotation.java
@@ -74,7 +74,7 @@ public void setDbReferences(Set<DatabaseReference> dbReferences) {
 	 */
 	public void addDBReference(String dbReferenceRepresentingString) {
 		if (this.dbReferences == null) {
-			this.dbReferences = new HashSet<DatabaseReference>();
+			this.dbReferences = new HashSet<>();
 		}
 		dbReferences.add(new DatabaseReference(dbReferenceRepresentingString));
 	}
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
index 494d8290a2..ce403bf4aa 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
@@ -94,9 +94,9 @@ public class StockholmStructure {
 	public StockholmStructure() {
 		fileAnnotation = new StockholmFileAnnotation();
 		consAnnotation = new StockholmConsensusAnnotation();
-		sequences = new HashMap<String, StringBuffer>();
-		seqsAnnotation = new HashMap<String, StockholmSequenceAnnotation>();
-		resAnnotation = new HashMap<String, StockholmResidueAnnotation>();
+		sequences = new HashMap<>();
+		seqsAnnotation = new HashMap<>();
+		resAnnotation = new HashMap<>();
 	}
 
 	public StockholmFileAnnotation getFileAnnotation() {
@@ -235,10 +235,11 @@ public List<AbstractSequence<? extends AbstractCompound>> getBioSequences(boolea
 		if (forcedSequenceType != null && !(forcedSequenceType.equals(PFAM) || forcedSequenceType.equals(RFAM))) {
 			throw new IllegalArgumentException("Illegal Argument " + forcedSequenceType);
 		}
-		List<AbstractSequence<? extends AbstractCompound>> seqs = new ArrayList<AbstractSequence<? extends AbstractCompound>>();
-		for (String sequencename : sequences.keySet()) {
-			AbstractSequence<? extends AbstractCompound> seq = null;
-			String sequence = sequences.get(sequencename).toString();
+		List<AbstractSequence<? extends AbstractCompound>> seqs = new ArrayList<>();
+		for (Map.Entry<String, StringBuffer> entry : sequences.entrySet()) {
+            String sequencename = entry.getKey();
+            AbstractSequence<? extends AbstractCompound> seq;
+			String sequence = entry.getValue().toString();
 			if (ignoreCase) {
 				sequence = sequence.toUpperCase();
 			}
@@ -308,16 +309,16 @@ private String[] splitSeqName(String sequenceName) {
 
 	@Override
 	public String toString() {
-		StringBuffer result = new StringBuffer();
+		StringBuilder result = new StringBuilder();
 		List<AbstractSequence<? extends AbstractCompound>> bioSeqs = getBioSequences(false);
 		int sequenceLength = -1;
 		for (AbstractSequence<? extends AbstractCompound> sequence : bioSeqs) {
 			String sequenceAsString = sequence.getSequenceAsString();
 			sequenceLength = sequenceAsString.length();
 			if (sequenceLength > 50) {
-				result.append(sequenceAsString.substring(0, 40));
+				result.append(sequenceAsString, 0, 40);
 				result.append("...");
-				result.append(sequenceAsString.substring(sequenceLength - 3, sequenceLength));
+				result.append(sequenceAsString, sequenceLength - 3, sequenceLength);
 			} else {
 				result.append(sequenceAsString);
 			}
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java
index edba157916..bb7aeaa16f 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java
@@ -62,8 +62,11 @@ public enum Last {
 	 */
 	public static class Cut {
 
-		private int queryIndex;
-		private int[][] targetIndices, tiLast, ti1, ti2;
+		private final int queryIndex;
+		private int[][] targetIndices;
+		private int[][] tiLast;
+		private final int[][] ti1;
+		private final int[][] ti2;
 
 		public Cut(int queryIndex, int[] dim) {
 			this.queryIndex = queryIndex;
@@ -171,7 +174,7 @@ public static int addAnchors(Cut[] cuts, int[] scores, boolean addScore, int[] a
 		for (Cut c : cuts) {
 			anchors[c.getQueryIndex()] = c.getTargetIndex(zMax);
 		}
-		return addScore ? (int) subscore : 0;
+		return addScore ? subscore : 0;
 	}
 
 	public static Cut[] getCuts(int k, Subproblem subproblem, int[] dim, boolean anchor0) {
@@ -244,11 +247,11 @@ public int getQueryStartIndex() {
 		public boolean isStartAnchored() {
 			return isAnchored;
 		}
-		private int queryStartIndex; // [0]
-		private int targetStartIndex; // [1]
-		private int queryEndIndex; // [2]
-		private int targetEndIndex; // [3]
-		private boolean isAnchored;
+		private final int queryStartIndex; // [0]
+		private final int targetStartIndex; // [1]
+		private final int queryEndIndex; // [2]
+		private final int targetEndIndex; // [3]
+		private final boolean isAnchored;
 		public Subproblem(int queryStartIndex, int targetStartIndex, int queryEndIndex, int targetEndIndex) {
 			this(queryStartIndex, targetStartIndex, queryEndIndex, targetEndIndex, false);
 		}
@@ -267,8 +270,8 @@ public Subproblem(int queryStartIndex, int targetStartIndex, int queryEndIndex,
 		 * @return list alignment subproblems
 		 */
 		public static List<Subproblem> getSubproblems(List<Anchor> anchors, int querySequenceLength, int targetSequenceLength) {
-			Collections.sort(anchors, new Anchor.QueryIndexComparator());
-			List<Subproblem> list = new ArrayList<Subproblem>();
+			anchors.sort(new Anchor.QueryIndexComparator());
+			List<Subproblem> list = new ArrayList<>();
 			Anchor last = new Anchor(-1, -1); // sentinal anchor
 			boolean isAnchored = false;
 			for (int i = 0; i < anchors.size(); i++) {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java
index 41b9502782..73a7650ae2 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java
@@ -34,6 +34,7 @@
 import org.biojava.nbio.core.sequence.template.Sequence;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 /**
@@ -96,9 +97,7 @@ public AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty,
 	 */
 	public int[] getAnchors() {
 		int[] anchor = new int[getScoreMatrixDimensions()[0] - 1];
-		for (int i = 0; i < anchor.length; i++) {
-			anchor[i] = -1;
-		}
+        Arrays.fill(anchor, -1);
 		for (int i = 0; i < anchors.size(); i++) {
 			anchor[anchors.get(i).getQueryIndex()] = anchors.get(i).getTargetIndex();
 		}
@@ -111,7 +110,7 @@ public int[] getAnchors() {
 	 * @param anchors list of points that are tied to the given indices in the target
 	 */
 	public void setAnchors(int[] anchors) {
-		super.anchors = new ArrayList<Anchor>();
+		super.anchors = new ArrayList<>();
 		if (anchors != null) {
 			for (int i = 0; i < anchors.length; i++) {
 				if (anchors[i] >= 0) {
@@ -133,7 +132,7 @@ public void addAnchor(int queryIndex, int targetIndex) {
 
 	@Override
 	protected void setProfile(List<Step> sx, List<Step> sy) {
-		profile = pair = new SimpleSequencePair<S, C>(getQuery(), getTarget(), sx, sy);
+		profile = pair = new SimpleSequencePair<>(getQuery(), getTarget(), sx, sy);
 	}
 
 }
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java
index 3ff44d8a8c..363d543d34 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java
@@ -42,7 +42,7 @@
  */
 public class GuanUberbacher<S extends Sequence<C>, C extends Compound> extends AnchoredPairwiseSequenceAligner<S, C> {
 
-	private static int defaultCutsPerSection = 10;
+	private static final int defaultCutsPerSection = 10;
 
 	/**
 	 * Sets the default number of cuts added to each section during each pass.
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
index b5e6f6188c..5179c87729 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
@@ -55,7 +55,7 @@ public abstract class AbstractMatrixAligner<S extends Sequence<C>, C extends Com
 	protected GapPenalty gapPenalty;
 	private SubstitutionMatrix<C> subMatrix;
 	private boolean local, storingScoreMatrix;
-	protected List<Anchor> anchors = new ArrayList<Anchor>();
+	protected List<Anchor> anchors = new ArrayList<>();
 	protected int cutsPerSection;
 
 	// output fields
@@ -218,8 +218,8 @@ private String scoreMatrixToString(int[][][] scores) {
 		CompoundSet<C> compoundSet = getCompoundSet();
 		int lengthCompound = compoundSet.getMaxSingleCompoundStringLength(), lengthRest =
 				Math.max(Math.max(Integer.toString(min).length(), Integer.toString(max).length()), lengthCompound) + 1;
-		String padCompound = "%" + Integer.toString(lengthCompound) + "s",
-				padRest = "%" + Integer.toString(lengthRest);
+		String padCompound = "%" + lengthCompound + "s",
+				padRest = "%" + lengthRest;
 		List<C> query = getCompoundsOfQuery(), target = getCompoundsOfTarget();
 		for (int type = 0; type < scores[0][0].length; type++) {
 			if (type > 0) {
@@ -312,7 +312,7 @@ protected void align() {
 		}
 		boolean linear = (gapPenalty.getType() == GapPenalty.Type.LINEAR);
 		Last[][][] traceback = new Last[dim[0]][][];
-		List<Step> sx = new ArrayList<Step>(), sy = new ArrayList<Step>();
+		List<Step> sx = new ArrayList<>(), sy = new ArrayList<>();
 
 		if (!local) {
 			xyMax = new int[] { dim[0] - 1, dim[1] - 1 };
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java
index 8c86470608..abd765b089 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java
@@ -137,12 +137,12 @@ protected CompoundSet<C> getCompoundSet() {
 
 	@Override
 	protected List<C> getCompoundsOfQuery() {
-		return (query == null) ? new ArrayList<C>() : query.getAsList();
+		return (query == null) ? new ArrayList<>() : query.getAsList();
 	}
 
 	@Override
 	protected List<C> getCompoundsOfTarget() {
-		return (target == null) ? new ArrayList<C>() : target.getAsList();
+		return (target == null) ? new ArrayList<>() : target.getAsList();
 	}
 
 	@Override
@@ -176,7 +176,7 @@ protected void reset() {
 				maxt += getSubstitutionMatrix().getValue(c, c);
 			}
 			max = Math.max(maxq, maxt);
-			score = min = isLocal() ? 0 : (int) (2 * getGapPenalty().getOpenPenalty() + (query.getLength() +
+			score = min = isLocal() ? 0 : (2 * getGapPenalty().getOpenPenalty() + (query.getLength() +
 					target.getLength()) * getGapPenalty().getExtensionPenalty());
 		}
 	}
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
index 01cba48463..aa3e47b824 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
@@ -189,13 +189,13 @@ protected CompoundSet<C> getCompoundSet() {
 	@Override
 	protected List<C> getCompoundsOfQuery() {
 		// TODO replace with consensus sequence
-		return (query == null) ? new ArrayList<C>() : query.getAlignedSequence(1).getAsList();
+		return (query == null) ? new ArrayList<>() : query.getAlignedSequence(1).getAsList();
 	}
 
 	@Override
 	protected List<C> getCompoundsOfTarget() {
 		// TODO replace with consensus sequence
-		return (target == null) ? new ArrayList<C>() : target.getAlignedSequence(1).getAsList();
+		return (target == null) ? new ArrayList<>() : target.getAlignedSequence(1).getAsList();
 	}
 
 	@Override
@@ -248,7 +248,7 @@ protected void reset() {
 				maxt += getSubstitutionScore(tfrac[i], tfrac[i]);
 			}
 			max = Math.max(maxq, maxt);
-			score = min = isLocal() ? 0 : (int) (2 * getGapPenalty().getOpenPenalty() + (query.getLength() +
+			score = min = isLocal() ? 0 : (2 * getGapPenalty().getOpenPenalty() + (query.getLength() +
 					target.getLength()) * getGapPenalty().getExtensionPenalty());
 		}
 	}
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java
index e1c4616620..6725a47f5f 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java
@@ -39,7 +39,7 @@
 public class CallablePairwiseSequenceAligner<S extends Sequence<C>, C extends Compound>
 		implements Callable<SequencePair<S, C>> {
 
-	private PairwiseSequenceAligner<S, C> psa;
+	private final PairwiseSequenceAligner<S, C> psa;
 
 	/**
 	 * Creates a pairwise sequence alignment task for simplified parallel execution.
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceScorer.java
index d5d3d4b243..4d8d833bcd 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceScorer.java
@@ -37,7 +37,7 @@
  */
 public class CallablePairwiseSequenceScorer<S extends Sequence<C>, C extends Compound> implements Callable<Double> {
 
-	private PairwiseSequenceScorer<S, C> pss;
+	private final PairwiseSequenceScorer<S, C> pss;
 
 	/**
 	 * Creates a pairwise sequence scoring task for simplified parallel execution.
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java
index 063426a91a..27a0c812d3 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java
@@ -39,7 +39,7 @@
 public class CallableProfileProfileAligner<S extends Sequence<C>, C extends Compound>
 		implements Callable<ProfilePair<S, C>> {
 
-	private ProfileProfileAligner<S, C> ppa;
+	private final ProfileProfileAligner<S, C> ppa;
 
 	/**
 	 * Creates a profile-profile alignment task for simplified parallel execution.
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/GapPenalty.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/GapPenalty.java
index 1c3aab1978..ef8fe96133 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/GapPenalty.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/GapPenalty.java
@@ -39,9 +39,9 @@ public interface GapPenalty {
 	 *  <li>DYNAMIC, if penalty values change during alignment
 	 * </ul>
 	 */
-	enum Type {CONSTANT, LINEAR, AFFINE, DYNAMIC};
+	enum Type {CONSTANT, LINEAR, AFFINE, DYNAMIC}
 
-	/**
+    /**
 	 * Returns penalty given when an already open gap elongates by a single element
 	 *
 	 * @return gap extension penalty
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java
index dc8ead79a7..9071b4e857 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java
@@ -101,7 +101,7 @@ public final static float PID(String seq1, String seq2, int start, int end) {
 	 * @return true if it is a gap, false otherwise
 	 */
 	public static final boolean isGap(char c) {
-		return (c == '-' || c == '.' || c == ' ') ? true : false;
+		return c == '-' || c == '.' || c == ' ';
 	}
 
 }
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceTreeEvaluator.java b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceTreeEvaluator.java
index ec9e274ab6..8a7d649949 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceTreeEvaluator.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceTreeEvaluator.java
@@ -66,8 +66,8 @@ private DistanceTreeEvaluator() {
 	public static double evaluate(Phylogeny tree, DistanceMatrix matrix) {
 		int numSequences = matrix.getSize();
 		List<PhylogenyNode> externalNodes = tree.getExternalNodes();
-		HashMap<String, PhylogenyNode> externalNodesHashMap = new HashMap<String, PhylogenyNode>();
-		Set<PhylogenyNode> path = new HashSet<PhylogenyNode>();
+		HashMap<String, PhylogenyNode> externalNodesHashMap = new HashMap<>();
+		Set<PhylogenyNode> path = new HashSet<>();
 
 		for (PhylogenyNode node : externalNodes) {
 			externalNodesHashMap.put(node.getName(), node);
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java
index 74cdf2e2f4..047f8efbdb 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java
@@ -64,14 +64,9 @@ public static <C extends Sequence<D>, D extends Compound> Msa convert(
 
 		// Convert the biojava MSA to a FASTA String
 		OutputStream os = new ByteArrayOutputStream();
-		FastaWriter<C, D> fastaW = new FastaWriter<C, D>(os,
+		FastaWriter<C, D> fastaW = new FastaWriter<>(os,
 				msa.getAlignedSequences(),
-				new FastaHeaderFormatInterface<C, D>() {
-					@Override
-					public String getHeader(C sequence) {
-						return sequence.getAccession().toString();
-					};
-				});
+				sequence -> sequence.getAccession().toString());
 
 		fastaW.process();
 		String fastaMSA = os.toString();
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/TreeConstructorType.java b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/TreeConstructorType.java
index d3f632046b..ba12f8251c 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/TreeConstructorType.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/TreeConstructorType.java
@@ -38,5 +38,5 @@ public enum TreeConstructorType {
 	UPGMA,
 
 	/** What does this stand for? (Aleix: Nov 2015) */
-	AV;
+	AV
 }
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/TreeType.java b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/TreeType.java
index 1f2896e923..d380219465 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/TreeType.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/TreeType.java
@@ -41,7 +41,7 @@ public enum TreeType {
 	/** Description name of the Tree Type */
 	protected final String name;
 
-	private TreeType(String name){
+	TreeType(String name){
 		this.name = name;
 	}
 }
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllGlobal.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllGlobal.java
index 9deee78c08..1671027958 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllGlobal.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllGlobal.java
@@ -45,7 +45,7 @@ public static void main(String[] args) {
 	}
 
 	private static void alignAllGlobal(String[] ids) throws Exception {
-		List<ProteinSequence> lst = new ArrayList<ProteinSequence>();
+		List<ProteinSequence> lst = new ArrayList<>();
 		for (String id : ids) {
 			lst.add(getSequenceForId(id));
 		}
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllLocal.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllLocal.java
index a56463159e..117a2be947 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllLocal.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllLocal.java
@@ -45,7 +45,7 @@ public static void main(String[] args) {
 	}
 
 	private static void alignAllLocal(String[] ids) throws Exception {
-		List<ProteinSequence> lst = new ArrayList<ProteinSequence>();
+		List<ProteinSequence> lst = new ArrayList<>();
 		for (String id : ids) {
 			lst.add(getSequenceForId(id));
 		}
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSA.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSA.java
index cfe3fcc05e..24085e698d 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSA.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSA.java
@@ -42,7 +42,7 @@ public static void main(String[] args) {
 	}
 
 	private static void multipleSequenceAlignment(String[] ids) throws Exception {
-		List<ProteinSequence> lst = new ArrayList<ProteinSequence>();
+		List<ProteinSequence> lst = new ArrayList<>();
 		for (String id : ids) {
 			lst.add(getSequenceForId(id));
 		}
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSAProfiler.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSAProfiler.java
index 55a4c7d0ec..46964a2b67 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSAProfiler.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSAProfiler.java
@@ -81,7 +81,7 @@ public static void main(String[] args) throws Exception {
 		Profiler profiler = new Profiler();
 
 		System.out.printf("Loading sequences from %s... ", args[0]);
-		List<ProteinSequence> list = new ArrayList<ProteinSequence>();
+		List<ProteinSequence> list = new ArrayList<>();
 		list.addAll(FastaReaderHelper.readFastaProteinSequence(new File(args[0])).values());
 		if (args.length > 1 && Integer.parseInt(args[1]) < list.size()) {
 			System.out.printf("%s/%d", args[1], list.size());
@@ -106,7 +106,7 @@ public static void main(String[] args) throws Exception {
 		profiler.setCheckpoint();
 
 		System.out.print("Stage 2: hierarchical clustering into a guide tree... ");
-		GuideTree<ProteinSequence, AminoAcidCompound> tree = new GuideTree<ProteinSequence, AminoAcidCompound>(list,
+		GuideTree<ProteinSequence, AminoAcidCompound> tree = new GuideTree<>(list,
 				scorers);
 		scorers = null;
 		System.out.printf("%d ms using %d kB%n%n%s%n%n", profiler.getTimeSinceCheckpoint()/1000000,
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalIdentityScorerTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalIdentityScorerTest.java
index 08bf9c73f8..b36a0ffd82 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalIdentityScorerTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalIdentityScorerTest.java
@@ -52,20 +52,20 @@ public void setup() throws CompoundNotFoundException {
 		target = new ProteinSequence("RDG");
 		gaps = new SimpleGapPenalty((short) 10, (short) 1);
 		blosum62 = SubstitutionMatrixHelper.getBlosum62();
-		alignment = new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(query, target, gaps, blosum62);
-		self = new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(query, query, gaps, blosum62);
-		scorer1 = new FractionalIdentityScorer<ProteinSequence, AminoAcidCompound>(alignment);
-		scorer2 = new FractionalIdentityScorer<ProteinSequence, AminoAcidCompound>(self);
+		alignment = new NeedlemanWunsch<>(query, target, gaps, blosum62);
+		self = new NeedlemanWunsch<>(query, query, gaps, blosum62);
+		scorer1 = new FractionalIdentityScorer<>(alignment);
+		scorer2 = new FractionalIdentityScorer<>(self);
 	}
 
 	@Test
 	public void testFractionalIdentityScorerPairwiseSequenceAlignerOfSC() {
-		assertNotNull(new FractionalIdentityScorer<ProteinSequence, AminoAcidCompound>(alignment));
+		assertNotNull(new FractionalIdentityScorer<>(alignment));
 	}
 
 	@Test
 	public void testFractionalIdentityScorerSequencePairOfSC() {
-		assertNotNull(new FractionalIdentityScorer<ProteinSequence, AminoAcidCompound>(alignment.getPair()));
+		assertNotNull(new FractionalIdentityScorer<>(alignment.getPair()));
 	}
 
 	@Test
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalSimilarityScorerTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalSimilarityScorerTest.java
index 26d7615d44..752d17e13f 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalSimilarityScorerTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalSimilarityScorerTest.java
@@ -53,20 +53,20 @@ public void setup() throws CompoundNotFoundException {
 		target = new ProteinSequence("RADG");
 		gaps = new SimpleGapPenalty((short) 2, (short) 1);
 		blosum62 = SubstitutionMatrixHelper.getBlosum62();
-		alignment = new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(query, target, gaps, blosum62);
-		self = new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(query, query, gaps, blosum62);
-		scorer1 = new FractionalSimilarityScorer<ProteinSequence, AminoAcidCompound>(alignment);
-		scorer2 = new FractionalSimilarityScorer<ProteinSequence, AminoAcidCompound>(self);
+		alignment = new NeedlemanWunsch<>(query, target, gaps, blosum62);
+		self = new NeedlemanWunsch<>(query, query, gaps, blosum62);
+		scorer1 = new FractionalSimilarityScorer<>(alignment);
+		scorer2 = new FractionalSimilarityScorer<>(self);
 	}
 
 	@Test
 	public void testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC() {
-		assertNotNull(new FractionalSimilarityScorer<ProteinSequence, AminoAcidCompound>(alignment));
+		assertNotNull(new FractionalSimilarityScorer<>(alignment));
 	}
 
 	@Test
 	public void testFractionalSimilarityScorerSequencePairOfSC() {
-		assertNotNull(new FractionalSimilarityScorer<ProteinSequence, AminoAcidCompound>(alignment.getPair()));
+		assertNotNull(new FractionalSimilarityScorer<>(alignment.getPair()));
 	}
 
 	@Test
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/GuideTreeTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/GuideTreeTest.java
index 08adf113ec..1c5bf3df99 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/GuideTreeTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/GuideTreeTest.java
@@ -49,11 +49,11 @@ public class GuideTreeTest {
 
 	@Before
 	public void setup() throws CompoundNotFoundException {
-		proteins = Arrays.asList(new ProteinSequence[] {new ProteinSequence("ARND"), new ProteinSequence("ARND"),
-				new ProteinSequence("HILK"), new ProteinSequence("ANDR")});
+		proteins = Arrays.asList(new ProteinSequence("ARND"), new ProteinSequence("ARND"),
+				new ProteinSequence("HILK"), new ProteinSequence("ANDR"));
 		gaps = new SimpleGapPenalty((short) 2, (short) 1);
 		blosum62 = SubstitutionMatrixHelper.getBlosum62();
-		tree = new GuideTree<ProteinSequence, AminoAcidCompound>(proteins, Alignments.getAllPairsScorers(proteins,
+		tree = new GuideTree<>(proteins, Alignments.getAllPairsScorers(proteins,
 				PairwiseSequenceScorerType.GLOBAL_IDENTITIES, gaps, blosum62));
 	}
 
@@ -112,12 +112,13 @@ public void testIterator() {
 			switch (i++) {
 			case 0: assertEquals(n.getName(), "1"); break;
 			case 1: assertEquals(n.getName(), "2"); break;
-			case 2: assertEquals(n.getName(), ""); break;
+			case 2:
+                case 6:
+                case 4:
+                    assertEquals(n.getName(), ""); break;
 			case 3: assertEquals(n.getName(), "3"); break;
-			case 4: assertEquals(n.getName(), ""); break;
-			case 5: assertEquals(n.getName(), "4"); break;
-			case 6: assertEquals(n.getName(), ""); break;
-			}
+                case 5: assertEquals(n.getName(), "4"); break;
+            }
 		}
 	}
 
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/NeedlemanWunschTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/NeedlemanWunschTest.java
index 5b44fc25f4..5382edabb3 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/NeedlemanWunschTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/NeedlemanWunschTest.java
@@ -57,15 +57,15 @@ public void setup() throws CompoundNotFoundException {
 		target = new ProteinSequence("RDG");
 		gaps = new SimpleGapPenalty(10, 1);
 		blosum62 = SubstitutionMatrixHelper.getBlosum62();
-		alignment = new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(query, target, gaps, blosum62);
-		self = new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(query, query, gaps, blosum62);
+		alignment = new NeedlemanWunsch<>(query, target, gaps, blosum62);
+		self = new NeedlemanWunsch<>(query, query, gaps, blosum62);
 	}
 
 	@Test
 	public void testComplex() throws Exception {
 
 		short match = 2, gop = -5, gep = -3; // 2, 5, and 3 are coprime; -2 is the mismatch score
-		SimpleSubstitutionMatrix<NucleotideCompound> mx = new SimpleSubstitutionMatrix<NucleotideCompound>(new DNACompoundSet(), match, (short)-match);
+		SimpleSubstitutionMatrix<NucleotideCompound> mx = new SimpleSubstitutionMatrix<>(new DNACompoundSet(), match, (short) -match);
 
 		DNASequence a = new DNASequence("CGTAT  ATATCGCGCGCGCGATATATATATCT TCTCTAAAAAAA".replaceAll(" ", ""));
 		DNASequence b = new DNASequence("GGTATATATATCGCGCGCACGAT TATATATCTCTCTCTAAAAAAA".replaceAll(" ", ""));
@@ -88,7 +88,7 @@ public void testComplex() throws Exception {
 	@Test
 	public void testNeedlemanWunsch() {
 		NeedlemanWunsch<ProteinSequence, AminoAcidCompound> nw =
-				new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>();
+				new NeedlemanWunsch<>();
 		nw.setQuery(query);
 		nw.setTarget(target);
 		nw.setGapPenalty(gaps);
@@ -229,7 +229,7 @@ public void testGetPair() {
 	public void should_align_all_anchored() throws CompoundNotFoundException {
 		DNASequence query = new DNASequence("ACG", AmbiguityDNACompoundSet.getDNACompoundSet());
 		DNASequence target = new DNASequence("CGT", AmbiguityDNACompoundSet.getDNACompoundSet());
-		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)0, (short)10), SubstitutionMatrixHelper.getNuc4_4());
+		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<>(query, target, new SimpleGapPenalty((short) 0, (short) 10), SubstitutionMatrixHelper.getNuc4_4());
 		aligner.setAnchors(new int[] { 0, 1, 2} );
 		assertEquals(String.format("ACG%nCGT%n"), aligner.getPair().toString());
 	}
@@ -241,7 +241,7 @@ public void should_align_all_anchored() throws CompoundNotFoundException {
 	public void should_align_starting_anchor() throws CompoundNotFoundException {
 		DNASequence query = new DNASequence("AAT", AmbiguityDNACompoundSet.getDNACompoundSet());
 		DNASequence target = new DNASequence("AATT", AmbiguityDNACompoundSet.getDNACompoundSet());
-		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)0, (short)10), SubstitutionMatrixHelper.getNuc4_4());
+		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<>(query, target, new SimpleGapPenalty((short) 0, (short) 10), SubstitutionMatrixHelper.getNuc4_4());
 		aligner.setAnchors(new int[] { 1, -1, -1} );
 		assertEquals(String.format("-AAT%nAATT%n"), aligner.getPair().toString());
 	}
@@ -253,7 +253,7 @@ public void should_align_starting_anchor() throws CompoundNotFoundException {
 	public void should_align_ending_anchor() throws CompoundNotFoundException {
 		DNASequence query = new DNASequence("AAG", AmbiguityDNACompoundSet.getDNACompoundSet());
 		DNASequence target = new DNASequence("AATT", AmbiguityDNACompoundSet.getDNACompoundSet());
-		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)0, (short)10), SubstitutionMatrixHelper.getNuc4_4());
+		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<>(query, target, new SimpleGapPenalty((short) 0, (short) 10), SubstitutionMatrixHelper.getNuc4_4());
 		aligner.addAnchor(2, 3);
 		assertEquals(String.format("AA-G%nAATT%n"), aligner.getPair().toString());
 	}
@@ -265,7 +265,7 @@ public void should_align_ending_anchor() throws CompoundNotFoundException {
 	public void should_align_middle_anchor() throws CompoundNotFoundException {
 		DNASequence query = new DNASequence("ACTTT", AmbiguityDNACompoundSet.getDNACompoundSet());
 		DNASequence target = new DNASequence("ACGTTT", AmbiguityDNACompoundSet.getDNACompoundSet());
-		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)0, (short)10), SubstitutionMatrixHelper.getNuc4_4());
+		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<>(query, target, new SimpleGapPenalty((short) 0, (short) 10), SubstitutionMatrixHelper.getNuc4_4());
 		aligner.setAnchors(new int[] { -1, 2, -1} );
 		assertEquals(String.format("A-CTTT%nACGTTT%n"), aligner.getPair().toString());
 	}
@@ -277,7 +277,7 @@ public void should_align_middle_anchor() throws CompoundNotFoundException {
 	public void should_align_multiple_anchors() throws CompoundNotFoundException {
 		DNASequence query = new DNASequence("ACGT", AmbiguityDNACompoundSet.getDNACompoundSet());
 		DNASequence target = new DNASequence("ATACGT", AmbiguityDNACompoundSet.getDNACompoundSet());
-		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)0, (short)10), SubstitutionMatrixHelper.getNuc4_4());
+		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<>(query, target, new SimpleGapPenalty((short) 0, (short) 10), SubstitutionMatrixHelper.getNuc4_4());
 		aligner.addAnchor(0, 0);
 		aligner.addAnchor(1, 1);
 		aligner.addAnchor(2, 2);
@@ -292,8 +292,8 @@ public void should_align_multiple_anchors() throws CompoundNotFoundException {
 	public void anchors_should_not_change_score() throws CompoundNotFoundException {
 		DNASequence query = new DNASequence("ACGT", AmbiguityDNACompoundSet.getDNACompoundSet());
 		DNASequence target = new DNASequence("ACGT", AmbiguityDNACompoundSet.getDNACompoundSet());
-		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)5, (short)10), SubstitutionMatrixHelper.getNuc4_4());
-		NeedlemanWunsch<DNASequence, NucleotideCompound> anchored = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)5, (short)10), SubstitutionMatrixHelper.getNuc4_4());
+		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<>(query, target, new SimpleGapPenalty((short) 5, (short) 10), SubstitutionMatrixHelper.getNuc4_4());
+		NeedlemanWunsch<DNASequence, NucleotideCompound> anchored = new NeedlemanWunsch<>(query, target, new SimpleGapPenalty((short) 5, (short) 10), SubstitutionMatrixHelper.getNuc4_4());
 		anchored.addAnchor(0, 0);
 		anchored.addAnchor(1, 1);
 		anchored.addAnchor(2, 2);
@@ -308,7 +308,7 @@ public void anchors_should_not_change_score() throws CompoundNotFoundException {
 	public void testAnchoredDNAAlignment() throws CompoundNotFoundException {
 		DNASequence query = new DNASequence(  "ACGTACCGGTTTT", DNACompoundSet.getDNACompoundSet());
 		DNASequence target = new DNASequence("TACGTCCGGTTACGTACGTT", DNACompoundSet.getDNACompoundSet());
-		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)5, (short)2), SubstitutionMatrixHelper.getNuc4_4());
+		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner = new NeedlemanWunsch<>(query, target, new SimpleGapPenalty((short) 5, (short) 2), SubstitutionMatrixHelper.getNuc4_4());
 		assertEquals(String.format("-ACGTACCGGTT-------TT%nTACGT-CCGGTTACGTACGTT%n"), aligner.getPair().toString());
 	}
 
@@ -335,7 +335,7 @@ public void testIntOverflowBug() throws CompoundNotFoundException {
 				AmbiguityDNACompoundSet.getDNACompoundSet());
 
 		NeedlemanWunsch<DNASequence, NucleotideCompound> aligner =
-				new NeedlemanWunsch<DNASequence, NucleotideCompound>(query, target, gap, matrix);
+				new NeedlemanWunsch<>(query, target, gap, matrix);
 
 
 		//System.out.println("getScore: " + aligner.getScore());
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleProfilePairTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleProfilePairTest.java
index 5d4e9acd53..3a75f71f68 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleProfilePairTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleProfilePairTest.java
@@ -57,34 +57,31 @@ public void setup() throws CompoundNotFoundException {
 		protein4 = new ProteinSequence("ANDR");
 		gaps = new SimpleGapPenalty((short) 2, (short) 1);
 		blosum62 = SubstitutionMatrixHelper.getBlosum62();
-		pair1 = new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(protein1, protein2, gaps, blosum62).getPair();
-		pair2 = new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(protein3, protein4, gaps, blosum62).getPair();
+		pair1 = new NeedlemanWunsch<>(protein1, protein2, gaps, blosum62).getPair();
+		pair2 = new NeedlemanWunsch<>(protein3, protein4, gaps, blosum62).getPair();
 	}
 
 	@Test
 	public void testSimpleProfilePair() {
 		ProfilePair<ProteinSequence, AminoAcidCompound> all =
-				new SimpleProfilePair<ProteinSequence, AminoAcidCompound>(pair1, pair2, Arrays.asList(new Step[] {
-				Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.GAP}), Arrays.asList(
-				new Step[] {Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND}));
+				new SimpleProfilePair<>(pair1, pair2, Arrays.asList(Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.GAP), Arrays.asList(
+                        Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND));
 		assertEquals(all.toString(), String.format("ARND--%nARND--%n--HILK%nA-ND-R%n"));
 	}
 
 	@Test
 	public void testGetQuery() {
 		ProfilePair<ProteinSequence, AminoAcidCompound> all =
-				new SimpleProfilePair<ProteinSequence, AminoAcidCompound>(pair1, pair2, Arrays.asList(new Step[] {
-				Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.GAP}), Arrays.asList(
-				new Step[] {Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND}));
+				new SimpleProfilePair<>(pair1, pair2, Arrays.asList(Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.GAP), Arrays.asList(
+                        Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND));
 		assertEquals(all.getQuery(), pair1);
 	}
 
 	@Test
 	public void testGetTarget() {
 		ProfilePair<ProteinSequence, AminoAcidCompound> all =
-				new SimpleProfilePair<ProteinSequence, AminoAcidCompound>(pair1, pair2, Arrays.asList(new Step[] {
-				Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.GAP}), Arrays.asList(
-				new Step[] {Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND}));
+				new SimpleProfilePair<>(pair1, pair2, Arrays.asList(Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.GAP), Arrays.asList(
+                        Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND));
 		assertEquals(all.getTarget(), pair2);
 	}
 
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleProfileProfileAlignerTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleProfileProfileAlignerTest.java
index 625e954730..de3f91694e 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleProfileProfileAlignerTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleProfileProfileAlignerTest.java
@@ -56,22 +56,22 @@ public void setup() throws CompoundNotFoundException {
 		protein4 = new ProteinSequence("ANDR");
 		gaps = new SimpleGapPenalty(2, 1);
 		blosum62 = SubstitutionMatrixHelper.getBlosum62();
-		prof1 = new SimpleProfile<ProteinSequence, AminoAcidCompound>(protein1);
-		prof2 = new SimpleProfile<ProteinSequence, AminoAcidCompound>(protein2);
-		prof3 = new SimpleProfile<ProteinSequence, AminoAcidCompound>(protein3);
-		prof4 = new SimpleProfile<ProteinSequence, AminoAcidCompound>(protein4);
-		sppa1 = new SimpleProfileProfileAligner<ProteinSequence, AminoAcidCompound>(prof1, prof2, gaps, blosum62);
+		prof1 = new SimpleProfile<>(protein1);
+		prof2 = new SimpleProfile<>(protein2);
+		prof3 = new SimpleProfile<>(protein3);
+		prof4 = new SimpleProfile<>(protein4);
+		sppa1 = new SimpleProfileProfileAligner<>(prof1, prof2, gaps, blosum62);
 		pp1 = sppa1.getPair();
-		sppa2 = new SimpleProfileProfileAligner<ProteinSequence, AminoAcidCompound>(prof3, prof4, gaps, blosum62);
+		sppa2 = new SimpleProfileProfileAligner<>(prof3, prof4, gaps, blosum62);
 		pp2 = sppa2.getPair();
-		sppa3 = new SimpleProfileProfileAligner<ProteinSequence, AminoAcidCompound>(pp1, pp2, gaps, blosum62);
+		sppa3 = new SimpleProfileProfileAligner<>(pp1, pp2, gaps, blosum62);
 		all = sppa3.getPair();
 	}
 
 	@Test
 	public void testSimpleProfileProfileAligner() {
 		SimpleProfileProfileAligner<ProteinSequence, AminoAcidCompound> alig =
-				new SimpleProfileProfileAligner<ProteinSequence, AminoAcidCompound>();
+				new SimpleProfileProfileAligner<>();
 		alig.setQuery(prof1);
 		alig.setTarget(prof2);
 		alig.setGapPenalty(gaps);
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleSubstitutionMatrixTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleSubstitutionMatrixTest.java
index 72ed4137d7..702bc4960f 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleSubstitutionMatrixTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleSubstitutionMatrixTest.java
@@ -42,7 +42,7 @@ public class SimpleSubstitutionMatrixTest {
 
 	@Test(expected=FileNotFoundException.class)
 	public void testSimpleSubstitutionMatrixNotFound() throws FileNotFoundException {
-		new SimpleSubstitutionMatrix<AminoAcidCompound>(AminoAcidCompoundSet.getAminoAcidCompoundSet(),
+		new SimpleSubstitutionMatrix<>(AminoAcidCompoundSet.getAminoAcidCompoundSet(),
 				new File("blosum63.txt"));
 	}
 
@@ -51,7 +51,7 @@ public void test() throws CompoundNotFoundException {
 		NucleotideCompound A = new DNASequence("A").getCompoundAt(1);
 		NucleotideCompound a = new DNASequence("a").getCompoundAt(1);
 		NucleotideCompound c = new DNASequence("c").getCompoundAt(1);
-		SubstitutionMatrix<NucleotideCompound> matrix = new SimpleSubstitutionMatrix<NucleotideCompound>(DNACompoundSet.getDNACompoundSet(), (short)1, (short)0);
+		SubstitutionMatrix<NucleotideCompound> matrix = new SimpleSubstitutionMatrix<>(DNACompoundSet.getDNACompoundSet(), (short) 1, (short) 0);
 		assertEquals(1, (matrix.getValue(A, A)));
 		assertEquals(1, (matrix.getValue(a, a)));
 		assertEquals(1, (matrix.getValue(A, a)));
@@ -70,7 +70,7 @@ public void testSimpleSubstitutionMatrix() {
 	@Test
 	public void testSimpleSubstitutionMatrixCompoundSetOfCStringString() {
 		DNACompoundSet dnacs = DNACompoundSet.getDNACompoundSet();
-		SubstitutionMatrix<NucleotideCompound> dnaTest = new SimpleSubstitutionMatrix<NucleotideCompound>(dnacs,
+		SubstitutionMatrix<NucleotideCompound> dnaTest = new SimpleSubstitutionMatrix<>(dnacs,
 				"# Test\nA C G T\nA 5 0 0 0\nC 0 5 0 0\nG 0 0 5 0\nT 0 0 0 1\n", "DNA Test");
 		short[][] matrix = dnaTest.getMatrix();
 		assertEquals(matrix[1][1], 5);
@@ -83,7 +83,7 @@ public void testSimpleSubstitutionMatrixCompoundSetOfCStringString() {
 
 	@Test
 	public void testSimpleSubstitutionMatrixCompoundSetOfCShortShort() {
-		SubstitutionMatrix<AminoAcidCompound> matrix = new SimpleSubstitutionMatrix<AminoAcidCompound>(
+		SubstitutionMatrix<AminoAcidCompound> matrix = new SimpleSubstitutionMatrix<>(
 				AminoAcidCompoundSet.getAminoAcidCompoundSet(), (short) 5, (short) 1);
 		assertEquals(matrix.getName(), "IDENTITY_5_1");
 	}
@@ -106,7 +106,7 @@ public void testSetName() {
 
 	@Test
 	public void testToString() {
-		SubstitutionMatrix<NucleotideCompound> matrix = new SimpleSubstitutionMatrix<NucleotideCompound>(
+		SubstitutionMatrix<NucleotideCompound> matrix = new SimpleSubstitutionMatrix<>(
 				DNACompoundSet.getDNACompoundSet(),
 				"# Test\nA C  G T\nA 5  0 0 0\nC 0 5 0 0 \nG 0 0 5 0\n    T 0     0 0 1\n", "DNAtest");
 		assertEquals(matrix.toString().substring(0,6), "# Test");
@@ -119,7 +119,7 @@ public void testToString() {
 	@Test
 	public void testCaseEquivalence() {
 		DNACompoundSet dnacs = DNACompoundSet.getDNACompoundSet();
-		SubstitutionMatrix<NucleotideCompound> dnaTest = new SimpleSubstitutionMatrix<NucleotideCompound>(dnacs,
+		SubstitutionMatrix<NucleotideCompound> dnaTest = new SimpleSubstitutionMatrix<>(dnacs,
 				"# Test\nA C G T\nA 5 0 0 0\nC 0 5 0 0\nG 0 0 5 0\nT 0 0 0 1\n", "DNA Test");
 		@SuppressWarnings("unused")
 		short[][] matrix = dnaTest.getMatrix();
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SmithWatermanTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SmithWatermanTest.java
index a3335b500e..c51d294525 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SmithWatermanTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SmithWatermanTest.java
@@ -49,14 +49,14 @@ public void setup() throws CompoundNotFoundException {
 		target = new ProteinSequence("ERDNKGFPS");
 		gaps = new SimpleGapPenalty((short) 2, (short) 1);
 		blosum62 = SubstitutionMatrixHelper.getBlosum62();
-		alignment = new SmithWaterman<ProteinSequence, AminoAcidCompound>(query, target, gaps, blosum62);
-		self = new SmithWaterman<ProteinSequence, AminoAcidCompound>(query, query, gaps, blosum62);
+		alignment = new SmithWaterman<>(query, target, gaps, blosum62);
+		self = new SmithWaterman<>(query, query, gaps, blosum62);
 	}
 
 	@Test
 	public void testSmithWaterman() {
 		SmithWaterman<ProteinSequence, AminoAcidCompound> alig =
-				new SmithWaterman<ProteinSequence, AminoAcidCompound>();
+				new SmithWaterman<>();
 		alig.setQuery(query);
 		alig.setTarget(target);
 		alig.setGapPenalty(gaps);
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java
index a50d8c4cde..cb21de52b4 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java
@@ -57,7 +57,7 @@ public void testDNAAlignment() {
 
 			Profile<DNASequence, NucleotideCompound> profile = Alignments.getMultipleSequenceAlignment(lst);
 
-			Assert.assertTrue(profile.getSize() == 10);
+			Assert.assertEquals(10, profile.getSize());
 
 			Assert.assertTrue(profile.getAlignedSequence(1).getSequenceAsString().length() > 50);
 
@@ -77,11 +77,10 @@ private static List<DNASequence> getDNAFASTAFile() throws Exception {
 		InputStream inStream = TestDNAAlignment.class.getResourceAsStream(String.format("/dna-fasta.txt"));
 		LinkedHashMap<String, DNASequence> fastas = FastaReaderHelper.readFastaDNASequence(inStream);
 
-		List<DNASequence> sequences = new ArrayList<DNASequence>();
+		List<DNASequence> sequences = new ArrayList<>();
 
-		for (String key : fastas.keySet()) {
-			DNASequence seq = fastas.get(key);
-			sequences.add(seq);
+		for (DNASequence seq : fastas.values()) {
+            sequences.add(seq);
 		}
 
 		return sequences;
@@ -96,7 +95,7 @@ public void testDNAMultipleAlignmentWithMixedCompoundSets() throws CompoundNotFo
 		DNASequence target = new DNASequence("ACTGACGTGTAGCTGACTGA", DNACompoundSet.getDNACompoundSet());
 		DNASequence query = new DNASequence("ACTGACGTGTAGCTGACTGTA", AmbiguityDNACompoundSet.getDNACompoundSet());
 
-		List<DNASequence> lst = new ArrayList<DNASequence>();
+		List<DNASequence> lst = new ArrayList<>();
 		lst.add(target);
 		lst.add(query);
 
@@ -163,6 +162,6 @@ public void testLinearAlignment() throws CompoundNotFoundException {
 		SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();
 		SimpleGapPenalty gapP = new SimpleGapPenalty((short)0, (short)3);
 		PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = Alignments.getPairwiseAligner(query, target, PairwiseSequenceAlignerType.GLOBAL, gapP, matrix);
-		Assert.assertEquals(String.format("GTAAAA-G----------%nG-AAAACGTTTTTTTTTT%n"), aligner.getPair().toString());;
+		Assert.assertEquals(String.format("GTAAAA-G----------%nG-AAAACGTTTTTTTTTT%n"), aligner.getPair().toString());
 	}
 }
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestSubOptimalMSA.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestSubOptimalMSA.java
index 13a14120a5..1785d45e53 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestSubOptimalMSA.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestSubOptimalMSA.java
@@ -36,7 +36,7 @@
 
 public class TestSubOptimalMSA {
 
-	private List<DNASequence> sequences = new ArrayList<DNASequence>();
+	private final List<DNASequence> sequences = new ArrayList<>();
 
 	@Before
 	public void setUp() {
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/aaindex/TestAAINDEXLoading.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/aaindex/TestAAINDEXLoading.java
index 1dbcc8cfcf..ba380cce44 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/aaindex/TestAAINDEXLoading.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/aaindex/TestAAINDEXLoading.java
@@ -63,7 +63,7 @@ public void testSDMmatrix(){
 
 		SubstitutionMatrix<AminoAcidCompound> sdm = SubstitutionMatrixHelper.getMatrixFromAAINDEX(matrixName);
 
-		int scale = 1;
+		int scale;
 		if ( sdm instanceof ScaledSubstitutionMatrix) {
 			ScaledSubstitutionMatrix scaledSDM = (ScaledSubstitutionMatrix)sdm;
 			scale = scaledSDM.getScale();
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/io/TestStockholmParser.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/io/TestStockholmParser.java
index 2e888705bf..67ac48522a 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/io/TestStockholmParser.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/io/TestStockholmParser.java
@@ -78,10 +78,10 @@ public void testPiwi(){
 
 			StockholmStructure data = fileParser.parse(inStream);
 
-			Assert.assertTrue("Did not get enough sequences!", data.getBioSequences(false).size() == 20);
+            Assert.assertEquals("Did not get enough sequences!", 20, data.getBioSequences(false).size());
 
 			AbstractSequence<?> seq = data.getBioSequences(false).get(0);
-			Assert.assertTrue(seq != null);
+            Assert.assertNotNull(seq);
 
 			Assert.assertTrue(seq.getSequenceAsString().length() > 20);
 
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/routines/AlignerHelperTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/routines/AlignerHelperTest.java
index 9d12abb897..ae3308ac6c 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/routines/AlignerHelperTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/routines/AlignerHelperTest.java
@@ -28,8 +28,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.*;
 
 /**
  *
@@ -62,7 +61,7 @@ public void getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cu
 	}
 	@Test
 	public void getSubproblems_should_return_score_indicies_of_alignment_subproblems() {
-		List<Anchor> anchors = new ArrayList<Anchor>();
+		List<Anchor> anchors = new ArrayList<>();
 		anchors.add(new Anchor(1, 2));
 		anchors.add(new Anchor(5, 5));
 		List<Subproblem> problems = AlignerHelper.Subproblem.getSubproblems(anchors, 10, 15);
@@ -82,18 +81,18 @@ public void getSubproblems_should_return_score_indicies_of_alignment_subproblems
 	}
 	@Test
 	public void getSubproblems_should_allow_zero_anchors() {
-		List<Anchor> anchors = new ArrayList<Anchor>();
+		List<Anchor> anchors = new ArrayList<>();
 		List<Subproblem> problems = AlignerHelper.Subproblem.getSubproblems(anchors, 10, 15);
 		assertEquals(1, problems.size());
 		assertEquals(0, problems.get(0).getQueryStartIndex());
 		assertEquals(0, problems.get(0).getTargetStartIndex());
 		assertEquals(10, problems.get(0).getQueryEndIndex());
 		assertEquals(15, problems.get(0).getTargetEndIndex());
-		assertEquals(false, problems.get(0).isStartAnchored());
+		assertFalse(problems.get(0).isStartAnchored());
 	}
 	@Test
 	public void getSubproblems_should_allow_start_and_end_anchors() {
-		List<Anchor> anchors = new ArrayList<Anchor>();
+		List<Anchor> anchors = new ArrayList<>();
 		anchors.add(new Anchor(0, 0));
 		anchors.add(new Anchor(9, 14));
 		List<Subproblem> problems = AlignerHelper.Subproblem.getSubproblems(anchors, 10, 15);
@@ -102,21 +101,21 @@ public void getSubproblems_should_allow_start_and_end_anchors() {
 		assertEquals(0, problems.get(0).getTargetStartIndex());
 		assertEquals(0, problems.get(0).getQueryEndIndex());
 		assertEquals(0, problems.get(0).getTargetEndIndex());
-		assertEquals(false, problems.get(0).isStartAnchored());
+		assertFalse(problems.get(0).isStartAnchored());
 		assertEquals(1, problems.get(1).getQueryStartIndex());
 		assertEquals(1, problems.get(1).getTargetStartIndex());
 		assertEquals(9, problems.get(1).getQueryEndIndex());
 		assertEquals(14, problems.get(1).getTargetEndIndex());
-		assertEquals(true, problems.get(1).isStartAnchored());
+		assertTrue(problems.get(1).isStartAnchored());
 		assertEquals(10, problems.get(2).getQueryStartIndex());
 		assertEquals(15, problems.get(2).getTargetStartIndex());
 		assertEquals(10, problems.get(2).getQueryEndIndex());
 		assertEquals(15, problems.get(2).getTargetEndIndex());
-		assertEquals(true, problems.get(2).isStartAnchored());
+		assertTrue(problems.get(2).isStartAnchored());
 	}
 	@Test
 	public void getSubproblems_should_allow_adjacent_anchors() {
-		List<Anchor> anchors = new ArrayList<Anchor>();
+		List<Anchor> anchors = new ArrayList<>();
 		anchors.add(new Anchor(1, 1));
 		anchors.add(new Anchor(2, 3));
 		List<Subproblem> problems = AlignerHelper.Subproblem.getSubproblems(anchors, 10, 15);
@@ -132,14 +131,14 @@ public void getSubproblems_should_allow_adjacent_anchors() {
 	}
 	@Test(expected=IllegalArgumentException.class)
 	public void getSubproblems_should_not_allow_repeated_anchors() {
-		List<Anchor> anchors = new ArrayList<Anchor>();
+		List<Anchor> anchors = new ArrayList<>();
 		anchors.add(new Anchor(1, 1));
 		anchors.add(new Anchor(1, 2));
 		AlignerHelper.Subproblem.getSubproblems(anchors, 10, 15);
 	}
 	@Test(expected=IllegalArgumentException.class)
 	public void getSubproblems_should_not_allow_unalignable_anchors() {
-		List<Anchor> anchors = new ArrayList<Anchor>();
+		List<Anchor> anchors = new ArrayList<>();
 		anchors.add(new Anchor(1, 2));
 		anchors.add(new Anchor(2, 1));
 		AlignerHelper.Subproblem.getSubproblems(anchors, 10, 15);
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/routines/GuanUberbacherTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/routines/GuanUberbacherTest.java
index 5ecb525231..f97e84d16e 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/routines/GuanUberbacherTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/routines/GuanUberbacherTest.java
@@ -54,14 +54,14 @@ public void setup() throws CompoundNotFoundException {
 		target = new ProteinSequence("RDG");
 		gaps = new SimpleGapPenalty(10, 1);
 		blosum62 = SubstitutionMatrixHelper.getBlosum62();
-		alignment = new GuanUberbacher<ProteinSequence, AminoAcidCompound>(query, target, gaps, blosum62);
-		self = new GuanUberbacher<ProteinSequence, AminoAcidCompound>(query, query, gaps, blosum62);
+		alignment = new GuanUberbacher<>(query, target, gaps, blosum62);
+		self = new GuanUberbacher<>(query, query, gaps, blosum62);
 	}
 
 	@Test
 	public void testGuanUberbacher() {
 		GuanUberbacher<ProteinSequence, AminoAcidCompound> gu =
-				new GuanUberbacher<ProteinSequence, AminoAcidCompound>();
+				new GuanUberbacher<>();
 		gu.setQuery(query);
 		gu.setTarget(target);
 		gu.setGapPenalty(gaps);
@@ -111,7 +111,7 @@ public void testGetPair() {
 	public void should_align_shorter_query() throws CompoundNotFoundException {
 		DNASequence query = new DNASequence("A", AmbiguityDNACompoundSet.getDNACompoundSet());
 		DNASequence target = new DNASequence("AT", AmbiguityDNACompoundSet.getDNACompoundSet());
-		GuanUberbacher<DNASequence, NucleotideCompound> aligner = new GuanUberbacher<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)5, (short)2), SubstitutionMatrixHelper.getNuc4_4());
+		GuanUberbacher<DNASequence, NucleotideCompound> aligner = new GuanUberbacher<>(query, target, new SimpleGapPenalty((short) 5, (short) 2), SubstitutionMatrixHelper.getNuc4_4());
 		assertEquals(String.format("A-%nAT%n"), aligner.getPair().toString());
 	}
 	/**
@@ -121,7 +121,7 @@ public void should_align_shorter_query() throws CompoundNotFoundException {
 	public void should_align_shorter_target() throws CompoundNotFoundException {
 		DNASequence query = new DNASequence("AT", AmbiguityDNACompoundSet.getDNACompoundSet());
 		DNASequence target = new DNASequence("A", AmbiguityDNACompoundSet.getDNACompoundSet());
-		GuanUberbacher<DNASequence, NucleotideCompound> aligner = new GuanUberbacher<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)5, (short)2), SubstitutionMatrixHelper.getNuc4_4());
+		GuanUberbacher<DNASequence, NucleotideCompound> aligner = new GuanUberbacher<>(query, target, new SimpleGapPenalty((short) 5, (short) 2), SubstitutionMatrixHelper.getNuc4_4());
 		assertEquals(String.format("AT%nA-%n"), aligner.getPair().toString());
 	}
 	/**
@@ -131,7 +131,7 @@ public void should_align_shorter_target() throws CompoundNotFoundException {
 	public void should_align_multiple_cuts() throws CompoundNotFoundException {
 		DNASequence query = new DNASequence("AAT", AmbiguityDNACompoundSet.getDNACompoundSet());
 		DNASequence target = new DNASequence("AATG", AmbiguityDNACompoundSet.getDNACompoundSet());
-		GuanUberbacher<DNASequence, NucleotideCompound> aligner = new GuanUberbacher<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)0, (short)2), SubstitutionMatrixHelper.getNuc4_4());
+		GuanUberbacher<DNASequence, NucleotideCompound> aligner = new GuanUberbacher<>(query, target, new SimpleGapPenalty((short) 0, (short) 2), SubstitutionMatrixHelper.getNuc4_4());
 		aligner.setCutsPerSection(2); // 3 bases with 2 cuts
 		assertEquals(String.format("AAT-%nAATG%n"), aligner.getPair().toString());
 	}
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestDistanceTreeEvaluator.java b/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestDistanceTreeEvaluator.java
index 3c129e0c22..1b006690fc 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestDistanceTreeEvaluator.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestDistanceTreeEvaluator.java
@@ -35,7 +35,7 @@
 public class TestDistanceTreeEvaluator {
 
 	@Test
-	public void testErrorFree() throws Exception {
+	public void testErrorFree() {
 
 		// Create a perfect additive distance matrix
 		BasicSymmetricalDistanceMatrix DM = new BasicSymmetricalDistanceMatrix(
@@ -44,7 +44,7 @@ public void testErrorFree() throws Exception {
 		// dAB = 0.8, dBC = 0.4, dAC = 0.8
 		for (int i = 0; i < 3; i++) {
 			char id = (char) ('A' + i);
-			DM.setIdentifier(i, id + "");
+			DM.setIdentifier(i, String.valueOf(id));
 			for (int j = i; j < 3; j++) {
 				if (i == j) {
 					DM.setValue(i, j, 0.0);
@@ -66,7 +66,7 @@ public void testErrorFree() throws Exception {
 	}
 
 	@Test
-	public void testErrorEstimation() throws Exception {
+	public void testErrorEstimation() {
 
 		// Matrix taken from forester test
 		BasicSymmetricalDistanceMatrix m = new BasicSymmetricalDistanceMatrix(4);
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestForesterWrapper.java b/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestForesterWrapper.java
index c4fe468852..8d4e2c563f 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestForesterWrapper.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestForesterWrapper.java
@@ -55,11 +55,11 @@ public void testMSAconversion() throws Exception {
 				.getResourceAsStream("/1u6d_symm.fasta");
 
 		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader =
-				new FastaReader<ProteinSequence, AminoAcidCompound>(
-				inStream,
-				new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
-				new ProteinSequenceCreator(AminoAcidCompoundSet
-						.getAminoAcidCompoundSet()));
+				new FastaReader<>(
+						inStream,
+						new GenericFastaHeaderParser<>(),
+						new ProteinSequenceCreator(AminoAcidCompoundSet
+								.getAminoAcidCompoundSet()));
 
 		LinkedHashMap<String, ProteinSequence> proteinSequences = fastaReader
 				.process();
@@ -67,7 +67,7 @@ public void testMSAconversion() throws Exception {
 		inStream.close();
 
 		MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> msa =
-				new MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound>();
+				new MultipleSequenceAlignment<>();
 
 		String expected = "";
 		for (ProteinSequence proteinSequence : proteinSequences.values()) {
@@ -79,14 +79,9 @@ public void testMSAconversion() throws Exception {
 		// Convert the biojava MSA to a FASTA String
 		OutputStream os = new ByteArrayOutputStream();
 		FastaWriter<ProteinSequence, AminoAcidCompound> fastaW =
-				new FastaWriter<ProteinSequence, AminoAcidCompound>(os,
-				msa.getAlignedSequences(),
-				new FastaHeaderFormatInterface<ProteinSequence, AminoAcidCompound>() {
-					@Override
-					public String getHeader(ProteinSequence sequence) {
-						return sequence.getAccession().toString();
-					};
-				});
+				new FastaWriter<>(os,
+						msa.getAlignedSequences(),
+						sequence -> sequence.getAccession().toString());
 		fastaW.process();
 		String biojava = os.toString();
 
diff --git a/biojava-core/src/main/java/demo/DemoSixFrameTranslation.java b/biojava-core/src/main/java/demo/DemoSixFrameTranslation.java
index 354e0bea26..ae98073d1a 100644
--- a/biojava-core/src/main/java/demo/DemoSixFrameTranslation.java
+++ b/biojava-core/src/main/java/demo/DemoSixFrameTranslation.java
@@ -106,9 +106,9 @@ public static void main(String[] args){
 			CompoundSet<NucleotideCompound> nucleotideCompoundSet = AmbiguityRNACompoundSet.getRNACompoundSet();
 
 			FastaReader<DNASequence, NucleotideCompound> proxy =
-					new FastaReader<DNASequence, NucleotideCompound>(
+					new FastaReader<>(
 							stream,
-							new GenericFastaHeaderParser<DNASequence, NucleotideCompound>(),
+							new GenericFastaHeaderParser<>(),
 							new DNASequenceCreator(ambiguityDNACompoundSet));
 
 			// has only one entry in this example, but could be easily extended to parse a FASTA file with multiple sequences
diff --git a/biojava-core/src/main/java/demo/ParseFastaFileDemo.java b/biojava-core/src/main/java/demo/ParseFastaFileDemo.java
index 5951ed3ad6..f201adc24f 100644
--- a/biojava-core/src/main/java/demo/ParseFastaFileDemo.java
+++ b/biojava-core/src/main/java/demo/ParseFastaFileDemo.java
@@ -24,6 +24,8 @@
 import java.io.File;
 import java.io.InputStream;
 import java.util.LinkedHashMap;
+import java.util.Map;
+
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
@@ -94,9 +96,9 @@ public static void main(String[] args) throws Exception {
 		InputStream inStream = isp.getInputStream(f);
 
 
-		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
 				inStream,
-				new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+				new GenericFastaHeaderParser<>(),
 				new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
 
 		LinkedHashMap<String, ProteinSequence> b;
@@ -104,9 +106,9 @@ public static void main(String[] args) throws Exception {
 		int nrSeq = 0;
 
 		while ((b = fastaReader.process(100)) != null) {
-			for (String key : b.keySet()) {
+			for (Map.Entry<String, ProteinSequence> entry : b.entrySet()) {
 				nrSeq++;
-				System.out.println(nrSeq + " : " + key + " " + b.get(key));
+				System.out.println(nrSeq + " : " + entry.getKey() + " " + entry.getValue());
 				if ( nrSeq % 100000 == 0)
 					System.out.println(nrSeq );
 			}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
index 8980fdad7b..81ab206cde 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
@@ -54,8 +54,10 @@ public class SimpleAlignedSequence<S extends Sequence<C>, C extends Compound> im
 
 	// always stored
 	private AlignedSequence<S, C> prev;
-	private S original;
-	private int length, numBefore, numAfter;
+	private final S original;
+	private final int length;
+	private int numBefore;
+	private int numAfter;
 	private Location location;
 
 	// cached (lazily initialized)
@@ -266,8 +268,9 @@ public boolean isGap(int alignmentIndex) {
 
 	// methods for Sequence
 
+	@SafeVarargs
 	@Override
-	public int countCompounds(C... compounds) {
+	public final int countCompounds(C... compounds) {
 		int count = 0;
 		List<C> search = Arrays.asList(compounds);
 		for (C compound : getAsList()) {
@@ -285,7 +288,7 @@ public AccessionID getAccession() {
 
 	@Override
 	public List<C> getAsList() {
-		List<C> compounds = new ArrayList<C>();
+		List<C> compounds = new ArrayList<>();
 		for (int i = 1; i <= length; i++) {
 			compounds.add(getCompoundAt(i));
 		}
@@ -382,7 +385,7 @@ public String toString() {
 
 	// helper method to initialize the location
 	private void setLocation(List<Step> steps) {
-		List<Location> sublocations = new ArrayList<Location>();
+		List<Location> sublocations = new ArrayList<>();
 		int start = 0, step = 0, oStep = numBefore+numAfter, oMax = this.original.getLength(), pStep = 0, pMax =
 				(prev == null) ? 0 : prev.getLength();
 		boolean inGap = true;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
index 7cd7ef1bf5..81f1c09ac1 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
@@ -57,7 +57,7 @@ public class SimpleProfile<S extends Sequence<C>, C extends Compound> implements
 
 	private List<AlignedSequence<S, C>> list;
 	private List<S> originals;
-	private int length;
+	private final int length;
 
 	/**
 	 * Creates a pair profile for the given already aligned sequences.
@@ -70,11 +70,11 @@ protected SimpleProfile(AlignedSequence<S, C> query, AlignedSequence<S, C> targe
 		if (query.getLength() != target.getLength()) {
 			throw new IllegalArgumentException("Aligned sequences differ in size");
 		}
-		list = new ArrayList<AlignedSequence<S, C>>();
+		list = new ArrayList<>();
 		list.add(query);
 		list.add(target);
 		list = Collections.unmodifiableList(list);
-		originals = new ArrayList<S>();
+		originals = new ArrayList<>();
 		originals.add(query.getOriginalSequence());
 		originals.add(target.getOriginalSequence());
 		originals = Collections.unmodifiableList(originals);
@@ -87,14 +87,14 @@ protected SimpleProfile(AlignedSequence<S, C> query, AlignedSequence<S, C> targe
 	 * @param sequence sequence to seed profile
 	 */
 	public SimpleProfile(S sequence) {
-		List<Step> s = new ArrayList<Step>();
+		List<Step> s = new ArrayList<>();
 		for (int i = 0; i < sequence.getLength(); i++) {
 			s.add(Step.COMPOUND);
 		}
-		list = new ArrayList<AlignedSequence<S, C>>();
-		list.add(new SimpleAlignedSequence<S, C>(sequence, s));
+		list = new ArrayList<>();
+		list.add(new SimpleAlignedSequence<>(sequence, s));
 		list = Collections.unmodifiableList(list);
-		originals = new ArrayList<S>();
+		originals = new ArrayList<>();
 		originals.add(sequence);
 		originals = Collections.unmodifiableList(originals);
 		length = sequence.getLength();
@@ -117,11 +117,11 @@ protected SimpleProfile(S query, S target, List<Step> sx, int xb, int xa, List<S
 		if (sx.size() != sy.size()) {
 			throw new IllegalArgumentException("Alignments differ in size");
 		}
-		list = new ArrayList<AlignedSequence<S, C>>();
-		list.add(new SimpleAlignedSequence<S, C>(query, sx, xb, xa));
-		list.add(new SimpleAlignedSequence<S, C>(target, sy, yb, ya));
+		list = new ArrayList<>();
+		list.add(new SimpleAlignedSequence<>(query, sx, xb, xa));
+		list.add(new SimpleAlignedSequence<>(target, sy, yb, ya));
 		list = Collections.unmodifiableList(list);
-		originals = new ArrayList<S>();
+		originals = new ArrayList<>();
 		originals.add(query);
 		originals.add(target);
 		originals = Collections.unmodifiableList(originals);
@@ -141,15 +141,15 @@ protected SimpleProfile(Profile<S, C> query, Profile<S, C> target, List<Step> sx
 		if (sx.size() != sy.size()) {
 			throw new IllegalArgumentException("Alignments differ in size");
 		}
-		list = new ArrayList<AlignedSequence<S, C>>();
+		list = new ArrayList<>();
 		for (AlignedSequence<S, C> s : query) {
-			list.add(new SimpleAlignedSequence<S, C>(s, sx));
+			list.add(new SimpleAlignedSequence<>(s, sx));
 		}
 		for (AlignedSequence<S, C> s : target) {
-			list.add(new SimpleAlignedSequence<S, C>(s, sy));
+			list.add(new SimpleAlignedSequence<>(s, sy));
 		}
 		list = Collections.unmodifiableList(list);
-		originals = new ArrayList<S>();
+		originals = new ArrayList<>();
 		originals.addAll(query.getOriginalSequences());
 		originals.addAll(target.getOriginalSequences());
 		originals = Collections.unmodifiableList(originals);
@@ -163,8 +163,8 @@ protected SimpleProfile(Profile<S, C> query, Profile<S, C> target, List<Step> sx
 	 * collection is empty.
 	 */
 	public SimpleProfile(Collection<AlignedSequence<S,C>> alignedSequences) {
-		list = new ArrayList<AlignedSequence<S,C>>();
-		originals = new ArrayList<S>();
+		list = new ArrayList<>();
+		originals = new ArrayList<>();
 
 		Iterator<AlignedSequence<S,C>> itr = alignedSequences.iterator();
 		if(!itr.hasNext()) {
@@ -213,16 +213,17 @@ public List<AlignedSequence<S, C>> getAlignedSequences() {
 
 	@Override
 	public List<AlignedSequence<S, C>> getAlignedSequences(int... listIndices) {
-		List<AlignedSequence<S, C>> tempList = new ArrayList<AlignedSequence<S, C>>();
+		List<AlignedSequence<S, C>> tempList = new ArrayList<>();
 		for (int i : listIndices) {
 			tempList.add(getAlignedSequence(i));
 		}
 		return Collections.unmodifiableList(tempList);
 	}
 
+	@SafeVarargs
 	@Override
-	public List<AlignedSequence<S, C>> getAlignedSequences(S... sequences) {
-		List<AlignedSequence<S, C>> tempList = new ArrayList<AlignedSequence<S, C>>();
+	public final List<AlignedSequence<S, C>> getAlignedSequences(S... sequences) {
+		List<AlignedSequence<S, C>> tempList = new ArrayList<>();
 		for (S s : sequences) {
 			tempList.add(getAlignedSequence(s));
 		}
@@ -262,7 +263,7 @@ public int[] getCompoundCountsAt(int alignmentIndex, List<C> compounds) {
 	@Override
 	public List<C> getCompoundsAt(int alignmentIndex) {
 		// TODO handle circular alignments
-		List<C> column = new ArrayList<C>();
+		List<C> column = new ArrayList<>();
 		for (AlignedSequence<S, C> s : list) {
 			column.add(s.getCompoundAt(alignmentIndex));
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfilePair.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfilePair.java
index 8d1479bacf..5c5296228c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfilePair.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfilePair.java
@@ -46,7 +46,8 @@ public class SimpleProfilePair<S extends Sequence<C>, C extends Compound> extend
 
 	private static final long serialVersionUID = 1L;
 
-	private Profile<S, C> query, target;
+	private final Profile<S, C> query;
+    private final Profile<S, C> target;
 
 	/**
 	 * Creates a pair profile for the given profiles.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java
index 6e2e5bff56..a9f400f054 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java
@@ -53,7 +53,7 @@ public class AAIndexFileParser {
 
 
 	public AAIndexFileParser(){
-		matrices  = new HashMap<String, SubstitutionMatrix<AminoAcidCompound>>();
+		matrices  = new HashMap<>();
 	}
 
 	/** parse an inputStream that points to an AAINDEX database file
@@ -71,7 +71,7 @@ public void parse(InputStream inputStream) throws IOException {
 		inMatrix = false;
 
 		BufferedReader buf = new BufferedReader (new InputStreamReader (inputStream));
-		String line = null;
+		String line;
 		line = buf.readLine();
 
 		while (  line != null ) {
@@ -125,10 +125,10 @@ private void processScores(String line) {
 			}
 
 
-			Float score = Float.parseFloat(values[i]);
+			float score = Float.parseFloat(values[i]);
 			score = scale * score;
 
-			Short s = (short) Math.round(score);
+			short s = (short) Math.round(score);
 
 			matrix[currentRowPos][i] = s;
 
@@ -150,7 +150,7 @@ private void processScores(String line) {
 		}
 	}
 
-	private int determineScale(String value) {
+	private static int determineScale(String value) {
 
 		String[] spl = value.split("\\.");
 
@@ -177,8 +177,8 @@ private void initMatrix(String line) {
 
 		matrix = new short[nrRows][nrCols];
 
-		rows = new ArrayList<AminoAcidCompound>();
-		cols = new ArrayList<AminoAcidCompound>();
+		rows = new ArrayList<>();
+		cols = new ArrayList<>();
 
 
 		//System.out.println(">" + currentRows+"<");
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexProvider.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexProvider.java
index 32b5994c60..9eecd9580d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexProvider.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexProvider.java
@@ -26,5 +26,5 @@
 
 public interface AAIndexProvider {
 
-	public SubstitutionMatrix<AminoAcidCompound> getMatrix(String matrixName);
+	SubstitutionMatrix<AminoAcidCompound> getMatrix(String matrixName);
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java
index ee26384bfa..86042a9d38 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java
@@ -52,7 +52,7 @@ public class ScaledSubstitutionMatrix implements
 	private String description, name;
 	private short[][] matrix;
 	private short max, min;
-	private AminoAcidCompoundSet compoundSet;
+	private final AminoAcidCompoundSet compoundSet;
 
 	private List<AminoAcidCompound> rows, cols;
 
@@ -164,8 +164,8 @@ public String getMatrixAsString() {
 			int lengthCompound = compoundSet.getMaxSingleCompoundStringLength(), lengthRest =
 					Math.max(Math.max(Short.toString(min).length(), Short.toString(max).length()), lengthCompound) + 1;
 
-			String padCompound = "%" + Integer.toString(lengthCompound) + "s",
-					padRest = "%" + Integer.toString(lengthRest);
+			String padCompound = "%" + lengthCompound + "s",
+					padRest = "%" + lengthRest;
 
 			for (int i = 0; i < lengthCompound; i++) {
 				s.append(" ");
@@ -216,7 +216,7 @@ public SubstitutionMatrix<AminoAcidCompound> normalizeMatrix(short scale) {
 	@Override
 	public Map<AminoAcidCompound, Short> getRow(AminoAcidCompound row) {
 		int rowIndex = rows.indexOf(row);
-		Map<AminoAcidCompound, Short> map = new HashMap<AminoAcidCompound, Short>();
+		Map<AminoAcidCompound, Short> map = new HashMap<>();
 		for (int colIndex = 0; colIndex < matrix[rowIndex].length; colIndex++) {
 			map.put(cols.get(colIndex), matrix[rowIndex][colIndex]);
 		}
@@ -226,7 +226,7 @@ public Map<AminoAcidCompound, Short> getRow(AminoAcidCompound row) {
 	@Override
 	public Map<AminoAcidCompound, Short> getColumn(AminoAcidCompound column) {
 		int colIndex = cols.indexOf(column);
-		Map<AminoAcidCompound, Short> map = new HashMap<AminoAcidCompound, Short>();
+		Map<AminoAcidCompound, Short> map = new HashMap<>();
 		for (int i = 0; i < matrix.length; i++) {
 			map.put(rows.get(i), matrix[i][colIndex]);
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java
index 8eb897219e..8f9e8dbf52 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java
@@ -50,14 +50,15 @@ public class SimpleSubstitutionMatrix<C extends Compound> implements Substitutio
 
 	private static final String comment = "#";
 
-	private CompoundSet<C> compoundSet;
+	private final CompoundSet<C> compoundSet;
 	private String description, name;
-	private short[][] matrix;
+	private final short[][] matrix;
 	private short max, min;
-	private List<C> rows, cols;
+	private final List<C> rows;
+	private final List<C> cols;
 
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum62() {
-		return new SimpleSubstitutionMatrix<AminoAcidCompound>(AminoAcidCompoundSet.getAminoAcidCompoundSet(), new InputStreamReader(
+		return new SimpleSubstitutionMatrix<>(AminoAcidCompoundSet.getAminoAcidCompoundSet(), new InputStreamReader(
 				SimpleSubstitutionMatrix.class.getResourceAsStream("/matrices/blosum62.txt")), "blosum62");
 	}
 
@@ -126,10 +127,10 @@ private SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, Scanner input, Stri
 		this.name = name;
 		max = Short.MIN_VALUE;
 		min = Short.MAX_VALUE;
-		rows = new ArrayList<C>();
-		cols = new ArrayList<C>();
+		rows = new ArrayList<>();
+		cols = new ArrayList<>();
 		StringBuilder descriptionIn = new StringBuilder();
-		List<short[]> matrixIn = new ArrayList<short[]>();
+		List<short[]> matrixIn = new ArrayList<>();
 		while(input.hasNextLine()) {
 			String line = input.nextLine();
 			if (line.startsWith(comment)) {
@@ -184,8 +185,8 @@ public String getMatrixAsString() {
 		StringBuilder s = new StringBuilder();
 		int lengthCompound = compoundSet.getMaxSingleCompoundStringLength(), lengthRest =
 				Math.max(Math.max(Short.toString(min).length(), Short.toString(max).length()), lengthCompound) + 1;
-		String padCompound = "%" + Integer.toString(lengthCompound) + "s",
-				padRest = "%" + Integer.toString(lengthRest);
+		String padCompound = "%" + lengthCompound + "s",
+				padRest = "%" + lengthRest;
 		for (int i = 0; i < lengthCompound; i++) {
 			s.append(" ");
 		}
@@ -288,7 +289,7 @@ public String toString() {
 	@Override
 	public Map<C, Short> getRow(C row) {
 		int rowIndex = rows.indexOf(row);
-		Map<C, Short> map = new HashMap<C, Short>();
+		Map<C, Short> map = new HashMap<>();
 		for (int colIndex = 0; colIndex < matrix[rowIndex].length; colIndex++) {
 			map.put(cols.get(colIndex), matrix[rowIndex][colIndex]);
 		}
@@ -298,7 +299,7 @@ public Map<C, Short> getRow(C row) {
 	@Override
 	public Map<C, Short> getColumn(C column) {
 		int colIndex = cols.indexOf(column);
-		Map<C, Short> map = new HashMap<C, Short>();
+		Map<C, Short> map = new HashMap<>();
 		for (int i = 0; i < matrix.length; i++) {
 			map.put(rows.get(i), matrix[i][colIndex]);
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java
index 7b629e7352..067ecee1b1 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java
@@ -48,10 +48,10 @@ public class SubstitutionMatrixHelper implements Serializable {
 	 */
 	private static final long serialVersionUID = 148491724604653225L;
 
-	private static Map<String, SubstitutionMatrix<AminoAcidCompound>> aminoAcidMatrices =
-			new HashMap<String, SubstitutionMatrix<AminoAcidCompound>>();
-	private static Map<String, SubstitutionMatrix<NucleotideCompound>> nucleotideMatrices =
-			new HashMap<String, SubstitutionMatrix<NucleotideCompound>>();
+	private static final Map<String, SubstitutionMatrix<AminoAcidCompound>> aminoAcidMatrices =
+			new HashMap<>();
+	private static final Map<String, SubstitutionMatrix<NucleotideCompound>> nucleotideMatrices =
+			new HashMap<>();
 
 	// prevents instantiation
 	private SubstitutionMatrixHelper() { }
@@ -251,7 +251,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getAminoAcidSubstitutionMatr
 	// reads in an amino acid substitution matrix, if necessary
 	private static SubstitutionMatrix<AminoAcidCompound> getAminoAcidMatrix(String file) {
 		if (!aminoAcidMatrices.containsKey(file)) {
-			aminoAcidMatrices.put(file, new SimpleSubstitutionMatrix<AminoAcidCompound>(
+			aminoAcidMatrices.put(file, new SimpleSubstitutionMatrix<>(
 					AminoAcidCompoundSet.getAminoAcidCompoundSet(), getReader(file), file));
 		}
 		return aminoAcidMatrices.get(file);
@@ -260,7 +260,7 @@ private static SubstitutionMatrix<AminoAcidCompound> getAminoAcidMatrix(String f
 	// reads in a nucleotide substitution matrix, if necessary
 	private static SubstitutionMatrix<NucleotideCompound> getNucleotideMatrix(String file) {
 		if (!nucleotideMatrices.containsKey(file)) {
-			nucleotideMatrices.put(file, new SimpleSubstitutionMatrix<NucleotideCompound>(
+			nucleotideMatrices.put(file, new SimpleSubstitutionMatrix<>(
 					AmbiguityDNACompoundSet.getDNACompoundSet(), getReader(file), file));
 		}
 		return nucleotideMatrices.get(file);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hit.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hit.java
index bf5ee54c69..6505ba50c9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hit.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hit.java
@@ -23,6 +23,7 @@
 import java.util.Iterator;
 import java.util.List;
 import java.util.NoSuchElementException;
+import java.util.Objects;
 
 import org.biojava.nbio.core.sequence.template.Sequence;
 
@@ -47,7 +48,7 @@ public abstract class Hit implements Iterable<Hsp>{
 	 */
 	private final int hitLen;
 	private final List<Hsp> hsps;
-	private Sequence hitSequence;
+	private final Sequence hitSequence;
 
 
 
@@ -85,7 +86,7 @@ public boolean equals(Object obj) {
 		if (this.hitLen != other.hitLen) {
 			return false;
 		}
-		if (this.hsps != other.hsps && (this.hsps == null || !this.hsps.equals(other.hsps))) {
+		if (!Objects.equals(this.hsps, other.hsps)) {
 			return false;
 		}
 		return true;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
index 8245c635c3..1a648eebbd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
@@ -22,6 +22,8 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Objects;
+
 import org.biojava.nbio.core.alignment.SimpleAlignedSequence;
 import org.biojava.nbio.core.alignment.SimpleSequencePair;
 import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
@@ -51,25 +53,25 @@
 
 public abstract class Hsp <S extends Sequence<C>, C extends Compound> {
 	private static final Logger logger = LoggerFactory.getLogger(Hsp.class);
-	private Integer hspNum;
-	private Double hspBitScore;
-	private Integer hspScore;
-	private Double hspEvalue;
-	private Integer hspQueryFrom;
-	private Integer hspQueryTo;
-	private Integer hspHitFrom;
-	private Integer hspHitTo;
-	private Integer hspQueryFrame;
-	private Integer hspHitFrame;
+	private final Integer hspNum;
+	private final Double hspBitScore;
+	private final Integer hspScore;
+	private final Double hspEvalue;
+	private final Integer hspQueryFrom;
+	private final Integer hspQueryTo;
+	private final Integer hspHitFrom;
+	private final Integer hspHitTo;
+	private final Integer hspQueryFrame;
+	private final Integer hspHitFrame;
 	private Integer hspIdentity;
-	private Integer hspPositive;
-	private Integer hspGaps;
+	private final Integer hspPositive;
+	private final Integer hspGaps;
 	private Integer hspAlignLen;
-	private String hspQseq;
-	private String hspHseq;
-	private String hspIdentityString;
-	private Double percentageIdentity = null;
-	private Integer mismatchCount = null;
+	private final String hspQseq;
+	private final String hspHseq;
+	private final String hspIdentityString;
+	private Double percentageIdentity;
+	private Integer mismatchCount;
 	private SimpleSequencePair<S, C> returnAln;
 
 	@Override
@@ -98,13 +100,13 @@ public boolean equals(Object obj) {
 			return false;
 		}
 		final Hsp<?, ?> other = (Hsp<?, ?>) obj;
-		if ((this.hspQseq == null) ? (other.hspQseq != null) : !this.hspQseq.equals(other.hspQseq)) {
+		if (!Objects.equals(this.hspQseq, other.hspQseq)) {
 			return false;
 		}
-		if ((this.hspHseq == null) ? (other.hspHseq != null) : !this.hspHseq.equals(other.hspHseq)) {
+		if (!Objects.equals(this.hspHseq, other.hspHseq)) {
 			return false;
 		}
-		if ((this.hspIdentityString == null) ? (other.hspIdentityString != null) : !this.hspIdentityString.equals(other.hspIdentityString)) {
+		if (!Objects.equals(this.hspIdentityString, other.hspIdentityString)) {
 			return false;
 		}
 		return true;
@@ -115,17 +117,15 @@ public SequencePair<S,C> getAlignment(){
 
 		SimpleAlignedSequence<S,C> alignedQuery, alignedHit;
 		// queryFrom e hitTo?
-		int numBefore, numAfter;
+//		int numBefore, numAfter;
 
 		alignedQuery = new SimpleAlignedSequence(getSequence(hspQseq), getAlignmentsSteps(hspQseq));
 		alignedHit = new SimpleAlignedSequence(getSequence(hspHseq), getAlignmentsSteps(hspHseq));
 
-		returnAln = new SimpleSequencePair<S, C>(alignedQuery, alignedHit);
-
-		return returnAln;
+		return returnAln = new SimpleSequencePair<>(alignedQuery, alignedHit);
 	}
 
-	private Sequence getSequence(String gappedSequenceString){
+	private static Sequence getSequence(String gappedSequenceString){
 		if (gappedSequenceString == null) return null;
 
 		Sequence returnSeq = null;
@@ -145,7 +145,7 @@ else if (sequenceString.matches("^[ACUG]+$"))
 	}
 
 	private List<Step> getAlignmentsSteps(String gappedSequenceString){
-		List<Step> returnList = new ArrayList<Step>();
+		List<Step> returnList = new ArrayList<>();
 
 		for (char c: gappedSequenceString.toCharArray()){
 			if (c=='-') returnList.add(Step.GAP); else returnList.add(Step.COMPOUND);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java
index aa1b432b57..37e604dab6 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java
@@ -20,11 +20,7 @@
  */
 package org.biojava.nbio.core.search.io;
 
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
-import java.util.NoSuchElementException;
+import java.util.*;
 
 import org.biojava.nbio.core.sequence.template.Sequence;
 
@@ -41,20 +37,20 @@
  */
 
 public abstract class Result implements Iterable<Hit>{
-	private String program;
-	private String version;
-	private String reference;
-	private String dbFile;
+	private final String program;
+	private final String version;
+	private final String reference;
+	private final String dbFile;
 
-	private HashMap<String,String> programSpecificParameters;
+	private final HashMap<String,String> programSpecificParameters;
 
-	private int iterationNumber;
-	private String queryID;
-	private String queryDef;
-	private int queryLength;
-	private Sequence querySequence;
-	private List<Hit> hits;
-	private int hitCounter = -1;
+	private final int iterationNumber;
+	private final String queryID;
+	private final String queryDef;
+	private final int queryLength;
+	private final Sequence querySequence;
+	private final List<Hit> hits;
+	private final int hitCounter = -1;
 
 	public Result(String program, String version, String reference, String dbFile, HashMap<String, String> programSpecificParameters, int iterationNumber, String queryID, String queryDef, int queryLength, List<Hit> hits, Sequence querySequence) {
 		this.program = program;
@@ -94,13 +90,13 @@ public boolean equals(Object obj) {
 			return false;
 		}
 		final Result other = (Result) obj;
-		if ((this.queryID == null) ? (other.queryID != null) : !this.queryID.equals(other.queryID)) {
+		if (!Objects.equals(this.queryID, other.queryID)) {
 			return false;
 		}
-		if ((this.queryDef == null) ? (other.queryDef != null) : !this.queryDef.equals(other.queryDef)) {
+		if (!Objects.equals(this.queryDef, other.queryDef)) {
 			return false;
 		}
-		if (this.hits != other.hits && (this.hits == null || !this.hits.equals(other.hits))) {
+		if (!Objects.equals(this.hits, other.hits)) {
 			return false;
 		}
 		return true;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java
index 479df1ac4d..d769fe7358 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java
@@ -59,7 +59,7 @@ public interface ResultFactory {
 	 * @param results
 	 * @throws Exception
 	 */
-	void storeObjects(List<Result> results) throws IOException, ParseException;
+	void storeObjects(List<Result> results);
 
 	/**
 	 * Specify the collection of sequences objects used as queries in the Search run.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
index 52654720d9..9e34739361 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
@@ -55,7 +55,7 @@ public class SearchIO implements Iterable<Result>{
 	 */
 	private List<Result> results;
 
-	private final String NOT_SUPPORTED_FILE_EXCEPTION =
+	private static final String NOT_SUPPORTED_FILE_EXCEPTION =
 			"This extension is not associated with any parser. You can try to specify a ResultFactory object.";
 
 	/**
@@ -140,7 +140,7 @@ public void writeResults() throws IOException, ParseException {
 	 */
 	private ResultFactory guessFactory(File f){
 		if (extensionFactoryAssociation == null){
-			extensionFactoryAssociation = new HashMap<String, ResultFactory>();
+			extensionFactoryAssociation = new HashMap<>();
 			ServiceLoader<ResultFactory> impl = ServiceLoader.load(ResultFactory.class);
 			for (ResultFactory loadedImpl : impl) {
 				List<String> fileExtensions = loadedImpl.getFileExtensions();
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java
index 410fad0fce..cd32503354 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java
@@ -48,7 +48,7 @@
  */
 
 public class BlastTabularParser implements ResultFactory {
-	private final String blastReference =
+	private static final String blastReference =
 			"Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), A greedy algorithm for aligning DNA sequences&quot;, J Comput Biol 2000; 7(1-2):203-14.";
 	/**
 	 * Tries to define a different level of consistency during parsing.
@@ -71,7 +71,7 @@ private enum PARSING_CONSISTENCY {
 
 	// data imported private:
 	int queryIdNumber = 0;
-	HashMap<String,String> queryIdMapping = new HashMap<String,String>();
+	HashMap<String,String> queryIdMapping = new HashMap<>();
 	String programName=null, queryName = null, databaseFile = null;
 	private String queryId      ;
 	private String subjectId    ;
@@ -89,7 +89,7 @@ private enum PARSING_CONSISTENCY {
 
 	@Override
 	public List<String> getFileExtensions() {
-		List<String> l = new ArrayList<String>();
+		List<String> l = new ArrayList<>();
 		l.add("blasttabular");
 		l.add("blasttxt");
 		return l;
@@ -102,7 +102,7 @@ public void setFile(File f) {
 
 	@Override
 	public List<Result> createObjects(double maxEScore) throws IOException, ParseException {
-		List<Result> results = new ArrayList<Result>();
+		List<Result> results = new ArrayList<>();
 
 		log.info("Query for hits");
 		LineNumberReader  lnr = new LineNumberReader(new FileReader(targetFile));
@@ -126,13 +126,13 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
 						.setQueryDef(queryName)
 						.setReference(blastReference);
 
-				List<Hit> hits = new ArrayList<Hit>();
+				List<Hit> hits = new ArrayList<>();
 
 				String currentQueryId = queryId;
 				while (currentQueryId.equals(queryId) && lineNumber < fileLinesCount){
 					BlastHitBuilder hitBuilder = new BlastHitBuilder();
 
-					List<Hsp> hsps = new ArrayList<Hsp>();
+					List<Hsp> hsps = new ArrayList<>();
 
 					String currentSubjectId=subjectId;
 					while (currentSubjectId.equals(subjectId) && lineNumber < fileLinesCount){
@@ -217,7 +217,7 @@ private String fetchData(Scanner scanner){
 	}
 
 	@Override
-	public void storeObjects(List<Result> results) throws IOException, ParseException {
+	public void storeObjects(List<Result> results) {
 		throw new UnsupportedOperationException("Not supported yet.");
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
index 1b30639b80..bdb2396fe1 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
@@ -105,7 +105,7 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
 			ArrayList<Element> IterationsList = XMLHelper.selectElements(blastDoc.getDocumentElement(), "BlastOutput_iterations/Iteration[Iteration_hits]");
 			logger.info(IterationsList.size() + " results");
 
-			resultsCollection = new ArrayList<Result>();
+			resultsCollection = new ArrayList<>();
 			for (Element element : IterationsList) {
 				BlastResultBuilder resultBuilder = new BlastResultBuilder();
 				// will add BlastOutput* key sections in the result object
@@ -131,7 +131,7 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
 				Element iterationHitsElement = XMLHelper.selectSingleElement(element, "Iteration_hits");
 				ArrayList<Element> hitList = XMLHelper.selectElements(iterationHitsElement, "Hit");
 
-				hitsCollection = new ArrayList<Hit>();
+				hitsCollection = new ArrayList<>();
 				for (Element hitElement : hitList) {
 					BlastHitBuilder blastHitBuilder = new BlastHitBuilder();
 					blastHitBuilder
@@ -148,9 +148,9 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
 					Element hithspsElement = XMLHelper.selectSingleElement(hitElement, "Hit_hsps");
 					ArrayList<Element> hspList = XMLHelper.selectElements(hithspsElement, "Hsp");
 
-					hspsCollection = new ArrayList<Hsp>();
+					hspsCollection = new ArrayList<>();
 					for (Element hspElement : hspList) {
-						Double evalue = new Double(XMLHelper.selectSingleElement(hspElement, "Hsp_evalue").getTextContent());
+						double evalue = new Double(XMLHelper.selectSingleElement(hspElement, "Hsp_evalue").getTextContent());
 
 						// add the new hsp only if it pass the specified threshold. It can save lot of memory and some parsing time
 						if (evalue <= maxEScore) {
@@ -195,7 +195,7 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
 
 	@Override
 	public List<String> getFileExtensions(){
-		ArrayList<String> extensions = new ArrayList<String>(1);
+		ArrayList<String> extensions = new ArrayList<>(1);
 		extensions.add("blastxml");
 		return extensions;
 	}
@@ -215,7 +215,7 @@ public void setDatabaseReferences(List<Sequence> sequences) {
 	 */
 	private void mapIds() {
 		if (queryReferences != null) {
-			queryReferencesMap = new HashMap<String,Sequence>(queryReferences.size());
+			queryReferencesMap = new HashMap<>(queryReferences.size());
 			for (int counter=0; counter < queryReferences.size() ; counter ++){
 				String id = "Query_"+(counter+1);
 				queryReferencesMap.put(id, queryReferences.get(counter));
@@ -223,7 +223,7 @@ private void mapIds() {
 		}
 
 		if (databaseReferences != null) {
-			databaseReferencesMap = new HashMap<String,Sequence>(databaseReferences.size());
+			databaseReferencesMap = new HashMap<>(databaseReferences.size());
 			for (int counter=0; counter < databaseReferences.size() ; counter ++){
 				// this is strange: while Query_id are 1 based, Hit (database) id are 0 based
 				String id = "gnl|BL_ORD_ID|"+(counter);
@@ -233,7 +233,7 @@ private void mapIds() {
 	}
 
 	@Override
-	public void storeObjects(List<Result> results) throws IOException, ParseException {
+	public void storeObjects(List<Result> results) {
 		throw new UnsupportedOperationException("This parser does not support writing yet.");
 	}
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java
index c54c6930a8..397f1f1d5a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java
@@ -36,7 +36,7 @@
  */
 public class AccessionID {
 
-	private String id = null;
+	private String id;
 	private DataSource source = DataSource.LOCAL;
 	private Integer version;
 	private String identifier = null;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java
index 5973dd386e..9aeb3ae08c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java
@@ -37,7 +37,7 @@
 public class CDSSequence extends DNASequence {
 
 	//private static final Logger log = Logger.getLogger(CDSSequence.class.getName());
-	Integer phase = 0; // 0, 1, 2
+	Integer phase; // 0, 1, 2
 	TranscriptSequence parentTranscriptSequence;
 
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ChromosomeSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ChromosomeSequence.java
index f53c539137..eeae4281a4 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ChromosomeSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ChromosomeSequence.java
@@ -37,7 +37,7 @@
 public class ChromosomeSequence extends DNASequence {
 
 	private int chromosomeNumber;
-	private LinkedHashMap<String, GeneSequence> geneSequenceHashMap = new LinkedHashMap<String, GeneSequence>();
+	private final LinkedHashMap<String, GeneSequence> geneSequenceHashMap = new LinkedHashMap<>();
 
 	/**
 	 * Empty constructor used by tools that need a proper Bean that allows the actual
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DNASequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DNASequence.java
index a8d072b4a1..9f77194fce 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DNASequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DNASequence.java
@@ -136,14 +136,14 @@ public int getGCCount() {
 	 * Returns a Sequence which runs in the current reverse order
 	 */
 	public SequenceView<NucleotideCompound> getReverse() {
-		return new ReversedSequenceView<NucleotideCompound>(this);
+		return new ReversedSequenceView<>(this);
 	}
 
 	/**
 	 * Returns a Sequence which will complement every base
 	 */
 	public SequenceView<NucleotideCompound> getComplement() {
-		return new ComplementSequenceView<NucleotideCompound>(this);
+		return new ComplementSequenceView<>(this);
 	}
 
 	/**
@@ -172,7 +172,7 @@ public static void main(String[] args) throws Exception {
 		logger.info("DNA Sequence: {}", dnaSequence.toString());
 
 		StringProxySequenceReader<NucleotideCompound> sequenceStringProxyLoader =
-				new StringProxySequenceReader<NucleotideCompound>("GCTA", DNACompoundSet.getDNACompoundSet());
+				new StringProxySequenceReader<>("GCTA", DNACompoundSet.getDNACompoundSet());
 		DNASequence dnaSequenceFromProxy = new DNASequence(sequenceStringProxyLoader);
 		logger.info("DNA Sequence from Proxy: {}", dnaSequenceFromProxy.toString());
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java
index db1f4fd26f..04511fe7f1 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java
@@ -41,14 +41,14 @@ public class GeneSequence extends DNASequence {
 
 	private final static Logger logger = LoggerFactory.getLogger(GeneSequence.class);
 
-	private final LinkedHashMap<String, TranscriptSequence> transcriptSequenceHashMap = new LinkedHashMap<String, TranscriptSequence>();
-	private final LinkedHashMap<String, IntronSequence> intronSequenceHashMap = new LinkedHashMap<String, IntronSequence>();
-	private final LinkedHashMap<String, ExonSequence> exonSequenceHashMap = new LinkedHashMap<String, ExonSequence>();
-	private final ArrayList<IntronSequence> intronSequenceList = new ArrayList<IntronSequence>();
-	private final ArrayList<ExonSequence> exonSequenceList = new ArrayList<ExonSequence>();
+	private final LinkedHashMap<String, TranscriptSequence> transcriptSequenceHashMap = new LinkedHashMap<>();
+	private final LinkedHashMap<String, IntronSequence> intronSequenceHashMap = new LinkedHashMap<>();
+	private final LinkedHashMap<String, ExonSequence> exonSequenceHashMap = new LinkedHashMap<>();
+	private final ArrayList<IntronSequence> intronSequenceList = new ArrayList<>();
+	private final ArrayList<ExonSequence> exonSequenceList = new ArrayList<>();
 	boolean intronAdded = false; // need to deal with the problem that typically introns are not added when validating the list and adding in introns as the regions not included in exons
 	private Strand strand = Strand.UNDEFINED;
-	private ChromosomeSequence chromosomeSequence;
+	private final ChromosomeSequence chromosomeSequence;
 
 	/**
 	 * A class that keeps track of the details of a GeneSequence which is difficult to properly model. Two important concepts that is difficult
@@ -102,7 +102,7 @@ public void addIntronsUsingExons() throws Exception {
 		}
 		ExonComparator exonComparator = new ExonComparator();
 		//sort based on start position and sense;
-		Collections.sort(exonSequenceList, exonComparator);
+		exonSequenceList.sort(exonComparator);
 		int shift = -1;
 		if (getStrand() == Strand.NEGATIVE) {
 			shift = 1;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.java
index 1ab060d23e..bc30122aea 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.java
@@ -42,7 +42,7 @@
  */
 public class MultipleSequenceAlignment<S extends Sequence<C>, C extends Compound> implements LightweightProfile<S, C> {
 
-	private List<S> sequences = new ArrayList<S>();
+	private final List<S> sequences = new ArrayList<>();
 	private Integer length = null;
 
 	/**
@@ -98,7 +98,7 @@ public List<S> getAlignedSequences() {
 	 */
 	@Override
 	public List<C> getCompoundsAt(int alignmentIndex) {
-		List<C> column = new ArrayList<C>();
+		List<C> column = new ArrayList<>();
 		for (S s : sequences) {
 			column.add(s.getCompoundAt(alignmentIndex));
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
index e3abbea6bd..acdbfa9396 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
@@ -161,9 +161,9 @@ private DNASequence getRawParentSequence(String accessId) throws IOException {
 		InputStream is = url.openConnection().getInputStream();
 
 		FastaReader<DNASequence, NucleotideCompound> parentReader
-				= new FastaReader<DNASequence, NucleotideCompound>(is,
-						new PlainFastaHeaderParser<DNASequence, NucleotideCompound>(),
-						new DNASequenceCreator(AmbiguityDNACompoundSet.getDNACompoundSet()));
+				= new FastaReader<>(is,
+				new PlainFastaHeaderParser<>(),
+				new DNASequenceCreator(AmbiguityDNACompoundSet.getDNACompoundSet()));
 		LinkedHashMap<String, DNASequence> seq = parentReader.process();
 
 		DNASequence parentSeq = null;
@@ -203,7 +203,7 @@ public static void main(String[] args) throws Exception {
 		ProteinSequence proteinSequence = new ProteinSequence("ARNDCEQGHILKMFPSTWYVBZJX");
 		logger.info("Protein Sequence: {}", proteinSequence.toString());
 
-		StringProxySequenceReader<AminoAcidCompound> sequenceStringProxyLoader = new StringProxySequenceReader<AminoAcidCompound>("XRNDCEQGHILKMFPSTWYVBZJA", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+		StringProxySequenceReader<AminoAcidCompound> sequenceStringProxyLoader = new StringProxySequenceReader<>("XRNDCEQGHILKMFPSTWYVBZJA", AminoAcidCompoundSet.getAminoAcidCompoundSet());
 		ProteinSequence proteinSequenceFromProxy = new ProteinSequence(sequenceStringProxyLoader);
 		logger.info("Protein Sequence from Proxy: {}", proteinSequenceFromProxy.toString());
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/RNASequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/RNASequence.java
index e44e884552..fb6f602d5e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/RNASequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/RNASequence.java
@@ -86,7 +86,7 @@ public RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader,
 	 * @return
 	 */
 	public SequenceView<NucleotideCompound> getReverseComplement() {
-		return new ComplementSequenceView<NucleotideCompound>(getInverse());
+		return new ComplementSequenceView<>(getInverse());
 	}
 
 	/**
@@ -97,7 +97,7 @@ public SequenceView<NucleotideCompound> getReverseComplement() {
 	 */
 	@Override
 public SequenceView<NucleotideCompound> getInverse() {
-		return new ReversedSequenceView<NucleotideCompound>(this);
+		return new ReversedSequenceView<>(this);
 	}
 
 	/**
@@ -105,7 +105,7 @@ public SequenceView<NucleotideCompound> getInverse() {
 	 * @return
 	 */
 	public SequenceView<NucleotideCompound> getComplement() {
-		return new ComplementSequenceView<NucleotideCompound>(this);
+		return new ComplementSequenceView<>(this);
 	}
 
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/SequenceOptimizationHints.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/SequenceOptimizationHints.java
index 0fab276028..6e7c131902 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/SequenceOptimizationHints.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/SequenceOptimizationHints.java
@@ -68,13 +68,13 @@ public static void setSequenceCollection(SequenceCollection aSequenceColection)
 
 	public enum SequenceUsage {
 
-		FULL_SEQUENCE_DATA, SUB_SEQUENCE_DATA, MINIMAL_SEQUENCE_DATA;
-	}
+		FULL_SEQUENCE_DATA, SUB_SEQUENCE_DATA, MINIMAL_SEQUENCE_DATA
+    }
 
 	public enum SequenceCollection {
 
-		ALL_SEQUENCES, VARIABLE_SEQUENCES, MINIMINAL_SEQUENCES;
-	}
+		ALL_SEQUENCES, VARIABLE_SEQUENCES, MINIMINAL_SEQUENCES
+    }
 
 	static private SequenceUsage sequenceUsage = SequenceUsage.FULL_SEQUENCE_DATA;
 	static private SequenceCollection sequenceCollection = SequenceCollection.ALL_SEQUENCES;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StartCodonSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StartCodonSequence.java
index eb3d37674a..279970a3a8 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StartCodonSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StartCodonSequence.java
@@ -29,7 +29,7 @@
  * @author Scooter Willis
  */
 public class StartCodonSequence extends DNASequence {
-public DNASequence parentGeneSequence = null;
+public DNASequence parentGeneSequence;
 
 
 	public StartCodonSequence(TranscriptSequence parentGeneSequence, int begin, int end){
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StopCodonSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StopCodonSequence.java
index 636d8548e0..b2c71b790e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StopCodonSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StopCodonSequence.java
@@ -30,7 +30,7 @@
  */
 public class StopCodonSequence extends DNASequence {
 
-public DNASequence parentGeneSequence = null;
+public DNASequence parentGeneSequence;
 
 
 	public StopCodonSequence(TranscriptSequence parentGeneSequence, int begin, int end){
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/Strand.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/Strand.java
index f4816adf7a..032983893d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/Strand.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/Strand.java
@@ -33,7 +33,7 @@ public enum Strand {
 	private final String stringRepresentation;
 	private final int numericRepresentation;
 
-	private Strand(String stringRepresentation, int numericRepresentation) {
+	Strand(String stringRepresentation, int numericRepresentation) {
 		this.stringRepresentation = stringRepresentation;
 		this.numericRepresentation = numericRepresentation;
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TaxonomyID.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TaxonomyID.java
index 64784727bd..402df2ca0a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TaxonomyID.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TaxonomyID.java
@@ -30,8 +30,8 @@
 public class TaxonomyID {
 
 
-	private String id = null;
-	DataSource dataSource = DataSource.UNKNOWN;
+	private String id;
+	DataSource dataSource;
 
 	public TaxonomyID(String id, DataSource dataSource) {
 		this.id = id;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java
index 29e6e60140..f7aeb796cf 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java
@@ -41,11 +41,11 @@ public class TranscriptSequence extends DNASequence {
 
 	private final static Logger logger = LoggerFactory.getLogger(TranscriptSequence.class);
 
-	private final ArrayList<CDSSequence> cdsSequenceList = new ArrayList<CDSSequence>();
-	private final LinkedHashMap<String, CDSSequence> cdsSequenceHashMap = new LinkedHashMap<String, CDSSequence>();
+	private final ArrayList<CDSSequence> cdsSequenceList = new ArrayList<>();
+	private final LinkedHashMap<String, CDSSequence> cdsSequenceHashMap = new LinkedHashMap<>();
 	private StartCodonSequence startCodonSequence = null;
 	private StopCodonSequence stopCodonSequence = null;
-	private GeneSequence parentGeneSequence = null;
+	private GeneSequence parentGeneSequence;
 
 	/**
 	 *
@@ -113,7 +113,7 @@ public CDSSequence addCDS(AccessionID accession, int begin, int end, int phase)
 		CDSSequence cdsSequence = new CDSSequence(this, begin, end, phase); //sense should be the same as parent
 		cdsSequence.setAccession(accession);
 		cdsSequenceList.add(cdsSequence);
-		Collections.sort(cdsSequenceList, new CDSComparator());
+		cdsSequenceList.sort(new CDSComparator());
 		cdsSequenceHashMap.put(accession.getID(), cdsSequence);
 		return cdsSequence;
 	}
@@ -137,16 +137,16 @@ public CDSSequence addCDS(AccessionID accession, int begin, int end, int phase)
 	 * @return
 	 */
 	public ArrayList<ProteinSequence> getProteinCDSSequences() {
-		ArrayList<ProteinSequence> proteinSequenceList = new ArrayList<ProteinSequence>();
+		ArrayList<ProteinSequence> proteinSequenceList = new ArrayList<>();
 		for (int i = 0; i < cdsSequenceList.size(); i++) {
 			CDSSequence cdsSequence = cdsSequenceList.get(i);
 			String codingSequence = cdsSequence.getCodingSequence();
 			//          logger.debug("CDS {} {} = {}", getStrand(), cdsSequence.getPhase(), codingSequence);
 			if (this.getStrand() == Strand.NEGATIVE) {
 				if (cdsSequence.phase == 1) {
-					codingSequence = codingSequence.substring(1, codingSequence.length());
+					codingSequence = codingSequence.substring(1);
 				} else if (cdsSequence.phase == 2) {
-					codingSequence = codingSequence.substring(2, codingSequence.length());
+					codingSequence = codingSequence.substring(2);
 				}
 				if (i < cdsSequenceList.size() - 1) {
 					CDSSequence nextCDSSequence = cdsSequenceList.get(i + 1);
@@ -160,9 +160,9 @@ public ArrayList<ProteinSequence> getProteinCDSSequences() {
 				}
 			} else {
 				if (cdsSequence.phase == 1) {
-					codingSequence = codingSequence.substring(1, codingSequence.length());
+					codingSequence = codingSequence.substring(1);
 				} else if (cdsSequence.phase == 2) {
-					codingSequence = codingSequence.substring(2, codingSequence.length());
+					codingSequence = codingSequence.substring(2);
 				}
 				if (i < cdsSequenceList.size() - 1) {
 					CDSSequence nextCDSSequence = cdsSequenceList.get(i + 1);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java
index 8252f27198..125fb362e8 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java
@@ -44,11 +44,11 @@ public class AminoAcidCompoundSet implements CompoundSet<AminoAcidCompound>, Ser
 	 *
 	 */
 	private static final long serialVersionUID = 4000344194364133456L;
-	private final Map<String, AminoAcidCompound> aminoAcidCompoundCache = new HashMap<String, AminoAcidCompound>();
-	private final Map<String, AminoAcidCompound> aminoAcidCompoundCache3Letter = new HashMap<String, AminoAcidCompound>();
+	private final Map<String, AminoAcidCompound> aminoAcidCompoundCache = new HashMap<>();
+	private final Map<String, AminoAcidCompound> aminoAcidCompoundCache3Letter = new HashMap<>();
 
 	private final Map<AminoAcidCompound, Set<AminoAcidCompound>> equivalentsCache =
-			new HashMap<AminoAcidCompound, Set<AminoAcidCompound>>();
+			new HashMap<>();
 
 	public AminoAcidCompoundSet() {
 		aminoAcidCompoundCache.put("A", new AminoAcidCompound(this, "A", "Ala", "Alanine", 71.0788f));
@@ -90,9 +90,8 @@ public AminoAcidCompoundSet() {
 		//which then does the actual conversion to Pyl.
 		aminoAcidCompoundCache.put("O", new AminoAcidCompound(this, "O", "Pyl", "Pyrrolysine", 255.3172f));
 
-		for(String oneLtr : aminoAcidCompoundCache.keySet()) {
-			AminoAcidCompound aa = aminoAcidCompoundCache.get(oneLtr);
-			String threeLtr = aa.getLongName().toUpperCase();
+		for(AminoAcidCompound aa : aminoAcidCompoundCache.values()) {
+            String threeLtr = aa.getLongName().toUpperCase();
 			aminoAcidCompoundCache3Letter.put(threeLtr, aa);
 		}
 	}
@@ -154,7 +153,7 @@ public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound)
 			addAmbiguousEquivalents("I", "L", "J");
 			// ambiguous gaps
 			AminoAcidCompound gap1, gap2, gap3;
-			Set<AminoAcidCompound> gaps = new HashSet<AminoAcidCompound>();
+			Set<AminoAcidCompound> gaps = new HashSet<>();
 			gaps.add(gap1 = aminoAcidCompoundCache.get("-"));
 			gaps.add(gap2 = aminoAcidCompoundCache.get("."));
 			gaps.add(gap3 = aminoAcidCompoundCache.get("_"));
@@ -162,7 +161,7 @@ public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound)
 			equivalentsCache.put(gap2, gaps);
 			equivalentsCache.put(gap3, gaps);
 			// X is never equivalent, even to itself
-			equivalentsCache.put(aminoAcidCompoundCache.get("X"), new HashSet<AminoAcidCompound>());
+			equivalentsCache.put(aminoAcidCompoundCache.get("X"), new HashSet<>());
 		}
 		return equivalentsCache.get(compound);
 	}
@@ -172,18 +171,18 @@ private void addAmbiguousEquivalents(String one, String two, String either) {
 		Set<AminoAcidCompound> equivalents;
 		AminoAcidCompound cOne, cTwo, cEither;
 
-		equivalents = new HashSet<AminoAcidCompound>();
+		equivalents = new HashSet<>();
 		equivalents.add(cOne = aminoAcidCompoundCache.get(one));
 		equivalents.add(cTwo = aminoAcidCompoundCache.get(two));
 		equivalents.add(cEither = aminoAcidCompoundCache.get(either));
 		equivalentsCache.put(cEither, equivalents);
 
-		equivalents = new HashSet<AminoAcidCompound>();
+		equivalents = new HashSet<>();
 		equivalents.add(cOne);
 		equivalents.add(cEither);
 		equivalentsCache.put(cOne, equivalents);
 
-		equivalents = new HashSet<AminoAcidCompound>();
+		equivalents = new HashSet<>();
 		equivalents.add(cTwo);
 		equivalents.add(cEither);
 		equivalentsCache.put(cTwo, equivalents);
@@ -206,7 +205,7 @@ public boolean isValidSequence(Sequence<AminoAcidCompound> sequence) {
 
 	@Override
 	public List<AminoAcidCompound> getAllCompounds() {
-		return new ArrayList<AminoAcidCompound>(aminoAcidCompoundCache.values());
+		return new ArrayList<>(aminoAcidCompoundCache.values());
 	}
 
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/NucleotideCompound.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/NucleotideCompound.java
index 786c79f812..6ed0cbb270 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/NucleotideCompound.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/NucleotideCompound.java
@@ -30,6 +30,7 @@
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.CompoundSet;
 
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.Set;
 
@@ -51,14 +52,14 @@ public NucleotideCompound(String base, CompoundSet<NucleotideCompound> compoundS
 	  super(base);
 	  this.compoundSet = compoundSet;
 	  this.complementStr = complementStr;
-	  this.constituents = unmodifiableSet(new HashSet<NucleotideCompound>(asList(this)));
+	  this.constituents = unmodifiableSet(new HashSet<>(Collections.singletonList(this)));
 	}
 
 	public NucleotideCompound(String base, CompoundSet<NucleotideCompound> compoundSet, String complementStr, NucleotideCompound[] constituents) {
 		super(base);
 		this.compoundSet = compoundSet;
 		this.complementStr = complementStr;
-		this.constituents = unmodifiableSet(new HashSet<NucleotideCompound>(asList(constituents)));
+		this.constituents = unmodifiableSet(new HashSet<>(asList(constituents)));
 	}
 
 	@Override
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java
index 19923effed..bbce920b82 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java
@@ -58,7 +58,7 @@ public interface Edit<C extends Compound> {
 	 * with a target Sequence. These ends can be of 0 length but conceptionally
 	 * they can still exist.
 	 */
-	public static abstract class AbstractEdit<C extends Compound> implements Edit<C> {
+	abstract class AbstractEdit<C extends Compound> implements Edit<C> {
 
 		private final static Logger logger = LoggerFactory.getLogger(AbstractEdit.class);
 
@@ -78,15 +78,15 @@ public static abstract class AbstractEdit<C extends Compound> implements Edit<C>
 		@Override
 		public Sequence<C> edit(Sequence<C> editingSequence) {
 			Sequence<C> targetSequence = getTargetSequence(editingSequence);
-			List<Sequence<C>> sequences = new ArrayList<Sequence<C>>();
+			List<Sequence<C>> sequences = new ArrayList<>();
 
 			sequences.add(getFivePrime(editingSequence));
 			sequences.add(targetSequence);
 			sequences.add(getThreePrime(editingSequence));
 
-			return new JoiningSequenceReader<C>(sequences);
+			return new JoiningSequenceReader<>(sequences);
 		}
-		private int start = -1;
+		private int start;
 		private int end = -1;
 		private String stringSequence;
 		private Sequence<C> sequence;
@@ -119,8 +119,8 @@ protected void setSequence(Sequence<C> sequence) {
 		public Sequence<C> getTargetSequence(Sequence<C> editingSequence) {
 			if (sequence == null && stringSequence != null) {
 				try {
-					sequence = new BasicSequence<C>(
-								stringSequence, editingSequence.getCompoundSet());
+					sequence = new BasicSequence<>(
+							stringSequence, editingSequence.getCompoundSet());
 				} catch (CompoundNotFoundException e) {
 					// TODO is there a better way to handle this exception?
 					logger.error("Problem setting sequence, some unrecognised compounds: {}", e.getMessage());
@@ -136,7 +136,7 @@ public Sequence<C> getTargetSequence(Sequence<C> editingSequence) {
 		protected Sequence<C> getEmptySequence(Sequence<C> editingSequence) {
 			Sequence<C> s = null;
 			try {
-				s = new BasicSequence<C>("", editingSequence.getCompoundSet());
+				s = new BasicSequence<>("", editingSequence.getCompoundSet());
 			} catch (CompoundNotFoundException e) {
 				// should not happen
 				logger.error("Could not construct empty sequence. {}. This is most likely a bug.", e.getMessage());
@@ -156,7 +156,7 @@ public int getEnd() {
 	/**
 	 * Implementation which allows for the deletion of bases from a Sequence
 	 */
-	public static class Delete<C extends Compound> extends AbstractEdit<C> {
+	class Delete<C extends Compound> extends AbstractEdit<C> {
 
 		public Delete(int position) {
 			this(position, position);
@@ -209,7 +209,7 @@ protected Sequence<C> getThreePrime(Sequence<C> editingSequence) {
 	 * The code will raise exceptions if you attempt a single base edit
 	 * with an insertion.
 	 */
-	public static class Insert<C extends Compound> extends AbstractEdit<C> {
+	class Insert<C extends Compound> extends AbstractEdit<C> {
 
 		private final boolean singlePosition;
 
@@ -285,7 +285,7 @@ protected Sequence<C> getThreePrime(Sequence<C> editingSequence) {
 	 * presence of a CompoundSet to parse a String (if given) which means
 	 * the eventual length of a Sequence is a lazy operation.
 	 */
-	public static class Substitute<C extends Compound> extends AbstractEdit<C> {
+	class Substitute<C extends Compound> extends AbstractEdit<C> {
 
 		public Substitute(String sequence, int position) {
 			super(position);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
index d601c573b0..f32148dbc1 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
@@ -40,15 +40,15 @@
  */
 public abstract class AbstractFeature<S extends AbstractSequence<C>, C extends Compound>
 		implements FeatureInterface<S, C> {
-	List<FeatureInterface<S, C>> childrenFeatures = new ArrayList<FeatureInterface<S, C>>();
+	List<FeatureInterface<S, C>> childrenFeatures = new ArrayList<>();
 	FeatureInterface<S, C> parentFeature;
 	AbstractLocation sequenceLocation;
-	String type = "";
-	String source = "";
+	String type;
+	String source;
 	private String description = "";
 	private String shortDescription = "";
 	private Object userObject = null;
-	private Map<String, List<Qualifier>> Qualifiers = new HashMap<String, List<Qualifier>>();
+	private Map<String, List<Qualifier>> Qualifiers = new HashMap<>();
 
 	/**
 	 * A feature has a type and a source
@@ -196,28 +196,24 @@ public void setShortDescription(String shortDescription) {
 	 * of overlapping features so they are delivered in a proper order.
 	 */
 
-	public static final Comparator<FeatureInterface<?, ?>> LOCATION_LENGTH = new Comparator<FeatureInterface<?, ?>>() {
-
-		@Override
-		public int compare(FeatureInterface<?, ?> e1, FeatureInterface<?, ?> e2) {
-			double v1 = e1.getLocations().getStart().getPosition();
-			double v2 = e2.getLocations().getStart().getPosition();
-			if (v1 < v2) {
+	public static final Comparator<FeatureInterface<?, ?>> LOCATION_LENGTH = (e1, e2) -> {
+		double v1 = e1.getLocations().getStart().getPosition();
+		double v2 = e2.getLocations().getStart().getPosition();
+		if (v1 < v2) {
+			return -1;
+		} else if (v1 > v2) {
+			return 1;
+		} else {
+			double end1 = e1.getLocations().getEnd().getPosition();
+			double end2 = e2.getLocations().getEnd().getPosition();
+			if(end1 > end2)
 				return -1;
-			} else if (v1 > v2) {
+			else if(end1 < end2)
 				return 1;
-			} else {
-				double end1 = e1.getLocations().getEnd().getPosition();
-				double end2 = e2.getLocations().getEnd().getPosition();
-				if(end1 > end2)
-					return -1;
-				else if(end1 < end2)
-					return 1;
-				else
-				return 0;
-			}
-
+			else
+			return 0;
 		}
+
 	};
 
 	 /**
@@ -225,33 +221,23 @@ else if(end1 < end2)
 	 *
 	 */
 
-	static public final Comparator<FeatureInterface<?, ?>> LENGTH = new Comparator<FeatureInterface<?, ?>>() {
-
-		@Override
-		public int compare(FeatureInterface<?, ?> e1, FeatureInterface<?, ?> e2) {
-			double v1 = Math.abs(e1.getLocations().getEnd().getPosition()- e1.getLocations().getStart().getPosition());
-			double v2 = Math.abs(e2.getLocations().getEnd().getPosition() -  e2.getLocations().getStart().getPosition());
-			if (v1 < v2) {
-				return -1;
-			} else if (v1 > v2) {
-				return 1;
-			} else {
-				return 0;
-			}
-
+	static public final Comparator<FeatureInterface<?, ?>> LENGTH = (e1, e2) -> {
+		double v1 = Math.abs(e1.getLocations().getEnd().getPosition()- e1.getLocations().getStart().getPosition());
+		double v2 = Math.abs(e2.getLocations().getEnd().getPosition() -  e2.getLocations().getStart().getPosition());
+		if (v1 < v2) {
+			return -1;
+		} else if (v1 > v2) {
+			return 1;
+		} else {
+			return 0;
 		}
+
 	};
 
 	/**
 	 * Sort features by type
 	 */
-	public static final Comparator<FeatureInterface<?, ?>> TYPE = new Comparator<FeatureInterface<?, ?>>() {
-
-		@Override
-		public int compare(FeatureInterface<?, ?> o1, FeatureInterface<?, ?> o2) {
-			return o1.getType().compareTo(o2.getType());
-		}
-	};
+	public static final Comparator<FeatureInterface<?, ?>> TYPE = (o1, o2) -> o1.getType().compareTo(o2.getType());
 
 	/**
 	 * @return the userObject
@@ -292,7 +278,7 @@ public void addQualifier(String key, Qualifier qualifier) {
 			vals.add(qualifier);
 			Qualifiers.put(key, vals);
 		} else {
-			List<Qualifier> vals = new ArrayList<Qualifier>();
+			List<Qualifier> vals = new ArrayList<>();
 			vals.add(qualifier);
 			Qualifiers.put(key, vals);
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java
index ce8793c561..28b14712ca 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java
@@ -37,9 +37,9 @@
  * @author Paolo Pavan
  */
 public class DBReferenceInfo extends Qualifier {
-	private LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>();
-	private String database = "";
-	private String id = "";
+	private LinkedHashMap<String, String> properties = new LinkedHashMap<>();
+	private String database;
+	private String id;
 
 	/**
 	 * The source database and id
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.java
index 0cb3ea5d8c..ceb6e34509 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.java
@@ -32,5 +32,5 @@
  */
 public interface DatabaseReferenceInterface {
 
-	public LinkedHashMap<String,ArrayList<DBReferenceInfo>> getDatabaseReferences();
+	LinkedHashMap<String,ArrayList<DBReferenceInfo>> getDatabaseReferences();
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java
index c270cc74e7..3b49341d22 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java
@@ -46,11 +46,11 @@ public class FeatureDbReferenceInfo<S extends AbstractSequence<C>, C extends Com
 
 	private AbstractLocation location;
 	private FeatureInterface<S,C> parentFeature;
-	private List<FeatureInterface<S, C>> childrenFeatures = new ArrayList<FeatureInterface<S, C>>();
+	private List<FeatureInterface<S, C>> childrenFeatures = new ArrayList<>();
 	private String description = "";
 	private String shortDescription = "";
 	private Object userObject;
-	private Map<String, List<Qualifier>> qualifiers = new HashMap<String,List<Qualifier>>();
+	private Map<String, List<Qualifier>> qualifiers = new HashMap<>();
 
 
 	public FeatureDbReferenceInfo(String database, String id) {
@@ -150,7 +150,7 @@ public void setQualifiers(Map<String, List<Qualifier>> qualifiers) {
 	@Override
 	public void addQualifier(String key, Qualifier qualifier) {
 		if (qualifiers == null) {
-			qualifiers = new HashMap<String, List<Qualifier>>();
+			qualifiers = new HashMap<>();
 		}
 		// Check for key. Update list of values
 		if (qualifiers.containsKey(key)){
@@ -158,7 +158,7 @@ public void addQualifier(String key, Qualifier qualifier) {
 			vals.add(qualifier);
 			qualifiers.put(key, vals);
 		} else {
-			List<Qualifier> vals = new ArrayList<Qualifier>();
+			List<Qualifier> vals = new ArrayList<>();
 			vals.add(qualifier);
 			qualifiers.put(key, vals);
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
index 47564bcefa..da05c79668 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
@@ -47,21 +47,21 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 * @return
 	 */
 
-	public String getShortDescription();
+    String getShortDescription();
 
 	/**
 	 * Set the short description that can be used to describe the feature
 	 * @param shortDescription
 	 */
 
-	public void setShortDescription(String shortDescription);
+    void setShortDescription(String shortDescription);
 
 	  /**
 	 * Get the description that can be used to describe the feature
 	 * @return
 	 */
 
-	public String getDescription();
+      String getDescription();
 
 
 	  /**
@@ -69,7 +69,7 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 * @return
 	 */
 
-	public void setDescription(String description);
+      void setDescription(String description);
 
 		/**
 	 * The location(s) of this feature where the location should contain a reference to parent and sequence etc.
@@ -80,7 +80,7 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 *
 	 * @return a Location anchoring this feature
 	 */
-	public AbstractLocation getLocations();
+        AbstractLocation getLocations();
 
 		/**
 	 * The new location for this feature.
@@ -93,14 +93,14 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 * @param loc the new Location for this feature
 	 *
 	 */
-	public void setLocation(AbstractLocation loc);
+        void setLocation(AbstractLocation loc);
 
 		/**
 	 * The type of the feature.
 	 *
 	 * @return the type of this sequence
 	 */
-	public String getType();
+        String getType();
 
 	/**
 	 * Change the type of this feature.
@@ -108,7 +108,7 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 * @param type  new type String
 	 *
 	 */
-	public void setType(String type);
+    void setType(String type);
 
 
 		/**
@@ -116,7 +116,7 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 *
 	 * @return the source, or generator
 	 */
-	public String getSource();
+        String getSource();
 
 	/**
 	 * Change the source of the FeatureInterface.
@@ -124,46 +124,46 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 * @param source the new source String
 	 *
 	 */
-	public void setSource(String source);
+    void setSource(String source);
 
 	/**
 	 * Set the parent feature
 	 * @param feature
 	 */
 
-	public void setParentFeature(FeatureInterface<S, C> feature);
+    void setParentFeature(FeatureInterface<S, C> feature);
 
 	/**
 	 * Get the parent feature
 	 * @return
 	 */
 
-	public FeatureInterface<S, C> getParentFeature();
+    FeatureInterface<S, C> getParentFeature();
 
 	/**
 	 * Get the features contained by this feature
 	 * @return
 	 */
 
-	public List<FeatureInterface<S, C>> getChildrenFeatures();
+    List<FeatureInterface<S, C>> getChildrenFeatures();
 
 	/**
 	 * Set the children features
 	 * @param features
 	 */
 
-	public void setChildrenFeatures(List<FeatureInterface<S, C>> features);
+    void setChildrenFeatures(List<FeatureInterface<S, C>> features);
 
 
 		/**
 	 * @return the userObject
 	 */
-	public Object getUserObject();
+        Object getUserObject();
 
 	/**
 	 * @param userObject the userObject to set
 	 */
-	public void setUserObject(Object userObject);
+    void setUserObject(Object userObject);
 
 
 	/**
@@ -171,19 +171,19 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 * @return
 	 */
 
-	public Map<String, List<Qualifier>> getQualifiers();
+    Map<String, List<Qualifier>> getQualifiers();
 
 	/**
 	 * Set the qualifiers
 	 * @param qualifiers
 	 */
 
-	public void setQualifiers(Map<String, List<Qualifier>> qualifiers);
+    void setQualifiers(Map<String, List<Qualifier>> qualifiers);
 	/**
 	 * Add a qualifier
 	 * @param qualifier
 	 */
 
-	public void addQualifier(String key, Qualifier qualifier);
+    void addQualifier(String key, Qualifier qualifier);
 
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java
index 9674d1abee..54e8afeac6 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java
@@ -36,5 +36,5 @@ public interface FeaturesKeyWordInterface {
 	 *
 	 * @return
 	 */
-	public ArrayList<String> getKeyWords() ;
+    ArrayList<String> getKeyWords() ;
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QualityFeature.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QualityFeature.java
index 7eec33a62a..0e7da9a97b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QualityFeature.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QualityFeature.java
@@ -37,7 +37,7 @@
  */
 public class QualityFeature<S extends AbstractSequence<C>, C extends Compound> extends AbstractFeature<S, C> {
 
-	private List<Number> qualities = new ArrayList<Number>();
+	private List<Number> qualities = new ArrayList<>();
 
 	/**
 	 * @param type
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java
index bce00e2729..524bdfdaa3 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java
@@ -35,7 +35,7 @@
  */
 public class QuantityFeature<S extends AbstractSequence<C>, C extends Compound> extends AbstractFeature<S, C> {
 
-	private List<Number> quantities = new ArrayList<Number>();
+	private List<Number> quantities = new ArrayList<>();
 
 	/**
 	 *
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java
index d2cebd7cd1..08d49ee686 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java
@@ -55,7 +55,12 @@ public class ABITrace {
 
 	//the next three lines are the important persistent data
 	private String sequence;
-	private int A[], G[], C[], T[], baseCalls[], qCalls[];
+	private int[] A;
+    private int[] G;
+    private int[] C;
+    private int[] T;
+    private int[] baseCalls;
+    private int[] qCalls;
 	private int traceLength, seqLength;
 
 	//This is the actual file data.
@@ -110,7 +115,7 @@ public ABITrace( URL ABIFile ) throws IOException
 	 * @throws IOException if there is a problem reading from the BufferedInputStream
 	 */
 	private void ABITraceInit(BufferedInputStream bis) throws IOException{
-		byte[] bytes = null;
+		byte[] bytes;
 		ByteArrayOutputStream baos = new ByteArrayOutputStream();
 		int b;
 		while ((b = bis.read()) >= 0)
@@ -191,16 +196,17 @@ public AbstractSequence<NucleotideCompound> getSequence() throws CompoundNotFoun
 	 * @throws CompoundNotFoundException if the base is not valid
 	 */
 	public int[] getTrace (String base) throws CompoundNotFoundException {
-		if (base.equals("A")) {
-			return A;
-		} else if (base.equals("C")) {
-			return C;
-		} else if (base.equals("G")) {
-			return G;
-		} else if (base.equals("T")) {
-			return T;
-		} else {
-			throw new CompoundNotFoundException("Don't know base: " + base);
+		switch (base) {
+			case "A":
+				return A;
+			case "C":
+				return C;
+			case "G":
+				return G;
+			case "T":
+				return T;
+			default:
+				throw new CompoundNotFoundException("Don't know base: " + base);
 		}
 	}
 
@@ -320,9 +326,9 @@ private int transmute(int ya, int height, double scale) {
 	 * @return - scaling factor
 	 */
 	private double calculateScale(int height) {
-		double newScale = 0.0;
-		double max = (double) getMaximum();
-		double ht = (double) height;
+		double newScale;
+		double max = getMaximum();
+		double ht = height;
 		newScale = ((ht - 50.0)) / max;
 		return newScale;
 	}
@@ -366,9 +372,9 @@ private void initData(byte[] fileData) {
 	 * traces into their arrays.
 	 */
 	private void setTraces() {
-		int pointers[] = new int[4]; //alphabetical, 0=A, 1=C, 2=G, 3=T
-		int datas[] = new int[4];
-		char order[] = new char[4];
+		int[] pointers = new int[4]; //alphabetical, 0=A, 1=C, 2=G, 3=T
+		int[] datas = new int[4];
+		char[] order = new char[4];
 
 		datas[0] = DATA9;
 		datas[1] = DATA10;
@@ -413,10 +419,10 @@ private void setTraces() {
 			DataInputStream dis = new DataInputStream(new ByteArrayInputStream(qq));
 			for (int x = 0; x <= traceLength - 1; x++) {
 				try {
-					if (i == 0) A[x] = (int) dis.readShort();
-					if (i == 1) C[x] = (int) dis.readShort();
-					if (i == 2) G[x] = (int) dis.readShort();
-					if (i == 3) T[x] = (int) dis.readShort();
+					if (i == 0) A[x] = dis.readShort();
+					if (i == 1) C[x] = dis.readShort();
+					if (i == 2) G[x] = dis.readShort();
+					if (i == 3) T[x] = dis.readShort();
 				} catch (IOException e)//This shouldn't happen. If it does something must be seriously wrong.
 				{
 					throw new IllegalStateException("Unexpected IOException encountered while manipulating internal streams.");
@@ -430,7 +436,7 @@ private void setTraces() {
 	 * Fetch the sequence from the trace data.
 	 */
 	private void setSeq() {
-		char tempseq[] = new char[seqLength];
+		char[] tempseq = new char[seqLength];
 		for (int x = 0; x <= seqLength - 1; ++x) {
 			tempseq[x] = (char) traceData[PBAS2 + x];
 		}
@@ -447,7 +453,7 @@ private void setQcalls() {
 		DataInputStream dis = new DataInputStream(new ByteArrayInputStream(qq));
 		for (int i = 0; i <= seqLength - 1; ++i) {
 			try {
-				qCalls[i] = (int) dis.readByte();
+				qCalls[i] = dis.readByte();
 			} catch (IOException e)//This shouldn't happen. If it does something must be seriously wrong.
 			{
 				throw new IllegalStateException("Unexpected IOException encountered while manipulating internal streams.");
@@ -465,7 +471,7 @@ private void setBasecalls() {
 		DataInputStream dis = new DataInputStream(new ByteArrayInputStream(qq));
 		for (int i = 0; i <= seqLength - 1; ++i) {
 			try {
-				baseCalls[i] = (int) dis.readShort();
+				baseCalls[i] = dis.readShort();
 			} catch (IOException e)//This shouldn't happen. If it does something must be seriously wrong.
 			{
 				throw new IllegalStateException("Unexpected IOException encountered while manipulating internal streams.");
@@ -540,7 +546,7 @@ private void setIndex() {
 	 * @return - int beginning at pointer in trace array
 	 */
 	private int getIntAt(int pointer) {
-		int out = 0;
+		int out;
 		byte[] temp = new byte[4];
 		getSubArray(temp, pointer);
 		try {
@@ -560,9 +566,7 @@ private int getIntAt(int pointer) {
 	 * @param traceDataOffset - starting point
 	 */
 	private void getSubArray(byte[] b, int traceDataOffset) {
-		for (int x = 0; x <= b.length - 1; x++) {
-			b[x] = traceData[traceDataOffset + x];
-		}
+		System.arraycopy(traceData, traceDataOffset + 0, b, 0, b.length - 1 + 1);
 	}
 
 	/**
@@ -573,7 +577,7 @@ private void getSubArray(byte[] b, int traceDataOffset) {
 	 * @return - if format of ABI file is correct
 	 */
 	private boolean isABI() {
-		char ABI[] = new char[4];
+		char[] ABI = new char[4];
 
 		for (int i = 0; i <= 2; i++) {
 			ABI[i] = (char) traceData[i];
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java
index e8b56ba29b..3dc587fc22 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java
@@ -76,8 +76,12 @@ public class BufferedReaderBytesRead extends Reader {
 	private boolean skipLF = false;
 	/** The skipLF flag when the mark was set */
 	private boolean markedSkipLF = false;
-	private static int defaultCharBufferSize = 8192;
-	private static int defaultExpectedLineLength = 80;
+
+	private static final int defaultCharBufferSize =
+			16 * 1024;
+			//8192;
+
+	private static final int defaultExpectedLineLength = 80;
 	long bytesRead = 0;
 
 	/**
@@ -146,16 +150,14 @@ private void fill() throws IOException {
 				if (readAheadLimit <= cb.length) {
 					/* Shuffle in the current buffer */
 					System.arraycopy(cb, markedChar, cb, 0, delta);
-					markedChar = 0;
-					dst = delta;
 				} else {
 					/* Reallocate buffer to accommodate read-ahead limit */
 					char[] ncb = new char[readAheadLimit];
 					System.arraycopy(cb, markedChar, ncb, 0, delta);
 					cb = ncb;
-					markedChar = 0;
-					dst = delta;
 				}
+				markedChar = 0;
+				dst = delta;
 				nextChar = nChars = delta;
 			}
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java
index 54865cb132..c3ebb861ae 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java
@@ -92,7 +92,7 @@ public AbstractSequence<AminoAcidCompound> getSequence(String sequence,
 	public AbstractSequence<AminoAcidCompound> getSequence(
 			List<AminoAcidCompound> list) {
 		AbstractSequence<AminoAcidCompound> seq =super.getSequence(list);
-		Collection<Object> strCase = new ArrayList<Object>(seq.getLength());
+		Collection<Object> strCase = new ArrayList<>(seq.getLength());
 		for(int i=0;i<seq.getLength();i++) {
 			strCase.add(true);
 		}
@@ -109,7 +109,7 @@ public AbstractSequence<AminoAcidCompound> getSequence(
 	 * This list contains only Booleans.
 	 */
 	private static List<Object> getStringCase(String str) {
-		List<Object> types = new ArrayList<Object>(str.length());
+		List<Object> types = new ArrayList<>(str.length());
 		for(int i=0;i<str.length();i++) {
 			types.add(Character.isUpperCase(str.charAt(i)));
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/DNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/DNASequenceCreator.java
index 48eab7cb23..78a5dd4832 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/DNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/DNASequenceCreator.java
@@ -83,7 +83,7 @@ public AbstractSequence<NucleotideCompound> getSequence(
 	@Override
 public AbstractSequence<NucleotideCompound> getSequence(
 			List<NucleotideCompound> list) {
-		ArrayListProxySequenceReader<NucleotideCompound> store = new ArrayListProxySequenceReader<NucleotideCompound>();
+		ArrayListProxySequenceReader<NucleotideCompound> store = new ArrayListProxySequenceReader<>();
 		store.setCompoundSet(compoundSet);
 		store.setContents(list);
 		return new DNASequence(store);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java
index 741bc2c26f..bfd8dd4305 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java
@@ -42,11 +42,11 @@ public class FastaGeneWriter {
 
 	private final static Logger logger = LoggerFactory.getLogger(FastaGeneWriter.class);
 
-	boolean showExonUppercase = false;
+	boolean showExonUppercase;
 	OutputStream os;
 	Collection<GeneSequence> sequences;
 	FastaHeaderFormatInterface<GeneSequence, NucleotideCompound> headerFormat;
-	private int lineLength = 60;
+	private int lineLength;
 /**
  *
  * @param os
@@ -86,7 +86,7 @@ public void process() throws Exception {
 			os.write(lineSep);
 
 			int compoundCount = 0;
-			String seq = "";
+			String seq;
 			//GeneSequence currently has a strand attribute to indicate direction
 
 			seq = sequence.getSequence5PrimeTo3Prime().getSequenceAsString();
@@ -95,8 +95,8 @@ public void process() throws Exception {
 				int geneBioBegin = sequence.getBioBegin();
 				int geneBioEnd = sequence.getBioEnd();
 				for (ExonSequence exonSequence : sequence.getExonSequences()) {
-					int featureBioBegin = 0;
-					int featureBioEnd = 0;
+					int featureBioBegin;
+					int featureBioEnd;
 					if (sequence.getStrand() != Strand.NEGATIVE) {
 						featureBioBegin = exonSequence.getBioBegin() - geneBioBegin;
 						featureBioEnd = exonSequence.getBioEnd() - geneBioBegin;
@@ -156,7 +156,7 @@ public void setLineLength(int lineLength) {
 	public static void main(String[] args) {
 
 		try {
-			ArrayList<GeneSequence> sequences = new ArrayList<GeneSequence>();
+			ArrayList<GeneSequence> sequences = new ArrayList<>();
 			ChromosomeSequence seq1 = new ChromosomeSequence("ATATATATATATATATATATATATATATATATACGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCATATATATATATATATATATATACGCGCGCGCGCGCGCGCATATATATATATATATATATATATATATATATACGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCATATATATATATATATATATATACGCGCGCGCGCGCGCGC");
 			GeneSequence gene1 = seq1.addGene(new AccessionID("gene1"), 1, 20, Strand.POSITIVE);
 
@@ -170,7 +170,7 @@ public static void main(String[] args) {
 			sequences.add(gene2);
 
 
-			FastaGeneWriter fastaWriter = new FastaGeneWriter(System.out, sequences, new GenericFastaHeaderFormat<GeneSequence, NucleotideCompound>(), true);
+			FastaGeneWriter fastaWriter = new FastaGeneWriter(System.out, sequences, new GenericFastaHeaderFormat<>(), true);
 			fastaWriter.process();
 
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
index 4ad7dbeb9c..39b061688a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
@@ -35,6 +35,7 @@
 import java.io.*;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
+import java.util.Map;
 
 /**
  * Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the
@@ -148,7 +149,7 @@ public LinkedHashMap<String,S> process(int max) throws IOException {
 		boolean keepGoing = true;
 
 
-		LinkedHashMap<String,S> sequences = new LinkedHashMap<String,S>();
+		LinkedHashMap<String,S> sequences = new LinkedHashMap<>();
 
 		do {
 			line = line.trim(); // nice to have but probably not needed
@@ -238,7 +239,7 @@ public static void main(String[] args) {
 
 			if ( is == null)
 				System.err.println("Could not get input file " + inputFile);
-			FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(is, new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+			FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(is, new GenericFastaHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
 			LinkedHashMap<String,ProteinSequence> proteinSequences = fastaReader.process();
 			is.close();
 
@@ -247,9 +248,9 @@ public static void main(String[] args) {
 
 			File file = new File(inputFile);
 			FastaReader<ProteinSequence,AminoAcidCompound> fastaProxyReader =
-					new FastaReader<ProteinSequence,AminoAcidCompound>(
+					new FastaReader<>(
 							file,
-							new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>(),
+							new GenericFastaHeaderParser<>(),
 							new FileProxyProteinSequenceCreator(
 									file,
 									AminoAcidCompoundSet.getAminoAcidCompoundSet(),
@@ -258,9 +259,9 @@ public static void main(String[] args) {
 					);
 			LinkedHashMap<String,ProteinSequence> proteinProxySequences = fastaProxyReader.process();
 
-			for(String key : proteinProxySequences.keySet()){
-				ProteinSequence proteinSequence = proteinProxySequences.get(key);
-				logger.info("Protein Proxy Sequence Key: {}", key);
+			for(Map.Entry<String, ProteinSequence> entry : proteinProxySequences.entrySet()){
+				ProteinSequence proteinSequence = entry.getValue();
+				logger.info("Protein Proxy Sequence Key: {}", entry.getKey());
 //                if(key.equals("Q98SJ1_CHICK/15-61")){
 //                    int dummy = 1;
 //                }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
index 4338ff5375..825b2ba545 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
@@ -57,15 +57,15 @@ public static LinkedHashMap<String, DNASequence> readFastaDNASequence(File file,
 		}
 
 		FastaReader<DNASequence, NucleotideCompound> fastaProxyReader =
-				new FastaReader<DNASequence, NucleotideCompound>(
+				new FastaReader<>(
 						file,
-						new GenericFastaHeaderParser<DNASequence, NucleotideCompound>(),
+						new GenericFastaHeaderParser<>(),
 						new FileProxyDNASequenceCreator(
 								file,
 								DNACompoundSet.getDNACompoundSet(),
 								new FastaSequenceParser()
-							)
-					);
+						)
+				);
 		return fastaProxyReader.process();
 
 	}
@@ -85,15 +85,15 @@ public static LinkedHashMap<String, RNASequence> readFastaRNASequence(File file,
 		}
 
 		FastaReader<RNASequence, NucleotideCompound> fastaProxyReader =
-				new FastaReader<RNASequence, NucleotideCompound>(
+				new FastaReader<>(
 						file,
-						new GenericFastaHeaderParser<RNASequence, NucleotideCompound>(),
+						new GenericFastaHeaderParser<>(),
 						new FileProxyRNASequenceCreator(
 								file,
 								RNACompoundSet.getRNACompoundSet(),
 								new FastaSequenceParser()
-							)
-					);
+						)
+				);
 		return fastaProxyReader.process();
 
 	}
@@ -124,9 +124,9 @@ public static LinkedHashMap<String, ProteinSequence> readFastaProteinSequence(
 	 */
 	public static LinkedHashMap<String, ProteinSequence> readFastaProteinSequence(
 			InputStream inStream) throws IOException {
-		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
 				inStream,
-				new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+				new GenericFastaHeaderParser<>(),
 				new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
 		return fastaReader.process();
 	}
@@ -139,9 +139,9 @@ public static LinkedHashMap<String, ProteinSequence> readFastaProteinSequence(
 	 */
 	public static LinkedHashMap<String, DNASequence> readFastaDNASequence(
 			InputStream inStream) throws IOException {
-		FastaReader<DNASequence, NucleotideCompound> fastaReader = new FastaReader<DNASequence, NucleotideCompound>(
+		FastaReader<DNASequence, NucleotideCompound> fastaReader = new FastaReader<>(
 				inStream,
-				new GenericFastaHeaderParser<DNASequence, NucleotideCompound>(),
+				new GenericFastaHeaderParser<>(),
 				new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
 		return fastaReader.process();
 	}
@@ -168,9 +168,9 @@ public static LinkedHashMap<String, DNASequence> readFastaDNASequence(
 	 */
 	public static LinkedHashMap<String, RNASequence> readFastaRNASequence(
 			InputStream inStream) throws IOException {
-		FastaReader<RNASequence, NucleotideCompound> fastaReader = new FastaReader<RNASequence, NucleotideCompound>(
+		FastaReader<RNASequence, NucleotideCompound> fastaReader = new FastaReader<>(
 				inStream,
-				new GenericFastaHeaderParser<RNASequence, NucleotideCompound>(),
+				new GenericFastaHeaderParser<>(),
 				new RNASequenceCreator(RNACompoundSet.getRNACompoundSet()));
 		return fastaReader.process();
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
index 5bdc0df018..5be5b1973f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
@@ -103,7 +103,7 @@ public void process() throws IOException {
 			os.write(lineSep);
 
 			int compoundCount = 0;
-			String seq = "";
+			String seq;
 
 			seq = sequence.getSequenceAsString();
 
@@ -133,7 +133,7 @@ public static void main(String[] args) {
 			FileInputStream is = new FileInputStream("/Users/Scooter/scripps/dyadic/c1-454Scaffolds.faa");
 
 
-			FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(is, new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+			FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(is, new GenericFastaHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
 			LinkedHashMap<String, ProteinSequence> proteinSequences = fastaReader.process();
 			is.close();
 
@@ -144,7 +144,7 @@ public static void main(String[] args) {
 
 			BufferedOutputStream bo = new BufferedOutputStream(fileOutputStream);
 			long start = System.currentTimeMillis();
-			FastaWriter<ProteinSequence, AminoAcidCompound> fastaWriter = new FastaWriter<ProteinSequence, AminoAcidCompound>(bo, proteinSequences.values(), new GenericFastaHeaderFormat<ProteinSequence, AminoAcidCompound>());
+			FastaWriter<ProteinSequence, AminoAcidCompound> fastaWriter = new FastaWriter<>(bo, proteinSequences.values(), new GenericFastaHeaderFormat<>());
 			fastaWriter.process();
 			bo.close();
 			long end = System.currentTimeMillis();
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java
index 966d723728..1e3ec619cf 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java
@@ -71,9 +71,9 @@ public static void writeProteinSequence(File file,
 	public static void writeProteinSequence(OutputStream outputStream,
 			Collection<ProteinSequence> proteinSequences) throws Exception {
 
-		FastaWriter<ProteinSequence, AminoAcidCompound> fastaWriter = new FastaWriter<ProteinSequence, AminoAcidCompound>(
+		FastaWriter<ProteinSequence, AminoAcidCompound> fastaWriter = new FastaWriter<>(
 				outputStream, proteinSequences,
-				new GenericFastaHeaderFormat<ProteinSequence, AminoAcidCompound>());
+				new GenericFastaHeaderFormat<>());
 		fastaWriter.process();
 
 	}
@@ -103,7 +103,7 @@ public static void writeGeneSequence(File file, Collection<GeneSequence> geneSeq
 	public static void writeGeneSequence(OutputStream outputStream, Collection<GeneSequence> geneSequences,boolean showExonUppercase) throws Exception {
 		FastaGeneWriter fastaWriter = new FastaGeneWriter(
 				outputStream, geneSequences,
-				new GenericFastaHeaderFormat<GeneSequence, NucleotideCompound>(),showExonUppercase);
+				new GenericFastaHeaderFormat<>(),showExonUppercase);
 		fastaWriter.process();
 
 	}
@@ -132,9 +132,9 @@ public static void writeNucleotideSequence(File file, Collection<DNASequence> dn
 	 */
 
 	public static void writeNucleotideSequence(OutputStream outputStream, Collection<DNASequence> dnaSequences) throws Exception {
-		FastaWriter<DNASequence, NucleotideCompound> fastaWriter = new FastaWriter<DNASequence, NucleotideCompound>(
+		FastaWriter<DNASequence, NucleotideCompound> fastaWriter = new FastaWriter<>(
 				outputStream, dnaSequences,
-				new GenericFastaHeaderFormat<DNASequence, NucleotideCompound>());
+				new GenericFastaHeaderFormat<>());
 		fastaWriter.process();
 
 	}
@@ -170,7 +170,7 @@ public static void writeSequence(OutputStream outputStream, Sequence<?> sequence
 	 */
 
 	private static Collection<Sequence<?>> singleSeqToCollection(Sequence<?> sequence) {
-		Collection<Sequence<?>> sequences = new ArrayList<Sequence<?>>();
+		Collection<Sequence<?>> sequences = new ArrayList<>();
 		sequences.add(sequence);
 		return sequences;
 	}
@@ -188,19 +188,11 @@ public static void writeSequences(OutputStream outputStream,
 			Collection<Sequence<?>> sequences) throws Exception {
 
 		FastaHeaderFormatInterface<Sequence<?>, Compound> fhfi =
-				new FastaHeaderFormatInterface<Sequence<?>, Compound>() {
-
-					@Override
-					public String getHeader(Sequence<?> sequence) {
-						return sequence.getAccession().toString();
-					}
-
-					;
-				};
+				sequence -> sequence.getAccession().toString();
 
 		FastaWriter<Sequence<?>, Compound> fastaWriter =
-				new FastaWriter<Sequence<?>, Compound>(outputStream,
-				sequences, fhfi);
+				new FastaWriter<>(outputStream,
+						sequences, fhfi);
 
 		fastaWriter.process();
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
index fb89f1c4e3..d077eaa007 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
@@ -50,8 +50,8 @@
 public class FileProxyDNASequenceCreator implements
 		SequenceCreatorInterface<NucleotideCompound> {
 
-	CompoundSet<NucleotideCompound> compoundSet = null;
-	File file = null;
+	CompoundSet<NucleotideCompound> compoundSet;
+	File file;
 	SequenceParserInterface sequenceParser;
 
 	/**
@@ -78,7 +78,7 @@ public FileProxyDNASequenceCreator(File file,
 	 */
 	@Override
 	public AbstractSequence<NucleotideCompound> getSequence(String sequence, long index ) throws CompoundNotFoundException, IOException {
-		SequenceFileProxyLoader<NucleotideCompound> sequenceFileProxyLoader = new SequenceFileProxyLoader<NucleotideCompound>(
+		SequenceFileProxyLoader<NucleotideCompound> sequenceFileProxyLoader = new SequenceFileProxyLoader<>(
 				file,
 				sequenceParser,
 				index,
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java
index 7db550683f..5048850579 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java
@@ -76,13 +76,13 @@ public FileProxyProteinSequenceCreator(File file, CompoundSet<AminoAcidCompound>
 	@Override
 	public AbstractSequence<AminoAcidCompound> getSequence(String sequence, long index) throws CompoundNotFoundException, IOException {
 		SequenceFileProxyLoader<AminoAcidCompound> sequenceFileProxyLoader =
-				new SequenceFileProxyLoader<AminoAcidCompound>(
+				new SequenceFileProxyLoader<>(
 						file,
 						sequenceParser,
 						index,
 						sequence.length(),
 						compoundSet
-						);
+				);
 		return new ProteinSequence(sequenceFileProxyLoader, compoundSet);
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
index 4be68696fb..7d117ffaa4 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
@@ -50,8 +50,8 @@
 public class FileProxyRNASequenceCreator implements
 		SequenceCreatorInterface<NucleotideCompound> {
 
-	CompoundSet<NucleotideCompound> compoundSet = null;
-	File file = null;
+	CompoundSet<NucleotideCompound> compoundSet;
+	File file;
 	SequenceParserInterface sequenceParser;
 
 	/**
@@ -78,7 +78,7 @@ public FileProxyRNASequenceCreator(File file,
 	 */
 	@Override
 	public AbstractSequence<NucleotideCompound> getSequence(String sequence, long index ) throws CompoundNotFoundException, IOException {
-		SequenceFileProxyLoader<NucleotideCompound> sequenceFileProxyLoader = new SequenceFileProxyLoader<NucleotideCompound>(
+		SequenceFileProxyLoader<NucleotideCompound> sequenceFileProxyLoader = new SequenceFileProxyLoader<>(
 				file,
 				sequenceParser,
 				index,
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
index 951cce40c0..d8c88bd1b2 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
@@ -55,9 +55,9 @@
  */
 public class GenbankReader<S extends AbstractSequence<C>, C extends Compound> {
 
-	private SequenceCreatorInterface<C> sequenceCreator;
-	private GenbankSequenceParser<S,C> genbankParser;
-	private BufferedReader bufferedReader;
+	private final SequenceCreatorInterface<C> sequenceCreator;
+	private final GenbankSequenceParser<S,C> genbankParser;
+	private final BufferedReader bufferedReader;
 	private boolean closed;
 	private final Logger logger = LoggerFactory.getLogger(this.getClass());
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
index 51c1f7593b..3e8e4e8241 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
@@ -61,15 +61,15 @@ public static LinkedHashMap<String, DNASequence> readGenbankDNASequence(File fil
 		}
 
 		GenbankReader<DNASequence, NucleotideCompound> GenbankProxyReader =
-				new GenbankReader<DNASequence, NucleotideCompound>(
+				new GenbankReader<>(
 						file,
-						new GenericGenbankHeaderParser<DNASequence, NucleotideCompound>(),
+						new GenericGenbankHeaderParser<>(),
 						new FileProxyDNASequenceCreator(
 								file,
 								DNACompoundSet.getDNACompoundSet(),
 								new GenbankSequenceParser<AbstractSequence<NucleotideCompound>, NucleotideCompound>()
-							)
-					);
+						)
+				);
 		return GenbankProxyReader.process();
 
 	}
@@ -89,15 +89,15 @@ public static LinkedHashMap<String, ProteinSequence> readGenbankProteinSequence(
 		}
 
 		GenbankReader<ProteinSequence, AminoAcidCompound> GenbankProxyReader =
-				new GenbankReader<ProteinSequence, AminoAcidCompound>(
+				new GenbankReader<>(
 						file,
-						new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
+						new GenericGenbankHeaderParser<>(),
 						new FileProxyProteinSequenceCreator(
 								file,
 								AminoAcidCompoundSet.getAminoAcidCompoundSet(),
 								new GenbankSequenceParser<AbstractSequence<AminoAcidCompound>, AminoAcidCompound>()
-							)
-					);
+						)
+				);
 		return GenbankProxyReader.process();
 
 	}
@@ -117,15 +117,15 @@ public static LinkedHashMap<String, RNASequence> readGenbankRNASequence(File fil
 		}
 
 		GenbankReader<RNASequence, NucleotideCompound> GenbankProxyReader =
-				new GenbankReader<RNASequence, NucleotideCompound>(
+				new GenbankReader<>(
 						file,
-						new GenericGenbankHeaderParser<RNASequence, NucleotideCompound>(),
+						new GenericGenbankHeaderParser<>(),
 						new FileProxyRNASequenceCreator(
 								file,
 								RNACompoundSet.getRNACompoundSet(),
 								new GenbankSequenceParser<AbstractSequence<NucleotideCompound>, NucleotideCompound>()
-							)
-					);
+						)
+				);
 		return GenbankProxyReader.process();
 
 	}
@@ -156,9 +156,9 @@ public static LinkedHashMap<String, ProteinSequence> readGenbankProteinSequence(
 	 */
 	public static LinkedHashMap<String, ProteinSequence> readGenbankProteinSequence(
 			InputStream inStream) throws Exception {
-		GenbankReader<ProteinSequence, AminoAcidCompound> GenbankReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(
+		GenbankReader<ProteinSequence, AminoAcidCompound> GenbankReader = new GenbankReader<>(
 				inStream,
-				new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
+				new GenericGenbankHeaderParser<>(),
 				new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
 		return GenbankReader.process();
 	}
@@ -171,9 +171,9 @@ public static LinkedHashMap<String, ProteinSequence> readGenbankProteinSequence(
 	 */
 	public static LinkedHashMap<String, DNASequence> readGenbankDNASequence(
 			InputStream inStream) throws Exception {
-		GenbankReader<DNASequence, NucleotideCompound> GenbankReader = new GenbankReader<DNASequence, NucleotideCompound>(
+		GenbankReader<DNASequence, NucleotideCompound> GenbankReader = new GenbankReader<>(
 				inStream,
-				new GenericGenbankHeaderParser<DNASequence, NucleotideCompound>(),
+				new GenericGenbankHeaderParser<>(),
 				new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
 		return GenbankReader.process();
 	}
@@ -199,9 +199,9 @@ public static LinkedHashMap<String, DNASequence> readGenbankDNASequence(
 	 */
 	public static LinkedHashMap<String, RNASequence> readGenbankRNASequence(
 			InputStream inStream) throws Exception {
-		GenbankReader<RNASequence, NucleotideCompound> GenbankReader = new GenbankReader<RNASequence, NucleotideCompound>(
+		GenbankReader<RNASequence, NucleotideCompound> GenbankReader = new GenbankReader<>(
 				inStream,
-				new GenericGenbankHeaderParser<RNASequence, NucleotideCompound>(),
+				new GenericGenbankHeaderParser<>(),
 				new RNASequenceCreator(RNACompoundSet.getRNACompoundSet()));
 		return GenbankReader.process();
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
index 9641a38894..700b50a087 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
@@ -75,7 +75,7 @@ public class GenbankSequenceParser<S extends AbstractSequence<C>, C extends Comp
 	 */
 	private HashMap<String, ArrayList<AbstractFeature>> featureCollection;
 
-	private Logger log = LoggerFactory.getLogger(getClass());
+	private final Logger log = LoggerFactory.getLogger(getClass());
 
 	// this is a compoundset parsed from header.
 	private CompoundSet<?> compoundType;
@@ -138,7 +138,7 @@ public class GenbankSequenceParser<S extends AbstractSequence<C>, C extends Comp
 
 
 	private String parse(BufferedReader bufferedReader) {
-		String sectionKey = null;
+		String sectionKey;
 		List<String[]> section;
 		// Get an ordered list of key->value pairs in array-tuples
 		do {
@@ -153,165 +153,187 @@ private String parse(BufferedReader bufferedReader) {
 				throw new ParserException(Messages.SECTIONKEYNULL);
 			}
 			// process section-by-section
-			if (sectionKey.equals(LOCUS_TAG)) {
-				String loc = section.get(0)[1];
-				header = loc;
-				Matcher m = lp.matcher(loc);
-				if (m.matches()) {
-					headerParser.setName(m.group(1));
-					headerParser.setAccession(m.group(1)); // default if no accession found
-
-					String lengthUnits = m.group(2);
-					String type = m.group(5);
-
-					if (lengthUnits.equalsIgnoreCase("aa")) {
-						compoundType = AminoAcidCompoundSet.getAminoAcidCompoundSet();
-					} else if (lengthUnits.equalsIgnoreCase("bp")) {
-						if (type != null) {
-							if (type.contains("RNA")) {
-								compoundType = RNACompoundSet.getRNACompoundSet();
+			switch (sectionKey) {
+				case LOCUS_TAG: {
+					String loc = section.get(0)[1];
+					header = loc;
+					Matcher m = lp.matcher(loc);
+					if (m.matches()) {
+						headerParser.setName(m.group(1));
+						headerParser.setAccession(m.group(1)); // default if no accession found
+
+						String lengthUnits = m.group(2);
+						String type = m.group(5);
+
+						if (lengthUnits.equalsIgnoreCase("aa")) {
+							compoundType = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+						} else if (lengthUnits.equalsIgnoreCase("bp")) {
+							if (type != null) {
+								if (type.contains("RNA")) {
+									compoundType = RNACompoundSet.getRNACompoundSet();
+								} else {
+									compoundType = DNACompoundSet.getDNACompoundSet();
+								}
 							} else {
 								compoundType = DNACompoundSet.getDNACompoundSet();
 							}
-						} else {
-							compoundType = DNACompoundSet.getDNACompoundSet();
 						}
-					}
 
-					log.debug("compound type: {}", compoundType.getClass().getSimpleName());
+						log.debug("compound type: {}", compoundType.getClass().getSimpleName());
 
-				} else {
-					throw new ParserException("Bad locus line");
-				}
-			} else if (sectionKey.equals(DEFINITION_TAG)) {
-				headerParser.setDescription(section.get(0)[1]);
-			} else if (sectionKey.equals(ACCESSION_TAG)) {
-				// if multiple accessions, store only first as accession,
-				// and store rest in annotation
-				String[] accs = section.get(0)[1].split("\\s+");
-				accession = accs[0].trim();
-				headerParser.setAccession(accession);
-			} else if (sectionKey.equals(VERSION_TAG)) {
-				String ver = section.get(0)[1];
-				Matcher m = vp.matcher(ver);
-				if (m.matches()) {
-					String verAcc = m.group(1);
-					if (!accession.equals(verAcc)) {
-						// the version refers to a different accession!
-						// believe the version line, and store the original
-						// accession away in the additional accession set
-						accession = verAcc;
-					}
-					if (m.group(3) != null) {
-						headerParser.setVersion(Integer.parseInt(m.group(3)));
-					}
-					if (m.group(5) != null) {
-						headerParser.setIdentifier(m.group(5));
+					} else {
+						throw new ParserException("Bad locus line");
 					}
-				} else {
-					throw new ParserException("Bad version line");
+					break;
 				}
-			} else if (sectionKey.equals(KEYWORDS_TAG)) {
-			} else if (sectionKey.equals(SOURCE_TAG)) {
-				// ignore - can get all this from the first feature
-			} else if (sectionKey.equals(REFERENCE_TAG)) {
-				if (!section.isEmpty()) {
-					GenbankReference genbankReference = new GenbankReference();
-					for (String[] ref : section) {
-						if (ref[0].equals(AUTHORS_TAG)) {
-							genbankReference.setAuthors(ref[1]);
-						} else if (ref[0].equals(TITLE_TAG)) {
-							genbankReference.setTitle(ref[1]);
-						} else if (ref[0].equals(JOURNAL_TAG)) {
-							genbankReference.setJournal(ref[1]);
+				case DEFINITION_TAG:
+					headerParser.setDescription(section.get(0)[1]);
+					break;
+				case ACCESSION_TAG:
+					// if multiple accessions, store only first as accession,
+					// and store rest in annotation
+					String[] accs = section.get(0)[1].split("\\s+");
+					accession = accs[0].trim();
+					headerParser.setAccession(accession);
+					break;
+				case VERSION_TAG: {
+					String ver = section.get(0)[1];
+					Matcher m = vp.matcher(ver);
+					if (m.matches()) {
+						String verAcc = m.group(1);
+						if (!accession.equals(verAcc)) {
+							// the version refers to a different accession!
+							// believe the version line, and store the original
+							// accession away in the additional accession set
+							accession = verAcc;
+						}
+						if (m.group(3) != null) {
+							headerParser.setVersion(Integer.parseInt(m.group(3)));
+						}
+						if (m.group(5) != null) {
+							headerParser.setIdentifier(m.group(5));
 						}
+					} else {
+						throw new ParserException("Bad version line");
 					}
-					headerParser.addReference(genbankReference);
+					break;
 				}
-			} else if (sectionKey.equals(COMMENT_TAG)) {
-				// Set up some comments
-				headerParser.setComment(section.get(0)[1]);
-			} else if (sectionKey.equals(FEATURE_TAG)) {
-				// starting from second line of input, start a new feature whenever we come across
-				// a key that does not start with /
-				AbstractFeature gbFeature = null;
-				for (int i = 1; i < section.size(); i++) {
-					String key = section.get(i)[0];
-					String val = section.get(i)[1];
-					if (key.startsWith("/")) {
-						if (gbFeature == null) {
-							throw new ParserException("Malformed GenBank file: found a qualifier without feature.");
-						}
-						key = key.substring(1); // strip leading slash
-						val = val.replaceAll("\\s*[\\n\\r]+\\s*", " ").trim();
-						if (val.endsWith("\"")) {
-							val = val.substring(1, val.length() - 1); // strip quotes
+				case KEYWORDS_TAG:
+					break;
+				case SOURCE_TAG:
+					// ignore - can get all this from the first feature
+					break;
+				case REFERENCE_TAG:
+					if (!section.isEmpty()) {
+						GenbankReference genbankReference = new GenbankReference();
+						for (String[] ref : section) {
+							switch (ref[0]) {
+								case AUTHORS_TAG:
+									genbankReference.setAuthors(ref[1]);
+									break;
+								case TITLE_TAG:
+									genbankReference.setTitle(ref[1]);
+									break;
+								case JOURNAL_TAG:
+									genbankReference.setJournal(ref[1]);
+									break;
+							}
 						}
-						// parameter on old feature
-						if (key.equals("db_xref")) {
-							Matcher m = dbxp.matcher(val);
-							if (m.matches()) {
-								String dbname = m.group(1);
-								String raccession = m.group(2);
-								Qualifier xref = new DBReferenceInfo(dbname, raccession);
-								gbFeature.addQualifier(key, xref);
-
-								ArrayList<DBReferenceInfo> listDBEntry = new ArrayList<DBReferenceInfo>();
-								listDBEntry.add((DBReferenceInfo) xref);
-								mapDB.put(key, listDBEntry);
-							} else {
-								throw new ParserException("Bad dbxref");
+						headerParser.addReference(genbankReference);
+					}
+					break;
+				case COMMENT_TAG:
+					// Set up some comments
+					headerParser.setComment(section.get(0)[1]);
+					break;
+				case FEATURE_TAG:
+					// starting from second line of input, start a new feature whenever we come across
+					// a key that does not start with /
+					AbstractFeature gbFeature = null;
+					for (int i = 1; i < section.size(); i++) {
+						String key = section.get(i)[0];
+						String val = section.get(i)[1];
+						if (key.startsWith("/")) {
+							if (gbFeature == null) {
+								throw new ParserException("Malformed GenBank file: found a qualifier without feature.");
 							}
-						} else if (key.equalsIgnoreCase("organism")) {
-							Qualifier q = new Qualifier(key, val.replace('\n', ' '));
-							gbFeature.addQualifier(key, q);
-						} else {
-							if (key.equalsIgnoreCase("translation")) {
-								// strip spaces from sequence
-								val = val.replaceAll("\\s+", "");
-								Qualifier q = new Qualifier(key, val);
+							key = key.substring(1); // strip leading slash
+							val = val.replaceAll("\\s*[\\n\\r]+\\s*", " ").trim();
+							if (val.endsWith("\"")) {
+								val = val.substring(1, val.length() - 1); // strip quotes
+							}
+							// parameter on old feature
+							if (key.equals("db_xref")) {
+								Matcher m = dbxp.matcher(val);
+								if (m.matches()) {
+									String dbname = m.group(1);
+									String raccession = m.group(2);
+									Qualifier xref = new DBReferenceInfo(dbname, raccession);
+									gbFeature.addQualifier(key, xref);
+
+									ArrayList<DBReferenceInfo> listDBEntry = new ArrayList<>();
+									listDBEntry.add((DBReferenceInfo) xref);
+									mapDB.put(key, listDBEntry);
+								} else {
+									throw new ParserException("Bad dbxref");
+								}
+							} else if (key.equalsIgnoreCase("organism")) {
+								Qualifier q = new Qualifier(key, val.replace('\n', ' '));
 								gbFeature.addQualifier(key, q);
 							} else {
-								Qualifier q = new Qualifier(key, val);
-								gbFeature.addQualifier(key, q);
+								if (key.equalsIgnoreCase("translation")) {
+									// strip spaces from sequence
+									val = val.replaceAll("\\s+", "");
+									Qualifier q = new Qualifier(key, val);
+									gbFeature.addQualifier(key, q);
+								} else {
+									Qualifier q = new Qualifier(key, val);
+									gbFeature.addQualifier(key, q);
+								}
 							}
+						} else {
+							// new feature!
+							gbFeature = new TextFeature(key, val, key, key);
+							Location l =
+									locationParser.parse(val);
+							gbFeature.setLocation((AbstractLocation) l);
+
+							if (!featureCollection.containsKey(key)) {
+								featureCollection.put(key, new ArrayList());
+							}
+							featureCollection.get(key).add(gbFeature);
 						}
-					} else {
-						// new feature!
-						gbFeature = new TextFeature(key, val, key, key);
-						Location l =
-								locationParser.parse(val);
-						gbFeature.setLocation((AbstractLocation)l);
-
-						if (!featureCollection.containsKey(key)) {
-							featureCollection.put(key, new ArrayList());
-						}
-						featureCollection.get(key).add(gbFeature);
 					}
-				}
-			} else if (sectionKey.equals(BASE_COUNT_TAG)) {
-				// ignore - can calculate from sequence content later if needed
-			} else if (sectionKey.equals(START_SEQUENCE_TAG)) {
-				// our first line is ignorable as it is the ORIGIN tag
-				// the second line onwards conveniently have the number as
-				// the [0] tuple, and sequence string as [1] so all we have
-				// to do is concat the [1] parts and then strip out spaces,
-				// and replace '.' and '~' with '-' for our parser.
-				StringBuffer seq = new StringBuffer();
-				for (int i = 1; i < section.size(); i++) {
-					seq.append(section.get(i)[1]);
-				}
-				seqData = seq.toString().replaceAll("\\s+", "").replaceAll("[\\.|~]", "-").toUpperCase();
-			} else if(sectionKey.equals(DBSOURCE)) {
-				//TODO
-			} else if(sectionKey.equals(PRIMARY)) {
-				//TODO
-			} else if(sectionKey.equals(DBLINK)) {
-				//TODO
-			} else {
-				if(!sectionKey.equals(END_SEQUENCE_TAG)) {
-					log.info("found unknown section key: "+sectionKey);
-				}
+					break;
+				case BASE_COUNT_TAG:
+					// ignore - can calculate from sequence content later if needed
+					break;
+				case START_SEQUENCE_TAG:
+					// our first line is ignorable as it is the ORIGIN tag
+					// the second line onwards conveniently have the number as
+					// the [0] tuple, and sequence string as [1] so all we have
+					// to do is concat the [1] parts and then strip out spaces,
+					// and replace '.' and '~' with '-' for our parser.
+					StringBuilder seq = new StringBuilder();
+					for (int i = 1; i < section.size(); i++) {
+						seq.append(section.get(i)[1]);
+					}
+					seqData = seq.toString().replaceAll("\\s+", "").replaceAll("[\\.|~]", "-").toUpperCase();
+					break;
+				case DBSOURCE:
+					//TODO
+					break;
+				case PRIMARY:
+					//TODO
+					break;
+				case DBLINK:
+					//TODO
+					break;
+				default:
+					if (!sectionKey.equals(END_SEQUENCE_TAG)) {
+						log.info("found unknown section key: " + sectionKey);
+					}
+					break;
 			}
 		} while (!sectionKey.equals(END_SEQUENCE_TAG));
 		return seqData;
@@ -326,8 +348,8 @@ private String parse(BufferedReader bufferedReader) {
 	// reads an indented section, combining split lines and creating a list of
 	// key->value tuples
 	private List<String[]> readSection(BufferedReader bufferedReader) {
-		List<String[]> section = new ArrayList<String[]>();
-		String line = "";
+		List<String[]> section = new ArrayList<>();
+		String line;
 
 		String currKey = null;
 		StringBuffer currVal = new StringBuffer();
@@ -385,19 +407,17 @@ private List<String[]> readSection(BufferedReader bufferedReader) {
 					}
 				}
 			}
-		} catch (IOException e) {
-			throw new ParserException(e.getMessage());
-		} catch (RuntimeException e) {
+		} catch (IOException | RuntimeException e) {
 			throw new ParserException(e.getMessage());
 		}
 		return section;
 	}
 
 	@Override
-	public String getSequence(BufferedReader bufferedReader, int sequenceLength) throws IOException {
-		featureCollection = new HashMap<String, ArrayList<AbstractFeature>>();
-		mapDB = new LinkedHashMap<String, ArrayList<DBReferenceInfo>>();
-		headerParser = new GenericGenbankHeaderParser<S, C>();
+	public String getSequence(BufferedReader bufferedReader, int sequenceLength) {
+		featureCollection = new HashMap<>();
+		mapDB = new LinkedHashMap<>();
+		headerParser = new GenericGenbankHeaderParser<>();
 		try {
 			parse(bufferedReader);
 		} catch (ParserException e) {
@@ -421,7 +441,7 @@ public LinkedHashMap<String, ArrayList<DBReferenceInfo>> getDatabaseReferences()
 	}
 
 	public ArrayList<String> getKeyWords() {
-		return new ArrayList<String>(featureCollection.keySet());
+		return new ArrayList<>(featureCollection.keySet());
 	}
 
 	public ArrayList<AbstractFeature> getFeatures(String keyword) {
@@ -432,8 +452,8 @@ public HashMap<String, ArrayList<AbstractFeature>> getFeatures() {
 	}
 
 	public void parseFeatures(AbstractSequence<C> sequence) {
-		for (String k: featureCollection.keySet())
-			for (AbstractFeature f: featureCollection.get(k))
+		for (ArrayList<AbstractFeature> abstractFeatures : featureCollection.values())
+			for (AbstractFeature f: abstractFeatures)
 				sequence.addFeature(f);
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java
index cab8d23db1..b3ad294c47 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java
@@ -85,7 +85,7 @@ public GenbankWriter(OutputStream os, Collection<S> sequences,
 	 * @param lineSeparator
 	 */
 
-	public void process() throws Exception {
+	public void process() {
 		// Loosely based on code from Howard Salis
 		// TODO - Force lower case?
 		// boolean closeit = false;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java
index 19e26bd3a7..4894daf38a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java
@@ -76,10 +76,10 @@ public static void writeProteinSequence(File file,
 	public static void writeProteinSequence(OutputStream outputStream,
 			Collection<ProteinSequence> proteinSequences) throws Exception {
 
-		GenbankWriter<ProteinSequence, AminoAcidCompound> genbankWriter = new GenbankWriter<ProteinSequence, AminoAcidCompound>(
+		GenbankWriter<ProteinSequence, AminoAcidCompound> genbankWriter = new GenbankWriter<>(
 				outputStream,
 				proteinSequences,
-				new GenericGenbankHeaderFormat<ProteinSequence, AminoAcidCompound>());
+				new GenericGenbankHeaderFormat<>());
 		genbankWriter.process();
 
 	}
@@ -126,10 +126,10 @@ public static void writeNucleotideSequence(OutputStream outputStream,
 	public static void writeNucleotideSequence(OutputStream outputStream,
 			Collection<DNASequence> dnaSequences, String seqType)
 			throws Exception {
-		GenericGenbankHeaderFormat<DNASequence, NucleotideCompound> genericGenbankHeaderFormat = new GenericGenbankHeaderFormat<DNASequence, NucleotideCompound>(
+		GenericGenbankHeaderFormat<DNASequence, NucleotideCompound> genericGenbankHeaderFormat = new GenericGenbankHeaderFormat<>(
 				seqType);
 		// genericGenbankHeaderFormat.setLineSeparator(lineSep);
-		GenbankWriter<DNASequence, NucleotideCompound> genbankWriter = new GenbankWriter<DNASequence, NucleotideCompound>(
+		GenbankWriter<DNASequence, NucleotideCompound> genbankWriter = new GenbankWriter<>(
 				outputStream, dnaSequences, genericGenbankHeaderFormat);
 		// genbankWriter.setLineSeparator(lineSep);
 		genbankWriter.process();
@@ -171,7 +171,7 @@ public static void writeSequence(OutputStream outputStream,
 
 	private static Collection<Sequence<?>> singleSeqToCollection(
 			Sequence<?> sequence) {
-		Collection<Sequence<?>> sequences = new ArrayList<Sequence<?>>();
+		Collection<Sequence<?>> sequences = new ArrayList<>();
 		sequences.add(sequence);
 		return sequences;
 	}
@@ -191,17 +191,9 @@ private static Collection<Sequence<?>> singleSeqToCollection(
 	public static void writeSequences(OutputStream outputStream,
 			Collection<Sequence<?>> sequences) throws Exception {
 
-		GenbankHeaderFormatInterface<Sequence<?>, Compound> fhfi = new GenbankHeaderFormatInterface<Sequence<?>, Compound>() {
+		GenbankHeaderFormatInterface<Sequence<?>, Compound> fhfi = sequence -> sequence.getAccession().toString();
 
-			@Override
-			public String getHeader(Sequence<?> sequence) {
-				return sequence.getAccession().toString();
-			}
-
-			;
-		};
-
-		GenbankWriter<Sequence<?>, Compound> genbankWriter = new GenbankWriter<Sequence<?>, Compound>(
+		GenbankWriter<Sequence<?>, Compound> genbankWriter = new GenbankWriter<>(
 				outputStream, sequences, fhfi);
 
 		genbankWriter.process();
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java
index 1a83dee701..e13f06d7ba 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java
@@ -71,8 +71,8 @@ public class GenericFastaHeaderParser<S extends AbstractSequence<C>, C extends C
 	 */
 	private String[] getHeaderValues(String header) {
 		String[] data = new String[0];
-		ArrayList<String> values = new ArrayList<String>();
-		StringBuffer sb = new StringBuffer();
+		ArrayList<String> values = new ArrayList<>();
+		StringBuilder sb = new StringBuilder();
 		//commented out 1/11/2012 to resolve an issue where headers do contain a length= at the end that are not recognized
 		//if(header.indexOf("length=") != -1){
 		//    data = new String[1];
@@ -152,7 +152,7 @@ public void parseHeader(String header, S sequence) {
 			String[] pdbe = data[0].split(" ");
 			String[] pdbaccession = pdbe[0].split(":");
 			sequence.setAccession(new AccessionID(pdbaccession[1], DataSource.PDBe));
-		} else if (data[0].indexOf(":") != -1 && data.length > 1 && data[1].equals("PDBID")) {
+		} else if (data[0].contains(":") && data.length > 1 && data[1].equals("PDBID")) {
 			sequence.setAccession(new AccessionID(data[0], DataSource.PDB2));
 		} else if (data[0].equalsIgnoreCase("pat")) {
 			sequence.setAccession(new AccessionID(data[2], DataSource.PATENTS));
@@ -178,7 +178,7 @@ public void parseHeader(String header, S sequence) {
 	public static void main(String[] args) {
 
 		logger.info("parseHeader");
-		String header = "";
+		String header;
 		ProteinSequence sequence = null;
 		try {
 			sequence = new ProteinSequence("");
@@ -187,7 +187,7 @@ public static void main(String[] args) {
 			logger.error("Could not create empty protein sequence. Error: {}. This is most likely a bug.",e.getMessage());
 		}
 		GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound> instance =
-		  new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>();
+				new GenericFastaHeaderParser<>();
 
 		header = "gi|gi-number|gb|accession|locus";
 		instance.parseHeader(header, sequence);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.java
index a19c9f648c..bef63c559f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.java
@@ -36,7 +36,7 @@ public class GenericGenbankHeaderFormat<S extends AbstractSequence<C>, C extends
 		GenbankHeaderFormatInterface<S, C> {
 	private static final int HEADER_WIDTH = 12;
 	private static final String lineSep = "%n";
-	private String seqType = null;
+	private String seqType;
 
 	public GenericGenbankHeaderFormat() {
 		seqType = null;
@@ -169,8 +169,8 @@ private String _write_the_first_line(S sequence) {
 					+ " is too long");
 		}
 
-		String units = "";
-		String mol_type = "";
+		String units;
+		String mol_type;
 		if (sequence.getCompoundSet() instanceof DNACompoundSet) {
 			units = "bp";
 			mol_type = "DNA";
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java
index 7c828b54f2..443443e62e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java
@@ -43,8 +43,8 @@ public class GenericGenbankHeaderParser<S extends AbstractSequence<C>, C extends
 	@SuppressWarnings("unused")
 	private int version;
 	private boolean versionSeen;
-	private ArrayList<String> comments = new ArrayList<>();
-	private List<AbstractReference> references = new ArrayList<>();
+	private final ArrayList<String> comments = new ArrayList<>();
+	private final List<AbstractReference> references = new ArrayList<>();
 
 	/**
 	 * Parse the header and set the values in the sequence
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java
index 97e37f30cd..98a5952858 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java
@@ -56,7 +56,7 @@ public class GenericInsdcHeaderFormat<S extends AbstractSequence<C>, C extends C
 	 * @param quote
 	 */
 	private String _write_feature_qualifier(String key, String value, boolean quote) {
-		String line = "";
+		String line;
 		if(null == value) {
 			line = QUALIFIER_INDENT_STR + "/" + key + lineSep;
 			return line;
@@ -195,7 +195,7 @@ private String _insdc_feature_location_string(FeatureInterface<AbstractSequence<
 			}
 			StringBuilder sb = new StringBuilder();
 			Formatter formatter = new Formatter(sb,Locale.US);
-			ArrayList<String> locations = new ArrayList<String>();
+			ArrayList<String> locations = new ArrayList<>();
 			for(FeatureInterface<AbstractSequence<C>, C> f  : feature.getChildrenFeatures()) {
 				locations.add(_insdc_location_string_ignoring_strand_and_subfeatures(f.getLocations(), record_length));
 			}
@@ -208,7 +208,7 @@ private String _insdc_feature_location_string(FeatureInterface<AbstractSequence<
 		//This covers typical forward strand features, and also an evil mixed strand:
 		StringBuilder sb = new StringBuilder();
 		Formatter formatter = new Formatter(sb,Locale.US);
-		ArrayList<String> locations = new ArrayList<String>();
+		ArrayList<String> locations = new ArrayList<>();
 		for(FeatureInterface<AbstractSequence<C>, C> f  : feature.getChildrenFeatures()) {
 			locations.add(_insdc_location_string_ignoring_strand_and_subfeatures(f.getLocations(), record_length));
 		}
@@ -340,14 +340,14 @@ raise ValueError("Expected a SeqFeature position object.")
 	 */
 	protected ArrayList<String> _split_multi_line(String text, int max_len) {
 		// TODO Auto-generated method stub
-		ArrayList<String> output = new ArrayList<String>();
+		ArrayList<String> output = new ArrayList<>();
 		text = text.trim();
 		if(text.length() <= max_len) {
 			output.add(text);
 			return output;
 		}
 
-		ArrayList<String> words = new ArrayList<String>();
+		ArrayList<String> words = new ArrayList<>();
 		Collections.addAll(words, text.split("\\s+"));
 		while(!words.isEmpty()) {
 			text = words.remove(0);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
index 8f1b449283..51c10918dd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
@@ -86,7 +86,7 @@ public static IUPACParser getInstance() {
 
 	public static final String      IUPAC_LOCATION = "org/biojava/nbio/core/sequence/iupac.txt";
 
-	private InputStream              is;
+	private final InputStream              is;
 	private List<IUPACTable>         tables;
 	private Map<String, IUPACTable>  nameLookup;
 	private Map<Integer, IUPACTable> idLookup;
@@ -134,8 +134,8 @@ public IUPACTable getTable(Integer id) {
 
 	private void populateLookups() {
 		if(nameLookup == null) {
-			nameLookup = new HashMap<String, IUPACTable>();
-			idLookup = new HashMap<Integer, IUPACTable>();
+			nameLookup = new HashMap<>();
+			idLookup = new HashMap<>();
 			for(IUPACTable t: getTables()) {
 				nameLookup.put(t.getName(), t);
 				idLookup.put(t.getId(), t);
@@ -144,7 +144,7 @@ private void populateLookups() {
 	}
 
 	private List<IUPACTable> parseTables() {
-		List<IUPACTable> localTables = new ArrayList<IUPACTable>();
+		List<IUPACTable> localTables = new ArrayList<>();
 		List<String> lines = IOUtils.getList(is);
 		Integer id = null;
 		String name, aa, starts, baseone, basetwo, basethree;
@@ -158,24 +158,26 @@ private List<IUPACTable> parseTables() {
 			}
 			else {
 				String[] keyValue = line.split("\\s*=\\s*");
-				if (keyValue[0].equals("AAs")) {
-					aa = keyValue[1];
-				}
-				else if (keyValue[0].equals("Starts")) {
-					starts = keyValue[1];
-				}
-				else if (keyValue[0].equals("Base1")) {
-					baseone = keyValue[1];
-				}
-				else if (keyValue[0].equals("Base2")) {
-					basetwo = keyValue[1];
-				}
-				else if (keyValue[0].equals("Base3")) {
-					basethree = keyValue[1];
-				}
-				else {
-					name = keyValue[0];
-					id = Integer.parseInt(keyValue[1]);
+				switch (keyValue[0]) {
+					case "AAs":
+						aa = keyValue[1];
+						break;
+					case "Starts":
+						starts = keyValue[1];
+						break;
+					case "Base1":
+						baseone = keyValue[1];
+						break;
+					case "Base2":
+						basetwo = keyValue[1];
+						break;
+					case "Base3":
+						basethree = keyValue[1];
+						break;
+					default:
+						name = keyValue[0];
+						id = Integer.parseInt(keyValue[1]);
+						break;
 				}
 			}
 		}
@@ -198,7 +200,7 @@ public static class IUPACTable implements Table {
 		private final String       baseTwo;
 		private final String       baseThree;
 
-		private final List<Codon>  codons    = new ArrayList<Codon>();
+		private final List<Codon>  codons    = new ArrayList<>();
 		private CompoundSet<Codon> compounds = null;
 
 		public IUPACTable(String name, int id, String aminoAcidString,
@@ -328,7 +330,7 @@ public CompoundSet<Codon> getCodonCompoundSet(
 		}
 
 		private List<List<String>> codonStrings() {
-			List<List<String>> codons = new ArrayList<List<String>>();
+			List<List<String>> codons = new ArrayList<>();
 			for (int i = 0; i < baseOne.length(); i++) {
 				List<String> codon = Arrays.asList(Character
 						.toString(baseOne.charAt(i)),
@@ -348,7 +350,7 @@ private List<String> startCodons() {
 		}
 
 		private List<String> split(String string) {
-			List<String> split = new ArrayList<String>();
+			List<String> split = new ArrayList<>();
 			for (int i = 0; i < string.length(); i++) {
 				split.add(Character.toString(string.charAt(i)));
 			}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java
index c40e3efa2a..fe9e7cba9d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java
@@ -42,7 +42,7 @@
 public class ProteinSequenceCreator implements
 		SequenceCreatorInterface<AminoAcidCompound> {
 
-	private CompoundSet<AminoAcidCompound> compoundSet;
+	private final CompoundSet<AminoAcidCompound> compoundSet;
 /**
  *
  * @param compoundSet
@@ -70,7 +70,7 @@ public AbstractSequence<AminoAcidCompound> getSequence(String sequence,
 	@Override
 public AbstractSequence<AminoAcidCompound> getSequence(
 			List<AminoAcidCompound> list) {
-		ArrayListProxySequenceReader<AminoAcidCompound> store = new ArrayListProxySequenceReader<AminoAcidCompound>();
+		ArrayListProxySequenceReader<AminoAcidCompound> store = new ArrayListProxySequenceReader<>();
 		store.setCompoundSet(compoundSet);
 		store.setContents(list);
 		return new ProteinSequence(store);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java
index 96abe9cd35..32d20da1ee 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java
@@ -78,7 +78,7 @@ public AbstractSequence<NucleotideCompound> getSequence(
 	@Override
 public AbstractSequence<NucleotideCompound> getSequence(List<NucleotideCompound> list) {
 		ArrayListProxySequenceReader<NucleotideCompound> store =
-			new ArrayListProxySequenceReader<NucleotideCompound>();
+				new ArrayListProxySequenceReader<>();
 		store.setCompoundSet(compoundSet);
 		store.setContents(list);
 		return new RNASequence(store);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblReader.java
index 45e50cd9ea..f0f73caf21 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblReader.java
@@ -46,7 +46,7 @@ public class EmblReader {
 	public static EmblRecord process(File file) throws IOException {
 
 		EmblRecord emblRecord = new EmblRecord();
-		StringBuilder sequence = new StringBuilder("");
+		StringBuilder sequence = new StringBuilder();
 		LinkedList<EmblReference> emblReferences = new LinkedList<>();
 		EmblReference emblReference = new EmblReference();
 		LinkedList<String> accessionNumber = new LinkedList<>();
@@ -59,13 +59,13 @@ public static EmblRecord process(File file) throws IOException {
 			throw new IllegalArgumentException("the file can't be a directory");
 
 		try (FileReader fileReader = new FileReader(file)) {
-			String line = "";
+			String line;
 			String lineIdentifier;
 			String lineInfo;
 			try (BufferedReader bufferedReader = new BufferedReader(fileReader)) {
 				while ((line = bufferedReader.readLine()) != null) {
 					if (line.length() > 1) {
-						lineInfo = line.substring(2, line.length()).trim();
+						lineInfo = line.substring(2).trim();
 						lineIdentifier = line.substring(0, 2);
 						if (lineIdentifier.equals("ID"))
 							emblRecord.setEmblId(populateID(lineInfo));
@@ -129,22 +129,30 @@ private static void populateSequence(String line, StringBuilder sequence) {
 
 	private static void populateEmblReferences(String lineIdentifier, String lineInfo, EmblReference emblReference
 			, LinkedList<EmblReference> emblReferences) {
-		if (lineIdentifier.equals("RN"))
-			emblReference.setReferenceNumber(lineInfo);
-		else if (lineIdentifier.equals("RP"))
-			emblReference.setReferencePosition(lineInfo);
-		else if (lineIdentifier.equals("RX"))
-			emblReference.setReferenceCrossReference(lineInfo);
-		else if (lineIdentifier.equals("RG"))
-			emblReference.setReferenceGroup(lineInfo);
-		else if (lineIdentifier.equals("RA"))
-			emblReference.setReferenceAuthor(lineInfo);
-		else if (lineIdentifier.equals("RT"))
-			emblReference.setReferenceTitle(lineInfo);
-		else if (lineIdentifier.equals("RL")) {
-			emblReference.setReferenceLocation(lineInfo);
-			emblReferences.add(emblReference.copyEmblReference(emblReference));
-		}
+        switch (lineIdentifier) {
+            case "RN":
+                emblReference.setReferenceNumber(lineInfo);
+                break;
+            case "RP":
+                emblReference.setReferencePosition(lineInfo);
+                break;
+            case "RX":
+                emblReference.setReferenceCrossReference(lineInfo);
+                break;
+            case "RG":
+                emblReference.setReferenceGroup(lineInfo);
+                break;
+            case "RA":
+                emblReference.setReferenceAuthor(lineInfo);
+                break;
+            case "RT":
+                emblReference.setReferenceTitle(lineInfo);
+                break;
+            case "RL":
+                emblReference.setReferenceLocation(lineInfo);
+                emblReferences.add(emblReference.copyEmblReference(emblReference));
+                break;
+        }
 	}
 
 	private static void populateAccessionNumber(String line, LinkedList<String> accessionNumber) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java
index a0bb6af6d3..5b1937a2d5 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java
@@ -35,5 +35,5 @@ public interface FastaHeaderFormatInterface<S extends Sequence<?>, C extends Com
 	 * @param sequence
 	 * @return
 	 */
-	public String getHeader(S sequence);
+    String getHeader(S sequence);
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java
index 5e08a424bf..6556845f08 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java
@@ -36,8 +36,8 @@ public interface GenbankHeaderFormatInterface<S extends Sequence<?>, C extends C
 	 * @param sequence
 	 * @return
 	 */
-	public static final String UNKNOWN_DNA = "UNK";
+    String UNKNOWN_DNA = "UNK";
 
-	public String getHeader(S sequence);
+	String getHeader(S sequence);
 
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java
index 9ec26dc225..0f9730decd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java
@@ -43,7 +43,7 @@ public interface SequenceCreatorInterface<C extends Compound> {
 	 * @throws CompoundNotFoundException
 	 * @throws IOException
 	 */
-	public AbstractSequence<C> getSequence(String sequence, long index) throws CompoundNotFoundException, IOException;
+    AbstractSequence<C> getSequence(String sequence, long index) throws CompoundNotFoundException, IOException;
 
 	/**
 	 *
@@ -51,13 +51,13 @@ public interface SequenceCreatorInterface<C extends Compound> {
 	 * @param index
 	 * @return
 	 */
-	public AbstractSequence<C> getSequence(ProxySequenceReader<C> proxyLoader, long index);
+    AbstractSequence<C> getSequence(ProxySequenceReader<C> proxyLoader, long index);
 
 	/**
 	 *
 	 * @param list
 	 * @return
 	 */
-	public AbstractSequence<C> getSequence(List<C> list);
+    AbstractSequence<C> getSequence(List<C> list);
 
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java
index dba9d7ca3d..f501543176 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java
@@ -35,5 +35,5 @@ public interface SequenceHeaderParserInterface<S extends Sequence<?>, C extends
 	 * @param header
 	 * @param sequence
 	 */
-	public void parseHeader(String header, S sequence);
+    void parseHeader(String header, S sequence);
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
index fd536e2802..af982f4846 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
@@ -37,5 +37,5 @@ public interface SequenceParserInterface {
 	 * @return
 	 * @throws Exception
 	 */
-	public String getSequence(BufferedReader bufferedReader,int sequenceLength) throws IOException;
+    String getSequence(BufferedReader bufferedReader, int sequenceLength) throws IOException;
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java
index a798fcc6c3..dbd2a29245 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java
@@ -70,7 +70,7 @@ public static void close(Closeable c) {
 	public static void copy(InputStream input, OutputStream output)
 			throws IOException {
 		byte[] buffer = new byte[BUFFER];
-		int n = 0;
+		int n;
 		while (-1 != (n = input.read(buffer))) {
 			output.write(buffer, 0, n);
 		}
@@ -110,13 +110,8 @@ public static void processReader(BufferedReader br, ReaderProcessor processor) t
 	 * @throws ParserException Can throw this if we cannot parse the given reader
 	 */
 	public static List<String> getList(BufferedReader br) throws ParserException {
-		final List<String> list = new ArrayList<String>();
-		processReader(br, new ReaderProcessor() {
-			@Override
-			public void process(String line) {
-				list.add(line);
-			}
-		});
+		final List<String> list = new ArrayList<>();
+		processReader(br, line -> list.add(line));
 		return list;
 	}
 
@@ -183,8 +178,8 @@ public static InputStream openFile(File file) throws IOException {
 	 *
 	 * @author ayates
 	 */
-	public static interface ReaderProcessor {
-		void process(String line) throws IOException;
+	public interface ReaderProcessor {
+		void process(String line);
 	}
 
 	/**
@@ -330,14 +325,10 @@ public static String getPDBLegend() {
 	 * @throws IOException If any I/O exception occurs while printing; this method does not catch any exceptions
 	 */
 	public static void print(String string, File file) throws IOException {
-		PrintWriter out = null;
-		try {
-			out = new PrintWriter(new BufferedWriter(new FileWriter(file)));
+		try (PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(file)))) {
 			out.print(string);
 			out.flush();
 			out.close();
-		} finally {
-			if (out != null) out.close();
 		}
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
index 2b74f9cacd..93233c3e91 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
@@ -69,10 +69,10 @@ public class GenbankProxySequenceReader<C extends Compound> extends StringProxyS
 
 	private static final String eutilBaseURL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"; //
 	private String genbankDirectoryCache = null;
-	private GenbankSequenceParser<AbstractSequence<C>, C> genbankParser;
-	private GenericGenbankHeaderParser<AbstractSequence<C>, C> headerParser;
-	private String header;
-	private HashMap<String, ArrayList<AbstractFeature>> features;
+	private final GenbankSequenceParser<AbstractSequence<C>, C> genbankParser;
+	private final GenericGenbankHeaderParser<AbstractSequence<C>, C> headerParser;
+	private final String header;
+	private final HashMap<String, ArrayList<AbstractFeature>> features;
 
 
 	/**
@@ -92,7 +92,7 @@ public GenbankProxySequenceReader(
 		String db = compoundSet instanceof AminoAcidCompoundSet ? "protein" : "nuccore";
 
 		InputStream inStream = getBufferedInputStream(accessionID, db);
-		genbankParser = new GenbankSequenceParser<AbstractSequence<C>, C>();
+		genbankParser = new GenbankSequenceParser<>();
 
 		setContents(genbankParser.getSequence(new BufferedReader(new InputStreamReader(inStream)), 0));
 		headerParser = genbankParser.getSequenceHeaderParser();
@@ -110,7 +110,7 @@ public GenbankProxySequenceReader(
 	}
 
 	private BufferedInputStream getBufferedInputStream(String accessionID, String db) throws IOException, InterruptedException {
-		BufferedInputStream inStream = null;
+		BufferedInputStream inStream;
 		if (genbankDirectoryCache != null && genbankDirectoryCache.length() > 0) {
 			File f = new File(genbankDirectoryCache + File.separatorChar + accessionID + ".gb");
 			if (f.exists()) {
@@ -199,7 +199,7 @@ public ArrayList<String> getKeyWords() {
 	public static void main(String[] args) throws Throwable {
 
 		GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
-				= new GenbankProxySequenceReader<AminoAcidCompound>("/tmp", "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+				= new GenbankProxySequenceReader<>("/tmp", "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
 		ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
 		genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
 		logger.info("Sequence ({},{})={}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
@@ -208,7 +208,7 @@ public static void main(String[] args) throws Throwable {
 		proteinSequence.getFeatures();
 
 		GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
-				= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "NM_001126", DNACompoundSet.getDNACompoundSet());
+				= new GenbankProxySequenceReader<>("/tmp", "NM_001126", DNACompoundSet.getDNACompoundSet());
 		DNASequence dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		dnaSequence.setAccession(new AccessionID("NM_001126"));
@@ -217,7 +217,7 @@ public static void main(String[] args) throws Throwable {
 		logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
 
 		genbankDNAReader
-				= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "NM_000266", DNACompoundSet.getDNACompoundSet());
+				= new GenbankProxySequenceReader<>("/tmp", "NM_000266", DNACompoundSet.getDNACompoundSet());
 		dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
@@ -225,7 +225,7 @@ public static void main(String[] args) throws Throwable {
 		logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
 
 		genbankDNAReader
-				= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "AV254721", DNACompoundSet.getDNACompoundSet());
+				= new GenbankProxySequenceReader<>("/tmp", "AV254721", DNACompoundSet.getDNACompoundSet());
 		dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
@@ -233,7 +233,7 @@ public static void main(String[] args) throws Throwable {
 		logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
 
 		genbankDNAReader
-				= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "AV254721.2", DNACompoundSet.getDNACompoundSet());
+				= new GenbankProxySequenceReader<>("/tmp", "AV254721.2", DNACompoundSet.getDNACompoundSet());
 		dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
@@ -241,7 +241,7 @@ public static void main(String[] args) throws Throwable {
 		logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
 
 		genbankDNAReader
-				= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "U49845", DNACompoundSet.getDNACompoundSet());
+				= new GenbankProxySequenceReader<>("/tmp", "U49845", DNACompoundSet.getDNACompoundSet());
 		dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
@@ -249,7 +249,7 @@ public static void main(String[] args) throws Throwable {
 		logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
 
 		genbankDNAReader
-				= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "GI:1293613", DNACompoundSet.getDNACompoundSet());
+				= new GenbankProxySequenceReader<>("/tmp", "GI:1293613", DNACompoundSet.getDNACompoundSet());
 		dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
@@ -257,7 +257,7 @@ public static void main(String[] args) throws Throwable {
 		logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
 
 		genbankDNAReader
-				= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "14109166", DNACompoundSet.getDNACompoundSet());
+				= new GenbankProxySequenceReader<>("/tmp", "14109166", DNACompoundSet.getDNACompoundSet());
 		dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
index 78c08b7795..c7fe81733f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
@@ -57,10 +57,10 @@ public class SequenceFileProxyLoader<C extends Compound> implements ProxySequenc
 
 	SequenceParserInterface sequenceParser;
 	private CompoundSet<C> compoundSet;
-	private List<C> parsedCompounds = new ArrayList<C>();
+	private final List<C> parsedCompounds = new ArrayList<>();
 	File file;
-	long sequenceStartIndex = -1;
-	int sequenceLength = -1;
+	long sequenceStartIndex;
+	int sequenceLength;
 	//private boolean initialized = false;
 
 	/**
@@ -204,7 +204,7 @@ public String getSequenceAsString() {
 	 */
 	public String getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand strand) {
 
-		SequenceAsStringHelper<C> sequenceAsStringHelper = new SequenceAsStringHelper<C>();
+		SequenceAsStringHelper<C> sequenceAsStringHelper = new SequenceAsStringHelper<>();
 		return sequenceAsStringHelper.getSequenceAsString(this.parsedCompounds, compoundSet, bioBegin, bioEnd, strand);
 	}
 
@@ -260,7 +260,7 @@ public int hashCode(){
 	@Override
 	public SequenceView<C> getSubSequence(final Integer bioBegin, final Integer bioEnd) {
 
-		return new SequenceProxyView<C>(SequenceFileProxyLoader.this, bioBegin, bioEnd);
+		return new SequenceProxyView<>(SequenceFileProxyLoader.this, bioBegin, bioEnd);
 	}
 
 	/**
@@ -296,8 +296,9 @@ public AccessionID getAccession() {
 	 * @param compounds
 	 * @return
 	 */
+	@SafeVarargs
 	@Override
-	public int countCompounds(C... compounds) {
+	public final int countCompounds(C... compounds) {
 		return SequenceMixin.countCompounds(this, compounds);
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
index 57c793ddc1..ee16f3c1d3 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
@@ -46,7 +46,7 @@ public class StringProxySequenceReader<C extends Compound> implements ProxySeque
 
 	private String sequence;
 	private CompoundSet<C> compoundSet;
-	private List<C> parsedCompounds = new ArrayList<C>();
+	private final List<C> parsedCompounds = new ArrayList<>();
 
 	public StringProxySequenceReader() {}
 
@@ -126,13 +126,13 @@ public List<C> getAsList() {
 
 
 	public String getSequenceAsString(Integer bioBegin, Integer bioEnd,Strand strand) {
-		SequenceAsStringHelper<C> sequenceAsStringHelper = new SequenceAsStringHelper<C>();
+		SequenceAsStringHelper<C> sequenceAsStringHelper = new SequenceAsStringHelper<>();
 		return sequenceAsStringHelper.getSequenceAsString(this.parsedCompounds, compoundSet, bioBegin, bioEnd, strand);
 	}
 
 	@Override
 	public SequenceView<C> getSubSequence(final Integer bioBegin, final Integer bioEnd) {
-		return new SequenceProxyView<C>(StringProxySequenceReader.this,bioBegin,bioEnd);
+		return new SequenceProxyView<>(StringProxySequenceReader.this, bioBegin, bioEnd);
 	}
 
 	@Override
@@ -152,8 +152,9 @@ public AccessionID getAccession() {
 	}
 
 
+	@SafeVarargs
 	@Override
-	public int countCompounds(C... compounds) {
+	public final int countCompounds(C... compounds) {
 		throw new UnsupportedOperationException("Not supported yet.");
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
index f7f51d89bb..f0ca633ab5 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
@@ -82,7 +82,7 @@ public class UniprotProxySequenceReader<C extends Compound> implements ProxySequ
 	private static String uniprotDirectoryCache = null;
 	private String sequence;
 	private CompoundSet<C> compoundSet;
-	private List<C> parsedCompounds = new ArrayList<C>();
+	private final List<C> parsedCompounds = new ArrayList<>();
 	Document uniprotDoc;
 
 	/**
@@ -128,7 +128,7 @@ public UniprotProxySequenceReader(Document document, CompoundSet<C> compoundSet)
 	public static <C extends Compound> UniprotProxySequenceReader<C> parseUniprotXMLString(String xml, CompoundSet<C> compoundSet) {
 		try {
 			Document document = XMLHelper.inputStreamToDocument(new ByteArrayInputStream(xml.getBytes()));
-			return new UniprotProxySequenceReader<C>(document, compoundSet);
+			return new UniprotProxySequenceReader<>(document, compoundSet);
 		} catch (Exception e) {
 			logger.error("Exception on xml parse of: {}", xml);
 		}
@@ -284,7 +284,7 @@ public SequenceView<C> getInverse() {
 	 * @return
 	 */
 	public String getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand strand) {
-		SequenceAsStringHelper<C> sequenceAsStringHelper = new SequenceAsStringHelper<C>();
+		SequenceAsStringHelper<C> sequenceAsStringHelper = new SequenceAsStringHelper<>();
 		return sequenceAsStringHelper.getSequenceAsString(this.parsedCompounds, compoundSet, bioBegin, bioEnd, strand);
 	}
 
@@ -296,7 +296,7 @@ public String getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand stran
 	 */
 	@Override
 	public SequenceView<C> getSubSequence(final Integer bioBegin, final Integer bioEnd) {
-		return new SequenceProxyView<C>(UniprotProxySequenceReader.this, bioBegin, bioEnd);
+		return new SequenceProxyView<>(UniprotProxySequenceReader.this, bioBegin, bioEnd);
 	}
 
 	/**
@@ -344,7 +344,7 @@ public AccessionID getAccession() {
 	 * @throws XPathExpressionException
 	 */
 	public ArrayList<AccessionID> getAccessions() throws XPathExpressionException {
-		ArrayList<AccessionID> accessionList = new ArrayList<AccessionID>();
+		ArrayList<AccessionID> accessionList = new ArrayList<>();
 		if (uniprotDoc == null) {
 			return accessionList;
 		}
@@ -376,7 +376,7 @@ public ArrayList<String> getAliases() throws XPathExpressionException {
 	 * @throws XPathExpressionException
 	 */
 	public ArrayList<String> getProteinAliases() throws XPathExpressionException {
-		ArrayList<String> aliasList = new ArrayList<String>();
+		ArrayList<String> aliasList = new ArrayList<>();
 		if (uniprotDoc == null) {
 			return aliasList;
 		}
@@ -479,7 +479,7 @@ private void getProteinAliasesFromElement(ArrayList<String> aliasList, Element e
 	 * @throws XPathExpressionException
 	 */
 	public ArrayList<String> getGeneAliases() throws XPathExpressionException {
-		ArrayList<String> aliasList = new ArrayList<String>();
+		ArrayList<String> aliasList = new ArrayList<>();
 		if (uniprotDoc == null) {
 			return aliasList;
 		}
@@ -500,8 +500,9 @@ public ArrayList<String> getGeneAliases() throws XPathExpressionException {
 	 * @param compounds
 	 * @return
 	 */
+	@SafeVarargs
 	@Override
-	public int countCompounds(C... compounds) {
+	public final int countCompounds(C... compounds) {
 		throw new UnsupportedOperationException("Not supported yet.");
 	}
 
@@ -538,9 +539,7 @@ private Document getUniprotXML(String accession) throws IOException, CompoundNot
 			//       logger.debug(sb.toString());
 			Document document = XMLHelper.inputStreamToDocument(new ByteArrayInputStream(sb.toString().getBytes()));
 			return document;
-		} catch (SAXException e) {
-			logger.error("Exception on xml parse of: {}", sb.toString());
-		} catch (ParserConfigurationException e) {
+		} catch (SAXException | ParserConfigurationException e) {
 			logger.error("Exception on xml parse of: {}", sb.toString());
 		}
 		return null;
@@ -609,12 +608,12 @@ private static HttpURLConnection openURLConnection(URL url) throws IOException {
 	}
 
 	private StringBuilder fetchUniprotXML(String uniprotURL)
-			throws IOException, CompoundNotFoundException {
+			throws IOException {
 
 		StringBuilder sb = new StringBuilder();
 		URL uniprot = new URL(uniprotURL);
 		int attempt = 5;
-		List<String> errorCodes = new ArrayList<String>();
+		List<String> errorCodes = new ArrayList<>();
 		while(attempt > 0) {
 			HttpURLConnection uniprotConnection = openURLConnection(uniprot);
 			int statusCode = uniprotConnection.getResponseCode();
@@ -722,7 +721,7 @@ public static void setUniprotDirectoryCache(String aUniprotDirectoryCache) {
 	public static void main(String[] args) {
 
 		try {
-			UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<AminoAcidCompound>("YA745_GIBZE", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+			UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<>("YA745_GIBZE", AminoAcidCompoundSet.getAminoAcidCompoundSet());
 			ProteinSequence proteinSequence = new ProteinSequence(uniprotSequence);
 			logger.info("Accession: {}", proteinSequence.getAccession().getID());
 			logger.info("Sequence: {}", proteinSequence.getSequenceAsString());
@@ -791,7 +790,7 @@ public String getOrganismName() {
 	 */
 	@Override
 	public ArrayList<String> getKeyWords() {
-		ArrayList<String> keyWordsList = new ArrayList<String>();
+		ArrayList<String> keyWordsList = new ArrayList<>();
 		if (uniprotDoc == null) {
 			return keyWordsList;
 		}
@@ -805,7 +804,7 @@ public ArrayList<String> getKeyWords() {
 			}
 		} catch (XPathExpressionException e) {
 			logger.error("Problems while parsing keywords in UniProt XML: {}. No keywords will be available.",e.getMessage());
-			return new ArrayList<String>();
+			return new ArrayList<>();
 		}
 
 		return keyWordsList;
@@ -817,7 +816,7 @@ public ArrayList<String> getKeyWords() {
 	 */
 	@Override
 	public LinkedHashMap<String, ArrayList<DBReferenceInfo>> getDatabaseReferences()  {
-		LinkedHashMap<String, ArrayList<DBReferenceInfo>> databaseReferencesHashMap = new LinkedHashMap<String, ArrayList<DBReferenceInfo>>();
+		LinkedHashMap<String, ArrayList<DBReferenceInfo>> databaseReferencesHashMap = new LinkedHashMap<>();
 		if (uniprotDoc == null) {
 			return databaseReferencesHashMap;
 		}
@@ -829,11 +828,7 @@ public LinkedHashMap<String, ArrayList<DBReferenceInfo>> getDatabaseReferences()
 			for (Element element : dbreferenceElementList) {
 				String type = element.getAttribute("type");
 				String id = element.getAttribute("id");
-				ArrayList<DBReferenceInfo> idlist = databaseReferencesHashMap.get(type);
-				if (idlist == null) {
-					idlist = new ArrayList<DBReferenceInfo>();
-					databaseReferencesHashMap.put(type, idlist);
-				}
+				ArrayList<DBReferenceInfo> idlist = databaseReferencesHashMap.computeIfAbsent(type, k -> new ArrayList<>());
 				DBReferenceInfo dbreferenceInfo = new DBReferenceInfo(type, id);
 				ArrayList<Element> propertyElementList = XMLHelper.selectElements(element, "property");
 				for (Element propertyElement : propertyElementList) {
@@ -846,7 +841,7 @@ public LinkedHashMap<String, ArrayList<DBReferenceInfo>> getDatabaseReferences()
 			}
 		} catch (XPathExpressionException e) {
 			logger.error("Problems while parsing db references in UniProt XML: {}. No db references will be available.",e.getMessage());
-			return new LinkedHashMap<String, ArrayList<DBReferenceInfo>>();
+			return new LinkedHashMap<>();
 		}
 
 		return databaseReferencesHashMap;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java
index 7a97c7ad1c..8dc999a66d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java
@@ -36,32 +36,17 @@ public class FuzzyPoint extends SimplePoint {
 	/**
 	 * Always uses the min point to resolve a location
 	 */
-	public static final Resolver<FuzzyPoint> MIN_RESOLVER = new Resolver<FuzzyPoint>() {
-		@Override
-		public int resolve(FuzzyPoint point) {
-			return point.getMin();
-		}
-	};
+	public static final Resolver<FuzzyPoint> MIN_RESOLVER = point -> point.getMin();
 
 	/**
 	 * Always uses the max point to resolve a location
 	 */
-	public static final Resolver<FuzzyPoint> MAX_RESOLVER = new Resolver<FuzzyPoint>() {
-		@Override
-		public int resolve(FuzzyPoint point) {
-			return point.getMax();
-		}
-	};
+	public static final Resolver<FuzzyPoint> MAX_RESOLVER = point -> point.getMax();
 
 	/**
 	 * Combines min and max and then gets the mean of it
 	 */
-	public static final Resolver<FuzzyPoint> MEAN_RESOLVER = new Resolver<FuzzyPoint>() {
-		@Override
-		public int resolve(FuzzyPoint point) {
-			return (point.getMin() + point.getMax()) / 2;
-		}
-	};
+	public static final Resolver<FuzzyPoint> MEAN_RESOLVER = point -> (point.getMin() + point.getMax()) / 2;
 
 	private final int min;
 	private final int max;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
index 2e8217ea43..b2178c5ac9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
@@ -59,7 +59,7 @@ public class InsdcParser <S extends AbstractSequence<C>, C extends Compound>{
 	//protected static final Pattern singleLocationPattern = Pattern.compile("(?:[A-Z]([A-Za-z\\.0-9_]*?):)?(<?)(\\d+)(\\.{2}|\\^)?(>?)(\\d+)?(>?)?");
 
 	// fixed issue #254
-	protected static final Pattern singleLocationPattern = Pattern.compile("(?:([A-Za-z\\.0-9_]*?):)?(<?)(\\d+)(\\.{2}|\\^)?(>?)(\\d+)?(>?)?");
+	protected static final Pattern singleLocationPattern = Pattern.compile("(?:([A-Za-z.0-9_]*?):)?(<?)(\\d+)(\\.{2}|\\^)?(>?)(\\d+)?(>?)?");
 	/**
 	 * Decodes a split pattern. Split patterns are a composition of multiple
 	 * locationsString qualified by actions: join(location,location, ...
@@ -96,11 +96,11 @@ public class InsdcParser <S extends AbstractSequence<C>, C extends Compound>{
 	protected Integer featureGlobalStart, featureGlobalEnd;
 
 	//private S referenceSequence = new org.biojava.nbio.core.sequence.DNASequence();
-	private AbstractSequence referenceSequence = new DNASequence();
+	private final AbstractSequence referenceSequence = new DNASequence();
 
 	enum complexFeaturesAppendEnum {
 
-		FLATTEN, HIERARCHICAL;
+		FLATTEN, HIERARCHICAL
 	}
 	/**
 	 * define the mode in which complex features should be appended in FLATTEN
@@ -160,17 +160,16 @@ public Location parse(String locationString) throws ParserException {
 	 * @param reader The source of the data; assumes that end of the reader
 	 * stream is the end of the location string to parse
 	 * @return The parsed location
-	 * @throws IOException Thrown with any reader error
 	 * @throws ParserException Thrown with any error with parsing locations
 	 */
-	public List<AbstractLocation> parse(Reader reader) throws IOException, ParserException {
+	public List<AbstractLocation> parse(Reader reader) throws ParserException {
 		// use parse(String s) instead!
 		return null;
 	}
 
 	private List<Location> parseLocationString(String string, int versus) throws ParserException {
 		Matcher m;
-		List<Location> boundedLocationsCollection = new ArrayList<Location>();
+		List<Location> boundedLocationsCollection = new ArrayList<>();
 
 		//String[] tokens = string.split(locationSplitPattern);
 		List<String> tokens = splitString(string);
@@ -265,7 +264,7 @@ private List<Location> parseLocationString(String string, int versus) throws Par
 
 
 	private List<String> splitString(String input) {
-		List<String> result = new ArrayList<String>();
+		List<String> result = new ArrayList<>();
 		int start = 0;
 		int openedParenthesis = 0;
 		for (int current = 0; current < input.length(); current++) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java
index efb02f6c64..e2a405badf 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java
@@ -153,7 +153,7 @@ public static Location circularLocation(int start, int end, Strand strand, int l
 			end = (length * (numberOfPasses + 1)) + modEnd;
 		}
 
-		List<Location> locations = new ArrayList<Location>();
+		List<Location> locations = new ArrayList<>();
 		locations.add(new SimpleLocation(modStart, length, strand));
 		for (int i = 0; i < numberOfPasses; i++) {
 			locations.add(new SimpleLocation(1, length, strand));
@@ -163,7 +163,7 @@ public static Location circularLocation(int start, int end, Strand strand, int l
 				new SimplePoint(end), strand, true, false, locations);
 	}
 
-	private static interface LocationPredicate {
+	private interface LocationPredicate {
 		boolean accept(Location previous, Location current);
 	}
 
@@ -172,12 +172,9 @@ private static interface LocationPredicate {
 	 * lowest start
 	 */
 	public static Location getMin(List<Location> locations) {
-		return scanLocations(locations, new LocationPredicate() {
-			@Override
-			public boolean accept(Location previous, Location current) {
-				int res = current.getStart().compareTo(previous.getStart());
-				return res < 0;
-			}
+		return scanLocations(locations, (previous, current) -> {
+			int res = current.getStart().compareTo(previous.getStart());
+			return res < 0;
 		});
 	}
 
@@ -186,12 +183,9 @@ public boolean accept(Location previous, Location current) {
 	 * highest end
 	 */
 	public static Location getMax(List<Location> locations) {
-		return scanLocations(locations, new LocationPredicate() {
-			@Override
-			public boolean accept(Location previous, Location current) {
-				int res = current.getEnd().compareTo(previous.getEnd());
-				return res > 0;
-			}
+		return scanLocations(locations, (previous, current) -> {
+			int res = current.getEnd().compareTo(previous.getEnd());
+			return res > 0;
 		});
 	}
 
@@ -283,7 +277,7 @@ public static boolean detectCicular(List<Location> subLocations) {
 	 * @return Returns a boolean indicating if this is consistently accessioned
 	 */
 	public static boolean consistentAccessions(List<Location> subLocations) {
-		Set<AccessionID> set = new HashSet<AccessionID>();
+		Set<AccessionID> set = new HashSet<>();
 		for(Location sub: subLocations) {
 			set.add(sub.getAccession());
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimpleLocation.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimpleLocation.java
index 2175ba4282..f0bdd8a438 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimpleLocation.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimpleLocation.java
@@ -61,7 +61,7 @@ public SimpleLocation(int start, int end, Strand strand, List<Location> subLocat
 
 	public SimpleLocation(Point start, Point end, Strand strand) {
 
-		super(start, end, strand, false, false, new ArrayList<Location>());
+		super(start, end, strand, false, false, new ArrayList<>());
 	}
 
 	public SimpleLocation(Point start, Point end, Strand strand, AccessionID accession) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
index 10ee98d1e8..11a16ccb9b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
@@ -224,7 +224,7 @@ public Iterator<Location> iterator() {
 			list = getSubLocations();
 		}
 		else {
-			list = new ArrayList<Location>();
+			list = new ArrayList<>();
 			list.add(this);
 		}
 		return list.iterator();
@@ -245,7 +245,7 @@ public List<Location> getRelevantSubLocations() {
 	 * Here to allow for recursion
 	 */
 	private List<Location> getAllSubLocations(Location location) {
-		List<Location> flatSubLocations = new ArrayList<Location>();
+		List<Location> flatSubLocations = new ArrayList<>();
 		for (Location l : location.getSubLocations()) {
 			if (l.isComplex()) {
 				flatSubLocations.addAll(getAllSubLocations(l));
@@ -311,11 +311,11 @@ public boolean isBetweenCompounds() {
 	@Override
 	public <C extends Compound> Sequence<C> getSubSequence(Sequence<C> sequence) {
 		if(isCircular()) {
-			List<Sequence<C>> sequences = new ArrayList<Sequence<C>>();
+			List<Sequence<C>> sequences = new ArrayList<>();
 			for(Location l: this) {
 				sequences.add(l.getSubSequence(sequence));
 			}
-			return new JoiningSequenceReader<C>(sequence.getCompoundSet(), sequences);
+			return new JoiningSequenceReader<>(sequence.getCompoundSet(), sequences);
 		}
 		return reverseSequence(sequence.getSubSequence(
 				getStart().getPosition(), getEnd().getPosition()));
@@ -327,11 +327,11 @@ public <C extends Compound> Sequence<C> getSubSequence(Sequence<C> sequence) {
 
 	@Override
 	public <C extends Compound> Sequence<C> getRelevantSubSequence(Sequence<C> sequence) {
-		List<Sequence<C>> sequences = new ArrayList<Sequence<C>>();
+		List<Sequence<C>> sequences = new ArrayList<>();
 		for(Location l: getRelevantSubLocations()) {
 			sequences.add(l.getSubSequence(sequence));
 		}
-		return new JoiningSequenceReader<C>(sequence.getCompoundSet(), sequences);
+		return new JoiningSequenceReader<>(sequence.getCompoundSet(), sequences);
 	}
 
 	/**
@@ -345,12 +345,12 @@ protected <C extends Compound> Sequence<C> reverseSequence(Sequence<C> sequence)
 			return sequence;
 		}
 
-		Sequence<C> reversed = new ReversedSequenceView<C>(sequence);
+		Sequence<C> reversed = new ReversedSequenceView<>(sequence);
 		// "safe" operation as we have tried to check this
 		if(canComplement(sequence)) {
 			Sequence<ComplementCompound> casted = (Sequence<ComplementCompound>) reversed;
 			ComplementSequenceView<ComplementCompound> complement =
-					new ComplementSequenceView<ComplementCompound>(casted);
+					new ComplementSequenceView<>(casted);
 			return (Sequence<C>)complement;
 		}
 		return reversed;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java
index 25cdf48f05..d57cab35dd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java
@@ -45,7 +45,7 @@ public interface Location extends Iterable<Location>, Accessioned {
 	 * Basic location which is set to the minimum and maximum bounds of
 	 * {@link Integer}. {@link Strand} is set to {@link Strand#UNDEFINED}.
 	 */
-	public static final Location EMPTY =
+	Location EMPTY =
 			new SimpleLocation(Integer.MIN_VALUE, Integer.MAX_VALUE, Strand.UNDEFINED);
 
 	/**
@@ -128,7 +128,7 @@ public interface Location extends Iterable<Location>, Accessioned {
 	 * Helper methods for use with the Location classes. Taking its
 	 * inspiration from the RichSequence.Tools class from the old BioJava
 	 */
-	public static class Tools {
+	class Tools {
 
 		/**
 		 * Used for building a location from a series of sub-locations
@@ -206,7 +206,7 @@ public static Location circularLocation(int start, int end, Strand strand, int l
 				end = (length * (numberOfPasses + 1)) + modEnd;
 			}
 
-			List<Location> locations = new ArrayList<Location>();
+			List<Location> locations = new ArrayList<>();
 			locations.add(new SimpleLocation(modStart, length, strand));
 			for (int i = 0; i < numberOfPasses; i++) {
 				locations.add(new SimpleLocation(1, length, strand));
@@ -216,7 +216,7 @@ public static Location circularLocation(int start, int end, Strand strand, int l
 					new SimplePoint(end), strand, true, false, locations);
 		}
 
-		private static interface LocationPredicate {
+		private interface LocationPredicate {
 
 			boolean accept(Location previous, Location current);
 		}
@@ -226,13 +226,9 @@ private static interface LocationPredicate {
 		 * lowest start
 		 */
 		public static Location getMin(List<Location> locations) {
-			return scanLocations(locations, new LocationPredicate() {
-
-				@Override
-				public boolean accept(Location previous, Location current) {
-					int res = current.getStart().compareTo(previous.getStart());
-					return res < 0;
-				}
+			return scanLocations(locations, (previous, current) -> {
+				int res = current.getStart().compareTo(previous.getStart());
+				return res < 0;
 			});
 		}
 
@@ -241,13 +237,9 @@ public boolean accept(Location previous, Location current) {
 		 * highest end
 		 */
 		public static Location getMax(List<Location> locations) {
-			return scanLocations(locations, new LocationPredicate() {
-
-				@Override
-				public boolean accept(Location previous, Location current) {
-					int res = current.getEnd().compareTo(previous.getEnd());
-					return res > 0;
-				}
+			return scanLocations(locations, (previous, current) -> {
+				int res = current.getEnd().compareTo(previous.getEnd());
+				return res > 0;
 			});
 		}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Point.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Point.java
index 52cefa711e..04cdd07398 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Point.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Point.java
@@ -29,7 +29,7 @@ public interface Point extends Comparable<Point> {
 	/**
 	 * Used to resolve a position about a point
 	 */
-	public interface Resolver<T extends Point> {
+    interface Resolver<T extends Point> {
 		int resolve(T point);
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java
index 48ecb8aff4..aa4356cd25 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java
@@ -44,7 +44,7 @@
 public class ArrayListSequenceReader<C extends Compound> implements SequenceReader<C> {
 
 	private CompoundSet<C> compoundSet;
-	private ArrayList<C> parsedCompounds = new ArrayList<C>();
+	private final ArrayList<C> parsedCompounds = new ArrayList<>();
 
 	private volatile Integer hashcode = null;
 
@@ -95,7 +95,7 @@ public String getSequenceAsString() {
 	 */
 	public String getSequenceAsString(Integer begin, Integer end, Strand strand) {
 		// TODO Optimise/cache.
-		SequenceAsStringHelper<C> sequenceAsStringHelper = new SequenceAsStringHelper<C>();
+		SequenceAsStringHelper<C> sequenceAsStringHelper = new SequenceAsStringHelper<>();
 		return sequenceAsStringHelper.getSequenceAsString(this.parsedCompounds, compoundSet, begin, end, strand);
 	}
 
@@ -182,15 +182,14 @@ public CompoundSet<C> getCompoundSet() {
 	public void setContents(String sequence) throws CompoundNotFoundException {
 		// Horrendously inefficient - pretty much the way the old BJ did things.
 		// TODO Should be optimised.
-		this.parsedCompounds.clear();
-		hashcode = null;
-		int maxCompoundLength = compoundSet.getMaxSingleCompoundStringLength();
-		boolean maxCompundLengthEqual1 = true;
-		if (maxCompoundLength > 1) {
-			maxCompundLengthEqual1 = false;
-		}
 		int length = sequence.length();
+		parsedCompounds.clear();
 		parsedCompounds.ensureCapacity(length); //get the array size correct
+
+		hashcode = null;
+		int maxCompoundLength = compoundSet.getMaxSingleCompoundStringLength();
+		boolean maxCompundLengthEqual1 = maxCompoundLength <= 1;
+
 		for (int i = 0; i < length;) {
 			String compoundStr = null;
 			C compound = null;
@@ -219,9 +218,7 @@ public void setContents(String sequence) throws CompoundNotFoundException {
 	 */
 	public void setContents(List<C> list) {
 		parsedCompounds.clear();
-		for (C c : list) {
-			parsedCompounds.add(c);
-		}
+		parsedCompounds.addAll(list);
 	}
 
 	/**
@@ -232,7 +229,7 @@ public void setContents(List<C> list) {
 	 */
 	@Override
 	public SequenceView<C> getSubSequence(final Integer bioBegin, final Integer bioEnd) {
-		return new SequenceProxyView<C>(ArrayListSequenceReader.this, bioBegin, bioEnd);
+		return new SequenceProxyView<>(ArrayListSequenceReader.this, bioBegin, bioEnd);
 	}
 
 	/**
@@ -249,8 +246,9 @@ public AccessionID getAccession() {
 	 * @param compounds
 	 * @return
 	 */
+	@SafeVarargs
 	@Override
-	public int countCompounds(C... compounds) {
+	public final int countCompounds(C... compounds) {
 		return SequenceMixin.countCompounds(this, compounds);
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
index 326c8589c8..d3922f8d3d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
@@ -75,15 +75,16 @@ public void setCompoundSet(CompoundSet<C> compoundSet) {
 	 * Class is immutable & so this is unsupported
 	 */
 	@Override
-	public void setContents(String sequence) throws CompoundNotFoundException {
+	public void setContents(String sequence) {
 		throw new UnsupportedOperationException(getClass().getSimpleName() + " is an immutable data structure; cannot reset contents");
 	}
 
 	/**
 	 * Counts the number of times a compound appears in this sequence store
 	 */
+	@SafeVarargs
 	@Override
-	public int countCompounds(C... compounds) {
+	public final int countCompounds(C... compounds) {
 		return SequenceMixin.countCompounds(this, compounds);
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.java
index 83f4c5dfd2..86bb3039a9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.java
@@ -43,7 +43,7 @@
 public class FourBitSequenceReader<C extends Compound> extends BitSequenceReader<C> {
 
 	public FourBitSequenceReader(Sequence<C> sequence) {
-		super(new FourBitArrayWorker<C>(sequence), sequence.getAccession());
+		super(new FourBitArrayWorker<>(sequence), sequence.getAccession());
 	}
 
 	public FourBitSequenceReader(String sequence, CompoundSet<C> compoundSet) {
@@ -51,7 +51,7 @@ public FourBitSequenceReader(String sequence, CompoundSet<C> compoundSet) {
 	}
 
 	public FourBitSequenceReader(String sequence, CompoundSet<C> compoundSet, AccessionID accession) {
-		super(new FourBitArrayWorker<C>(sequence, compoundSet), accession);
+		super(new FourBitArrayWorker<>(sequence, compoundSet), accession);
 	}
 
 	public FourBitSequenceReader(FourBitArrayWorker<C> worker) {
@@ -114,7 +114,7 @@ protected int compoundsPerDatatype() {
 		@Override
 		protected Map<C, Integer> generateCompoundsToIndex() {
 			final CompoundSet<C> cs = getCompoundSet();
-			Map<C, Integer> map = new HashMap<C, Integer>();
+			Map<C, Integer> map = new HashMap<>();
 			int index = 0;
 			for (C currentCompound : sortedCompounds(cs)) {
 				C upperCasedCompound = getOptionalUpperCasedCompound(currentCompound, cs);
@@ -132,7 +132,7 @@ protected Map<C, Integer> generateCompoundsToIndex() {
 		}
 
 		private C getOptionalUpperCasedCompound(C currentCompound, CompoundSet<C> cs) {
-			C upperCasedCompound = null;
+			C upperCasedCompound;
 			String upperCasedString = cs.getStringForCompound(currentCompound).toUpperCase();
 			if (cs.getCompoundForString(upperCasedString) == null) {
 				upperCasedCompound = currentCompound;
@@ -143,16 +143,11 @@ private C getOptionalUpperCasedCompound(C currentCompound, CompoundSet<C> cs) {
 		}
 
 		private List<C> sortedCompounds(final CompoundSet<C> cs) {
-			List<C> compounds = new ArrayList<C>(cs.getAllCompounds());
-			Collections.sort(compounds, new Comparator<C>() {
-
-
-				@Override
-				public int compare(C o1, C o2) {
-					String s1 = cs.getStringForCompound(o1);
-					String s2 = cs.getStringForCompound(o2);
-					return s1.compareTo(s2);
-				}
+			List<C> compounds = new ArrayList<>(cs.getAllCompounds());
+			compounds.sort((o1, o2) -> {
+				String s1 = cs.getStringForCompound(o1);
+				String s2 = cs.getStringForCompound(o2);
+				return s1.compareTo(s2);
 			});
 			return compounds;
 		}
@@ -165,7 +160,7 @@ public int compare(C o1, C o2) {
 		protected List<C> generateIndexToCompounds() {
 			CompoundSet<C> cs = getCompoundSet();
 			Map<C, Integer> lookup = getCompoundsToIndexLookup();
-			Map<Integer, C> tempMap = new HashMap<Integer, C>();
+			Map<Integer, C> tempMap = new HashMap<>();
 			//First get the reverse lookup working
 			for (C compound : lookup.keySet()) {
 				C upperCasedCompound = getOptionalUpperCasedCompound(compound, cs);
@@ -174,8 +169,8 @@ protected List<C> generateIndexToCompounds() {
 			}
 
 			//Then populate the results by going back through the sorted integer keys
-			List<C> compounds = new ArrayList<C>();
-			List<Integer> keys = new ArrayList<Integer>(tempMap.keySet());
+			List<C> compounds = new ArrayList<>();
+			List<Integer> keys = new ArrayList<>(tempMap.keySet());
 			Collections.sort(keys);
 			for (Integer key : keys) {
 				compounds.add(tempMap.get(key));
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
index 5c5a3999d9..4de2e003bf 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
@@ -61,6 +61,7 @@ public class JoiningSequenceReader<C extends Compound> implements ProxySequenceR
 	 * available during construction otherwise we will throw an illegal
 	 * state exception).
 	 */
+	@SafeVarargs
 	public JoiningSequenceReader(Sequence<C>... sequences) {
 		this(Arrays.asList(sequences));
 	}
@@ -76,6 +77,7 @@ public JoiningSequenceReader(List<Sequence<C>> sequences) {
 		this.compoundSet = grepCompoundSet();
 	}
 
+	@SafeVarargs
 	public JoiningSequenceReader(CompoundSet<C> compoundSet, Sequence<C>... sequences) {
 		this(compoundSet, Arrays.asList(sequences));
 	}
@@ -86,7 +88,7 @@ public JoiningSequenceReader(CompoundSet<C> compoundSet, List<Sequence<C>> seque
 	}
 
 	private List<Sequence<C>> grepSequences(List<Sequence<C>> sequences) {
-		List<Sequence<C>> seqs = new ArrayList<Sequence<C>>();
+		List<Sequence<C>> seqs = new ArrayList<>();
 		for (Sequence<C> s : sequences) {
 			if (s.getLength() != 0) {
 				seqs.add(s);
@@ -277,13 +279,14 @@ public void setCompoundSet(CompoundSet<C> compoundSet) {
 
 
 	@Override
-	public void setContents(String sequence) throws CompoundNotFoundException {
+	public void setContents(String sequence) {
 		throw new UnsupportedOperationException();
 	}
 
 
+	@SafeVarargs
 	@Override
-	public int countCompounds(C... compounds) {
+	public final int countCompounds(C... compounds) {
 		return SequenceMixin.countCompounds(this, compounds);
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
index 554b7b8361..23db800fd5 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
@@ -74,7 +74,7 @@ public void setCompoundSet(CompoundSet<C> compoundSet) {
 	 */
 
 	@Override
-	public void setContents(String sequence) throws CompoundNotFoundException {
+	public void setContents(String sequence) {
 		throw new UnsupportedOperationException("Not supported.");
 	}
 
@@ -146,7 +146,7 @@ public List<C> getAsList() {
 
 	@Override
 	public SequenceView<C> getSubSequence(Integer start, Integer end) {
-		return new SequenceProxyView<C>(this, start, end);
+		return new SequenceProxyView<>(this, start, end);
 	}
 
 	/**
@@ -171,8 +171,9 @@ public AccessionID getAccession() {
 	 * Delegates to {@link SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) }
 	 */
 
+	@SafeVarargs
 	@Override
-	public int countCompounds(C... compounds) {
+	public final int countCompounds(C... compounds) {
 		return SequenceMixin.countCompounds(this, compounds);
 	}
 
@@ -182,7 +183,7 @@ public int countCompounds(C... compounds) {
 
 	@Override
 	public Iterator<C> iterator() {
-		return new SequenceMixin.SequenceIterator<C>(this);
+		return new SequenceMixin.SequenceIterator<>(this);
 	}
 
 	@Override
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/TwoBitSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/TwoBitSequenceReader.java
index c73482d04b..c17a634309 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/TwoBitSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/TwoBitSequenceReader.java
@@ -50,7 +50,7 @@
 public class TwoBitSequenceReader<C extends NucleotideCompound> extends BitSequenceReader<C> {
 
 	public TwoBitSequenceReader(Sequence<C> sequence) {
-		super(new TwoBitArrayWorker<C>(sequence), sequence.getAccession());
+		super(new TwoBitArrayWorker<>(sequence), sequence.getAccession());
 	}
 
 	public TwoBitSequenceReader(String sequence, CompoundSet<C> compoundSet) {
@@ -58,7 +58,7 @@ public TwoBitSequenceReader(String sequence, CompoundSet<C> compoundSet) {
 	}
 
 	public TwoBitSequenceReader(String sequence, CompoundSet<C> compoundSet, AccessionID accession) {
-		super(new TwoBitArrayWorker<C>(sequence, compoundSet), accession);
+		super(new TwoBitArrayWorker<>(sequence, compoundSet), accession);
 	}
 
 	public TwoBitSequenceReader(TwoBitArrayWorker<C> worker) {
@@ -138,7 +138,7 @@ protected Map<C, Integer> generateCompoundsToIndex() {
 		@Override
 		protected List<C> generateIndexToCompounds() {
 			CompoundSet<C> cs = getCompoundSet();
-			List<C> result = new ArrayList<C>();
+			List<C> result = new ArrayList<>();
 			result.add( cs.getCompoundForString("T"));
 
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
index 579153a2fd..08415bb48b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
@@ -39,11 +39,11 @@ public abstract class AbstractCompoundSet<C extends Compound> implements Compoun
 
 	private final static Logger logger = LoggerFactory.getLogger(AbstractCompoundSet.class);
 
-	private Map<CharSequence, C> charSeqToCompound = new HashMap<CharSequence, C>();
+	private final Map<CharSequence, C> charSeqToCompound = new HashMap<>();
 	private int maxCompoundCharSequenceLength = -1;
 	private Boolean compoundStringLengthEqual = null;
 
-	Map<C,Set<C>> equivalentsMap = new HashMap<C, Set<C>>();
+	Map<C,Set<C>> equivalentsMap = new HashMap<>();
 
 	protected void addCompound(C compound, C lowerCasedCompound, Iterable<C> equivalents) {
 		addCompound(compound);
@@ -60,18 +60,15 @@ protected void addCompound(C compound, C lowerCasedCompound, Iterable<C> equival
 		}
 	}
 
-	protected void addCompound(C compound, C lowerCasedCompound, C... equivalents) {
-		List<C> equiv = new ArrayList<C>(equivalents.length);
+	@SafeVarargs
+	protected final void addCompound(C compound, C lowerCasedCompound, C... equivalents) {
+		List<C> equiv = new ArrayList<>(equivalents.length);
 		equiv.addAll(Arrays.asList(equivalents));
 		addCompound(compound, lowerCasedCompound, equiv);
 	}
 
 	protected void addEquivalent(C compound, C equivalent) {
-	 Set<C> s = equivalentsMap.get(compound);
-	 if ( s == null){
-		 s = new HashSet<C>();
-		 equivalentsMap.put(compound, s);
-	 }
+		Set<C> s = equivalentsMap.computeIfAbsent(compound, k -> new HashSet<>());
 
 		s.add( equivalent);
 	}
@@ -170,7 +167,7 @@ public boolean isValidSequence(Sequence<C> sequence) {
 
 	@Override
 public List<C> getAllCompounds() {
-		return new ArrayList<C>(charSeqToCompound.values());
+		return new ArrayList<>(charSeqToCompound.values());
 	}
 
 	private void assertCompound(C compound) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.java
index e11af2b1de..cdfde5944f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.java
@@ -37,7 +37,7 @@ public abstract class AbstractCompoundTranslator<F extends Compound, T extends C
 	public AbstractCompoundTranslator(SequenceCreatorInterface<T> creator,
 			CompoundSet<F> fromCompoundSet, CompoundSet<T> toCompoundSet) {
 		this.creator = creator;
-		this.mapper = new HashMap<F, List<T>>();
+		this.mapper = new HashMap<>();
 		this.fromCompoundSet = fromCompoundSet;
 		this.toCompoundSet = toCompoundSet;
 	}
@@ -62,14 +62,11 @@ protected void addStrings(String source, String... targets) {
 		}
 	}
 
-	protected void addCompounds(F source, T... targets) {
+	@SafeVarargs
+	protected final void addCompounds(F source, T... targets) {
 
-	 List<T> l = mapper.get(source);
-	 if ( l == null) {
-		 l = new ArrayList<T>();
-		 mapper.put(source, l);
-	 }
-		 l.addAll(Arrays.asList(targets));
+		List<T> l = mapper.computeIfAbsent(source, k -> new ArrayList<>());
+		l.addAll(Arrays.asList(targets));
 	}
 
 	@Override
@@ -97,7 +94,7 @@ else if (compounds.size() > 1) {
 
 		@Override
 	public List<Sequence<T>> createSequences(Sequence<F> originalSequence) {
-		List<List<T>> workingList = new ArrayList<List<T>>();
+		List<List<T>> workingList = new ArrayList<>();
 		for (F source : originalSequence) {
 			List<T> compounds = translateMany(source);
 
@@ -126,7 +123,7 @@ public List<Sequence<T>> createSequences(Sequence<F> originalSequence) {
 
 	protected void addCompoundsToList(List<T> compounds, List<List<T>> workingList) {
 		int size = compounds.size();
-		List<List<T>> currentWorkingList = new ArrayList<List<T>>();
+		List<List<T>> currentWorkingList = new ArrayList<>();
 		for (int i = 0; i < size; i++) {
 			boolean last = (i == (size - 1));
 			// If last run we add the compound to the top set of lists & then
@@ -147,7 +144,7 @@ protected void addCompoundsToList(List<T> compounds, List<List<T>> workingList)
 	}
 
 	protected List<Sequence<T>> workingListToSequences(List<List<T>> workingList) {
-		List<Sequence<T>> sequences = new ArrayList<Sequence<T>>();
+		List<Sequence<T>> sequences = new ArrayList<>();
 		for (List<T> seqList : workingList) {
 			sequences.add(getCreator().getSequence(seqList));
 		}
@@ -155,9 +152,9 @@ protected List<Sequence<T>> workingListToSequences(List<List<T>> workingList) {
 	}
 
 	private List<List<T>> duplicateList(List<List<T>> incoming) {
-		List<List<T>> outgoing = new ArrayList<List<T>>();
+		List<List<T>> outgoing = new ArrayList<>();
 		for (List<T> current : incoming) {
-			outgoing.add(new ArrayList<T>(current));
+			outgoing.add(new ArrayList<>(current));
 		}
 		return outgoing;
 	}
@@ -165,7 +162,7 @@ private List<List<T>> duplicateList(List<List<T>> incoming) {
 	protected void addCompoundToLists(List<List<T>> list, T compound) {
 
 		if (list.isEmpty()) {
-			list.add(new ArrayList<T>());
+			list.add(new ArrayList<>());
 		}
 
 		for (List<T> current : list) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java
index cb682ef347..a279a67437 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java
@@ -45,7 +45,7 @@ protected void addNucleotideCompound(String base, String complement, String... e
 		C upper = newNucleotideCompound(base.toUpperCase(), complement.toUpperCase(), upperEquivalents);
 		C lower = newNucleotideCompound(base.toLowerCase(), complement.toLowerCase(), lowerEquivalents);
 
-		List<C> equivalentCompounds = new ArrayList<C>();
+		List<C> equivalentCompounds = new ArrayList<>();
 
 		for(int i=0; i<equivalents.length; i++) {
 			equivalentCompounds.add(getCompoundForString(upperEquivalents[i]));
@@ -64,9 +64,9 @@ protected void addNucleotideCompound(String base, String complement, String... e
 	 */
 	@SuppressWarnings("unchecked")
 	protected void calculateIndirectAmbiguities() {
-		Map<NucleotideCompound, List<NucleotideCompound>> equivalentsMap = new HashMap<NucleotideCompound, List<NucleotideCompound>>();
+		Map<NucleotideCompound, List<NucleotideCompound>> equivalentsMap = new HashMap<>();
 
-		List<NucleotideCompound> ambiguousCompounds = new ArrayList<NucleotideCompound>();
+		List<NucleotideCompound> ambiguousCompounds = new ArrayList<>();
 		for(NucleotideCompound compound: getAllCompounds()) {
 			if (!compound.isAmbiguous()) {
 				continue;
@@ -101,8 +101,9 @@ protected void calculateIndirectAmbiguities() {
 
 		//And once it's all done start adding them to the equivalents map
 
-		for ( NucleotideCompound key: equivalentsMap.keySet()){
-			List<NucleotideCompound> vals = equivalentsMap.get(key);
+		for (Map.Entry<NucleotideCompound, List<NucleotideCompound>> entry : equivalentsMap.entrySet()){
+            NucleotideCompound key = entry.getKey();
+            List<NucleotideCompound> vals = entry.getValue();
 			for (NucleotideCompound value: vals){
 				addEquivalent((C)key,(C)value);
 				addEquivalent((C)value,(C)key);
@@ -116,12 +117,8 @@ private void checkAdd(
 		NucleotideCompound value) {
 
 
-			List<NucleotideCompound> listS = equivalentsMap.get(key);
-			if ( listS == null){
-				listS = new ArrayList<NucleotideCompound>();
-				equivalentsMap.put(key, listS);
-			}
-			listS.add(value);
+		List<NucleotideCompound> listS = equivalentsMap.computeIfAbsent(key, k -> new ArrayList<>());
+		listS.add(value);
 
 
 }
@@ -139,7 +136,7 @@ private NucleotideCompound toLowerCase(NucleotideCompound compound) {
 	 * @return The ambiguity symbol which represents this set of nucleotides best
 	 */
 	public NucleotideCompound getAmbiguity(NucleotideCompound... compounds) {
-		Set<NucleotideCompound> settedCompounds = new HashSet<NucleotideCompound>();
+		Set<NucleotideCompound> settedCompounds = new HashSet<>();
 		for(NucleotideCompound compound: compounds) {
 			for(NucleotideCompound subCompound: compound.getConstituents()) {
 				settedCompounds.add(getCompoundForString(subCompound.getBase().toUpperCase()));
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
index 7e0228a976..5c3c614e09 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
@@ -65,15 +65,15 @@ public abstract class AbstractSequence<C extends Compound> implements Sequence<C
 	private Integer bioEnd = null;
 	private AbstractSequence<?> parentSequence = null;
 	private String source = null;
-	private ArrayList<String> notesList = new ArrayList<String>();
+	private ArrayList<String> notesList = new ArrayList<>();
 	private Double sequenceScore = null;
 	private FeaturesKeyWordInterface featuresKeyWord = null;
 	private DatabaseReferenceInterface databaseReferences = null;
 	private FeatureRetriever featureRetriever = null;
-	private ArrayList<FeatureInterface<AbstractSequence<C>, C>> features =
-			new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
-	private LinkedHashMap<String, ArrayList<FeatureInterface<AbstractSequence<C>, C>>> groupedFeatures =
-			new LinkedHashMap<String, ArrayList<FeatureInterface<AbstractSequence<C>, C>>>();
+	private final ArrayList<FeatureInterface<AbstractSequence<C>, C>> features =
+			new ArrayList<>();
+	private final LinkedHashMap<String, ArrayList<FeatureInterface<AbstractSequence<C>, C>>> groupedFeatures =
+			new LinkedHashMap<>();
 	private List<String> comments = new ArrayList<>();
 	private List<AbstractReference> references;
 
@@ -88,7 +88,7 @@ public AbstractSequence() {
 	 */
 	public AbstractSequence(String seqString, CompoundSet<C> compoundSet) throws CompoundNotFoundException {
 		setCompoundSet(compoundSet);
-		sequenceStorage = new ArrayListSequenceReader<C>();
+		sequenceStorage = new ArrayListSequenceReader<>();
 		sequenceStorage.setCompoundSet(this.getCompoundSet());
 		sequenceStorage.setContents(seqString);
 	}
@@ -127,8 +127,8 @@ public void setProxySequenceReader(SequenceReader<C> proxyLoader) {
 		if (proxyLoader instanceof FeatureRetriever) {
 			this.setFeatureRetriever((FeatureRetriever) sequenceStorage);
 			HashMap<String, ArrayList<AbstractFeature>> ff = getFeatureRetriever().getFeatures();
-			for (String k: ff.keySet()){
-				for (AbstractFeature f: ff.get(k)){
+			for (ArrayList<AbstractFeature> abstractFeatures : ff.values()){
+				for (AbstractFeature f: abstractFeatures){
 					this.addFeature(f);
 				}
 			}
@@ -349,7 +349,7 @@ public void setReferences(List<AbstractReference> references) {
 	 */
 	public List<FeatureInterface<AbstractSequence<C>, C>> getFeatures(String featureType, int bioSequencePosition) {
 		ArrayList<FeatureInterface<AbstractSequence<C>, C>> featureHits =
-				new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
+				new ArrayList<>();
 		List<FeatureInterface<AbstractSequence<C>, C>> features = getFeaturesByType(featureType);
 		if (features != null) {
 			for (FeatureInterface<AbstractSequence<C>, C> feature : features) {
@@ -368,7 +368,7 @@ public List<FeatureInterface<AbstractSequence<C>, C>> getFeatures(String feature
 	 */
 	public List<FeatureInterface<AbstractSequence<C>, C>> getFeatures(int bioSequencePosition) {
 		ArrayList<FeatureInterface<AbstractSequence<C>, C>> featureHits =
-				new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
+				new ArrayList<>();
 		if (features != null) {
 			for (FeatureInterface<AbstractSequence<C>, C> feature : features) {
 				if (bioSequencePosition >= feature.getLocations().getStart().getPosition() && bioSequencePosition <= feature.getLocations().getEnd().getPosition()) {
@@ -396,7 +396,7 @@ public List<FeatureInterface<AbstractSequence<C>, C>> getFeatures() {
 	 */
 	public void addFeature(int bioStart, int bioEnd, FeatureInterface<AbstractSequence<C>, C> feature) {
 		SequenceLocation<AbstractSequence<C>, C> sequenceLocation =
-				new SequenceLocation<AbstractSequence<C>, C>(bioStart, bioEnd, this);
+				new SequenceLocation<>(bioStart, bioEnd, this);
 		feature.setLocation(sequenceLocation);
 		addFeature(feature);
 	}
@@ -409,14 +409,10 @@ public void addFeature(int bioStart, int bioEnd, FeatureInterface<AbstractSequen
 	 */
 	public void addFeature(FeatureInterface<AbstractSequence<C>, C> feature) {
 		features.add(feature);
-		ArrayList<FeatureInterface<AbstractSequence<C>, C>> featureList = groupedFeatures.get(feature.getType());
-		if (featureList == null) {
-			featureList = new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
-			groupedFeatures.put(feature.getType(), featureList);
-		}
+		ArrayList<FeatureInterface<AbstractSequence<C>, C>> featureList = groupedFeatures.computeIfAbsent(feature.getType(), k -> new ArrayList<>());
 		featureList.add(feature);
-		Collections.sort(features, AbstractFeature.LOCATION_LENGTH);
-		Collections.sort(featureList, AbstractFeature.LOCATION_LENGTH);
+		features.sort(AbstractFeature.LOCATION_LENGTH);
+		featureList.sort(AbstractFeature.LOCATION_LENGTH);
 	}
 
 	/**
@@ -442,7 +438,7 @@ public void removeFeature(FeatureInterface<AbstractSequence<C>, C> feature) {
 	public List<FeatureInterface<AbstractSequence<C>, C>> getFeaturesByType(String type) {
 		List<FeatureInterface<AbstractSequence<C>, C>> features = groupedFeatures.get(type);
 		if (features == null) {
-			features = new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
+			features = new ArrayList<>();
 		}
 		return features;
 	}
@@ -503,7 +499,7 @@ public void setFeatureRetriever(FeatureRetriever featureRetriever) {
 
 	public enum AnnotationType {
 
-		CURATED, PREDICTED, UNKNOWN;
+		CURATED, PREDICTED, UNKNOWN
 	}
 
 	/**
@@ -604,7 +600,7 @@ private SequenceReader<C> getSequenceStorage() {
 			//return parentSequence.getSequenceStorage();
 
 			if ( this.compoundSet.equals(parentSequence.getCompoundSet())){
-				sequenceStorage = new ArrayListSequenceReader<C>();
+				sequenceStorage = new ArrayListSequenceReader<>();
 				sequenceStorage.setCompoundSet(this.getCompoundSet());
 				try {
 					sequenceStorage.setContents(parentSequence.getSequenceAsString());
@@ -701,7 +697,7 @@ public int getLength() {
 	 */
 	@Override
 	public SequenceView<C> getSubSequence(final Integer bioStart, final Integer bioEnd) {
-		return new SequenceProxyView<C>(this, bioStart, bioEnd);
+		return new SequenceProxyView<>(this, bioStart, bioEnd);
 	}
 
 	/**
@@ -718,8 +714,9 @@ public Iterator<C> iterator() {
 	 * @param compounds
 	 * @return
 	 */
+	@SafeVarargs
 	@Override
-	public int countCompounds(C... compounds) {
+	public final int countCompounds(C... compounds) {
 		return SequenceMixin.countCompounds(this, compounds);
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/ComplementCompound.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/ComplementCompound.java
index 66b0e29e32..74873d286d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/ComplementCompound.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/ComplementCompound.java
@@ -29,5 +29,5 @@
 
 public interface ComplementCompound extends Compound {
 
-	public ComplementCompound getComplement();
+	ComplementCompound getComplement();
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java
index 6dbeda2208..eb2db9da93 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java
@@ -28,21 +28,21 @@
 
 public interface Compound {
 
-	public boolean equalsIgnoreCase(Compound compound);
+	boolean equalsIgnoreCase(Compound compound);
 
-	public String getDescription();
+	String getDescription();
 
-	public void setDescription(String description);
+	void setDescription(String description);
 
-	public String getShortName();
+	String getShortName();
 
-	public void setShortName(String shortName);
+	void setShortName(String shortName);
 
-	public String getLongName();
+	String getLongName();
 
-	public void setLongName(String longName);
+	void setLongName(String longName);
 
-	public Float getMolecularWeight();
+	Float getMolecularWeight();
 
-	public void setMolecularWeight(Float molecularWeight);
+	void setMolecularWeight(Float molecularWeight);
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/CompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/CompoundSet.java
index 2dbc40603a..1710d0c358 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/CompoundSet.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/CompoundSet.java
@@ -34,31 +34,31 @@ public interface CompoundSet<C extends Compound> {
 	/**
 	 * Returns the maximum size of a compound String this set holds
 	 */
-	public int getMaxSingleCompoundStringLength();
+    int getMaxSingleCompoundStringLength();
 
 	/**
 	 * Returns true if all String representations of Compounds are of the
 	 * same length.
 	 */
-	public boolean isCompoundStringLengthEqual();
+    boolean isCompoundStringLengthEqual();
 
 	/**
 	 * Return null if not recognised. Throw IllegalArgumentException if string
 	 * is longer than maximum allowed by {@link #getStringForCompound(Compound)}.
 	 */
-	public C getCompoundForString(String string);
+    C getCompoundForString(String string);
 
-	public String getStringForCompound(C compound);
+	String getStringForCompound(C compound);
 
-	public boolean compoundsEquivalent(C compoundOne, C compoundTwo);
+	boolean compoundsEquivalent(C compoundOne, C compoundTwo);
 
-	public boolean isValidSequence(Sequence<C> sequence);
+	boolean isValidSequence(Sequence<C> sequence);
 
-	public Set<C> getEquivalentCompounds(C compound);
+	Set<C> getEquivalentCompounds(C compound);
 
-	public boolean hasCompound(C compound);
+	boolean hasCompound(C compound);
 
-	public List<C> getAllCompounds();
+	List<C> getAllCompounds();
 
 	boolean isComplementable();
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Sequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Sequence.java
index f05ed60ec7..da15aabb68 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Sequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Sequence.java
@@ -41,7 +41,7 @@ public interface Sequence<C extends Compound> extends Iterable<C>, Accessioned {
 	/**
 	 * Returns the length of the Sequence
 	 */
-	public int getLength();
+    int getLength();
 
 	/**
 	 * Returns the Compound at the given biological index
@@ -49,7 +49,7 @@ public interface Sequence<C extends Compound> extends Iterable<C>, Accessioned {
 	 * @param position Biological index (1 to n)
 	 * @return Compound at the specified position
 	 */
-	public C getCompoundAt(int position);
+    C getCompoundAt(int position);
 
 	/**
 	 * Scans through the Sequence looking for the first occurrence of the given
@@ -58,7 +58,7 @@ public interface Sequence<C extends Compound> extends Iterable<C>, Accessioned {
 	 * @param compound Compounds to look for
 	 * @return Index of the first position of the compound in the sequence (1 to n)
 	 */
-	public int getIndexOf(C compound);
+    int getIndexOf(C compound);
 
 /**
 	 * Scans through the Sequence looking for the last occurrence of the given
@@ -67,17 +67,17 @@ public interface Sequence<C extends Compound> extends Iterable<C>, Accessioned {
 	 * @param compound Compounds to look for
 	 * @return Index of the last position of the compound in the sequence (1 to n)
 	 */
-	public int getLastIndexOf(C compound);
+int getLastIndexOf(C compound);
 
 	/**
 	 * Returns the String representation of the Sequence
 	 */
-	public String getSequenceAsString();
+    String getSequenceAsString();
 
 	/**
 	 * Returns the Sequence as a List of compounds
 	 */
-	public List<C> getAsList();
+    List<C> getAsList();
 
 	/**
 	 * Returns a portion of the sequence from the different positions. This is
@@ -87,12 +87,12 @@ public interface Sequence<C extends Compound> extends Iterable<C>, Accessioned {
 	 * @param end Biological end; must be less than length + 1
 	 * @return A SequenceView of the offset
 	 */
-	public SequenceView<C> getSubSequence(Integer start, Integer end);
+    SequenceView<C> getSubSequence(Integer start, Integer end);
 
 	/**
 	 * Gets the compound set used to back this Sequence
 	 */
-	public CompoundSet<C> getCompoundSet();
+    CompoundSet<C> getCompoundSet();
 
 	/**
 	 * Returns the number of times we found a compound in the Sequence
@@ -100,12 +100,12 @@ public interface Sequence<C extends Compound> extends Iterable<C>, Accessioned {
 	 * @param compounds Vargs of the compounds to count
 	 * @return Number of times a compound was found
 	 */
-	public int countCompounds(C... compounds);
+    int countCompounds(C... compounds);
 
 	/**
 	 * Does the <em>right thing</em> to get the inverse of the current
 	 * Sequence. This means either reversing the Sequence and optionally
 	 * complementing the Sequence.
 	 */
-	public SequenceView<C> getInverse();
+    SequenceView<C> getInverse();
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java
index d6efc03817..979f29278a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java
@@ -59,6 +59,7 @@ public class SequenceMixin {
 	 * @param <C> The type of compound we are looking for
 	 * @return The number of times the given compounds appear in this Sequence
 	 */
+	@SafeVarargs
 	public static <C extends Compound> int countCompounds(
 			Sequence<C> sequence, C... compounds) {
 		int count = 0;
@@ -113,7 +114,7 @@ public static int countAT(Sequence<NucleotideCompound> sequence) {
 	 * sequence. Any compound not in the Map will return a fraction of 0.
 	 */
 	public static <C extends Compound> Map<C, Double> getDistribution(Sequence<C> sequence) {
-		Map<C, Double> results = new HashMap<C, Double>();
+		Map<C, Double> results = new HashMap<>();
 		Map<C, Integer> composition = getComposition(sequence);
 		double length = sequence.getLength();
 		for (Map.Entry<C, Integer> entry : composition.entrySet()) {
@@ -133,7 +134,7 @@ public static <C extends Compound> Map<C, Double> getDistribution(Sequence<C> se
 	 * @return Counts for the instances of all compounds in the sequence
 	 */
 	public static <C extends Compound> Map<C, Integer> getComposition(Sequence<C> sequence) {
-		Map<C, Integer> results = new HashMap<C, Integer>();
+		Map<C, Integer> results = new HashMap<>();
 
 		for (C currentCompound : sequence) {
 			Integer currentInteger = results.get(currentCompound);
@@ -187,7 +188,7 @@ public static <C extends Compound> String toString(Sequence<C> sequence) {
 	 * the Compounds of that {@link Sequence}.
 	 */
 	public static <C extends Compound> List<C> toList(Sequence<C> sequence) {
-		List<C> list = new ArrayList<C>(sequence.getLength());
+		List<C> list = new ArrayList<>(sequence.getLength());
 		for (C compound : sequence) {
 			list.add(compound);
 		}
@@ -218,7 +219,7 @@ public static <C extends Compound> int indexOf(Sequence<C> sequence,
 	 */
 	public static <C extends Compound> int lastIndexOf(Sequence<C> sequence,
 			C compound) {
-		int index = indexOf(new ReversedSequenceView<C>(sequence), compound);
+		int index = indexOf(new ReversedSequenceView<>(sequence), compound);
 		return (sequence.getLength() - index)+1;
 	}
 
@@ -229,7 +230,7 @@ public static <C extends Compound> int lastIndexOf(Sequence<C> sequence,
 	 */
 	public static <C extends Compound> Iterator<C> createIterator(
 			Sequence<C> sequence) {
-		return new SequenceIterator<C>(sequence);
+		return new SequenceIterator<>(sequence);
 	}
 
 	/**
@@ -237,7 +238,7 @@ public static <C extends Compound> Iterator<C> createIterator(
 	 */
 	public static <C extends Compound> SequenceView<C> createSubSequence(
 			Sequence<C> sequence, int start, int end) {
-		return new SequenceProxyView<C>(sequence, start, end);
+		return new SequenceProxyView<>(sequence, start, end);
 	}
 
 	/**
@@ -250,7 +251,7 @@ public static <C extends Compound> SequenceView<C> createSubSequence(
 	public static <C extends Compound> Sequence<C> shuffle(Sequence<C> sequence) {
 		List<C> compounds = sequence.getAsList();
 		Collections.shuffle(compounds);
-		return new ArrayListSequenceReader<C>(compounds,
+		return new ArrayListSequenceReader<>(compounds,
 				sequence.getCompoundSet());
 	}
 
@@ -275,8 +276,8 @@ public static <C extends Compound> String checksum(Sequence<C> sequence) {
 	 * @return The list of non-overlapping K-mers
 	 */
 	public static <C extends Compound> List<SequenceView<C>> nonOverlappingKmers(Sequence<C> sequence, int kmer) {
-		List<SequenceView<C>> l = new ArrayList<SequenceView<C>>();
-		WindowedSequence<C> w = new WindowedSequence<C>(sequence, kmer);
+		List<SequenceView<C>> l = new ArrayList<>();
+		WindowedSequence<C> w = new WindowedSequence<>(sequence, kmer);
 		for(SequenceView<C> view: w) {
 			l.add(view);
 		}
@@ -293,17 +294,17 @@ public static <C extends Compound> List<SequenceView<C>> nonOverlappingKmers(Seq
 	 * @return The list of overlapping K-mers
 	 */
 	public static <C extends Compound> List<SequenceView<C>> overlappingKmers(Sequence<C> sequence, int kmer) {
-		List<SequenceView<C>> l = new ArrayList<SequenceView<C>>();
+		List<SequenceView<C>> l = new ArrayList<>();
 		List<Iterator<SequenceView<C>>> windows
-				= new ArrayList<Iterator<SequenceView<C>>>();
+				= new ArrayList<>();
 
 		for(int i=1; i<=kmer; i++) {
 			if(i == 1) {
-				windows.add(new WindowedSequence<C>(sequence, kmer).iterator());
+				windows.add(new WindowedSequence<>(sequence, kmer).iterator());
 			}
 			else {
 				SequenceView<C> sv = sequence.getSubSequence(i, sequence.getLength());
-				windows.add(new WindowedSequence<C>(sv, kmer).iterator());
+				windows.add(new WindowedSequence<>(sv, kmer).iterator());
 			}
 		}
 
@@ -333,7 +334,7 @@ public static <C extends Compound> List<SequenceView<C>> overlappingKmers(Sequen
 	 */
 	@SuppressWarnings({ "unchecked" })
 	public static <C extends Compound> SequenceView<C> inverse(Sequence<C> sequence) {
-		SequenceView<C> reverse = new ReversedSequenceView<C>(sequence);
+		SequenceView<C> reverse = new ReversedSequenceView<>(sequence);
 		if(sequence.getCompoundSet().isComplementable()) {
 			return new ComplementSequenceView(reverse);
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java
index f6e51dfad7..57c0d5cbc3 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java
@@ -117,12 +117,12 @@ public CompoundSet<C> getCompoundSet() {
 
 	@Override
 	public SequenceView<C> getSubSequence(final Integer bioStart, final Integer bioEnd) {
-		return new SequenceProxyView<C>(this, bioStart, bioEnd);
+		return new SequenceProxyView<>(this, bioStart, bioEnd);
 	}
 
 	@Override
 	public Iterator<C> iterator() {
-		return new SequenceMixin.SequenceIterator<C>(this);
+		return new SequenceMixin.SequenceIterator<>(this);
 	}
 
 	@Override
@@ -175,8 +175,9 @@ public void setBioEnd(Integer bioEnd) {
 		this.bioEnd = bioEnd;
 	}
 
+	@SafeVarargs
 	@Override
-	public int countCompounds(C... compounds) {
+	public final int countCompounds(C... compounds) {
 		return SequenceMixin.countCompounds(this, compounds);
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceReader.java
index 48eb728a94..e8380598b3 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceReader.java
@@ -29,7 +29,7 @@
 
 public interface SequenceReader<C extends Compound> extends Sequence<C> {
 
-	public void setCompoundSet(CompoundSet<C> compoundSet);
+	void setCompoundSet(CompoundSet<C> compoundSet);
 
-	public void setContents(String sequence) throws CompoundNotFoundException;
+	void setContents(String sequence) throws CompoundNotFoundException;
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceView.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceView.java
index 4f98899355..7c2228e17f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceView.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceView.java
@@ -28,15 +28,15 @@
 
 public interface SequenceView<C extends Compound> extends Sequence<C> {
 
-	public Sequence<C> getViewedSequence();
+	Sequence<C> getViewedSequence();
 
 	/**
 	 * 1-indexed, inclusive.
 	 */
-	public Integer getBioStart();
+    Integer getBioStart();
 
 	/**
 	 * 1-indexed, inclusive.
 	 */
-	public Integer getBioEnd();
+    Integer getBioEnd();
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/DNAToRNATranslator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/DNAToRNATranslator.java
index 0016c86507..baafa9419d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/DNAToRNATranslator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/DNAToRNATranslator.java
@@ -65,7 +65,7 @@ public DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound> rnaCreato
 		@Override
 		public List<Sequence<NucleotideCompound>> createSequences(Sequence<NucleotideCompound> originalSequence) {
 				if(shortCutTranslation) {
-						List<Sequence<NucleotideCompound>> result = new ArrayList<Sequence<NucleotideCompound>>(1);
+						List<Sequence<NucleotideCompound>> result = new ArrayList<>(1);
 						result.add(wrapToRna(originalSequence));
 						return result;
 				}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Frame.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Frame.java
index 8f35c0eb03..c60695015e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Frame.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Frame.java
@@ -42,7 +42,7 @@ public enum Frame {
 	private final boolean reverse;
 	private final int start;
 
-	private Frame(int start, boolean reverse) {
+	Frame(int start, boolean reverse) {
 		this.start = start;
 		this.reverse = reverse;
 	}
@@ -83,7 +83,7 @@ public static Frame[] getAllFrames() {
 	public <C extends NucleotideCompound> Sequence<C> wrap(Sequence<C> incoming) {
 		Sequence<C> reversed;
 		if(reverse) {
-			reversed = new ComplementSequenceView<C>(new ReversedSequenceView<C>(incoming));
+			reversed = new ComplementSequenceView<>(new ReversedSequenceView<>(incoming));
 		}
 		else {
 			reversed = incoming;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.java
index e748b41387..56ee596811 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.java
@@ -81,20 +81,16 @@ public RNAToAminoAcidTranslator(
 		this.initMetOnly = initMetOnly;
 		this.translateNCodons = translateNCodons;
 
-		quickLookup = new HashMap<Table.CaseInsensitiveTriplet, Codon>(codons
+		quickLookup = new HashMap<>(codons
 				.getAllCompounds().size());
-		aminoAcidToCodon = new HashMap<AminoAcidCompound, List<Codon>>();
+		aminoAcidToCodon = new HashMap<>();
 
 		List<Codon> codonList = table.getCodons(nucleotides, aminoAcids);
 		for (Codon codon : codonList) {
 			quickLookup.put(codon.getTriplet(), codon);
 			codonArray[codon.getTriplet().intValue()] = codon;
 
-			List<Codon> codonL = aminoAcidToCodon.get(codon.getAminoAcid());
-			if (codonL == null) {
-				codonL = new ArrayList<Codon>();
-				aminoAcidToCodon.put(codon.getAminoAcid(), codonL);
-			}
+			List<Codon> codonL = aminoAcidToCodon.computeIfAbsent(codon.getAminoAcid(), k -> new ArrayList<>());
 			codonL.add(codon);
 
 		}
@@ -114,9 +110,9 @@ public RNAToAminoAcidTranslator(
 	public List<Sequence<AminoAcidCompound>> createSequences(
 			Sequence<NucleotideCompound> originalSequence) {
 
-		List<List<AminoAcidCompound>> workingList = new ArrayList<List<AminoAcidCompound>>();
+		List<List<AminoAcidCompound>> workingList = new ArrayList<>();
 
-		Iterable<SequenceView<NucleotideCompound>> iter = new WindowedSequence<NucleotideCompound>(
+		Iterable<SequenceView<NucleotideCompound>> iter = new WindowedSequence<>(
 				originalSequence, 3);
 
 		boolean first = true;
@@ -132,7 +128,7 @@ public List<Sequence<AminoAcidCompound>> createSequences(
 					element.getCompoundAt(i++), element.getCompoundAt(i++),
 					element.getCompoundAt(i++));
 
-			Codon target = null;
+			Codon target;
 
 			target = quickLookup.get(triplet);
 
@@ -152,7 +148,7 @@ public List<Sequence<AminoAcidCompound>> createSequences(
 					}
 				}
 
-				addCompoundsToList(Arrays.asList(aminoAcid), workingList);
+				addCompoundsToList(Collections.singletonList(aminoAcid), workingList);
 			}
 
 			if (doTranslate && stopAtStopCodons && target.isStop()) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
index 7d75a10d6a..7ebdc1a2ff 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
@@ -64,7 +64,7 @@ CompoundSet<Codon> getCodonCompoundSet(
 	 * @author ayates
 	 *
 	 */
-	public static class Codon implements Compound {
+	class Codon implements Compound {
 
 		private final CaseInsensitiveTriplet triplet;
 		private final boolean start;
@@ -191,7 +191,7 @@ public void setShortName(String shortName) {
 	 * Class used to hold three nucleotides together and allow for equality
 	 * to be assessed in a case insensitive manner.
 	 */
-	public static class CaseInsensitiveTriplet {
+	class CaseInsensitiveTriplet {
 
 		private final NucleotideCompound one;
 		private final NucleotideCompound two;
@@ -199,7 +199,7 @@ public static class CaseInsensitiveTriplet {
 
 		private transient boolean hashSet = false;
 		private transient int hash;
-		private transient boolean stringSet = false;
+		private final transient boolean stringSet = false;
 		private transient String stringify;
 
 		public CaseInsensitiveTriplet(NucleotideCompound one,
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java
index 0ca5bc6f1a..162d760f05 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java
@@ -125,7 +125,7 @@ public Sequence<AminoAcidCompound> translate(
 	 */
 	public Map<Frame, Sequence<AminoAcidCompound>> multipleFrameTranslation(
 			Sequence<NucleotideCompound> dna, Frame... frames) {
-		Map<Frame, Sequence<AminoAcidCompound>> results = new EnumMap<Frame, Sequence<AminoAcidCompound>>(
+		Map<Frame, Sequence<AminoAcidCompound>> results = new EnumMap<>(
 				Frame.class);
 		for (Frame frame : frames) {
 			Sequence<NucleotideCompound> rna = getDnaRnaTranslator()
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/RnaSequenceView.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/RnaSequenceView.java
index b0c00d6a60..48fea9da1e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/RnaSequenceView.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/RnaSequenceView.java
@@ -39,7 +39,7 @@
  */
 public class RnaSequenceView extends SequenceProxyView<NucleotideCompound> implements ProxySequenceReader<NucleotideCompound> {
 
-	private CompoundSet<NucleotideCompound> rnaCompounds;
+	private final CompoundSet<NucleotideCompound> rnaCompounds;
 	private Map<NucleotideCompound, NucleotideCompound> dnaToRna = null;
 	private Map<NucleotideCompound, NucleotideCompound> rnaToDna = null;
 
@@ -90,9 +90,9 @@ public Map<NucleotideCompound, NucleotideCompound> getDnaToRna() {
 
 	protected void buildTranslators() {
 		Map<NucleotideCompound, NucleotideCompound> localDnaToRna =
-				new HashMap<NucleotideCompound, NucleotideCompound>();
+				new HashMap<>();
 		Map<NucleotideCompound, NucleotideCompound> localRnaToDna =
-				new HashMap<NucleotideCompound, NucleotideCompound>();
+				new HashMap<>();
 
 		NucleotideCompound thymine =
 				getViewedSequence().getCompoundSet().getCompoundForString("T");
@@ -124,7 +124,7 @@ public void setCompoundSet(CompoundSet<NucleotideCompound> compoundSet) {
 	}
 
 	@Override
-	public void setContents(String sequence) throws CompoundNotFoundException {
+	public void setContents(String sequence) {
 		throw new UnsupportedOperationException("Unsupported operation; create a new viewed sequence");
 	}
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/WindowedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/WindowedSequence.java
index 72e2111407..9b21da105a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/WindowedSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/WindowedSequence.java
@@ -115,7 +115,7 @@ public SequenceView<C> get(int index) {
 	 */
 	@Override
 	public Iterator<SequenceView<C>> iterator() {
-		return new WindowedSequenceIterator<C>(this);
+		return new WindowedSequenceIterator<>(this);
 	}
 
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/CRC64Checksum.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/CRC64Checksum.java
index 3e99fec10b..81e0a9339d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/CRC64Checksum.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/CRC64Checksum.java
@@ -81,7 +81,7 @@ public long getValue() {
 	 */
 	@Override
 	public String toString() {
-		StringBuffer builder = new StringBuffer();
+		StringBuilder builder = new StringBuilder();
 		builder.append(Long.toHexString(crc >>> 4));
 		builder.append(Long.toHexString(crc & 0xF));
 		for (int i = 16 - builder.length(); i > 0; --i)
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/ConcurrencyTools.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/ConcurrencyTools.java
index 3e849a38a4..303da24403 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/ConcurrencyTools.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/ConcurrencyTools.java
@@ -94,7 +94,7 @@ public static void setThreadPoolSingle() {
 	public static void setThreadPoolSize(int threads) {
 		setThreadPool(   new ThreadPoolExecutor(threads, threads,
 									  0L, TimeUnit.MILLISECONDS,
-									  new LinkedBlockingQueue<Runnable>()));
+				new LinkedBlockingQueue<>()));
 
 
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
index 2fd6f3f9e0..beb86f865c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
@@ -61,36 +61,25 @@ public static void copy(File src, File dst) throws IOException {
 		// Took following recipe from
 		// http://stackoverflow.com/questions/106770/standard-concise-way-to-copy-a-file-in-java
 		// The nio package seems to be the most efficient way to copy a file
-		FileChannel source = null;
-		FileChannel destination = null;
 
-		try {
-			// we need the supress warnings here (the warning that the stream is not closed is harmless)
-			// see http://stackoverflow.com/questions/12970407/does-filechannel-close-close-the-underlying-stream
-			source = new FileInputStream(src).getChannel();
-			destination = new FileOutputStream(dst).getChannel();
-			destination.transferFrom(source, 0, source.size());
-		} finally {
-			if (source != null) {
-				source.close();
-			}
-			if (destination != null) {
-				destination.close();
-			}
-		}
+        try (FileChannel source = new FileInputStream(src).getChannel(); FileChannel destination = new FileOutputStream(dst).getChannel()) {
+            // we need the supress warnings here (the warning that the stream is not closed is harmless)
+            // see http://stackoverflow.com/questions/12970407/does-filechannel-close-close-the-underlying-stream
+            destination.transferFrom(source, 0, source.size());
+        }
 	}
 
 	public static String getFileExtension(File f) {
 		String fileName = f.getName();
-		String ext = "";
+		String ext;
 		int mid = fileName.lastIndexOf(".");
-		ext = fileName.substring(mid + 1, fileName.length());
+		ext = fileName.substring(mid + 1);
 		return ext;
 	}
 
 	public static String getFilePrefix(File f) {
 		String fileName = f.getName();
-		String fname = "";
+		String fname;
 
 		int mid = fileName.indexOf(".");
 		fname = fileName.substring(0, mid);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java
index e8feeec8ac..0ca9f46c3e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java
@@ -44,7 +44,7 @@ public class FlatFileCache {
 	/**
 	 * The cache singleton.
 	 */
-	private static SoftHashMap<String, byte[]> cache = new SoftHashMap<String, byte[]>(0);
+	private static final SoftHashMap<String, byte[]> cache = new SoftHashMap<>(0);
 
 
 	// no public constructor;
@@ -73,7 +73,7 @@ public  static void addToCache(String key, File fileToCache){
 
 			// Read in the bytes
 			int offset = 0;
-			int numRead = 0;
+			int numRead;
 			while (offset < bytes.length
 					&& (numRead=is.read(bytes, offset, bytes.length-offset)) >= 0) {
 				offset += numRead;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/InputStreamProvider.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/InputStreamProvider.java
index f129dedb0b..8b7731ae5c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/InputStreamProvider.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/InputStreamProvider.java
@@ -100,7 +100,7 @@ public InputStream getInputStream(String pathToFile)
 	 * @return the magic number
 	 * @throws IOException
 	 */
-	private int getMagicNumber(InputStream in)
+	private static int getMagicNumber(InputStream in)
 	throws IOException {
 
 
@@ -118,7 +118,7 @@ private int getMagicNumber(InputStream in)
 	public InputStream getInputStream(URL u)
 	throws IOException{
 
-		int magic = 0;
+		int magic;
 
 
 		InputStream inStream = u.openStream();
@@ -160,7 +160,7 @@ public  InputStream getInputStream(File f)
 		// use the magic numbers to determine the compression type,
 		// use file extension only as 2nd choice
 
-		int magic = 0;
+		int magic;
 
 
 		InputStream test = getInputStreamFromFile(f);
@@ -168,7 +168,7 @@ public  InputStream getInputStream(File f)
 		test.close();
 
 
-		InputStream inputStream = null;
+		InputStream inputStream;
 
 		String fileName = f.getName();
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java
index 0027dbc7b4..4a55867c1a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java
@@ -34,17 +34,17 @@
  */
 
 public class PrettyXMLWriter implements XMLWriter {
-	private int indentUnit = 2;
+	private final int indentUnit = 2;
 
-	private PrintWriter writer;
+	private final PrintWriter writer;
 	private boolean isOpeningTag = false;
 	private boolean afterNewline = true;
 	private int indent = 0;
 
-	private Map<String, String> namespacePrefixes = new HashMap<String, String>();
+	private final Map<String, String> namespacePrefixes = new HashMap<>();
 	private int namespaceSeed = 0;
-	private LinkedList<List<String>> namespaceBindings = new LinkedList<List<String>>();
-	private List<String> namespacesDeclared = new ArrayList<String>();
+	private final LinkedList<List<String>> namespaceBindings = new LinkedList<>();
+	private final List<String> namespacesDeclared = new ArrayList<>();
 
 	public PrettyXMLWriter(PrintWriter writer) {
 		this.writer = writer;
@@ -64,10 +64,9 @@ public void declareNamespace(String nsURI, String prefixHint)
 		}
 	}
 
-	private void handleDeclaredNamespaces()
-		throws IOException
+	private void handleDeclaredNamespaces() throws IOException
 	{
-		if (namespacesDeclared.size() == 0) {
+		if (namespacesDeclared.size() > 0) {
 			for (Iterator<String> nsi = namespacesDeclared.iterator(); nsi.hasNext(); ) {
 				String nsURI = nsi.next();
 				if (!namespacePrefixes.containsKey(nsURI)) {
@@ -79,9 +78,7 @@ private void handleDeclaredNamespaces()
 		}
 	}
 
-	protected void writeIndent()
-		throws IOException
-	{
+	protected void writeIndent() {
 		for (int i = 0; i < indent * indentUnit; ++i) {
 			writer.write(' ');
 		}
@@ -108,7 +105,7 @@ private String allocPrefix(String nsURI) {
 		namespacePrefixes.put(nsURI, prefix);
 		List<String> bindings = namespaceBindings.getLast();
 		if (bindings == null) {
-			bindings = new ArrayList<String>();
+			bindings = new ArrayList<>();
 			namespaceBindings.removeLast();
 			namespaceBindings.add(bindings);
 		}
@@ -270,9 +267,7 @@ public void print(String data)
 	}
 
 	@Override
-	public void printRaw(String data)
-		throws IOException
-	{
+	public void printRaw(String data) {
 	writer.println(data);
 	}
 
@@ -312,18 +307,14 @@ protected void printAttributeValue(String data)
 	}
 	}
 
-	protected void numericalEntity(char c)
-		throws IOException
-	{
+	protected void numericalEntity(char c) {
 	writer.print("&#");
 	writer.print((int) c);
 	writer.print(';');
 	}
 
 	@Override
-	public void close()
-		throws IOException
-	{
+	public void close() {
 		writer.close();
 	}
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java
index ca58257f48..20aa61164a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java
@@ -38,11 +38,11 @@ public class SingleLinkageClusterer {
 
 	private static final Logger logger = LoggerFactory.getLogger(SingleLinkageClusterer.class);
 
-	private class LinkedPair {
+	private static class LinkedPair {
 
-		private int first;
-		private int second;
-		private double closestDistance;
+		private final int first;
+		private final int second;
+		private final double closestDistance;
 
 		public LinkedPair(int first, int second, double minDistance) {
 			this.first = first;
@@ -65,7 +65,7 @@ public double getClosestDistance() {
 		@Override
 		public String toString() {
 
-			String closestDistStr = null;
+			String closestDistStr;
 			if (closestDistance==Double.MAX_VALUE) {
 				closestDistStr = String.format("%6s", "inf");
 			} else {
@@ -77,11 +77,11 @@ public String toString() {
 
 	}
 
-	private double[][] matrix;
+	private final double[][] matrix;
 
-	private boolean isScoreMatrix;
+	private final boolean isScoreMatrix;
 
-	private int numItems;
+	private final int numItems;
 
 	private LinkedPair[] dendrogram;
 
@@ -190,7 +190,7 @@ private double getDistance(int first, int second) {
 	private void updateIndicesToCheck(int m) {
 
 		if (indicesToCheck==null) {
-			indicesToCheck = new ArrayList<Integer>(numItems);
+			indicesToCheck = new ArrayList<>(numItems);
 
 			for (int i=0;i<numItems;i++) {
 				indicesToCheck.add(i);
@@ -215,7 +215,7 @@ private LinkedPair getClosestPair() {
 
 					if (matrix[i][j]>=max) {
 						max = matrix[i][j];
-						closestPair = new LinkedPair(i,j,max);
+						closestPair = new LinkedPair(i, j, max);
 					}
 
 				}
@@ -229,7 +229,7 @@ private LinkedPair getClosestPair() {
 
 					if (matrix[i][j]<=min) {
 						min = matrix[i][j];
-						closestPair = new LinkedPair(i,j,min);
+						closestPair = new LinkedPair(i, j, min);
 					}
 
 				}
@@ -250,7 +250,7 @@ public Map<Integer, Set<Integer>> getClusters(double cutoff) {
 			clusterIt();
 		}
 
-		Map<Integer, Set<Integer>> clusters = new TreeMap<Integer, Set<Integer>>();
+		Map<Integer, Set<Integer>> clusters = new TreeMap<>();
 
 		int clusterId = 1;
 
@@ -276,7 +276,7 @@ public Map<Integer, Set<Integer>> getClusters(double cutoff) {
 
 				if (firstClusterId==-1 && secondClusterId==-1) {
 					// neither member is in a cluster yet, let's assign a new cluster and put them both in
-					Set<Integer> members = new TreeSet<Integer>();
+					Set<Integer> members = new TreeSet<>();
 					members.add(dendrogram[i].getFirst());
 					members.add(dendrogram[i].getSecond());
 					clusters.put(clusterId, members);
@@ -295,16 +295,12 @@ public Map<Integer, Set<Integer>> getClusters(double cutoff) {
 					if (firstCluster.size()<secondCluster.size()) {
 						logger.debug("Joining cluster "+firstClusterId+" to cluster "+secondClusterId);
 						// we join first onto second
-						for (int member : firstCluster) {
-							secondCluster.add(member);
-						}
+						secondCluster.addAll(firstCluster);
 						clusters.remove(firstClusterId);
 					} else {
 						logger.debug("Joining cluster "+secondClusterId+" to cluster "+firstClusterId);
 						// we join second onto first
-						for (int member : secondCluster) {
-							firstCluster.add(member);
-						}
+						firstCluster.addAll(secondCluster);
 						clusters.remove(secondClusterId);
 					}
 				}
@@ -319,10 +315,10 @@ public Map<Integer, Set<Integer>> getClusters(double cutoff) {
 		}
 
 		// reassigning cluster numbers by creating a new map (there can be gaps in the numbering if cluster-joining happened)
-		Map<Integer,Set<Integer>> finalClusters = new TreeMap<Integer, Set<Integer>>();
+		Map<Integer,Set<Integer>> finalClusters = new TreeMap<>();
 		int newClusterId = 1;
-		for (int oldClusterId:clusters.keySet()) {
-			finalClusters.put(newClusterId, clusters.get(oldClusterId));
+		for (Set<Integer> integers : clusters.values()) {
+			finalClusters.put(newClusterId, integers);
 			newClusterId++;
 		}
 
@@ -336,7 +332,7 @@ public Map<Integer, Set<Integer>> getClusters(double cutoff) {
 				}
 			}
 			if (!isAlreadyClustered) {
-				Set<Integer> members = new TreeSet<Integer>();
+				Set<Integer> members = new TreeSet<>();
 				members.add(i);
 				finalClusters.put(newClusterId, members);
 				newClusterId++;
@@ -367,9 +363,9 @@ private boolean isWithinCutoff(int i, double cutoff) {
 
 	private String clustersToString(Map<Integer,Set<Integer>> finalClusters) {
 		StringBuilder sb = new StringBuilder();
-		for (int cId:finalClusters.keySet()) {
-			sb.append(cId).append(": ");
-			for (int member:finalClusters.get(cId)) {
+		for (Map.Entry<Integer, Set<Integer>> entry : finalClusters.entrySet()) {
+			sb.append((int) entry.getKey()).append(": ");
+			for (int member: entry.getValue()) {
 				sb.append(member).append(" ");
 			}
 			sb.append("\n");
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
index b13c246baa..d26e1144c5 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
@@ -41,7 +41,7 @@ public class SoftHashMap<K, V> extends AbstractMap<K, V> {
 
 	/** The internal HashMap that stores SoftReference to actual data. */
 
-	private final Map<K, SoftReference<V>> map = new HashMap<K, SoftReference<V>>();
+	private final Map<K, SoftReference<V>> map = new HashMap<>();
 
 	/** Maximum Number of references you dont want GC to collect. */
 
@@ -49,11 +49,11 @@ public class SoftHashMap<K, V> extends AbstractMap<K, V> {
 
 	/** The FIFO list of hard references, order of last access. */
 
-	private final LinkedList<V> hardCache = new LinkedList<V>();
+	private final LinkedList<V> hardCache = new LinkedList<>();
 
 	/** Reference queue for cleared SoftReference objects. */
 
-	private final ReferenceQueue<V> queue = new ReferenceQueue<V>();
+	private final ReferenceQueue<V> queue = new ReferenceQueue<>();
 
 	public SoftHashMap() {
 
@@ -215,7 +215,7 @@ public synchronized V put(K key, V value) {
 
 		logger.debug("Putting {} on cache. size: {}", key, size());
 
-		map.put(key, new SoftValue<K, V>(value, key, queue));
+		map.put(key, new SoftValue<>(value, key, queue));
 
 		return value;
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java
index f8aef6b35e..bd30662768 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java
@@ -75,7 +75,7 @@ public static String convertStreamToString(InputStream stream) {
 		BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
 		StringBuilder sb = new StringBuilder();
 
-		String line = null;
+		String line;
 		try {
 			while ((line = reader.readLine()) != null) {
 
@@ -136,24 +136,18 @@ public static boolean equalsToIgnoreEndline(String expected, String actual) {
 
 
 	public static boolean equalsToXml(String expected, String actual) {
-		Document expectedDocument=null;
-		Document actualDocument=null;
+		Document expectedDocument;
+		Document actualDocument;
 		try {
 			DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
 			DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
 			expectedDocument = documentBuilder.parse(new ByteArrayInputStream(expected.getBytes()));
 			actualDocument = documentBuilder.parse(new ByteArrayInputStream(actual.getBytes()));
-		} catch (ParserConfigurationException e) {
-			logger.error("Exception: ", e);
-			throw new RuntimeException("Couldn't Parse XML", e);
-		} catch (SAXException e) {
-			logger.error("Exception: ", e);
-			throw new RuntimeException("Couldn't Parse XML", e);
-		} catch (IOException e) {
+		} catch (ParserConfigurationException | IOException | SAXException e) {
 			logger.error("Exception: ", e);
 			throw new RuntimeException("Couldn't Parse XML", e);
 		}
-		final DocumentType doctype1 = expectedDocument.getDoctype();
+        final DocumentType doctype1 = expectedDocument.getDoctype();
 		final DocumentType doctype2 = actualDocument.getDoctype();
 		if (doctype1==null ^ doctype2 == null) {
 			return false;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/UncompressInputStream.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/UncompressInputStream.java
index 07708f0f4d..98cc49fa26 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/UncompressInputStream.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/UncompressInputStream.java
@@ -176,7 +176,7 @@ public synchronized int read(byte[] buf, int off, int len)
 		// empty stack if stuff still left
 		int s_size = l_stack.length - l_stackp;
 		if (s_size > 0) {
-			int num = (s_size >= len) ? len : s_size;
+			int num = Math.min(s_size, len);
 			System.arraycopy(l_stack, l_stackp, buf, off, num);
 			off += num;
 			len -= num;
@@ -304,7 +304,7 @@ public synchronized int read(byte[] buf, int off, int len)
 				// And put them out in forward order
 
 				s_size = l_stack.length - l_stackp;
-				int num = (s_size >= len) ? len : s_size;
+				int num = Math.min(s_size, len);
 				System.arraycopy(l_stack, l_stackp, buf, off, num);
 				off += num;
 				len -= num;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java
index 7d9e1cad63..525c5b09da 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java
@@ -123,7 +123,7 @@ static public Element selectParentElement(Element element, String parentName) {
 	}
 
 	static public Element selectSingleElement(Element element, String xpathExpression) throws XPathExpressionException {
-		if (xpathExpression.indexOf("/") == -1) {
+		if (!xpathExpression.contains("/")) {
 			NodeList nodeList = element.getChildNodes();
 			for (int i = 0; i < nodeList.getLength(); i++) {
 				Node node = nodeList.item(i);
@@ -145,11 +145,11 @@ static public Element selectSingleElement(Element element, String xpathExpressio
 	}
 
 	static public ArrayList<Element> selectElements(Element element, String xpathExpression) throws XPathExpressionException {
-		ArrayList<Element> resultVector = new ArrayList<Element>();
+		ArrayList<Element> resultVector = new ArrayList<>();
 		if (element == null) {
 			return resultVector;
 		}
-		if (xpathExpression.indexOf("/") == -1) {
+		if (!xpathExpression.contains("/")) {
 			NodeList nodeList = element.getChildNodes();
 			for (int i = 0; i < nodeList.getLength(); i++) {
 				Node node = nodeList.item(i);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
index b6d51d1f25..d5875aa2e4 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
@@ -38,7 +38,7 @@ public interface XMLWriter {
 	 * @param s a string of data to include verbatim in the XML stream
 	 */
 
-	public void printRaw(String s) throws IOException;
+    void printRaw(String s);
 
 	/**
 	 * Open a new namespace-qualified XML tag.
@@ -47,7 +47,7 @@ public interface XMLWriter {
 	 * @param localName The name of the tag
 	 */
 
-	public void openTag(String nsURI, String localName) throws IOException;
+    void openTag(String nsURI, String localName) throws IOException;
 
 	/**
 	 * Open a new unqualified XML tag.  This may also be used if you want
@@ -56,7 +56,7 @@ public interface XMLWriter {
 	 * @param name The name of the tag.
 	 */
 
-	public void openTag(String name) throws IOException;
+    void openTag(String name) throws IOException;
 
 	/**
 	 * Add an attribute to an element.  This will throw an exception if it's not
@@ -67,7 +67,7 @@ public interface XMLWriter {
 	 * @param value The textual value of the attribute
 	 */
 
-	public void attribute(String nsURI, String localName, String value) throws IOException;
+    void attribute(String nsURI, String localName, String value) throws IOException;
 
 	/**
 	 * Add an un-qualified attribute to an element.  This will throw an exception if it's not
@@ -77,19 +77,19 @@ public interface XMLWriter {
 	 * @param value The textual value of the attribute
 	 */
 
-	public void attribute(String qName, String value) throws IOException;
+    void attribute(String qName, String value) throws IOException;
 
 	/**
 	 * Prints some textual content in an element.
 	 */
 
-	public void print(String data) throws IOException;
+    void print(String data) throws IOException;
 
 	/**
 	 * Prints some textual content, terminated with a newline character.
 	 */
 
-	public void println(String data) throws IOException;
+    void println(String data) throws IOException;
 
 	/**
 	 * Closes an element
@@ -98,7 +98,7 @@ public interface XMLWriter {
 	 * @param qName The name of the tag
 	 */
 
-	public void closeTag(String nsURI, String qName) throws IOException;
+    void closeTag(String nsURI, String qName) throws IOException;
 
 	/**
 	 * Closes an un-qualified element.
@@ -106,7 +106,7 @@ public interface XMLWriter {
 	 * @param name The tag name
 	 */
 
-	public void closeTag(String name) throws IOException;
+    void closeTag(String name) throws IOException;
 
 	/**
 	 * Hints that a namespace is going to be used in a sub-tree.  Use this method
@@ -121,7 +121,7 @@ public interface XMLWriter {
 	 * @param prefixHint A suggested prefix-string for this namespace.
 	 */
 
-	public void declareNamespace(String nsURI, String prefixHint) throws IOException;
+    void declareNamespace(String nsURI, String prefixHint) throws IOException;
 
 	/**
 	 * Close this XMLWriter, and it's underlying stream.
@@ -129,5 +129,5 @@ public interface XMLWriter {
 	 * @since 1.4
 	 */
 
-	public void close() throws IOException;
+    void close();
 }
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/TestAmbiguityCompoundSet.java b/biojava-core/src/test/java/org/biojava/nbio/core/TestAmbiguityCompoundSet.java
index 56abb5d802..9ce712581a 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/TestAmbiguityCompoundSet.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/TestAmbiguityCompoundSet.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.core;
 
-import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.DNASequence;
 import org.biojava.nbio.core.sequence.RNASequence;
 import org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet;
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java
index 8bbc64c182..43a87c4c3e 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java
@@ -49,32 +49,29 @@ public class SimpleAlignedSequenceTest {
 	public void setup() throws CompoundNotFoundException {
 		go = new ProteinSequence("ARND");
 		lo = new ProteinSequence("CEQGHILKM");
-		global = new SimpleAlignedSequence<ProteinSequence, AminoAcidCompound>(go, Arrays.asList(new Step[] {
-				Step.GAP, Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND, Step.GAP}));
-		local = new SimpleAlignedSequence<ProteinSequence, AminoAcidCompound>(lo, Arrays.asList(new Step[] {
-				Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.GAP, Step.COMPOUND, Step.GAP, Step.COMPOUND,
-				Step.COMPOUND}), 1, 3);
-		local2 = new SimpleAlignedSequence<ProteinSequence, AminoAcidCompound>(go, Arrays.asList(new Step[] {
-				Step.COMPOUND, Step.COMPOUND, Step.COMPOUND}), 1, 0);
+		global = new SimpleAlignedSequence<>(go, Arrays.asList(Step.GAP, Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND, Step.GAP));
+		local = new SimpleAlignedSequence<>(lo, Arrays.asList(Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.GAP, Step.COMPOUND, Step.GAP, Step.COMPOUND,
+                Step.COMPOUND), 1, 3);
+		local2 = new SimpleAlignedSequence<>(go, Arrays.asList(Step.COMPOUND, Step.COMPOUND, Step.COMPOUND), 1, 0);
 		cs = AminoAcidCompoundSet.getAminoAcidCompoundSet();
 	}
 
 	@Test(expected=IllegalArgumentException.class)
 	public void testSimpleAlignedSequenceLocal() {
-		new SimpleAlignedSequence<ProteinSequence, AminoAcidCompound>(lo, Arrays.asList(new Step[] {Step.COMPOUND,
-				Step.COMPOUND, Step.GAP, Step.GAP, Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND}));
+		new SimpleAlignedSequence<>(lo, Arrays.asList(Step.COMPOUND,
+                Step.COMPOUND, Step.GAP, Step.GAP, Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND));
 	}
 
 	@Test(expected=IllegalArgumentException.class)
 	public void testSimpleAlignedSequenceLong() {
-		new SimpleAlignedSequence<ProteinSequence, AminoAcidCompound>(go, Arrays.asList(new Step[] {Step.GAP,
-				Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP}));
+		new SimpleAlignedSequence<>(go, Arrays.asList(Step.GAP,
+                Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP));
 	}
 
 	@Test(expected=IllegalArgumentException.class)
 	public void testSimpleAlignedSequenceShort() {
-		new SimpleAlignedSequence<ProteinSequence, AminoAcidCompound>(go, Arrays.asList(new Step[] {Step.GAP,
-				Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.GAP}));
+		new SimpleAlignedSequence<>(go, Arrays.asList(Step.GAP,
+                Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.GAP));
 	}
 
 	@Test
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleProfileTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleProfileTest.java
index cfd857ac29..65a619e10a 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleProfileTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleProfileTest.java
@@ -52,20 +52,17 @@ public void setup() throws CompoundNotFoundException {
 		target = new ProteinSequence("RDG");
 		query.setAccession(new AccessionID("Query"));
 		target.setAccession(new AccessionID("Target"));
-		global = new SimpleProfile<ProteinSequence, AminoAcidCompound>(query, target, Arrays.asList(new Step[] {
-				Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP}), 0, 0, Arrays.asList(
-				new Step[] {Step.GAP, Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND}), 0, 0);
-		local = new SimpleProfile<ProteinSequence, AminoAcidCompound>(query, target, Arrays.asList(new Step[] {
-				Step.COMPOUND, Step.COMPOUND, Step.COMPOUND}), 1, 0, Arrays.asList(new Step[] { Step.COMPOUND,
-				Step.GAP, Step.COMPOUND}), 0, 1);
-		single = new SimpleProfile<ProteinSequence, AminoAcidCompound>(query);
+		global = new SimpleProfile<>(query, target, Arrays.asList(Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP), 0, 0, Arrays.asList(
+                Step.GAP, Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND), 0, 0);
+		local = new SimpleProfile<>(query, target, Arrays.asList(Step.COMPOUND, Step.COMPOUND, Step.COMPOUND), 1, 0, Arrays.asList(Step.COMPOUND,
+                Step.GAP, Step.COMPOUND), 0, 1);
+		single = new SimpleProfile<>(query);
 	}
 
 	@Test(expected=IllegalArgumentException.class)
 	public void testSimpleProfile() {
-		new SimpleProfile<ProteinSequence, AminoAcidCompound>(query, target, Arrays.asList(new Step[] {
-				Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP}), 0, 0, Arrays.asList(
-				new Step[] {Step.GAP, Step.COMPOUND, Step.GAP, Step.COMPOUND}), 0, 0);
+		new SimpleProfile<>(query, target, Arrays.asList(Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP), 0, 0, Arrays.asList(
+                Step.GAP, Step.COMPOUND, Step.GAP, Step.COMPOUND), 0, 0);
 	}
 
 	@Test
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleSequencePairTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleSequencePairTest.java
index 2c9aedfa91..9cea8140bf 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleSequencePairTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleSequencePairTest.java
@@ -44,12 +44,9 @@ public class SimpleSequencePairTest {
 	public void setup() throws CompoundNotFoundException {
 		query = new ProteinSequence("ARND");
 		target = new ProteinSequence("RDG");
-		global = new SimpleSequencePair<ProteinSequence, AminoAcidCompound>(query, target, Arrays.asList(new Step[] {
-				Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP}), Arrays.asList(new Step[] {
-				Step.GAP, Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND}));
-		local = new SimpleSequencePair<ProteinSequence, AminoAcidCompound>(query, target, Arrays.asList(new Step[] {
-				Step.COMPOUND, Step.COMPOUND, Step.COMPOUND}), 1, 0, Arrays.asList(new Step[] { Step.COMPOUND,
-				Step.GAP, Step.COMPOUND}), 0, 1);
+		global = new SimpleSequencePair<>(query, target, Arrays.asList(Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP), Arrays.asList(Step.GAP, Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND));
+		local = new SimpleSequencePair<>(query, target, Arrays.asList(Step.COMPOUND, Step.COMPOUND, Step.COMPOUND), 1, 0, Arrays.asList(Step.COMPOUND,
+                Step.GAP, Step.COMPOUND), 0, 1);
 	}
 
 	@Test
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java b/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
index 75992962d1..c09956fb40 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
@@ -42,9 +42,9 @@ private void testProcessAll(String path) throws Exception {
 		ClasspathResource r = new ClasspathResource(path);
 		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
 		try( InputStream inStream = r.getInputStream() ) {
-			fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+			fastaReader = new FastaReader<>(
 					inStream,
-					new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+					new GenericFastaHeaderParser<>(),
 					new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
 			LinkedHashMap<String, ProteinSequence> sequences = fastaReader.process();
 			assertThat(sequences,is(notNullValue()));
@@ -82,9 +82,9 @@ private void testProcess1(String path) throws Exception {
 		ClasspathResource r = new ClasspathResource(path);
 		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
 		try( InputStream inStream = r.getInputStream() ) {
-			fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+			fastaReader = new FastaReader<>(
 					inStream,
-					new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+					new GenericFastaHeaderParser<>(),
 					new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
 			LinkedHashMap<String,ProteinSequence> out1 = fastaReader.process(1);
 			assertThat(out1,is(notNullValue()));
@@ -124,9 +124,9 @@ private void testProcess2(String path) throws Exception {
 		ClasspathResource r = new ClasspathResource(path);
 		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
 		try( InputStream inStream = r.getInputStream() ) {
-			fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+			fastaReader = new FastaReader<>(
 					inStream,
-					new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+					new GenericFastaHeaderParser<>(),
 					new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
 			LinkedHashMap<String,ProteinSequence> out1 = fastaReader.process(1);
 			assertThat(out1,is(notNullValue()));
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastTabularParserTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastTabularParserTest.java
index c8343b3060..a5ac5c311f 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastTabularParserTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastTabularParserTest.java
@@ -67,7 +67,7 @@ public void testGetFileExtensions() {
 		System.out.println("getFileExtensions");
 		BlastTabularParser instance = new BlastTabularParser();
 
-		List<String> expResult = new ArrayList<String>();
+		List<String> expResult = new ArrayList<>();
 		expResult.add("blasttabular");
 		expResult.add("blasttxt");
 
@@ -143,7 +143,7 @@ public void testCreateObjects() throws Exception {
 				.setHspBitScore(2894)
 				.createBlastHsp();
 
-		List<Hsp> hsplist = new ArrayList<Hsp>();
+		List<Hsp> hsplist = new ArrayList<>();
 		hsplist.add(hsp1Hit1Res1);
 		hsplist.add(hsp1Hit1Res2);
 
@@ -151,7 +151,7 @@ public void testCreateObjects() throws Exception {
 				.setHitDef("CP000411")
 				.setHsps(hsplist)
 				.createBlastHit();
-		List<Hit> hitlist = new ArrayList<Hit>();
+		List<Hit> hitlist = new ArrayList<>();
 		hitlist.add(hit1Res1);
 
 		BlastResult res1 = new BlastResultBuilder()
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java
index 45de0dbd19..89c73b4d7e 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java
@@ -120,7 +120,7 @@ public void testCreateObjects() throws Exception {
 				.setHspHseq("TTAAATTGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGTGGCGTGCCTAATACATGCAAGTCGTACGCTAGCCGCTGAATTGATCCTTCGGGTGAAGTGAGGCAATGACTAGAGTGGCGAACTGGTGAGTAACACGTAAGAAACCTGCCCTTTAGTGGGGGATAACATTTGGAAACAGATGCTAATACCGCGTAACAACAAATCACACATGTGATCTGTTTGAAAGGTCCTTTTGGATCGCTAGAGGATGGTCTTGCGGCGTATTAGCTTGTTGGTAGGGTAGAAGCCTACCAAGGCAATGATGCGTAGCCGAGTTGAGAGACTGGCCGGCCACATTGGGACTGAGACACTGCCCAAACTCCTACGGGAGGCTGCAGTAGGGAATTTTCCGCAATGCACGAAAGTGTGACGGAGCGACGCCGCGTGTGTGATGAAGGCTTTCGGGTCGTAAAGCACTGTTGTAAGGGAAGAATAACTGAATTCAGAGAAAGTTTTCAGCTTGACGGTACCTTACCAGAAAGGGATGGCTAAATACGTGCCAGCAGCCGCGGTAATACGTATGTCCCGAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGACGGTTTATTAAGTCTGATGTGAAATCCCGAGGCCCAACCTCGGAACTGCATTGGAAACTGATTTACTTGAGTGCGATAGAGGCAAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATGTGGAAGAACACCAGTGGCGAAAGCGGCTTGCTAGATCGTAACTGACGTTGAGGCTCGAAAGTATGGGTAGCAAACGGGATTAGATACCCCGGTAGTCCATACCGTAAACGATGGGTGCTAGTTGTTAAGAGGTTTCCGCCTCCTAGTGACGTAGCAAACGCATTAAGCACCCCGCCTGAGGAGTACGGCCGCAAGGCTAAAACTTAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGATACGCGAAAAACCTTACCAGGTCTTGACATACCAATGATCGCTTTTGTAATGAAAGCTTTTCTTCGGAACATTGGATACAGGTGGTGCATGGTCGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTATTAGTTGCCAGCATTTAGTTGGGCACTCTAATGAGACTGCCGGTGATAAACCGGAGGAAGGTGGGGACGACGTCAGATCATCATGCCCCTTATGACCTGGGCAACACACGTGCTACAATGGGAAGTACAACGAGTCGCAAACCGGCGACGGTAAGCTAATCTCTTAAAACTTCTCTCAGTTCGGACTGGAGTCTGCAACTCGACTCCACGAAGGCGGAATCGCTAGTAATCGCGAATCAGCATGTCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCAAATCATGGGAGTCGGAAGTACCCAAAGTCGCTTGGCTAACTTTTAGAGGCCGGTGCCTAAGGTAAAATCGATGACTGGGATTAAGTCGTAACAAGGTAGCCGTAGGAGAACCTGCGGCTGGATCACCTCCTTTCT")
 				.setHspIdentityString("|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||")
 				.createBlastHsp();
-		List<Hsp> hsplist = new ArrayList<Hsp>();
+		List<Hsp> hsplist = new ArrayList<>();
 		hsplist.add(hsp1hit1res1);
 		hsplist.add(hsp1hit1res1);
 
@@ -133,7 +133,7 @@ public void testCreateObjects() throws Exception {
 				.setHsps(hsplist)
 				.createBlastHit();
 
-		List<Hit> hitlist = new ArrayList<Hit>();
+		List<Hit> hitlist = new ArrayList<>();
 		hitlist.add(hit1res1);
 
 		BlastResult res1 = new BlastResultBuilder()
@@ -200,7 +200,7 @@ public void testGetFileExtensions() {
 	 * Test of storeObjects method, of class BlastXMLParser.
 	 */
 	@Test
-	public void testStoreObjects() throws Exception {
+	public void testStoreObjects() {
 		// not implemented yet
 	}
 }
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/DNATest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/DNATest.java
index f112284740..e2190ce7db 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/DNATest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/DNATest.java
@@ -43,8 +43,8 @@
 
 public class DNATest {
 
-	private DNACompoundSet set = new DNACompoundSet();
-	private AmbiguityDNACompoundSet ambiguity = new AmbiguityDNACompoundSet();
+	private final DNACompoundSet set = new DNACompoundSet();
+	private final AmbiguityDNACompoundSet ambiguity = new AmbiguityDNACompoundSet();
 
 	@Test
 	public void reverseComplement() throws CompoundNotFoundException {
@@ -54,17 +54,17 @@ public void reverseComplement() throws CompoundNotFoundException {
 
 	@Test
 	public void complement() throws CompoundNotFoundException {
-		String s = new ComplementSequenceView<NucleotideCompound>(getSeq()).getSequenceAsString();
+		String s = new ComplementSequenceView<>(getSeq()).getSequenceAsString();
 		assertThat("Complemented sequence not as expected", s, is("TACG"));
 	}
 
 	@Test
 	public void reverse() throws CompoundNotFoundException {
-		SequenceView<NucleotideCompound> r = new ReversedSequenceView<NucleotideCompound>(getSeq());
+		SequenceView<NucleotideCompound> r = new ReversedSequenceView<>(getSeq());
 		assertThat("Reversed sequence not as expected", r.getSequenceAsString(), is("CGTA"));
 		assertThat("Base at 2 not right", r.getCompoundAt(2).toString(), is("G"));
 
-		List<String> actual = new ArrayList<String>();
+		List<String> actual = new ArrayList<>();
 		List<String> expected = Arrays.asList("C", "G", "T", "A");
 		for (NucleotideCompound c : r) {
 			actual.add(c.toString());
@@ -165,11 +165,11 @@ public void twoBit() throws CompoundNotFoundException {
 		String expected = "ATGCAACTGA";
 		DNASequence seq = getSeq(expected);
 		SequenceReader<NucleotideCompound> twoBitFromSeq =
-				new TwoBitSequenceReader<NucleotideCompound>(seq);
+				new TwoBitSequenceReader<>(seq);
 
 		//being cheeky here & getting compound set from seq
 		SequenceReader<NucleotideCompound> twoBitFromString =
-				new TwoBitSequenceReader<NucleotideCompound>(expected, seq.getCompoundSet());
+				new TwoBitSequenceReader<>(expected, seq.getCompoundSet());
 
 		assertThat("TwoBit from Sequence not as expected", twoBitFromSeq.getSequenceAsString(), is(expected));
 		assertThat("TwoBit from String not as expected", twoBitFromString.getSequenceAsString(), is(expected));
@@ -180,11 +180,11 @@ public void fourBit() throws CompoundNotFoundException {
 		String expected = "ATGCAACTGA";
 		DNASequence seq = getSeq(expected);
 		SequenceReader<NucleotideCompound> bitFromSeq =
-				new FourBitSequenceReader<NucleotideCompound>(seq);
+				new FourBitSequenceReader<>(seq);
 
 		//being cheeky here & getting compound set from seq
 		SequenceReader<NucleotideCompound> bitFromString =
-				new FourBitSequenceReader<NucleotideCompound>(expected, seq.getCompoundSet());
+				new FourBitSequenceReader<>(expected, seq.getCompoundSet());
 
 		assertThat("FourBit from Sequence not as expected", bitFromSeq.getSequenceAsString(), is(expected));
 		assertThat("FourBit from String not as expected", bitFromString.getSequenceAsString(), is(expected));
@@ -193,7 +193,7 @@ public void fourBit() throws CompoundNotFoundException {
 	@Test(expected = IllegalStateException.class)
 	public void badTwoBit() throws CompoundNotFoundException {
 		DNASequence seq = getSeq();
-		new TwoBitSequenceReader<NucleotideCompound>("ATNGC", seq.getCompoundSet());
+		new TwoBitSequenceReader<>("ATNGC", seq.getCompoundSet());
 	}
 
 	@Test
@@ -203,7 +203,7 @@ public void singleCompoundSequence() {
 		NucleotideCompound n = cs.getCompoundForString("N");
 		int length = 1000;
 
-		ProxySequenceReader<NucleotideCompound> sr = new SingleCompoundSequenceReader<NucleotideCompound>(n, cs, length);
+		ProxySequenceReader<NucleotideCompound> sr = new SingleCompoundSequenceReader<>(n, cs, length);
 		DNASequence seq = new DNASequence(sr);
 
 		int intCount = 0;
@@ -268,8 +268,8 @@ public void sequenceEquality() throws CompoundNotFoundException {
 		assertTrue("Asserting sequences are identical ignoring case & case different", SequenceMixin.sequenceEqualityIgnoreCase(d, getSeq("aTgC")));
 		assertFalse("Sequence lengths differ", SequenceMixin.sequenceEquality(d, getSeq("ATG")));
 
-		DNASequence bsr = new DNASequence(new TwoBitSequenceReader<NucleotideCompound>("ATGC", DNACompoundSet.getDNACompoundSet()));
-		DNASequence bsrCI = new DNASequence(new TwoBitSequenceReader<NucleotideCompound>("ATGc", DNACompoundSet.getDNACompoundSet()));
+		DNASequence bsr = new DNASequence(new TwoBitSequenceReader<>("ATGC", DNACompoundSet.getDNACompoundSet()));
+		DNASequence bsrCI = new DNASequence(new TwoBitSequenceReader<>("ATGc", DNACompoundSet.getDNACompoundSet()));
 
 		assertTrue("Asserting sequences are identical; backing stores differ", SequenceMixin.sequenceEquality(d, bsr));
 		assertTrue("Asserting sequences are identical ignoring case; backing stores differ", SequenceMixin.sequenceEqualityIgnoreCase(d, bsrCI));
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/JoiningSequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/JoiningSequenceReaderTest.java
index 899247ebc6..353daaed51 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/JoiningSequenceReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/JoiningSequenceReaderTest.java
@@ -34,13 +34,13 @@ public class JoiningSequenceReaderTest {
 	@Test
 	public void canScan() throws CompoundNotFoundException {
 		JoiningSequenceReader<NucleotideCompound> seq =
-			new JoiningSequenceReader<NucleotideCompound>(
-					new DNASequence("AAAA"),
-					new DNASequence("GGG"),
-					new JoiningSequenceReader<NucleotideCompound>(new DNASequence("A"), new DNASequence("C")),
-					new DNASequence("TT"),
-					new DNASequence("C")
-		);
+				new JoiningSequenceReader<>(
+						new DNASequence("AAAA"),
+						new DNASequence("GGG"),
+						new JoiningSequenceReader<>(new DNASequence("A"), new DNASequence("C")),
+						new DNASequence("TT"),
+						new DNASequence("C")
+				);
 
 		String expected = "AAAAGGGACTTC";
 
@@ -59,12 +59,12 @@ public void canScan() throws CompoundNotFoundException {
 	@Test
 	public void empty() throws CompoundNotFoundException {
 		JoiningSequenceReader<NucleotideCompound> seq =
-			new JoiningSequenceReader<NucleotideCompound>(
-					new DNASequence(""),
-					new DNASequence(""),
-					new DNASequence("A"),
-					new DNASequence("")
-			);
+				new JoiningSequenceReader<>(
+						new DNASequence(""),
+						new DNASequence(""),
+						new DNASequence("A"),
+						new DNASequence("")
+				);
 		assertEquals("Testing empty sequences", "A", seq.getSequenceAsString());
 	}
 }
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignmentTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignmentTest.java
index 20acfc2cd2..ea922decf6 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignmentTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignmentTest.java
@@ -43,11 +43,11 @@ public class MultipleSequenceAlignmentTest {
 
 	@Before
 	public void setup() throws CompoundNotFoundException {
-		msaProteins = new MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound>();
+		msaProteins = new MultipleSequenceAlignment<>();
 		for (int i = 0; i < 8; i++) {
 			msaProteins.addAlignedSequence(new ProteinSequence("ARNDCEQGHILKMFPSTWYVBZJX"));
 		}
-		msaDNA = new MultipleSequenceAlignment<DNASequence, NucleotideCompound>();
+		msaDNA = new MultipleSequenceAlignment<>();
 		for (int i = 0; i < 7; i++) {
 			msaDNA.addAlignedSequence(new DNASequence("ATCGATCGATCGATCG"));
 		}
@@ -56,13 +56,13 @@ public void setup() throws CompoundNotFoundException {
 	@Test
 	public void testGetCompoundsAt() {
 		AminoAcidCompound aminoAcid = AminoAcidCompoundSet.getAminoAcidCompoundSet().getCompoundForString("N");
-		List<AminoAcidCompound> colProteins = new ArrayList<AminoAcidCompound>();
+		List<AminoAcidCompound> colProteins = new ArrayList<>();
 		for (int i = 0; i < 8; i++) {
 			colProteins.add(aminoAcid);
 		}
 		assertEquals(msaProteins.getCompoundsAt(3), colProteins);
 		NucleotideCompound nucleotide = DNACompoundSet.getDNACompoundSet().getCompoundForString("C");
-		List<NucleotideCompound> colDNA = new ArrayList<NucleotideCompound>();
+		List<NucleotideCompound> colDNA = new ArrayList<>();
 		for (int i = 0; i < 7; i++) {
 			colDNA.add(nucleotide);
 		}
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TestSequenceEquals.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TestSequenceEquals.java
index 5fe57374d1..3f0fcc53a5 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TestSequenceEquals.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TestSequenceEquals.java
@@ -39,23 +39,23 @@ public void testSameCompounds() throws Exception{
 		ProteinSequence seq2 = new ProteinSequence("ARNDCEQGHILKMFPSTWYVBZJXARNDCEQGHILKMFPSTWYVBZJX");
 
 
-		assertFalse(seq1.equals(seq2));
+        assertNotEquals(seq1, seq2);
 
-		assertTrue(seq1.equals(seq1));
+        assertEquals(seq1, seq1);
 
-		assertTrue(seq2.equals(seq2));
+        assertEquals(seq2, seq2);
 
 
 		ProteinSequence seq3 = new ProteinSequence("ARNDCEQGHILKMFPSTWYVBZJX");
 
-		assertTrue(seq3.equals(seq1));
+        assertEquals(seq3, seq1);
 
-		assertFalse(seq2.equals(seq3));
+        assertNotEquals(seq2, seq3);
 
 
 		DNASequence dnaSeq = new DNASequence("ATGGCGGCGCTGAGCGGT");
 
-		assertFalse(seq1.equals(dnaSeq));
+        assertNotEquals(seq1, dnaSeq);
 
 
 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TranslationTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TranslationTest.java
index 00c520d586..b0113bfdfa 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TranslationTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TranslationTest.java
@@ -51,8 +51,8 @@ public class TranslationTest {
 
 	private final static Logger logger = LoggerFactory.getLogger(TranslationTest.class);
 
-	private static DNACompoundSet dnaCs = DNACompoundSet.getDNACompoundSet();
-	private static AminoAcidCompoundSet aaCs = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+	private static final DNACompoundSet dnaCs = DNACompoundSet.getDNACompoundSet();
+	private static final AminoAcidCompoundSet aaCs = AminoAcidCompoundSet.getAminoAcidCompoundSet();
 	private static DNASequence brca2Dna;
 	private static Sequence<AminoAcidCompound> brca2Pep;
 	private static Sequence<NucleotideCompound> volvoxDna;
@@ -70,20 +70,20 @@ public static void parseSequences() {
 				"org/biojava/nbio/core/sequence/volvox-peptide.fasta").getInputStream();
 
 		try {
-			FastaReader<DNASequence, NucleotideCompound> dnaReader = new FastaReader<DNASequence, NucleotideCompound>(cdsIs,
-					new GenericFastaHeaderParser<DNASequence, NucleotideCompound>(), new DNASequenceCreator(dnaCs));
+			FastaReader<DNASequence, NucleotideCompound> dnaReader = new FastaReader<>(cdsIs,
+					new GenericFastaHeaderParser<>(), new DNASequenceCreator(dnaCs));
 			brca2Dna = dnaReader.process().values().iterator().next();
-			FastaReader<ProteinSequence, AminoAcidCompound> pReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
-					pepIs, new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(), new ProteinSequenceCreator(
-							aaCs));
+			FastaReader<ProteinSequence, AminoAcidCompound> pReader = new FastaReader<>(
+					pepIs, new GenericFastaHeaderParser<>(), new ProteinSequenceCreator(
+					aaCs));
 			brca2Pep = pReader.process().values().iterator().next();
 
-			FastaReader<DNASequence, NucleotideCompound> volvoxDnaReader = new FastaReader<DNASequence, NucleotideCompound>(volDnaIs,
-					new GenericFastaHeaderParser<DNASequence, NucleotideCompound>(), new DNASequenceCreator(dnaCs));
+			FastaReader<DNASequence, NucleotideCompound> volvoxDnaReader = new FastaReader<>(volDnaIs,
+					new GenericFastaHeaderParser<>(), new DNASequenceCreator(dnaCs));
 			volvoxDna = volvoxDnaReader.process().values().iterator().next();
-			FastaReader<ProteinSequence, AminoAcidCompound> volvoxPepReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
-					volPepIs, new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(), new ProteinSequenceCreator(
-							aaCs));
+			FastaReader<ProteinSequence, AminoAcidCompound> volvoxPepReader = new FastaReader<>(
+					volPepIs, new GenericFastaHeaderParser<>(), new ProteinSequenceCreator(
+					aaCs));
 			volvoxPep = volvoxPepReader.process().values().iterator().next();
 		}
 		catch (IOException e) {
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundTest.java
index ce0cee1691..bcc3e09c2a 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundTest.java
@@ -29,7 +29,7 @@
 
 public class AmbiguityDNACompoundTest {
 
-	private AmbiguityDNACompoundSet set = AmbiguityDNACompoundSet.getDNACompoundSet();
+	private final AmbiguityDNACompoundSet set = AmbiguityDNACompoundSet.getDNACompoundSet();
 
 	@Test
 	public void testAmbiguity() {
@@ -44,7 +44,7 @@ public void testBasicAmbiguity() {
 	}
 
 	private NucleotideCompound[] getCompounds(String... compoundStrings) {
-		List<NucleotideCompound> c = new ArrayList<NucleotideCompound>();
+		List<NucleotideCompound> c = new ArrayList<>();
 		for(String s: compoundStrings) {
 			c.add(set.getCompoundForString(s));
 		}
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/ABITracerTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/ABITracerTest.java
index 89aef23cbb..66cef29fac 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/ABITracerTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/ABITracerTest.java
@@ -32,19 +32,19 @@
  */
 public class ABITracerTest {
 
-	private String sequence = "GGGCGAGCKYYAYATTTTGGCAAGAATTGAGCTCTATGGCCACAACCATGGTGAGCAAGGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCAAGGTGCACATGGAGGGCTCCGTGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCCCCTCAGTTCATGTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGACTACTTGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGAGGACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCGAGTTCATCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTAATGCAGAAGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGCGCCCTGAAGGGCGAGATCAAGCAGAGGCTGAAGCTGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTACAACGTCAACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAACAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTACAAGGGCGGCAGCGGCATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAARACCCGCGCCGAGGTGAARTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAAGGGGCAYCGCACCTTTC";
-	private int[] qual = {20, 3, 4, 4, 4, 6, 4, 4, 0, 0, 0, 6, 0, 10, 20, 26, 22, 17, 21, 31, 29, 32, 28, 18, 23, 17, 19, 35, 36, 50, 39, 50, 50, 50, 50, 50, 25, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 39, 33, 20, 35, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 50, 35, 31, 23, 28, 31, 21, 43, 39, 35, 24, 30, 26, 35, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 31, 24, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 43, 43, 50, 50, 50, 50, 50, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 35, 50, 50, 50, 50, 31, 36, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 40, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 40, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 50, 43, 43, 50, 43, 43, 50, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 50, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 28, 28, 35, 28, 28, 35, 28, 28, 35, 28, 28, 35, 28, 28, 35, 28, 21, 28, 35, 28, 28, 35, 35, 35, 35, 35, 37, 38, 21, 28, 35, 28, 28, 35, 35, 35, 35, 35, 35, 35, 36, 36, 21, 39, 35, 35, 35, 39, 35, 37, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 28, 28, 35, 35, 28, 28, 35, 35, 35, 36, 36, 22, 39, 35, 35, 35, 35, 35, 35, 37, 38, 28, 35, 21, 36, 36, 37, 35, 35, 20, 39, 39, 35, 35, 35, 35, 37, 38, 28, 35, 37, 34, 35, 24, 24, 27, 25, 20, 24, 37, 35, 27, 21, 20, 21, 27, 17, 20, 24, 32, 26, 20, 12, 20, 10, 20, 24, 25, 23, 20, 32, 24, 24, 23, 20, 24, 23, 18, 34, 34, 34, 22, 26, 24, 24, 18, 22, 22, 23, 25, 20, 12, 20, 24, 23, 24, 23, 22, 20, 20, 0, 20, 24, 23, 20, 8, 10, 4, 20, 20, 3, 7, 19, 20, 4, 4, 7, 7, 0, 7, 11, 18, 8, 3, 23, 23, 20, 11, 4, 20, 18, 12, 20, 20, 20, 4, 20, 4, 2, 3, 21, 21, 21, 21, 10, 15, 14, 15, 19, 2, 4, 3, 6, 11, 3, 4, 6, 21, 16, 20, 11, 1, 4, 12, 0, 15, 8, 1, 3, 3, 12, 1, 11, 20, 4};
-	private int[] base = {2, 13, 38, 51, 67, 78, 92, 118, 138, 162, 181, 191, 210, 222, 239, 253, 266, 280, 288, 304, 317, 333, 347, 359, 375, 386, 394, 406, 418, 433, 444, 457, 472, 482, 496, 506, 519, 529, 544, 557, 569, 579, 590, 601, 614, 626, 638, 649, 663, 673, 686, 706, 715, 731, 740, 753, 765, 777, 787, 799, 813, 826, 838, 854, 863, 876, 892, 901, 913, 929, 937, 948, 960, 970, 981, 993, 1004, 1017, 1034, 1045, 1056, 1068, 1080, 1091, 1103, 1115, 1126, 1138, 1148, 1160, 1177, 1187, 1199, 1211, 1222, 1232, 1243, 1254, 1268, 1279, 1294, 1307, 1319, 1330, 1341, 1352, 1362, 1374, 1388, 1398, 1411, 1422, 1433, 1444, 1456, 1466, 1479, 1497, 1506, 1519, 1531, 1543, 1556, 1567, 1578, 1589, 1604, 1614, 1630, 1641, 1651, 1662, 1675, 1688, 1700, 1711, 1721, 1732, 1748, 1758, 1772, 1784, 1795, 1806, 1820, 1830, 1844, 1855, 1866, 1877, 1892, 1902, 1914, 1926, 1939, 1950, 1965, 1974, 1986, 1999, 2011, 2023, 2037, 2047, 2059, 2072, 2084, 2096, 2107, 2120, 2132, 2144, 2156, 2169, 2180, 2191, 2202, 2217, 2227, 2239, 2251, 2264, 2275, 2286, 2297, 2309, 2321, 2332, 2347, 2358, 2369, 2381, 2394, 2406, 2417, 2429, 2439, 2452, 2465, 2476, 2490, 2501, 2512, 2524, 2536, 2546, 2560, 2570, 2581, 2593, 2605, 2616, 2628, 2640, 2653, 2664, 2676, 2688, 2700, 2712, 2723, 2735, 2748, 2759, 2772, 2784, 2795, 2808, 2820, 2831, 2842, 2854, 2866, 2878, 2888, 2901, 2913, 2927, 2936, 2947, 2958, 2970, 2982, 2994, 3005, 3019, 3030, 3041, 3053, 3064, 3077, 3088, 3099, 3110, 3123, 3135, 3146, 3157, 3168, 3179, 3192, 3203, 3214, 3226, 3238, 3251, 3263, 3275, 3286, 3297, 3308, 3320, 3331, 3344, 3356, 3368, 3380, 3391, 3402, 3415, 3426, 3440, 3451, 3462, 3474, 3485, 3496, 3508, 3520, 3532, 3543, 3556, 3569, 3580, 3593, 3604, 3615, 3626, 3638, 3650, 3661, 3673, 3684, 3698, 3709, 3721, 3732, 3744, 3756, 3767, 3779, 3792, 3803, 3814, 3827, 3838, 3850, 3862, 3873, 3885, 3897, 3909, 3920, 3932, 3943, 3955, 3966, 3980, 3990, 4002, 4014, 4026, 4038, 4050, 4061, 4072, 4083, 4095, 4107, 4119, 4131, 4143, 4156, 4167, 4179, 4191, 4203, 4215, 4227, 4238, 4252, 4262, 4274, 4287, 4298, 4310, 4321, 4333, 4345, 4356, 4370, 4381, 4393, 4406, 4417, 4428, 4440, 4453, 4464, 4477, 4489, 4500, 4513, 4524, 4536, 4548, 4560, 4573, 4583, 4595, 4607, 4620, 4631, 4645, 4655, 4667, 4679, 4690, 4702, 4714, 4728, 4739, 4750, 4762, 4774, 4786, 4798, 4810, 4821, 4833, 4845, 4857, 4869, 4880, 4892, 4905, 4916, 4927, 4940, 4952, 4963, 4977, 4988, 5000, 5012, 5023, 5034, 5045, 5057, 5069, 5081, 5093, 5104, 5115, 5127, 5139, 5151, 5163, 5176, 5188, 5199, 5211, 5223, 5235, 5247, 5259, 5272, 5283, 5296, 5308, 5320, 5331, 5343, 5354, 5366, 5378, 5390, 5402, 5414, 5426, 5438, 5450, 5462, 5474, 5486, 5497, 5510, 5521, 5532, 5544, 5557, 5569, 5581, 5592, 5604, 5617, 5629, 5641, 5652, 5663, 5676, 5687, 5699, 5712, 5724, 5735, 5748, 5760, 5771, 5784, 5794, 5806, 5817, 5829, 5841, 5853, 5866, 5879, 5891, 5903, 5916, 5928, 5941, 5952, 5964, 5976, 5988, 6000, 6012, 6024, 6036, 6048, 6060, 6072, 6085, 6096, 6109, 6121, 6133, 6146, 6157, 6168, 6180, 6192, 6203, 6215, 6227, 6239, 6251, 6265, 6276, 6289, 6302, 6313, 6325, 6337, 6349, 6361, 6374, 6386, 6398, 6410, 6422, 6436, 6448, 6459, 6471, 6483, 6495, 6507, 6520, 6532, 6545, 6555, 6567, 6579, 6591, 6603, 6615, 6627, 6640, 6652, 6664, 6676, 6688, 6700, 6713, 6726, 6738, 6749, 6761, 6774, 6786, 6799, 6811, 6823, 6835, 6848, 6859, 6871, 6883, 6895, 6907, 6920, 6933, 6945, 6956, 6968, 6980, 6992, 7005, 7016, 7030, 7042, 7053, 7066, 7079, 7091, 7104, 7115, 7128, 7140, 7152, 7163, 7175, 7187, 7200, 7212, 7224, 7235, 7248, 7260, 7272, 7285, 7297, 7309, 7321, 7333, 7345, 7358, 7370, 7382, 7394, 7406, 7419, 7431, 7443, 7455, 7468, 7480, 7492, 7505, 7517, 7530, 7542, 7554, 7566, 7578, 7591, 7603, 7615, 7628, 7640, 7653, 7666, 7677, 7690, 7702, 7714, 7727, 7738, 7750, 7762, 7775, 7786, 7799, 7812, 7823, 7836, 7848, 7859, 7871, 7884, 7896, 7909, 7921, 7933, 7946, 7958, 7971, 7984, 7996, 8007, 8019, 8032, 8044, 8056, 8069, 8081, 8094, 8107, 8119, 8131, 8143, 8155, 8167, 8179, 8192, 8205, 8218, 8230, 8244, 8255, 8267, 8279, 8291, 8303, 8315, 8328, 8340, 8353, 8366, 8378, 8392, 8404, 8417, 8431, 8443, 8455, 8467, 8479, 8492, 8504, 8516, 8529, 8543, 8555, 8567, 8580, 8593, 8606, 8619, 8632, 8644, 8658, 8670, 8683, 8695, 8708, 8721, 8733, 8746, 8759, 8771, 8783, 8795, 8808, 8821, 8833, 8845, 8858, 8871, 8885, 8898, 8910, 8923, 8936, 8949, 8960, 8973, 8986, 9000, 9012, 9025, 9038, 9051, 9064, 9076, 9089, 9102, 9114, 9126, 9139, 9151, 9164, 9177, 9191, 9204, 9217, 9230, 9243, 9255, 9268, 9281, 9294, 9307, 9320, 9333, 9345, 9358, 9371, 9384, 9398, 9412, 9424, 9437, 9450, 9462, 9475, 9488, 9501, 9514, 9528, 9542, 9554, 9567, 9581, 9593, 9606, 9619, 9632, 9645, 9658, 9671, 9682, 9695, 9708, 9721, 9735, 9749, 9762, 9776, 9789, 9802, 9815, 9828, 9842, 9855, 9867, 9880, 9893, 9906, 9920, 9933, 9947, 9960, 9974, 9987, 10000, 10014, 10027, 10040, 10054, 10067, 10081, 10095, 10107, 10120, 10134, 10148, 10161, 10175, 10188, 10201, 10214, 10228, 10241, 10254, 10267, 10280, 10294, 10309, 10322, 10335, 10348, 10362, 10374, 10387, 10401, 10415, 10428, 10441, 10455, 10469, 10482, 10497, 10510, 10523, 10537, 10551, 10565, 10579, 10593, 10606, 10621, 10634, 10647, 10661, 10675, 10689, 10704, 10719, 10732, 10746, 10760, 10774, 10788, 10802, 10815, 10829, 10843, 10856, 10871, 10884, 10898, 10913, 10927, 10940, 10955, 10970, 10984, 10999, 11013, 11027, 11042, 11056, 11071, 11086, 11100, 11114, 11128, 11142, 11158, 11171, 11186, 11200, 11213, 11228, 11241, 11255, 11270, 11284, 11299, 11314, 11328, 11342, 11356, 11370, 11385, 11399, 11413, 11429, 11445, 11460, 11474, 11489, 11503, 11518, 11533, 11549, 11563, 11577, 11592, 11607, 11621, 11637, 11651, 11665, 11680, 11694, 11708, 11725, 11740, 11754, 11768, 11784, 11798, 11813, 11828, 11843, 11858, 11874, 11888, 11904, 11920, 11933, 11948, 11964, 11979, 11993, 12009, 12024, 12041, 12058, 12071, 12087, 12102, 12117, 12132, 12148, 12165, 12179, 12195, 12210, 12226, 12241, 12256, 12273, 12288, 12304, 12320, 12335, 12350, 12365, 12382, 12398, 12414, 12430, 12446, 12462, 12478, 12495, 12511, 12525, 12541, 12556, 12575, 12591, 12605, 12622, 12638, 12653, 12671, 12686, 12705, 12721, 12739, 12756, 12772, 12788, 12806, 12822, 12839, 12855, 12873, 12890, 12908, 12923, 12941, 12960, 12975, 12992, 13009, 13024, 13040, 13059, 13076, 13092, 13109, 13128, 13145, 13161, 13179, 13194, 13216, 13233, 13249, 13266, 13287, 13303, 13322, 13337, 13357, 13375, 13392, 13410, 13424, 13446, 13465, 13480, 13499, 13517, 13533, 13559, 13575, 13595, 13612, 13632, 13650, 13670, 13687, 13706, 13726, 13744, 13765, 13783, 13803, 13822, 13841, 13860, 13879, 13897, 13917, 13936, 13960, 13979, 13996, 14019, 14040, 14057, 14077, 14102, 14122, 14141, 14163, 14184, 14202, 14225, 14244, 14265, 14287, 14312, 14336, 14356, 14375, 14393, 14420, 14438, 14465, 14483, 14500, 14536, 14555, 14575, 14604, 14619, 14648, 14668, 14691, 14725, 14748, 14770, 14788, 14818, 14840, 14862, 14888, 14921, 14939, 14969, 14996, 15022, 15051, 15075, 15098, 15130, 15149, 15167, 15218, 15237, 15276, 15297, 15333, 15356, 15379, 15418, 15447, 15481, 15508, 15530, 15574, 15599, 15643, 15680, 15697, 15743, 15759, 15775, 15813, 15845, 15877, 15911, 15931, 15968, 16014, 16049, 16077, 16088, 16138, 16149, 16185, 16200, 16241, 16280, 16296};
+	private final String sequence = "GGGCGAGCKYYAYATTTTGGCAAGAATTGAGCTCTATGGCCACAACCATGGTGAGCAAGGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCAAGGTGCACATGGAGGGCTCCGTGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCCCCTCAGTTCATGTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGACTACTTGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGAGGACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCGAGTTCATCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTAATGCAGAAGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGCGCCCTGAAGGGCGAGATCAAGCAGAGGCTGAAGCTGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTACAACGTCAACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAACAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTACAAGGGCGGCAGCGGCATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAARACCCGCGCCGAGGTGAARTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAAGGGGCAYCGCACCTTTC";
+	private final int[] qual = {20, 3, 4, 4, 4, 6, 4, 4, 0, 0, 0, 6, 0, 10, 20, 26, 22, 17, 21, 31, 29, 32, 28, 18, 23, 17, 19, 35, 36, 50, 39, 50, 50, 50, 50, 50, 25, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 39, 33, 20, 35, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 50, 35, 31, 23, 28, 31, 21, 43, 39, 35, 24, 30, 26, 35, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 31, 24, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 43, 43, 50, 50, 50, 50, 50, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 35, 50, 50, 50, 50, 31, 36, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 40, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 40, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 50, 43, 43, 50, 43, 43, 50, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 50, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 28, 28, 35, 28, 28, 35, 28, 28, 35, 28, 28, 35, 28, 28, 35, 28, 21, 28, 35, 28, 28, 35, 35, 35, 35, 35, 37, 38, 21, 28, 35, 28, 28, 35, 35, 35, 35, 35, 35, 35, 36, 36, 21, 39, 35, 35, 35, 39, 35, 37, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 28, 28, 35, 35, 28, 28, 35, 35, 35, 36, 36, 22, 39, 35, 35, 35, 35, 35, 35, 37, 38, 28, 35, 21, 36, 36, 37, 35, 35, 20, 39, 39, 35, 35, 35, 35, 37, 38, 28, 35, 37, 34, 35, 24, 24, 27, 25, 20, 24, 37, 35, 27, 21, 20, 21, 27, 17, 20, 24, 32, 26, 20, 12, 20, 10, 20, 24, 25, 23, 20, 32, 24, 24, 23, 20, 24, 23, 18, 34, 34, 34, 22, 26, 24, 24, 18, 22, 22, 23, 25, 20, 12, 20, 24, 23, 24, 23, 22, 20, 20, 0, 20, 24, 23, 20, 8, 10, 4, 20, 20, 3, 7, 19, 20, 4, 4, 7, 7, 0, 7, 11, 18, 8, 3, 23, 23, 20, 11, 4, 20, 18, 12, 20, 20, 20, 4, 20, 4, 2, 3, 21, 21, 21, 21, 10, 15, 14, 15, 19, 2, 4, 3, 6, 11, 3, 4, 6, 21, 16, 20, 11, 1, 4, 12, 0, 15, 8, 1, 3, 3, 12, 1, 11, 20, 4};
+	private final int[] base = {2, 13, 38, 51, 67, 78, 92, 118, 138, 162, 181, 191, 210, 222, 239, 253, 266, 280, 288, 304, 317, 333, 347, 359, 375, 386, 394, 406, 418, 433, 444, 457, 472, 482, 496, 506, 519, 529, 544, 557, 569, 579, 590, 601, 614, 626, 638, 649, 663, 673, 686, 706, 715, 731, 740, 753, 765, 777, 787, 799, 813, 826, 838, 854, 863, 876, 892, 901, 913, 929, 937, 948, 960, 970, 981, 993, 1004, 1017, 1034, 1045, 1056, 1068, 1080, 1091, 1103, 1115, 1126, 1138, 1148, 1160, 1177, 1187, 1199, 1211, 1222, 1232, 1243, 1254, 1268, 1279, 1294, 1307, 1319, 1330, 1341, 1352, 1362, 1374, 1388, 1398, 1411, 1422, 1433, 1444, 1456, 1466, 1479, 1497, 1506, 1519, 1531, 1543, 1556, 1567, 1578, 1589, 1604, 1614, 1630, 1641, 1651, 1662, 1675, 1688, 1700, 1711, 1721, 1732, 1748, 1758, 1772, 1784, 1795, 1806, 1820, 1830, 1844, 1855, 1866, 1877, 1892, 1902, 1914, 1926, 1939, 1950, 1965, 1974, 1986, 1999, 2011, 2023, 2037, 2047, 2059, 2072, 2084, 2096, 2107, 2120, 2132, 2144, 2156, 2169, 2180, 2191, 2202, 2217, 2227, 2239, 2251, 2264, 2275, 2286, 2297, 2309, 2321, 2332, 2347, 2358, 2369, 2381, 2394, 2406, 2417, 2429, 2439, 2452, 2465, 2476, 2490, 2501, 2512, 2524, 2536, 2546, 2560, 2570, 2581, 2593, 2605, 2616, 2628, 2640, 2653, 2664, 2676, 2688, 2700, 2712, 2723, 2735, 2748, 2759, 2772, 2784, 2795, 2808, 2820, 2831, 2842, 2854, 2866, 2878, 2888, 2901, 2913, 2927, 2936, 2947, 2958, 2970, 2982, 2994, 3005, 3019, 3030, 3041, 3053, 3064, 3077, 3088, 3099, 3110, 3123, 3135, 3146, 3157, 3168, 3179, 3192, 3203, 3214, 3226, 3238, 3251, 3263, 3275, 3286, 3297, 3308, 3320, 3331, 3344, 3356, 3368, 3380, 3391, 3402, 3415, 3426, 3440, 3451, 3462, 3474, 3485, 3496, 3508, 3520, 3532, 3543, 3556, 3569, 3580, 3593, 3604, 3615, 3626, 3638, 3650, 3661, 3673, 3684, 3698, 3709, 3721, 3732, 3744, 3756, 3767, 3779, 3792, 3803, 3814, 3827, 3838, 3850, 3862, 3873, 3885, 3897, 3909, 3920, 3932, 3943, 3955, 3966, 3980, 3990, 4002, 4014, 4026, 4038, 4050, 4061, 4072, 4083, 4095, 4107, 4119, 4131, 4143, 4156, 4167, 4179, 4191, 4203, 4215, 4227, 4238, 4252, 4262, 4274, 4287, 4298, 4310, 4321, 4333, 4345, 4356, 4370, 4381, 4393, 4406, 4417, 4428, 4440, 4453, 4464, 4477, 4489, 4500, 4513, 4524, 4536, 4548, 4560, 4573, 4583, 4595, 4607, 4620, 4631, 4645, 4655, 4667, 4679, 4690, 4702, 4714, 4728, 4739, 4750, 4762, 4774, 4786, 4798, 4810, 4821, 4833, 4845, 4857, 4869, 4880, 4892, 4905, 4916, 4927, 4940, 4952, 4963, 4977, 4988, 5000, 5012, 5023, 5034, 5045, 5057, 5069, 5081, 5093, 5104, 5115, 5127, 5139, 5151, 5163, 5176, 5188, 5199, 5211, 5223, 5235, 5247, 5259, 5272, 5283, 5296, 5308, 5320, 5331, 5343, 5354, 5366, 5378, 5390, 5402, 5414, 5426, 5438, 5450, 5462, 5474, 5486, 5497, 5510, 5521, 5532, 5544, 5557, 5569, 5581, 5592, 5604, 5617, 5629, 5641, 5652, 5663, 5676, 5687, 5699, 5712, 5724, 5735, 5748, 5760, 5771, 5784, 5794, 5806, 5817, 5829, 5841, 5853, 5866, 5879, 5891, 5903, 5916, 5928, 5941, 5952, 5964, 5976, 5988, 6000, 6012, 6024, 6036, 6048, 6060, 6072, 6085, 6096, 6109, 6121, 6133, 6146, 6157, 6168, 6180, 6192, 6203, 6215, 6227, 6239, 6251, 6265, 6276, 6289, 6302, 6313, 6325, 6337, 6349, 6361, 6374, 6386, 6398, 6410, 6422, 6436, 6448, 6459, 6471, 6483, 6495, 6507, 6520, 6532, 6545, 6555, 6567, 6579, 6591, 6603, 6615, 6627, 6640, 6652, 6664, 6676, 6688, 6700, 6713, 6726, 6738, 6749, 6761, 6774, 6786, 6799, 6811, 6823, 6835, 6848, 6859, 6871, 6883, 6895, 6907, 6920, 6933, 6945, 6956, 6968, 6980, 6992, 7005, 7016, 7030, 7042, 7053, 7066, 7079, 7091, 7104, 7115, 7128, 7140, 7152, 7163, 7175, 7187, 7200, 7212, 7224, 7235, 7248, 7260, 7272, 7285, 7297, 7309, 7321, 7333, 7345, 7358, 7370, 7382, 7394, 7406, 7419, 7431, 7443, 7455, 7468, 7480, 7492, 7505, 7517, 7530, 7542, 7554, 7566, 7578, 7591, 7603, 7615, 7628, 7640, 7653, 7666, 7677, 7690, 7702, 7714, 7727, 7738, 7750, 7762, 7775, 7786, 7799, 7812, 7823, 7836, 7848, 7859, 7871, 7884, 7896, 7909, 7921, 7933, 7946, 7958, 7971, 7984, 7996, 8007, 8019, 8032, 8044, 8056, 8069, 8081, 8094, 8107, 8119, 8131, 8143, 8155, 8167, 8179, 8192, 8205, 8218, 8230, 8244, 8255, 8267, 8279, 8291, 8303, 8315, 8328, 8340, 8353, 8366, 8378, 8392, 8404, 8417, 8431, 8443, 8455, 8467, 8479, 8492, 8504, 8516, 8529, 8543, 8555, 8567, 8580, 8593, 8606, 8619, 8632, 8644, 8658, 8670, 8683, 8695, 8708, 8721, 8733, 8746, 8759, 8771, 8783, 8795, 8808, 8821, 8833, 8845, 8858, 8871, 8885, 8898, 8910, 8923, 8936, 8949, 8960, 8973, 8986, 9000, 9012, 9025, 9038, 9051, 9064, 9076, 9089, 9102, 9114, 9126, 9139, 9151, 9164, 9177, 9191, 9204, 9217, 9230, 9243, 9255, 9268, 9281, 9294, 9307, 9320, 9333, 9345, 9358, 9371, 9384, 9398, 9412, 9424, 9437, 9450, 9462, 9475, 9488, 9501, 9514, 9528, 9542, 9554, 9567, 9581, 9593, 9606, 9619, 9632, 9645, 9658, 9671, 9682, 9695, 9708, 9721, 9735, 9749, 9762, 9776, 9789, 9802, 9815, 9828, 9842, 9855, 9867, 9880, 9893, 9906, 9920, 9933, 9947, 9960, 9974, 9987, 10000, 10014, 10027, 10040, 10054, 10067, 10081, 10095, 10107, 10120, 10134, 10148, 10161, 10175, 10188, 10201, 10214, 10228, 10241, 10254, 10267, 10280, 10294, 10309, 10322, 10335, 10348, 10362, 10374, 10387, 10401, 10415, 10428, 10441, 10455, 10469, 10482, 10497, 10510, 10523, 10537, 10551, 10565, 10579, 10593, 10606, 10621, 10634, 10647, 10661, 10675, 10689, 10704, 10719, 10732, 10746, 10760, 10774, 10788, 10802, 10815, 10829, 10843, 10856, 10871, 10884, 10898, 10913, 10927, 10940, 10955, 10970, 10984, 10999, 11013, 11027, 11042, 11056, 11071, 11086, 11100, 11114, 11128, 11142, 11158, 11171, 11186, 11200, 11213, 11228, 11241, 11255, 11270, 11284, 11299, 11314, 11328, 11342, 11356, 11370, 11385, 11399, 11413, 11429, 11445, 11460, 11474, 11489, 11503, 11518, 11533, 11549, 11563, 11577, 11592, 11607, 11621, 11637, 11651, 11665, 11680, 11694, 11708, 11725, 11740, 11754, 11768, 11784, 11798, 11813, 11828, 11843, 11858, 11874, 11888, 11904, 11920, 11933, 11948, 11964, 11979, 11993, 12009, 12024, 12041, 12058, 12071, 12087, 12102, 12117, 12132, 12148, 12165, 12179, 12195, 12210, 12226, 12241, 12256, 12273, 12288, 12304, 12320, 12335, 12350, 12365, 12382, 12398, 12414, 12430, 12446, 12462, 12478, 12495, 12511, 12525, 12541, 12556, 12575, 12591, 12605, 12622, 12638, 12653, 12671, 12686, 12705, 12721, 12739, 12756, 12772, 12788, 12806, 12822, 12839, 12855, 12873, 12890, 12908, 12923, 12941, 12960, 12975, 12992, 13009, 13024, 13040, 13059, 13076, 13092, 13109, 13128, 13145, 13161, 13179, 13194, 13216, 13233, 13249, 13266, 13287, 13303, 13322, 13337, 13357, 13375, 13392, 13410, 13424, 13446, 13465, 13480, 13499, 13517, 13533, 13559, 13575, 13595, 13612, 13632, 13650, 13670, 13687, 13706, 13726, 13744, 13765, 13783, 13803, 13822, 13841, 13860, 13879, 13897, 13917, 13936, 13960, 13979, 13996, 14019, 14040, 14057, 14077, 14102, 14122, 14141, 14163, 14184, 14202, 14225, 14244, 14265, 14287, 14312, 14336, 14356, 14375, 14393, 14420, 14438, 14465, 14483, 14500, 14536, 14555, 14575, 14604, 14619, 14648, 14668, 14691, 14725, 14748, 14770, 14788, 14818, 14840, 14862, 14888, 14921, 14939, 14969, 14996, 15022, 15051, 15075, 15098, 15130, 15149, 15167, 15218, 15237, 15276, 15297, 15333, 15356, 15379, 15418, 15447, 15481, 15508, 15530, 15574, 15599, 15643, 15680, 15697, 15743, 15759, 15775, 15813, 15845, 15877, 15911, 15931, 15968, 16014, 16049, 16077, 16088, 16138, 16149, 16185, 16200, 16241, 16280, 16296};
 
 	public ABITracerTest() {
 	}
 
 	@BeforeClass
-	public static void setUpClass() throws Exception {
+	public static void setUpClass() {
 	}
 
 	@AfterClass
-	public static void tearDownClass() throws Exception {
+	public static void tearDownClass() {
 	}
 
 	@Before
@@ -84,7 +84,7 @@ public void testLocal() throws Exception {
 		Assert.assertEquals(1165, tracer.getSequenceLength());
 
 		//Test sequence of tracer for file 3730.ab1
-		Assert.assertTrue(sequence.equals(tracer.getSequence().getSequenceAsString()));
+		Assert.assertEquals(sequence, tracer.getSequence().getSequenceAsString());
 		//Test array that represents the quality of tracer for file 3730.ab1
 		Assert.assertArrayEquals(qual, tracer.getQcalls());
 		//Test array that represents the baseline of tracer for file 3730.ab1
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java
index 0222b54c47..1be322de07 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java
@@ -30,7 +30,6 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.LinkedHashMap;
-import java.util.logging.Level;
 
 /**
  *
@@ -44,11 +43,11 @@ public FastaReaderTest() {
 	}
 
 	@BeforeClass
-	public static void setUpClass() throws Exception {
+	public static void setUpClass() {
 	}
 
 	@AfterClass
-	public static void tearDownClass() throws Exception {
+	public static void tearDownClass() {
 	}
 
 	@Before
@@ -69,7 +68,7 @@ public void testProcess() throws Exception {
 		Assert.assertNotNull(inStream);
 
 
-		FastaReader<ProteinSequence,AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence,AminoAcidCompound>(inStream, new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+		FastaReader<ProteinSequence,AminoAcidCompound> fastaReader = new FastaReader<>(inStream, new GenericFastaHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
 		LinkedHashMap<String,ProteinSequence> proteinSequences = fastaReader.process();
 		inStream.close();
 
@@ -78,9 +77,8 @@ public void testProcess() throws Exception {
 		Assert.assertEquals(proteinSequences.size(), 283);
 
 		int seqNum = 0;
-		for(String id:proteinSequences.keySet()) {
-			ProteinSequence proteinSequence = proteinSequences.get(id);
-			switch(seqNum) {
+		for(ProteinSequence proteinSequence : proteinSequences.values()) {
+            switch(seqNum) {
 				case 0:
 					Assert.assertEquals(proteinSequence.getAccession().getID(), "A2D504_ATEGE/1-46");
 					Assert.assertEquals(proteinSequence.getSequenceAsString(), "-----------------FK-N----LP-LED----------------Q----ITL--IQY-----------SWM----------------------CL-SSFA------LSWRSYK---HTNSQFLYFAPDLVF-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------");
@@ -106,7 +104,7 @@ public void processIntTest() throws Exception {
 		logger.info("process(int)");
 		InputStream inStream = this.getClass().getResourceAsStream("/PF00104_small.fasta");
 		Assert.assertNotNull(inStream);
-		FastaReader<ProteinSequence,AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence,AminoAcidCompound>(inStream, new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+		FastaReader<ProteinSequence,AminoAcidCompound> fastaReader = new FastaReader<>(inStream, new GenericFastaHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
 		LinkedHashMap<String,ProteinSequence> proteinSequences = fastaReader.process(200);
 
 		//Should have 200 sequences
@@ -114,9 +112,8 @@ public void processIntTest() throws Exception {
 		Assert.assertEquals(proteinSequences.size(), 200);
 
 		int seqNum = 0;
-		for(String id:proteinSequences.keySet()) {
-			ProteinSequence proteinSequence = proteinSequences.get(id);
-			switch(seqNum) {
+		for(ProteinSequence proteinSequence : proteinSequences.values()) {
+            switch(seqNum) {
 				case 0:
 					Assert.assertEquals(proteinSequence.getAccession().getID(), "A2D504_ATEGE/1-46");
 					Assert.assertEquals(proteinSequence.getSequenceAsString(), "-----------------FK-N----LP-LED----------------Q----ITL--IQY-----------SWM----------------------CL-SSFA------LSWRSYK---HTNSQFLYFAPDLVF-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------");
@@ -134,9 +131,8 @@ public void processIntTest() throws Exception {
 		proteinSequences = fastaReader.process(200);
 		Assert.assertEquals(proteinSequences.size(), 83);
 		seqNum = 0;
-		for(String id:proteinSequences.keySet()) {
-			ProteinSequence proteinSequence = proteinSequences.get(id);
-			switch(seqNum) {
+		for(ProteinSequence proteinSequence : proteinSequences.values()) {
+            switch(seqNum) {
 				case 0:
 					Assert.assertEquals(proteinSequence.getAccession().getID(), "RARA_CANFA/233-413");
 					Assert.assertEquals(proteinSequence.getSequenceAsString(), "TKCIIKTVEFAKQL-PGFT-T----LT-IAD----------------Q----ITL--LKA-----------ACL----------------------DI-LILR------ICTRYTP---EQDTMTFSEGLTLN-------------------------------------------------------------------------------------------------------------------------------------------------------------RTQMHKAGFGPLTDLVFAFA-NQL-LPL-E-MDDAET--------------------GLLSA-ICLI-CGDRQD-------------------------------------------LEQP--DRVDMLQEPLLEALKV-Y-----VRK---------RR---PS----------------------------RP------H--------MFP-KMLMKITD-LRSIS-----------------AKG-AERV--ITLKMEIPG--SMP--PLI-------QEM---");
@@ -164,9 +160,9 @@ public void testSmallFasta() throws IOException {
 
 		InputStream inStream = this.getClass().getResourceAsStream("/test.fasta");
 
-		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
 				inStream,
-				new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+				new GenericFastaHeaderParser<>(),
 				new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
 
 		LinkedHashMap<String, ProteinSequence> b;
@@ -192,9 +188,9 @@ public void testSmallFasta2() throws IOException {
 
 		InputStream inStream = this.getClass().getResourceAsStream("/test.fasta");
 
-		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
 				inStream,
-				new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+				new GenericFastaHeaderParser<>(),
 				new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
 
 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
index d6018a5eaf..b04357f6ee 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
@@ -46,11 +46,11 @@ public GenbankCookbookTest() {
 	}
 
 	@BeforeClass
-	public static void setUpClass() throws Exception {
+	public static void setUpClass() {
 	}
 
 	@AfterClass
-	public static void tearDownClass() throws Exception {
+	public static void tearDownClass() {
 	}
 
 	@Before
@@ -71,13 +71,13 @@ public void testProcess() throws Throwable {
 		 */
 		//Try with the GenbankProxySequenceReader
 		GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
-				= new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"), "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+				= new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"), "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
 		ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
 		genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
 		//logger.info("Sequence({},{}) = {}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
 
 	GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
-	= new GenbankProxySequenceReader<NucleotideCompound>(System.getProperty("java.io.tmpdir"), "NM_001126", DNACompoundSet.getDNACompoundSet());
+	= new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"), "NM_001126", DNACompoundSet.getDNACompoundSet());
 	DNASequence dnaSequence = new DNASequence(genbankDNAReader);
 	genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 	//logger.info("Sequence({},{}) = {}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
@@ -104,9 +104,9 @@ public void testProcess() throws Throwable {
 		 */
 		//Try reading with the GanbankReader
 
-		GenbankReader<DNASequence, NucleotideCompound> dnaReader = new GenbankReader<DNASequence, NucleotideCompound>(
+		GenbankReader<DNASequence, NucleotideCompound> dnaReader = new GenbankReader<>(
 				dnaResource.getInputStream(),
-				new GenericGenbankHeaderParser<DNASequence, NucleotideCompound>(),
+				new GenericGenbankHeaderParser<>(),
 				new DNASequenceCreator(DNACompoundSet.getDNACompoundSet())
 		);
 		dnaSequences = dnaReader.process();
@@ -114,9 +114,9 @@ public void testProcess() throws Throwable {
 		logger.debug("DNA Sequence: {}", dnaSequences);
 
 
-		GenbankReader<ProteinSequence, AminoAcidCompound> protReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(
+		GenbankReader<ProteinSequence, AminoAcidCompound> protReader = new GenbankReader<>(
 				protResource.getInputStream(),
-				new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
+				new GenericGenbankHeaderParser<>(),
 				new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())
 		);
 		protSequences = protReader.process();
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
index 5bcbecf672..e94d8bc0f7 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
@@ -72,11 +72,11 @@ public GenbankReaderTest() {
 	}
 
 	@BeforeClass
-	public static void setUpClass() throws Exception {
+	public static void setUpClass() {
 	}
 
 	@AfterClass
-	public static void tearDownClass() throws Exception {
+	public static void tearDownClass() {
 	}
 
 	@Before
@@ -169,7 +169,7 @@ public void testProcess() throws Exception {
 	 * The underlying {@link InputStream} should remain open until the last call.
 	 */
 	@Test
-	public void testPartialProcess() throws IOException, CompoundNotFoundException, NoSuchFieldException {
+	public void testPartialProcess() throws IOException, CompoundNotFoundException {
 		CheckableInputStream inStream = new CheckableInputStream(this.getClass().getResourceAsStream("/two-dnaseqs.gb"));
 
 		GenbankReader<DNASequence, NucleotideCompound> genbankDNA
@@ -217,7 +217,7 @@ public void CDStest() throws Exception {
 		assertTrue(inStream.isclosed());
 
 
-		Assert.assertTrue(proteinSequences.size() == 1);
+		assertEquals(1, proteinSequences.size());
 		logger.debug("protein sequences: {}", proteinSequences);
 
 		ProteinSequence protein = new ArrayList<>(proteinSequences.values()).get(0);
@@ -228,7 +228,7 @@ public void CDStest() throws Exception {
 		List<Qualifier> dbrefs = quals.get("db_xref");
 
 		Assert.assertNotNull(codedBy);
-		Assert.assertTrue(!codedBy.isEmpty());
+		assertFalse(codedBy.isEmpty());
 		assertEquals(codedBy, "NM_000266.2:503..904");
 		assertEquals(5, dbrefs.size());
 
@@ -353,7 +353,7 @@ public void testLegacyLocusCompatable() throws IOException, CompoundNotFoundExce
 	/**
 	 * Helper class to be able to verify the closed state of the input stream.
 	 */
-	private class CheckableInputStream extends BufferedInputStream {
+	private static class CheckableInputStream extends BufferedInputStream {
 
 		private boolean closed;
 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankWriterTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankWriterTest.java
index 6b54346226..9ac1f1b830 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankWriterTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankWriterTest.java
@@ -49,10 +49,8 @@ public void testProcess() throws Exception {
 		//File dnaFile = new File("src/test/resources/NM_000266.gb");
 		LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence( inStream );
 		ByteArrayOutputStream fragwriter = new ByteArrayOutputStream();
-		ArrayList<DNASequence> seqs = new ArrayList<DNASequence>();
-		for(DNASequence seq : dnaSequences.values()) {
-			seqs.add(seq);
-		}
+		ArrayList<DNASequence> seqs = new ArrayList<>();
+        seqs.addAll(dnaSequences.values());
 		GenbankWriterHelper.writeNucleotideSequence(fragwriter, seqs,
 				GenbankWriterHelper.LINEAR_DNA);
 		//System.out.println(fragwriter.toString());
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParserTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParserTest.java
index 1d41e734ac..13d27418f9 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParserTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParserTest.java
@@ -42,11 +42,11 @@ public GenericFastaHeaderParserTest() {
 	}
 
 	@BeforeClass
-	public static void setUpClass() throws Exception {
+	public static void setUpClass() {
 	}
 
 	@AfterClass
-	public static void tearDownClass() throws Exception {
+	public static void tearDownClass() {
 	}
 
 	@Before
@@ -78,9 +78,9 @@ public void tearDown() {
 	@Test
 	public void testParseHeader() throws CompoundNotFoundException {
 		logger.info("parseHeader");
-		String header = "";
+		String header;
 		ProteinSequence sequence = new ProteinSequence("");
-		GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound> instance = new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>();
+		GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound> instance = new GenericFastaHeaderParser<>();
 
 		header = "gi|gi-number|gb|accession|locus";
 		instance.parseHeader(header, sequence);
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
index 647d86df4d..edcba6c41b 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
@@ -55,7 +55,7 @@
 @RunWith(Parameterized.class)
 public class GenbankProxySequenceReaderTest {
 
-	private String gi;
+	private final String gi;
 	private final static Logger logger = LoggerFactory.getLogger(GenbankProxySequenceReaderTest.class);
 
 	public GenbankProxySequenceReaderTest(String gi) {
@@ -166,7 +166,7 @@ so it should be done here (manualy).
 			logger.info("CDS: {}", CDS);
 			String codedBy = CDS.getQualifiers().get("coded_by").get(0).getValue();
 			Assert.assertNotNull(codedBy);
-			Assert.assertTrue(!codedBy.isEmpty());
+			Assert.assertFalse(codedBy.isEmpty());
 			logger.info("\t\tcoded_by: {}", codedBy);
 		}
 
@@ -205,7 +205,7 @@ public void testProteinSequenceFactoring() throws Exception {
 					 That test is always failed
 					 */
 					//Assert.assertTrue(parentSeq.getAccession());
-					Assert.assertTrue(!parentSeq.getSequenceAsString().isEmpty());
+					Assert.assertFalse(parentSeq.getSequenceAsString().isEmpty());
 				}
 			}
 		} else {
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
index 4150e90ffc..e7967abe81 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
@@ -48,9 +48,9 @@ public void testWrongSequence() throws Exception {
 		String wrongGi = "34567";
 
 		GenbankProxySequenceReader<AminoAcidCompound> genbankReader
-				= new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
-						wrongGi,
-						AminoAcidCompoundSet.getAminoAcidCompoundSet());
+				= new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"),
+				wrongGi,
+				AminoAcidCompoundSet.getAminoAcidCompoundSet());
 
 		ProteinSequence seq = new ProteinSequence(genbankReader);
 	}
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/InsdcParserTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/InsdcParserTest.java
index 01094c84ba..99b6b96793 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/InsdcParserTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/InsdcParserTest.java
@@ -38,9 +38,9 @@
 @RunWith(Parameterized.class)
 public class InsdcParserTest {
 
-	private Logger log = LoggerFactory.getLogger(getClass());
-	private String data;
-	private String expected;
+	private final Logger log = LoggerFactory.getLogger(getClass());
+	private final String data;
+	private final String expected;
 
 	public InsdcParserTest(String data, String expected) {
 		this.data = data;
@@ -58,10 +58,9 @@ public static Collection<String[]> data() {
 	/**
 	 * Test for issue #254
 	 *
-	 * @throws Exception
 	 */
 	@Test
-	public void extractAccessionTest() throws Exception {
+	public void extractAccessionTest() {
 		log.info("test accession");
 		log.debug("data: '{}'   expected: '{}'", data, expected);
 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/LocationParserTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/LocationParserTest.java
index 3c562498b5..14cf3ebaaa 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/LocationParserTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/LocationParserTest.java
@@ -54,7 +54,7 @@ public class LocationParserTest {
 
 	public static final InsdcParser PARSER = new InsdcParser();
 
-	private Logger log = LoggerFactory.getLogger(getClass());
+	private final Logger log = LoggerFactory.getLogger(getClass());
 
 	@Test
 	@Ignore
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/TargetedLocationParserTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/TargetedLocationParserTest.java
index 6ea7c9f869..0f0267c8de 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/TargetedLocationParserTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/TargetedLocationParserTest.java
@@ -40,10 +40,10 @@
 @RunWith(Parameterized.class)
 public class TargetedLocationParserTest {
 
-	private Data request;
+	private final Data request;
 
 	public static class Data {
-		private String Insdc;
+		private final String Insdc;
 
 		/**
 		 * Parser data input. Based on that input it should be able to identity the origin and wanted target
@@ -55,10 +55,10 @@ public static class Data {
 		public Data(String gi, CompoundSet<?> originType, String Insdc, CompoundSet<?> compound) {
 			this.Insdc = Insdc;
 		}
-	};
+	}
 
 	@Parameterized.Parameters
-	public static Collection<Data[]> getLocations() throws Exception {
+	public static Collection<Data[]> getLocations() {
 
 
 		Data[][] out = new Data[][]{
@@ -85,7 +85,7 @@ public TargetedLocationParserTest(Data request) {
 
 
 	@Test
-	public void locationTest() throws Exception {
+	public void locationTest() {
 
 		InsdcParser parser = new InsdcParser(DataSource.GENBANK);
 		Location loc = parser.parse(request.Insdc);
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/views/WindowViewTests.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/views/WindowViewTests.java
index 90d4da3a01..e27962adb4 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/views/WindowViewTests.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/views/WindowViewTests.java
@@ -38,7 +38,7 @@ public class WindowViewTests {
 	@Test
 	public void basicWindow() throws CompoundNotFoundException {
 		RNASequence rna = new RNASequence("AUGCCU");
-		WindowedSequence<NucleotideCompound> window = new WindowedSequence<NucleotideCompound>(rna, 3);
+		WindowedSequence<NucleotideCompound> window = new WindowedSequence<>(rna, 3);
 
 		Iterator<SequenceView<NucleotideCompound>> iter = window.iterator();
 		assertTrue("hasNext() returns true", iter.hasNext());
@@ -57,8 +57,8 @@ public void basicWindow() throws CompoundNotFoundException {
 	@Test
 	public void reaminderWindow() throws CompoundNotFoundException {
 		RNASequence rna = new RNASequence("AUGCC");
-		WindowedSequence<NucleotideCompound> window = new WindowedSequence<NucleotideCompound>(rna, 3);
-		List<SequenceView<NucleotideCompound>> list = new ArrayList<SequenceView<NucleotideCompound>>();
+		WindowedSequence<NucleotideCompound> window = new WindowedSequence<>(rna, 3);
+		List<SequenceView<NucleotideCompound>> list = new ArrayList<>();
 		for(SequenceView<NucleotideCompound> c: window) {
 			list.add(c);
 		}
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/util/TestUncompressInputStream.java b/biojava-core/src/test/java/org/biojava/nbio/core/util/TestUncompressInputStream.java
index 470eacfbbf..be889f6ba3 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/util/TestUncompressInputStream.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/util/TestUncompressInputStream.java
@@ -60,7 +60,7 @@ public void testUncompression() throws Exception {
 		ByteArrayOutputStream obaos = new ByteArrayOutputStream();
 		try (BufferedInputStream oin = new BufferedInputStream(
 				this.getClass().getClassLoader()
-				.getResourceAsStream(ORIG_OF_BIGGER_TEST_FILE));) {
+				.getResourceAsStream(ORIG_OF_BIGGER_TEST_FILE))) {
 			byte[] buf = new byte[100000];
 			int len;
 			while ((len = oin.read(buf)) >= 0)
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java
index 7f7294801e..e6a7459918 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java
@@ -28,10 +28,7 @@
 
 import java.io.File;
 import java.io.FileWriter;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.LinkedHashMap;
+import java.util.*;
 
 /**
  *
@@ -42,13 +39,13 @@ public class GeneFeatureHelper {
 	private static final Logger logger = LoggerFactory.getLogger(GeneFeatureHelper.class);
 
 	static public LinkedHashMap<String, ChromosomeSequence> loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(File fastaSequenceFile, File uppercaseFastaFile, boolean throwExceptionGeneNotFound) throws Exception {
-		LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList = new LinkedHashMap<String, ChromosomeSequence>();
+		LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList = new LinkedHashMap<>();
 		LinkedHashMap<String, DNASequence> dnaSequenceList = FastaReaderHelper.readFastaDNASequence(fastaSequenceFile);
-		for (String accession : dnaSequenceList.keySet()) {
-			DNASequence contigSequence = dnaSequenceList.get(accession);
+		for (Map.Entry<String, DNASequence> entry : dnaSequenceList.entrySet()) {
+			DNASequence contigSequence = entry.getValue();
 			ChromosomeSequence chromsomeSequence = new ChromosomeSequence(contigSequence.getSequenceAsString());
 			chromsomeSequence.setAccession(contigSequence.getAccession());
-			chromosomeSequenceList.put(accession, chromsomeSequence);
+			chromosomeSequenceList.put(entry.getKey(), chromsomeSequence);
 		}
 
 
@@ -91,7 +88,7 @@ static public LinkedHashMap<String, ChromosomeSequence> loadFastaAddGeneFeatures
 						dnaSequence.getAccession().toString(), contigDNASequence.getAccession().toString(), bioStart, bioEnd, strand);
 				ChromosomeSequence chromosomeSequence = chromosomeSequenceList.get(accession);
 
-				ArrayList<Integer> exonBoundries = new ArrayList<Integer>();
+				ArrayList<Integer> exonBoundries = new ArrayList<>();
 
 				//look for transitions from lowercase to upper case
 				for (int i = 0; i < geneSequence.length(); i++) {
@@ -314,12 +311,12 @@ static public void addGeneIDGFF2GeneFeatures(LinkedHashMap<String, ChromosomeSeq
 	}
 
 	static public LinkedHashMap<String, ChromosomeSequence> getChromosomeSequenceFromDNASequence(LinkedHashMap<String, DNASequence> dnaSequenceList) {
-		LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList = new LinkedHashMap<String, ChromosomeSequence>();
-		for (String key : dnaSequenceList.keySet()) {
-			DNASequence dnaSequence = dnaSequenceList.get(key);
+		LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList = new LinkedHashMap<>();
+		for (Map.Entry<String, DNASequence> entry : dnaSequenceList.entrySet()) {
+			DNASequence dnaSequence = entry.getValue();
 			ChromosomeSequence chromosomeSequence = new ChromosomeSequence(dnaSequence.getProxySequenceReader()); //we want the underlying sequence but don't need storage
 			chromosomeSequence.setAccession(dnaSequence.getAccession());
-			chromosomeSequenceList.put(key, chromosomeSequence);
+			chromosomeSequenceList.put(entry.getKey(), chromosomeSequence);
 		}
 		return chromosomeSequenceList;
 	}
@@ -361,10 +358,10 @@ static public void addGmodGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSeque
 		for (FeatureI f : mRNAFeatures) {
 			String geneID;
 			String geneNote = null;
-			String geneSource = null;
-			String sequenceName = null;
-			ChromosomeSequence seq = null;
-			GeneSequence geneSequence = null;
+			String geneSource;
+			String sequenceName;
+			ChromosomeSequence seq;
+			GeneSequence geneSequence;
 
 			Feature mRNAFeature = (Feature) f;
 			String mRNAID = mRNAFeature.getAttribute("ID");
@@ -835,8 +832,8 @@ static public void addGeneMarkGTFGeneFeatures(LinkedHashMap<String, ChromosomeSe
 
 	}
 
-	static public LinkedHashMap<String, ProteinSequence> getProteinSequences(Collection<ChromosomeSequence> chromosomeSequences) throws Exception {
-		LinkedHashMap<String, ProteinSequence> proteinSequenceHashMap = new LinkedHashMap<String, ProteinSequence>();
+	static public LinkedHashMap<String, ProteinSequence> getProteinSequences(Collection<ChromosomeSequence> chromosomeSequences) {
+		LinkedHashMap<String, ProteinSequence> proteinSequenceHashMap = new LinkedHashMap<>();
 		for (ChromosomeSequence dnaSequence : chromosomeSequences) {
 			for (GeneSequence geneSequence : dnaSequence.getGeneSequences().values()) {
 				for (TranscriptSequence transcriptSequence : geneSequence.getTranscripts().values()) {
@@ -864,8 +861,8 @@ static public LinkedHashMap<String, ProteinSequence> getProteinSequences(Collect
 		return proteinSequenceHashMap;
 	}
 
-	static public LinkedHashMap<String, GeneSequence> getGeneSequences(Collection<ChromosomeSequence> chromosomeSequences) throws Exception {
-		LinkedHashMap<String, GeneSequence> geneSequenceHashMap = new LinkedHashMap<String, GeneSequence>();
+	static public LinkedHashMap<String, GeneSequence> getGeneSequences(Collection<ChromosomeSequence> chromosomeSequences) {
+		LinkedHashMap<String, GeneSequence> geneSequenceHashMap = new LinkedHashMap<>();
 		for (ChromosomeSequence chromosomeSequence : chromosomeSequences) {
 			for (GeneSequence geneSequence : chromosomeSequence.getGeneSequences().values()) {
 				geneSequenceHashMap.put(geneSequence.getAccession().getID(), geneSequence);
@@ -875,7 +872,7 @@ static public LinkedHashMap<String, GeneSequence> getGeneSequences(Collection<Ch
 		return geneSequenceHashMap;
 	}
 
-	public static void main(String[] args) throws Exception {
+	public static void main(String[] args) {
 /*        if (false) {
 			LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList = GeneFeatureHelper.loadFastaAddGeneFeaturesFromGeneMarkGTF(new File("Scaffolds.fna"), new File("genemark_hmm.gtf"));
 			LinkedHashMap<String, ProteinSequence> proteinSequenceList = GeneFeatureHelper.getProteinSequences(chromosomeSequenceList.values());
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java
index 88881b37eb..831a8875bc 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java
@@ -25,6 +25,7 @@
 import java.io.File;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
+import java.util.Map;
 
 /**
  *
@@ -33,13 +34,13 @@
 public class BlastHomologyHits {
 
 	static public LinkedHashMap<String, ArrayList<String>> getMatches(File xmlBlastHits, double ecutoff) throws Exception {
-		LinkedHashMap<String, ArrayList<String>> homologyHits = new LinkedHashMap<String, ArrayList<String>>();
+		LinkedHashMap<String, ArrayList<String>> homologyHits = new LinkedHashMap<>();
 		BlastXMLQuery blastXMLQuery = new BlastXMLQuery(xmlBlastHits.getAbsolutePath());
 		LinkedHashMap<String, ArrayList<String>> hits = blastXMLQuery.getHitsQueryDef(ecutoff);
-		for (String accessionid : hits.keySet()) {
-			String[] data = accessionid.split(" "); // deal with notes/comments in blast results
+		for (Map.Entry<String, ArrayList<String>> entry : hits.entrySet()) {
+			String[] data = entry.getKey().split(" "); // deal with notes/comments in blast results
 			String id = data[0];
-			ArrayList<String> uniprotProteinHits = hits.get(accessionid);
+			ArrayList<String> uniprotProteinHits = entry.getValue();
 			homologyHits.put(id, uniprotProteinHits);
 
 		}
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
index 0910b6b68d..7efaf5de2f 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
@@ -41,6 +41,7 @@
 import java.io.OutputStream;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
+import java.util.Map;
 
 /**
  *
@@ -56,12 +57,13 @@ public void process(File xmlBlastHits, double ecutoff, LinkedHashMap<String, Gen
 		process(hits, geneSequenceHashMap, gff3Output);
 	}
 
-	public void process(LinkedHashMap<String, ArrayList<String>> hits, LinkedHashMap<String, GeneSequence> geneSequenceHashMap, OutputStream gff3Output) throws Exception {
+	public void process(LinkedHashMap<String, ArrayList<String>> hits, LinkedHashMap<String, GeneSequence> geneSequenceHashMap, OutputStream gff3Output) {
 		int size = hits.size();
 		int index = 0;
 //		HashMap<String, String> scaffoldsReferencedHashMap = new HashMap<String, String>();
-		for (String accessionid : hits.keySet()) {
-			index++;
+		for (Map.Entry<String, ArrayList<String>> stringArrayListEntry : hits.entrySet()) {
+            String accessionid = stringArrayListEntry.getKey();
+            index++;
 			if (index == 12) {
 				index = 12;
 			}
@@ -75,9 +77,9 @@ public void process(LinkedHashMap<String, ArrayList<String>> hits, LinkedHashMap
 					logger.error("Not found " + id);
 					continue;
 				}
-				ArrayList<String> uniprotProteinHits = hits.get(accessionid);
+				ArrayList<String> uniprotProteinHits = stringArrayListEntry.getValue();
 				String uniprotBestHit = uniprotProteinHits.get(0);
-				UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<AminoAcidCompound>(uniprotBestHit, AminoAcidCompoundSet.getAminoAcidCompoundSet());
+				UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<>(uniprotBestHit, AminoAcidCompoundSet.getAminoAcidCompoundSet());
 
 				ProteinSequence proteinSequence = new ProteinSequence(uniprotSequence);
 				String hitSequence = proteinSequence.getSequenceAsString();
@@ -87,7 +89,7 @@ public void process(LinkedHashMap<String, ArrayList<String>> hits, LinkedHashMap
 					String predictedProteinSequence = transcriptSequence.getProteinSequence().getSequenceAsString();
 					ArrayList<ProteinSequence> cdsProteinList = transcriptSequence.getProteinCDSSequences();
 
-					ArrayList<CDSSequence> cdsSequenceList = new ArrayList<CDSSequence>(transcriptSequence.getCDSSequences().values());
+					ArrayList<CDSSequence> cdsSequenceList = new ArrayList<>(transcriptSequence.getCDSSequences().values());
 					String testSequence = "";
 					for (ProteinSequence cdsProteinSequence : cdsProteinList) {
 						testSequence = testSequence + cdsProteinSequence.getSequenceAsString();
@@ -140,7 +142,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
 						proteinIndex = proteinIndex + seq.length();
 						if (startIndex != null && endIndex != null && startIndex != endIndex) {
 							CDSSequence cdsSequence = cdsSequenceList.get(i);
-							String hitLabel = "";
+							String hitLabel;
 							if (transcriptSequence.getStrand() == Strand.POSITIVE) {
 								hitLabel = uniprotBestHit + "_" + startIndex + "_" + endIndex;
 							} else {
@@ -227,11 +229,11 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
 											notes = notes + " " + note.getId();
 											geneSequence.addNote(note.getId()); // add note/keyword which can be output in fasta header if needed
 											LinkedHashMap<String, String> properties = note.getProperties();
-											for (String propertytype : properties.keySet()) {
-												if (propertytype.equals("evidence")) {
+											for (Map.Entry<String, String> entry : properties.entrySet()) {
+												if (entry.getKey().equals("evidence")) {
 													continue;
 												}
-												String property = properties.get(propertytype);
+												String property = entry.getValue();
 
 												if (property.startsWith("C:")) {
 													continue; // skip over the location
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReader.java
index 17ca61205c..e6326dc29e 100755
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReader.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReader.java
@@ -27,6 +27,7 @@
 import java.io.*;
 import java.net.URL;
 import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
 import java.util.List;
 
 /**
@@ -100,7 +101,7 @@ public final Iterable<Fastq> read(final URL url) throws IOException
 		Collect collect = new Collect();
 		try
 		{
-			reader = Resources.asCharSource(url, Charset.forName("UTF-8")).openBufferedStream();
+			reader = Resources.asCharSource(url, StandardCharsets.UTF_8).openBufferedStream();
 			stream(reader, collect);
 		}
 		finally
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriter.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriter.java
index 5df7443995..f438cfec63 100755
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriter.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriter.java
@@ -100,27 +100,11 @@ public final void write(final File file, final Iterable<Fastq> fastq) throws IOE
 		{
 			throw new IllegalArgumentException("fastq must not be null");
 		}
-		Writer writer = null;
-		try
-		{
-			writer = new BufferedWriter(new FileWriter(file));
-			append(writer, fastq);
-		}
-		finally
-		{
-			if (writer != null)
-			{
-				try
-				{
-					writer.close();
-				}
-				catch (IOException e)
-				{
-					// ignore
-				}
-			}
-		}
-	}
+        try (Writer writer = new BufferedWriter(new FileWriter(file))) {
+            append(writer, fastq);
+        }
+        // ignore
+    }
 
 	@Override
 	public final void write(final OutputStream outputStream, final Fastq... fastq) throws IOException
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqParser.java
index 52f5141df2..b636415775 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqParser.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqParser.java
@@ -122,8 +122,8 @@ public Object getResult()
 		@Override
 		public boolean processLine(final String line) throws IOException
 		{
-			String sequence = null;
-			String quality = null;
+			String sequence;
+			String quality;
 			switch (state)
 			{
 			case DESCRIPTION:
@@ -192,7 +192,7 @@ public boolean processLine(final String line) throws IOException
 	}
 
 	/** Parser state. */
-	private static enum State
+	private enum State
 	{
 		/** Description parser state. */
 		DESCRIPTION,
@@ -207,6 +207,6 @@ private static enum State
 		QUALITY,
 
 		/** Complete parser state. */
-		COMPLETE;
-	};
+		COMPLETE
+	}
 }
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqTools.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqTools.java
index 437d7bd435..78191a7655 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqTools.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqTools.java
@@ -133,7 +133,7 @@ public static QualityFeature<AbstractSequence<NucleotideCompound>, NucleotideCom
 		{
 			throw new IllegalArgumentException("fastq must not be null");
 		}
-		QualityFeature<AbstractSequence<NucleotideCompound>, NucleotideCompound> qualityScores = new QualityFeature<AbstractSequence<NucleotideCompound>, NucleotideCompound>("qualityScores", "sequencing");
+		QualityFeature<AbstractSequence<NucleotideCompound>, NucleotideCompound> qualityScores = new QualityFeature<>("qualityScores", "sequencing");
 		qualityScores.setQualities(toList(qualityScores(fastq)));
 		return qualityScores;
 	}
@@ -153,7 +153,7 @@ public static QuantityFeature<AbstractSequence<NucleotideCompound>, NucleotideCo
 		{
 			throw new IllegalArgumentException("fastq must not be null");
 		}
-		QuantityFeature<AbstractSequence<NucleotideCompound>, NucleotideCompound> errorProbabilities = new QuantityFeature<AbstractSequence<NucleotideCompound>, NucleotideCompound>("errorProbabilities", "sequencing");
+		QuantityFeature<AbstractSequence<NucleotideCompound>, NucleotideCompound> errorProbabilities = new QuantityFeature<>("errorProbabilities", "sequencing");
 		errorProbabilities.setQuantities(toList(errorProbabilities(fastq)));
 		return errorProbabilities;
 	}
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqVariant.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqVariant.java
index efffbf4f78..8df5972166 100755
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqVariant.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqVariant.java
@@ -186,7 +186,7 @@ public double errorProbability(final int qualityScore)
 
 
 	/** Map of FASTQ sequence format variants keyed by name and lowercase-with-dashes name. */
-	private static final Map<String, FastqVariant> FASTQ_VARIANTS = new HashMap<String, FastqVariant>(6);
+	private static final Map<String, FastqVariant> FASTQ_VARIANTS = new HashMap<>(6);
 
 	static
 	{
@@ -206,7 +206,7 @@ public double errorProbability(final int qualityScore)
 	 *
 	 * @param description description of this FASTQ sequence format variant, must not be null
 	 */
-	private FastqVariant(final String description)
+	FastqVariant(final String description)
 	{
 		if (description == null)
 		{
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/ParseListener.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/ParseListener.java
index f03f77fc92..14890b9ead 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/ParseListener.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/ParseListener.java
@@ -33,9 +33,8 @@ public interface ParseListener
 	 * Notify this parse listener of a description line.
 	 *
 	 * @param description description line
-	 * @throws IOException if an I/O error occurs
-	 */
-	void description(String description) throws IOException;
+     */
+	void description(String description);
 
 	/**
 	 * Notify this parse listener of a sequence line.
@@ -47,9 +46,8 @@ public interface ParseListener
 	 * </p>
 	 *
 	 * @param sequence sequence line
-	 * @throws IOException if an I/O error occurs
-	 */
-	void sequence(String sequence) throws IOException;
+     */
+	void sequence(String sequence);
 
 	/**
 	 * Notify this parse listener of an additional sequence line.
@@ -60,9 +58,8 @@ public interface ParseListener
 	 * </p>
 	 *
 	 * @param sequence additional sequence line
-	 * @throws IOException if an I/O error occurs
-	 */
-	void appendSequence(String sequence) throws IOException;
+     */
+	void appendSequence(String sequence);
 
 	/**
 	 * Notify this parse listener of a repeat description line.
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/StreamingFastqParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/StreamingFastqParser.java
index a0455381ed..c22db24fc7 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/StreamingFastqParser.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/StreamingFastqParser.java
@@ -58,20 +58,17 @@ static void stream(final Readable readable, final FastqVariant variant, final St
 		FastqParser.parse(readable, new ParseListener()
 			{
 				@Override
-				public void description(final String description) throws IOException
-				{
+				public void description(final String description) {
 					builder.withDescription(description);
 				}
 
 				@Override
-				public void sequence(final String sequence) throws IOException
-				{
+				public void sequence(final String sequence) {
 					builder.withSequence(sequence);
 				}
 
 				@Override
-				public void appendSequence(final String sequence) throws IOException
-				{
+				public void appendSequence(final String sequence) {
 					builder.appendSequence(sequence);
 				}
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/cytoband/CytobandParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/cytoband/CytobandParser.java
index 560566b0b2..5655976e2f 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/cytoband/CytobandParser.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/cytoband/CytobandParser.java
@@ -52,11 +52,10 @@ public static void main(String[] args) {
 		try {
 			SortedSet<Cytoband> cytobands = me.getAllCytobands(new URL(
 					DEFAULT_LOCATION));
-			SortedSet<StainType> types = new TreeSet<StainType>();
+			SortedSet<StainType> types = new TreeSet<>();
 			for (Cytoband c : cytobands) {
 				logger.info("Cytoband: {}", c);
-				if (!types.contains(c.getType()))
-					types.add(c.getType());
+                types.add(c.getType());
 			}
 			logger.info("Strain Type: {}", types);
 		} catch (Exception e) {
@@ -76,8 +75,8 @@ public SortedSet<Cytoband> getAllCytobands(InputStream instream)
 			throws IOException {
 		BufferedReader reader = new BufferedReader(new InputStreamReader(
 				instream));
-		String line = null;
-		SortedSet<Cytoband> cytobands = new TreeSet<Cytoband>();
+		String line;
+		SortedSet<Cytoband> cytobands = new TreeSet<>();
 		while ((line = reader.readLine()) != null) {
 			String[] spl = line.split("\t");
 			if (spl.length != 5) {
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java
index a573a7062d..c6ba1a0d4c 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java
@@ -42,7 +42,7 @@ public class GeneIDXMLReader {
 
 	private static final Logger logger = LoggerFactory.getLogger(GeneIDXMLReader.class);
 
-	Document geneidDoc = null;
+	Document geneidDoc;
 
 	public GeneIDXMLReader(String geneidXMLFile) throws Exception {
 		logger.info("Start read of {}", geneidXMLFile);
@@ -51,7 +51,7 @@ public GeneIDXMLReader(String geneidXMLFile) throws Exception {
 	}
 
 	public LinkedHashMap<String, ProteinSequence> getProteinSequences() throws Exception {
-		LinkedHashMap<String, ProteinSequence> proteinSequenceList = new LinkedHashMap<String, ProteinSequence>();
+		LinkedHashMap<String, ProteinSequence> proteinSequenceList = new LinkedHashMap<>();
 		ArrayList<Element> elementList = XMLHelper.selectElements(geneidDoc.getDocumentElement(), "prediction/gene/protein");
 		logger.info("{} hits", elementList.size());
 
@@ -68,7 +68,7 @@ public LinkedHashMap<String, ProteinSequence> getProteinSequences() throws Excep
 	}
 
 	public LinkedHashMap<String, DNASequence> getDNACodingSequences() throws Exception {
-		LinkedHashMap<String, DNASequence> dnaSequenceList = new LinkedHashMap<String, DNASequence>();
+		LinkedHashMap<String, DNASequence> dnaSequenceList = new LinkedHashMap<>();
 		ArrayList<Element> elementList = XMLHelper.selectElements(geneidDoc.getDocumentElement(), "prediction/gene/cDNA");
 		logger.info("{} hits", elementList.size());
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
index df6a1a4373..368d3e6d84 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
@@ -79,9 +79,9 @@ public static List<GeneChromosomePosition> getChromosomeMappings() throws IOExce
 	public static List<GeneChromosomePosition> getChromosomeMappings(InputStream inStream) throws IOException {
 		BufferedReader reader = new BufferedReader(new InputStreamReader(inStream));
 
-		ArrayList<GeneChromosomePosition> gcps = new ArrayList<GeneChromosomePosition>();
+		ArrayList<GeneChromosomePosition> gcps = new ArrayList<>();
 
-		String line = null;
+		String line;
 		while ((line = reader.readLine()) != null) {
 			GeneChromosomePosition gcp = getGeneChromosomePosition(line);
 			if ( gcp != null)
@@ -126,7 +126,7 @@ private static GeneChromosomePosition getGeneChromosomePosition(String line) {
 
 	private static List<Integer> getIntegerList(String lst){
 		String[] spl = lst.split(",");
-		ArrayList<Integer> l = new ArrayList<Integer>();
+		ArrayList<Integer> l = new ArrayList<>();
 		for (String s : spl){
 			l.add(Integer.parseInt(s));
 		}
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.java
index e9158c015a..1e13df5107 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.java
@@ -92,7 +92,7 @@ public static List<GeneName> getGeneNames() throws IOException{
 	 */
 	public static List<GeneName> getGeneNames(InputStream inStream) throws IOException{
 
-		ArrayList<GeneName> geneNames = new ArrayList<GeneName>();
+		ArrayList<GeneName> geneNames = new ArrayList<>();
 		BufferedReader reader = new BufferedReader(new InputStreamReader(inStream));
 
 		// skip reading first line (it is the legend)
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java
index 9d750f850e..b498fb0e86 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java
@@ -51,8 +51,6 @@ public String seqname() {
 		return mSeqname;
 	}
 
-	;
-
 	/**
 	 * Get source (aka method). (GFF field 2). This is often the name of
 	 * the program or procedure that created the features.
@@ -63,8 +61,6 @@ public String source() {
 		return mSource;
 	}
 
-	;
-
 	/**
 	 * Get feature type, such as "exon" or "CDS". (GFF field 3).
 	 *
@@ -75,8 +71,6 @@ public String type() {
 		return mType;
 	}
 
-	;
-
 	/**
 	 * Get location of feature. Note that feature objects have
 	 * no link or reference to the actual sequence object to which
@@ -98,8 +92,6 @@ public double score() {
 		return mScore;
 	}
 
-	;
-
 	/**
 	 * Get frame (aka phase). (GFF field 8). Specifies the offset of the
 	 * first nucleotide of the first in-frame codon, assuming this feature
@@ -113,8 +105,6 @@ public int frame() {
 		return mFrame;
 	}
 
-	;
-
 	/**
 	 * Get the string of key/value attributes. (GFF field 9). The format and
 	 * meaning of this field varies from flavor to flavor of GFF/GTF. This method
@@ -127,13 +117,11 @@ public String attributes() {
 		return mAttributes;
 	}
 
-	;
-
 	@SuppressWarnings("unused")
 	private Feature() {
 	}
 
-	;        //unavailable
+	//unavailable
 
 	/**
 	 * Make a copy of the specified feature. The mappings in the userMap() HashMap
@@ -153,7 +141,7 @@ public Feature(Feature feature) {
 		mFrame = feature.mFrame;
 		mAttributes = feature.mAttributes;
 		initAttributeHashMap();
-		mUserMap = new HashMap<String, String>(feature.mUserMap);
+		mUserMap = new HashMap<>(feature.mUserMap);
 	}
 
 	/**
@@ -177,7 +165,7 @@ public Feature(String seqname, String source, String type, Location location, Do
 		mFrame = frame;
 		mAttributes = attributes;
 		initAttributeHashMap();
-		mUserMap = new HashMap<String, String>();
+		mUserMap = new HashMap<>();
 
 	}
 
@@ -199,7 +187,7 @@ public HashMap<String, String> userData() {
 		return mUserMap;
 	}
 
-	 HashMap<String,String> attributeHashMap = new HashMap<String,String>();
+	 HashMap<String,String> attributeHashMap = new HashMap<>();
 
 	private void initAttributeHashMap(){
 	   String[] values = mAttributes.split(";");
@@ -300,7 +288,7 @@ public String toString() {
 		s += mType + '\t';
 		s += mLocation.start() + "\t";
 		s += mLocation.end() + "\t";
-		s += Double.toString(mScore) + "\t";
+		s += mScore + "\t";
 
 		if (mFrame == -1) {
 			s += ".\t";
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java
index 1383276ce2..bcdc0bc32b 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java
@@ -38,7 +38,7 @@ public class FeatureHelper {
 	 */
 	static public LinkedHashMap<String,FeatureList> buildFeatureAtrributeIndex(String attribute,FeatureList list){
 
-		LinkedHashMap<String,FeatureList> featureHashMap = new LinkedHashMap<String,FeatureList>();
+		LinkedHashMap<String,FeatureList> featureHashMap = new LinkedHashMap<>();
 		FeatureList featureList = list.selectByAttribute(attribute);
 		for(FeatureI feature : featureList){
 			String value = feature.getAttribute(attribute);
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureI.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureI.java
index 9fa7c02061..0e9c35359e 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureI.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureI.java
@@ -36,7 +36,7 @@ public interface FeatureI
 	 *
 	 * @return The location.
 	 */
-	public Location location();
+    Location location();
 
 	/**
 	 * Get the group id of the feature. The group id is defined in the GFF1
@@ -50,21 +50,21 @@ public interface FeatureI
 	 *
 	 * @return The group id. This may be an empty string.
 	 */
-	public String group();
+    String group();
 
 	/**
 	 * Get the feature type, for example, "exon", "CDS", etc.
 	 *
 	 * @return The type.
 	 */
-	public String type();
+    String type();
 
 	/**
 	 * Get the sequence name.
 	 *
 	 * @return Sequence name.
 	 */
-	public String seqname();
+    String seqname();
 
 	/**
 	 * Get the attribute value for this key.
@@ -72,7 +72,7 @@ public interface FeatureI
 	 * @param key The key.
 	 * @return The corresponding value. Null if the key has no value defined .
 	 */
-	public String getAttribute( String key );
+    String getAttribute(String key);
 
 
 	/**
@@ -81,7 +81,7 @@ public interface FeatureI
 	 * @param key The key.
 	 * @return True if a value is defined for this key.
 	 */
-	public boolean hasAttribute( String key );
+    boolean hasAttribute(String key);
 
 	/**
 	 * Check if the feature attributes include the specified key/value pair.
@@ -90,7 +90,7 @@ public interface FeatureI
 	 * @param value The value.
 	 * @return True if the feature's value for this key matches the specified value.
 	 */
-	public boolean hasAttribute( String key, String value );
+    boolean hasAttribute(String key, String value);
 
 	/**
 	 * A string representation of the feature.
@@ -98,15 +98,15 @@ public interface FeatureI
 	 * @return The string.
 	 */
 	@Override
-	public String toString();
+    String toString();
 
 	/**
 	 * Get HashMap of user data.
 	 *
 	 * @return The user HashMap.
 	 */
-	public  HashMap<String, String> userData();
+    HashMap<String, String> userData();
 
-	public HashMap<String, String> getAttributes();
+	HashMap<String, String> getAttributes();
 
 }
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java
index 19b7afec93..1910b0eee7 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java
@@ -40,7 +40,7 @@
 @SuppressWarnings("serial")
 public class FeatureList extends ArrayList<FeatureI> {
 
-	 Map<String, Map<String,List<FeatureI>>> featindex = new HashMap<String,Map<String,List<FeatureI>>>();
+	 Map<String, Map<String,List<FeatureI>>> featindex = new HashMap<>();
 	Location mLocation;			//genomic location (union of feature locations)
 
 	/**
@@ -81,11 +81,11 @@ public boolean add(FeatureI feature) {
 			if (featindex.containsKey(entry.getKey())){
 				Map<String,List<FeatureI>> feat = featindex.get(entry.getKey());
 				if (feat==null){
-					feat= new HashMap<String,List<FeatureI>>();
+					feat= new HashMap<>();
 				}
 				List<FeatureI> features = feat.get(entry.getValue());
 				if (features==null){
-					features = new ArrayList<FeatureI>();
+					features = new ArrayList<>();
 				}
 				features.add(feature);
 				feat.put(entry.getValue(), features);
@@ -103,9 +103,7 @@ public boolean add(FeatureI feature) {
 	 * @param list The collection of FeatureI objects.
 	 */
 	public void add(Collection<FeatureI> list) {
-		for (FeatureI f : list) {
-			add(f);
-		}
+		this.addAll(list);
 	}
 
 	/**
@@ -185,7 +183,7 @@ public String splice(DNASequence sequence) {
 	 * the order of features in the list.
 	 */
 	public Collection<String> groupValues() {
-		Set<String> set = new HashSet<String>();
+		Set<String> set = new HashSet<>();
 		for (FeatureI f : this) {
 			//enter in a set -- removes duplicates
 			set.add(f.group());
@@ -207,10 +205,10 @@ public Collection<String> attributeValues(String key) {
 		if (featindex.containsKey(key)){
 			Map<String, List<FeatureI>> map = featindex.get(key);
 			Collection<String> result = map.keySet();
-			if (result == null) result = new HashSet<String>();
+			if (result == null) result = new HashSet<>();
 			return Collections.unmodifiableCollection(result);
 		}
-		LinkedHashMap<String, String> hash = new LinkedHashMap<String, String>();
+		LinkedHashMap<String, String> hash = new LinkedHashMap<>();
 		for (FeatureI f : this) {
 			//enter as a key -- removes duplicates
 			hash.put(f.getAttribute(key), null);
@@ -353,8 +351,7 @@ public FeatureList selectByUserData(String key) {
 	 * on the same strand as the specified location will be considered for inclusion.
 	 * @return The new list of features that overlap the location.
 	 */
-	public FeatureList selectOverlapping(String seqname, Location location, boolean useBothStrands)
-			throws Exception {
+	public FeatureList selectOverlapping(String seqname, Location location, boolean useBothStrands) {
 		FeatureList list = new FeatureList();
 
 		for (FeatureI feature : this) {
@@ -468,7 +465,7 @@ public String toString() {
 	/**
 	 * used by sort routine
 	 */
-	private class FeatureComparator implements Comparator<FeatureI>, Serializable {
+	private static class FeatureComparator implements Comparator<FeatureI>, Serializable {
 	private static final long serialVersionUID = 1;
 
 		@Override
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Reader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Reader.java
index a0f5b573f8..049dc68a55 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Reader.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Reader.java
@@ -100,7 +100,7 @@ public static FeatureList read(String filename, List<String> indexes) throws IOE
 
 
 	public static FeatureList read(String filename) throws IOException {
-	   return read(filename,new ArrayList<String>(0));
+	   return read(filename, new ArrayList<>(0));
 	}
 
 
@@ -122,7 +122,7 @@ private static Feature parseLine(String s) {
 
 		String locEnd =line[4].trim();
 
-		Double score;
+		double score;
 
 		try {
 			score = Double.parseDouble(line[5].trim());
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
index c4bc070f21..4e38a1a166 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
@@ -29,6 +29,7 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.LinkedHashMap;
+import java.util.Map;
 
 /**
  *
@@ -45,9 +46,10 @@ public class GFF3Writer {
 	public void write(OutputStream outputStream, LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList) throws Exception {
 
 		outputStream.write("##gff-version 3\n".getBytes());
-		for (String key : chromosomeSequenceList.keySet()) {
-			ChromosomeSequence chromosomeSequence = chromosomeSequenceList.get(key);
-			String gff3line = "";
+		for (Map.Entry<String, ChromosomeSequence> entry : chromosomeSequenceList.entrySet()) {
+            String key = entry.getKey();
+            ChromosomeSequence chromosomeSequence = entry.getValue();
+			String gff3line;
 	//         if(source.length() == 0){
 	//             Collection<GeneSequence> genes = chromosomeSequence.getGeneSequences().values();
 	//             for(GeneSequence gene : genes){
@@ -94,8 +96,8 @@ public void write(OutputStream outputStream, LinkedHashMap<String, ChromosomeSeq
 					outputStream.write(gff3line.getBytes());
 
 					String transcriptParentName = geneSequence.getAccession().getID() + "." + transcriptIndex;
-					ArrayList<CDSSequence> cdsSequenceList = new ArrayList<CDSSequence>(transcriptSequence.getCDSSequences().values());
-					Collections.sort(cdsSequenceList, new SequenceComparator());
+					ArrayList<CDSSequence> cdsSequenceList = new ArrayList<>(transcriptSequence.getCDSSequences().values());
+					cdsSequenceList.sort(new SequenceComparator());
 					for (CDSSequence cdsSequence : cdsSequenceList) {
 						gff3line = key + "\t" + cdsSequence.getSource() + "\t" + "CDS" + "\t" + cdsSequence.getBioBegin() + "\t" + cdsSequence.getBioEnd() + "\t";
 						score = cdsSequence.getSequenceScore();
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.java
index c7f59de102..2cd712b0a5 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.java
@@ -93,7 +93,7 @@ private static Feature parseLine(String s) {
 		//FIXME update to use regex split on tabs
 		//FIXME better errors on parse failures
 
-		int start = 0;
+		int start;
 		int end = 0;
 
 		start = end;
@@ -116,7 +116,7 @@ private static Feature parseLine(String s) {
 		end = s.indexOf('\t', start);
 		String locEnd = s.substring(start, end);
 
-		Double score;
+		double score;
 		start = end + 1;
 		end = s.indexOf('\t', start);
 		try {
@@ -145,7 +145,7 @@ private static Feature parseLine(String s) {
 		//grab everything until end of line (or # comment)
 		start = end + 1;
 		end = s.indexOf('#', start);
-		String attributes = null;
+		String attributes;
 		if (end < 0) {
 			attributes = new String(s.substring(start));
 		} else {
@@ -170,9 +170,8 @@ public static void write(FeatureList features, String filename) throws IOExcepti
 
 		BufferedWriter bw = new BufferedWriter(new FileWriter(filename));
 
-		ListIterator<FeatureI> iter = features.listIterator();
-		while (iter.hasNext()) {
-			Feature feature = (Feature) iter.next();
+		for (FeatureI featureI : features) {
+			Feature feature = (Feature) featureI;
 			writeLine(feature, bw);
 		}
 
@@ -186,7 +185,7 @@ private static void writeLine(Feature f, BufferedWriter bw) throws IOException {
 
 		s += f.location().bioStart() + "\t";
 		s += f.location().bioEnd() + "\t";
-		s += Double.toString(f.score()) + "\t";
+		s += f.score() + "\t";
 		s += f.location().bioStrand() + "\t";
 
 		if (f.frame() == -1) {
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.java
index 8f0f53b026..2808383979 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.java
@@ -93,7 +93,7 @@ public static FeatureList read(String filename) throws IOException {
 	private static Feature parseLine(String s) {
 		//FIXME update to use regex split on tabs
 		//FIXME better errors on parse failures
-		int start = 0;
+		int start;
 		int end = 0;
 
 		start = end;
@@ -116,7 +116,7 @@ private static Feature parseLine(String s) {
 		end = s.indexOf('\t', start);
 		String locEnd = s.substring(start, end);
 
-		Double score;
+		double score;
 		start = end + 1;
 		end = s.indexOf('\t', start);
 		try {
@@ -145,7 +145,7 @@ private static Feature parseLine(String s) {
 		//grab everything until end of line (or # comment)
 		start = end + 1;
 		end = s.indexOf('#', start);
-		String attributes = null;
+		String attributes;
 		if (end < 0) {
 			attributes = new String(s.substring(start));
 		} else {
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/LocIterator.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/LocIterator.java
index c8ffd98974..06c94a92d6 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/LocIterator.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/LocIterator.java
@@ -44,9 +44,9 @@ public class LocIterator implements Iterator<Location> {
 	int mIncrement;
 
 	@SuppressWarnings("unused")
-	private LocIterator() {};
+	private LocIterator() {}
 
-	/**
+    /**
 	 * Construct an iterator that slides a window over a Location.
 	 *
 	 * @param bounds The location over which to iterate.
@@ -138,7 +138,7 @@ public boolean hasNext()
 	 */
 	public Location remainder()
 	{
-		Location remainder= null;
+		Location remainder;
 
 		if( mPosition == 0 )
 		{
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
index 91e71463f8..483295572e 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
@@ -69,8 +69,8 @@
 public class Location implements Iterable<Location>
 {
 
-	private int mStart;
-	private int mEnd;
+	private final int mStart;
+	private final int mEnd;
 
 
 	/**
@@ -267,8 +267,8 @@ public Location union( Location other )
 		}
 		else
 		{
-			int start= (other.mStart < mStart)? other.mStart: mStart;
-			int end= (other.mEnd > mEnd)? other.mEnd: mEnd;
+			int start= Math.min(other.mStart, mStart);
+			int end= Math.max(other.mEnd, mEnd);
 
 			return new Location( start, end );
 		}
@@ -368,15 +368,7 @@ public Iterable<Location> window( final int windowSize, final int increment )
 		final Location loc= this;
 
 		//return iterable anonymous inner class
-		return new Iterable<Location> ()
-			{
-				@Override
-				public LocIterator iterator()
-				{
-					return new LocIterator( loc, windowSize, increment );
-				}
-
-			};
+		return () -> new LocIterator( loc, windowSize, increment );
 	}
 
 	/**
@@ -503,7 +495,7 @@ public Location prefix( Location other )
 		{
 			if( other.mStart >= mStart )
 			{
-				return new Location( mStart, (other.mStart < mEnd)? other.mStart: mEnd );
+				return new Location( mStart, Math.min(other.mStart, mEnd));
 			}
 			else
 			{
@@ -531,7 +523,7 @@ public Location suffix( Location other )
 		{
 			if( other.mEnd <= mEnd )
 			{
-				return new Location( (other.mEnd > mStart)? other.mEnd: mStart, mEnd );
+				return new Location(Math.max(other.mEnd, mStart), mEnd );
 			}
 			else
 			{
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitFacade.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitFacade.java
index 71dfc4174f..6dbf1f0ba3 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitFacade.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitFacade.java
@@ -28,7 +28,7 @@
  */
 public class TwoBitFacade {
 
-	private TwoBitParser twoBitParser = null;
+	private TwoBitParser twoBitParser;
 
 
 	/**
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java
index 4f5733037d..b66dd3b014 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java
@@ -48,11 +48,11 @@ public class TwoBitParser extends InputStream {
 
 	public int DEFAULT_BUFFER_SIZE = 10000;
 	//
-	private RandomAccessFile raf;
-	private File f;
+	private final RandomAccessFile raf;
+	private final File f;
 	private boolean reverse = false;
-	private String[] seq_names;
-	private HashMap<String,Long> seq2pos = new HashMap<String,Long>();
+	private final String[] seq_names;
+	private final HashMap<String,Long> seq2pos = new HashMap<>();
 	private String cur_seq_name;
 	private long[][] cur_nn_blocks;
 	private long[][] cur_mask_blocks;
@@ -98,7 +98,7 @@ else if(sign==0x4327411A) {
 		}
 	}
 	private long readFourBytes() throws Exception {
-		long ret = 0;
+		long ret;
 		if(!reverse) {
 			ret = raf.read();
 			ret += raf.read()*0x100;
@@ -170,7 +170,7 @@ public void setCurrentSequence(String seq_name) throws Exception {
 	 * Method resets current position to the begining of sequence stream.
 	 */
 	@Override
-	public synchronized void reset() throws IOException {
+	public synchronized void reset() {
 		cur_seq_pos = 0;
 		cur_nn_block_num = (cur_nn_blocks.length>0)?0:-1;
 		cur_mask_block_num = (cur_mask_blocks.length>0)?0:-1;
@@ -228,7 +228,7 @@ public int read() throws IOException {
 		else if(bit_num==3) {
 			file_pos++;
 		}
-		char ret = 'N';
+		char ret;
 		if((cur_nn_block_num>=0)&&
 				(cur_nn_blocks[cur_nn_block_num][0]<=cur_seq_pos)) {
 			if(cur_bits[bit_num]!=0) {
@@ -297,7 +297,7 @@ public synchronized long skip(long n) throws IOException {
 	 * new current sequence.
 	 */
 	@Override
-	public void close() throws IOException {
+	public void close() {
 		cur_seq_name = null;
 		cur_nn_blocks = null;
 		cur_mask_blocks = null;
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java
index ff5e1318d0..61d5475037 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java
@@ -38,7 +38,7 @@ public class BlastXMLQuery {
 
 	private static final Logger logger = LoggerFactory.getLogger(BlastXMLQuery.class);
 
-	Document blastDoc = null;
+	Document blastDoc;
 
 	public BlastXMLQuery(String blastFile) throws Exception {
 		logger.info("Start read of {}", blastFile);
@@ -47,7 +47,7 @@ public BlastXMLQuery(String blastFile) throws Exception {
 	}
 
 	public LinkedHashMap<String, ArrayList<String>> getHitsQueryDef(double maxEScore) throws Exception {
-		LinkedHashMap<String, ArrayList<String>> hitsHashMap = new LinkedHashMap<String, ArrayList<String>>();
+		LinkedHashMap<String, ArrayList<String>> hitsHashMap = new LinkedHashMap<>();
 		logger.info("Query for hits");
 		ArrayList<Element> elementList = XMLHelper.selectElements(blastDoc.getDocumentElement(), "BlastOutput_iterations/Iteration[Iteration_hits]");
 		logger.info("{} hits", elementList.size());
@@ -67,11 +67,7 @@ public LinkedHashMap<String, ArrayList<String>> getHitsQueryDef(double maxEScore
 					String value = evalueElement.getTextContent();
 					double evalue = Double.parseDouble(value);
 					if (evalue <= maxEScore) {
-						ArrayList<String> hits = hitsHashMap.get(querydef);
-						if (hits == null) {
-							hits = new ArrayList<String>();
-							hitsHashMap.put(querydef, hits);
-						}
+						ArrayList<String> hits = hitsHashMap.computeIfAbsent(querydef, k -> new ArrayList<>());
 						hits.add(hitaccession);
 					}
 				}
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/uniprot/UniprotToFasta.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/uniprot/UniprotToFasta.java
index 66a9d2a086..2806e83d9d 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/uniprot/UniprotToFasta.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/uniprot/UniprotToFasta.java
@@ -67,10 +67,10 @@ public void process( String uniprotDatFileName,String fastaFileName ) throws Exc
 			String line = br.readLine();
 			String id = "";
 			StringBuffer sequence = new StringBuffer();
-			ArrayList<ProteinSequence> seqCodingRegionsList = new ArrayList<ProteinSequence>();
+			ArrayList<ProteinSequence> seqCodingRegionsList = new ArrayList<>();
 			int count = 0;
-			HashMap<String,String> uniqueGenes = new HashMap<String,String>();
-			HashMap<String,String> uniqueSpecies = new HashMap<String,String>();
+			HashMap<String,String> uniqueGenes = new HashMap<>();
+			HashMap<String,String> uniqueSpecies = new HashMap<>();
 			while(line != null){
 				if(line.startsWith("ID")){
 					String[] data = line.split(" ");
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
index a63a78a236..aa91bf2ad5 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
@@ -112,7 +112,7 @@ private static String formatExonStructureForward(GeneChromosomePosition chromPos
 			}
 		}
 		s.append("Coding Length: ");
-		s.append((codingLength-3)+"");
+		s.append(String.valueOf(codingLength - 3));
 		s.append(newline);
 		return s.toString();
 	}
@@ -242,7 +242,7 @@ public static ChromPos getChromosomePosForCDScoordinate(int cdsNucleotidePositio
 		int cdsEnd = chromPos.getCdsEnd();
 
 
-		ChromPos chromosomePos = null;
+		ChromPos chromosomePos;
 
 		if (chromPos.getOrientation().equals('+'))
 
@@ -333,7 +333,7 @@ public static ChromPos getChromPosReverse(int cdsPos, List<Integer> exonStarts,
 
 				if ( debug ) {
 
-					StringBuffer b = new StringBuffer();
+					StringBuilder b = new StringBuilder();
 
 					b.append("     UTR         :" + format(cdsEnd + 1) + " - " + format(end) + newline);
 					if (tmpstart == start)
@@ -706,7 +706,7 @@ private static List<Range<Integer>> getCDSExonRangesReverse(GeneChromosomePositi
 			}
 		}
 		if ( debug ) {
-			s.append("CDS length: ").append(Integer.toString(codingLength - 3));
+			s.append("CDS length: ").append((codingLength - 3));
 			s.append(newline);
 			logger.debug(s.toString());
 		}
@@ -821,7 +821,7 @@ public static int getCDSPosForward(int chromPos, List<Integer> exonStarts, List<
 		List<Range<Integer>> cdsRegions = getCDSRegions(exonStarts, exonEnds, cdsStart, cdsEnd);
 
 		int codingLength = 0;
-		int lengthExon = 0;
+		int lengthExon;
 		for (Range<Integer> range : cdsRegions) {
 
 			int start = range.lowerEndpoint();
@@ -868,7 +868,7 @@ public static int getCDSPosReverse(int chromPos, List<Integer> exonStarts, List<
 		List<Range<Integer>> cdsRegions = getCDSRegions(exonStarts, exonEnds, cdsStart, cdsEnd);
 
 		int codingLength = 0;
-		int lengthExon = 0;
+		int lengthExon;
 		for ( int i=cdsRegions.size()-1; i>=0; i-- ) {
 
 			int start = cdsRegions.get(i).lowerEndpoint();
@@ -899,8 +899,8 @@ public static int getCDSPosReverse(int chromPos, List<Integer> exonStarts, List<
 	public static List<Range<Integer>> getCDSRegions(List<Integer> origExonStarts, List<Integer> origExonEnds, int cdsStart, int cdsEnd) {
 
 		// remove exons that are fully landed in UTRs
-		List<Integer> exonStarts = new ArrayList<Integer>(origExonStarts);
-		List<Integer> exonEnds = new ArrayList<Integer>(origExonEnds);
+		List<Integer> exonStarts = new ArrayList<>(origExonStarts);
+		List<Integer> exonEnds = new ArrayList<>(origExonEnds);
 
 		int j=0;
 		for (int i = 0; i < origExonStarts.size(); i++) {
@@ -920,7 +920,7 @@ public static List<Range<Integer>> getCDSRegions(List<Integer> origExonStarts, L
 		exonEnds.remove(nExons-1);
 		exonEnds.add(cdsEnd);
 
-		List<Range<Integer>> cdsRegion = new ArrayList<Range<Integer>>();
+		List<Range<Integer>> cdsRegion = new ArrayList<>();
 		for ( int i=0; i<nExons; i++ ) {
 			Range<Integer> r = Range.closed(exonStarts.get(i), exonEnds.get(i));
 			cdsRegion.add(r);
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ProteinMappingTools.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ProteinMappingTools.java
index 8fdb093c54..bff7888d08 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ProteinMappingTools.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ProteinMappingTools.java
@@ -44,7 +44,7 @@ public static ProteinSequence convertDNAtoProteinSequence(String dnaSequence) th
 	 *
 	 * @return the protein sequence
 	 */
-	public static ProteinSequence convertDNAtoProteinSequence(DNASequence dnaSequence) throws CompoundNotFoundException {
+	public static ProteinSequence convertDNAtoProteinSequence(DNASequence dnaSequence) {
 		RNASequence mRNA = dnaSequence.getRNASequence();
 		return mRNA.getProteinSequence();
 	}
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java
index 4948a62c76..ff733d1d06 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java
@@ -40,7 +40,7 @@ public class SplitFasta {
 
 	private static final Logger logger = LoggerFactory.getLogger(SplitFasta.class);
 
-	public void processNucleotides(File fastaFileName,String uniqueid, File outputDirectory ) throws Exception{
+	public static void processNucleotides(File fastaFileName, String uniqueid, File outputDirectory) throws Exception{
 		if(!outputDirectory.exists())
 			outputDirectory.mkdirs();
 
@@ -52,7 +52,7 @@ public void processNucleotides(File fastaFileName,String uniqueid, File outputDi
 			}else{
 				fileName = fileName + uniqueid + dnaSequence.getAccession().getID() + ".fna";
 			}
-			ArrayList<DNASequence> dnaList = new ArrayList<DNASequence>();
+			ArrayList<DNASequence> dnaList = new ArrayList<>();
 			dnaList.add(dnaSequence);
 			FastaWriterHelper.writeNucleotideSequence(new File(fileName), dnaList);
 		}
@@ -62,7 +62,7 @@ public void processNucleotides(File fastaFileName,String uniqueid, File outputDi
 		public static void main( String[] args ){
 		try{
 			SplitFasta splitFasta = new SplitFasta();
-			splitFasta.processNucleotides(new File("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/454Scaffolds.fna"), "", new File("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/individual"));
+			SplitFasta.processNucleotides(new File("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/454Scaffolds.fna"), "", new File("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/individual"));
 		}catch(Exception e){
 			logger.error("Exception: ", e);
 		}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/FeatureListTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/FeatureListTest.java
index 6e1cae5d8b..ed554272ba 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/FeatureListTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/FeatureListTest.java
@@ -35,8 +35,7 @@
  */
 public class FeatureListTest {
 	@Test
-	public void testAddIndex() throws Exception
-	{
+	public void testAddIndex() {
 		FeatureList fl = new FeatureList();
 		fl.add(new Feature("seqname", "source", "type", new Location(1, 2), (double)0, 0, "gene_id \"gene_id_1\"; transcript_id \"transcript_id_1\";"));
 		fl.addIndex("transcript_id");
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
index db4fa31328..1bb9d1ed4b 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
@@ -48,11 +48,11 @@ public class GeneFeatureHelperTest {
 	private static final Logger logger = LoggerFactory.getLogger(GeneFeatureHelperTest.class);
 
 	@Before
-	public void setUp() throws Exception {
+	public void setUp() {
 	}
 
 	@After
-	public void tearDown() throws Exception {
+	public void tearDown() {
 	}
 
 	@Test
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
index 8a19d041e4..a7b47ae0a3 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
@@ -74,9 +74,9 @@ public void testAK1() {
 				if ( ! pos.getGenebankId().equals("NM_000476"))
 					continue;
 
-				Assert.assertTrue(pos.getGeneName().equals(geneName));
-				Assert.assertTrue(pos.getOrientation().equals('-'));
-				Assert.assertTrue(pos.getChromosome().equals("chr9"));
+				Assert.assertEquals(pos.getGeneName(), geneName);
+				Assert.assertEquals('-', (char) pos.getOrientation());
+				Assert.assertEquals("chr9", pos.getChromosome());
 
 				List<Range<Integer>> cdsranges = ChromosomeMappingTools.getCDSExonRanges(pos);
 
@@ -90,14 +90,14 @@ public void testAK1() {
 
 				int cdslength = ChromosomeMappingTools.getCDSLength(pos);
 
-				Assert.assertTrue("CDS length should be 582, but is " + cdslength, cdslength == (uniProtLength * 3));
+				Assert.assertEquals("CDS length should be 582, but is " + cdslength, cdslength, (uniProtLength * 3));
 
 				List<Range<Integer>> chromranges = ChromosomeMappingTools.getChromosomalRangesForCDS(pos);
 
 				// we are reverse strand. reverse the order
 				chromranges = Lists.reverse(chromranges);
 
-				Assert.assertTrue(chromranges.size() == 6);
+				Assert.assertEquals(6, chromranges.size());
 
 				// compare with https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=CCDS6881
 				validateExon(0,127868008,127868076, chromranges  );
@@ -129,16 +129,16 @@ public void testHBA(){
 				if ( ! pos.getGeneName().equals(geneName))
 					continue;
 
-				Assert.assertTrue(pos.getGeneName().equals("HBA1"));
-				Assert.assertTrue(pos.getGenebankId().equals("NM_000558"));
-				Assert.assertTrue(pos.getChromosome().equals("chr16"));
-				Assert.assertTrue(pos.getTranscriptionStart().equals(176650));
-				Assert.assertTrue(pos.getTranscriptionEnd().equals(177522));
-				Assert.assertTrue(pos.getOrientation().equals('+'));
+				Assert.assertEquals("HBA1", pos.getGeneName());
+				Assert.assertEquals("NM_000558", pos.getGenebankId());
+				Assert.assertEquals("chr16", pos.getChromosome());
+				Assert.assertEquals(176650, (int) pos.getTranscriptionStart());
+				Assert.assertEquals(177522, (int) pos.getTranscriptionEnd());
+				Assert.assertEquals('+', (char) pos.getOrientation());
 
 				List<Range<Integer>> cdsranges = ChromosomeMappingTools.getCDSExonRanges(pos);
 
-				Assert.assertTrue(cdsranges.size() == 3);
+				Assert.assertEquals(3, cdsranges.size());
 
 				validateExon(0,0,95,cdsranges);
 				validateExon(1,95,300,cdsranges);
@@ -163,8 +163,8 @@ public void testHBA(){
 	private void validateExon(int exonNr, int start, int stop, List<Range<Integer>> cdsranges) {
 
 		Range<Integer> exon = cdsranges.get(exonNr);
-		Assert.assertTrue("Exon " + exonNr + " boundary " + exon.lowerEndpoint() + " does not match " + start, exon.lowerEndpoint().equals(start));
-		Assert.assertTrue("Exon " + exonNr + " boundary " + exon.upperEndpoint() + " does not match " + stop, exon.upperEndpoint().equals(stop));
+		Assert.assertEquals("Exon " + exonNr + " boundary " + exon.lowerEndpoint() + " does not match " + start, (int) exon.lowerEndpoint(), start);
+		Assert.assertEquals("Exon " + exonNr + " boundary " + exon.upperEndpoint() + " does not match " + stop, (int) exon.upperEndpoint(), stop);
 
 	}
 
@@ -336,39 +336,39 @@ public void testMappingCromosomePosTomRNAMultiUTRs() {
 	@Test
 	public void testGenomeMappingToolGetCDSRanges(){
 
-		List<Integer> lst1 = new ArrayList<>(Arrays.asList( new Integer[]{86346823, 86352858, 86354529}));
-		List<Integer> lst2 = new ArrayList<>(Arrays.asList(new Integer[]{86348878, 86352984, 86354692}));
+		List<Integer> lst1 = new ArrayList<>(Arrays.asList(86346823, 86352858, 86354529));
+		List<Integer> lst2 = new ArrayList<>(Arrays.asList(86348878, 86352984, 86354692));
 
-		Integer cdsStart=86348749, cdsEnd=86387027;
+		int cdsStart=86348749, cdsEnd=86387027;
 
 		List<Range<Integer>> result = ChromosomeMappingTools.getCDSRegions(lst1,lst2,cdsStart,cdsEnd);
 
 		// makes sure the first list does not get  changed;
-		Assert.assertTrue(lst1.get(0) == 86346823);
+		Assert.assertEquals(86346823, (int) lst1.get(0));
 
 
-		Assert.assertTrue(result.get(0).lowerEndpoint() == 86348749);
-		Assert.assertTrue(result.get(1).lowerEndpoint() == 86352858);
-		Assert.assertTrue(result.get(2).lowerEndpoint() == 86354529);
+		Assert.assertEquals(86348749, (int) result.get(0).lowerEndpoint());
+		Assert.assertEquals(86352858, (int) result.get(1).lowerEndpoint());
+		Assert.assertEquals(86354529, (int) result.get(2).lowerEndpoint());
 
-		Assert.assertTrue(result.get(0).upperEndpoint() == 86348878);
-		Assert.assertTrue(result.get(1).upperEndpoint() == 86352984);
-		Assert.assertTrue(result.get(2).upperEndpoint() == 86387027);
+		Assert.assertEquals(86348878, (int) result.get(0).upperEndpoint());
+		Assert.assertEquals(86352984, (int) result.get(1).upperEndpoint());
+		Assert.assertEquals(86387027, (int) result.get(2).upperEndpoint());
 
 	}
 
 	@Test
 	public void testGenomeMappingToolGetCDSRangesSERINC2(){
 
-		List<Integer> lst1 = new ArrayList<>(Arrays.asList( new Integer[]{31413812, 31415872, 31423692}));
-		List<Integer> lst2 = new ArrayList<>(Arrays.asList(new Integer[]{31414777, 31415907, 31423854}));
+		List<Integer> lst1 = new ArrayList<>(Arrays.asList(31413812, 31415872, 31423692));
+		List<Integer> lst2 = new ArrayList<>(Arrays.asList(31414777, 31415907, 31423854));
 
-		Integer cdsStart=31423818, cdsEnd=31434199;
+		int cdsStart=31423818, cdsEnd=31434199;
 
 		List<Range<Integer>> result = ChromosomeMappingTools.getCDSRegions(lst1,lst2,cdsStart,cdsEnd);
 
 		// makes sure the first list does not get  changed;
-		Assert.assertTrue(result.get(0).lowerEndpoint() == 31423818);
+		Assert.assertEquals(31423818, (int) result.get(0).lowerEndpoint());
 
 	}
 }
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestLocation.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestLocation.java
index 1289cb757e..f1ff2b1636 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestLocation.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestLocation.java
@@ -64,11 +64,11 @@ public void testLocation() {
 
 		//isBefore
 		assertTrue( r2_5.isBefore( r5_8 ));
-		assertTrue( !r2_5.isBefore( r4_7 ));
+        assertFalse(r2_5.isBefore(r4_7));
 
 		//isAfter
 		assertTrue(r5_8.isAfter( r2_5 ));
-		assertTrue(!r5_8.isAfter( r4_7 ));
+        assertFalse(r5_8.isAfter(r4_7));
 
 		//contains
 		assertTrue(p15_19.contains( p16_19 ));
@@ -76,8 +76,8 @@ public void testLocation() {
 		//overlaps
 		assertTrue(r2_5.overlaps( r4_7 ));
 		assertTrue(r2_5.overlaps( r0_3 ));
-		assertTrue(!r5_8.overlaps( r2_5 ));
-		assertTrue(!r2_5.overlaps( r5_8 ));
+        assertFalse(r5_8.overlaps(r2_5));
+        assertFalse(r2_5.overlaps(r5_8));
 
 
 		//prefix
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReaderTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReaderTest.java
index 6dbfbe968c..c87079a1da 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReaderTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReaderTest.java
@@ -312,35 +312,17 @@ public void testMultipleWrappedQuality() throws Exception
 	}
 
 	@Test
-	public void testErrorExamples() throws Exception
-	{
+	public void testErrorExamples() {
 		FastqReader reader = createFastqReader();
 		for (String errorExample : ERROR_EXAMPLES)
 		{
-			InputStream inputStream = getClass().getResourceAsStream(errorExample);
-			try
-			{
+			try (InputStream inputStream = getClass().getResourceAsStream(errorExample)) {
 				reader.read(inputStream);
 				Assert.fail("error example " + errorExample + " expected IOException");
-			}
-			catch (IOException e)
-			{
+			} catch (IOException e) {
 				// expected
 			}
-			finally
-			{
-				if (inputStream != null)
-				{
-					try
-					{
-						inputStream.close();
-					}
-					catch (IOException e)
-					{
-						// ignore
-					}
-				}
-			}
+			// ignore
 		}
 	}
 
@@ -351,37 +333,37 @@ public void testParse() throws Exception
 		final String input = "";
 		reader.parse(new StringReader(input), new ParseListener() {
 						 @Override
-						 public void description(final String description) throws IOException {
+						 public void description(final String description) {
 							 // empty
 						 }
 
 						 @Override
-						 public void sequence(final String sequence) throws IOException {
+						 public void sequence(final String sequence) {
 							 // empty
 						 }
 
 						 @Override
-						 public void appendSequence(final String sequence) throws IOException {
+						 public void appendSequence(final String sequence) {
 							 // empty
 						 }
 
 						 @Override
-						 public void repeatDescription(final String repeatDescription) throws IOException {
+						 public void repeatDescription(final String repeatDescription) {
 							 // empty
 						 }
 
 						 @Override
-						 public void quality(final String quality) throws IOException {
+						 public void quality(final String quality) {
 							 // empty
 						 }
 
 						 @Override
-						 public void appendQuality(final String quality) throws IOException {
+						 public void appendQuality(final String quality) {
 							 // empty
 						 }
 
 						 @Override
-						 public void complete() throws IOException {
+						 public void complete() {
 							 // empty
 						 }
 					 });
@@ -393,39 +375,39 @@ public void testParseNullReadable() throws Exception
 		FastqReader reader = createFastqReader();
 		try
 		{
-			reader.parse((Readable) null, new ParseListener() {
+			reader.parse(null, new ParseListener() {
 							 @Override
-							 public void description(final String description) throws IOException {
+							 public void description(final String description) {
 								 // empty
 							 }
 
 							 @Override
-							 public void sequence(final String sequence) throws IOException {
+							 public void sequence(final String sequence) {
 								 // empty
 							 }
 
 							 @Override
-							 public void appendSequence(final String sequence) throws IOException {
+							 public void appendSequence(final String sequence) {
 								 // empty
 							 }
 
 							 @Override
-							 public void repeatDescription(final String repeatDescription) throws IOException {
+							 public void repeatDescription(final String repeatDescription) {
 								 // empty
 							 }
 
 							 @Override
-							 public void quality(final String quality) throws IOException {
+							 public void quality(final String quality) {
 								 // empty
 							 }
 
 							 @Override
-							 public void appendQuality(final String quality) throws IOException {
+							 public void appendQuality(final String quality) {
 								 // empty
 							 }
 
 							 @Override
-							 public void complete() throws IOException {
+							 public void complete() {
 								 // empty
 							 }
 						 });
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriterTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriterTest.java
index b2596dd51b..b3f39fa927 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriterTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriterTest.java
@@ -79,7 +79,7 @@ public void testAppendVararg() throws Exception
 
 		try
 		{
-			writer.append((Appendable) null, fastq0);
+			writer.append(null, fastq0);
 			Assert.fail("append(null,) expected IllegalArgumentException");
 		}
 		catch (IllegalArgumentException e)
@@ -96,7 +96,7 @@ public void testAppendIterable() throws Exception
 		Fastq fastq0 = createFastq();
 		Fastq fastq1 = createFastq();
 		Fastq fastq2 = createFastq();
-		List<Fastq> list = new ArrayList<Fastq>();
+		List<Fastq> list = new ArrayList<>();
 		Assert.assertSame(appendable, writer.append(appendable, list));
 		list.add(fastq0);
 		Assert.assertSame(appendable, writer.append(appendable, list));
@@ -109,7 +109,7 @@ public void testAppendIterable() throws Exception
 
 		try
 		{
-			writer.append((Appendable) null, list);
+			writer.append(null, list);
 			Assert.fail("append(null,) expected IllegalArgumentException");
 		}
 		catch (IllegalArgumentException e)
@@ -163,7 +163,7 @@ public void testWriteFileIterable() throws Exception
 		Fastq fastq0 = createFastq();
 		Fastq fastq1 = createFastq();
 		Fastq fastq2 = createFastq();
-		List<Fastq> list = new ArrayList<Fastq>();
+		List<Fastq> list = new ArrayList<>();
 		File file0 = File.createTempFile("abstractFastqWriterTest", null);
 		writer.write(file0, list);
 
@@ -238,7 +238,7 @@ public void testWriteOutputStreamIterable() throws Exception
 		Fastq fastq1 = createFastq();
 		Fastq fastq2 = createFastq();
 		OutputStream outputStream = new ByteArrayOutputStream();
-		List<Fastq> list = new ArrayList<Fastq>();
+		List<Fastq> list = new ArrayList<>();
 		writer.write(outputStream, list);
 		list.add(fastq0);
 		writer.write(outputStream, list);
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/ConvertTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/ConvertTest.java
index 0c6775a659..fb634ac088 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/ConvertTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/ConvertTest.java
@@ -99,7 +99,7 @@ public void testConvert() throws Exception
 		}
 	}
 
-	private final class FastqVariantPair
+	private static final class FastqVariantPair
 	{
 		final FastqVariant variant1;
 		final FastqVariant variant2;
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqBuilderTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqBuilderTest.java
index b013e996d2..e2af4e776d 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqBuilderTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqBuilderTest.java
@@ -316,7 +316,7 @@ public void testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull()
 			.withQuality("0123")
 			.withVariant(FastqVariant.FASTQ_SOLEXA);
 
-		Assert.assertEquals(false, fastqBuilder.sequenceAndQualityLengthsMatch());
+        Assert.assertFalse(fastqBuilder.sequenceAndQualityLengthsMatch());
 	}
 
 	@Test
@@ -327,7 +327,7 @@ public void testBuildNonMatchingSequenceQualityScoreLengthsQualityNull()
 			.withSequence("ACTG")
 			.withVariant(FastqVariant.FASTQ_SOLEXA);
 
-		Assert.assertEquals(false, fastqBuilder.sequenceAndQualityLengthsMatch());
+        Assert.assertFalse(fastqBuilder.sequenceAndQualityLengthsMatch());
 	}
 
 	@Test
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqTest.java
index b6fc3c98b0..d3454718e2 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqTest.java
@@ -77,7 +77,7 @@ public void testConstructor()
 	public void testDescription()
 	{
 		Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
-		Assert.assertTrue(fastq.getDescription() != null);
+        Assert.assertNotNull(fastq.getDescription());
 		Assert.assertEquals("description", fastq.getDescription());
 	}
 
@@ -85,7 +85,7 @@ public void testDescription()
 	public void testSequence()
 	{
 		Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
-		Assert.assertTrue(fastq.getSequence() != null);
+        Assert.assertNotNull(fastq.getSequence());
 		Assert.assertEquals("sequence", fastq.getSequence());
 	}
 
@@ -93,7 +93,7 @@ public void testSequence()
 	public void testQuality()
 	{
 		Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
-		Assert.assertTrue(fastq.getQuality() != null);
+        Assert.assertNotNull(fastq.getQuality());
 		Assert.assertEquals("quality_", fastq.getQuality());
 	}
 
@@ -101,7 +101,7 @@ public void testQuality()
 	public void testVariant()
 	{
 		Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
-		Assert.assertTrue(fastq.getVariant() != null);
+        Assert.assertNotNull(fastq.getVariant());
 		Assert.assertEquals(FastqVariant.FASTQ_SANGER, fastq.getVariant());
 	}
 
@@ -117,15 +117,15 @@ public void testEquals()
 		Fastq fastq0 = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
 		Fastq fastq1 = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);
 
-		Assert.assertFalse(fastq0.equals(null));
-		Assert.assertFalse(fastq1.equals(null));
-		Assert.assertFalse(fastq0.equals(new Object()));
-		Assert.assertFalse(fastq1.equals(new Object()));
-		Assert.assertTrue(fastq0.equals(fastq0));
-		Assert.assertTrue(fastq1.equals(fastq1));
-		Assert.assertFalse(fastq0 == fastq1);
-		Assert.assertFalse(fastq0.equals(fastq1));
-		Assert.assertFalse(fastq1.equals(fastq0));
+        Assert.assertNotEquals(null, fastq0);
+        Assert.assertNotEquals(null, fastq1);
+        Assert.assertNotEquals(fastq0, new Object());
+        Assert.assertNotEquals(fastq1, new Object());
+        Assert.assertEquals(fastq0, fastq0);
+        Assert.assertEquals(fastq1, fastq1);
+        Assert.assertNotSame(fastq0, fastq1);
+        Assert.assertNotEquals(fastq0, fastq1);
+        Assert.assertNotEquals(fastq1, fastq0);
 	}
 
 	@Test
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqToolsTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqToolsTest.java
index 469601e624..2e4150e60d 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqToolsTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqToolsTest.java
@@ -505,14 +505,14 @@ public void testConvertQualitiesIlluminaToSolexa()
 	@Test
 	public void testToList()
 	{
-		List<String> list = new ArrayList<String>();
+		List<String> list = new ArrayList<>();
 		Assert.assertSame(list, FastqTools.toList(list));
 	}
 
 	@Test
 	public void testToListNotAList()
 	{
-		Collection<String> collection = new HashSet<String>();
+		Collection<String> collection = new HashSet<>();
 		Assert.assertTrue(FastqTools.toList(collection) instanceof List);
 		Assert.assertNotSame(collection, FastqTools.toList(collection));
 	}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqVariantTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqVariantTest.java
index f8b0855a8e..a1705057d6 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqVariantTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqVariantTest.java
@@ -66,9 +66,9 @@ public void testIsIllumina()
 	@Test
 	public void testParseFastqVariant()
 	{
-		Assert.assertEquals(null, parseFastqVariant(null));
-		Assert.assertEquals(null, parseFastqVariant(""));
-		Assert.assertEquals(null, parseFastqVariant("not a valid FASTQ variant"));
+        Assert.assertNull(parseFastqVariant(null));
+        Assert.assertNull(parseFastqVariant(""));
+        Assert.assertNull(parseFastqVariant("not a valid FASTQ variant"));
 		Assert.assertEquals(FASTQ_SANGER, parseFastqVariant("FASTQ_SANGER"));
 		Assert.assertEquals(FASTQ_SANGER, parseFastqVariant("fastq-sanger"));
 	}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqReaderTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqReaderTest.java
index d7b0a8b9d2..1a67f2a9d7 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqReaderTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqReaderTest.java
@@ -59,8 +59,7 @@ public FastqWriter createFastqWriter()
 	}
 
 	@Test
-	public void testValidateDescription() throws Exception
-	{
+	public void testValidateDescription() {
 		IlluminaFastqReader reader = new IlluminaFastqReader();
 		URL invalidDescription = getClass().getResource("illumina-invalid-description.fastq");
 		try
@@ -75,8 +74,7 @@ public void testValidateDescription() throws Exception
 	}
 
 	@Test
-	public void testValidateRepeatDescription() throws Exception
-	{
+	public void testValidateRepeatDescription() {
 		IlluminaFastqReader reader = new IlluminaFastqReader();
 		URL invalidRepeatDescription = getClass().getResource("illumina-invalid-repeat-description.fastq");
 		try
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SangerFastqReaderTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SangerFastqReaderTest.java
index af6f67319f..e5d66dbc80 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SangerFastqReaderTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SangerFastqReaderTest.java
@@ -58,8 +58,7 @@ public FastqWriter createFastqWriter()
 		return new SangerFastqWriter();
 	}
 
-	public void testValidateDescription() throws Exception
-	{
+	public void testValidateDescription() {
 		SangerFastqReader reader = new SangerFastqReader();
 		URL invalidDescription = getClass().getResource("sanger-invalid-description.fastq");
 		try
@@ -74,8 +73,7 @@ public void testValidateDescription() throws Exception
 	}
 
 	@Test
-	public void testValidateRepeatDescription() throws Exception
-	{
+	public void testValidateRepeatDescription() {
 		SangerFastqReader reader = new SangerFastqReader();
 		URL invalidRepeatDescription = getClass().getResource("sanger-invalid-repeat-description.fastq");
 		try
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SolexaFastqReaderTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SolexaFastqReaderTest.java
index 5f6f041c84..25909e97dd 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SolexaFastqReaderTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/SolexaFastqReaderTest.java
@@ -60,8 +60,7 @@ public FastqWriter createFastqWriter()
 	}
 
 	@Test
-	public void testValidateDescription() throws Exception
-	{
+	public void testValidateDescription() {
 		SolexaFastqReader reader = new SolexaFastqReader();
 		URL invalidDescription = getClass().getResource("solexa-invalid-description.fastq");
 		try
@@ -76,8 +75,7 @@ public void testValidateDescription() throws Exception
 	}
 
 	@Test
-	public void testValidateRepeatDescription() throws Exception
-	{
+	public void testValidateRepeatDescription() {
 		SolexaFastqReader reader = new SolexaFastqReader();
 		URL invalidRepeatDescription = getClass().getResource("solexa-invalid-repeat-description.fastq");
 		try
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/StreamingFastqParserTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/StreamingFastqParserTest.java
index a80f44a43d..6818977adb 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/StreamingFastqParserTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/StreamingFastqParserTest.java
@@ -36,11 +36,8 @@ public void testStreamNullReadable() throws Exception
 	{
 		try
 		{
-			StreamingFastqParser.stream((Readable) null, FastqVariant.FASTQ_SANGER, new StreamListener() {
-				@Override
-				public void fastq(final Fastq fastq) {
-					// empty
-				}
+			StreamingFastqParser.stream(null, FastqVariant.FASTQ_SANGER, fastq -> {
+				// empty
 			});
 			Assert.fail("stream(null,,) expected IllegalArgumentException");
 		}
@@ -56,11 +53,8 @@ public void testStreamNullVariant() throws Exception
 		try
 		{
 			final String input = "";
-			StreamingFastqParser.stream(new StringReader(input), null, new StreamListener() {
-				@Override
-				public void fastq(final Fastq fastq) {
-					// empty
-				}
+			StreamingFastqParser.stream(new StringReader(input), null, fastq -> {
+				// empty
 			});
 			Assert.fail("stream(null,,) expected IllegalArgumentException");
 		}
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/MMcifTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/MMcifTest.java
index 4947e0077a..a83bfe1fd0 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/MMcifTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/MMcifTest.java
@@ -106,7 +106,7 @@ private void comparePDB2cif(String id, String chainId) throws IOException {
 
 
 		// load the PDB file via the PDB parser
-		Structure pdbStructure = null;
+		Structure pdbStructure;
 		InputStream pinStream = this.getClass().getResourceAsStream("/"+id+".pdb");
 		assertNotNull(inStream);
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/PDBFileParserTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/PDBFileParserTest.java
index 7bc3c2846d..f94b5faaaf 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/PDBFileParserTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/PDBFileParserTest.java
@@ -108,7 +108,7 @@ public void testCorrectFloatingPointDisplay() throws IOException {
 		Structure s = parser.parsePDBFile(br);
 		String pdb = s.toPDB();
 
-		assertTrue("the created PDB file does not match the input file", pdb.equals(t));
+        assertEquals("the created PDB file does not match the input file", pdb, t);
 
 
 	}
@@ -304,7 +304,7 @@ public void testSITE() throws IOException {
 			//				System.out.println("Got:");
 			//				System.out.println(remark800.toString());
 		}
-		assertTrue("the created PDB REMARK800 section does not match the input file", remark800.toString().equals(remark800Test));
+        assertEquals("the created PDB REMARK800 section does not match the input file", remark800.toString(), remark800Test);
 
 		if (!sites.toString().equals(sitesTest)) {
 			System.out.println("Expected:");
@@ -331,7 +331,7 @@ public void testMultiLineJRNL() throws IOException {
 
 
 		BufferedReader br = new BufferedReader(new StringReader(jrnlString));
-		Structure s = null;
+		Structure s;
 
 		s = parser.parsePDBFile(br);
 
@@ -357,7 +357,7 @@ public void testIncorrectDateFormatMultiLineJRNL() throws IOException{
 
 
 		BufferedReader br = new BufferedReader(new StringReader(jrnlString));
-		Structure s = null;
+		Structure s;
 		s = parser.parsePDBFile(br);
 		//    String jrnl = s.getJournalArticle().toString();
 		//            System.out.println(jrnl);
@@ -380,7 +380,7 @@ public void testInvalidFormatREFsectionJRNL() throws IOException{
 
 
 		BufferedReader br = new BufferedReader(new StringReader(jrnlString));
-		Structure s = null;
+		Structure s;
 		s = parser.parsePDBFile(br);
 		// String jrnl = s.getJournalArticle().toString();
 		//            System.out.println(jrnl);
@@ -406,7 +406,7 @@ public void testSecondMultiLineJRNL() throws IOException{
 
 
 		BufferedReader br = new BufferedReader(new StringReader(jrnlString));
-		Structure s = null;
+		Structure s;
 		s = parser.parsePDBFile(br);
 		// String jrnl = s.getJournalArticle().toString();
 		//            System.out.println(jrnl);
@@ -433,7 +433,7 @@ public void testSingleLineJRNL() throws IOException{
 
 
 		BufferedReader br = new BufferedReader(new StringReader(jrnlString));
-		Structure s = null;
+		Structure s;
 		s = parser.parsePDBFile(br);
 		//   String jrnl = s.getJournalArticle().toString();
 		//            System.out.println(jrnl);
@@ -459,7 +459,7 @@ public void testToBePublishedJRNL() throws IOException{
 
 
 		BufferedReader br = new BufferedReader(new StringReader(jrnlString));
-		Structure s = null;
+		Structure s;
 		s = parser.parsePDBFile(br);
 
 		JournalArticle journalArticle = s.getJournalArticle();
@@ -552,7 +552,7 @@ public void testCorrectAtomNamePadding() throws IOException {
 		String pdb = s.toPDB();
 
 
-		assertTrue("the created PDB file does not match the input file", pdb.equals(atomLines));
+        assertEquals("the created PDB file does not match the input file", pdb, atomLines);
 
 	}
 
@@ -619,13 +619,13 @@ public void testMissingElements() throws IOException {
 		BufferedReader br = new BufferedReader(new StringReader(missingElement));
 		Structure s = parser.parsePDBFile(br);
 		String pdb = s.toPDB();
-		assertTrue("the Element column has not been filled correctly", pdb.equals(original));
+        assertEquals("the Element column has not been filled correctly", pdb, original);
 
 
 		br = new BufferedReader(new StringReader(emptyElement));
 		s = parser.parsePDBFile(br);
 		pdb = s.toPDB();
-		assertTrue("the Element column has not been filled correctly", pdb.equals(original));
+        assertEquals("the Element column has not been filled correctly", pdb, original);
 
 	}
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java
index 15198acbfa..cfb11a465e 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java
@@ -98,10 +98,9 @@ public void testSeqResParsing() {
 
 	/**
 	 * Tests if a PDB file can be parsed
-	 * @throws Exception
 	 */
 	@Test
-	public void testReadPDBFile() throws Exception {
+	public void testReadPDBFile() {
 
 		assertEquals("pdb code not set!","5PTI",structure.getPDBCode());
 
@@ -126,7 +125,7 @@ public void testReadPDBFile() throws Exception {
 	}
 
 	@Test
-	public void testSSBondParsing() throws Exception {
+	public void testSSBondParsing() {
 		assertNotNull(structure);
 
 		List<Bond> ssbonds = structure.getSSBonds();
@@ -164,16 +163,15 @@ private void assertDisulfideBond(String expectedChainId1, String expectedChainId
 
 	/**
 	 * Tests that standard amino acids are working properly
-	 * @throws Exception
 	 */
 	@Test
-	public void testStandardAmino() throws Exception {
+	public void testStandardAmino() {
 
 		AminoAcid arg = StandardAminoAcid.getAminoAcid("ARG");
-		assertTrue(arg.size() == 11 );
+		assertEquals(11, arg.size());
 
 		AminoAcid gly = StandardAminoAcid.getAminoAcid("G");
-		assertTrue(gly.size() == 4);
+		assertEquals(4, gly.size());
 
 	}
 
@@ -182,7 +180,7 @@ public void testPDBHeader(){
 
 		PDBHeader header = structure.getPDBHeader();
 		String classification = header.getClassification();
-		assertTrue(classification.equals("PROTEINASE INHIBITOR (TRYPSIN)"));
+		assertEquals("PROTEINASE INHIBITOR (TRYPSIN)", classification);
 
 		String idCode = header.getIdCode();
 		assertEquals("the idCode in the Header is " + idCode + " and not 5PTI, as expected","5PTI",idCode);
@@ -208,7 +206,7 @@ public void testPDBHeader(){
 		//assertEquals("did not find the right number of compounds! ", 2, compounds.size());
 
 		EntityInfo comp = compounds.get(0);
-		assertEquals("did not get the right compounds info",true,comp.getDescription().startsWith("TRYPSIN INHIBITOR"));
+		assertTrue("did not get the right compounds info", comp.getDescription().startsWith("TRYPSIN INHIBITOR"));
 
 		List<String> chainIds = comp.getChainIds();
 		List<Chain> chains    = comp.getChains();
@@ -237,14 +235,14 @@ public void testCreateVirtualCBAtom(){
 	}
 
 	@Test
-	public void testMutation() throws Exception {
+	public void testMutation() {
 
 		Group g1 = (Group)structure.getChainByIndex(0).getAtomGroup(21).clone();
-		assertTrue(g1 != null);
+		assertNotNull(g1);
 
 
 		Group g2 = (Group)structure.getChainByIndex(0).getAtomGroup(53).clone();
-		assertTrue(g2 != null);
+		assertNotNull(g2);
 
 
 		assertEquals("The group at position 22 is not a PHE","PHE", g1.getPDBName());
@@ -292,13 +290,13 @@ public void testMutation() throws Exception {
 	}
 
 	@Test
-	public void testElement() throws Exception {
+	public void testElement() {
 		// there should be no wild card elements
 		// in a structure (!= Element.R)
 		for (Chain c: structure.getChains()) {
 			for (Group g: c.getAtomGroups()) {
 				for (Atom a: g.getAtoms()) {
-					assertFalse(a.getElement().equals(Element.R));
+					assertNotEquals(a.getElement(), Element.R);
 				}
 			}
 		}
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1a4w.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1a4w.java
index 870c74a13a..5a67cbf67f 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1a4w.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1a4w.java
@@ -82,7 +82,7 @@ public void test1a4wPDBFile() throws IOException
 
 
 
-		Structure structure2 = null;
+		Structure structure2;
 
 		InputStream inStream = this.getClass().getResourceAsStream("/1a4w.cif");
 		Assert.assertNotNull(inStream);
@@ -132,15 +132,15 @@ private void testStructure(Structure structure){
 		//System.out.println(structure);
 		Assert.assertTrue("chain " + a.getName() + " length should be 26. was: " + a.getAtomGroups(GroupType.AMINOACID).size(), (a.getAtomGroups(GroupType.AMINOACID).size() == 26));
 
-		Assert.assertTrue("chain " + a.getName() + " seqres length should be 36. was: " + a.getSeqResLength(), a.getSeqResLength() == 36);
+        Assert.assertEquals("chain " + a.getName() + " seqres length should be 36. was: " + a.getSeqResLength(), 36, a.getSeqResLength());
 
 		Assert.assertTrue("chain " + b.getName() + " length should be 248. was: " + b.getAtomGroups(GroupType.AMINOACID).size(), (b.getAtomGroups(GroupType.AMINOACID).size() == 248));
 
-		Assert.assertTrue("chain " + b.getName() + " seqres length should be 259. was: " + b.getSeqResLength(), b.getSeqResLength() == 259);
+        Assert.assertEquals("chain " + b.getName() + " seqres length should be 259. was: " + b.getSeqResLength(), 259, b.getSeqResLength());
 
 		Assert.assertTrue("chain " + c.getName() + " length should be 9. was: " + c.getAtomGroups(GroupType.AMINOACID).size(), (c.getAtomGroups(GroupType.AMINOACID).size() == 9));
 
-		Assert.assertTrue("chain " + c.getName() + " seqres length should be 12. was: " + c.getSeqResLength(), c.getSeqResLength() == 12);
+        Assert.assertEquals("chain " + c.getName() + " seqres length should be 12. was: " + c.getSeqResLength(), 12, c.getSeqResLength());
 
 		Assert.assertEquals("chain " + c.getName() + " seqres sequences is not correct!", "NGDFEEIPEEYL", c.getSeqResSequence());
 	}
@@ -253,14 +253,18 @@ public void testSiteGroups(){
 					// before biojava 5.0 we were asserting for same chain, but now the DAR residue is in its own nonpoly chain, can't do it anymore
 					//assertEquals(c2, g.getChain());
 					String pdbName = g.getPDBName();
-					if ( pdbName.equals("DAR")) {
-						darPresent = true;
-						//System.out.println("darPresent");
+					switch (pdbName) {
+						case "DAR":
+							darPresent = true;
+							//System.out.println("darPresent");
+							break;
+						case "GLY":
+							glyPresent = true;
+							break;
+						case "H2O":
+							noWater = false;
+							break;
 					}
-					else if ( pdbName.equals("GLY"))
-						glyPresent = true;
-					else if ( pdbName.equals("H2O"))
-						noWater = false;
 				}
 			}
 		}
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/AlignmentToolsTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/AlignmentToolsTest.java
index 339f1e4eee..3c46c1b258 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/AlignmentToolsTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/AlignmentToolsTest.java
@@ -97,7 +97,7 @@ public void testGetSymmetryOrderForMaps() {
 		final float minimumMetricChange = .5f;// be liberal, since we have small alignments
 
 		// noisy C3 alignment
-		Map<Integer,Integer> alignment1 = new HashMap<Integer,Integer>();
+		Map<Integer,Integer> alignment1 = new HashMap<>();
 		alignment1.put(1, 5);
 		alignment1.put(2, 6);
 		alignment1.put(4, 7);
@@ -107,14 +107,14 @@ public void testGetSymmetryOrderForMaps() {
 		alignment1.put(10, 3);
 		alignment1.put(11, 4);
 
-		Map<Integer,Integer> identity = new AlignmentTools.IdentityMap<Integer>();
+		Map<Integer,Integer> identity = new AlignmentTools.IdentityMap<>();
 
 		order = AlignmentTools.getSymmetryOrder(alignment1, identity, maxSymmetry, minimumMetricChange);
 		Assert.assertEquals("Wrong order for alignment 1", 3, order);
 
 		// sequential alignment. Should be order 1, but we report this as "no symmetry"
 		//TODO Change default return value in getSymmetry
-		Map<Integer,Integer> alignment2 = new HashMap<Integer,Integer>();
+		Map<Integer,Integer> alignment2 = new HashMap<>();
 		for(int i=1;i<10;i++) {
 			alignment2.put(i, i+1);
 		}
@@ -123,7 +123,7 @@ public void testGetSymmetryOrderForMaps() {
 		Assert.assertEquals("Wrong order for alignment 2", 1, order);
 
 		// now try to get symmetry order with an imperfect identity
-		Map<Integer,Integer> alignment3 = new HashMap<Integer,Integer>();
+		Map<Integer,Integer> alignment3 = new HashMap<>();
 		alignment3.put(1, 15);
 		alignment3.put(2, 16);
 		alignment3.put(4, 17);
@@ -133,7 +133,7 @@ public void testGetSymmetryOrderForMaps() {
 		alignment3.put(10, 13);
 		alignment3.put(11, 14);
 
-		Map<Integer,Integer> identityMinus10 = new HashMap<Integer,Integer>();
+		Map<Integer,Integer> identityMinus10 = new HashMap<>();
 		for(int i=1;i<=11;i++) {
 			identityMinus10.put(i+10, i);
 		}
@@ -155,7 +155,7 @@ public void testGetSymmetryOrderForMaps() {
 	@Test
 	public void testGuessSequentialAlignment() {
 		// noisy C3 alignment
-		Map<Integer,Integer> alignment1 = new HashMap<Integer,Integer>();
+		Map<Integer,Integer> alignment1 = new HashMap<>();
 		alignment1.put(1, 5);
 		alignment1.put(2, 6);
 		alignment1.put(4, 7);
@@ -166,7 +166,7 @@ public void testGuessSequentialAlignment() {
 		alignment1.put(11, 4);
 
 		// Sequential version of the alignment
-		Map<Integer,Integer> sequentialForward = new HashMap<Integer,Integer>();
+		Map<Integer,Integer> sequentialForward = new HashMap<>();
 		sequentialForward.put(1, 2);
 		sequentialForward.put(2, 3);
 		sequentialForward.put(4, 4);
@@ -177,7 +177,7 @@ public void testGuessSequentialAlignment() {
 		sequentialForward.put(11, 11);
 
 		// inverse of sequentialForward
-		Map<Integer,Integer> sequentialBackward = new HashMap<Integer,Integer>();
+		Map<Integer,Integer> sequentialBackward = new HashMap<>();
 		sequentialBackward.put(2, 1);
 		sequentialBackward.put(3, 2);
 		sequentialBackward.put(4, 4);
@@ -254,7 +254,7 @@ public void testGetSymmetryOrderWithCECP() throws IOException, StructureExceptio
 	@Test
 	public void testApplyAlignment() {
 		// noisy C3 alignment
-		Map<Integer,Integer> alignment1 = new HashMap<Integer,Integer>();
+		Map<Integer,Integer> alignment1 = new HashMap<>();
 		alignment1.put(1, 5);
 		alignment1.put(2, 6);
 		alignment1.put(4, 7);
@@ -264,7 +264,7 @@ public void testApplyAlignment() {
 		alignment1.put(10, 3);
 		alignment1.put(11, 4);
 
-		Map<Integer,Integer> image1 = new HashMap<Integer,Integer>();
+		Map<Integer,Integer> image1 = new HashMap<>();
 		image1.put(1, null);
 		image1.put(2, 9);
 		image1.put(4, 11);
@@ -284,7 +284,7 @@ public void testApplyAlignment() {
 	@Test
 	public void testApplyAlignmentNonIdentical() {
 		// noisy C3 alignment
-		Map<Integer,Integer> alignment1 = new HashMap<Integer,Integer>();
+		Map<Integer,Integer> alignment1 = new HashMap<>();
 		alignment1.put(1, 15);
 		alignment1.put(2, 16);
 		alignment1.put(4, 17);
@@ -294,7 +294,7 @@ public void testApplyAlignmentNonIdentical() {
 		alignment1.put(10, 13);
 		alignment1.put(11, 14);
 
-		Map<Integer,Integer> image1 = new HashMap<Integer,Integer>();
+		Map<Integer,Integer> image1 = new HashMap<>();
 		image1.put(1, null);
 		image1.put(2, 19);
 		image1.put(4, 21);
@@ -306,7 +306,7 @@ public void testApplyAlignmentNonIdentical() {
 		//image1.put(5, null);
 		//image1.put(3, null);
 
-		Map<Integer,Integer> identity1 = new HashMap<Integer, Integer>();
+		Map<Integer,Integer> identity1 = new HashMap<>();
 		for(int i=1;i<12;i++) {
 			identity1.put(i+10,i);
 		}
@@ -320,7 +320,7 @@ public void testToConciseAlignmentString() {
 		String result,expected;
 		int i=0;
 
-		test = new HashMap<Integer, Integer>();
+		test = new HashMap<>();
 		test.put(1, 2);
 		test.put(2, 3);
 		test.put(3, 4);
@@ -331,7 +331,7 @@ public void testToConciseAlignmentString() {
 		Assert.assertEquals((i++) + ". Linear strings.", expected, result);
 
 
-		test = new HashMap<Integer, Integer>();
+		test = new HashMap<>();
 		test.put(1, 2);
 		test.put(2, 3);
 		test.put(3, 1);
@@ -341,7 +341,7 @@ public void testToConciseAlignmentString() {
 		result = AlignmentTools.toConciseAlignmentString(test);
 		Assert.assertEquals((i++) + ". Cycles.", expected, result);
 
-		test = new HashMap<Integer, Integer>();
+		test = new HashMap<>();
 		test.put(1, 2);
 		test.put(2, 3);
 		test.put(3, 1);
@@ -351,7 +351,7 @@ public void testToConciseAlignmentString() {
 		result = AlignmentTools.toConciseAlignmentString(test);
 		Assert.assertEquals((i++) + ". Complex.", expected, result);
 
-		test = new HashMap<Integer, Integer>();
+		test = new HashMap<>();
 		test.put(1, 2);
 		test.put(2, 3);
 		test.put(3, 4);
@@ -376,7 +376,7 @@ public void testToConciseAlignmentString() {
 		result = AlignmentTools.toConciseAlignmentString(test);
 		Assert.assertEquals((i++) + ". Sub-optimal arrangement", expected, result);
 
-		Map <Integer,Double> test2 = new HashMap<Integer, Double>();
+		Map <Integer,Double> test2 = new HashMap<>();
 		test2.put(1, 12.);
 		test2.put(2, 13.);
 		test2.put(3, 14.);
@@ -409,7 +409,7 @@ public void testUpdateSuperposition() throws IOException, StructureException {
 		Atom[] ca2 = StructureTools.getRepresentativeAtomArray(s);
 		StringBuilder sb = new StringBuilder();
 		BufferedReader br = new BufferedReader(new FileReader("src/test/resources/align/31BI_symm_align.xml"));
-		String line = "";
+		String line;
 		while ((line = br.readLine()) != null) {
 			sb.append(line);
 		}
@@ -429,7 +429,7 @@ public void testUpdateSuperposition() throws IOException, StructureException {
 	 */
 	public static class OffsetMap extends AbstractMap<Double,Integer>
 	{
-		private int offset;
+		private final int offset;
 		public OffsetMap(int offset) {
 			this.offset = offset;
 		}
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/FlipAFPChainTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/FlipAFPChainTest.java
index 6213503c64..b3f0752f86 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/FlipAFPChainTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/FlipAFPChainTest.java
@@ -139,8 +139,7 @@ private void flip(String name1, String name2, String algorithmName) throws Struc
 	 * @param ca2
 	 * @return
 	 */
-	private double getRMSD(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
-	throws StructureException {
+	private double getRMSD(AFPChain afpChain, Atom[] ca1, Atom[] ca2) {
 
 		Atom[] ca2clone = StructureTools.cloneAtomArray(ca2);
 		rotateAtoms2(afpChain,ca2clone);
@@ -150,9 +149,9 @@ private double getRMSD(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
 		Atom[] catmp1 = AFPAlignmentDisplay.getAlignedAtoms1(afpChain, ca1);
 		Atom[] catmp2 = AFPAlignmentDisplay.getAlignedAtoms2(afpChain, ca2clone);
 
-		assertTrue(catmp1.length == catmp2.length);
+		assertEquals(catmp1.length, catmp2.length);
 
-		assertTrue(catmp1.length == afpChain.getNrEQR());
+		assertEquals(catmp1.length, afpChain.getNrEQR());
 
 		return Calc.rmsd(catmp1,catmp2);
 	}
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/TestSimilarityCalc.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/TestSimilarityCalc.java
index 48e905a9e5..00ecaa6c3b 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/TestSimilarityCalc.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/TestSimilarityCalc.java
@@ -26,14 +26,12 @@
 import org.biojava.nbio.structure.align.StructureAlignment;
 import org.biojava.nbio.structure.align.StructureAlignmentFactory;
 import org.biojava.nbio.structure.align.model.AFPChain;
-import org.biojava.nbio.structure.align.model.AfpChainWriter;
 import org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters;
 import org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.junit.Test;
 
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.junit.Assert.*;
 
 
 /**
@@ -49,8 +47,8 @@ public void testSimilarityDisplay(){
 
 		AtomCache cache = new AtomCache();
 
-		Structure structure1 = null;
-		Structure structure2 = null;
+		Structure structure1;
+		Structure structure2;
 
 		try {
 
@@ -71,9 +69,9 @@ public void testSimilarityDisplay(){
 			afpChain.setName2(name2);
 
 
-			assertTrue(afpChain.getAlnLength() == 71);
+			assertEquals(71, afpChain.getAlnLength());
 
-			assertTrue(afpChain.getAlnLength() == 71);
+			assertEquals(71, afpChain.getAlnLength());
 			assertTrue(afpChain.getSimilarity() > .57);
 			assertTrue(afpChain.getSimilarity() <= .6);
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/ce/OptimalCECPMainTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/ce/OptimalCECPMainTest.java
index bf7ee56be4..76f9005b47 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/ce/OptimalCECPMainTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/ce/OptimalCECPMainTest.java
@@ -44,13 +44,13 @@
  */
 public class OptimalCECPMainTest {
 
-	private AtomCache cache = new AtomCache();
+	private final AtomCache cache = new AtomCache();
 
 	/* (non-Javadoc)
 	 * @see junit.framework.TestCase#setUp()
 	 */
 	@Before
-	public void setUp() throws Exception {
+	public void setUp() {
 	}
 
 	/**
@@ -183,22 +183,22 @@ public void testPermuteArray() throws Exception {
 		arrP = Arrays.copyOf(arr0, arr0.length);
 		Assert.assertTrue("Shallow equals!", Arrays.deepEquals(arr0, arrP));
 		permuteArray.invoke(null, arrP, 0);
-		Assert.assertTrue(String.format("Permuting by 0 gave %s%s%s%s%s%s", (Object[]) arrP),
+		Assert.assertTrue(String.format("Permuting by 0 gave %s%s%s%s%s%s", arrP),
 				Arrays.deepEquals(arr0, arrP));
 
 		arrP = Arrays.copyOf(arr0, arr0.length);
 		permuteArray.invoke(null, arrP, 1);
-		Assert.assertTrue(String.format("Permuting by 1 gave %s%s%s%s%s%s", (Object[]) arrP),
+		Assert.assertTrue(String.format("Permuting by 1 gave %s%s%s%s%s%s", arrP),
 				Arrays.deepEquals(arr1, arrP));
 
 		arrP = Arrays.copyOf(arr0, arr0.length);
 		permuteArray.invoke(null, arrP, 5);
-		Assert.assertTrue(String.format("Permuting by 7 gave %s%s%s%s%s%s", (Object[]) arrP),
+		Assert.assertTrue(String.format("Permuting by 7 gave %s%s%s%s%s%s", arrP),
 				Arrays.deepEquals(arr5, arrP));
 
 		arrP = Arrays.copyOf(arr0, arr0.length);
 		permuteArray.invoke(null, arrP, -1);
-		Assert.assertTrue(String.format("Permuting by -1 gave %s%s%s%s%s%s", (Object[]) arrP),
+		Assert.assertTrue(String.format("Permuting by -1 gave %s%s%s%s%s%s", arrP),
 				Arrays.deepEquals(arr5, arrP));
 
 		try {
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/AFPChainSerialisationTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/AFPChainSerialisationTest.java
index 9d0bc303b7..dadba4d471 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/AFPChainSerialisationTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/AFPChainSerialisationTest.java
@@ -148,13 +148,13 @@ private void testAlignment(String name1, String name2, Atom[] ca1, Atom[] ca2, b
 		int blockNum = afpChain.getBlockNum();
 		int[] optLen = afpChain.getOptLen();
 
-		assertTrue("The nr of aligned blocks is not the same! " + blockNum + " " + newChain.getBlockNum() , blockNum == newChain.getBlockNum());
+		assertEquals("The nr of aligned blocks is not the same! " + blockNum + " " + newChain.getBlockNum(), blockNum, newChain.getBlockNum());
 
 
 
 		for ( int i =0 ; i < blockNum ; i++){
 			int newLenI = newChain.getOptLen()[i];
-			assertTrue("The values in the optLen field don't match! pos:" + i + " orig:" + optLen[i] + " new:" +  newLenI,optLen[i] == newLenI);
+			assertEquals("The values in the optLen field don't match! pos:" + i + " orig:" + optLen[i] + " new:" + newLenI, optLen[i], newLenI);
 		}
 
 		// test the internal optAlign data structure:
@@ -170,8 +170,8 @@ private void testAlignment(String name1, String name2, Atom[] ca1, Atom[] ca2, b
 				int n1 = optAln2[i][0][j];
 				int n2 = optAln2[i][1][j];
 
-				assertTrue(p1 == n1);
-				assertTrue(p2 == n2);
+				assertEquals(p1, n1);
+				assertEquals(p2, n2);
 
 			}
 		}
@@ -187,7 +187,7 @@ private void testAlignment(String name1, String name2, Atom[] ca1, Atom[] ca2, b
 	}
 
 
-	private AFPChain doAlign(String name1, String name2, Atom[] ca1, Atom[] ca2 , boolean doRigid) throws StructureException,IOException{
+	private AFPChain doAlign(String name1, String name2, Atom[] ca1, Atom[] ca2 , boolean doRigid) throws StructureException {
 		FatCatParameters params = new FatCatParameters();
 
 		FatCat fatCat = new FatCat();
@@ -222,14 +222,14 @@ public String[] align (String name1, String name2, Atom[] ca1, Atom[] ca2 , bool
 
 	@org.junit.Test
 	public void testMulti() throws IOException, StructureException {
-		Atom[] ca1 = null;
-		Atom[] ca2 = null;
-		Atom[] ca3 = null;
-		Atom[] ca4 = null;
-		Atom[] ca5 = null;
-		Atom[] ca6 = null;
-		String[] result1 = null;
-		String[] result2 = null;
+		Atom[] ca1;
+		Atom[] ca2;
+		Atom[] ca3;
+		Atom[] ca4;
+		Atom[] ca5;
+		Atom[] ca6;
+		String[] result1;
+		String[] result2;
 
 		String name1 = "5pti.A";
 		String name2 = "1znf.A";
@@ -264,7 +264,7 @@ public void testMulti() throws IOException, StructureException {
 		//WARNING: THE ORDER CAN CHANGE: order of elements in XML is not necessarily the same!
 		AFPChain[] chains = AFPChainXMLParser.parseMultiXML(xmlNew);
 
-		assertTrue(chains.length == 2);
+		assertEquals(2, chains.length);
 
 		// recreate the correct chains...
 		AFPChain new1 = getAfpFor(name1,chains);
@@ -273,16 +273,16 @@ public void testMulti() throws IOException, StructureException {
 		assertNotNull(new1);
 		assertNotNull(new2);
 
-		assertTrue(new1.getName1().equals(name1));
+		assertEquals(new1.getName1(), name1);
 		//System.out.println(new2.getName1() + " " + new2.getName2() + " "+ name3);
-		assertTrue(new2.getName1().equals(name3));
+		assertEquals(new2.getName1(), name3);
 
 
 		AFPChainXMLParser.rebuildAFPChain(new1, ca1, ca3);
 		String fatcat1 = new1.toFatcat(ca1, ca3);
 		assertEquals(fatcat1, result1[0]);
 		String xmlnew1 = AFPChainXMLConverter.toXML(new1, ca1, ca3);
-		assertTrue(xmlnew1.equals(result1[1]));
+		assertEquals(xmlnew1, result1[1]);
 
 		AFPChainXMLParser.rebuildAFPChain(new2, ca4, ca6);
 		String fatcat2 = new2.toFatcat(ca4, ca6);
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/FlipAFPChainTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/FlipAFPChainTest.java
index 41a03bee70..cf58a0c3c1 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/FlipAFPChainTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/FlipAFPChainTest.java
@@ -118,7 +118,7 @@ private void align (StructureAlignment algorithm, String name1, String name2)
 		Assert.assertNotNull("could not get nr. of eqr: ", afpChain.getNrEQR());
 		Assert.assertNotNull("could not get nr. of eqr: ", origFlip.getNrEQR());
 
-		Assert.assertTrue("The nr. of equivalent positions is not equal!", afpChain.getNrEQR() == origFlip.getNrEQR());
+		Assert.assertEquals("The nr. of equivalent positions is not equal!", afpChain.getNrEQR(), origFlip.getNrEQR());
 
 		Atom shift1 = afpChain.getBlockShiftVector()[0];
 		Atom shift2 = origFlip.getBlockShiftVector()[0];
@@ -158,8 +158,7 @@ private void align (StructureAlignment algorithm, String name1, String name2)
 	 * @param ca2
 	 * @return
 	 */
-	private double getRMSD(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
-			throws StructureException {
+	private double getRMSD(AFPChain afpChain, Atom[] ca1, Atom[] ca2) {
 
 		Atom[] ca2clone = StructureTools.cloneAtomArray(ca2);
 		rotateAtoms2(afpChain,ca2clone);
@@ -169,9 +168,9 @@ private double getRMSD(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
 		Atom[] catmp1 = AFPAlignmentDisplay.getAlignedAtoms1(afpChain, ca1);
 		Atom[] catmp2 = AFPAlignmentDisplay.getAlignedAtoms2(afpChain, ca2clone);
 
-		Assert.assertTrue(catmp1.length == catmp2.length);
+		Assert.assertEquals(catmp1.length, catmp2.length);
 
-		Assert.assertTrue(catmp1.length == afpChain.getNrEQR());
+		Assert.assertEquals(catmp1.length, afpChain.getNrEQR());
 
 		return Calc.rmsd(catmp1,catmp2);
 	}
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/MyTestHelper.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/MyTestHelper.java
index 1905b173af..0fc48c7a5e 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/MyTestHelper.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/MyTestHelper.java
@@ -41,7 +41,7 @@ public class MyTestHelper
 
 	public static String compareAlignment(String pdb1, String chain1, String pdb2, String chain2, String originalOutput, boolean doRigid){
 
-		AFPChain afpChain = null;
+		AFPChain afpChain;
 
 		PDBFileReader pdbpars = new PDBFileReader();
 		pdbpars.setPath(pdbPath);
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java
index 5a4709e2e0..3016dc7737 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java
@@ -86,7 +86,7 @@ private void compare(String name1, String name2, boolean doRigid){
 			//Atom[] shifts1 = afpChain.getBlockShiftVector();
 			double[] blockRmsd = afpChain.getBlockRmsd();
 
-			assertTrue( afpChain.getBlockNum() == newChain.getBlockNum());
+			assertEquals(afpChain.getBlockNum(), newChain.getBlockNum());
 
 			// make sure the XML conversion worked OK.
 			for ( int i = 0 ; i < newChain.getBlockNum();i++) {
@@ -96,7 +96,7 @@ private void compare(String name1, String name2, boolean doRigid){
 				assertTrue(compareRmsd(blockRmsd[i], newChain.getBlockRmsd()[i]) );
 			}
 
-			assertTrue(afpChain.getOptLength() == newChain.getOptLength());
+			assertEquals(afpChain.getOptLength(), newChain.getOptLength());
 
 			// get the aligned blocks and check RMSD
 			int[] blockSize =afpChain.getBlockSize();
@@ -122,9 +122,7 @@ private void compare(String name1, String name2, boolean doRigid){
 
 			}
 
-		} catch (IOException e){
-			fail(e.getMessage());
-		} catch (StructureException e){
+		} catch (IOException | StructureException e){
 			fail(e.getMessage());
 		}
 
@@ -161,9 +159,9 @@ private void compareBlock(int blockNr, AFPChain afpChain, AFPChain newChain,
 
 		// get the eqr atoms of block X:
 		int[] optLen =afpChain.getOptLen();
-		List<Atom> eqrPos1 = new ArrayList<Atom>();
-		List<Atom> eqrPos2 = new ArrayList<Atom>();
-		List<Atom> eqrPos2copy = new ArrayList<Atom>();
+		List<Atom> eqrPos1 = new ArrayList<>();
+		List<Atom> eqrPos2 = new ArrayList<>();
+		List<Atom> eqrPos2copy = new ArrayList<>();
 		for ( int z = 0 ; z < blocks2[blockNr][0].length && z < optLen[blockNr] ; z++){
 			int pos1 = blocks2[blockNr][0][z];
 			int pos2 = blocks2[blockNr][1][z];
@@ -177,15 +175,15 @@ private void compareBlock(int blockNr, AFPChain afpChain, AFPChain newChain,
 			eqrPos2copy.add(c3);
 		}
 
-		assertTrue("The nr of Atoms in block " + blockNr + " does not match the expected nr. Expected:" + afpChain.getOptLen()[blockNr] + " but found: " + eqrPos2.size() , eqrPos2.size() == afpChain.getOptLen()[blockNr]);
+		assertEquals("The nr of Atoms in block " + blockNr + " does not match the expected nr. Expected:" + afpChain.getOptLen()[blockNr] + " but found: " + eqrPos2.size(), eqrPos2.size(), afpChain.getOptLen()[blockNr]);
 
 
 
 		// THIS IS ROTATING the coordinates according to what is in the file.
 
-		Atom[] blockSet1 = eqrPos1.toArray(new Atom[eqrPos1.size()]);
-		Atom[] blockSet2 = eqrPos2.toArray(new Atom[eqrPos2.size()]);
-		Atom[] blockSet2copy = eqrPos2copy.toArray(new Atom[eqrPos2copy.size()]);
+		Atom[] blockSet1 = eqrPos1.toArray(new Atom[0]);
+		Atom[] blockSet2 = eqrPos2.toArray(new Atom[0]);
+		Atom[] blockSet2copy = eqrPos2copy.toArray(new Atom[0]);
 
 
 		//System.out.println(shift );
@@ -248,7 +246,7 @@ private void compareBlock(int blockNr, AFPChain afpChain, AFPChain newChain,
 
 	}
 
-	private boolean compareVectors(Atom atom1, Atom atom2) throws StructureException {
+	private boolean compareVectors(Atom atom1, Atom atom2) {
 
 		//System.out.println(Math.abs(atom1.getX()-  atom2.getX()));
 		assertTrue("The X coordinates are too far apart!", Math.abs(atom1.getX()-  atom2.getX()) < 0.01);
@@ -270,7 +268,7 @@ private boolean compareMatrices(Matrix matrix1, Matrix matrix2) {
 
 	}
 
-	private AFPChain getAlignment (String name1, String name2, Atom[] ca1, Atom[] ca2 , boolean doRigid) throws StructureException,IOException{
+	private AFPChain getAlignment (String name1, String name2, Atom[] ca1, Atom[] ca2 , boolean doRigid) throws StructureException {
 		FatCatParameters params = new FatCatParameters();
 
 		StructureAlignment fatCat ;
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestOutputStrings.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestOutputStrings.java
index 4917d67cf3..e50d0c3135 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestOutputStrings.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestOutputStrings.java
@@ -207,28 +207,7 @@ public void test1buz1aliFlexible(){
 		String pdb2 = "1ali";
 		String chain2 ="A";
 
-		String originalOutput ="Align 1buzA.pdb 116 with 1aliA.pdb 446" +newline +
-		"Twists 1 ini-len 64 ini-rmsd 3.12 opt-equ 88 opt-rmsd 3.34 chain-rmsd 5.32 Score 103.72 align-len 199 gaps 111 (55.78%)" +newline +
-		"P-value 3.26e-01 Afp-num 15578 Identity 6.25% Similarity 25.89%" +newline +
-		"Block  0 afp  1 score 23.14 rmsd  0.76 gap 0 (0.00%)" +newline +
-		"Block  1 afp  7 score 100.08 rmsd  3.32 gap 17 (0.23%)" +newline +
-		"" +newline +
-		"                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" +newline +
-		"Chain 1:    5 DMNVKESVLCIRLTGELDH---------------------------------HTAETLKQKVTQSLEKDD" +newline +
-		"              1 11111111111111                                    222222222222222222" +newline +
-		"Chain 2:  246 VTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEK" +newline +
-		"" +newline +
-		"                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" +newline +
-		"Chain 1:   42 IRHIVLNLEDLS------------FMDSSGLGVILGRYKQIK-QIGGEMVVCAISPAVKRLFDMSGLFKI" +newline +
-		"              222222222222            222222222222222222 2222222222222              " +newline +
-		"Chain 2:  316 GFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPG" +newline +
-		"" +newline +
-		"                  .    :    .    :    .    :    .    :    .    :    ." +newline +
-		"Chain 1:   99 I---------------------------------RFEQSE--------QQALLTLGVAS" +newline +
-		"                                                22            222222 2222" +newline +
-		"Chain 2:  386 LTQALNTKDGAVMVMSYGNSEEDSQENTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKA" +newline +
-		"" +newline +
-		"Note: positions are from PDB; the numbers between alignments are block index" +newline ;
+		String originalOutput = "Align 1buzA.pdb 116 with 1aliA.pdb 446" + newline + "Twists 1 ini-len 64 ini-rmsd 3.12 opt-equ 88 opt-rmsd 3.34 chain-rmsd 5.32 Score 103.72 align-len 199 gaps 111 (55.78%)" + newline + "P-value 3.26e-01 Afp-num 15578 Identity 6.25% Similarity 25.89%" + newline + "Block  0 afp  1 score 23.14 rmsd  0.76 gap 0 (0.00%)" + newline + "Block  1 afp  7 score 100.08 rmsd  3.32 gap 17 (0.23%)" + newline + "" + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:    5 DMNVKESVLCIRLTGELDH---------------------------------HTAETLKQKVTQSLEKDD" + newline + "              1 11111111111111                                    222222222222222222" + newline + "Chain 2:  246 VTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEK" + newline + "" + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:   42 IRHIVLNLEDLS------------FMDSSGLGVILGRYKQIK-QIGGEMVVCAISPAVKRLFDMSGLFKI" + newline + "              222222222222            222222222222222222 2222222222222              " + newline + "Chain 2:  316 GFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPG" + newline + "" + newline + "                  .    :    .    :    .    :    .    :    .    :    ." + newline + "Chain 1:   99 I---------------------------------RFEQSE--------QQALLTLGVAS" + newline + "                                                22            222222 2222" + newline + "Chain 2:  386 LTQALNTKDGAVMVMSYGNSEEDSQENTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKA" + newline + newline + "Note: positions are from PDB; the numbers between alignments are block index" + newline;
 
 		String result = MyTestHelper.compareAlignment(pdb1, chain1, pdb2, chain2, originalOutput,false);
 		if (! result.equals("")){
@@ -327,23 +306,7 @@ public void test1a641hngFlexible(){
 		String pdb2 = "1hng";
 		String chain2 ="B";
 
-		String originalOutput="Align 1a64A.pdb 94 with 1hngB.pdb 175" +newline +
-		"Twists 1 ini-len 88 ini-rmsd 1.84 opt-equ 94 opt-rmsd 0.64 chain-rmsd 20.77 Score 235.94 align-len 96 gaps 2 (2.08%)" +newline +
-		"P-value 4.23e-13 Afp-num 6497 Identity 98.94% Similarity 100.00%" +newline +
-		"Block  0 afp  5 score 118.80 rmsd  0.75 gap 0 (0.00%)" +newline +
-		"Block  1 afp  6 score 143.14 rmsd  0.46 gap 0 (0.00%)" +newline +
-		"" +newline +
-		"                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" +newline +
-		"Chain 1:    4 GTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKR--KPFLKSGAFEILANGDLKIKNLTRDDS" +newline +
-		"              11111111111111111111111111111111111111111  222222222222222222222222222" +newline +
-		"Chain 2:    4 GTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKMKPFLKSGAFEILANGDLKIKNLTRDDS" +newline +
-		"" +newline +
-		"                  .    :    .    :    ." +newline +
-		"Chain 1:   74 GTYNVTVYSTNGTRILDKALDLRILE" +newline +
-		"              22222222222222222222222222" +newline +
-		"Chain 2:   74 GTYNVTVYSTNGTRILNKALDLRILE" +newline +
-		"" +newline +
-		"Note: positions are from PDB; the numbers between alignments are block index" +newline ;
+		String originalOutput= "Align 1a64A.pdb 94 with 1hngB.pdb 175" + newline + "Twists 1 ini-len 88 ini-rmsd 1.84 opt-equ 94 opt-rmsd 0.64 chain-rmsd 20.77 Score 235.94 align-len 96 gaps 2 (2.08%)" + newline + "P-value 4.23e-13 Afp-num 6497 Identity 98.94% Similarity 100.00%" + newline + "Block  0 afp  5 score 118.80 rmsd  0.75 gap 0 (0.00%)" + newline + "Block  1 afp  6 score 143.14 rmsd  0.46 gap 0 (0.00%)" + newline + "" + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:    4 GTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKR--KPFLKSGAFEILANGDLKIKNLTRDDS" + newline + "              11111111111111111111111111111111111111111  222222222222222222222222222" + newline + "Chain 2:    4 GTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKMKPFLKSGAFEILANGDLKIKNLTRDDS" + newline + "" + newline + "                  .    :    .    :    ." + newline + "Chain 1:   74 GTYNVTVYSTNGTRILDKALDLRILE" + newline + "              22222222222222222222222222" + newline + "Chain 2:   74 GTYNVTVYSTNGTRILNKALDLRILE" + newline + newline + "Note: positions are from PDB; the numbers between alignments are block index" + newline;
 		String result = MyTestHelper.compareAlignment(pdb1, chain1, pdb2, chain2, originalOutput,false);
 		if (! result.equals("")){
 			String msg = "the created alignment images are not identical! ";
@@ -509,28 +472,7 @@ public void test1a211hwgFlexible(){
 		String pdb2 = "1hwg";
 		String chain2 ="C";
 
-		String originalOutput="Align 1a21A.pdb 194 with 1hwgC.pdb 191" +newline +
-		"Twists 1 ini-len 120 ini-rmsd 3.04 opt-equ 150 opt-rmsd 2.96 chain-rmsd 4.21 Score 233.34 align-len 210 gaps 60 (28.57%)" +newline +
-		"P-value 1.15e-05 Afp-num 12696 Identity 11.98% Similarity 23.95%" +newline +
-		"Block  0 afp  4 score 66.42 rmsd  2.03 gap 6 (0.16%)" +newline +
-		"Block  1 afp 11 score 184.29 rmsd  3.24 gap 69 (0.44%)" +newline +
-		"" +newline +
-		"                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" +newline +
-		"Chain 1:    6 RAYNLTWKSTN-FKTILEWEPKSIDHVYTVQISTRLENWKSKCFLTAE---TECDLTDEVVKDVGQTYMA" +newline +
-		"              11111111111 111111111     111111111111111111       222222222   222222 " +newline +
-		"Chain 2:   32 EPKFTKCRSPERETFSCHWTD-----PIQLFYTRRNQEWKECPDYVSAGENSCYFNSSFT---SIWIPYC" +newline +
-		"" +newline +
-		"                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" +newline +
-		"Chain 1:   72 RVLSYPARNTTGFPEEPPFRNSPEFTPYLDTNLGQPTIQSFEQVG-------TKLNVTVQDARTLVTFLS" +newline +
-		"                                    22222222222222222222222       222222222222   222" +newline +
-		"Chain 2:  109 IKLTSNGGTVDE----------KCFSVDEIVQPDPPIALNWTLLNVSLTGIHADIQVRWEAPRN---ADI" +newline +
-		"" +newline +
-		"                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" +newline +
-		"Chain 1:  141 LRAVFGKDLNYTLYYWR-----KKTAT-TNTNEFLIDVDKGE-NYCFSVQAVIPSRKRKQRSPESLTECT" +newline +
-		"              222222  222222222     22222 22222222222222 2222222222222  222222222222" +newline +
-		"Chain 2:  166 QKGWMV--LEYELQYKEVNETKWKMMDPILTTSVPVYSLKVDKEYEVRVRSKQRNS--GNYGEFSEVLYV" +newline +
-		"" +newline +
-		"Note: positions are from PDB; the numbers between alignments are block index" +newline;
+		String originalOutput= "Align 1a21A.pdb 194 with 1hwgC.pdb 191" + newline + "Twists 1 ini-len 120 ini-rmsd 3.04 opt-equ 150 opt-rmsd 2.96 chain-rmsd 4.21 Score 233.34 align-len 210 gaps 60 (28.57%)" + newline + "P-value 1.15e-05 Afp-num 12696 Identity 11.98% Similarity 23.95%" + newline + "Block  0 afp  4 score 66.42 rmsd  2.03 gap 6 (0.16%)" + newline + "Block  1 afp 11 score 184.29 rmsd  3.24 gap 69 (0.44%)" + newline + "" + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:    6 RAYNLTWKSTN-FKTILEWEPKSIDHVYTVQISTRLENWKSKCFLTAE---TECDLTDEVVKDVGQTYMA" + newline + "              11111111111 111111111     111111111111111111       222222222   222222 " + newline + "Chain 2:   32 EPKFTKCRSPERETFSCHWTD-----PIQLFYTRRNQEWKECPDYVSAGENSCYFNSSFT---SIWIPYC" + newline + "" + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:   72 RVLSYPARNTTGFPEEPPFRNSPEFTPYLDTNLGQPTIQSFEQVG-------TKLNVTVQDARTLVTFLS" + newline + "                                    22222222222222222222222       222222222222   222" + newline + "Chain 2:  109 IKLTSNGGTVDE----------KCFSVDEIVQPDPPIALNWTLLNVSLTGIHADIQVRWEAPRN---ADI" + newline + "" + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:  141 LRAVFGKDLNYTLYYWR-----KKTAT-TNTNEFLIDVDKGE-NYCFSVQAVIPSRKRKQRSPESLTECT" + newline + "              222222  222222222     22222 22222222222222 2222222222222  222222222222" + newline + "Chain 2:  166 QKGWMV--LEYELQYKEVNETKWKMMDPILTTSVPVYSLKVDKEYEVRVRSKQRNS--GNYGEFSEVLYV" + newline + newline + "Note: positions are from PDB; the numbers between alignments are block index" + newline;
 
 		String result = MyTestHelper.compareAlignment(pdb1, chain1, pdb2, chain2, originalOutput,false);
 		if (! result.equals("")){
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java
index 8ab3f29fb3..439f86cbf8 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java
@@ -148,7 +148,7 @@ public void testByPDB() throws IOException {
 
 	private void matchNames(String pdbId,String[] expected,List<EcodDomain> actual) {
 		assertEquals("Wrong number of domains for "+pdbId, expected.length, actual.size());
-		Set<String> exp = new HashSet<String>(Arrays.asList(expected));
+		Set<String> exp = new HashSet<>(Arrays.asList(expected));
 		for(EcodDomain d : actual) {
 			assertTrue("Unexpected domain "+d.getDomainId()+" in "+pdbId,exp.contains(d.getDomainId()));
 		}
@@ -175,7 +175,7 @@ public void testParsing() throws IOException {
 		}
 		expected = new EcodDomain(
 				//				Long uid, String domainId, Boolean manual,
-				20669l, "e1lyw.1", false,
+                20669L, "e1lyw.1", false,
 				//				Integer xGroup, Integer hGroup, Integer tGroup, Integer fGroup, String pdbId,
 				1,1,1,fGroup,"1lyw",
 				//				String chainName, String range, String seqId, String architectureName,
@@ -184,7 +184,7 @@ public void testParsing() throws IOException {
 				"cradle loop barrel", "RIFT-related","acid protease",
 				//				String fGroupName, Boolean isAssembly, List<String> ligands
 				fGroupName,
-				20669l, Collections.singleton("EPE")
+                20669L, Collections.singleton("EPE")
 				);
 		assertEquals(ecodId,expected,domain);
 
@@ -195,13 +195,13 @@ public void testParsing() throws IOException {
 	}
 
 	@Test
-	public void testMultithreaded() throws IOException {
+	public void testMultithreaded() {
 		final EcodInstallation ecod = (EcodInstallation) EcodFactory.getEcodDatabase(VERSION);
 		ecod.clear();
 		String[] ecodIds = new String[] {
 				"e4s1gA1", "e4umoB1", "e4v0cA1", "e4v1af1", "e3j7yj1", "e4wfcA1","e4b0jP1",
 		};
-		List<Future<EcodDomain>> futureDomains = new ArrayList<Future<EcodDomain>>();
+		List<Future<EcodDomain>> futureDomains = new ArrayList<>();
 		for(final String ecodId : ecodIds) {
 			Callable<EcodDomain> job = new Callable<EcodDomain>() {
 				@Override
@@ -246,8 +246,8 @@ public void testFilterByHierarchy() throws IOException {
 		Set<String> expected,actual;
 
 		// expected members through at least develop133
-		expected = new HashSet<String>(Arrays.asList(
-				"e4il6R1 e4pj0R1 e4pj0r1 e4ub6R1 e4ub8R1".split(" ") ));
+		expected = new HashSet<>(Arrays.asList(
+				"e4il6R1 e4pj0R1 e4pj0r1 e4ub6R1 e4ub8R1".split(" ")));
 		// expanded by develop204
 		if( ecod.getVersion().compareToIgnoreCase("develop204") >= 0) {
 			expected.addAll(Arrays.asList(
@@ -256,21 +256,21 @@ public void testFilterByHierarchy() throws IOException {
 		}
 
 		filtered = ecod.filterByHierarchy("6106.1.1");
-		actual = new HashSet<String>();
+		actual = new HashSet<>();
 		for(EcodDomain d : filtered) {
 			actual.add(d.getDomainId());
 		}
 		assertEquals(expected,actual);
 
 		filtered = ecod.filterByHierarchy("6106.1");
-		actual = new HashSet<String>();
+		actual = new HashSet<>();
 		for(EcodDomain d : filtered) {
 			actual.add(d.getDomainId());
 		}
 		assertEquals(expected,actual);
 
 		filtered = ecod.filterByHierarchy("6106");
-		actual = new HashSet<String>();
+		actual = new HashSet<>();
 		for(EcodDomain d : filtered) {
 			actual.add(d.getDomainId());
 		}
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java
index 96d7e31d62..d8ae01bc2a 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java
@@ -85,11 +85,7 @@ private static int testVersion(String ecodVersion) throws IOException {
 			try {
 				struct = cache.getStructure(d.getPdbId());
 				ca1 = StructureTools.getRepresentativeAtomArray(struct);
-			} catch (IOException e) {
-				logger.error("Error getting structure for "+d.getDomainId(),e);
-				errors++;
-				continue;
-			} catch (StructureException e) {
+			} catch (IOException | StructureException e) {
 				logger.error("Error getting structure for "+d.getDomainId(),e);
 				errors++;
 				continue;
@@ -128,12 +124,11 @@ private static int testVersion(String ecodVersion) throws IOException {
 						Group g = struct.getPolyChainByPDB(range.getStart().getChainName()).getGroupByPDB(range.getStart());
 						if(g!=null) {
 							logger.warn("No CA atom for starting residue "+d.getDomainId()+"_"+range);
-							clean = false;
-						} else {
+                        } else {
 							logger.error("Start doesn't exist for "+d.getDomainId()+"_"+range.toString());
-							clean = false;
-						}
-					}
+                        }
+                        clean = false;
+                    }
 				} catch(Exception e) {
 					logger.error("Start doesn't exist for "+d.getDomainId()+"_"+range.toString(),e);
 					clean = false;
@@ -147,12 +142,11 @@ private static int testVersion(String ecodVersion) throws IOException {
 						} catch(StructureException e ) {}
 						if(g!=null) {
 							logger.warn("No CA atom for ending residue "+d.getDomainId()+"_"+range);
-							clean = false;
-						} else {
+                        } else {
 							logger.error("End doesn't exist for "+d.getDomainId()+"_"+range.toString());
-							clean = false;
-						}
-					}
+                        }
+                        clean = false;
+                    }
 				} catch(Exception e) {
 					logger.error("End doesn't exist for "+d.getDomainId()+"_"+range.toString(),e);
 					clean = false;
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/LoadOldXMLfileTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/LoadOldXMLfileTest.java
index 69c52dd2de..97f10a7ca4 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/LoadOldXMLfileTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/LoadOldXMLfileTest.java
@@ -94,7 +94,7 @@ public static String convertStreamToString(InputStream stream) throws IOExceptio
 		BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
 		StringBuilder sb = new StringBuilder();
 
-		String line = null;
+		String line;
 
 		while ((line = reader.readLine()) != null) {
 		  sb.append(line).append("\n");
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java
index 23a73a7ae8..6f394a34b8 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java
@@ -191,8 +191,8 @@ public void test4OPJ() throws IOException, StructureException {
 			List<Chain> model = multiModelBioAssemblies.get(0).getModel(modelIdx);
 			for (Chain c:model) {
 				System.out.println(c.getId()+" "+c.getName());
-				assertTrue(!c.getId().contains("_"));
-				assertTrue(!c.getName().contains("_"));
+                assertFalse(c.getId().contains("_"));
+                assertFalse(c.getName().contains("_"));
 			}
 
 		}
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java
index daadcc7023..6450f9ed44 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java
@@ -100,9 +100,9 @@ public static void setUpBeforeClass() {
 			(cache.getPath().equals(System.getProperty("java.io.tmpdir")+File.separator))    ) {
 
 			throw new IllegalArgumentException("PDB_DIR has not been set or it is set to the default temp directory. Please set PDB_DIR to run this test");
-		};
+		}
 
-		params = new FileParsingParameters();
+        params = new FileParsingParameters();
 		cache.setFileParsingParams(params);
 		cache.setObsoleteBehavior(ObsoleteBehavior.THROW_EXCEPTION);
 	}
@@ -130,7 +130,7 @@ public void testVeryLongPdbVsMmCif() throws IOException, StructureException {
 	@Ignore
 	@Test
 	public void testSingle() throws IOException, StructureException {
-		testAll(Arrays.asList("4kro"));
+		testAll(Collections.singletonList("4kro"));
 	}
 
 	@After
@@ -141,7 +141,7 @@ public void printInfo() {
 
 	private void testAll(List<String> pdbIds) throws IOException, StructureException {
 
-		pdbIdsWithMismatchingMolIds = new HashSet<String>();
+		pdbIdsWithMismatchingMolIds = new HashSet<>();
 
 		long start = System.currentTimeMillis();
 
@@ -358,7 +358,7 @@ private void testHeader(Structure sPdb, Structure sCif) {
 
 
 			if (ciPdb.getNcsOperators()==null) {
-				assertTrue(ciCif.getNcsOperators()==null);
+				assertNull(ciCif.getNcsOperators());
 			} else {
 
 				Matrix4d[] ncsOpersPdb = ciPdb.getNcsOperators();
@@ -393,18 +393,19 @@ private void testHeader(Structure sPdb, Structure sCif) {
 					hPdb.getNrBioAssemblies(),batPdb.size());
 			assertEquals("Size of bioassemblies maps don't coincide",batPdb.size(), batCif.size());
 
-			for (int id:batPdb.keySet()) {
+			for (Map.Entry<Integer, BioAssemblyInfo> entry : batPdb.entrySet()) {
+				int id = entry.getKey();
 				assertTrue("Bioassembly id is not contained in mmCIF",batCif.containsKey(id));
 				// there's an inconsistency in 4amh pdb vs mmCIF in mmSize
 				if (sPdb.getPDBCode().equalsIgnoreCase("4amh")) continue;
 
 				assertEquals("Macromolecular size of assembly "+id+" doesn't coincide",
-						batPdb.get(id).getMacromolecularSize(), batCif.get(id).getMacromolecularSize());
+						entry.getValue().getMacromolecularSize(), batCif.get(id).getMacromolecularSize());
 			}
 		}
 	}
 
-	private void testChains(Structure sPdb, Structure sCif) throws StructureException {
+	private void testChains(Structure sPdb, Structure sCif) {
 		assertNotNull(sPdb.getChains());
 		assertNotNull(sCif.getChains());
 
@@ -432,7 +433,7 @@ private void testChains(Structure sPdb, Structure sCif) throws StructureExceptio
 
 
 
-		Set<String> chainIds = new TreeSet<String>();
+		Set<String> chainIds = new TreeSet<>();
 		for (Chain chain:sPdb.getPolyChains()){
 			chainIds.add(chain.getName());
 		}
@@ -601,7 +602,7 @@ private List<String> readTestSetFile(String testSetFile) throws IOException {
 		InputStream inStream = this.getClass().getResourceAsStream(testSetFile);
 		BufferedReader br = new BufferedReader(new InputStreamReader(inStream));
 
-		List<String> list = new ArrayList<String>();
+		List<String> list = new ArrayList<>();
 
 		String line;
 		while ((line=br.readLine())!=null) {
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/BerkeleyScopInstallationTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/BerkeleyScopInstallationTest.java
index 96c01ae03c..5d47b6bbdb 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/BerkeleyScopInstallationTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/BerkeleyScopInstallationTest.java
@@ -42,7 +42,7 @@ public BerkeleyScopInstallationTest(String tag,ScopDatabase scop) {
 	}
 	@Parameters(name="{0}")
 	public static Collection<Object[]> availableDatabases() {
-		ArrayList<Object[]> databases = new ArrayList<Object[]>();
+		ArrayList<Object[]> databases = new ArrayList<>();
 		ScopInstallation scop;
 
 		for(String version : new String[] {
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/RemoteScopInstallationTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/RemoteScopInstallationTest.java
index 2abe7d63ae..74cd9df51c 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/RemoteScopInstallationTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/RemoteScopInstallationTest.java
@@ -46,7 +46,7 @@ public RemoteScopInstallationTest(String tag,ScopDatabase scop) {
 	//@Parameters
 	@Parameters(name="{0}")
 	public static Collection<Object[]> availableDatabases() {
-		ArrayList<Object[]> databases = new ArrayList<Object[]>();
+		ArrayList<Object[]> databases = new ArrayList<>();
 		RemoteScopInstallation scop;
 		for(String version : new String[] {
 				ScopFactory.LATEST_VERSION,
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDatabaseTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDatabaseTest.java
index 2a34d017f1..30a5c6e738 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDatabaseTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDatabaseTest.java
@@ -94,7 +94,7 @@ public void traverseHierarchy()
 		desc = scop.getScopDescriptionBySunid(node.getSunid());
 		assertEquals(tag,46487,node.getSunid());
 		assertEquals(tag,"-",desc.getName());
-		assertTrue(tag,Pattern.matches("Human \\(Homo sapiens\\)( \\[TaxId: 9606\\])?",desc.getDescription()));
+		assertTrue(tag,Pattern.matches("Human \\(Homo sapiens\\)( \\[TaxId: 9606])?",desc.getDescription()));
 		assertEquals(tag,"a.1.1.2",desc.getClassificationId());
 
 		node = scop.getScopNode(node.getParentSunid());
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopInstallationTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopInstallationTest.java
index c1c940da84..c1b7e3be5b 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopInstallationTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopInstallationTest.java
@@ -47,7 +47,7 @@ public ScopInstallationTest(String tag,ScopDatabase scop) {
 	//@Parameters
 	@Parameters(name="{0}")
 	public static Collection<Object[]> availableDatabases() {
-		ArrayList<Object[]> databases = new ArrayList<Object[]>();
+		ArrayList<Object[]> databases = new ArrayList<>();
 		ScopInstallation scop;
 
 		for(String version : new String[] {
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopTest.java
index f7d5e8fdee..8405c83837 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopTest.java
@@ -98,11 +98,11 @@ private void runSCOPTests() throws IOException, StructureException {
 
 		List<ScopDomain> domains = scop.getDomainsForPDB("4HHB");
 
-		assertTrue(domains.size() == 4);
+        assertEquals(4, domains.size());
 
 		// test case sensitivity;
 		List<ScopDomain> domains2 = scop.getDomainsForPDB("4hhb");
-		assertTrue(domains2.size() == domains.size());
+        assertEquals(domains2.size(), domains.size());
 
 		//System.out.println(domains);
 
@@ -110,7 +110,7 @@ private void runSCOPTests() throws IOException, StructureException {
 		String scop1m02 = "d1m02a_	1m02	A:	k.36.1.1	74353	cl=58788,cf=75796,sf=75797,fa=75798,dm=75799,sp=75800,px=74353";
 
 		List<ScopDomain> domains1m02 = scop.getDomainsForPDB("1m02");
-		assertTrue(domains1m02.size() == 1);
+        assertEquals(1, domains1m02.size());
 		ScopDomain d1 = domains1m02.get(0);
 
 		assertNotNull(d1);
@@ -119,7 +119,7 @@ private void runSCOPTests() throws IOException, StructureException {
 
 
 		List<ScopDomain> domains1cdg = scop.getDomainsForPDB("1CDG");
-		assertTrue(domains1cdg.size() == 4);
+        assertEquals(4, domains1cdg.size());
 		ScopDomain d2 = domains1cdg.get(0);
 		assertEquals("Wrong SCOP Id", "d1cdga1", d2.getScopId());
 		AtomCache cache = new AtomCache();
@@ -146,7 +146,7 @@ private void runSCOPTests() throws IOException, StructureException {
 
 		// check a domain with multiple ranges
 		List<ScopDomain> domains1xzp = scop.getDomainsForPDB("1xzp");
-		assertTrue(domains1xzp.size() ==4 );
+        assertEquals(4, domains1xzp.size());
 
 
 
@@ -163,7 +163,7 @@ private void runSCOPTests() throws IOException, StructureException {
 		// check insertion codes
 
 		List<ScopDomain> domains2bq6 = scop.getDomainsForPDB("2bq6");
-		assertTrue(domains2bq6.size() == 2);
+        assertEquals(2, domains2bq6.size());
 		ScopDomain target = scop.getDomainByScopID("d2bq6a1");
 
 		assertNotNull(target);
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java
index a5cd0a9fb4..b244c864ab 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java
@@ -267,7 +267,7 @@ public void testLocal() throws IOException, StructureException {
 			for (QuatSymmetryResults local:foundLocal) {
 				logger.info("Found stoichiometry "+local.getStoichiometry().toString()+" with symmetry "+local.getSymmetry());
 				assertTrue("Stoichiometry "+local.getStoichiometry().toString()+" not expected for "+testIds.get(iTest),
-						refLocal.keySet().contains(local.getStoichiometry().toString()));
+						refLocal.containsKey(local.getStoichiometry().toString()));
 
 				assertEquals("Symmetry "+local.getSymmetry()+" with stoichiometry "+local.getStoichiometry().toString()+
 								" not expected for "+testIds.get(iTest),
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java b/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java
index 71604d9bb3..7452b9b737 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java
@@ -82,7 +82,7 @@ public File[] getLocalFiles(){
 
 		File dir = getLocalDir();
 
-		List<File> files = new ArrayList<File>();
+		List<File> files = new ArrayList<>();
 		for ( String f : rfiles) {
 
 
@@ -98,7 +98,7 @@ public File[] getLocalFiles(){
 
 		}
 
-		return files.toArray(new File[files.size()]);
+		return files.toArray(new File[0]);
 	}
 
 
@@ -170,7 +170,7 @@ public void downloadFile(URL u, File localFile) throws IOException {
 
 		FileOutputStream w = new FileOutputStream(tmp);
 
-		int i= 0;
+		int i;
 		byte[] bytesIn = new byte[300000];
 		while ((i = in.read(bytesIn)) >= 0) {
 			w.write(bytesIn,0,i);
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Site.java b/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Site.java
index ca5e4a5f2f..d22cce8ff2 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Site.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Site.java
@@ -25,6 +25,7 @@
 
 import java.io.*;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 import java.util.zip.GZIPInputStream;
 
@@ -48,11 +49,11 @@ public static List<Site> parseSites(File f) throws IOException {
 		Reader decoder = new InputStreamReader(gzipStream);
 		BufferedReader buf = new BufferedReader(decoder);
 
-		String line = null;
+		String line;
 
-		List<Site > data = new ArrayList<Site>();
+		List<Site > data = new ArrayList<>();
 
-		List<String> headerFields = null;
+		List<String> headerFields;
 
 		int proteinIndex = -1;
 		int uniprotIndex = -1;
@@ -131,11 +132,8 @@ public static List<Site> parseSites(File f) throws IOException {
 	private static List<String> parseHeaderFields(String line) {
 		String[] spl = line.split("\t");
 
-		List<String> h = new ArrayList<String>();
-		for (String s: spl){
-			h.add(s);
-
-		}
+		List<String> h = new ArrayList<>();
+        h.addAll(Arrays.asList(spl));
 
 		return h;
 	}
@@ -215,7 +213,7 @@ public void setOrganism(String organism) {
 
 	@Override
 	public String toString() {
-		StringBuffer s = new StringBuffer();
+		StringBuilder s = new StringBuilder();
 
 		s.append("Site{" +
 				"protein='" + protein + '\'');
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java
index ff4b0abb82..4a35ff5218 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java
@@ -50,10 +50,10 @@ public final class Component {
 	 */
 	private static void lazyInit() {
 		if (components==null) {
-			components = new HashSet<Component>();
-			nonTerminalComps = new HashMap<Set<String>, Component>();
-			nTerminalAminoAcids = new HashMap<Set<String>, Component>();
-			cTerminalAminoAcids = new HashMap<Set<String>, Component>();
+			components = new HashSet<>();
+			nonTerminalComps = new HashMap<>();
+			nTerminalAminoAcids = new HashMap<>();
+			cTerminalAminoAcids = new HashMap<>();
 		}
 	}
 
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationCategory.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationCategory.java
index 89d9bd9720..170cf5cdbf 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationCategory.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationCategory.java
@@ -93,7 +93,7 @@ public boolean isCrossLink() {
 	/**
 	 * The variable is the same as the &ltType&gt; in the ptm_list XML file.
 	 */
-	private String label;
+	private final String label;
 
 	private String desc;
 
@@ -106,9 +106,9 @@ public static ModificationCategory getByLabel(String label) {
 		return mapLabelCat.get(label);
 	}
 
-	private static Map<String, ModificationCategory> mapLabelCat;
+	private static final Map<String, ModificationCategory> mapLabelCat;
 	static {
-		mapLabelCat = new HashMap<String, ModificationCategory>();
+		mapLabelCat = new HashMap<>();
 		for (ModificationCategory cat:ModificationCategory.values()) {
 			mapLabelCat.put(cat.label, cat);
 		}
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationCondition.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationCondition.java
index 3afc2f171a..ce4b0a491b 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationCondition.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationCondition.java
@@ -37,11 +37,11 @@ public interface ModificationCondition {
 	 *
 	 * @return the involved components.
 	 */
-	public List<Component> getComponents();
+    List<Component> getComponents();
 
 	/**
 	 *
 	 * @return a list of all {Link ModificationLinkage}s.
 	 */
-	public List<ModificationLinkage> getLinkages();
+    List<ModificationLinkage> getLinkages();
 }
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationConditionImpl.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationConditionImpl.java
index 2af28ed33f..5cb7857bdd 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationConditionImpl.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationConditionImpl.java
@@ -49,7 +49,7 @@ public ModificationConditionImpl(final List<Component> components,
 
 
 		if (components.size() > 1) {
-			Set<Integer> indices = new HashSet<Integer>();
+			Set<Integer> indices = new HashSet<>();
 			for (ModificationLinkage linkage : linkages) {
 				indices.add(linkage.getIndexOfComponent1());
 				indices.add(linkage.getIndexOfComponent2());
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationOccurrenceType.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationOccurrenceType.java
index 30a4bad4e0..fde9dcee68 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationOccurrenceType.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationOccurrenceType.java
@@ -60,7 +60,7 @@ public String toString() {
 	/**
 	 * The variable is the same as the &ltOccurrence&gt; in the ptm_list XML file.
 	 */
-	private String label;
+	private final String label;
 
 	/**
 	 *
@@ -71,9 +71,9 @@ public static ModificationOccurrenceType getByLabel(String label) {
 		return mapLabelOcc.get(label);
 	}
 
-	private static Map<String, ModificationOccurrenceType> mapLabelOcc;
+	private static final Map<String, ModificationOccurrenceType> mapLabelOcc;
 	static {
-		mapLabelOcc = new HashMap<String, ModificationOccurrenceType>();
+		mapLabelOcc = new HashMap<>();
 		for (ModificationOccurrenceType occ:ModificationOccurrenceType.values()) {
 			mapLabelOcc.put(occ.label, occ);
 		}
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModification.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModification.java
index b173f63f11..6f5b15633f 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModification.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModification.java
@@ -39,84 +39,84 @@ public interface ProteinModification {
 	 *
 	 * @return modification id.
 	 */
-	public String getId();
+    String getId();
 
 	/**
 	 *
 	 * @return Protein Data Bank Chemical Component ID.
 	 */
-	public String getPdbccId();
+    String getPdbccId();
 
 	/**
 	 *
 	 * @return Protein Data Bank Chemical Component name.
 	 */
-	public String getPdbccName();
+    String getPdbccName();
 
 	/**
 	 *
 	 * @return RESID ID.
 	 */
-	public String getResidId();
+    String getResidId();
 
 	/**
 	 *
 	 * @return RESID name.
 	 */
-	public String getResidName();
+    String getResidName();
 
 	/**
 	 *
 	 * @return PSI-MOD ID.
 	 */
-	public String getPsimodId();
+    String getPsimodId();
 
 	/**
 	 *
 	 * @return PSI-MOD name.
 	 */
-	public String getPsimodName();
+    String getPsimodName();
 
 	/**
 	 *
 	 * @return Systematic name.
 	 */
-	public String getSystematicName();
+    String getSystematicName();
 
 	/**
 	 *
 	 * @return Description.
 	 */
-	public String getDescription();
+    String getDescription();
 
 	/**
 	 *
 	 * @return a set of keywords.
 	 */
-	public Set<String> getKeywords();
+    Set<String> getKeywords();
 
 	/**
 	 *
 	 * @return {@link ModificationCondition}
 	 */
-	public ModificationCondition getCondition();
+    ModificationCondition getCondition();
 
 	/**
 	 *
 	 * @return formula of the modified residue.
 	 */
-	public String getFormula();
+    String getFormula();
 
 	/**
 	 *
 	 * @return the modification category.
 	 */
-	public ModificationCategory getCategory();
+    ModificationCategory getCategory();
 
 	/**
 	 *
 	 * @return the modification occurrence type.
 	 */
-	public ModificationOccurrenceType getOccurrenceType();
+    ModificationOccurrenceType getOccurrenceType();
 
 }
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationImpl.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationImpl.java
index a06ee41936..dd4f11d41f 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationImpl.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationImpl.java
@@ -251,7 +251,7 @@ public static class Builder {
 		private String sysName = null;
 		private String formula = null;
 
-		private Set<String> keywords = new LinkedHashSet<String>();
+		private Set<String> keywords = new LinkedHashSet<>();
 
 		/**
 		 *
@@ -289,7 +289,7 @@ public Builder(final ProteinModification copyFrom) {
 			this.sysName = copyFrom.getSystematicName();
 			this.formula = copyFrom.getFormula();
 
-			this.keywords = new LinkedHashSet<String>(copyFrom.getKeywords());
+			this.keywords = new LinkedHashSet<>(copyFrom.getKeywords());
 		}
 
 		public Builder setCategory(final ModificationCategory cat) {
@@ -448,7 +448,7 @@ private ProteinModificationImpl(Builder builder) {
 		this.sysName = builder.sysName;
 		this.formula = builder.formula;
 
-		this.keywords = new LinkedHashSet<String>(builder.keywords);
+		this.keywords = new LinkedHashSet<>(builder.keywords);
 	}
 
 	@Override
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java
index 54babab8e1..95e08fe90f 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java
@@ -55,7 +55,7 @@ public class ProteinModificationRegistry {
 	private static Map<ModificationCategory, Set<ProteinModification>> byCategory = null;
 	private static Map<ModificationOccurrenceType, Set<ProteinModification>> byOccurrenceType = null;
 
-	private static String DIR_XML_PTM_LIST = "ptm_list.xml";
+	private static final String DIR_XML_PTM_LIST = "ptm_list.xml";
 
 
 
@@ -109,22 +109,22 @@ private static synchronized void lazyInit() {
 	private static synchronized void lazyInit(InputStream inStream) {
 		if (registry==null) {
 
-			registry = 	new HashSet<ProteinModification>();
-			byId = new HashMap<String, ProteinModification>();
-			byResidId = new HashMap<String, Set<ProteinModification>>();
-			byPsimodId = new HashMap<String, Set<ProteinModification>>();
-			byPdbccId = new HashMap<String, Set<ProteinModification>>();
-			byKeyword = new HashMap<String, Set<ProteinModification>>();
-			byComponent = new HashMap<Component, Set<ProteinModification>>();
-			byCategory = new EnumMap<ModificationCategory, Set<ProteinModification>>(
+			registry = new HashSet<>();
+			byId = new HashMap<>();
+			byResidId = new HashMap<>();
+			byPsimodId = new HashMap<>();
+			byPdbccId = new HashMap<>();
+			byKeyword = new HashMap<>();
+			byComponent = new HashMap<>();
+			byCategory = new EnumMap<>(
 					ModificationCategory.class);
 			for (ModificationCategory cat:ModificationCategory.values()) {
-				byCategory.put(cat, new HashSet<ProteinModification>());
+				byCategory.put(cat, new HashSet<>());
 			}
-			byOccurrenceType = new EnumMap<ModificationOccurrenceType, Set<ProteinModification>>(
+			byOccurrenceType = new EnumMap<>(
 					ModificationOccurrenceType.class);
 			for (ModificationOccurrenceType occ:ModificationOccurrenceType.values()) {
-				byOccurrenceType.put(occ, new HashSet<ProteinModification>());
+				byOccurrenceType.put(occ, new HashSet<>());
 			}
 			registerCommonProteinModifications(inStream);
 		}
@@ -156,50 +156,30 @@ public static void register(final ProteinModification modification) {
 		ModificationCondition condition = modification.getCondition();
 		List<Component> comps = condition.getComponents();
 		for (Component comp:comps) {
-			Set<ProteinModification> mods = byComponent.get(comp);
-			if (mods==null) {
-				mods = new HashSet<ProteinModification>();
-				byComponent.put(comp, mods);
-			}
+			Set<ProteinModification> mods = byComponent.computeIfAbsent(comp, k -> new HashSet<>());
 			mods.add(modification);
 		}
 
 		String pdbccId = modification.getPdbccId();
 		if (pdbccId!=null) {
-			Set<ProteinModification> mods = byPdbccId.get(pdbccId);
-			if (mods==null) {
-				mods = new HashSet<ProteinModification>();
-				byPdbccId.put(pdbccId, mods);
-			}
+			Set<ProteinModification> mods = byPdbccId.computeIfAbsent(pdbccId, k -> new HashSet<>());
 			mods.add(modification);
 		}
 
 		String residId = modification.getResidId();
 		if (residId!=null) {
-			Set<ProteinModification> mods = byResidId.get(residId);
-			if (mods==null) {
-				mods = new HashSet<ProteinModification>();
-				byResidId.put(residId, mods);
-			}
+			Set<ProteinModification> mods = byResidId.computeIfAbsent(residId, k -> new HashSet<>());
 			mods.add(modification);
 		}
 
 		String psimodId = modification.getPsimodId();
 		if (psimodId!=null) {
-			Set<ProteinModification> mods = byPsimodId.get(psimodId);
-			if (mods==null) {
-				mods = new HashSet<ProteinModification>();
-				byPsimodId.put(psimodId, mods);
-			}
+			Set<ProteinModification> mods = byPsimodId.computeIfAbsent(psimodId, k -> new HashSet<>());
 			mods.add(modification);
 		}
 
 		for (String keyword : modification.getKeywords()) {
-			Set<ProteinModification> mods = byKeyword.get(keyword);
-			if (mods==null) {
-				mods = new HashSet<ProteinModification>();
-				byKeyword.put(keyword, mods);
-			}
+			Set<ProteinModification> mods = byKeyword.computeIfAbsent(keyword, k -> new HashSet<>());
 			mods.add(modification);
 		}
 	}
@@ -308,7 +288,7 @@ public static Set<ProteinModification> getByComponent(final Component comp1,
 		if (comps.length==0) {
 			return Collections.unmodifiableSet(mods);
 		} else {
-			Set<ProteinModification> ret = new HashSet<ProteinModification>(mods);
+			Set<ProteinModification> ret = new HashSet<>(mods);
 			for (Component comp:comps) {
 				mods = byComponent.get(comp);
 				if (mods==null) {
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ComponentXMLConverter.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ComponentXMLConverter.java
index 138488b650..87e0314d50 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ComponentXMLConverter.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ComponentXMLConverter.java
@@ -46,8 +46,8 @@ public static String toXML(Component component) throws IOException{
 	public static void toXML(Component component, PrettyXMLWriter xml) throws IOException{
 		xml.openTag("component");
 
-		xml.attribute("nTerminal" , component.isNTerminal()+"");
-		xml.attribute("cTerminal", component.isCTerminal()+"");
+		xml.attribute("nTerminal" , String.valueOf(component.isNTerminal()));
+		xml.attribute("cTerminal", String.valueOf(component.isCTerminal()));
 		for (String pdbccId : component.getPdbccIds()){
 			xml.openTag("pdbccID");
 			xml.attribute("id", pdbccId);
@@ -74,7 +74,7 @@ public static Component fromXML(Node componentN) {
 		boolean isNTerminal = Boolean.parseBoolean(nTerminalS);
 		boolean isCTerminal = Boolean.parseBoolean(cTerminalS);
 
-		Set<String>pdbccIds = new HashSet<String>();
+		Set<String>pdbccIds = new HashSet<>();
 
 		NodeList valList = componentN.getChildNodes();
 		int numChildren  = valList.getLength();
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java
index fb76e02340..cb795276a9 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java
@@ -110,7 +110,7 @@ public static ModifiedCompound fromXML(String xml){
 		ProteinModification modification = null;
 		//Collection<StructureAtomLinkage> linkages = new ArrayList<StructureAtomLinkage>();
 		StructureAtomLinkage[] linkages = null;
-		List<StructureGroup> structureGroups = new ArrayList<StructureGroup>();
+		List<StructureGroup> structureGroups = new ArrayList<>();
 		try
 		{
 			//Convert string to XML document
@@ -142,41 +142,41 @@ public static ModifiedCompound fromXML(String xml){
 					if(!listOfConditions.hasAttributes()) continue;
 
 
-					if ( listOfConditions.getNodeName().equals("proteinModification")) {
-						//modification = ProteinModificationXMLConverter.fromXML(listOfConditions);
-						String modId = getAttribute(listOfConditions, "id");
-						modification = ProteinModificationRegistry.getById(modId);
-						if (modification==null) {
-							logger.warn("Error: no modification information.");
-						}
-					} else if ( listOfConditions.getNodeName().equals("linkage")) {
-						double dist = Double.parseDouble(getAttribute(listOfConditions, "distance"));
-						int pos = Integer.parseInt(getAttribute(listOfConditions,"pos"));
-						int total = Integer.parseInt(getAttribute(listOfConditions,"total"));
-						if ( linkages == null)
-							linkages = new StructureAtomLinkage[total];
-
-						StructureAtom atom1 = getAtom("atom1", listOfConditions);
-						StructureAtom atom2 = getAtom("atom2",listOfConditions);
-						StructureAtomLinkage linkage = new StructureAtomLinkage(atom1, atom2, dist);
-						//linkages.add(linkage);
-						linkages[pos] = linkage;
-					} else if (listOfConditions.getNodeName().equals("structureGroup")) {
-						StructureGroup group = StructureGroupXMLConverter.fromXML(listOfConditions);
-						structureGroups.add(group);
+					switch (listOfConditions.getNodeName()) {
+						case "proteinModification":
+							//modification = ProteinModificationXMLConverter.fromXML(listOfConditions);
+							String modId = getAttribute(listOfConditions, "id");
+							modification = ProteinModificationRegistry.getById(modId);
+							if (modification == null) {
+								logger.warn("Error: no modification information.");
+							}
+							break;
+						case "linkage":
+							double dist = Double.parseDouble(getAttribute(listOfConditions, "distance"));
+							int pos = Integer.parseInt(getAttribute(listOfConditions, "pos"));
+							int total = Integer.parseInt(getAttribute(listOfConditions, "total"));
+							if (linkages == null)
+								linkages = new StructureAtomLinkage[total];
+
+							StructureAtom atom1 = getAtom("atom1", listOfConditions);
+							StructureAtom atom2 = getAtom("atom2", listOfConditions);
+							StructureAtomLinkage linkage = new StructureAtomLinkage(atom1, atom2, dist);
+							//linkages.add(linkage);
+							linkages[pos] = linkage;
+							break;
+						case "structureGroup":
+							StructureGroup group = StructureGroupXMLConverter.fromXML(listOfConditions);
+							structureGroups.add(group);
 //						logger.info("structureGroups size:" + structureGroups.size());
+							break;
 					}
 				}
 			}
 		} catch (SAXParseException err)	{
 			logger.error("** Parsing error, line: {}, uri: {}", err.getLineNumber (), err.getSystemId (), err);
-		}
-		catch (SAXException e) {
+		} catch (Throwable e) {
 			logger.error("Exception: ", e);
 		}
-		catch (Throwable t) {
-			logger.error("Exception: ", t);
-		}
 
 
 		if ( linkages != null) {
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ProteinModificationXmlReader.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ProteinModificationXmlReader.java
index 0a1c5f36e9..6f245e5c5a 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ProteinModificationXmlReader.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ProteinModificationXmlReader.java
@@ -110,7 +110,7 @@ public static void registerProteinModificationFromXml(InputStream isXml)
 			}
 
 			// condition
-			ModificationCondition condition = null;
+			ModificationCondition condition;
 			{
 				nodes = infoNodes.get("Condition");
 				if (nodes==null || nodes.size()!=1) {
@@ -121,14 +121,14 @@ public static void registerProteinModificationFromXml(InputStream isXml)
 				Node compsNode = nodes.get(0);
 
 				// keep track of the labels of component indices
-				Map<String,Integer> mapLabelComp = new HashMap<String,Integer>();
+				Map<String,Integer> mapLabelComp = new HashMap<>();
 
 				Map<String,List<Node>> compInfoNodes = getChildNodes(compsNode);
 
 				// components
 				List<Node> compNodes = compInfoNodes.get("Component");
 				int sizeComp = compNodes.size();
-				List<Component> comps = new ArrayList<Component>(sizeComp);
+				List<Component> comps = new ArrayList<>(sizeComp);
 				for (int iComp=0; iComp<sizeComp; iComp++) {
 					Node compNode = compNodes.get(iComp);
 					// comp label
@@ -146,7 +146,7 @@ public static void registerProteinModificationFromXml(InputStream isXml)
 					}
 
 					// comp PDBCC ID
-					Set<String> compIds = new HashSet<String>();
+					Set<String> compIds = new HashSet<>();
 					List<Node> compIdNodes = getChildNodes(compNode).get("Id");
 					if (compIdNodes!=null) {
 						for (Node compIdNode : compIdNodes) {
@@ -199,7 +199,7 @@ public static void registerProteinModificationFromXml(InputStream isXml)
 				List<ModificationLinkage> linkages = null;
 				if (bondNodes!=null) {
 					int sizeBonds = bondNodes.size();
-					linkages = new ArrayList<ModificationLinkage>(sizeBonds);
+					linkages = new ArrayList<>(sizeBonds);
 					for (int iBond=0; iBond<sizeBonds; iBond++) {
 						Node bondNode = bondNodes.get(iBond);
 						Map<String,List<Node>> bondChildNodes = getChildNodes(bondNode);
@@ -305,12 +305,16 @@ public static void registerProteinModificationFromXml(InputStream isXml)
 						xrefName = xrefNode.get(0).getTextContent();
 					}
 
-					if (xrefDb.equals("PDBCC")) {
-						modBuilder.setPdbccId(xrefId).setPdbccName(xrefName);
-					} else if (xrefDb.equals("RESID")) {
-						modBuilder.setResidId(xrefId).setResidName(xrefName);
-					} else if (xrefDb.equals("PSI-MOD")) {
-						modBuilder.setPsimodId(xrefId).setPsimodName(xrefName);
+					switch (xrefDb) {
+						case "PDBCC":
+							modBuilder.setPdbccId(xrefId).setPdbccName(xrefName);
+							break;
+						case "RESID":
+							modBuilder.setResidId(xrefId).setResidName(xrefName);
+							break;
+						case "PSI-MOD":
+							modBuilder.setPsimodId(xrefId).setPsimodName(xrefName);
+							break;
 					}
 				}
 			} // end of cross references
@@ -342,7 +346,7 @@ private static Map<String,List<Node>> getChildNodes(Node parent) {
 		if (parent==null)
 			return Collections.emptyMap();
 
-		Map<String,List<Node>> children = new HashMap<String,List<Node>>();
+		Map<String,List<Node>> children = new HashMap<>();
 
 		NodeList nodes = parent.getChildNodes();
 		int nNodes = nodes.getLength();
@@ -352,11 +356,7 @@ private static Map<String,List<Node>> getChildNodes(Node parent) {
 				continue;
 
 			String name = node.getNodeName();
-			List<Node> namesakes = children.get(name);
-			if (namesakes==null) {
-				namesakes = new ArrayList<Node>();
-				children.put(name, namesakes);
-			}
+			List<Node> namesakes = children.computeIfAbsent(name, k -> new ArrayList<>());
 			namesakes.add(node);
 		}
 
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/StructureGroupXMLConverter.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/StructureGroupXMLConverter.java
index 61a56e3b6b..def283f6ab 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/StructureGroupXMLConverter.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/StructureGroupXMLConverter.java
@@ -36,8 +36,8 @@ public static void toXML(StructureGroup group, PrettyXMLWriter xml) throws IOExc
 		xml.attribute("chainID", group.getChainId());
 		xml.attribute("pdbName", group.getPDBName());
 		if ( group.getInsCode() != null)
-			xml.attribute("insCode",group.getInsCode()+"");
-		xml.attribute("residueNr", group.getResidueNumber()+"");
+			xml.attribute("insCode", String.valueOf(group.getInsCode()));
+		xml.attribute("residueNr", String.valueOf(group.getResidueNumber()));
 		xml.attribute("isAminoAcid", Boolean.toString(group.isAminoAcid()));
 		xml.closeTag("structureGroup");
 	}
@@ -57,7 +57,7 @@ public static StructureGroup fromXML(Node n) {
 		resNum.setInsCode(insCode.charAt(0));
 		resNum.setSeqNum(Integer.parseInt(resN));
 
-		StructureGroup g = new StructureGroup(resNum, pdbName, Boolean.valueOf(isAminoAcid));
+		StructureGroup g = new StructureGroup(resNum, pdbName, Boolean.parseBoolean(isAminoAcid));
 		return g;
 	}
 
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java
index 164c3d86d9..5d9937d9d2 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java
@@ -41,32 +41,32 @@ public interface ModifiedCompound {
 	 *
 	 * @return a description
 	 */
-	public String getDescription();
+    String getDescription();
 
-	public void setDescription(String desc);
+	void setDescription(String desc);
 
 	/**
 	 *
 	 * @return {@link ProteinModificationBean} occurred on the residue.
 	 */
-	public ProteinModification getModification();
+    ProteinModification getModification();
 
-	public void setModification(ProteinModification modi);
+	void setModification(ProteinModification modi);
 
 	/**
 	 *
 	 * @return a set of involved group.
 	 */
-	public Set<StructureGroup> getGroups();
+    Set<StructureGroup> getGroups();
 
-	public void setGroups(Set<StructureGroup> groups);
+	void setGroups(Set<StructureGroup> groups);
 
 	/**
 	 *
 	 * @param isAminoAcid true if amino acids.
 	 * @return a set of involved group of the type.
 	 */
-	public Set<StructureGroup> getGroups(boolean isAminoAcid);
+    Set<StructureGroup> getGroups(boolean isAminoAcid);
 
 
 
@@ -76,13 +76,13 @@ public interface ModifiedCompound {
 	 * @see #getLinkedGroupPairs
 	 * @see StructureAtomLinkage
 	 */
-	public Set<StructureAtomLinkage> getAtomLinkages();
+    Set<StructureAtomLinkage> getAtomLinkages();
 
 	/** Set atom linkages
 	 *
 	 * @return
 	 */
-	public void setAtomLinkages(Set<StructureAtomLinkage> linkages);
+    void setAtomLinkages(Set<StructureAtomLinkage> linkages);
 
 	/**
 	 * Add a linkage. Add new the involved groups first using {@link addGroup}.
@@ -90,20 +90,20 @@ public interface ModifiedCompound {
 	 * @return true if this linkage was not already contained.
 	 * @see StructureAtomLinkage
 	 */
-	public boolean addAtomLinkage(StructureAtomLinkage linkage);
+    boolean addAtomLinkage(StructureAtomLinkage linkage);
 
 	/**
 	 * Add a collections of linkages.
 	 * @param linkages an atom linkage.
 	 */
-	public void addAtomLinkages(Collection<StructureAtomLinkage> linkages);
+    void addAtomLinkages(Collection<StructureAtomLinkage> linkages);
 
 
 	/**
 	 *
 	 * @return true if groups from multiple chains were involved
 	 */
-	public boolean crossChains();
+    boolean crossChains();
 
 
 }
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java
index e42d987e61..8e369f7c17 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java
@@ -75,7 +75,7 @@ public ModifiedCompoundImpl (
 			throw new IllegalArgumentException("Null argument(s)");
 		}
 
-		groups = new HashSet<StructureGroup>(1);
+		groups = new HashSet<>(1);
 		groups.add(modifiedResidue);
 
 		// is it possible that components be added by addLinkage later?
@@ -101,7 +101,7 @@ public ModifiedCompoundImpl( ProteinModification modification,
 			throw new IllegalArgumentException("at least one linkage.");
 		}
 
-		this.groups = new HashSet<StructureGroup>();
+		this.groups = new HashSet<>();
 
 		addAtomLinkages(linkages);
 
@@ -128,7 +128,7 @@ else if (originalModification.getCategory()!=ModificationCategory.UNDEFINED)
 			modification = originalModification;
 		else {
 			int nRes = 0;
-			Set<String> ligands = new HashSet<String>();
+			Set<String> ligands = new HashSet<>();
 			for (StructureGroup group : groups) {
 				if (group.isAminoAcid()) {
 					nRes ++;
@@ -174,7 +174,7 @@ public Set<StructureGroup> getGroups() {
 
 	@Override
 	public Set<StructureGroup> getGroups(boolean isAminoAcid) {
-		Set<StructureGroup> result = new HashSet<StructureGroup>();
+		Set<StructureGroup> result = new HashSet<>();
 		for (StructureGroup group : groups) {
 			if (group.isAminoAcid() == isAminoAcid) {
 				result.add(group);
@@ -194,7 +194,7 @@ public Set<StructureAtomLinkage> getAtomLinkages() {
 		if (atomLinkages==null) {
 			return Collections.emptySet();
 		} else {
-			Set<StructureAtomLinkage> result = new HashSet<StructureAtomLinkage>();
+			Set<StructureAtomLinkage> result = new HashSet<>();
 			for (Set<StructureAtomLinkage> linkages : atomLinkages.values()) {
 				result.addAll(linkages);
 			}
@@ -218,20 +218,20 @@ public boolean addAtomLinkage(StructureAtomLinkage linkage) {
 			throw new IllegalArgumentException("Null linkage");
 		}
 
-		Set<StructureGroup> gs = new HashSet<StructureGroup>(2);
+		Set<StructureGroup> gs = new HashSet<>(2);
 		gs.add(linkage.getAtom1().getGroup());
 		gs.add(linkage.getAtom2().getGroup());
 
 		if (atomLinkages==null) {
-			atomLinkages = new HashMap<Set<StructureGroup>, Set<StructureAtomLinkage>>();
+			atomLinkages = new HashMap<>();
 		}
 
 		Set<StructureAtomLinkage> linkages = atomLinkages.get(gs);
 		if (linkages == null) {
-			linkages = new HashSet<StructureAtomLinkage>();
+			linkages = new HashSet<>();
 			atomLinkages.put(gs, linkages);
 			groups.addAll(gs); // it's possible of new groups
-		};
+		}
 
 		return linkages.add(linkage);
 	}
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java
index fdfd8cf312..63e19579ea 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java
@@ -267,9 +267,9 @@ public void identify(final List<Chain> chains,
 		}
 
 
-		residues = new ArrayList<Group>();
-		List<Group> ligands = new ArrayList<Group>();
-		Map<Component, Set<Group>> mapCompGroups = new HashMap<Component, Set<Group>>();
+		residues = new ArrayList<>();
+		List<Group> ligands = new ArrayList<>();
+		Map<Component, Set<Group>> mapCompGroups = new HashMap<>();
 
 		for (Chain chain : chains) {
 
@@ -292,7 +292,7 @@ public void identify(final List<Chain> chains,
 			}
 			logger.warn("No amino acids found for {}. Either you did not parse the PDB file with alignSEQRES records, or this record does not contain any amino acids.", pdbId);
 		}
-		List<ModifiedCompound> modComps = new ArrayList<ModifiedCompound>();
+		List<ModifiedCompound> modComps = new ArrayList<>();
 
 		for (ProteinModification mod : potentialModifications) {
 			ModificationCondition condition = mod.getCondition();
@@ -333,10 +333,10 @@ public void identify(final List<Chain> chains,
 	}
 
 	private void reset() {
-		identifiedModifiedCompounds = new LinkedHashSet<ModifiedCompound>();
+		identifiedModifiedCompounds = new LinkedHashSet<>();
 		if (recordUnidentifiableModifiedCompounds) {
-			unidentifiableAtomLinkages = new LinkedHashSet<StructureAtomLinkage>();
-			unidentifiableModifiedResidues = new LinkedHashSet<StructureGroup>();
+			unidentifiableAtomLinkages = new LinkedHashSet<>();
+			unidentifiableModifiedResidues = new LinkedHashSet<>();
 		}
 
 	}
@@ -392,7 +392,7 @@ private void identifyAdditionalAttachments(ModifiedCompound mc,
 		// ligands to amino acid bonds for same modification of unknown category
 		// will be combined in mergeModComps()
 		// TODO: how about chain-chain links?
-		List<Group> identifiedGroups = new ArrayList<Group>();
+		List<Group> identifiedGroups = new ArrayList<>();
 		for (StructureGroup num : mc.getGroups(false)) {
 			Group group;
 			try {
@@ -464,7 +464,7 @@ private Group getGroup(StructureGroup num, List<Chain> chains) throws StructureE
 	 * Merge identified modified compounds if linked.
 	 */
 	private void mergeModComps(List<ModifiedCompound> modComps) {
-		TreeSet<Integer> remove = new TreeSet<Integer>();
+		TreeSet<Integer> remove = new TreeSet<>();
 		int n = modComps.size();
 		for (int icurr=1; icurr<n; icurr++) {
 			ModifiedCompound curr = modComps.get(icurr);
@@ -512,7 +512,7 @@ private void recordUnidentifiableAtomLinkages(List<ModifiedCompound> modComps,
 			List<Group> ligands) {
 
 		// first put identified linkages in a map for fast query
-		Set<StructureAtomLinkage> identifiedLinkages = new HashSet<StructureAtomLinkage>();
+		Set<StructureAtomLinkage> identifiedLinkages = new HashSet<>();
 		for (ModifiedCompound mc : modComps) {
 			identifiedLinkages.addAll(mc.getAtomLinkages());
 		}
@@ -555,7 +555,7 @@ private void recordUnidentifiableAtomLinkages(List<ModifiedCompound> modComps,
 	}
 
 	private void recordUnidentifiableModifiedResidues(List<ModifiedCompound> modComps) {
-		Set<StructureGroup> identifiedComps = new HashSet<StructureGroup>();
+		Set<StructureGroup> identifiedComps = new HashSet<>();
 		for (ModifiedCompound mc : modComps) {
 			identifiedComps.addAll(mc.getGroups(true));
 		}
@@ -592,18 +592,14 @@ private void addModificationGroups(
 			throw new IllegalArgumentException("Null argument(s).");
 		}
 
-		Map<Component,Set<Component>> mapSingleMultiComps = new HashMap<Component,Set<Component>>();
+		Map<Component,Set<Component>> mapSingleMultiComps = new HashMap<>();
 		for (ProteinModification mod : modifications) {
 			ModificationCondition condition = mod.getCondition();
 			for (Component comp : condition.getComponents()) {
 				for (String pdbccId : comp.getPdbccIds()) {
 					Component single = Component.of(Collections.singleton(pdbccId),
 							comp.isNTerminal(), comp.isCTerminal());
-					Set<Component> mult = mapSingleMultiComps.get(single);
-					if (mult == null) {
-						mult = new HashSet<Component>();
-						mapSingleMultiComps.put(single, mult);
-					}
+					Set<Component> mult = mapSingleMultiComps.computeIfAbsent(single, k -> new HashSet<>());
 					mult.add(comp);
 				}
 			}
@@ -619,11 +615,7 @@ private void addModificationGroups(
 						Component.of(pdbccId));
 
 				for (Component comp : unionComponentSet(ligandsWildCard, comps)) {
-					Set<Group> gs = saveTo.get(comp);
-					if (gs==null) {
-						gs = new LinkedHashSet<Group>();
-						saveTo.put(comp, gs);
-					}
+					Set<Group> gs = saveTo.computeIfAbsent(comp, k -> new LinkedHashSet<>());
 					gs.add(group);
 				}
 			}
@@ -645,11 +637,7 @@ private void addModificationGroups(
 						Component.of(pdbccId));
 
 				for (Component comp : unionComponentSet(residuesWildCard, comps)) {
-					Set<Group> gs = saveTo.get(comp);
-					if (gs==null) {
-						gs = new LinkedHashSet<Group>();
-						saveTo.put(comp, gs);
-					}
+					Set<Group> gs = saveTo.computeIfAbsent(comp, k -> new LinkedHashSet<>());
 					gs.add(group);
 				}
 			}
@@ -669,11 +657,7 @@ private void addModificationGroups(
 						Component.of(res.getPDBName(), true, false));
 
 				for (Component comp : unionComponentSet(nTermWildCard, comps)) {
-					Set<Group> gs = saveTo.get(comp);
-					if (gs==null) {
-						gs = new LinkedHashSet<Group>();
-						saveTo.put(comp, gs);
-					}
+					Set<Group> gs = saveTo.computeIfAbsent(comp, k -> new LinkedHashSet<>());
 					gs.add(res);
 				}
 			} while (iRes<nRes && ligands.contains(res));
@@ -691,11 +675,7 @@ private void addModificationGroups(
 						Component.of(res.getPDBName(), false, true));
 
 				for (Component comp : unionComponentSet(cTermWildCard, comps)) {
-					Set<Group> gs = saveTo.get(comp);
-					if (gs==null) {
-						gs = new LinkedHashSet<Group>();
-						saveTo.put(comp, gs);
-					}
+					Set<Group> gs = saveTo.computeIfAbsent(comp, k -> new LinkedHashSet<>());
 					gs.add(res);
 				}
 			} while (iRes>=0 && ligands.contains(res));
@@ -712,7 +692,7 @@ private Set<Component> unionComponentSet(Set<Component> set1, Set<Component> set
 		if (set2 == null)
 			return set1;
 
-		Set<Component> set = new HashSet<Component>(set1.size()+set2.size());
+		Set<Component> set = new HashSet<>(set1.size() + set2.size());
 		set.addAll(set1);
 		set.addAll(set2);
 
@@ -728,7 +708,7 @@ private List<List<Atom[]>> getMatchedAtomsOfLinkages(
 		int nLink = linkages.size();
 
 		List<List<Atom[]>> matchedAtomsOfLinkages =
-				new ArrayList<List<Atom[]>>(nLink);
+				new ArrayList<>(nLink);
 
 		for (int iLink=0; iLink<nLink; iLink++) {
 			ModificationLinkage linkage = linkages.get(iLink);
@@ -741,7 +721,7 @@ private List<List<Atom[]>> getMatchedAtomsOfLinkages(
 			Set<Group> groups1 = mapCompGroups.get(comp1);
 			Set<Group> groups2 = mapCompGroups.get(comp2);
 
-			List<Atom[]> list = new ArrayList<Atom[]>();
+			List<Atom[]> list = new ArrayList<>();
 
 			List<String> potentialNamesOfAtomOnGroup1 = linkage.getPDBNameOfPotentialAtomsOnComponent1();
 			for (String name : potentialNamesOfAtomOnGroup1) {
@@ -810,9 +790,9 @@ private void assembleLinkages(List<List<Atom[]>> matchedAtomsOfLinkages,
 
 		int nLink = matchedAtomsOfLinkages.size();
 		int[] indices = new int[nLink];
-		Set<ModifiedCompound> identifiedCompounds = new HashSet<ModifiedCompound>();
+		Set<ModifiedCompound> identifiedCompounds = new HashSet<>();
 		while (indices[0]<matchedAtomsOfLinkages.get(0).size()) {
-			List<Atom[]> atomLinkages = new ArrayList<Atom[]>(nLink);
+			List<Atom[]> atomLinkages = new ArrayList<>(nLink);
 			for (int iLink=0; iLink<nLink; iLink++) {
 				Atom[] atoms = matchedAtomsOfLinkages.get(iLink).get(indices[iLink]);
 				atomLinkages.add(atoms);
@@ -821,7 +801,7 @@ private void assembleLinkages(List<List<Atom[]>> matchedAtomsOfLinkages,
 				// matched
 
 				int n = atomLinkages.size();
-				List<StructureAtomLinkage> linkages = new ArrayList<StructureAtomLinkage>(n);
+				List<StructureAtomLinkage> linkages = new ArrayList<>(n);
 				for (int i=0; i<n; i++) {
 					Atom[] linkage = atomLinkages.get(i);
 					StructureAtomLinkage link = StructureUtil.getStructureAtomLinkage(
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureUtil.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureUtil.java
index 0245018ca2..0e42b77df3 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureUtil.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureUtil.java
@@ -180,7 +180,7 @@ public static List<Atom[]> findAtomLinkages(final Group group1,
 			throw new IllegalArgumentException("bondLengthTolerance cannot be negative.");
 		}
 
-		List<Atom[]> ret = new ArrayList<Atom[]>();
+		List<Atom[]> ret = new ArrayList<>();
 
 		if (potentialNamesOfAtomOnGroup1 == null) {
 			// if empty name, search for all atoms
@@ -282,8 +282,8 @@ private static boolean hasMetalBond(Atom a1, Atom a2, MetalBondDistance definiti
 
 		double distance = Calc.getDistance(a1,a2);
 
-		Float min = definition.getLowerLimit();
-		Float max = definition.getUpperLimit();
+		float min = definition.getLowerLimit();
+		float max = definition.getUpperLimit();
 
 		return ( min < distance && max > distance);
 
@@ -327,7 +327,7 @@ public static List<String> getAtomNames(Group group) {
 		}
 
 		int n = atoms.size();
-		List<String> ret = new ArrayList<String>(n);
+		List<String> ret = new ArrayList<>(n);
 		for (int i=0; i<n; i++) {
 			ret.add(atoms.get(i).getName());
 		}
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java
index 548da337cf..2f2fc65983 100644
--- a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java
+++ b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java
@@ -31,8 +31,7 @@
 import java.net.URL;
 import java.util.List;
 
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.junit.Assert.*;
 
 
 /**
@@ -102,7 +101,7 @@ public void testAcetylation() throws IOException {
 
 		for (Site s : sites) {
 
-			assertTrue(s.getResidue() != null);
+            assertNotNull(s.getResidue());
 
 		}
 
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ModifiedCompoundSerializationTest.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ModifiedCompoundSerializationTest.java
index b1bb17fd6e..ef66f6b13f 100644
--- a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ModifiedCompoundSerializationTest.java
+++ b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ModifiedCompoundSerializationTest.java
@@ -36,6 +36,7 @@
 import org.slf4j.LoggerFactory;
 
 import java.io.*;
+import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
@@ -144,7 +145,7 @@ public void test1CDG(){
 	public List<ModifiedCompound> testXMLSerialization(String pdbId){
 		String xml = null;
 		ModifiedCompound currentMC = null;
-		List<ModifiedCompound> all = new ArrayList<ModifiedCompound>();
+		List<ModifiedCompound> all = new ArrayList<>();
 		try {
 
 			Structure struc = TmpAtomCache.cache.getStructure(pdbId);
@@ -220,7 +221,7 @@ public String convertStreamToString(InputStream is)
 			char[] buffer = new char[1024];
 			try {
 				Reader reader = new BufferedReader(
-						new InputStreamReader(is, "UTF-8"));
+						new InputStreamReader(is, StandardCharsets.UTF_8));
 				int n;
 				while ((n = reader.read(buffer)) != -1) {
 					writer.write(buffer, 0, n);
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java
index cd7bd76a30..8e407f9cbd 100644
--- a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java
+++ b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java
@@ -477,7 +477,7 @@ private Set<ModifiedCompound> identifyAllModfications(Structure struc) {
 	 * http://www.biojava.org/wiki/BioJava:CookBook3:ProtMod
 	 */
 	private List<ResidueNumber> identifyPhosphosites(Structure struc) {
-		List<ResidueNumber> phosphosites = new ArrayList<ResidueNumber>();
+		List<ResidueNumber> phosphosites = new ArrayList<>();
 		ProteinModificationIdentifier parser = new ProteinModificationIdentifier();
 		parser.identify(struc, ProteinModificationRegistry.getByKeyword("phosphoprotein"));
 		Set<ModifiedCompound> mcs = parser.getIdentifiedModifiedCompound();
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationRegistryTest.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationRegistryTest.java
index 7590904de6..a25f76e8dc 100644
--- a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationRegistryTest.java
+++ b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationRegistryTest.java
@@ -49,7 +49,7 @@ public class ProteinModificationRegistryTest {
 	@Test
 	public void testRegisterModification() {
 		// define the involved components, in this case two cystines (CYS)
-		List<Component> components = new ArrayList<Component>(2);
+		List<Component> components = new ArrayList<>(2);
 		components.add(Component.of("CYS"));
 		components.add(Component.of("CYS"));
 
diff --git a/biojava-ontology/src/main/java/demo/ParseGO.java b/biojava-ontology/src/main/java/demo/ParseGO.java
index c16dffed89..b3397bccb3 100644
--- a/biojava-ontology/src/main/java/demo/ParseGO.java
+++ b/biojava-ontology/src/main/java/demo/ParseGO.java
@@ -56,11 +56,9 @@ public static void main(String[] args){
 			Ontology ontology = parser.parseOBO(oboFile, "BioSapiens", "the BioSapiens ontology");
 
 			Set<Term> keys = ontology.getTerms();
-			Iterator<Term> iter = keys.iterator();
-			while (iter.hasNext()){
-				Term t = iter.next();
-				logger.info("{} [{}]", t.getName(), t.getDescription());
-			}
+            for (Term t : keys) {
+                logger.info("{} [{}]", t.getName(), t.getDescription());
+            }
 		} catch (Exception e){
 			logger.error("Exception: ", e);
 		}
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/IntegerOntology.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/IntegerOntology.java
index c8ee792a5b..432400f979 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/IntegerOntology.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/IntegerOntology.java
@@ -117,14 +117,13 @@ public Set getRemoteTerms() {
 	}
 
 	@Override
-	public Term createTerm(String name) throws AlreadyExistsException,  IllegalArgumentException {
+	public Term createTerm(String name) throws IllegalArgumentException {
 		throw new IllegalArgumentException(getName() + " is immutable");
 	}
 
 	@Override
 	public Term createTerm(String name, String description)
 			throws
-			AlreadyExistsException,
 
 			IllegalArgumentException
 			{
@@ -134,7 +133,6 @@ public Term createTerm(String name, String description)
 	@Override
 	public Term createTerm(String name, String description, Object[] synonyms)
 			throws
-			AlreadyExistsException,
 
 			IllegalArgumentException
 			{
@@ -144,7 +142,6 @@ public Term createTerm(String name, String description, Object[] synonyms)
 	@Override
 	public Variable createVariable(String name, String description)
 			throws
-			AlreadyExistsException,
 
 			IllegalArgumentException
 			{
@@ -160,10 +157,7 @@ public Term importTerm(Term t, String name)
 	}
 
 	@Override
-	public Triple createTriple(Term subject, Term object, Term predicate, String name, String description)
-			throws
-			AlreadyExistsException
-			{
+	public Triple createTriple(Term subject, Term object, Term predicate, String name, String description) {
 		throw new IllegalArgumentException(getName() + " is immutable");
 			}
 
@@ -190,7 +184,7 @@ public boolean containsTerm(String name) {
 	}
 
 	public IntTerm resolveInt(int val) {
-		Integer i = new Integer(val);
+		Integer i = val;
 		IntTerm term = (IntTerm) termCache.get(i);
 
 		if(term == null) {
@@ -205,7 +199,7 @@ public final class IntTerm
 
 	implements Term {
 		private final int val;
-		private Set synonyms;
+		private final Set synonyms;
 
 		public IntTerm(int val) {
 			this(val, null);
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntoTools.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntoTools.java
index 1b1d7afd27..cd83cc2372 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntoTools.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntoTools.java
@@ -73,13 +73,7 @@ public final class OntoTools {
 	public static final Term PARTIAL_ORDER;
 
 	static {
-		DEFAULT_FACTORY = new OntologyFactory() {
-			@Override
-			public Ontology createOntology(String name, String desc)
-			throws OntologyException {
-				return new Ontology.Impl(name, desc);
-			}
-		};
+		DEFAULT_FACTORY = (name, desc) -> new Ontology.Impl(name, desc);
 
 		try {
 			BufferedReader reader = new BufferedReader(
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java
index 365aab4251..c63f9aad23 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java
@@ -51,14 +51,14 @@ public interface Ontology  {
 	 * @return the name of the ontology
 	 */
 
-	public String getName();
+	String getName();
 
 	/** Set the name for this ontology
 	 *
 	 * @param name - the name
 	 *
 	 */
-	public void setName(String name);
+	void setName(String name);
 
 	/**
 	 * Return a human-readable description of this ontology, or the empty
@@ -66,13 +66,13 @@ public interface Ontology  {
 	 * @return the description of the term
 	 */
 
-	public String getDescription();
+	String getDescription();
 
 	/** set the description of this ontology
 	 *
 	 * @param description
 	 */
-	public void setDescription(String description);
+	void setDescription(String description);
 
 
 
@@ -81,7 +81,7 @@ public interface Ontology  {
 	 * @return a Set of all Terms of the ontology.
 	 */
 
-	public Set<Term> getTerms();
+	Set<Term> getTerms();
 
 	/**
 	 * Fetch the term with the specified name.
@@ -91,7 +91,7 @@ public interface Ontology  {
 	 * @throws NoSuchElementException if no term exists with that name
 	 */
 
-	public Term getTerm(String name) throws NoSuchElementException;
+	Term getTerm(String name) throws NoSuchElementException;
 
 	/**
 	 * Return all triples from this ontology which match the supplied
@@ -104,7 +104,7 @@ public interface Ontology  {
 	 * @return a Set of triples
 	 */
 
-	public Set<Triple> getTriples(Term subject, Term object, Term predicate);
+	Set<Triple> getTriples(Term subject, Term object, Term predicate);
 
 	/**
 	 * Return the associated OntologyOps.
@@ -118,7 +118,7 @@ public interface Ontology  {
 	 * @return the OntologyOps instance associated with this instance.
 	 */
 
-	public OntologyOps getOps();
+	OntologyOps getOps();
 
 	/**
 	 * Create a new term in this ontology.
@@ -132,7 +132,7 @@ public interface Ontology  {
 	 * @throws ChangeVetoException
 	 */
 
-	public Term createTerm(String name)
+	Term createTerm(String name)
 			throws
 			AlreadyExistsException,
 
@@ -151,7 +151,7 @@ public Term createTerm(String name)
 	 * @throws ChangeVetoException
 	 */
 
-	public Term createTerm(String name, String description)
+	Term createTerm(String name, String description)
 			throws
 			AlreadyExistsException,
 
@@ -171,7 +171,7 @@ public Term createTerm(String name, String description)
 	 * @throws ChangeVetoException
 	 */
 
-	public Term createTerm(String name, String description, Object[] synonyms)
+	Term createTerm(String name, String description, Object[] synonyms)
 			throws
 			AlreadyExistsException,
 
@@ -190,7 +190,7 @@ public Term createTerm(String name, String description, Object[] synonyms)
 	 * @throws ChangeVetoException
 	 */
 
-	public Variable createVariable(String name, String description)
+	Variable createVariable(String name, String description)
 			throws
 			AlreadyExistsException,
 
@@ -212,7 +212,7 @@ public Variable createVariable(String name, String description)
 	 * @throws IllegalArgumentException
 	 */
 
-	public Term importTerm(Term t, String localName)
+	Term importTerm(Term t, String localName)
 			throws
 
 			IllegalArgumentException;
@@ -233,7 +233,7 @@ public Term importTerm(Term t, String localName)
 	 * @throws IllegalArgumentException if subject, object or predicate are not all
 	 *      from the same ontology
 	 */
-	public Triple createTriple(Term subject, Term object, Term predicate, String name, String description)
+	Triple createTriple(Term subject, Term object, Term predicate, String name, String description)
 			throws
 			AlreadyExistsException
 			;
@@ -246,7 +246,7 @@ public Triple createTriple(Term subject, Term object, Term predicate, String nam
 	 * @return true if contained
 	 */
 
-	public boolean containsTriple(Term subject, Term object, Term predicate);
+	boolean containsTriple(Term subject, Term object, Term predicate);
 
 	/**
 	 * Remove a term from an ontology, together with all triples which refer to it.
@@ -254,7 +254,7 @@ public Triple createTriple(Term subject, Term object, Term predicate, String nam
 	 * @throws ChangeVetoException
 	 */
 
-	public void deleteTerm(Term t) ;
+	void deleteTerm(Term t) ;
 
 	/**
 	 * Determines if this ontology currently contains a term named <code>name</code>
@@ -262,7 +262,7 @@ public Triple createTriple(Term subject, Term object, Term predicate, String nam
 	 * @return true is contained
 	 */
 
-	public boolean containsTerm(String name);
+	boolean containsTerm(String name);
 
 	/**
 	 * A basic in-memory implementation of an ontology
@@ -274,7 +274,7 @@ public Triple createTriple(Term subject, Term object, Term predicate, String nam
 
 	// AP: I am setting name and description to public changeable fields
 	// e.g during parsing of an .obo file we don't know them when the ontology is instanciated
-	public final class Impl
+	final class Impl
 
 	implements Ontology, java.io.Serializable {
 		/**
@@ -294,13 +294,13 @@ public final class Impl
 		private final OntologyOps ops;
 
 		{
-			terms            = new HashMap<String, Term>();
-			triples          = new HashSet<Triple>();
-			subjectTriples   = new HashMap<Term, Set<Triple>>();
-			objectTriples    = new HashMap<Term, Set<Triple>>();
-			relationTriples  = new HashMap<Term, Set<Triple>>();
-			remoteTerms      = new HashMap<Term, RemoteTerm>();
-			localRemoteTerms = new HashSet<Term>();
+			terms            = new HashMap<>();
+			triples          = new HashSet<>();
+			subjectTriples   = new HashMap<>();
+			objectTriples    = new HashMap<>();
+			relationTriples  = new HashMap<>();
+			remoteTerms      = new HashMap<>();
+			localRemoteTerms = new HashSet<>();
 		}
 
 		public Impl(String name, String description) {
@@ -337,7 +337,7 @@ public void setDescription(String description){
 
 		@Override
 		public Set<Term> getTerms() {
-			return new HashSet<Term>(terms.values());
+			return new HashSet<>(terms.values());
 		}
 
 		@Override
@@ -377,16 +377,15 @@ public Set<Triple> getTriples(Term subject, Term object, Term predicate) {
 			}
 		}
 
-		private Set<Triple> filterTriples(Set<Triple> base, Term subject, Term object, Term predicate) {
+		private static Set<Triple> filterTriples(Set<Triple> base, Term subject, Term object, Term predicate) {
 			if (base == null) {
 				return Collections.EMPTY_SET;
 			} else if (subject == null && object == null && predicate == null) {
-				return Collections.unmodifiableSet(new HashSet<Triple>(base));
+				return Collections.unmodifiableSet(new HashSet<>(base));
 			}
 
-			Set<Triple> retval = new HashSet<Triple>();
-			for (Iterator<Triple> i = base.iterator(); i.hasNext(); ) {
-				Triple t = i.next();
+			Set<Triple> retval = new HashSet<>();
+			for (Triple t : base) {
 				if (subject != null && t.getSubject() != subject) {
 					continue;
 				}
@@ -531,8 +530,7 @@ public Triple createTriple(Term subject,
 				String description)
 						throws
 						AlreadyExistsException,
-						IllegalArgumentException,
-						NullPointerException,
+				NullPointerException,
 						IllegalArgumentException
 						{
 			Triple t = new Triple.Impl(subject, object, predicate, name, description);
@@ -564,11 +562,7 @@ private void addTriple(Triple t) {
 		}
 
 		private void pushTriple(Map<Term,Set<Triple>> m, Term key, Triple t) {
-			Set<Triple> s = m.get(key);
-			if (s == null) {
-				s = new HashSet<Triple>();
-				m.put(key, s);
-			}
+			Set<Triple> s = m.computeIfAbsent(key, k -> new HashSet<>());
 			s.add(t);
 		}
 
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntologyFactory.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntologyFactory.java
index 1bac93c033..64f7d52221 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntologyFactory.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntologyFactory.java
@@ -34,8 +34,7 @@ public interface OntologyFactory {
 	 * @param description the description for the ontology
 	 * @return an Ontology
 	 * @throws NullPointerException if either name or description are null
-	 * @throws OntologyException if the ontology could not be created
 	 */
-	public Ontology createOntology(String name, String description)
-	throws OntologyException;
+    Ontology createOntology(String name, String description)
+	;
 }
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntologyOps.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntologyOps.java
index a4e1b243a0..97104b4620 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntologyOps.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntologyOps.java
@@ -49,5 +49,5 @@ public interface OntologyOps {
 	 *
 	 * @return a Set containing all remote terms in the ontology
 	 */
-	public Set getRemoteTerms();
+    Set getRemoteTerms();
 }
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntologyTerm.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntologyTerm.java
index 849bbc8ff0..e4256f46f8 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntologyTerm.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntologyTerm.java
@@ -52,7 +52,7 @@ public interface OntologyTerm extends Term {
 	 */
 
 	@Override
-	public Ontology getOntology();
+	Ontology getOntology();
 
 	/**
 	 * Simple in-memory implementation of a remote ontology term.
@@ -60,7 +60,7 @@ public interface OntologyTerm extends Term {
 	 * This can be used to implement Ontology.importTerm
 	 */
 
-	public final static class Impl
+	final class Impl
 
 	implements OntologyTerm, java.io.Serializable {
 
@@ -68,7 +68,7 @@ public final static class Impl
 		private final Ontology ontology;
 		private final Ontology target;
 
-		private Set synonyms;
+		private final Set synonyms;
 
 		public Impl(Ontology ontology, Ontology target) {
 			this(ontology, target, null);
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/RemoteTerm.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/RemoteTerm.java
index c003bb8ff3..e6a9721f30 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/RemoteTerm.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/RemoteTerm.java
@@ -60,7 +60,7 @@ public interface RemoteTerm extends Term {
 	 * @return the term
 	 */
 
-	public Term getRemoteTerm();
+	Term getRemoteTerm();
 
 	/**
 	 * Simple in-memory implementation of a remote ontology term.
@@ -68,7 +68,7 @@ public interface RemoteTerm extends Term {
 	 * This can be used to implement Ontology.importTerm
 	 */
 
-	public final static class Impl
+	final class Impl
 	extends AbstractTerm
 	implements RemoteTerm, java.io.Serializable {
 		/**
@@ -78,7 +78,7 @@ public final static class Impl
 		private final Ontology ontology;
 		private final Term remoteTerm;
 		private final String name;
-		private Set synonyms;
+		private final Set synonyms;
 
 		public Impl(Ontology ontology, Term remoteTerm, String name) {
 			this(ontology, remoteTerm, name, null);
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Synonym.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Synonym.java
index 968bac29e7..f2f2cd28df 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Synonym.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Synonym.java
@@ -45,12 +45,7 @@ public String toString(){
 		return txt;
 	}
 
-	public final static Comparator<Synonym> COMPARATOR = new Comparator<Synonym>() {
-		@Override
-		public int compare(Synonym a, Synonym b) {
-			return String.CASE_INSENSITIVE_ORDER.compare(a.toString(), b.toString());
-		}
-	};
+	public final static Comparator<Synonym> COMPARATOR = (a, b) -> String.CASE_INSENSITIVE_ORDER.compare(a.toString(), b.toString());
 
 	public Synonym() {
 	}
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java
index 387aa7c17a..dee4691177 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java
@@ -66,7 +66,7 @@ public interface Term extends Annotatable {
 	 * @return the name of the term
 	 */
 
-	public String getName();
+	String getName();
 
 	/**
 	 * Return a human-readable description of this term, or the empty string if
@@ -74,42 +74,42 @@ public interface Term extends Annotatable {
 	 * @return the description of the term
 	 */
 
-	public String getDescription();
+	String getDescription();
 
 	/** set the description of the term;
 	 *
 	 * @param description
 	 *
 	 */
-	public void setDescription(String description);
+	void setDescription(String description);
 
 	/**
 	 * Return the ontology in which this term exists.
 	 * @return the ontology
 	 */
 
-	public Ontology getOntology();
+	Ontology getOntology();
 
 	/**
 	 * Return the synonyms for this term.
 	 * @return the synonyms
 	 */
 
-	public Object[] getSynonyms();
+	Object[] getSynonyms();
 
 	/**
 	 * Add a synonym for this term.
 	 * @param synonym the synonym
 	 */
 
-	public void addSynonym(Object synonym);
+	void addSynonym(Object synonym);
 
 	/**
 	 * Remove a synonym for this term.
 	 * @param synonym
 	 */
 
-	public void removeSynonym(Object synonym);
+	void removeSynonym(Object synonym);
 
 	/**
 	 * Simple in-memory implementation of an ontology term.
@@ -117,7 +117,7 @@ public interface Term extends Annotatable {
 	 * This can be used to implement Ontology.createTerm
 	 */
 
-	public static class Impl
+	class Impl
 	extends AbstractTerm
 	implements Term, java.io.Serializable {
 		/**
@@ -155,7 +155,7 @@ public Impl(Ontology ontology, String name, String description, Object[] synonym
 			this.description = description;
 			this.ontology = ontology;
 
-			this.synonyms = new TreeSet<Object>();
+			this.synonyms = new TreeSet<>();
 			if (synonyms!=null) this.synonyms.addAll(Arrays.asList(synonyms));
 		}
 
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java
index 550c4d5651..5a1d2439c5 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java
@@ -51,21 +51,21 @@ public interface Triple
 	 * @return the subject term
 	 */
 
-	public Term getSubject();
+	Term getSubject();
 
 	/**
 	 * Return the object term of this triple.
 	 * @return the object term
 	 */
 
-	public Term getObject();
+	Term getObject();
 
 	/**
 	 * Return a Term which defines the type of relationship between the subject and object terms.
 	 * @return the predicate
 	 */
 
-	public Term getPredicate();
+	Term getPredicate();
 
 	/**
 	 * The hashcode for a Triple.
@@ -82,7 +82,7 @@ public interface Triple
 	 * </p>
 	 */
 	@Override
-	public int hashCode();
+	int hashCode();
 
 	/**
 	 * Check to see if an object is an equivalent Triple.
@@ -105,7 +105,7 @@ public interface Triple
 	 * </p>
 	 */
 	@Override
-	public boolean equals(Object obj);
+	boolean equals(Object obj);
 
 	/**
 	 * Basic in-memory implementation of a Triple in an ontology
@@ -114,7 +114,7 @@ public interface Triple
 	 * @see org.biojavax.ontology.SimpleComparableTriple
 	 */
 
-	public static final class Impl
+	final class Impl
 
 	implements Triple, java.io.Serializable {
 		/**
@@ -126,7 +126,7 @@ public static final class Impl
 		private final Term predicate;
 		private /*final*/ String name;
 		private /*final*/ String description;
-		private Set<Object> synonyms;
+		private final Set<Object> synonyms;
 
 		public Impl(Term subject, Term object, Term predicate) {
 			this(subject, object, predicate, null, null, null);
@@ -182,7 +182,7 @@ public Impl(Term subject,
 			this.name = name;
 			this.description = description;
 
-			this.synonyms = new TreeSet<Object>();
+			this.synonyms = new TreeSet<>();
 			if (synonyms!=null) this.synonyms.addAll(Arrays.asList(synonyms));
 		}
 
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Variable.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Variable.java
index 2c453f674b..014850d319 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Variable.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Variable.java
@@ -27,7 +27,7 @@
  */
 public interface Variable
 extends Term {
-	public static class Impl
+	class Impl
 	extends Term.Impl
 	implements Variable
 	{
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java
index 7754ec130a..0f861ed00d 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java
@@ -48,7 +48,7 @@ public Ontology parseGO(BufferedReader goFile,
 			Ontology onto = factory.createOntology(ontoName, ontoDescription);
 			Term isa = onto.importTerm(OntoTools.IS_A, null);
 			Term partof = null; // fixme: onto.importTerm(OntoTools.PART_OF, null);
-			List<Term> termStack = new ArrayList<Term>();
+			List<Term> termStack = new ArrayList<>();
 			String line;
 			while ((line = goFile.readLine()) != null) {
 				int leadSpaces = 0;
@@ -101,7 +101,7 @@ private void safeAddTriple(Ontology onto, Term s, Term o, Term p)
 	}
 
 	private Term parseTerm(Ontology onto, String s)
-		throws ParseException, AlreadyExistsException
+		throws AlreadyExistsException
 	{
 		int semi = s.indexOf(';');
 		int semi2 = s.indexOf(';', semi + 1);
@@ -122,7 +122,7 @@ private Term parseTerm(Ontology onto, String s)
 		} else {
 			Term t = onto.createTerm(termName, termDesc);
 			if (toke.hasMoreTokens()) {
-				List<String> secondaries = new ArrayList<String>();
+				List<String> secondaries = new ArrayList<>();
 				while (toke.hasMoreTokens()) {
 					secondaries.add(toke.nextToken());
 				}
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/OboParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/OboParser.java
index d772850e05..940a25bd3e 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/OboParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/OboParser.java
@@ -70,7 +70,6 @@ public class OboParser {
 	 * @param ontoDescription
 
 	 * @return the ontology represented as a BioJava ontology file
-	 * @throws ParseException
 	 * @throws IOException
 	 */
 	public Ontology parseOBO(
@@ -78,27 +77,26 @@ public Ontology parseOBO(
 			String ontoName,
 			String ontoDescription
 			)
-					throws ParseException, IOException {
+					throws IOException {
 
-		try {
+//		try {
 			OntologyFactory factory = OntoTools.getDefaultFactory();
-			Ontology ontology = factory.createOntology(ontoName, ontoDescription);
 
 			OboFileParser parser = new OboFileParser();
 
-			OboFileEventListener handler = new OboFileHandler(ontology);
+			Ontology ontology = factory.createOntology(ontoName, ontoDescription);
 
-			parser.addOboFileEventListener(handler);
+            parser.addOboFileEventListener(new OboFileHandler(ontology));
 			parser.parseOBO(oboFile);
 
 			return ontology;
 
-
-		} catch (AlreadyExistsException ex) {
-			throw new RuntimeException( "Duplication in ontology");
-		} catch (OntologyException ex) {
-			throw new RuntimeException(ex);
-		}
+//
+//		} catch (AlreadyExistsException ex) {
+//			throw new RuntimeException( "Duplication in ontology");
+//		} catch (OntologyException ex) {
+//			throw new RuntimeException(ex);
+//		}
 
 	}
 }
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java
index 2c0ed0a3ae..22ab4749ef 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java
@@ -140,7 +140,7 @@ public Ontology parse(BufferedReader in, OntologyFactory of)
 						Term relT = resolveTerm(predicate, onto);
 
 						Triple trip = resolveTriple(subT, objT, relT, onto);
-						trip = trip==null?null:trip; // prevent unused field error
+						trip = trip; // prevent unused field error
 					} catch (StringIndexOutOfBoundsException e) {
 						throw new IOException("Could not parse line: " + line);
 					}
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileEventListener.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileEventListener.java
index 7350b6a2cb..0e061bcf74 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileEventListener.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileEventListener.java
@@ -37,36 +37,36 @@ public interface OboFileEventListener {
 	 *
 	 *
 	 */
-	public void documentStart();
+    void documentStart();
 
 	/** end of parsing a new OBO file
 	 *
 	 *
 	 */
-	public void documentEnd();
+    void documentEnd();
 
 	/** parsed a new OBO file header
 	 *
 	 *
 	 */
-	public void newOboFileHeader();
+    void newOboFileHeader();
 
 	/** parsed a new stanza in the file
 	 *
 	 * @param stanza
 	 */
-	public void newStanza(String stanza);
+    void newStanza(String stanza);
 
 	/**found a new key in the file
 	 *
 	 * @param key
 	 * @param value
 	 */
-	public void newKey(String key, String value );
+    void newKey(String key, String value);
 
 	/** a new synonym has been found
 	 *
 	 * @param synonym
 	 */
-	public void newSynonym(Synonym synonym);
+    void newSynonym(Synonym synonym);
 }
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java
index 49e3c2b56c..c70d9f58e3 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java
@@ -91,7 +91,7 @@ public void documentEnd() {
 
 	@Override
 	public void documentStart() {
-		termStack = new ArrayList<Term>();
+		termStack = new ArrayList<>();
 	}
 
 	@Override
@@ -136,54 +136,68 @@ public void newKey(String key, String value) {
 				logger.warn("did not find ID for Term! ");
 				return;
 			}
-			if (key.equals(NAMESPACE)){
-				Annotation anno = currentTerm.getAnnotation();
-				anno.setProperty(NAMESPACE, value);
-			}
-			else if (key.equals(NAME)){
-				currentTerm.setDescription(value);
-			} else if (key.equals(DEF)){
-				//TODO
-				// set definition
-				Annotation anno = currentTerm.getAnnotation();
-				anno.setProperty(DEF, value);
-			} else if (key.equals(XREF_ANALOG)){
-				// set xref analog
-				Annotation anno = currentTerm.getAnnotation();
-				anno.setProperty(XREF_ANALOG, value);
-			} else if (key.equals(IS_OBSOLETE)) {
-				// ignore obsolete Terms...
-				//logger.info("obsolete: {}", currentTerm);
-				Annotation anno = currentTerm.getAnnotation();
-				anno.setProperty(IS_OBSOLETE, new Boolean(true));
-
-			} else if (key.equals(IS_A) ||
-					key.equals(RELATIONSHIP) ||
-					key.equals(DISJOINT_FROM) ||
-					key.equals(INTERSECTION_OF) ||
-					key.equals(SUBSET)) {
-				try {
-					Term object = (ontology.containsTerm(value) ?
-							ontology.getTerm(value): ontology.createTerm(value));
-					Term predicate = (ontology.containsTerm(key) ? ontology.getTerm(key) : ontology.createTerm(key));
-					ontology.createTriple(currentTerm, object, predicate, currentTerm + " " + predicate + " " + object, key+"-relationship");
-				} catch (AlreadyExistsException ex) {
+			switch (key) {
+				case NAMESPACE: {
+					Annotation anno = currentTerm.getAnnotation();
+					anno.setProperty(NAMESPACE, value);
+					break;
+				}
+				case NAME:
+					currentTerm.setDescription(value);
+					break;
+				case DEF: {
+					//TODO
+					// set definition
+					Annotation anno = currentTerm.getAnnotation();
+					anno.setProperty(DEF, value);
+					break;
+				}
+				case XREF_ANALOG: {
+					// set xref analog
+					Annotation anno = currentTerm.getAnnotation();
+					anno.setProperty(XREF_ANALOG, value);
+					break;
 				}
+				case IS_OBSOLETE: {
+					// ignore obsolete Terms...
+					//logger.info("obsolete: {}", currentTerm);
+					Annotation anno = currentTerm.getAnnotation();
+					anno.setProperty(IS_OBSOLETE, Boolean.TRUE);
 
-			} else if (key.equals(COMMENT)){
-				Annotation anno = currentTerm.getAnnotation();
-				anno.setProperty(COMMENT, value);
-			} else if (key.equals(ALT_ID)){
-				Annotation anno = currentTerm.getAnnotation();
-				anno.setProperty(ALT_ID, value);
-			}
-			else if (key.equals(REPLACED_BY)) {
-				Annotation anno = currentTerm.getAnnotation();
-				anno.setProperty(REPLACED_BY, value);
-			}
+					break;
+				}
+				case IS_A:
+				case RELATIONSHIP:
+				case DISJOINT_FROM:
+				case INTERSECTION_OF:
+				case SUBSET:
+					try {
+						Term object = (ontology.containsTerm(value) ?
+								ontology.getTerm(value) : ontology.createTerm(value));
+						Term predicate = (ontology.containsTerm(key) ? ontology.getTerm(key) : ontology.createTerm(key));
+						ontology.createTriple(currentTerm, object, predicate, currentTerm + " " + predicate + " " + object, key + "-relationship");
+					} catch (AlreadyExistsException ex) {
+					}
 
-			else {
-				//logger.info("unknown key {}", key);
+					break;
+				case COMMENT: {
+					Annotation anno = currentTerm.getAnnotation();
+					anno.setProperty(COMMENT, value);
+					break;
+				}
+				case ALT_ID: {
+					Annotation anno = currentTerm.getAnnotation();
+					anno.setProperty(ALT_ID, value);
+					break;
+				}
+				case REPLACED_BY: {
+					Annotation anno = currentTerm.getAnnotation();
+					anno.setProperty(REPLACED_BY, value);
+					break;
+				}
+				default:
+					//logger.info("unknown key {}", key);
+					break;
 			}
 
 
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
index 76b7d673c2..90d6f466c8 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
@@ -61,41 +61,39 @@ public class OboFileParser {
 
 
 	protected static final Map<Character, Character> escapeChars =
-		new HashMap<Character, Character>();
+			new HashMap<>();
 
 	protected static final Map<Character, Character> unescapeChars =
-		new HashMap<Character, Character>();
+			new HashMap<>();
 
 	static {
-		escapeChars.put(new Character('n'), new Character('\n'));
-		escapeChars.put(new Character('W'), new Character(' '));
-		escapeChars.put(new Character('t'), new Character('\t'));
-		escapeChars.put(new Character(':'), new Character(':'));
-		escapeChars.put(new Character(','), new Character(','));
-		escapeChars.put(new Character('"'), new Character('"'));
-		escapeChars.put(new Character('\''), new Character('\''));
-		escapeChars.put(new Character('\\'), new Character('\\'));
-		escapeChars.put(new Character('{'), new Character('{'));
-		escapeChars.put(new Character('}'), new Character('}'));
-		escapeChars.put(new Character('('), new Character('('));
-		escapeChars.put(new Character(')'), new Character(')'));
-		escapeChars.put(new Character('['), new Character('['));
-		escapeChars.put(new Character(']'), new Character(']'));
-		escapeChars.put(new Character('!'), new Character('!'));
-		Iterator <Character> it = escapeChars.keySet().iterator();
-		while (it.hasNext()) {
-			Character key = it.next();
+		escapeChars.put('n', '\n');
+		escapeChars.put('W', ' ');
+		escapeChars.put('t', '\t');
+		escapeChars.put(':', ':');
+		escapeChars.put(',', ',');
+		escapeChars.put('"', '"');
+		escapeChars.put('\'', '\'');
+		escapeChars.put('\\', '\\');
+		escapeChars.put('{', '{');
+		escapeChars.put('}', '}');
+		escapeChars.put('(', '(');
+		escapeChars.put(')', ')');
+		escapeChars.put('[', '[');
+		escapeChars.put(']', ']');
+		escapeChars.put('!', '!');
+		for (Character key : escapeChars.keySet()) {
 			Character value = escapeChars.get(key);
 			unescapeChars.put(value, key);
 		}
 	}
 
 	public static class SOPair {
-		public String str = null;
+		public String str;
 
-		public int index = -1;
+		public int index;
 
-		public int endIndex = -1;
+		public int endIndex;
 
 		public SOPair(String str, int index) {
 			this(str, index, -1);
@@ -114,7 +112,7 @@ public SOPair(String str, int index, int endIndex) {
 
 
 	public OboFileParser(){
-		listeners = new ArrayList<OboFileEventListener>();
+		listeners = new ArrayList<>();
 	}
 
 
@@ -166,7 +164,7 @@ public void parseOBO(BufferedReader oboFile) throws IOException{
 					lineEnd = line.length();
 
 				// find nested values
-				NestedValue nv = null;
+				NestedValue nv;
 
 				int trailingStartIndex = -1;
 				int trailingEndIndex = -1;
@@ -258,12 +256,17 @@ private Synonym parseSynonym(String key, String value) throws IOException{
 		StringTokenizer tokenizer = new StringTokenizer(leftovers, " \t");
 		int scope = Synonym.RELATED_SYNONYM;
 
-		if ( key.equals(OboFileHandler.EXACT_SYNONYM))
-			scope = Synonym.EXACT_SYNONYM;
-		else if ( key.equals(OboFileHandler.BROAD_SYNONYM))
-			scope = Synonym.BROAD_SYNONYM;
-		else if ( key.equals(OboFileHandler.NARROW_SYNONYM))
-			scope = Synonym.NARROW_SYNONYM;
+		switch (key) {
+			case OboFileHandler.EXACT_SYNONYM:
+				scope = Synonym.EXACT_SYNONYM;
+				break;
+			case OboFileHandler.BROAD_SYNONYM:
+				scope = Synonym.BROAD_SYNONYM;
+				break;
+			case OboFileHandler.NARROW_SYNONYM:
+				scope = Synonym.NARROW_SYNONYM;
+				break;
+		}
 
 
 		String catID = null;
@@ -271,19 +274,26 @@ else if ( key.equals(OboFileHandler.NARROW_SYNONYM))
 			String token = tokenizer.nextToken();
 			//logger.info("TOKEN:" +token);
 			if (i == 0) {
-				if (token.equals("RELATED"))
-					scope = Synonym.RELATED_SYNONYM;
-				else if (token.equals("UNSPECIFIED"))
-					scope = Synonym.RELATED_SYNONYM;
-				else if (token.equals("EXACT"))
-					scope = Synonym.EXACT_SYNONYM;
-				else if (token.equals("BROAD"))
-					scope = Synonym.BROAD_SYNONYM;
-				else if (token.equals("NARROW"))
-					scope = Synonym.NARROW_SYNONYM;
-				else
-					throw new IOException("Found unexpected scope "
-							+ "identifier " + token + line);
+				switch (token) {
+					case "RELATED":
+						scope = Synonym.RELATED_SYNONYM;
+						break;
+					case "UNSPECIFIED":
+						scope = Synonym.RELATED_SYNONYM;
+						break;
+					case "EXACT":
+						scope = Synonym.EXACT_SYNONYM;
+						break;
+					case "BROAD":
+						scope = Synonym.BROAD_SYNONYM;
+						break;
+					case "NARROW":
+						scope = Synonym.NARROW_SYNONYM;
+						break;
+					default:
+						throw new IOException("Found unexpected scope "
+								+ "identifier " + token + line);
+				}
 			} else if (i == 1) {
 				catID = token;
 			} else
@@ -316,7 +326,7 @@ else if (token.equals("NARROW"))
 	}
 
 	protected Map<String,Object>[] getDbxrefList(String line, int startoffset, int endoffset) throws IOException {
-		Vector<Map<String,Object>> temp = new Vector<Map<String,Object>>();
+		Vector<Map<String,Object>> temp = new Vector<>();
 		boolean stop = false;
 		while (!stop) {
 			int braceIndex = findUnescaped(line, '{', startoffset, endoffset);
@@ -343,7 +353,7 @@ protected Map<String,Object>[] getDbxrefList(String line, int startoffset, int e
 				startoffset++;
 				continue;
 			}
-			NestedValue nv = null;
+			NestedValue nv;
 			if (trailing) {
 				nv = new NestedValue();
 				endIndex = getNestedValue(nv, line, endIndex + 1);
@@ -367,7 +377,7 @@ protected Map<String,Object>[] getDbxrefList(String line, int startoffset, int e
 
 	protected Map<String,Object> parseXref(String line,
 			int startoffset, int endoffset) throws IOException {
-		String xref_str = null;
+		String xref_str;
 		String desc_str = null;
 
 		SOPair xref = unescape(line, '"', startoffset, endoffset, false);
@@ -381,7 +391,7 @@ protected Map<String,Object> parseXref(String line,
 		}
 
 
-		Map<String, Object> m = new HashMap<String, Object>();
+		Map<String, Object> m = new HashMap<>();
 		m.put("xref",xref_str);
 		m.put("desc",desc_str);
 		return m;
@@ -390,34 +400,28 @@ protected Map<String,Object> parseXref(String line,
 
 
 	private void triggerNewStanza(String stanza){
-		Iterator<OboFileEventListener> iter = listeners.iterator();
-		while (iter.hasNext()){
-			OboFileEventListener li = iter.next();
+		for (OboFileEventListener li : listeners) {
 			li.newStanza(stanza);
 		}
 	}
 
 	private void triggerNewKey(String key, String value){
-		Iterator<OboFileEventListener> iter = listeners.iterator();
-		while (iter.hasNext()){
-			OboFileEventListener li = iter.next();
+		for (OboFileEventListener li : listeners) {
 			li.newKey(key, value);
 		}
 	}
 
 	private void triggerNewSynonym(Synonym synonym){
-		Iterator<OboFileEventListener> iter = listeners.iterator();
-		while (iter.hasNext()){
-			OboFileEventListener li = iter.next();
+		for (OboFileEventListener li : listeners) {
 			li.newSynonym(synonym);
 		}
 	}
 
 	public static String escape(String str, boolean escapespaces) {
-		StringBuffer out = new StringBuffer();
+		StringBuilder out = new StringBuilder();
 		for (int i = 0; i < str.length(); i++) {
 			char c = str.charAt(i);
-			Object o = unescapeChars.get(new Character(c));
+			Object o = unescapeChars.get(c);
 			if (o == null)
 				out.append(c);
 			else {
@@ -441,7 +445,7 @@ public SOPair unescape(String str, char toChar, int startindex,
 
 	public SOPair unescape(String str, char toChar, int startindex,
 			int endindex, boolean mustFindChar) throws IOException {
-		StringBuffer out = new StringBuffer();
+		StringBuilder out = new StringBuilder();
 		int endValue = -1;
 		for (int i = startindex; i < endindex; i++) {
 			char c = str.charAt(i);
@@ -449,7 +453,7 @@ public SOPair unescape(String str, char toChar, int startindex,
 				i++;
 				c = str.charAt(i);
 				Character mapchar = escapeChars
-				.get(new Character(c));
+				.get(c);
 				if (mapchar == null)
 					throw new IOException("Unrecognized escape"
 							+ " character " + c + " found.");
@@ -615,9 +619,8 @@ public NestedValue() {
 	public String toString(){
 		String txt = "NestedValue: " ;
 		Set<Object> keys = propertyValues.keySet();
-		Iterator<Object> iter = keys.iterator();
-		while (iter.hasNext()){
-			String key = iter.next().toString();
+		for (Object o : keys) {
+			String key = o.toString();
 			String value = propertyValues.get(key).toString();
 			txt += " [" + key + ":" + value + "]";
 		}
@@ -636,9 +639,8 @@ public Properties getPropertyValues() {
 
 	public void addPropertyValue(Properties pv) {
 		Set<Object> keys = pv.keySet();
-		Iterator<Object> iter = keys.iterator();
-		while (iter.hasNext()){
-			String key = iter.next().toString();
+		for (Object o : keys) {
+			String key = o.toString();
 			String value = pv.get(key).toString();
 			propertyValues.setProperty(key, value);
 		}
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java
index d6f9374328..69e0630f9e 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java
@@ -135,7 +135,7 @@ public Set keys() {
 
 	@Override
 	public String toString() {
-		StringBuffer sb = new StringBuffer("{");
+		StringBuilder sb = new StringBuilder("{");
 		Map prop = getProperties();
 		Iterator i = prop.keySet().iterator();
 		if(i.hasNext()) {
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java
index fccf023371..dabfa9ebf8 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java
@@ -113,7 +113,7 @@ void setProperty(Object key, Object value)
 	 *
 	 */
 
-	public void removeProperty(Object key)
+    void removeProperty(Object key)
 			throws NoSuchElementException;
 
 	/**
@@ -157,6 +157,6 @@ public void removeProperty(Object key)
 	 * an implementation to have annotation even though it should implement
 	 * Annotatable.
 	 */
-	static final Annotation EMPTY_ANNOTATION = new EmptyAnnotation();
+    Annotation EMPTY_ANNOTATION = new EmptyAnnotation();
 }
 
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/KeyedWeakReference.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/KeyedWeakReference.java
index 46b345c368..6e10eae149 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/KeyedWeakReference.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/KeyedWeakReference.java
@@ -35,7 +35,7 @@
  */
 
 public class KeyedWeakReference extends WeakReference {
-	private Object key;
+	private final Object key;
 
 	public KeyedWeakReference(Object key, Object ref) {
 		super(ref);
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/SmallMap.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/SmallMap.java
index c1f37caae5..b00e4eadea 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/SmallMap.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/SmallMap.java
@@ -222,7 +222,7 @@ public void remove() {
 	}
 
 	private class MapEntry implements Map.Entry {
-		private int offset;
+		private final int offset;
 
 		private MapEntry(int offset) {
 			this.offset = offset;
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java
index 7762642c76..f3ece73302 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java
@@ -110,7 +110,7 @@ public Set entrySet() {
 	}
 
 	private class WVEntrySet extends AbstractSet {
-	private Set keyRefEntrySet;
+	private final Set keyRefEntrySet;
 
 	public WVEntrySet() {
 		super();
@@ -130,9 +130,9 @@ public Iterator iterator() {
 	}
 	}
 
-	private class WVEntryIterator implements Iterator {
+	private static class WVEntryIterator implements Iterator {
 	private Object cache;
-	private Iterator keyRefIterator;
+	private final Iterator keyRefIterator;
 
 	public WVEntryIterator(Iterator keyRefIterator) {
 		this.keyRefIterator = keyRefIterator;
@@ -182,8 +182,8 @@ private void primeCache() {
 	}
 
 	private static class WVMapEntry implements Map.Entry {
-	private Object key;
-	private Object value;
+	private final Object key;
+	private final Object value;
 
 	private WVMapEntry(Object key, Object value) {
 		this.key = key;
diff --git a/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestOboFileParsing.java b/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestOboFileParsing.java
index 8c8bf3e3e2..6fc38eb944 100644
--- a/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestOboFileParsing.java
+++ b/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestOboFileParsing.java
@@ -71,24 +71,22 @@ public void testParsingHPOOBO() throws Exception {
 
 		ontology = parser.parseOBO(oboFile, "Human_phenotype", "the Human Phenotype ontology");
 		Set<Term> keys = ontology.getTerms();
-		Iterator iter = keys.iterator();
-
-		while (iter.hasNext()){
-			Term term = (Term) iter.next();
-			if(term.getName().equals("HP:0000057")) {
-				Annotation anno = term.getAnnotation();
-				Assert.assertTrue(anno.containsProperty("replaced_by"));
-				Assert.assertEquals("HP:0008665", anno.getProperty("replaced_by"));
-			}
-			if(term.getName().equals("HP:0000006")) {
-				Assert.assertEquals("Autosomal dominant inheritance", term.getDescription());
-				Object[] syns = term.getSynonyms();
-				Assert.assertEquals(3,  syns.length);
-				Assert.assertEquals("Autosomal dominant", ((Synonym) syns[0]).getName());
-				Assert.assertEquals("Autosomal dominant form", ((Synonym) syns[1]).getName());
-				Assert.assertEquals("Autosomal dominant type", ((Synonym) syns[2]).getName());
-			}
-		}
+
+        for (Term term : keys) {
+            if (term.getName().equals("HP:0000057")) {
+                Annotation anno = term.getAnnotation();
+                Assert.assertTrue(anno.containsProperty("replaced_by"));
+                Assert.assertEquals("HP:0008665", anno.getProperty("replaced_by"));
+            }
+            if (term.getName().equals("HP:0000006")) {
+                Assert.assertEquals("Autosomal dominant inheritance", term.getDescription());
+                Object[] syns = term.getSynonyms();
+                Assert.assertEquals(3, syns.length);
+                Assert.assertEquals("Autosomal dominant", ((Synonym) syns[0]).getName());
+                Assert.assertEquals("Autosomal dominant form", ((Synonym) syns[1]).getName());
+                Assert.assertEquals("Autosomal dominant type", ((Synonym) syns[2]).getName());
+            }
+        }
 	}
 
 }
diff --git a/biojava-protein-disorder/src/main/java/demo/PredictDisorder.java b/biojava-protein-disorder/src/main/java/demo/PredictDisorder.java
index f6013dadd2..1678ebd418 100644
--- a/biojava-protein-disorder/src/main/java/demo/PredictDisorder.java
+++ b/biojava-protein-disorder/src/main/java/demo/PredictDisorder.java
@@ -59,7 +59,7 @@ public static void main(String[] args) throws Exception{
 	private static ProteinSequence getUniprot(String uniProtID) throws Exception {
 
 		AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
-		UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<AminoAcidCompound>(uniProtID,set);
+		UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<>(uniProtID, set);
 
 		ProteinSequence seq = new ProteinSequence(uniprotSequence);
 
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java
index 55b9bc5cc6..19aa512e88 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java
@@ -29,6 +29,7 @@
 import org.slf4j.LoggerFactory;
 
 import java.io.*;
+import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.regex.Matcher;
@@ -250,10 +251,10 @@ public static void writeFasta(final OutputStream outstream,
 	 */
 	public static List<FastaSequence> readFasta(final InputStream inStream)
 		throws IOException {
-	final List<FastaSequence> seqs = new ArrayList<FastaSequence>();
+	final List<FastaSequence> seqs = new ArrayList<>();
 
 	final BufferedReader infasta = new BufferedReader(
-		new InputStreamReader(inStream, "UTF8"), 16000);
+		new InputStreamReader(inStream, StandardCharsets.UTF_8), 16000);
 	final Pattern pattern = Pattern.compile("//s+");
 
 	String line;
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java
index 60b259aff2..f886cfec54 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java
@@ -58,9 +58,7 @@ public class Jronn implements Serializable {
 	static {
 		try {
 			loader.loadModels();
-		} catch (NumberFormatException e) {
-			throw new RuntimeException("Fails to load models!" + e.getMessage(), e);
-		} catch (IOException e) {
+		} catch (NumberFormatException | IOException e) {
 			throw new RuntimeException("Fails to load models!" + e.getMessage(), e);
 		}
 	}
@@ -157,7 +155,7 @@ public static float[] getDisorderScores(ProteinSequence sequence) {
 	 * @return
 	 */
 	public static FastaSequence convertProteinSequencetoFasta(ProteinSequence sequence){
-		StringBuffer buf = new StringBuffer();
+		StringBuilder buf = new StringBuilder();
 		for (AminoAcidCompound compound : sequence) {
 
 			String c = compound.getShortName();
@@ -175,14 +173,12 @@ public static FastaSequence convertProteinSequencetoFasta(ProteinSequence sequen
 	private static float[] predictSerial(FastaSequence fsequence) {
 		ORonn.validateSequenceForRonn(fsequence);
 		ORonn ronn;
-		float[] disorder = null;
+		float[] disorder;
 		try {
 			ronn = new ORonn(fsequence, loader);
 			disorder = ronn.call().getMeanScores();
 		} catch (NumberFormatException e) {
 			throw new RuntimeException("Jronn fails to load models " + e.getLocalizedMessage(), e);
-		} catch (IOException e) {
-			throw new RuntimeException("Jronn fails to load models " + e.getLocalizedMessage(), e);
 		}
 		return disorder;
 	}
@@ -215,7 +211,7 @@ public static Range[] scoresToRanges(float[] scores, float probability)  {
 
 		int count=0;
 		int regionLen=0;
-		List<Range> ranges = new ArrayList<Range>();
+		List<Range> ranges = new ArrayList<>();
 		for(float score: scores) {
 			count++;
 			// Round to 2 decimal points before comparison
@@ -233,7 +229,7 @@ public static Range[] scoresToRanges(float[] scores, float probability)  {
 		if(regionLen>1) {
 			ranges.add(new Range(count-regionLen+1, count,scores[scores.length-1]));
 		}
-		return ranges.toArray(new Range[ranges.size()]);
+		return ranges.toArray(new Range[0]);
 
 	}
 
@@ -246,7 +242,7 @@ public static Range[] scoresToRanges(float[] scores, float probability)  {
 	 * @see #getDisorder(FastaSequence)
 	 */
 	public static Map<FastaSequence,float[]> getDisorderScores(List<FastaSequence> sequences) {
-		Map<FastaSequence,float[]> results = new TreeMap<FastaSequence, float[]>();
+		Map<FastaSequence,float[]> results = new TreeMap<>();
 		for(FastaSequence fsequence : sequences) {
 			results.put(fsequence, predictSerial(fsequence));
 		}
@@ -261,7 +257,7 @@ public static Map<FastaSequence,float[]> getDisorderScores(List<FastaSequence> s
 	 * @see #getDisorder(FastaSequence)
 	 */
 	public static Map<FastaSequence,Range[]> getDisorder(List<FastaSequence> sequences) {
-		Map<FastaSequence,Range[]> disorderRanges = new TreeMap<FastaSequence,Range[]>();
+		Map<FastaSequence,Range[]> disorderRanges = new TreeMap<>();
 		for(FastaSequence fs: sequences) {
 			disorderRanges.put(fs, getDisorder(fs));
 		}
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java
index f6eb3aac47..345fb20cd5 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java
@@ -33,6 +33,7 @@
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.nio.charset.StandardCharsets;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Map;
@@ -95,7 +96,7 @@ public static class Model {
 	final float[] W;// = new float[RonnConstraint.maxD];
 
 	int numOfDBAAseq;
-	int modelNum = -1;
+	int modelNum;
 
 	public Model(final int modelNum, final int numberofSequence) {
 		this.modelNum = modelNum;
@@ -155,7 +156,7 @@ public String toString() {
 
 	}
 
-	private static final Map<Integer, Model> models = new HashMap<Integer, Model>();
+	private static final Map<Integer, Model> models = new HashMap<>();
 
 	public Model getModel(final int modelNum) {
 	return ModelLoader.models.get(modelNum);
@@ -167,8 +168,8 @@ void loadModels() throws NumberFormatException, IOException {
 			final BufferedReader bfr = new BufferedReader(
 					new InputStreamReader(ModelLoader.class.getResourceAsStream(
 							"model" + i + ".rec"),
-							"ISO-8859-1"));
-			String line = null;
+							StandardCharsets.ISO_8859_1));
+			String line;
 			line = bfr.readLine().trim();
 			final int numberOfSeqs = Integer.parseInt(line);
 			final Model model = new Model(i, numberOfSeqs);
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/NullOutputStream.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/NullOutputStream.java
index 572e4ddee6..3b9395fdd6 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/NullOutputStream.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/NullOutputStream.java
@@ -40,7 +40,7 @@
 public final class NullOutputStream extends OutputStream {
 
 	@Override
-	public void write(final int b) throws IOException {
+	public void write(final int b) {
 		// this methods does nothing.
 		// This is an intention
 	}
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonn.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonn.java
index 16dbcb72a1..8f5122eefd 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonn.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonn.java
@@ -91,8 +91,7 @@ public final class ORonn implements Callable<ORonn> {
 		timer = new Timer(TimeUnit.MILLISECONDS);
 	}
 	//This constructor is for API calls where the caller collects the results directly
-	ORonn(final FastaSequence sequence, final ModelLoader mloader) throws NumberFormatException,
-	IOException {
+	ORonn(final FastaSequence sequence, final ModelLoader mloader) throws NumberFormatException {
 		this.sequence = sequence;
 		this.mloader = mloader;
 		out = new PrintWriter(new NullOutputStream());
@@ -136,7 +135,7 @@ static boolean isValidSequence(final FastaSequence fsequence) {
 	}
 
 	@Override
-	public ORonn call() throws NumberFormatException, IOException {
+	public ORonn call() throws NumberFormatException {
 		final String seq = sequence.getSequence();
 		// Calculate for each model
 		for (int m = 0; m < ORonn.NUMBER_OF_MODELS; m++) {
@@ -190,7 +189,7 @@ float[] getMeanScores() {
 	 * sequence. Letters and values separated by tabulation in	this case.
 	 *
 	 */
-	static enum ResultLayout {
+	enum ResultLayout {
 		VERTICAL, HORIZONTAL
 	}
 
@@ -201,7 +200,7 @@ static void printUsage() {
 	static boolean isValidSequenceForRonn(final FastaSequence fsequence,
 			final PrintWriter stat) {
 		boolean valid = true;
-		String message = "";
+		String message;
 		if (!ORonn.isValidSequence(fsequence)) {
 			message = "IGNORING sequence "
 					+ fsequence.getId()
@@ -225,7 +224,7 @@ static boolean isValidSequenceForRonn(final FastaSequence fsequence,
 
 	static void validateSequenceForRonn(final FastaSequence fsequence) {
 
-		String message = "";
+		String message;
 		if (!ORonn.isValidSequence(fsequence)) {
 			message = "IGNORING sequence "
 					+ fsequence.getId()
@@ -353,7 +352,7 @@ static void predictParallel(final List<FastaSequence> fsequences,
 		// Do parallel execution
 		final ExecutorService executor = new ThreadPoolExecutor(prms
 				.getThreadNum(), prms.getThreadNum(), 0L, TimeUnit.SECONDS,
-				new SynchronousQueue<Runnable>(),
+				new SynchronousQueue<>(),
 				new ThreadPoolExecutor.CallerRunsPolicy());
 		try {
 			for (final FastaSequence sequence : fsequences) {
@@ -369,8 +368,7 @@ static void predictParallel(final List<FastaSequence> fsequences,
 				executor.submit(ronn);
 			}
 			executor.shutdown();
-			final int timeOut = (fsequences.size() < 60) ? 60 : fsequences
-					.size();
+			final int timeOut = Math.max(fsequences.size(), 60);
 			stat.println("All task submitted. Waiting for complition for "
 					+ "maximum of " + timeOut + " minutes");
 			executor.awaitTermination(timeOut, TimeUnit.MINUTES);
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java
index 41253be8c1..e5ef18de4c 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java
@@ -142,7 +142,7 @@ public void getScores(final File outfile) throws FileNotFoundException {
 	private final float[] align(final int sResidue, final int dIndex) {
 	int dResidue, r;
 	float maxScore = -1000000;
-	float rho1 = 0;
+	float rho1;
 	int maxIdx = 0;
 	float rho0 = 0;
 	short[] dbAARow = model.dbAA[dIndex];
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/RonnConstraint.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/RonnConstraint.java
index dacf3067bd..995ecbda6b 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/RonnConstraint.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/RonnConstraint.java
@@ -91,7 +91,7 @@ public final class RonnConstraint {
 		{ -2, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2,
 			-1, 2, 7 } };
 
-	public static enum Threshold {
+	public enum Threshold {
 	T0(0, RonnConstraint.THRESHOLD0), T1(1, RonnConstraint.THRESHOLD1), T2(
 		2, RonnConstraint.THRESHOLD2), T3(3, RonnConstraint.THRESHOLD3), T4(
 		4, RonnConstraint.THRESHOLD4), T5(5, RonnConstraint.THRESHOLD5), T6(
@@ -101,7 +101,7 @@ public static enum Threshold {
 	private final int tnum;
 	private final float[] values;
 
-	private Threshold(final int tnum, final float[] values) {
+	Threshold(final int tnum, final float[] values) {
 		this.tnum = tnum;
 		this.values = values;
 	}
diff --git a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/JronnTest.java b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/JronnTest.java
index 65bfc5ed36..2783477538 100644
--- a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/JronnTest.java
+++ b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/JronnTest.java
@@ -79,7 +79,7 @@ public void checkJronn() {
 	 * Credit Thomas Klambauer, but here have removed the implement of
 	 * AutoCloseable (Java 7) for BioJava support of Java 6.
 	 */
-	public class ScopedProperty {
+	public static class ScopedProperty {
 
 		private final String key;
 		private final String oldValue;
diff --git a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
index d3c50fd61b..6c8dca3379 100644
--- a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
+++ b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
@@ -96,7 +96,7 @@ private static ProteinSequence getUniprot(String uniProtID) throws CompoundNotFo
 
 		AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
 		UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence =
-				new UniprotProxySequenceReader<AminoAcidCompound>(uniProtID,set);
+				new UniprotProxySequenceReader<>(uniProtID, set);
 
 		ProteinSequence seq = new ProteinSequence(uniprotSequence);
 
diff --git a/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java b/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java
index 5327b18e2f..97f32828be 100644
--- a/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java
+++ b/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java
@@ -48,7 +48,7 @@
  */
 public class AFPFromFasta {
 
-	public static void main(String[] args) throws IOException, StructureException, Exception {
+	public static void main(String[] args) throws Exception {
 		Structure structure1 = StructureTools.getStructure("1w0p");
 		Structure structure2 = StructureTools.getStructure("1w0p");
 		String first = "alfdynatgdtefdspakqgwmqdntnngsgvltnadgmpawlvqgiggraqwtyslstnqhaqassfgwrmttemkvlsggmitnyyangtqrvlpiisldssgnlvvefegqtgrtvlatgtaateyhkfelvflpgsnpsasfyfdgklirdniqptaskQNMIVWGNGSSntdgvaayrdikfei------------------------------------------------------------------------------------------------------------------QGDVIf------------RGPDRIPSIVASsvTPGVVTAFAEKRVGGgdpgalsntNDIITRTSRDGGITWDTELNLTEQinvsdeFDFSDPRPIYDPs---SNTVLVSYARWPtdaaqngdrikpwmpNGIFYSVYDVASgnWQAPIDVTdqvkersfqiagwggselyrrntslnsqqdwqsnakirivdgaanqiqvadgsrkyvvtlsidesgglvanlngvsapiilqsehakvhsfhdyelqysalnhtttlfvdgqqittwagevsqenniqfgnadaqidgrlhvqkivltqqghnlvefdafylaqqtpevekdleklgwtkiktgntmslygNASVNPGpgHGITLtrqqnisgsqNGRLIYPAIVLdrfFLNVMSIYSDDGgsnwq-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGSTLpipfrwksssileTLEPSEADMVELQN--GDLLLTARLDFNQivngvny--SPRQQFLSKDGGITWSLLEANNANvfsnistgTVDASITRFEqsdgSHFLLFTNPQGnpagTNgr------------QNLGLWFSFDEG--VTWKGPIQ--LVNGasaysdiyqldsenaivivetdnsnmrilrmpitllkqklt";
diff --git a/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java b/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
index fbd3ecc74d..c63afe6cf0 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
@@ -24,6 +24,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.UnsupportedEncodingException;
+import java.nio.charset.StandardCharsets;
 
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
@@ -68,20 +69,15 @@ public static void getAlignmentFromFasta() throws StructureException {
 
 
 		InputStream fasta;
-		try {
-			fasta = new ByteArrayInputStream(fastaStr.getBytes("UTF-8"));
-		} catch (UnsupportedEncodingException e) {
-			e.printStackTrace();
-			return;
-		}
+        fasta = new ByteArrayInputStream(fastaStr.getBytes(StandardCharsets.UTF_8));
 
-		// Create a header parser to parse the header lines into valid structure accessions.
+        // Create a header parser to parse the header lines into valid structure accessions.
 		// The resulting accession can be anything interpretable by AtomCache.getStructure.
 		// Possible Examples: "4HHB" (whole structure), "d4hhba_" (SCOP domain),
 		//   "4HHB.A:1-15" (residue range)
 		// For this example, the built-in fasta parser will extract the correct accession.
 		SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound> headerParser;
-		headerParser = new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>();
+		headerParser = new GenericFastaHeaderParser<>();
 
 		// Create AtomCache to fetch structures from the PDB
 		AtomCache cache = new AtomCache();
@@ -96,10 +92,7 @@ public static void getAlignmentFromFasta() throws StructureException {
 				fasta, headerParser, creator, cache);
 		try {
 			parser.process();
-		} catch (IOException e) {
-			e.printStackTrace();
-			return;
-		} catch (StructureException e) {
+		} catch (IOException | StructureException e) {
 			e.printStackTrace();
 			return;
 		}
diff --git a/biojava-structure-gui/src/main/java/demo/DemoCE.java b/biojava-structure-gui/src/main/java/demo/DemoCE.java
index 5e2bb0aabb..81630472f0 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoCE.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoCE.java
@@ -60,8 +60,8 @@ public static void main(String[] args){
 
 		ChemCompGroupFactory.setChemCompProvider(prov);
 
-		Structure structure1 = null;
-		Structure structure2 = null;
+		Structure structure1;
+		Structure structure2;
 
 		try {
 
diff --git a/biojava-structure-gui/src/main/java/demo/DemoFATCAT.java b/biojava-structure-gui/src/main/java/demo/DemoFATCAT.java
index ac7a0542f6..173bd90436 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoFATCAT.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoFATCAT.java
@@ -53,8 +53,8 @@ public static void main(String[] args){
 
 		AtomCache cache = new AtomCache();
 
-		Structure structure1 = null;
-		Structure structure2 = null;
+		Structure structure1;
+		Structure structure2;
 
 		try {
 
diff --git a/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java b/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java
index 062bc6d8d7..6deb62bf8c 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java
@@ -48,7 +48,7 @@
  */
 public class DemoMultipleMC {
 
-	public static void main(String[] args) throws IOException, StructureException, InterruptedException, ExecutionException {
+	public static void main(String[] args) throws IOException, StructureException {
 
 		//ASP-proteinases (CEMC paper)
 		//List<String> names = Arrays.asList("3app", "4ape", "2apr", "5pep", "1psn", "4cms", "1bbs.A", "1smr.A", "2jxr.A", "1mpp", "2asi", "1am5");
@@ -97,9 +97,9 @@ public static void main(String[] args) throws IOException, StructureException, I
 		//Load the CA atoms of the structures
 		AtomCache cache = new AtomCache();
 
-		List<StructureIdentifier> identifiers = new ArrayList<StructureIdentifier>();
+		List<StructureIdentifier> identifiers = new ArrayList<>();
 
-		List<Atom[]> atomArrays = new ArrayList<Atom[]>();
+		List<Atom[]> atomArrays = new ArrayList<>();
 		for (String name:names)	{
 			atomArrays.add(cache.getAtoms(name));
 			identifiers.add(new SubstructureIdentifier(name));
diff --git a/biojava-structure-gui/src/main/java/demo/DemoRotationAxis.java b/biojava-structure-gui/src/main/java/demo/DemoRotationAxis.java
index 83b676eb8f..06faf0faf3 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoRotationAxis.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoRotationAxis.java
@@ -118,10 +118,8 @@ public static void main(String[] args) {
 			jmolPanel.evalString("draw ID z VECTOR {0,0,0} {0,0,5} WIDTH 0.5 COLOR blue \">z\";");
 			*/
 
-		} catch (IOException e) {
-			e.printStackTrace();
-		} catch (StructureException e) {
+		} catch (IOException | StructureException e) {
 			e.printStackTrace();
 		}
-	}
+    }
 }
diff --git a/biojava-structure-gui/src/main/java/demo/DemoSW3DAligner.java b/biojava-structure-gui/src/main/java/demo/DemoSW3DAligner.java
index bcb4ac1e96..cc9ef9b874 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoSW3DAligner.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoSW3DAligner.java
@@ -44,8 +44,8 @@ public static void main(String[] args){
 
 		AtomCache cache = new AtomCache();
 
-		Structure structure1 = null;
-		Structure structure2 = null;
+		Structure structure1;
+		Structure structure2;
 
 		try {
 
diff --git a/biojava-structure-gui/src/main/java/demo/DemoShowLargeAssembly.java b/biojava-structure-gui/src/main/java/demo/DemoShowLargeAssembly.java
index c626e90f8a..aa0c4ea87c 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoShowLargeAssembly.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoShowLargeAssembly.java
@@ -90,7 +90,7 @@ public static Structure  readStructure(String pdbId, int bioAssemblyId) {
 
 		// download missing files
 
-		Structure structure = null;
+		Structure structure;
 		try {
 			structure = StructureIO.getBiologicalAssembly(pdbId,bioAssemblyId);
 		} catch (Exception e){
diff --git a/biojava-structure-gui/src/main/java/demo/DemoShowValidationResults.java b/biojava-structure-gui/src/main/java/demo/DemoShowValidationResults.java
index 80001fd6bf..b88eac875a 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoShowValidationResults.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoShowValidationResults.java
@@ -46,7 +46,7 @@ public static void main(String[] args){
 
 	private static void showPdbValidation(String pdbId) {
 		try {
-			JAXBContext ctx = JAXBContext.newInstance(new Class[] {WwPDBValidationInformation.class});
+			JAXBContext ctx = JAXBContext.newInstance(WwPDBValidationInformation.class);
 
 			Unmarshaller um = ctx.createUnmarshaller();
 
@@ -87,7 +87,7 @@ private static void showPdbValidation(String pdbId) {
 					pos +="^" + iCode;
 				pos +=":" + chainId;
 
-				BigDecimal base = new BigDecimal(0.5);
+				BigDecimal base = new BigDecimal("0.5");
 
 				for (Clash clash : clashes){
 					String clashatom = clash.getAtom();
diff --git a/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java b/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java
index c99678d4b9..8f31e5ce66 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java
@@ -38,6 +38,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.UnsupportedEncodingException;
+import java.nio.charset.StandardCharsets;
 
 /**
  * Demo of how to use the {@link FastaStructureParser} class to read protein
@@ -60,20 +61,15 @@ public static void getStructureFromFasta() {
 			"KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA\n" +
 			"VHASLDKFLASVSTVLTSKYR\n";
 		InputStream fasta;
-		try {
-			fasta = new ByteArrayInputStream(fastaStr.getBytes("UTF-8"));
-		} catch (UnsupportedEncodingException e) {
-			e.printStackTrace();
-			return;
-		}
+        fasta = new ByteArrayInputStream(fastaStr.getBytes(StandardCharsets.UTF_8));
 
-		// Create a header parser to parse the header lines into valid structure accessions.
+        // Create a header parser to parse the header lines into valid structure accessions.
 		// The resulting accession can be anything interpretable by AtomCache.getStructure.
 		// Possible Examples: "4HHB" (whole structure), "d4hhba_" (SCOP domain),
 		//   "4HHB.A:1-15" (residue range)
 		// For this example, the built-in fasta parser will extract the correct accession.
 		SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound> headerParser;
-		headerParser = new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>();
+		headerParser = new GenericFastaHeaderParser<>();
 
 		// Create AtomCache to fetch structures from the PDB
 		AtomCache cache = new AtomCache();
@@ -88,10 +84,7 @@ public static void getStructureFromFasta() {
 				fasta, headerParser, creator, cache);
 		try {
 			parser.process();
-		} catch (IOException e) {
-			e.printStackTrace();
-			return;
-		} catch (StructureException e) {
+		} catch (IOException | StructureException e) {
 			e.printStackTrace();
 			return;
 		}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AboutDialog.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AboutDialog.java
index 1d978876cf..d364e00343 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AboutDialog.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AboutDialog.java
@@ -66,22 +66,18 @@ public void showDialog(){
 		vBox= Box.createVerticalBox();
 		vBox.add(scroll);
 
-		txt.addHyperlinkListener(new HyperlinkListener(){
-
-			@Override
-			public void hyperlinkUpdate(HyperlinkEvent e) {
-
-				if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
-					String href = e.getDescription();
-					BrowserOpener.showDocument(href);
-				}
-				if ( e.getEventType() == HyperlinkEvent.EventType.ENTERED) {
-					// change the mouse curor
-					vBox.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
-				}
-				if (e.getEventType() == HyperlinkEvent.EventType.EXITED) {
-					vBox.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
-				}
+		txt.addHyperlinkListener(e -> {
+
+			if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+				String href = e.getDescription();
+				BrowserOpener.showDocument(href);
+			}
+			if ( e.getEventType() == HyperlinkEvent.EventType.ENTERED) {
+				// change the mouse curor
+				vBox.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+			}
+			if (e.getEventType() == HyperlinkEvent.EventType.EXITED) {
+				vBox.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
 			}
 		});
 
@@ -90,17 +86,14 @@ public void hyperlinkUpdate(HyperlinkEvent e) {
 
 		JButton close = new JButton("Close");
 
-		close.addActionListener(new ActionListener(){
-			@Override
-			public void actionPerformed(ActionEvent event) {
-				Object source = event.getSource();
+		close.addActionListener(event -> {
+			Object source = event.getSource();
 
-				JButton but = (JButton)source;
-				Container parent = but.getParent().getParent().getParent().getParent().getParent().getParent() ;
+			JButton but = (JButton)source;
+			Container parent = but.getParent().getParent().getParent().getParent().getParent().getParent() ;
 
-				JDialog dia = (JDialog) parent;
-				dia.dispose();
-			}
+			JDialog dia = (JDialog) parent;
+			dia.dispose();
 		});
 
 		Box hBoxb = Box.createHorizontalBox();
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalcDB.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalcDB.java
index 74637e4617..61ab28273b 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalcDB.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalcDB.java
@@ -97,7 +97,7 @@ public AlignmentCalcDB(AlignmentGui parent, Structure s1,  String name1, UserCon
 	@Override
 	public void run() {
 
-		StructureAlignment algorithm = null;
+		StructureAlignment algorithm;
 
 		if ( parent != null )
 			algorithm = parent.getStructureAlignment();
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalculationRunnable.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalculationRunnable.java
index e50de3f637..d9559b2227 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalculationRunnable.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalculationRunnable.java
@@ -27,8 +27,8 @@
 public interface AlignmentCalculationRunnable extends Runnable
 {
 
-	public void interrupt();
-	public void cleanup();
-	public void setNrCPUs(int useNrCPUs);
+	void interrupt();
+	void cleanup();
+	void setNrCPUs(int useNrCPUs);
 
 }
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java
index c55e6689e3..f40ecfe9a2 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java
@@ -65,7 +65,7 @@
  */
 public class AlignmentGui extends JFrame{
 
-	private final static long serialVersionUID =0l;
+	private final static long serialVersionUID = 0L;
 
 	StructureAlignment algorithm;
 
@@ -82,7 +82,7 @@ public class AlignmentGui extends JFrame{
 	JProgressBar progress;
 
 
-	private DBSearchGUI dbsearch;
+	private final DBSearchGUI dbsearch;
 
 
 	public static void main(String[] args){
@@ -93,7 +93,7 @@ public static void main(String[] args){
 
 	static final ResourceManager resourceManager = ResourceManager.getResourceManager("ce");
 
-	private static final String MAIN_TITLE = "Pairwise Structure Alignment - Main - V." + resourceManager.getString("ce.version");;
+	private static final String MAIN_TITLE = "Pairwise Structure Alignment - Main - V." + resourceManager.getString("ce.version");
 
 	private static final AlignmentGui me = new AlignmentGui();
 
@@ -208,7 +208,7 @@ private Box setupAlgorithm()
 		algorithmList.setSelectedIndex(0);
 
 		Action actionAlgorithm = new AbstractAction("Algorithm") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			// This method is called when the button is pressed
 			@Override
 			public void actionPerformed(ActionEvent evt) {
@@ -226,7 +226,7 @@ public void actionPerformed(ActionEvent evt) {
 
 
 		Action paramAction = new AbstractAction("Parameters") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			// This method is called when the button is pressed
 			@Override
 			public void actionPerformed(ActionEvent evt) {
@@ -269,7 +269,7 @@ private Box initButtons(){
 		//        hBox42.add(Box.createGlue());
 		//        vBox.add(hBox42);
 		Action action1 = new AbstractAction("Align") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			// This method is called when the button is pressed
 			@Override
 			public void actionPerformed(ActionEvent evt) {
@@ -290,7 +290,7 @@ else if ( selectedIndex == 1)
 		JButton submitB = new JButton(action1);
 
 		Action action3 = new AbstractAction("Abort") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			// This method is called when the button is pressed
 			@Override
 			public void actionPerformed(ActionEvent evt) {
@@ -304,7 +304,7 @@ public void actionPerformed(ActionEvent evt) {
 		abortB.setEnabled(false);
 
 		Action action2 = new AbstractAction("Exit") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			// This method is called when the button is pressed
 			@Override
 			public void actionPerformed(ActionEvent evt) {
@@ -377,8 +377,8 @@ private void calcAlignment() {
 				return;
 			}
 
-			String name1 = "custom1";
-			String name2 = "custom2";
+			String name1;
+			String name2;
 
 			if  ( pos == 0){
 				name1 = tab1.getName1().getIdentifier();
@@ -400,9 +400,7 @@ private void calcAlignment() {
 			progress.setIndeterminate(true);
 			ProgressThreadDrawer drawer = new ProgressThreadDrawer(progress);
 			drawer.start();
-		} catch (StructureException e){
-			JOptionPane.showMessageDialog(null,"Could not align structures. Exception: " + e.getMessage());
-		} catch (IOException e) {
+		} catch (StructureException | IOException e){
 			JOptionPane.showMessageDialog(null,"Could not align structures. Exception: " + e.getMessage());
 		}
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java
index c603392c08..1e79061d78 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java
@@ -46,7 +46,7 @@ public ChooseDirAction (JTextField textField, UserConfiguration config){
 		this.config = config;
 		this.textField = textField;
 	}
-	public static final long serialVersionUID = 0l;
+	public static final long serialVersionUID = 0L;
 	// This method is called when the button is pressed
 	@Override
 	public void actionPerformed(ActionEvent evt) {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.java
index 637183a3af..32dd0d4b2c 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.java
@@ -48,7 +48,7 @@ public class ConfigPDBInstallPanel extends JPanel
 
 	JTextField pdbDir;
 
-	private static ConfigPDBInstallPanel instance = new ConfigPDBInstallPanel();
+	private static final ConfigPDBInstallPanel instance = new ConfigPDBInstallPanel();
 
 	static JDialog dialog;
 
@@ -137,22 +137,14 @@ public static void showDialog(){
 		vBox.add(Box.createGlue());
 
 		JButton apply = new JButton("Apply");
-		apply.addActionListener(new ActionListener(){
-			@Override
-		public void actionPerformed(ActionEvent event) {
-				instance.applyValues();
-				dialog.dispose();
-			}
+		apply.addActionListener(event -> {
+			instance.applyValues();
+			dialog.dispose();
 		});
 
 		JButton close = new JButton("Cancel");
 
-		close.addActionListener(new ActionListener(){
-			@Override
-		public void actionPerformed(ActionEvent event) {
-			  dialog.dispose();
-			}
-		});
+		close.addActionListener(event -> dialog.dispose());
 
 		Box hBoxb = Box.createHorizontalBox();
 		hBoxb.add(Box.createGlue());
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBResultTable.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBResultTable.java
index b71b040f8e..700b8707cd 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBResultTable.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBResultTable.java
@@ -96,7 +96,7 @@ public DBResultTable(){
 
 	public void show(BufferedReader in, UserConfiguration config) throws IOException{
 		String str;
-		List<String[]> tmpdat = new ArrayList<String[]>();
+		List<String[]> tmpdat = new ArrayList<>();
 		while ((str = in.readLine()) != null) {
 			if ( str.startsWith("#")) {
 				if ( str.startsWith("# algorithm:")) {
@@ -142,9 +142,7 @@ else if ( str.startsWith("#param:scoring=")){
 								ceParams.setScoringStrategy(scoreS);
 							}
 						}
-					} catch (IndexOutOfBoundsException e){
-						System.err.println("Unknown scoring strategy from line: " + str);
-					} catch (IllegalArgumentException e) {
+					} catch (IndexOutOfBoundsException | IllegalArgumentException e){
 						System.err.println("Unknown scoring strategy from line: " + str);
 					} catch (Exception e) {
 						System.err.println("Unknown parameter can't read parameters from line: " + str);
@@ -260,7 +258,7 @@ private void initAlgorithm(String algorithmName) {
 	}
 
 	private void outputSelection() {
-		StringBuffer output = new StringBuffer();
+		StringBuilder output = new StringBuilder();
 		output.append(String.format("Lead: %d, %d. ",
 				table.getSelectionModel().getLeadSelectionIndex(),
 				table.getColumnModel().getSelectionModel().
@@ -309,7 +307,7 @@ private void showAlignment( String name1, String name2){
 		}
 
 		try {
-			Structure structure1 = null;
+			Structure structure1;
 			if ( name1.equals("CUSTOM")) {
 				// user uploaded a custom PDB file...
 				structure1 = loadCustomStructure(userPath,userChain);
@@ -348,7 +346,7 @@ private void showAlignment( String name1, String name2){
 
 	private Structure loadCustomStructure(String userPath2, String userChain2) throws StructureException{
 		StructureIOFile reader = new PDBFileReader();
-		Structure s = null;
+		Structure s;
 		try {
 			s = reader.getStructure(userPath2);
 		} catch (IOException  e){
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBSearchGUI.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBSearchGUI.java
index 885a544d28..a17bb5cab4 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBSearchGUI.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBSearchGUI.java
@@ -155,30 +155,26 @@ private JPanel createListPane() {
 
 		dir.add(hBox);
 
-		chB.addActionListener(new ActionListener() {
-
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				JFileChooser chooser = new JFileChooser();
-				chooser.setMultiSelectionEnabled(false);
-				chooser.setDialogTitle("Select Output Directory");
-				chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
-				//
-				// disable the "All files" option.
-				//
-				chooser.setAcceptAllFileFilterUsed(false);
-				//
-
-
-				//				In response to a button click:
-				int returnVal = chooser.showSaveDialog(null);
-				if ( returnVal == JFileChooser.APPROVE_OPTION) {
-					File file = chooser.getSelectedFile();
-					outFileLocation.setText(file.getPath());
-					outFileLocation.repaint();
-				}
-
+		chB.addActionListener(e -> {
+			JFileChooser chooser = new JFileChooser();
+			chooser.setMultiSelectionEnabled(false);
+			chooser.setDialogTitle("Select Output Directory");
+			chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+			//
+			// disable the "All files" option.
+			//
+			chooser.setAcceptAllFileFilterUsed(false);
+			//
+
+
+			//				In response to a button click:
+			int returnVal = chooser.showSaveDialog(null);
+			if ( returnVal == JFileChooser.APPROVE_OPTION) {
+				File file = chooser.getSelectedFile();
+				outFileLocation.setText(file.getPath());
+				outFileLocation.repaint();
 			}
+
 		});
 
 		//tabP.addTab("Select Output Directory", null, dir,
@@ -203,18 +199,14 @@ private Box createDomainSelectPane() {
 		JComboBox domainList = new JComboBox(petStrings);
 		domainList.setSelectedIndex(0);
 		domainList.setToolTipText("Either align whole chains or SCOP domains and domains assigned with PDP, where no SCOP available.");
-		domainList.addActionListener(new ActionListener() {
+		domainList.addActionListener(arg0 -> {
+			JComboBox box = (JComboBox)arg0.getSource();
+			int index = box.getSelectedIndex();
+			if ( index == 0)
+				useDomainSplit = true;
+			else
+				useDomainSplit = false;
 
-			@Override
-			public void actionPerformed(ActionEvent arg0) {
-				JComboBox box = (JComboBox)arg0.getSource();
-				int index = box.getSelectedIndex();
-				if ( index == 0)
-					useDomainSplit = true;
-				else
-					useDomainSplit = false;
-
-			}
 		});
 
 		JLabel label= new JLabel("Domains:");
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
index 03aa7d5084..ddab5d5a5f 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
@@ -40,7 +40,6 @@
 import org.biojava.nbio.structure.align.gui.jmol.JmolTools;
 import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
 import org.biojava.nbio.structure.align.model.AFPChain;
-import org.biojava.nbio.structure.align.util.AFPAlignmentDisplay;
 import org.biojava.nbio.structure.align.util.AlignmentTools;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -56,7 +55,7 @@ public class DisplayAFP {
 
 	//TODO: same as getEqrPos??? !!!
 	public static final List<Integer> getEQRAlignmentPos(AFPChain afpChain){
-		List<Integer> lst = new ArrayList<Integer>();
+		List<Integer> lst = new ArrayList<>();
 
 		char[] s1 = afpChain.getAlnseq1();
 		char[] s2 = afpChain.getAlnseq2();
@@ -107,7 +106,7 @@ private static boolean isAlignedPosition(int i, char c1, char c2, boolean isFatC
 	 * @param ca
 	 */
 	public static final List<String> getPDBresnum(int aligPos, AFPChain afpChain, Atom[] ca){
-		List<String> lst = new ArrayList<String>();
+		List<String> lst = new ArrayList<>();
 		if ( aligPos > 1) {
 			System.err.println("multiple alignments not supported yet!");
 			return lst;
@@ -230,7 +229,7 @@ private static int getNextFatCatPos(AFPChain afpChain, int chainNr,
 
 				if(len > 0)     {
 
-					int lmax = (p1 - p1b - 1)>(p2 - p2b - 1)?(p1 - p1b - 1):(p2 - p2b - 1);
+					int lmax = Math.max((p1 - p1b - 1), (p2 - p2b - 1));
 
 					// lmax gives the length of an alignment gap
 
@@ -343,7 +342,7 @@ private static final int getUngappedFatCatPos(AFPChain afpChain, int chainNr, in
 
 				if(len > 0)     {
 
-					int lmax = (p1 - p1b - 1)>(p2 - p2b - 1)?(p1 - p1b - 1):(p2 - p2b - 1);
+					int lmax = Math.max((p1 - p1b - 1), (p2 - p2b - 1));
 
 					// lmax gives the length of an alignment gap
 
@@ -404,10 +403,9 @@ private static final int getUngappedFatCatPos(AFPChain afpChain, int chainNr, in
 	 * @param ca
 	 * @param hetatms
 	 * @return
-	 * @throws StructureException
 	 */
-	public static final Atom[] getAtomArray(Atom[] ca,List<Group> hetatms ) throws StructureException{
-		List<Atom> atoms = new ArrayList<Atom>();
+	public static final Atom[] getAtomArray(Atom[] ca,List<Group> hetatms ) {
+		List<Atom> atoms = new ArrayList<>();
 		Collections.addAll(atoms, ca);
 
 		logger.debug("got {} hetatoms", hetatms.size());
@@ -425,7 +423,7 @@ public static final Atom[] getAtomArray(Atom[] ca,List<Group> hetatms ) throws S
 			atoms.add(a);
 		}
 
-		Atom[] arr = atoms.toArray(new Atom[atoms.size()]);
+		Atom[] arr = atoms.toArray(new Atom[0]);
 
 		return arr;
 	}
@@ -436,7 +434,7 @@ public static final Atom[] getAtomArray(Atom[] ca,List<Group> hetatms ) throws S
 
 	public static final StructureAlignmentJmol display(AFPChain afpChain,Group[] twistedGroups, Atom[] ca1, Atom[] ca2,List<Group> hetatms1, List<Group> hetatms2 ) throws StructureException {
 
-		List<Atom> twistedAs = new ArrayList<Atom>();
+		List<Atom> twistedAs = new ArrayList<>();
 
 		for ( Group g: twistedGroups){
 			if ( g == null )
@@ -446,7 +444,7 @@ public static final StructureAlignmentJmol display(AFPChain afpChain,Group[] twi
 			Atom a = g.getAtom(0);
 			twistedAs.add(a);
 		}
-		Atom[] twistedAtoms = twistedAs.toArray(new Atom[twistedAs.size()]);
+		Atom[] twistedAtoms = twistedAs.toArray(new Atom[0]);
 		twistedAtoms = StructureTools.cloneAtomArray(twistedAtoms);
 
 		Atom[] arr1 = getAtomArray(ca1, hetatms1);
@@ -476,7 +474,7 @@ public static final StructureAlignmentJmol display(AFPChain afpChain,Group[] twi
 		return jmol;
 	}
 
-	public static void showAlignmentPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol) throws StructureException {
+	public static void showAlignmentPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol) {
 
 		AligPanel me = new AligPanel();
 		me.setAlignmentJmol(jmol);
@@ -560,7 +558,7 @@ public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1,
 
 		Group[] twistedGroups = AlignmentTools.prepareGroupsForDisplay(afpChain,ca1, ca2);
 
-		List<Atom> twistedAs = new ArrayList<Atom>();
+		List<Atom> twistedAs = new ArrayList<>();
 
 		for ( Group g: twistedGroups){
 			if ( g == null )
@@ -570,7 +568,7 @@ public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1,
 			Atom a = g.getAtom(0);
 			twistedAs.add(a);
 		}
-		Atom[] twistedAtoms = twistedAs.toArray(new Atom[twistedAs.size()]);
+		Atom[] twistedAtoms = twistedAs.toArray(new Atom[0]);
 
 		List<Group> hetatms  = StructureTools.getUnalignedGroups(ca1);
 		List<Group> hetatms2 = StructureTools.getUnalignedGroups(ca2);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java
index 22f4ad1822..cc1b3f15cf 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java
@@ -76,7 +76,7 @@ public DotPlotPanel(AFPChain alignment ){
 		int[][][] optAln = alignment.getOptAln(); // [block #][{0,1} chain index][pos]
 
 		for(;alignNumber < optAln.length;alignNumber++) {
-			List<int[]> alignPairs = new ArrayList<int[]>();
+			List<int[]> alignPairs = new ArrayList<>();
 			for(int pos = 0; pos<optAln[alignNumber][0].length; pos++ ) {
 				alignPairs.add( new int[] {
 						optAln[alignNumber][0][pos],
@@ -280,9 +280,7 @@ public static void main(String[] args) {
 			showDotPlotJFrame(afpChain);
 
 
-		} catch (StructureException e) {
-			e.printStackTrace();
-		} catch (IOException e) {
+		} catch (StructureException | IOException e) {
 			e.printStackTrace();
 		}
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIAlignmentProgressListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIAlignmentProgressListener.java
index 8bbf28aad2..8f2e6865f0 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIAlignmentProgressListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIAlignmentProgressListener.java
@@ -46,8 +46,8 @@ public class GUIAlignmentProgressListener extends JPanel implements AlignmentPro
 	int alignmentsProcessed;
 
 	JProgressBar progressBar;
-	private JTextArea taskOutput;
-	private JButton stopButton;
+	private final JTextArea taskOutput;
+	private final JButton stopButton;
 
 	FarmJob farmJob;
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIFarmJobRunnable.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIFarmJobRunnable.java
index 5a0006c29b..9120909128 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIFarmJobRunnable.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIFarmJobRunnable.java
@@ -74,12 +74,7 @@ public void run() {
 		t.start();
 
 
-		javax.swing.SwingUtilities.invokeLater(new Runnable() {
-	        @Override
-			public void run() {
-	            createAndShowGUI(progressListener);
-	        }
-		});
+		javax.swing.SwingUtilities.invokeLater(() -> createAndShowGUI(progressListener));
 
 	}
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/HelpDialog.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/HelpDialog.java
index 0a83191339..26f1bd540f 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/HelpDialog.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/HelpDialog.java
@@ -55,40 +55,33 @@ public void showDialog(){
 	      vBox= Box.createVerticalBox();
 	      vBox.add(scroll);
 
-	      txt.addHyperlinkListener(new HyperlinkListener(){
-
-	         @Override
-			public void hyperlinkUpdate(HyperlinkEvent e) {
-
-	             if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
-	                 String href = e.getDescription();
-	                 BrowserOpener.showDocument(href);
-	             }
-	             if ( e.getEventType() == HyperlinkEvent.EventType.ENTERED) {
-	                 // change the mouse curor
-	                 vBox.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
-	             }
-	             if (e.getEventType() == HyperlinkEvent.EventType.EXITED) {
-	                 vBox.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
-	             }
-	         }
-	     });
+	      txt.addHyperlinkListener(e -> {
+
+			  if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+				  String href = e.getDescription();
+				  BrowserOpener.showDocument(href);
+			  }
+			  if ( e.getEventType() == HyperlinkEvent.EventType.ENTERED) {
+				  // change the mouse curor
+				  vBox.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+			  }
+			  if (e.getEventType() == HyperlinkEvent.EventType.EXITED) {
+				  vBox.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+			  }
+		  });
 
 
 	      JButton close = new JButton("Close");
 
-	      close.addActionListener(new ActionListener(){
-	         @Override
-			public void actionPerformed(ActionEvent event) {
-	            Object source = event.getSource();
+	      close.addActionListener(event -> {
+			 Object source = event.getSource();
 
-	            JButton but = (JButton)source;
-	            Container parent = but.getParent().getParent().getParent().getParent().getParent().getParent() ;
+			 JButton but = (JButton)source;
+			 Container parent = but.getParent().getParent().getParent().getParent().getParent().getParent() ;
 
-	            JDialog dia = (JDialog) parent;
-	            dia.dispose();
-	         }
-	      });
+			 JDialog dia = (JDialog) parent;
+			 dia.dispose();
+		  });
 
 	      Box hBoxb = Box.createHorizontalBox();
 	      hBoxb.add(Box.createGlue());
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/JPrintPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/JPrintPanel.java
index 47ee654f2a..4ce35415b1 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/JPrintPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/JPrintPanel.java
@@ -40,7 +40,7 @@ public class JPrintPanel extends JPanel implements Printable,ActionListener{
 	private static final long serialVersionUID = -3337337068138131455L;
 
 	@Override
-	public int print(Graphics g, PageFormat pf, int pi) throws PrinterException {
+	public int print(Graphics g, PageFormat pf, int pi) {
 
 		if (pi >= 1) {
 			return Printable.NO_SUCH_PAGE;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java
index 91ca7571b4..307ddf3337 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java
@@ -61,7 +61,7 @@ public class MemoryMonitor extends JPanel {
 	boolean doControls;
 	JTextField tf;
 
-	public static final long serialVersionUID = 56289234782130l;
+	public static final long serialVersionUID = 56289234782130L;
 
 	public MemoryMonitor() {
 		setLayout(new BorderLayout());
@@ -103,28 +103,28 @@ public void mouseClicked(MouseEvent e) {
 	}
 
 
-	public class Surface extends JPanel implements Runnable {
+	public static class Surface extends JPanel implements Runnable {
 
-		public static final long serialVersionUID = 2387409854370432908l;
+		public static final long serialVersionUID = 2387409854370432908L;
 
 		public Thread thread;
 		public long sleepAmount = 1000;
 		private int w, h;
 		private BufferedImage bimg;
 		private Graphics2D big;
-		private Font font = new Font("Times New Roman", Font.PLAIN, 11);
-		private Runtime r = Runtime.getRuntime();
+		private final Font font = new Font("Times New Roman", Font.PLAIN, 11);
+		private final Runtime r = Runtime.getRuntime();
 		private int columnInc;
 		private int[] pts;
 		private int ptNum;
 		private int ascent, descent;
 		//private float freeMemory, totalMemory;
-		private Rectangle graphOutlineRect = new Rectangle();
-		private Rectangle2D mfRect = new Rectangle2D.Float();
-		private Rectangle2D muRect = new Rectangle2D.Float();
-		private Line2D graphLine = new Line2D.Float();
-		private Color graphColor = new Color(46, 139, 87);
-		private Color mfColor = new Color(0, 100, 0);
+		private final Rectangle graphOutlineRect = new Rectangle();
+		private final Rectangle2D mfRect = new Rectangle2D.Float();
+		private final Rectangle2D muRect = new Rectangle2D.Float();
+		private final Line2D graphLine = new Line2D.Float();
+		private final Color graphColor = new Color(46, 139, 87);
+		private final Color mfColor = new Color(0, 100, 0);
 		private String usedStr;
 
 
@@ -169,8 +169,8 @@ public void paint(Graphics g) {
 
 			// .. Draw allocated and used strings ..
 			big.setColor(Color.green);
-			big.drawString(String.valueOf((int) totalMemory/1024) + "K allocated",  4.0f, ascent+0.5f);
-			usedStr = String.valueOf(((int) (totalMemory - freeMemory))/1024)
+			big.drawString((int) totalMemory / 1024 + "K allocated",  4.0f, ascent+0.5f);
+			usedStr = ((int) (totalMemory - freeMemory)) / 1024
 					+ "K used";
 			big.drawString(usedStr, 4, h-descent);
 
@@ -234,7 +234,7 @@ public void paint(Graphics g) {
 				pts = new int[graphW];
 				ptNum = 0;
 			} else if (pts.length != graphW) {
-				int[] tmp = null;
+				int[] tmp;
 				if (ptNum < graphW) {
 					tmp = new int[ptNum];
 					System.arraycopy(pts, 0, tmp, 0, tmp.length);
@@ -259,9 +259,7 @@ public void paint(Graphics g) {
 				}
 				if (ptNum+2 == pts.length) {
 					// throw out oldest point
-					for (int j = 1;j < ptNum; j++) {
-						pts[j-1] = pts[j];
-					}
+					if (ptNum - 1 >= 0) System.arraycopy(pts, 1, pts, 0, ptNum - 1);
 					--ptNum;
 				} else {
 					ptNum++;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java
index 9484217af9..0abf5f2c52 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java
@@ -209,38 +209,34 @@ public static JMenuBar initJmolMenu(JFrame frame,
 	public static JMenuItem getDBResultMenuItem() {
 
 		ImageIcon saveicon = createImageIcon("/icons/kpdf.png");
-		JMenuItem saveI = null;
+		JMenuItem saveI;
 
 		if ( saveicon == null)
 			saveI = new JMenuItem(LOAD_DB_RESULTS);
 		else
 			saveI = new JMenuItem(LOAD_DB_RESULTS, saveicon);
 
-		saveI.addActionListener(new ActionListener() {
+		saveI.addActionListener(e -> {
+			final JFileChooser fc = new JFileChooser();
 
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				final JFileChooser fc = new JFileChooser();
-
-				//					In response to a button click:
-				int returnVal = fc.showOpenDialog(null);
-				if ( returnVal == JFileChooser.APPROVE_OPTION) {
-					File file = fc.getSelectedFile();
-
-					UserConfiguration config = WebStartMain.getWebStartConfig();
-					DBResultTable table = new DBResultTable();
-					table.show(file,config);
-				}
+			//					In response to a button click:
+			int returnVal = fc.showOpenDialog(null);
+			if ( returnVal == JFileChooser.APPROVE_OPTION) {
+				File file = fc.getSelectedFile();
 
+				UserConfiguration config = WebStartMain.getWebStartConfig();
+				DBResultTable table = new DBResultTable();
+				table.show(file,config);
 			}
-		} );
+
+		});
 
 		return saveI;
 	}
 
 	public static JMenuItem getShowPDBMenuItem() {
 		ImageIcon loadI = createImageIcon("/icons/background.png");
-		JMenuItem openI = null;
+		JMenuItem openI;
 
 		if ( loadI == null)
 			openI =new JMenuItem("Show By ID");
@@ -255,7 +251,7 @@ public static JMenuItem getShowPDBMenuItem() {
 
 	public static JMenuItem getOpenPDBMenuItem() {
 		ImageIcon loadI = createImageIcon("/icons/background.png");
-		JMenuItem openI = null;
+		JMenuItem openI;
 
 		if ( loadI == null)
 			openI =new JMenuItem("Open PDB file");
@@ -269,7 +265,7 @@ public static JMenuItem getOpenPDBMenuItem() {
 
 	public static JMenuItem getLoadMenuItem() {
 
-		JMenuItem loadF = null;
+		JMenuItem loadF;
 		ImageIcon loadI = createImageIcon("/icons/revert.png");
 		if ( loadI == null)
 			loadF = new JMenuItem(LOAD_ALIGNMENT_XML);
@@ -305,7 +301,7 @@ public static JMenuBar getAlignmentPanelMenu(JFrame frame,
 
 		ImageIcon saveicon = createImageIcon("/icons/filesave.png");
 
-		JMenuItem saveF = null;
+		JMenuItem saveF;
 
 		if (saveicon != null)
 			saveF = new JMenuItem("Save text display", saveicon);
@@ -400,7 +396,7 @@ public static JMenuBar getAlignmentTextMenu(JFrame frame,
 
 		ImageIcon saveicon = createImageIcon("/icons/filesave.png");
 
-		JMenuItem saveF = null;
+		JMenuItem saveF;
 
 		if (saveicon != null )
 			saveF = new JMenuItem("Save text display", saveicon);
@@ -487,7 +483,7 @@ public static JMenuItem getPrintMenuItem() {
 
 	public static JMenuItem getExportPDBMenuItem(AbstractAlignmentJmol parent) {
 		ImageIcon saveicon = createImageIcon("/icons/compfile.png");
-		JMenuItem exportI = null;
+		JMenuItem exportI;
 
 		if ( saveicon == null)
 			exportI = new JMenuItem("Export PDB file");
@@ -504,7 +500,7 @@ public static JMenuItem getSaveAlignmentMenuItem(AFPChain afpChain,
 			MultipleAlignment msa){
 
 		ImageIcon saveicon = createImageIcon("/icons/filesave.png");
-		JMenuItem saveF = null;
+		JMenuItem saveF;
 
 		if (saveicon == null)
 			saveF = new JMenuItem(SAVE_ALIGNMENT_XML);
@@ -522,7 +518,7 @@ public static JMenuItem getAboutMenuItem() {
 
 		ImageIcon helpIcon = createImageIcon("/icons/help.png");
 
-		JMenuItem aboutM = null;
+		JMenuItem aboutM;
 
 		if ( helpIcon == null)
 			aboutM = new  JMenuItem("About this Software");
@@ -530,14 +526,7 @@ public static JMenuItem getAboutMenuItem() {
 			aboutM = new  JMenuItem("About this Software", helpIcon);
 
 		aboutM.setMnemonic(KeyEvent.VK_A);
-		aboutM.addActionListener(new ActionListener(){
-
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				MenuCreator.showAboutDialog();
-
-			}
-		});
+		aboutM.addActionListener(e -> MenuCreator.showAboutDialog());
 		return aboutM;
 	}
 
@@ -547,7 +536,7 @@ private static JMenuItem getSystemInfoItem()
 
 		ImageIcon helpIcon = createImageIcon("/icons/help.png");
 
-		JMenuItem aboutM = null;
+		JMenuItem aboutM;
 
 		if ( helpIcon == null)
 			aboutM = new  JMenuItem("System Info");
@@ -555,14 +544,7 @@ private static JMenuItem getSystemInfoItem()
 			aboutM = new  JMenuItem("System Info", helpIcon);
 
 		aboutM.setMnemonic(KeyEvent.VK_S);
-		aboutM.addActionListener(new ActionListener(){
-
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				MenuCreator.showSystemInfo();
-
-			}
-		});
+		aboutM.addActionListener(e -> MenuCreator.showSystemInfo());
 		return aboutM;
 	}
 
@@ -579,15 +561,11 @@ public static JMenuItem getExitMenuItem(){
 			exitI = new JMenuItem("Quit",exitIcon);
 		exitI.setMnemonic(KeyEvent.VK_Q);
 		exitI.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_Q, keyMask));
-		exitI.addActionListener(new ActionListener(){
+		exitI.addActionListener(e -> {
+			String cmd = e.getActionCommand();
 
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				String cmd = e.getActionCommand();
-
-				if ( cmd.equals("Quit")){
-					System.exit(0);
-				}
+			if ( cmd.equals("Quit")){
+				System.exit(0);
 			}
 		});
 		return exitI;
@@ -607,14 +585,10 @@ public static JMenuItem getHelpMenuItem(){
 			helpM = new JMenuItem("Help", helpIcon);
 
 		helpM.setMnemonic(KeyEvent.VK_H);
-		helpM.addActionListener(new ActionListener(){
-
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				HelpDialog d = new HelpDialog();
-				d.showDialog();
+		helpM.addActionListener(e -> {
+			HelpDialog d = new HelpDialog();
+			d.showDialog();
 
-			}
 		});
 
 		return helpM;
@@ -635,7 +609,7 @@ public static JMenuItem getCloseMenuItem(JFrame frame){
 		closeI.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_W, keyMask));
 
 		class MyCloseListener implements ActionListener{
-			JFrame f;
+			final JFrame f;
 			MyCloseListener(JFrame frame){
 				f=frame;
 			}
@@ -713,14 +687,11 @@ protected static JMenuItem getPairwiseAlignmentMenuItem() {
 			pairI = new JMenuItem(PAIRWISE_ALIGN, alignIcon);
 		pairI.setMnemonic(KeyEvent.VK_N);
 		pairI.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_N, keyMask));
-		pairI.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				String cmd = e.getActionCommand();
+		pairI.addActionListener(e -> {
+			String cmd = e.getActionCommand();
 
-				if ( cmd.equals(PAIRWISE_ALIGN)){
-					MenuCreator.showPairDialog();
-				}
+			if ( cmd.equals(PAIRWISE_ALIGN)){
+				MenuCreator.showPairDialog();
 			}
 		});
 		return pairI;
@@ -736,14 +707,11 @@ protected static JMenuItem getMultipleAlignmentMenuItem() {
 			multipleI = new JMenuItem(MULTIPLE_ALIGN, alignIcon);
 		multipleI.setMnemonic(KeyEvent.VK_N);
 		multipleI.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_N, keyMask));
-		multipleI.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				String cmd = e.getActionCommand();
+		multipleI.addActionListener(e -> {
+			String cmd = e.getActionCommand();
 
-				if ( cmd.equals(MULTIPLE_ALIGN)){
-					MenuCreator.showMultipleDialog();
-				}
+			if ( cmd.equals(MULTIPLE_ALIGN)){
+				MenuCreator.showMultipleDialog();
 			}
 		});
 		return multipleI;
@@ -844,7 +812,7 @@ public static JMenuBar initAlignmentGUIMenu(JFrame frame) {
 	private static JMenuItem getMemoryMonitorItem() {
 		ImageIcon helpIcon = createImageIcon("/icons/help.png");
 
-		JMenuItem aboutM = null;
+		JMenuItem aboutM;
 
 		if ( helpIcon == null)
 			aboutM = new  JMenuItem("Memory Monitor");
@@ -852,14 +820,7 @@ private static JMenuItem getMemoryMonitorItem() {
 			aboutM = new  JMenuItem("Memory Monitor", helpIcon);
 
 		aboutM.setMnemonic(KeyEvent.VK_M);
-		aboutM.addActionListener(new ActionListener(){
-
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				MenuCreator.showMemoryMonitor();
-
-			}
-		});
+		aboutM.addActionListener(e -> MenuCreator.showMemoryMonitor());
 		return aboutM;
 	}
 
@@ -888,14 +849,7 @@ public void windowClosing(WindowEvent e) {}
 		Box b = Box.createHorizontalBox();
 		JButton b1 = new JButton("Run Garbage Collector");
 
-		b1.addActionListener(new ActionListener() {
-
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				System.gc();
-
-			}
-		});
+		b1.addActionListener(e -> System.gc());
 
 		b.add(b1);
 		b.add(Box.createGlue());
@@ -920,15 +874,11 @@ private static JMenuItem getConfigMenuItem() {
 		else
 			configI = new JMenuItem("Settings",configIcon);
 		configI.setMnemonic(KeyEvent.VK_S);
-		configI.addActionListener(new ActionListener(){
-
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				String cmd = e.getActionCommand();
+		configI.addActionListener(e -> {
+			String cmd = e.getActionCommand();
 
-				if ( cmd.equals("Settings")){
-					ConfigPDBInstallPanel.showDialog();
-				}
+			if ( cmd.equals("Settings")){
+				ConfigPDBInstallPanel.showDialog();
 			}
 		});
 		return configI;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.java
index e764a5e654..d3b2af0c6d 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.java
@@ -78,7 +78,7 @@ public void run() {
 				parent.getMultipleStructureAligner();
 		try {
 
-			List<Atom[]> atomArrays = new ArrayList<Atom[]>();
+			List<Atom[]> atomArrays = new ArrayList<>();
 			for (Structure s:structures){
 				Atom[] ca = StructureTools.getRepresentativeAtomArray(s);
 				atomArrays.add(ca);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.java
index 95a4ac248e..f523e9c574 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.java
@@ -64,14 +64,14 @@
  */
 public class MultipleAlignmentGUI extends JFrame {
 
-	private final static long serialVersionUID =0l;
+	private final static long serialVersionUID = 0L;
 	private final static String version = "1.0";
 
 	private MultipleStructureAligner multiple;
 	private StructureAlignment pairwise;
 
-	private SelectMultiplePanel tab;
-	private JTabbedPane tabPane;
+	private final SelectMultiplePanel tab;
+	private final JTabbedPane tabPane;
 
 	private Thread thread;
 	private AlignmentCalculationRunnable alicalc;
@@ -154,7 +154,7 @@ private Box setupPairwiseAlgorithm() {
 		algorithmList.setSelectedIndex(0);
 
 		Action actionAlgorithm = new AbstractAction("Algorithm") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			@Override
 			public void actionPerformed(ActionEvent evt) {
 				JComboBox cb = (JComboBox)evt.getSource();
@@ -165,7 +165,7 @@ public void actionPerformed(ActionEvent evt) {
 		algorithmList.addActionListener(actionAlgorithm);
 
 		Action paramAction = new AbstractAction("Parameters") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			@Override
 			public void actionPerformed(ActionEvent evt) {
 				StructureAlignment p = getPairwiseStructureAligner();
@@ -197,7 +197,7 @@ private Box setupMultipleAlgorithm() {
 		multList.setSelectedIndex(0);
 
 		Action actionMultiple = new AbstractAction("Algorithm") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			@Override
 			public void actionPerformed(ActionEvent evt) {
 				updateMultipleAlgorithm();
@@ -206,7 +206,7 @@ public void actionPerformed(ActionEvent evt) {
 		multList.addActionListener(actionMultiple);
 
 		Action paramAction = new AbstractAction("Parameters") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			@Override
 			public void actionPerformed(ActionEvent evt) {
 				MultipleStructureAligner m = getMultipleStructureAligner();
@@ -236,7 +236,7 @@ private Box initButtons(){
 		progress.setVisible(false);
 
 		Action action1 = new AbstractAction("Align") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			// This method is called when the button is pressed
 			@Override
 			public void actionPerformed(ActionEvent evt) {
@@ -246,7 +246,7 @@ public void actionPerformed(ActionEvent evt) {
 		JButton submitB = new JButton(action1);
 
 		Action action3 = new AbstractAction("Abort") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			// This method is called when the button is pressed
 			@Override
 			public void actionPerformed(ActionEvent evt) {
@@ -257,7 +257,7 @@ public void actionPerformed(ActionEvent evt) {
 		abortB.setEnabled(false);
 
 		Action action2 = new AbstractAction("Exit") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			// This method is called when the button is pressed
 			@Override
 			public void actionPerformed(ActionEvent evt) {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java
index fac312875f..44c000a2f4 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java
@@ -76,7 +76,7 @@ public class MultipleAlignmentJmolDisplay  {
 	public static List<String> getPDBresnum(int structNum,
 			MultipleAlignment multAln, Atom[] ca){
 
-		List<String> lst = new ArrayList<String>();
+		List<String> lst = new ArrayList<>();
 
 		for(Block block : multAln.getBlocks() ) {
 
@@ -99,11 +99,9 @@ else if (pos < ca.length) {
 	 *
 	 * @param multAln
 	 * @param jmol
-
-	 * @throws StructureException
 	 */
 	public static void showMultipleAligmentPanel(MultipleAlignment multAln,
-			AbstractAlignmentJmol jmol) throws StructureException {
+			AbstractAlignmentJmol jmol) {
 
 		MultipleAligPanel me = new MultipleAligPanel(multAln, jmol);
 		JFrame frame = new JFrame();
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyAlignmentLoadListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyAlignmentLoadListener.java
index 2a85930c27..366996b5fd 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyAlignmentLoadListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyAlignmentLoadListener.java
@@ -76,7 +76,7 @@ public void actionPerformed(ActionEvent evt) {
 				BufferedReader in = new BufferedReader(
 						new InputStreamReader(stream));
 
-				StringBuffer input = new StringBuffer();
+				StringBuilder input = new StringBuilder();
 				String str;
 				while ((str = in.readLine()) != null) {
 					input.append(str);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MySaveFileListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MySaveFileListener.java
index f93fba29df..3655a21b16 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MySaveFileListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MySaveFileListener.java
@@ -52,8 +52,8 @@
  */
 public class MySaveFileListener implements ActionListener {
 
-	private AFPChain afpChain;
-	private MultipleAlignment msa;
+	private final AFPChain afpChain;
+	private final MultipleAlignment msa;
 	private boolean printText;
 
 	public MySaveFileListener (AFPChain afpChain){
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ParameterGUI.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ParameterGUI.java
index 836e386ab4..e0bd5cbdf5 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ParameterGUI.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ParameterGUI.java
@@ -82,7 +82,7 @@ public ParameterGUI(ConfigStrucAligParams params, String algorithm) {
 		assert(names.size() == types.size());
 		assert(names.size() == helps.size());
 
-		textFields = new ArrayList<Component>();
+		textFields = new ArrayList<>();
 		Box vBox = Box.createVerticalBox();
 
 		for (int i = 0 ; i < keys.size(); i++){
@@ -146,32 +146,21 @@ public ParameterGUI(ConfigStrucAligParams params, String algorithm) {
 
 
 		JButton abort = new JButton("Cancel");
-		abort.addActionListener(new ActionListener(){
-			@Override
-			public void actionPerformed(ActionEvent event) {
-				destroy();
-				dispose();	         }
-		});
+		abort.addActionListener(event -> {
+			destroy();
+			dispose();	         });
 
 		JButton defaultB = new JButton("Default");
-		defaultB.addActionListener(new ActionListener(){
-			@Override
-			public void actionPerformed(ActionEvent event) {
-				setDefault();
-			}
-		});
+		defaultB.addActionListener(event -> setDefault());
 
 		JButton close = new JButton("Apply");
 
-		close.addActionListener(new ActionListener(){
-			@Override
-			public void actionPerformed(ActionEvent event) {
+		close.addActionListener(event -> {
 
-				storeParameters();
+			storeParameters();
 
-				destroy();
-				dispose();	         }
-		});
+			destroy();
+			dispose();	         });
 
 		Box hBox = Box.createHorizontalBox();
 		hBox.add(abort);
@@ -247,7 +236,7 @@ protected void storeParameters() {
 			Class type = types.get(i);
 			String key  = keys.get(i);
 			// String name = keys.get(i);
-			String value = null;
+			String value;
 			System.out.println(key);
 			if( type.isEnum() ) {
 				JComboBox field = (JComboBox)  textFields.get(i);
@@ -256,10 +245,10 @@ protected void storeParameters() {
 			} else if ( type == Boolean.class){
 				JComboBox field = (JComboBox)  textFields.get(i);
 				int sel = field.getSelectedIndex();
-				Boolean flag = true;
+				boolean flag = true;
 				if ( sel == 1 )
 					flag = false;
-				value = flag.toString();
+				value = Boolean.toString(flag);
 			} else {
 				JTextField field = (JTextField)textFields.get(i);
 				value = field.getText();
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/StructureLoaderThread.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/StructureLoaderThread.java
index fa4bba99f2..813866c8ad 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/StructureLoaderThread.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/StructureLoaderThread.java
@@ -52,7 +52,7 @@ protected String doInBackground() {
 		System.out.println("loading " + name );
 
 		AtomCache cache = new AtomCache(config.getPdbFilePath(),config.getCacheFilePath());
-		Structure s = null;
+		Structure s;
 		try {
 			if ( showBiolAssembly) {
 				s= StructureIO.getBiologicalAssembly(name);
@@ -97,29 +97,25 @@ public static void showProgressBar() {
 
 		if ( progressFrame == null){
 
-			SwingUtilities.invokeLater(new Runnable() {
+			SwingUtilities.invokeLater(() -> {
+				// TODO Auto-generated method stub
 
-				@Override
-				public void run() {
-					// TODO Auto-generated method stub
 
+				final JFrame frame = new JFrame("Loading ...");
+				final JProgressBar progressBar = new JProgressBar();
 
-					final JFrame frame = new JFrame("Loading ...");
-					final JProgressBar progressBar = new JProgressBar();
+				progressBar.setIndeterminate(true);
 
-					progressBar.setIndeterminate(true);
-
-					final JPanel contentPane = new JPanel();
-					contentPane.setBorder(BorderFactory.createEmptyBorder(10,10,10,10));
-					contentPane.setLayout(new BorderLayout());
-					contentPane.add(new JLabel("Loading ..."), BorderLayout.NORTH);
-					contentPane.add(progressBar, BorderLayout.CENTER);
-					frame.setContentPane(contentPane);
-					frame.pack();
-					frame.setLocationRelativeTo(null);
-					progressFrame = frame;
-					frame.setVisible(true);
-				}
+				final JPanel contentPane = new JPanel();
+				contentPane.setBorder(BorderFactory.createEmptyBorder(10,10,10,10));
+				contentPane.setLayout(new BorderLayout());
+				contentPane.add(new JLabel("Loading ..."), BorderLayout.NORTH);
+				contentPane.add(progressBar, BorderLayout.CENTER);
+				frame.setContentPane(contentPane);
+				frame.pack();
+				frame.setLocationRelativeTo(null);
+				progressFrame = frame;
+				frame.setVisible(true);
 			});
 
 		}
@@ -130,14 +126,10 @@ public void run() {
 	static JFrame progressFrame = null;
 	private void hideProgressBar() {
 
-		SwingUtilities.invokeLater(new Runnable() {
-
-			@Override
-			public void run() {
-				if ( progressFrame != null){
-					progressFrame.dispose();
-					progressFrame = null;
-				}
+		SwingUtilities.invokeLater(() -> {
+			if ( progressFrame != null){
+				progressFrame.dispose();
+				progressFrame = null;
 			}
 		});
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SystemInfo.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SystemInfo.java
index a899f485c8..dba6865fe1 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SystemInfo.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SystemInfo.java
@@ -212,11 +212,11 @@ public void addOneSystemProperty(
 					}
 				}
 				else if (isURLProperty(name)) {
-					StringBuffer    fixed = new StringBuffer();
+					StringBuilder fixed = new StringBuilder();
 					int     start   = 0;
-					int     hit     = 0;
+					int     hit;
 					while ((hit = propValue.indexOf('%', start)) >= 0) {
-						fixed.append(propValue.substring(start, hit));
+						fixed.append(propValue, start, hit);
 						int     value   =
 							Integer.parseInt(propValue.substring(hit + 1, hit + 3), 16);
 						fixed.append(((char) value));
@@ -280,22 +280,18 @@ public void showDialog(){
 		vBox= Box.createVerticalBox();
 		vBox.add(scroll);
 
-		txt.addHyperlinkListener(new HyperlinkListener(){
+		txt.addHyperlinkListener(e -> {
 
-			@Override
-		public void hyperlinkUpdate(HyperlinkEvent e) {
-
-				if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
-					String href = e.getDescription();
-					BrowserOpener.showDocument(href);
-				}
-				if ( e.getEventType() == HyperlinkEvent.EventType.ENTERED) {
-					// change the mouse curor
-					vBox.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
-				}
-				if (e.getEventType() == HyperlinkEvent.EventType.EXITED) {
-					vBox.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
-				}
+			if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+				String href = e.getDescription();
+				BrowserOpener.showDocument(href);
+			}
+			if ( e.getEventType() == HyperlinkEvent.EventType.ENTERED) {
+				// change the mouse curor
+				vBox.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+			}
+			if (e.getEventType() == HyperlinkEvent.EventType.EXITED) {
+				vBox.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
 			}
 		});
 
@@ -304,17 +300,14 @@ public void hyperlinkUpdate(HyperlinkEvent e) {
 
 		JButton close = new JButton("Close");
 
-		close.addActionListener(new ActionListener(){
-			@Override
-		public void actionPerformed(ActionEvent event) {
-				Object source = event.getSource();
+		close.addActionListener(event -> {
+			Object source = event.getSource();
 
-				JButton but = (JButton)source;
-				Container parent = but.getParent().getParent().getParent().getParent().getParent().getParent() ;
+			JButton but = (JButton)source;
+			Container parent = but.getParent().getParent().getParent().getParent().getParent().getParent() ;
 
-				JDialog dia = (JDialog) parent;
-				dia.dispose();
-			}
+			JDialog dia = (JDialog) parent;
+			dia.dispose();
 		});
 
 		Box hBoxb = Box.createHorizontalBox();
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.java
index 6eadd48dcd..bc98ffe2b8 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.java
@@ -63,11 +63,11 @@ public class AligPanel  extends JPrintPanel implements AlignmentPositionListener
 	private static final long serialVersionUID = -6892229111166263764L;
 
 	private AFPChain afpChain;
-	private AFPChainCoordManager coordManager ;
-	private Font seqFont;
-	private Font eqFont;
+	private final AFPChainCoordManager coordManager ;
+	private final Font seqFont;
+	private final Font eqFont;
 	private AbstractAlignmentJmol jmol;
-	private AligPanelMouseMotionListener mouseMoLi;
+	private final AligPanelMouseMotionListener mouseMoLi;
 
 	private BitSet selection;
 
@@ -89,7 +89,7 @@ public static void main(String[] args){
 
 		try {
 			BufferedReader in = new BufferedReader(new FileReader(file));
-			StringBuffer xml = new StringBuffer();
+			StringBuilder xml = new StringBuilder();
 			String str;
 			while ((str = in.readLine()) != null) {
 				xml.append(str);
@@ -279,7 +279,7 @@ public void paintComponent(Graphics g){
 
 						int colorPos = 0;
 						if (isFATCAT) {
-							int block = 0;
+							int block;
 							char s = symb[i];
 							try {
 								block = Integer.parseInt(String.valueOf(s)) - 1;
@@ -430,7 +430,7 @@ private void updateJmolDisplay() {
 
 		int size = afpChain.getAlnLength();
 
-		StringBuffer cmd = new StringBuffer("select ");
+		StringBuilder cmd = new StringBuilder("select ");
 
 		int nrSelected = 0;
 		try {
@@ -581,30 +581,42 @@ public void windowOpened(WindowEvent e) {
 public void actionPerformed(ActionEvent e) {
 		String cmd = e.getActionCommand();
 		// print is handled by superclass
-		if ( cmd.equals(MenuCreator.PRINT)) {
-			super.actionPerformed(e);
-		} else if (cmd.equals(MenuCreator.TEXT_ONLY)){
-			String result = AfpChainWriter.toWebSiteDisplay(afpChain, ca1, ca2);
-			DisplayAFP.showAlignmentImage(afpChain, result);
-		} else if ( cmd.equals(MenuCreator.PAIRS_ONLY)) {
-			String result = AfpChainWriter.toAlignedPairs(afpChain, ca1, ca2) ;
-			DisplayAFP.showAlignmentImage(afpChain, result);
-		} else if (cmd.equals(MenuCreator.FATCAT_TEXT)){
-			String result = afpChain.toFatcat(ca1, ca2);
-			result += AFPChain.newline;
-			result += afpChain.toRotMat();
-			DisplayAFP.showAlignmentImage(afpChain, result);
-		} else if ( cmd.equals(MenuCreator.SELECT_EQR)){
-			selectEQR();
-		} else if ( cmd.equals(MenuCreator.SIMILARITY_COLOR)){
-			colorBySimilarity(true);
-		} else if ( cmd.equals(MenuCreator.EQR_COLOR)){
-			colorBySimilarity(false);
-		} else if ( cmd.equals(MenuCreator.FATCAT_BLOCK)){
-			colorByAlignmentBlock();
-		}
-		else {
-			System.err.println("Unknown command:" + cmd);
+		switch (cmd) {
+			case MenuCreator.PRINT:
+				super.actionPerformed(e);
+				break;
+			case MenuCreator.TEXT_ONLY: {
+				String result = AfpChainWriter.toWebSiteDisplay(afpChain, ca1, ca2);
+				DisplayAFP.showAlignmentImage(afpChain, result);
+				break;
+			}
+			case MenuCreator.PAIRS_ONLY: {
+				String result = AfpChainWriter.toAlignedPairs(afpChain, ca1, ca2);
+				DisplayAFP.showAlignmentImage(afpChain, result);
+				break;
+			}
+			case MenuCreator.FATCAT_TEXT: {
+				String result = afpChain.toFatcat(ca1, ca2);
+				result += AFPChain.newline;
+				result += afpChain.toRotMat();
+				DisplayAFP.showAlignmentImage(afpChain, result);
+				break;
+			}
+			case MenuCreator.SELECT_EQR:
+				selectEQR();
+				break;
+			case MenuCreator.SIMILARITY_COLOR:
+				colorBySimilarity(true);
+				break;
+			case MenuCreator.EQR_COLOR:
+				colorBySimilarity(false);
+				break;
+			case MenuCreator.FATCAT_BLOCK:
+				colorByAlignmentBlock();
+				break;
+			default:
+				System.err.println("Unknown command:" + cmd);
+				break;
 		}
 
 	}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.java
index 9914f07d2a..83f1dda632 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.java
@@ -44,7 +44,7 @@ public class AligPanelMouseMotionListener implements MouseMotionListener, MouseL
 
 	public AligPanelMouseMotionListener(AligPanel parent){
 		this.parent = parent;
-		aligPosListeners = new ArrayList<AlignmentPositionListener>();
+		aligPosListeners = new ArrayList<>();
 		prevPos = -1;
 		isDragging = false;
 		selectionStart = null;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
index 1387bbd417..289ec9774c 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
@@ -77,11 +77,11 @@ public class MultipleAligPanel extends JPrintPanel
 	int size; 			//number of structures
 	int length; 		//number of aligned positions in sequence alignment
 
-	private Font seqFont;
-	private Font eqFont;
+	private final Font seqFont;
+	private final Font eqFont;
 
 	private AbstractAlignmentJmol jmol;
-	private MultipleAligPanelMouseMotionListener mouseMoLi;
+	private final MultipleAligPanelMouseMotionListener mouseMoLi;
 	private MultipleAlignmentCoordManager coordManager;
 
 	private BitSet selection;
@@ -120,10 +120,9 @@ public MultipleAligPanel(){
 	 * @param afpChain
 	 * @param ca1
 	 * @param ca2
-	 * @throws StructureException
 	 */
 	public MultipleAligPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
-			AbstractAlignmentJmol jmol) throws StructureException {
+			AbstractAlignmentJmol jmol) {
 
 		this();
 
@@ -139,7 +138,7 @@ public MultipleAligPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
 		this.multAln = ensemble.getMultipleAlignment(0);
 
 		//Create the sequence alignment and the structure-sequence mapping.
-		this.mapSeqToStruct = new ArrayList<Integer>();
+		this.mapSeqToStruct = new ArrayList<>();
 		this.alnSeq = MultipleAlignmentTools.getSequenceAlignment(
 				this.multAln, this.mapSeqToStruct);
 
@@ -162,7 +161,7 @@ public MultipleAligPanel(MultipleAlignment msa, AbstractAlignmentJmol jm) {
 		this.multAln = msa;
 
 		//Create the sequence alignment and the structure-sequence mapping.
-		this.mapSeqToStruct = new ArrayList<Integer>();
+		this.mapSeqToStruct = new ArrayList<>();
 		this.alnSeq = MultipleAlignmentTools.getSequenceAlignment(
 				this.multAln, this.mapSeqToStruct);
 
@@ -225,7 +224,7 @@ public void paintComponent(Graphics g){
 			else isGapped = true;
 
 			//Loop through every structure to get all the points
-			List<Point> points = new ArrayList<Point>();
+			List<Point> points = new ArrayList<>();
 			for (int str=0; str<size; str++) points.add(
 					coordManager.getPanelPos(str,i));
 			Point p1 = points.get(0);
@@ -351,7 +350,7 @@ private void updateJmolDisplay() {
 
 		if (jmol == null) return;
 
-		StringBuffer cmd = new StringBuffer("select ");
+		StringBuilder cmd = new StringBuilder("select ");
 		int nrSelected = 0;
 		for (int i=0; i<length; i++){
 			if (selection.get(i)){
@@ -437,27 +436,40 @@ public void windowOpened(WindowEvent e) {}
 	@Override
 	public void actionPerformed(ActionEvent e) {
 		String cmd = e.getActionCommand();
-		if ( cmd.equals(MenuCreator.PRINT)) {
-			super.actionPerformed(e);
-		} else if (cmd.equals(MenuCreator.FASTA_FORMAT)){
-			String result = MultipleAlignmentWriter.toFASTA(multAln);
-			MultipleAlignmentJmolDisplay.showAlignmentImage(multAln, result);
-		} else if ( cmd.equals(MenuCreator.PAIRS_ONLY)) {
-			String result = MultipleAlignmentWriter.toAlignedResidues(multAln);
-			MultipleAlignmentJmolDisplay.showAlignmentImage(multAln, result);
-		} else if (cmd.equals(MenuCreator.FATCAT_TEXT)){
-			String result = MultipleAlignmentWriter.toFatCat(multAln);
-			MultipleAlignmentJmolDisplay.showAlignmentImage(multAln, result);
-		} else if (cmd.equals(MenuCreator.SELECT_EQR)){
-			selectEQR();
-		} else if ( cmd.equals(MenuCreator.SIMILARITY_COLOR)){
-			colorBySimilarity(true);
-		} else if (cmd.equals(MenuCreator.EQR_COLOR)){
-			colorBySimilarity(false);
-		} else if ( cmd.equals(MenuCreator.FATCAT_BLOCK)){
-			colorByAlignmentBlock();
-		} else {
-			System.err.println("Unknown command:" + cmd);
+		switch (cmd) {
+			case MenuCreator.PRINT:
+				super.actionPerformed(e);
+				break;
+			case MenuCreator.FASTA_FORMAT: {
+				String result = MultipleAlignmentWriter.toFASTA(multAln);
+				MultipleAlignmentJmolDisplay.showAlignmentImage(multAln, result);
+				break;
+			}
+			case MenuCreator.PAIRS_ONLY: {
+				String result = MultipleAlignmentWriter.toAlignedResidues(multAln);
+				MultipleAlignmentJmolDisplay.showAlignmentImage(multAln, result);
+				break;
+			}
+			case MenuCreator.FATCAT_TEXT: {
+				String result = MultipleAlignmentWriter.toFatCat(multAln);
+				MultipleAlignmentJmolDisplay.showAlignmentImage(multAln, result);
+				break;
+			}
+			case MenuCreator.SELECT_EQR:
+				selectEQR();
+				break;
+			case MenuCreator.SIMILARITY_COLOR:
+				colorBySimilarity(true);
+				break;
+			case MenuCreator.EQR_COLOR:
+				colorBySimilarity(false);
+				break;
+			case MenuCreator.FATCAT_BLOCK:
+				colorByAlignmentBlock();
+				break;
+			default:
+				System.err.println("Unknown command:" + cmd);
+				break;
 		}
 	}
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanelMouseMotionListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanelMouseMotionListener.java
index c217458ffb..d4f605dcc8 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanelMouseMotionListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanelMouseMotionListener.java
@@ -42,7 +42,7 @@ public class MultipleAligPanelMouseMotionListener
 implements MouseMotionListener, MouseListener {
 
 	private MultipleAligPanel parent;
-	private List<AlignmentPositionListener> aligPosListeners;
+	private final List<AlignmentPositionListener> aligPosListeners;
 	private int prevPos;
 
 	private boolean isDragging ;
@@ -52,7 +52,7 @@ public class MultipleAligPanelMouseMotionListener
 
 	public MultipleAligPanelMouseMotionListener(MultipleAligPanel parent){
 		this.parent = parent;
-		aligPosListeners = new ArrayList<AlignmentPositionListener>();
+		aligPosListeners = new ArrayList<>();
 		prevPos = -1;
 		isDragging = false;
 		selectionStart = null;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAlignmentCoordManager.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAlignmentCoordManager.java
index 35c65c524c..e7f562487e 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAlignmentCoordManager.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAlignmentCoordManager.java
@@ -31,8 +31,8 @@
  */
 public class MultipleAlignmentCoordManager {
 
-	private int alignmentLength;     	//number of aligned residues
-	private int alignmentSize;			//number of strucures aligned
+	private final int alignmentLength;     	//number of aligned residues
+	private final int alignmentSize;			//number of strucures aligned
 
 	/**
 	 * Constructor.
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/AutoSuggestProvider.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/AutoSuggestProvider.java
index 88352df175..64105ca298 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/AutoSuggestProvider.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/AutoSuggestProvider.java
@@ -38,31 +38,31 @@ public interface AutoSuggestProvider {
 	 * @param userInput
 	 * @return list of suggestions
 	 */
-	public Vector<String> getSuggestion(String userInput);
+    Vector<String> getSuggestion(String userInput);
 
 
 	/** set the maximum number of suggestions to return
 	 *
 	 * @param maxNrSuggestions
 	 */
-	public void setMaxNrSuggestions(int maxNrSuggestions);
+    void setMaxNrSuggestions(int maxNrSuggestions);
 
 
 	/** Get the maximun nr of suggestions
 	 *
 	 * @return maxNrSuggestions
 	 */
-	public int getMaxNrSuggestions();
+    int getMaxNrSuggestions();
 
 
 	/** reset all suggestions
 	 *
 	 */
-	public void clear();
+    void clear();
 
 
 	/** Interrupt searching for suggestions
 	 *
 	 */
-	public void stop();
+    void stop();
 }
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/DefaultAutoSuggestProvider.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/DefaultAutoSuggestProvider.java
index 045ff5ce8d..1a87aa786a 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/DefaultAutoSuggestProvider.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/DefaultAutoSuggestProvider.java
@@ -30,7 +30,7 @@ public class DefaultAutoSuggestProvider implements AutoSuggestProvider {
 
 	@Override
 	public Vector<String> getSuggestion(String userInput) {
-		Vector<String> data = new Vector<String>();
+		Vector<String> data = new Vector<>();
 
 		data.add(userInput + " no AutoSuggestProvider registered yet!");
 		return data;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java
index 128ee39149..1cbaebf6c1 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java
@@ -247,7 +247,7 @@ private void init(){
 		lastWord = "";
 		regular = getFont();
 		busy = new Font(getFont().getName(), Font.ITALIC, getFont().getSize());
-		suggestions = new Vector<String>();
+		suggestions = new Vector<>();
 		defaultText = DEFAULT_TEXT;
 
 
@@ -340,7 +340,7 @@ private void updateLocation() {
 	 */
 	private class SuggestionFetcher extends SwingWorker<String, Object> {
 		/** flag used to stop the thread */
-		private AtomicBoolean stop = new AtomicBoolean(false);
+		private final AtomicBoolean stop = new AtomicBoolean(false);
 
 		String previousWord;
 		/**
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java
index d90fd0380f..24c47bb544 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java
@@ -47,7 +47,7 @@ public Vector<String> getSuggestion(String userInput) {
 
 		long timeS = System.currentTimeMillis();
 
-		List<ScopDomain> domains = new ArrayList<ScopDomain>();
+		List<ScopDomain> domains;
 
 		domains = getPossibleScopDomains(userInput);
 
@@ -55,7 +55,7 @@ public Vector<String> getSuggestion(String userInput) {
 
 		// convert domains to Strings
 
-		Vector<String> v=new Vector<String>();
+		Vector<String> v= new Vector<>();
 
 		int counter = 0;
 		for ( ScopDomain d : domains){
@@ -82,7 +82,7 @@ public Vector<String> getSuggestion(String userInput) {
 
 	private List<ScopDomain> getPossibleScopDomains(String userInput) {
 
-		List<ScopDomain> domains = new ArrayList<ScopDomain>();
+		List<ScopDomain> domains = new ArrayList<>();
 
 		ScopDatabase scop = ScopFactory.getSCOP();
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfo.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfo.java
index e90fafcf43..b4c27afb9b 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfo.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfo.java
@@ -40,7 +40,7 @@ public class AtomInfo {
 	String residueNumber;
 	int modelNumber;
 
-	private static Pattern inscodePatter ;
+	private static final Pattern inscodePatter ;
 	static {
 		inscodePatter = Pattern.compile("([0-9]+)([a-zA-Z]*)?");
 	}
@@ -106,17 +106,17 @@ public void setAtomName(String name) {
 
 	@Override
 	public String toString() {
-		String aa3 = "";
+		String aa3;
 		boolean printResName = true;
 
-		String chain1 ="";
-		String res1 = "";
+		String chain1;
+		String res1;
 
 		aa3 = residueName;
 		res1 = residueNumber;
 		chain1 = chainId;
 
-		StringBuffer buf = new StringBuffer();
+		StringBuilder buf = new StringBuilder();
 		if ( printResName) {
 			if ( !aa3.equals("")){
 				buf.append("[");
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfoParser.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfoParser.java
index ac4dd69120..ff8561276f 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfoParser.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfoParser.java
@@ -37,7 +37,7 @@ public class AtomInfoParser {
 
 	static {
 
-		String numberPattern = "\\[(.*)\\]([0-9^a-zA-Z]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?";
+		String numberPattern = "\\[(.*)]([0-9^a-zA-Z]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?";
 		pattern = Pattern.compile(numberPattern);
 
 	}
@@ -94,12 +94,12 @@ public static AtomInfo parse(String jmolAtomInfo){
 
 		String ci = " ";
 		if (chainId != null)
-			ci = chainId.substring(1,chainId.length());
+			ci = chainId.substring(1);
 		info.setChainId(ci);
 
 		int mn = 1;
 		if ( modelNumber != null)
-			mn = Integer.parseInt(modelNumber.substring(1,modelNumber.length()));
+			mn = Integer.parseInt(modelNumber.substring(1));
 		info.setModelNumber(mn);
 
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java
index b8b37c6251..57925259de 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java
@@ -135,9 +135,9 @@ public void setStructure(final Structure s, boolean useMmtf) {
 			try (
 					PipedOutputStream out = new PipedOutputStream();
 					// Viewer requires a BufferedInputStream for reflection
-					InputStream in = new BufferedInputStream(new PipedInputStream(out));
-					) {
-				new Thread((Runnable)() -> {
+					InputStream in = new BufferedInputStream(new PipedInputStream(out))
+			) {
+				new Thread(() -> {
 					try {
 						MmtfActions.writeToOutputStream(s,out);
 					} catch (Exception e) {
@@ -171,39 +171,7 @@ public void setStructure(final Structure s) {
 	 */
 	public void jmolColorByChain(){
 		String script =
-				"function color_by_chain(objtype, color_list) {"+ String.format("%n") +
-				""+ String.format("%n") +
-				"		 if (color_list) {"+ String.format("%n") +
-				"		   if (color_list.type == \"string\") {"+ String.format("%n") +
-				"		     color_list = color_list.split(\",\").trim();"+ String.format("%n") +
-				"		   }"+ String.format("%n") +
-				"		 } else {"+ String.format("%n") +
-				"		   color_list = [\"104BA9\",\"AA00A2\",\"C9F600\",\"FFA200\",\"284A7E\",\"7F207B\",\"9FB82E\",\"BF8B30\",\"052D6E\",\"6E0069\",\"83A000\",\"A66A00\",\"447BD4\",\"D435CD\",\"D8FA3F\",\"FFBA40\",\"6A93D4\",\"D460CF\",\"E1FA71\",\"FFCC73\"];"+ String.format("%n") +
-				"		 }"+ String.format("%n") +
-
-				"		 var cmd2 = \"\";"+ String.format("%n") +
-
-				"		 if (!objtype) {"+ String.format("%n") +
-				"		   var type_list  = [ \"backbone\",\"cartoon\",\"dots\",\"halo\",\"label\",\"meshribbon\",\"polyhedra\",\"rocket\",\"star\",\"strand\",\"strut\",\"trace\"];"+ String.format("%n") +
-				"		   cmd2 = \"color \" + type_list.join(\" none; color \") + \" none;\";"+ String.format("%n") +
-				"		   objtype = \"atoms\";"+ String.format("%n") +
-
-				"		 }"+ String.format("%n") +
-
-				"		 var chain_list  = script(\"show chain\").trim().lines;"+ String.format("%n") +
-				"		 var chain_count = chain_list.length;"+ String.format("%n") +
-
-				"		 var color_count = color_list.length;"+ String.format("%n") +
-				"		 var sel = {selected};"+ String.format("%n") +
-				"		 var cmds = \"\";"+ String.format("%n") +
-
-
-				"		 for (var chain_number=1; chain_number<=chain_count; chain_number++) {"+ String.format("%n") +
-				"		   // remember, Jmol arrays start with 1, but % can return 0"+ String.format("%n") +
-				"		   cmds += \"select sel and :\" + chain_list[chain_number] + \";color \" + objtype + \" [x\" + color_list[(chain_number-1) % color_count + 1] + \"];\" + cmd2;"+ String.format("%n") +
-				"		 }"+ String.format("%n") +
-				"		 script INLINE @{cmds + \"select sel\"}"+ String.format("%n") +
-				"}";
+				"function color_by_chain(objtype, color_list) {" + String.format("%n") + String.format("%n") + "		 if (color_list) {" + String.format("%n") + "		   if (color_list.type == \"string\") {" + String.format("%n") + "		     color_list = color_list.split(\",\").trim();" + String.format("%n") + "		   }" + String.format("%n") + "		 } else {" + String.format("%n") + "		   color_list = [\"104BA9\",\"AA00A2\",\"C9F600\",\"FFA200\",\"284A7E\",\"7F207B\",\"9FB82E\",\"BF8B30\",\"052D6E\",\"6E0069\",\"83A000\",\"A66A00\",\"447BD4\",\"D435CD\",\"D8FA3F\",\"FFBA40\",\"6A93D4\",\"D460CF\",\"E1FA71\",\"FFCC73\"];" + String.format("%n") + "		 }" + String.format("%n") + "		 var cmd2 = \"\";" + String.format("%n") + "		 if (!objtype) {" + String.format("%n") + "		   var type_list  = [ \"backbone\",\"cartoon\",\"dots\",\"halo\",\"label\",\"meshribbon\",\"polyhedra\",\"rocket\",\"star\",\"strand\",\"strut\",\"trace\"];" + String.format("%n") + "		   cmd2 = \"color \" + type_list.join(\" none; color \") + \" none;\";" + String.format("%n") + "		   objtype = \"atoms\";" + String.format("%n") + "		 }" + String.format("%n") + "		 var chain_list  = script(\"show chain\").trim().lines;" + String.format("%n") + "		 var chain_count = chain_list.length;" + String.format("%n") + "		 var color_count = color_list.length;" + String.format("%n") + "		 var sel = {selected};" + String.format("%n") + "		 var cmds = \"\";" + String.format("%n") + "		 for (var chain_number=1; chain_number<=chain_count; chain_number++) {" + String.format("%n") + "		   // remember, Jmol arrays start with 1, but % can return 0" + String.format("%n") + "		   cmds += \"select sel and :\" + chain_list[chain_number] + \";color \" + objtype + \" [x\" + color_list[(chain_number-1) % color_count + 1] + \"];\" + cmd2;" + String.format("%n") + "		 }" + String.format("%n") + "		 script INLINE @{cmds + \"select sel\"}" + String.format("%n") + "}";
 
 		executeCmd(script);
 	}
@@ -229,66 +197,86 @@ public void actionPerformed(ActionEvent event) {
 
 		String selectLigand = "select ligand;wireframe 0.16;spacefill 0.5; color cpk ;";
 
-		if ( value.equals("Cartoon")){
-			String script = "hide null; select all;  spacefill off; wireframe off; backbone off;" +
-					" cartoon on; " +
-					" select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
-					" select *.FE; spacefill 0.7; color cpk ; " +
-					" select *.CU; spacefill 0.7; color cpk ; " +
-					" select *.ZN; spacefill 0.7; color cpk ; " +
-					" select all; ";
-			this.executeCmd(script);
-		} else if (value.equals("Backbone")){
-			String script = "hide null; select all; spacefill off; wireframe off; backbone 0.4;" +
-					" cartoon off; " +
-					" select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
-					" select *.FE; spacefill 0.7; color cpk ; " +
-					" select *.CU; spacefill 0.7; color cpk ; " +
-					" select *.ZN; spacefill 0.7; color cpk ; " +
-					" select all; ";
-			this.executeCmd(script);
-		} else if (value.equals("CPK")){
-			String script = "hide null; select all; spacefill off; wireframe off; backbone off;" +
-					" cartoon off; cpk on;" +
-					" select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
-					" select *.FE; spacefill 0.7; color cpk ; " +
-					" select *.CU; spacefill 0.7; color cpk ; " +
-					" select *.ZN; spacefill 0.7; color cpk ; " +
-					" select all; ";
-			this.executeCmd(script);
-
-		} else if (value.equals("Ligands")){
-			this.executeCmd("restrict ligand; cartoon off; wireframe on;  display selected;");
-		} else if (value.equals("Ligands and Pocket")){
-			this.executeCmd(" select within (6.0,ligand); cartoon off; wireframe on; backbone off; display selected; ");
-		} else if ( value.equals("Ball and Stick")){
-			String script = "hide null; restrict not water;  wireframe 0.2; spacefill 25%;" +
-					" cartoon off; backbone off; " +
-					" select ligand; wireframe 0.16; spacefill 0.5; color cpk; " +
-					" select *.FE; spacefill 0.7; color cpk ; " +
-					" select *.CU; spacefill 0.7; color cpk ; " +
-					" select *.ZN; spacefill 0.7; color cpk ; " +
-					" select all; ";
-			this.executeCmd(script);
-		} else if ( value.equals("By Chain")){
-			jmolColorByChain();
-			String script = "hide null; select all;set defaultColors Jmol; color_by_chain(\"cartoon\"); color_by_chain(\"\"); " + selectLigand + "; select all; ";
-			this.executeCmd(script);
-		} else if ( value.equals("Rainbow")) {
-			this.executeCmd("hide null; select all; set defaultColors Jmol; color group; color cartoon group; " + selectLigand + "; select all; " );
-		} else if ( value.equals("Secondary Structure")){
-			this.executeCmd("hide null; select all; set defaultColors Jmol; color structure; color cartoon structure;" + selectLigand + "; select all; " );
-
-		} else if ( value.equals("By Element")){
-			this.executeCmd("hide null; select all; set defaultColors Jmol; color cpk; color cartoon cpk; " + selectLigand + "; select all; ");
-		} else if ( value.equals("By Amino Acid")){
-			this.executeCmd("hide null; select all; set defaultColors Jmol; color amino; color cartoon amino; " + selectLigand + "; select all; " );
-		} else if ( value.equals("Hydrophobicity") ){
-			this.executeCmd("hide null; set defaultColors Jmol; select hydrophobic; color red; color cartoon red; select not hydrophobic ; color blue ; color cartoon blue; "+ selectLigand+"; select all; ");
-		} else if ( value.equals("Suggest Domains")){
-			colorByPDP();
-		} else if ( value.equals("Show SCOP Domains")){
-			colorBySCOP();
+		switch (value) {
+			case "Cartoon": {
+				String script = "hide null; select all;  spacefill off; wireframe off; backbone off;" +
+						" cartoon on; " +
+						" select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
+						" select *.FE; spacefill 0.7; color cpk ; " +
+						" select *.CU; spacefill 0.7; color cpk ; " +
+						" select *.ZN; spacefill 0.7; color cpk ; " +
+						" select all; ";
+				this.executeCmd(script);
+				break;
+			}
+			case "Backbone": {
+				String script = "hide null; select all; spacefill off; wireframe off; backbone 0.4;" +
+						" cartoon off; " +
+						" select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
+						" select *.FE; spacefill 0.7; color cpk ; " +
+						" select *.CU; spacefill 0.7; color cpk ; " +
+						" select *.ZN; spacefill 0.7; color cpk ; " +
+						" select all; ";
+				this.executeCmd(script);
+				break;
+			}
+			case "CPK": {
+				String script = "hide null; select all; spacefill off; wireframe off; backbone off;" +
+						" cartoon off; cpk on;" +
+						" select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
+						" select *.FE; spacefill 0.7; color cpk ; " +
+						" select *.CU; spacefill 0.7; color cpk ; " +
+						" select *.ZN; spacefill 0.7; color cpk ; " +
+						" select all; ";
+				this.executeCmd(script);
+
+				break;
+			}
+			case "Ligands":
+				this.executeCmd("restrict ligand; cartoon off; wireframe on;  display selected;");
+				break;
+			case "Ligands and Pocket":
+				this.executeCmd(" select within (6.0,ligand); cartoon off; wireframe on; backbone off; display selected; ");
+				break;
+			case "Ball and Stick": {
+				String script = "hide null; restrict not water;  wireframe 0.2; spacefill 25%;" +
+						" cartoon off; backbone off; " +
+						" select ligand; wireframe 0.16; spacefill 0.5; color cpk; " +
+						" select *.FE; spacefill 0.7; color cpk ; " +
+						" select *.CU; spacefill 0.7; color cpk ; " +
+						" select *.ZN; spacefill 0.7; color cpk ; " +
+						" select all; ";
+				this.executeCmd(script);
+				break;
+			}
+			case "By Chain": {
+				jmolColorByChain();
+				String script = "hide null; select all;set defaultColors Jmol; color_by_chain(\"cartoon\"); color_by_chain(\"\"); " + selectLigand + "; select all; ";
+				this.executeCmd(script);
+				break;
+			}
+			case "Rainbow":
+				this.executeCmd("hide null; select all; set defaultColors Jmol; color group; color cartoon group; " + selectLigand + "; select all; ");
+				break;
+			case "Secondary Structure":
+				this.executeCmd("hide null; select all; set defaultColors Jmol; color structure; color cartoon structure;" + selectLigand + "; select all; ");
+
+				break;
+			case "By Element":
+				this.executeCmd("hide null; select all; set defaultColors Jmol; color cpk; color cartoon cpk; " + selectLigand + "; select all; ");
+				break;
+			case "By Amino Acid":
+				this.executeCmd("hide null; select all; set defaultColors Jmol; color amino; color cartoon amino; " + selectLigand + "; select all; ");
+				break;
+			case "Hydrophobicity":
+				this.executeCmd("hide null; set defaultColors Jmol; select hydrophobic; color red; color cartoon red; select not hydrophobic ; color blue ; color cartoon blue; " + selectLigand + "; select all; ");
+				break;
+			case "Suggest Domains":
+				colorByPDP();
+				break;
+			case "Show SCOP Domains":
+				colorBySCOP();
+				break;
 		}
 		evalString("restore selection; ");
 	}
@@ -361,7 +349,7 @@ private void colorByPDP() {
 					Group startG = ca[start].getGroup();
 					Group endG = ca[end].getGroup();
 					logger.debug("   Segment: " +startG.getResidueNumber() +":" + startG.getChainId() + " - " + endG.getResidueNumber()+":"+endG.getChainId() + " " + s);
-					String j1 = startG.getResidueNumber()+"";
+					String j1 = String.valueOf(startG.getResidueNumber());
 					String j2 = endG.getResidueNumber()+":"+endG.getChainId();
 					String script = " select  " +j1 +"-" +j2 +"/1;";
 					script += " color [" + c1.getRed() + ","+c1.getGreen() + "," +c1.getBlue()+"];";
@@ -407,7 +395,7 @@ public void destroy(){
 	}
 
 	public static class JmolLoggerAdapter implements LoggerInterface {
-		private Logger slf;
+		private final Logger slf;
 		public JmolLoggerAdapter(Logger slf) {
 			this.slf=slf;
 		}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolTools.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolTools.java
index 5a42f37cad..1630276b46 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolTools.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolTools.java
@@ -38,7 +38,7 @@ public static final String getPdbInfo(Atom a){
 		return getPdbInfo(a,true);
 	}
 
-	private static Pattern inscodePatter ;
+	private static final Pattern inscodePatter ;
 	static {
 		inscodePatter = Pattern.compile("([0-9]+)([a-zA-Z]*)?");
 	}
@@ -80,7 +80,7 @@ public static final String getPdbInfo(Atom a, boolean printResName){
 			}
 		}
 
-		StringBuffer buf = new StringBuffer();
+		StringBuilder buf = new StringBuilder();
 		if ( printResName) {
 			if ( !aa3.equals("")){
 				buf.append("[");
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
index fc7d209312..3b0a119ae1 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
@@ -76,8 +76,8 @@ public class MultipleAlignmentJmol extends AbstractAlignmentJmol {
 
 	private MultipleAlignment multAln;
 	private List<Atom[]> transformedAtoms;
-	private JCheckBox colorByBlocks;
-	private List<JCheckBox> selectedStructures;
+	private final JCheckBox colorByBlocks;
+	private final List<JCheckBox> selectedStructures;
 
 	private static final String LIGAND_DISPLAY_SCRIPT = "select ligand; wireframe 40; spacefill 120; color CPK;";
 
@@ -113,7 +113,7 @@ public MultipleAlignmentJmol(MultipleAlignment msa,
 		frame.setJMenuBar(menu);
 		this.multAln = msa;
 		this.transformedAtoms = rotatedAtoms;
-		this.selectedStructures = new ArrayList<JCheckBox>();
+		this.selectedStructures = new ArrayList<>();
 
 		frame.addWindowListener(new WindowAdapter() {
 
@@ -168,23 +168,19 @@ public void windowClosing(WindowEvent e) {
 			vBox.add(modelSelection);
 
 			JButton show = new JButton("Show Only: ");
-			show.addActionListener(new ActionListener() {
-
-				@Override
-				public void actionPerformed(ActionEvent e) {
-					jmolPanel.evalString("save selection;");
-					String cmd = getJmolString(multAln,
-							transformedAtoms, colorPalette,
-							colorByBlocks.isSelected());
-					cmd += "; restrict ";
-					for (int st = 0; st < multAln.size(); st++) {
-						if (selectedStructures.get(st).isSelected()) {
-							cmd += "*/" + (st + 1) + ", ";
-						}
+			show.addActionListener(e -> {
+				jmolPanel.evalString("save selection;");
+				String cmd = getJmolString(multAln,
+						transformedAtoms, colorPalette,
+						colorByBlocks.isSelected());
+				cmd += "; restrict ";
+				for (int st = 0; st < multAln.size(); st++) {
+					if (selectedStructures.get(st).isSelected()) {
+						cmd += "*/" + (st + 1) + ", ";
 					}
-					cmd += "none;";
-					jmolPanel.executeCmd(cmd + " restore selection;");
 				}
+				cmd += "none;";
+				jmolPanel.executeCmd(cmd + " restore selection;");
 			});
 			modelSelection.add(show);
 
@@ -228,29 +224,26 @@ public void actionPerformed(ActionEvent e) {
 		String[] cPalette = { "Spectral", "Set1", "Set2", "Pastel" };
 		JComboBox<String> palette = new JComboBox<>(cPalette);
 
-		palette.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-
-				@SuppressWarnings("unchecked")
-				JComboBox<String> source = (JComboBox<String>) e.getSource();
-				String value = source.getSelectedItem().toString();
-				evalString("save selection; select *; color grey; "
-						+ "select ligand; color CPK;");
-
-				if (value == "Set1") {
-					colorPalette = ColorBrewer.Set1;
-				} else if (value == "Set2") {
-					colorPalette = ColorBrewer.Set2;
-				} else if (value == "Spectral") {
-					colorPalette = ColorBrewer.Spectral;
-				} else if (value == "Pastel") {
-					colorPalette = ColorBrewer.Pastel1;
-				}
-				String script = getJmolString(multAln, transformedAtoms,
-						colorPalette, colorByBlocks.isSelected());
-				evalString(script + "; restore selection; ");
+		palette.addActionListener(e -> {
+
+			@SuppressWarnings("unchecked")
+			JComboBox<String> source = (JComboBox<String>) e.getSource();
+			String value = source.getSelectedItem().toString();
+			evalString("save selection; select *; color grey; "
+					+ "select ligand; color CPK;");
+
+			if (value == "Set1") {
+				colorPalette = ColorBrewer.Set1;
+			} else if (value == "Set2") {
+				colorPalette = ColorBrewer.Set2;
+			} else if (value == "Spectral") {
+				colorPalette = ColorBrewer.Spectral;
+			} else if (value == "Pastel") {
+				colorPalette = ColorBrewer.Pastel1;
 			}
+			String script = getJmolString(multAln, transformedAtoms,
+					colorPalette, colorByBlocks.isSelected());
+			evalString(script + "; restore selection; ");
 		});
 
 		hBox1.add(Box.createGlue());
@@ -262,45 +255,32 @@ public void actionPerformed(ActionEvent e) {
 		hBox2.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
 
 		JButton resetDisplay = new JButton("Reset Display");
-		resetDisplay.addActionListener(new ActionListener() {
+		resetDisplay.addActionListener(e -> {
+			logger.info("reset!!");
+			jmolPanel.executeCmd("restore STATE state_1");
 
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				logger.info("reset!!");
-				jmolPanel.executeCmd("restore STATE state_1");
-
-			}
 		});
 
 		hBox2.add(resetDisplay);
 		hBox2.add(Box.createGlue());
 
 		JCheckBox toggleSelection = new JCheckBox("Show Selection");
-		toggleSelection.addItemListener(new ItemListener() {
+		toggleSelection.addItemListener(e -> {
+			boolean showSelection = (e.getStateChange() == ItemEvent.SELECTED);
 
-			@Override
-			public void itemStateChanged(ItemEvent e) {
-				boolean showSelection = (e.getStateChange() == ItemEvent.SELECTED);
-
-				if (showSelection) {
-					jmolPanel.executeCmd("set display selected");
-				} else
-					jmolPanel.executeCmd("set display off");
-			}
+			if (showSelection) {
+				jmolPanel.executeCmd("set display selected");
+			} else
+				jmolPanel.executeCmd("set display off");
 		});
 		hBox2.add(toggleSelection);
 		hBox2.add(Box.createGlue());
 
 		colorByBlocks = new JCheckBox("Color By Block");
-		colorByBlocks.addItemListener(new ItemListener() {
-			@Override
-			public void itemStateChanged(ItemEvent e) {
-				evalString("save selection; "
-						+ getJmolString(multAln, transformedAtoms,
-								colorPalette, colorByBlocks.isSelected())
-						+ "; restore selection;");
-			}
-		});
+		colorByBlocks.addItemListener(e -> evalString("save selection; "
+				+ getJmolString(multAln, transformedAtoms,
+						colorPalette, colorByBlocks.isSelected())
+				+ "; restore selection;"));
 
 		hBox2.add(colorByBlocks);
 		hBox2.add(Box.createGlue());
@@ -375,37 +355,45 @@ public void actionPerformed(ActionEvent ae) {
 			return;
 		}
 		try {
-			if (cmd.equals(MenuCreator.TEXT_ONLY)) {
-				logger.warn("Option not available for MultipleAlignments");
-
-			} else if (cmd.equals(MenuCreator.PAIRS_ONLY)) {
-				String result = MultipleAlignmentWriter
-						.toAlignedResidues(multAln);
-				MultipleAlignmentJmolDisplay
-						.showAlignmentImage(multAln, result);
-
-			} else if (cmd.equals(MenuCreator.ALIGNMENT_PANEL)) {
-				MultipleAlignmentJmolDisplay.showMultipleAligmentPanel(multAln,
-						this);
-
-			} else if (cmd.equals(MenuCreator.FATCAT_TEXT)) {
-				String result = MultipleAlignmentWriter.toFatCat(multAln)
-						+ "\n";
-				result += MultipleAlignmentWriter.toTransformMatrices(multAln);
-				MultipleAlignmentJmolDisplay
-						.showAlignmentImage(multAln, result);
-
-			} else if (cmd.equals(MenuCreator.PHYLOGENETIC_TREE)) {
-
-				// Kimura, Structural and Fractional Dissimilarity Score
-				Phylogeny kimura = MultipleAlignmentTools
-						.getKimuraTree(multAln);
-				Phylogeny sdm = MultipleAlignmentTools.getHSDMTree(multAln);
-				// Phylogeny structural = MultipleAlignmentTools
-				// .getStructuralTree(multAln);
-
-				Archaeopteryx
-						.createApplication(new Phylogeny[] { kimura, sdm });
+			switch (cmd) {
+				case MenuCreator.TEXT_ONLY:
+					logger.warn("Option not available for MultipleAlignments");
+
+					break;
+				case MenuCreator.PAIRS_ONLY: {
+					String result = MultipleAlignmentWriter
+							.toAlignedResidues(multAln);
+					MultipleAlignmentJmolDisplay
+							.showAlignmentImage(multAln, result);
+
+					break;
+				}
+				case MenuCreator.ALIGNMENT_PANEL:
+					MultipleAlignmentJmolDisplay.showMultipleAligmentPanel(multAln,
+							this);
+
+					break;
+				case MenuCreator.FATCAT_TEXT: {
+					String result = MultipleAlignmentWriter.toFatCat(multAln)
+							+ "\n";
+					result += MultipleAlignmentWriter.toTransformMatrices(multAln);
+					MultipleAlignmentJmolDisplay
+							.showAlignmentImage(multAln, result);
+
+					break;
+				}
+				case MenuCreator.PHYLOGENETIC_TREE:
+
+					// Kimura, Structural and Fractional Dissimilarity Score
+					Phylogeny kimura = MultipleAlignmentTools
+							.getKimuraTree(multAln);
+					Phylogeny sdm = MultipleAlignmentTools.getHSDMTree(multAln);
+					// Phylogeny structural = MultipleAlignmentTools
+					// .getStructuralTree(multAln);
+
+					Archaeopteryx
+							.createApplication(new Phylogeny[]{kimura, sdm});
+					break;
 			}
 		} catch (Exception e) {
 			logger.error("Could not complete display option.", e);
@@ -426,13 +414,13 @@ public static String getJmolString(MultipleAlignment multAln,
 					colorPalette, colorByBlocks);
 		Color[] colors = colorPalette.getColorPalette(multAln.size());
 
-		StringBuffer j = new StringBuffer();
+		StringBuilder j = new StringBuilder();
 		j.append(DEFAULT_SCRIPT);
 
 		// Color the equivalent residues of every structure
-		StringBuffer sel = new StringBuffer();
+		StringBuilder sel = new StringBuilder();
 		sel.append("select *; color lightgrey; backbone 0.1; ");
-		List<List<String>> allPDB = new ArrayList<List<String>>();
+		List<List<String>> allPDB = new ArrayList<>();
 
 		// Get the aligned residues of every structure
 		for (int i = 0; i < multAln.size(); i++) {
@@ -508,7 +496,7 @@ private static void printJmolScript4Block(Atom[] atoms,
 			int str, int colorPos, int blockNum) {
 
 		// Obtain the residues aligned in this block of the structure
-		List<String> pdb = new ArrayList<String>();
+		List<String> pdb = new ArrayList<>();
 		for (int i = 0; i < alignRes.get(str).size(); i++) {
 
 			// Handle gaps - only color if it is not null
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java
index 6c47f80276..c762df85f6 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java
@@ -50,7 +50,7 @@ public class RasmolCommandListener
 	public RasmolCommandListener(JmolPanel panel, JTextField field){
 		textfield = field;
 		jmolPanel = panel;
-		history = new ArrayList<String>();
+		history = new ArrayList<>();
 		historyPosition = -2; // -2 = history = empty;
 	}
 
@@ -95,18 +95,20 @@ public void  mouseClicked(MouseEvent e){
 			textfield.setText("");
 			textfield.repaint();
 		}
-	};
+	}
 
 
 	@Override
-	public void  mouseExited(MouseEvent e){};
+	public void  mouseExited(MouseEvent e){}
+
 	@Override
-	public void  mouseReleased(MouseEvent e){};
+	public void  mouseReleased(MouseEvent e){}
+
 	@Override
-	public void  mousePressed(MouseEvent e){};
+	public void  mousePressed(MouseEvent e){}
 
 	@Override
-	public void  mouseEntered(MouseEvent e){};
+	public void  mouseEntered(MouseEvent e){}
 
 	/** takes care of the cursor up/down keys. triggers copying of stored
 	 * commands into the current textfield
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java
index 1b0ee9a6f8..aa9eedf736 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java
@@ -200,14 +200,10 @@ public void windowClosing(WindowEvent e) {
 
 		JButton resetDisplay = new JButton("Reset Display");
 
-		resetDisplay.addActionListener(new ActionListener() {
+		resetDisplay.addActionListener(e -> {
+			System.out.println("reset!!");
+			jmolPanel.executeCmd("restore STATE state_1");
 
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				System.out.println("reset!!");
-				jmolPanel.executeCmd("restore STATE state_1");
-
-			}
 		});
 
 		hBox2.add(resetDisplay);
@@ -216,21 +212,17 @@ public void actionPerformed(ActionEvent e) {
 
 		JCheckBox toggleSelection = new JCheckBox("Show Selection");
 		toggleSelection.addItemListener(
-				new ItemListener() {
-
-					@Override
-					public void itemStateChanged(ItemEvent e) {
-						boolean showSelection = (e.getStateChange() == ItemEvent.SELECTED);
-
-						if (showSelection){
-							jmolPanel.executeCmd("set display selected");
-						} else {
-							jmolPanel.executeCmd("set display off");
-						}
+				e -> {
+					boolean showSelection = (e.getStateChange() == ItemEvent.SELECTED);
 
+					if (showSelection){
+						jmolPanel.executeCmd("set display selected");
+					} else {
+						jmolPanel.executeCmd("set display off");
 					}
+
 				}
-				);
+		);
 
 
 
@@ -256,13 +248,13 @@ public void itemStateChanged(ItemEvent e) {
 		zoomSlider.setMajorTickSpacing(100);
 		zoomSlider.setPaintTicks(true);
 
-		Hashtable<Integer, JLabel> labelTable = new Hashtable<Integer, JLabel>();
-		labelTable.put(new Integer(0),new JLabel("0%"));
-		labelTable.put(new Integer(100),new JLabel("100%"));
-		labelTable.put(new Integer(200),new JLabel("200%"));
-		labelTable.put(new Integer(300),new JLabel("300%"));
-		labelTable.put(new Integer(400),new JLabel("400%"));
-		labelTable.put(new Integer(500),new JLabel("500%"));
+		Hashtable<Integer, JLabel> labelTable = new Hashtable<>();
+		labelTable.put(0,new JLabel("0%"));
+		labelTable.put(100,new JLabel("100%"));
+		labelTable.put(200,new JLabel("200%"));
+		labelTable.put(300,new JLabel("300%"));
+		labelTable.put(400,new JLabel("400%"));
+		labelTable.put(500,new JLabel("500%"));
 
 		zoomSlider.setLabelTable(labelTable);
 		zoomSlider.setPaintLabels(true);
@@ -273,21 +265,17 @@ public void itemStateChanged(ItemEvent e) {
 		// SPIN CHECKBOX
 		JCheckBox toggleSpin = new JCheckBox("Spin");
 		toggleSpin.addItemListener(
-				new ItemListener() {
-
-					@Override
-					public void itemStateChanged(ItemEvent e) {
-						boolean spinOn = (e.getStateChange() == ItemEvent.SELECTED);
-
-						if (spinOn){
-							jmolPanel.executeCmd("spin ON");
-						} else {
-							jmolPanel.executeCmd("spin OFF");
-						}
+				e -> {
+					boolean spinOn = (e.getStateChange() == ItemEvent.SELECTED);
 
+					if (spinOn){
+						jmolPanel.executeCmd("spin ON");
+					} else {
+						jmolPanel.executeCmd("spin OFF");
 					}
+
 				}
-				);
+		);
 
 
 		hBox3.add(toggleSpin);
@@ -370,47 +358,55 @@ public void destroy() {
 	@Override
 	public void actionPerformed(ActionEvent e) {
 		String cmd = e.getActionCommand();
-		if (cmd.equals(MenuCreator.TEXT_ONLY)) {
-			if (afpChain == null) {
-				System.err.println("Currently not viewing an alignment!");
-				return;
-			}
-			// Clone the AFPChain to not override the FatCat numbers in alnsymb
-			AFPChain textAFP = (AFPChain) afpChain.clone();
-			String result = AfpChainWriter.toWebSiteDisplay(textAFP, ca1, ca2);
+		switch (cmd) {
+			case MenuCreator.TEXT_ONLY: {
+				if (afpChain == null) {
+					System.err.println("Currently not viewing an alignment!");
+					return;
+				}
+				// Clone the AFPChain to not override the FatCat numbers in alnsymb
+				AFPChain textAFP = (AFPChain) afpChain.clone();
+				String result = AfpChainWriter.toWebSiteDisplay(textAFP, ca1, ca2);
 
-			DisplayAFP.showAlignmentImage(afpChain, result);
+				DisplayAFP.showAlignmentImage(afpChain, result);
 
-		} else if (cmd.equals(MenuCreator.PAIRS_ONLY)) {
-			if (afpChain == null) {
-				System.err.println("Currently not viewing an alignment!");
-				return;
+				break;
 			}
-			String result = AfpChainWriter.toAlignedPairs(afpChain, ca1, ca2);
+			case MenuCreator.PAIRS_ONLY: {
+				if (afpChain == null) {
+					System.err.println("Currently not viewing an alignment!");
+					return;
+				}
+				String result = AfpChainWriter.toAlignedPairs(afpChain, ca1, ca2);
 
-			DisplayAFP.showAlignmentImage(afpChain, result);
+				DisplayAFP.showAlignmentImage(afpChain, result);
 
-		} else if (cmd.equals(MenuCreator.ALIGNMENT_PANEL)) {
-			if (afpChain == null) {
-				System.err.println("Currently not viewing an alignment!");
-				return;
-			}
-			try {
-				DisplayAFP.showAlignmentPanel(afpChain, ca1, ca2, this);
-			} catch (Exception e1) {
-				e1.printStackTrace();
-				return;
+				break;
 			}
+			case MenuCreator.ALIGNMENT_PANEL:
+				if (afpChain == null) {
+					System.err.println("Currently not viewing an alignment!");
+					return;
+				}
+				try {
+					DisplayAFP.showAlignmentPanel(afpChain, ca1, ca2, this);
+				} catch (Exception e1) {
+					e1.printStackTrace();
+					return;
+				}
 
-		} else if (cmd.equals(MenuCreator.FATCAT_TEXT)) {
-			if (afpChain == null) {
-				System.err.println("Currently not viewing an alignment!");
-				return;
+				break;
+			case MenuCreator.FATCAT_TEXT: {
+				if (afpChain == null) {
+					System.err.println("Currently not viewing an alignment!");
+					return;
+				}
+				String result = afpChain.toFatcat(ca1, ca2);
+				result += AFPChain.newline;
+				result += afpChain.toRotMat();
+				DisplayAFP.showAlignmentImage(afpChain, result);
+				break;
 			}
-			String result = afpChain.toFatcat(ca1, ca2);
-			result += AFPChain.newline;
-			result += afpChain.toRotMat();
-			DisplayAFP.showAlignmentImage(afpChain, result);
 		}
 	}
 
@@ -420,11 +416,11 @@ public static String getJmolString(AFPChain afpChain, Atom[] ca1, Atom[] ca2) {
 			return getMultiBlockJmolScript(afpChain, ca1, ca2);
 		}
 
-		StringBuffer j = new StringBuffer();
+		StringBuilder j = new StringBuilder();
 		j.append(DEFAULT_SCRIPT);
 
 		// now color the equivalent residues ...
-		StringBuffer sel = new StringBuffer();
+		StringBuilder sel = new StringBuilder();
 		List<String> pdb1 = DisplayAFP.getPDBresnum(0, afpChain, ca1);
 		sel.append("select ");
 		int pos = 0;
@@ -465,7 +461,7 @@ public static String getJmolString(AFPChain afpChain, Atom[] ca1, Atom[] ca2) {
 		// Rasmol
 
 		// and now select the aligned residues...
-		StringBuffer buf = new StringBuffer("select ");
+		StringBuilder buf = new StringBuilder("select ");
 		int count = 0;
 		for (String res : pdb1) {
 			if (count > 0)
@@ -559,8 +555,8 @@ private static void printJmolScript4Block(Atom[] ca1, Atom[] ca2, int blockNum,
 		c1 = ColorUtils.getIntermediate(ColorUtils.orange, end1, blockNum, bk);
 		c2 = ColorUtils.getIntermediate(ColorUtils.cyan, end2, blockNum, bk);
 
-		List<String> pdb1 = new ArrayList<String>();
-		List<String> pdb2 = new ArrayList<String>();
+		List<String> pdb1 = new ArrayList<>();
+		List<String> pdb2 = new ArrayList<>();
 		for (int i = 0; i < optLen[bk]; i++) {
 			///
 			int pos1 = optAln[bk][0][i];
@@ -622,7 +618,7 @@ public List<Matrix> getDistanceMatrices() {
 	public void stateChanged(ChangeEvent e) {
 		JSlider source = (JSlider) e.getSource();
 		if (!source.getValueIsAdjusting()) {
-			int zoomValue = (int) source.getValue();
+			int zoomValue = source.getValue();
 			jmolPanel.executeCmd("zoom " + zoomValue);
 		}
 	}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/JNLPProxy.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/JNLPProxy.java
index 99e8a6eb3e..8b070a17dd 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/JNLPProxy.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/JNLPProxy.java
@@ -78,12 +78,12 @@ public static boolean  showDocument ( URL  url )
 	try
 	{
 		Method  method = basicServiceClass.getMethod (
-			"showDocument", new Class [ ] { URL.class } );
+			"showDocument", URL.class);
 
 		Boolean  resultBoolean = ( Boolean )
 			method.invoke ( basicServiceObject, new Object [ ] { url } );
 
-		boolean success = resultBoolean.booleanValue ( );
+		boolean success = resultBoolean;
 		if ( ! success )
 		System.out.println("invocation of method failed!");
 		return success;
@@ -109,10 +109,10 @@ private static Object  getBasicServiceObject ( )
 			= Class.forName ( "javax.jnlp.ServiceManager" );
 
 		Method  lookupMethod = serviceManagerClass.getMethod ( "lookup",
-			new Class [ ] { String.class } );
+                String.class);
 
 		return lookupMethod.invoke (
-			null, new Object [ ] { "javax.jnlp.BasicService" } );
+			null, "javax.jnlp.BasicService");
 	}
 	catch ( Exception  ex )
 	{
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java
index 27c0ceb322..c9fedcfbd8 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java
@@ -73,13 +73,7 @@ public static void main(String[] args){
 
 			// we did not get enough arguments, show the general user interface...
 
-			javax.swing.SwingUtilities.invokeLater(new Runnable() {
-				@Override
-				public void run() {
-
-					AlignmentGui.getInstance();
-				}
-			});
+			javax.swing.SwingUtilities.invokeLater(() -> AlignmentGui.getInstance());
 
 			return;
 
@@ -88,12 +82,7 @@ public void run() {
 		else if ( args.length < 3){
 			//String arg0 = args[0];
 
-			javax.swing.SwingUtilities.invokeLater(new Runnable() {
-				@Override
-				public void run() {
-					AlignmentGui.getInstance();
-				}
-			});
+			javax.swing.SwingUtilities.invokeLater(() -> AlignmentGui.getInstance());
 
 			return;
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java
index eeffe5b749..46b20d38f4 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java
@@ -149,35 +149,27 @@ public void windowClosing(WindowEvent e) {
 
 		JButton resetDisplay = new JButton("Reset Display");
 
-		resetDisplay.addActionListener(new ActionListener() {
+		resetDisplay.addActionListener(e -> {
+			System.out.println("reset!!");
+			jmolPanel.executeCmd("restore STATE state_1");
 
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				System.out.println("reset!!");
-				jmolPanel.executeCmd("restore STATE state_1");
-
-			}
 		});
 
 		hBox2.add(resetDisplay); hBox2.add(Box.createGlue());
 
 		JCheckBox toggleSelection = new JCheckBox("Show Selection");
 		toggleSelection.addItemListener(
-			    new ItemListener() {
-
-					@Override
-					public void itemStateChanged(ItemEvent e) {
-						  boolean showSelection = (e.getStateChange() == ItemEvent.SELECTED);
+				e -> {
+					  boolean showSelection = (e.getStateChange() == ItemEvent.SELECTED);
 
-						  if (showSelection){
-							  jmolPanel.executeCmd("set display selected");
-						  } else {
-							  jmolPanel.executeCmd("set display off");
-						  }
+					  if (showSelection){
+						  jmolPanel.executeCmd("set display selected");
+					  } else {
+						  jmolPanel.executeCmd("set display off");
+					  }
 
-					}
 				}
-			);
+		);
 
 
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JmolViewerImpl.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JmolViewerImpl.java
index e361a156c1..2c89da3895 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JmolViewerImpl.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JmolViewerImpl.java
@@ -203,10 +203,10 @@ static class JmolPanel extends JPanel {
 				adapterC = Class.forName(adapter);
 				smartAdapterC = Class.forName(smartAdapter);
 
-				Method m = viewerC.getMethod("allocateSimpleViewer", new Class[]{Component.class, adapterC});
+				Method m = viewerC.getMethod("allocateSimpleViewer", Component.class, adapterC);
 
-				Constructor constructor = smartAdapterC.getConstructor(new Class[]{});
-				adapterO = constructor.newInstance(new Object[]{});
+				Constructor constructor = smartAdapterC.getConstructor();
+				adapterO = constructor.newInstance();
 
 				//viewerC = JmolSimpleViewer.allocateSimpleViewer(this, adapter);
 				viewerO = m.invoke(viewerC, this, adapterO);
@@ -214,20 +214,12 @@ static class JmolPanel extends JPanel {
 				evalString = viewerC.getMethod("evalString", String.class);
 
 				renderScreenImage = viewerC.getMethod("renderScreenImage",
-						new Class[]{Graphics.class, Dimension.class, Rectangle.class});
+                        Graphics.class, Dimension.class, Rectangle.class);
 
-				openStringInline = viewerC.getMethod("openStringInline", new Class[]{String.class});
+				openStringInline = viewerC.getMethod("openStringInline", String.class);
 
-			} catch (InstantiationException ex) {
+			} catch (InstantiationException | NoSuchMethodException | InvocationTargetException | IllegalArgumentException | IllegalAccessException ex) {
 				logger.error("Exception caught", ex);
-			} catch (IllegalAccessException ex) {
-				logger.error("Exception caught", ex);
-			} catch (IllegalArgumentException ex) {
-				logger.error("Exception caught", ex);
-			} catch (InvocationTargetException ex) {
-				logger.error("Exception caught", ex);
-			} catch (NoSuchMethodException e) {
-				logger.error("Exception caught", e);
 			}
 
 			evalString("set scriptQueue on;");
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java
index b2c6917559..33662abe61 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java
@@ -198,7 +198,7 @@ public ScaleableMatrixPanel(){
 
 
 	protected static Map<String,ContinuousColorMapper> createGradients() {
-		SortedMap<String,ContinuousColorMapper> gradients = new TreeMap<String,ContinuousColorMapper>();
+		SortedMap<String,ContinuousColorMapper> gradients = new TreeMap<>();
 
 		int i = 0; //prepend number, since sorted alphabetically
 		ColorSpace hsv = HSVColorSpace.getHSVColorSpace();
@@ -379,7 +379,8 @@ protected class GradientRenderer extends JPanel
 	implements ListCellRenderer {
 
 		private static final long serialVersionUID = -2000575579184232365L;
-		private int min,max;
+		private final int min;
+		private final int max;
 		JLabel title;
 		JPanel gradientContainer;
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/Selection.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/Selection.java
index 902b172b2f..9247940df6 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/Selection.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/Selection.java
@@ -27,8 +27,8 @@
 public interface Selection {
 
 
-	public void clear();
-	public List<AtomInfo> getSelection();
-	public void setSelection(List<AtomInfo> selection);
+	void clear();
+	List<AtomInfo> getSelection();
+	void setSelection(List<AtomInfo> selection);
 
 }
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java
index dd4dc97cc4..d6eb415cc8 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java
@@ -232,7 +232,7 @@ public SequenceDisplay(StructurePairAligner structurePairAligner){
 
 		this.setLayout(new BoxLayout(this,BoxLayout.Y_AXIS));
 
-		apos = new ArrayList<AlignedPosition>();
+		apos = new ArrayList<>();
 	}
 
 	public void clearListeners(){
@@ -451,9 +451,7 @@ private void updatePercentageDisplay(){
 	private int getMaxSequenceLength(){
 		int l1 = panel1.getChain().getAtomGroups(GroupType.AMINOACID).size();
 		int l2 = panel2.getChain().getAtomGroups(GroupType.AMINOACID).size();
-		if ( l1 > l2)
-			return l1;
-		else return l2;
+        return Math.max(l1, l2);
 	}
 
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/StructureViewer.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/StructureViewer.java
index 43f608ef32..62d9369236 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/StructureViewer.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/StructureViewer.java
@@ -26,35 +26,35 @@
 
 public interface StructureViewer {
 
-	public void setStructure(Structure structure);
-	public void repaint();
-	public void setSelection(Selection selection);
-	public Selection getSelection();
+	void setStructure(Structure structure);
+	void repaint();
+	void setSelection(Selection selection);
+	Selection getSelection();
 
 	/** Apply this color to the current Selection
 	 *
 	 * @param red
 	 */
-	public void setColor(Color red);
-	public Color getColor();
+    void setColor(Color red);
+	Color getColor();
 
 
 	/** Apply this style to the current selection
 	 *
 	 * @param wireframe renderstyle
 	 */
-	public void setStyle(RenderStyle wireframe);
+    void setStyle(RenderStyle wireframe);
 
 	/** Clear the current display
 	 *
 	 *
 	 */
-	public void clear();
+    void clear();
 
 	/** Set the Zoom level
 	 *
 	 * @param i
 	 */
-	public void setZoom(int i);
+    void setZoom(int i);
 
 }
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/AlignmentPositionListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/AlignmentPositionListener.java
index 61ca8c5fd9..d955b67f3c 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/AlignmentPositionListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/AlignmentPositionListener.java
@@ -25,11 +25,11 @@
 
 public interface AlignmentPositionListener {
 
-	public void mouseOverPosition(AlignedPosition p);
-	public void positionSelected(AlignedPosition p);
-	public void toggleSelection(AlignedPosition p);
-	public void rangeSelected(AlignedPosition start , AlignedPosition end);
-	public void selectionLocked();
-	public void selectionUnlocked();
+	void mouseOverPosition(AlignedPosition p);
+	void positionSelected(AlignedPosition p);
+	void toggleSelection(AlignedPosition p);
+	void rangeSelected(AlignedPosition start, AlignedPosition end);
+	void selectionLocked();
+	void selectionUnlocked();
 
 }
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/JmolAlignedPositionListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/JmolAlignedPositionListener.java
index 14937adea2..e346fc9813 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/JmolAlignedPositionListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/JmolAlignedPositionListener.java
@@ -71,8 +71,8 @@ public void mouseOverPosition(AlignedPosition p) {
 			return;
 		}
 
-		String pdbpos1 ="";
-		String pdbpos2 = "";
+		String pdbpos1;
+		String pdbpos2;
 
 		if ( p1 >-1) {
 			Atom a = ca1[p1];
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java
index 8dc672ed36..54e1b341e5 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java
@@ -53,12 +53,12 @@
 public class AlternativeAlignmentFrame
 extends JFrame{
 
-	private static final long serialVersionUID=0l;
+	private static final long serialVersionUID= 0L;
 
 
 	private static final Logger logger = LoggerFactory.getLogger(AlternativeAlignmentFrame.class);
 
-	private static String[] columnNames = new String[]{"#","eqr","score", "rms", "gaps","cluster", "show distance matrix","show alignment"};
+	private static final String[] columnNames = new String[]{"#","eqr","score", "rms", "gaps","cluster", "show distance matrix","show alignment"};
 
 	AlternativeAlignment[] aligs;
 	JPanel panel;
@@ -126,12 +126,12 @@ private Object[][] getDataFromAligs(AlternativeAlignment[] aligs){
 		for ( int i=0;i< aligs.length;i++){
 			AlternativeAlignment alig = aligs[i];
 
-			data[i][0] = new Integer(i+1);
-			data[i][1] = new Integer(alig.getEqr());
-			data[i][2] = new Double(alig.getScore());
-			data[i][3] = new Double(alig.getRmsd());
-			data[i][4] = new Integer(alig.getGaps());
-			data[i][5] = new Integer(alig.getCluster());
+			data[i][0] = i + 1;
+			data[i][1] = alig.getEqr();
+			data[i][2] = (double) alig.getScore();
+			data[i][3] = alig.getRmsd();
+			data[i][4] = alig.getGaps();
+			data[i][5] = alig.getCluster();
 			JButton maxb = new JButton("Distance Matrix");
 			maxb.addMouseListener(new MatrixMouseListener(this,i));
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JButtonTableCellRenderer.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JButtonTableCellRenderer.java
index 586220728e..7466e76b89 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JButtonTableCellRenderer.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JButtonTableCellRenderer.java
@@ -27,7 +27,7 @@
 import java.awt.*;
 
 class JButtonTableCellRenderer implements TableCellRenderer {
-	private TableCellRenderer __defaultRenderer;
+	private final TableCellRenderer __defaultRenderer;
 
 	public JButtonTableCellRenderer(TableCellRenderer renderer) {
 		__defaultRenderer = renderer;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JTableDataButtonModel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JTableDataButtonModel.java
index 561d130bbf..23e877d88d 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JTableDataButtonModel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JTableDataButtonModel.java
@@ -26,7 +26,7 @@
 
 class JTableDataButtonModel extends AbstractTableModel {
 
-		public static final long serialVersionUID = 0l;
+		public static final long serialVersionUID = 0L;
 
 		Object[][] __rows;
 		String[]   __columns;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JTableMouseButtonListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JTableMouseButtonListener.java
index 5b8269a109..bb3bde4a7f 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JTableMouseButtonListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JTableMouseButtonListener.java
@@ -30,7 +30,7 @@
 
 class JTableMouseButtonListener implements MouseListener {
 
-	private JTable __table;
+	private final JTable __table;
 
 	private void __forwardEventToButton(MouseEvent e) {
 		TableColumnModel columnModel = __table.getColumnModel();
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/MenuCreator.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/MenuCreator.java
index ef945c5263..f149dd2152 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/MenuCreator.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/MenuCreator.java
@@ -56,32 +56,29 @@ public static JMenuBar initMenu(){
 
 		JMenuItem openI = new JMenuItem("Open");
 		openI.setMnemonic(KeyEvent.VK_O);
-		openI.addActionListener(new ActionListener(){
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				String cmd = e.getActionCommand();
-				if ( cmd.equals("Open")){
-					final JFileChooser fc = new JFileChooser();
+		openI.addActionListener(e -> {
+			String cmd = e.getActionCommand();
+			if ( cmd.equals("Open")){
+				final JFileChooser fc = new JFileChooser();
 
 //					In response to a button click:
-					int returnVal = fc.showOpenDialog(null);
-					if ( returnVal == JFileChooser.APPROVE_OPTION) {
-						File file = fc.getSelectedFile();
-
-						PDBFileReader reader = new PDBFileReader();
-						try {
-							Structure s = reader.getStructure(file);
-							BiojavaJmol jmol = new BiojavaJmol();
-							jmol.setStructure(s);
-							jmol.evalString("select * ; color chain;");
-							jmol.evalString("select *; spacefill off; wireframe off; backbone 0.4;  ");
-
-						} catch (Exception ex){
-							ex.printStackTrace();
-						}
+				int returnVal = fc.showOpenDialog(null);
+				if ( returnVal == JFileChooser.APPROVE_OPTION) {
+					File file1 = fc.getSelectedFile();
+
+					PDBFileReader reader = new PDBFileReader();
+					try {
+						Structure s = reader.getStructure(file1);
+						BiojavaJmol jmol = new BiojavaJmol();
+						jmol.setStructure(s);
+						jmol.evalString("select * ; color chain;");
+						jmol.evalString("select *; spacefill off; wireframe off; backbone 0.4;  ");
+
+					} catch (Exception ex){
+						ex.printStackTrace();
+					}
 
 
-					}
 				}
 			}
 		});
@@ -89,15 +86,11 @@ public void actionPerformed(ActionEvent e) {
 
 		JMenuItem exitI = new JMenuItem("Exit");
 		exitI.setMnemonic(KeyEvent.VK_X);
-		exitI.addActionListener(new ActionListener(){
-
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				String cmd = e.getActionCommand();
+		exitI.addActionListener(e -> {
+			String cmd = e.getActionCommand();
 
-				if ( cmd.equals("Exit")){
-					System.exit(0);
-				}
+			if ( cmd.equals("Exit")){
+				System.exit(0);
 			}
 		});
 
@@ -106,14 +99,11 @@ public void actionPerformed(ActionEvent e) {
 
 		JMenu align = new JMenu("Align");
 		JMenuItem pairI = new JMenuItem("2 protein structures");
-		pairI.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				String cmd = e.getActionCommand();
+		pairI.addActionListener(e -> {
+			String cmd = e.getActionCommand();
 
-				if ( cmd.equals("2 protein structures")){
-					MenuCreator.showPairDialog();
-				}
+			if ( cmd.equals("2 protein structures")){
+				MenuCreator.showPairDialog();
 			}
 		});
 
@@ -123,15 +113,11 @@ public void actionPerformed(ActionEvent e) {
 
 		JMenu about = new JMenu("About");
 		JMenuItem aboutI = new JMenuItem("PDBview");
-		aboutI.addActionListener(new ActionListener(){
-
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				String cmd = e.getActionCommand();
+		aboutI.addActionListener(e -> {
+			String cmd = e.getActionCommand();
 
-				if ( cmd.equals("PDBview")){
-					MenuCreator.showAboutDialog();
-				}
+			if ( cmd.equals("PDBview")){
+				MenuCreator.showAboutDialog();
 			}
 		});
 
@@ -177,17 +163,14 @@ private static void showAboutDialog(){
 
 		JButton close = new JButton("Close");
 
-		close.addActionListener(new ActionListener(){
-			@Override
-			public void actionPerformed(ActionEvent event) {
-				Object source = event.getSource();
+		close.addActionListener(event -> {
+			Object source = event.getSource();
 
-				JButton but = (JButton)source;
-				Container parent = but.getParent().getParent().getParent().getParent().getParent().getParent() ;
+			JButton but = (JButton)source;
+			Container parent = but.getParent().getParent().getParent().getParent().getParent().getParent() ;
 
-				JDialog dia = (JDialog) parent;
-				dia.dispose();
-			}
+			JDialog dia = (JDialog) parent;
+			dia.dispose();
 		});
 
 		Box hBoxb = Box.createHorizontalBox();
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBDirPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBDirPanel.java
index 7db9f67424..8bb3d57230 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBDirPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBDirPanel.java
@@ -225,7 +225,7 @@ public ChooseDirAction (JTextField textField){
 		super("Choose");
 		this.textField = textField;
 	}
-	public static final long serialVersionUID = 0l;
+	public static final long serialVersionUID = 0L;
 	// This method is called when the button is pressed
 	@Override
 	public void actionPerformed(ActionEvent evt) {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java
index 2c542f0797..95dcc1a8f6 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java
@@ -59,7 +59,7 @@ public class PDBUploadPanel
 
 
 
-	private JComboBox fileType ;
+	private final JComboBox fileType ;
 
 	JTextField filePath1;
 	JTextField filePath2;
@@ -129,7 +129,7 @@ public Structure getStructure2() throws StructureException{
 	private Structure getStructure(JTextField filePath,JTextField chainId) throws StructureException{
 		//PDBFileReader reader = new PDBFileReader();
 
-		StructureIOFile reader = null;
+		StructureIOFile reader;
 		String fileFormat = (String)fileType.getSelectedItem();
 		if ( fileFormat.equals(UserConfiguration.PDB_FORMAT)){
 			reader = new PDBFileReader();
@@ -141,7 +141,7 @@ private Structure getStructure(JTextField filePath,JTextField chainId) throws St
 
 		String path = filePath.getText();
 		File f = new File(path);
-		Structure s = null;
+		Structure s;
 		try {
 			s = reader.getStructure(f);
 		} catch (IOException  e){
@@ -206,7 +206,7 @@ public ChooseAction (JTextField textField){
 		super("Choose");
 		this.textField = textField;
 	}
-	public static final long serialVersionUID = 0l;
+	public static final long serialVersionUID = 0L;
 	// This method is called when the button is pressed
 	@Override
 	public void actionPerformed(ActionEvent evt) {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopSelectPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopSelectPanel.java
index a6571483a6..5ab2bff7c9 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopSelectPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopSelectPanel.java
@@ -125,7 +125,7 @@ public Structure getStructure2() throws StructureException
 		return getStructure(dom2.getText());
 	}
 
-	private Structure getStructure(String domainID) throws StructureException{
+	private Structure getStructure(String domainID) {
 		//PDBFileReader reader = new PDBFileReader();
 
 		if ( domainID == null || domainID.equals(""))
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java
index ae8d859951..502e6264ea 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java
@@ -90,7 +90,7 @@ private Box getDomainPanel(JTextField f){
 
 	public List<Structure> getStructures() throws StructureException {
 
-		List<Structure> structures = new ArrayList<Structure>();
+		List<Structure> structures = new ArrayList<>();
 
 		for (StructureIdentifier name:getNames()){
 			structures.add(getStructure(name));
@@ -100,7 +100,7 @@ public List<Structure> getStructures() throws StructureException {
 
 	public List<StructureIdentifier> getNames() {
 
-		List<StructureIdentifier> names = new ArrayList<StructureIdentifier>();
+		List<StructureIdentifier> names = new ArrayList<>();
 
 		String raw = input.getText().trim();
 		String[] split = raw.split(" ");
@@ -111,7 +111,7 @@ public List<StructureIdentifier> getNames() {
 		return names;
 	}
 
-	private Structure getStructure(StructureIdentifier name) throws StructureException{
+	private Structure getStructure(StructureIdentifier name) {
 
 		UserConfiguration config = WebStartMain.getWebStartConfig();
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceMouseListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceMouseListener.java
index e10331b9d5..11d7f2fd31 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceMouseListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceMouseListener.java
@@ -86,7 +86,7 @@ public SequenceMouseListener(SequenceDisplay parent) {
 
 		coordManager = new CoordManager();
 
-		alignmentPositionListeners = new ArrayList<AlignmentPositionListener>();
+		alignmentPositionListeners = new ArrayList<>();
 		//renderer.getLayeredPane().addMouseListener(popupFrame);
 
 	}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java
index bc29425c07..c969683c1c 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java
@@ -39,7 +39,7 @@
 public class SequenceScalePanel
 extends JPanel{
 
-	static final long serialVersionUID = 7893248902423l;
+	static final long serialVersionUID = 7893248902423L;
 
 	//private static final Logger logger = LoggerFactory.getLogger(SequenceScalePanel.class);
 
@@ -105,7 +105,7 @@ public SequenceScalePanel(int position) {
 		setPrefSize();
 		coordManager = new CoordManager();
 
-		apos = new ArrayList<AlignedPosition>();
+		apos = new ArrayList<>();
 
 	}
 
@@ -219,7 +219,7 @@ public void paintComponent(Graphics g){
 
 		setPaintDefaults(g2D);
 
-		int y = 1;
+		int y;
 
 
 		// draw the scale
@@ -378,7 +378,7 @@ protected void drawIdx(Graphics2D g2D, int y){
 		if ( scale <= 3)
 			lineH = 8;
 
-		int i = startpos;
+		int i;
 
 
 		// display the actual sequence!;
@@ -446,7 +446,7 @@ protected int drawSequence(Graphics2D g2D,  int y){
 
 			//g2D.setColor(SCALE_COLOR);
 
-			int i = startpos;
+			int i;
 
 			// display the actual sequence!;
 			for ( int gap = startpos ;   gap < apos.size() ;gap++){
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/StructurePairSelector.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/StructurePairSelector.java
index 1ced9fe59f..89710a6140 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/StructurePairSelector.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/StructurePairSelector.java
@@ -35,7 +35,7 @@
  */
 public interface StructurePairSelector {
 
-	public Structure getStructure1() throws StructureException, IOException;
-	public Structure getStructure2() throws StructureException, IOException;
+	Structure getStructure1() throws StructureException, IOException;
+	Structure getStructure2() throws StructureException, IOException;
 
 }
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ColorInterpolator.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ColorInterpolator.java
index 13aedf3b8c..33f04c1240 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ColorInterpolator.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ColorInterpolator.java
@@ -36,5 +36,5 @@ public interface ColorInterpolator {
 	 * @return The color between a and b
 	 * @throws IllegalArgumentException if mixing is not between 0 and 1
 	 */
-	public Color interpolate(Color a, Color b, float mixing);
+    Color interpolate(Color a, Color b, float mixing);
 }
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapper.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapper.java
index 8ee0c4e2c9..e5442627f0 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapper.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapper.java
@@ -37,5 +37,5 @@ public interface ContinuousColorMapper {
 	 * @param value The real to be mapped
 	 * @return The color corresponding to value
 	 */
-	public Color getColor(double value);
+    Color getColor(double value);
 }
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/DefaultMatrixMapper.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/DefaultMatrixMapper.java
index 3b9975d0c0..7b246173da 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/DefaultMatrixMapper.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/DefaultMatrixMapper.java
@@ -48,7 +48,7 @@ public DefaultMatrixMapper(double scale, float saturation ) {
 	 */
 	@Override
 	public Color getColor(double value) {
-		float hue = 1.0f;
+		float hue;
 		hue = (float)(1-(value/scalevalue));
 		if (hue < 0)
 			hue = 0;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientMapper.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientMapper.java
index 4678d68707..f28c74d053 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientMapper.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientMapper.java
@@ -51,7 +51,7 @@ public class GradientMapper implements ContinuousColorMapper, Map<Double, Color>
 	public static final int RAINBOW_GRADIENT = 4;
 	public static final int RAINBOW_INTENSITY_GRADIENT = 5;
 
-	private NavigableMap<Double,Color> mapping;
+	private final NavigableMap<Double,Color> mapping;
 	private ColorInterpolator interpolator;
 
 	public GradientMapper() {
@@ -61,7 +61,7 @@ public GradientMapper(Color negInf, Color posInf) {
 		this(negInf,posInf,ColorSpace.getInstance(ColorSpace.CS_sRGB));
 	}
 	public GradientMapper(Color negInf, Color posInf, ColorSpace cspace) {
-		mapping = new TreeMap<Double,Color>();
+		mapping = new TreeMap<>();
 		mapping.put(Double.NEGATIVE_INFINITY, negInf);
 		mapping.put(Double.POSITIVE_INFINITY, posInf);
 		interpolator = new LinearColorInterpolator(cspace);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientPanel.java
index 68690b58cb..7f88f732ca 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientPanel.java
@@ -26,8 +26,9 @@
 
 public class GradientPanel extends JPanel {
 	private static final long serialVersionUID = -6387922432121206731L;
-	private ContinuousColorMapper mapper;
-	private double min, max;
+	private final ContinuousColorMapper mapper;
+	private final double min;
+    private final double max;
 
 
 	public GradientPanel(ContinuousColorMapper mapper, double min, double max) {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java
index 9522ec7a15..c98b5812e3 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java
@@ -23,6 +23,7 @@
 
 import java.awt.*;
 import java.awt.color.ColorSpace;
+import java.util.Arrays;
 
 /**
  * @author Spencer Bliven
@@ -156,8 +157,7 @@ public void setColorSpace(ColorSpace colorSpace, InterpolationDirection[] dir) {
 
 	public void setColorSpace(ColorSpace colorSpace) {
 		InterpolationDirection[] dir = new InterpolationDirection[colorSpace.getNumComponents()];
-		for(int i=0;i<dir.length;i++)
-			dir[i] = InterpolationDirection.INNER;
+        Arrays.fill(dir, InterpolationDirection.INNER);
 		this.setColorSpace(colorSpace, dir);
 	}
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LogColorMapper.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LogColorMapper.java
index 89dac75045..7f26310d51 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LogColorMapper.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LogColorMapper.java
@@ -34,7 +34,7 @@
  */
 public class LogColorMapper extends ContinuousColorMapperTransform {
 
-	private int base;
+	private final int base;
 
 	/**
 	 * Creates a new LogColorMapper with base 10.
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
index f5fc7da991..91e570d6d1 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
@@ -239,7 +239,7 @@ public static String printSymmetryAxes(CeSymmResult symm,boolean allAxes)
 		for (Axis a : symmAxes) {
 			RotationAxis rot = a.getRotationAxis();
 			List<List<Integer>> cyclicForm = axes.getRepeatsCyclicForm(a);
-			List<Atom> repAtoms = new ArrayList<Atom>();
+			List<Atom> repAtoms = new ArrayList<>();
 			for(List<Integer> cycle : cyclicForm) {
 				for(Integer repeat : cycle) {
 					repAtoms.addAll(Arrays.asList(repeats.get(repeat)));
@@ -247,7 +247,7 @@ public static String printSymmetryAxes(CeSymmResult symm,boolean allAxes)
 			}
 
 			script += rot.getJmolScript(
-					repAtoms.toArray(new Atom[repAtoms.size()]), id);
+					repAtoms.toArray(new Atom[0]), id);
 			id++;
 		}
 
@@ -299,7 +299,7 @@ public static String printSymmetryGroup(CeSymmResult symm)
 	 */
 	public static String getSymmTitle(CeSymmResult result) {
 
-		StringBuffer buff = new StringBuffer();
+		StringBuilder buff = new StringBuilder();
 
 		// Add algorithm name and version
 		buff.append(result.getMultipleAlignment().getEnsemble()
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryGui.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryGui.java
index 7568141b55..8447d35702 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryGui.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryGui.java
@@ -65,19 +65,19 @@
  */
 public class SymmetryGui extends JFrame {
 
-	private final static long serialVersionUID = 0l;
+	private final static long serialVersionUID = 0L;
 
-	private CESymmParameters params = new CESymmParameters();
+	private final CESymmParameters params = new CESymmParameters();
 	private JButton abortB;
 
-	private SelectPDBPanel  tab1 ;
-	private PDBUploadPanel  tab2;
-	private ScopSelectPanel tab3;
+	private final SelectPDBPanel  tab1 ;
+	private final PDBUploadPanel  tab2;
+	private final ScopSelectPanel tab3;
 
 	private Thread thread;
 	private AlignmentCalculationRunnable alicalc;
-	private JTabbedPane masterPane;
-	private JTabbedPane tabPane;
+	private final JTabbedPane masterPane;
+	private final JTabbedPane tabPane;
 	private JProgressBar progress;
 
 	public static void main(String[] args){
@@ -159,7 +159,7 @@ private Box setupAlgorithm() {
 		algorithmList.setSelectedIndex(0);
 
 		Action paramAction = new AbstractAction("Parameters") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			// This method is called when the button is pressed
 			@Override
 			public void actionPerformed(ActionEvent evt) {
@@ -188,7 +188,7 @@ private Box initButtons(){
 		progress.setVisible(false);
 
 		Action action1 = new AbstractAction("Analyze") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			// This method is called when the button is pressed
 			@Override
 			public void actionPerformed(ActionEvent evt) {
@@ -206,7 +206,7 @@ public void actionPerformed(ActionEvent evt) {
 		JButton submitB = new JButton(action1);
 
 		Action action3 = new AbstractAction("Abort") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			// This method is called when the button is pressed
 			@Override
 			public void actionPerformed(ActionEvent evt) {
@@ -220,7 +220,7 @@ public void actionPerformed(ActionEvent evt) {
 		abortB.setEnabled(false);
 
 		Action action2 = new AbstractAction("Exit") {
-			public static final long serialVersionUID = 0l;
+			public static final long serialVersionUID = 0L;
 			// This method is called when the button is pressed
 			@Override
 			public void actionPerformed(ActionEvent evt) {
@@ -302,10 +302,7 @@ private void calcAlignment() {
 			progress.setIndeterminate(true);
 			ProgressThreadDrawer drawer = new ProgressThreadDrawer(progress);
 			drawer.start();
-		} catch (StructureException e){
-			JOptionPane.showMessageDialog(null,
-					"Could not align structures. Exception: " + e.getMessage());
-		} catch (IOException e) {
+		} catch (StructureException | IOException e){
 			JOptionPane.showMessageDialog(null,
 					"Could not align structures. Exception: " + e.getMessage());
 		}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java
index 1fdb882f7c..d6f617225d 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java
@@ -43,8 +43,8 @@
  */
 public class SymmetryListener implements ActionListener {
 
-	private MultipleAlignmentJmol jmol;
-	private CeSymmResult symm;
+	private final MultipleAlignmentJmol jmol;
+	private final CeSymmResult symm;
 
 	private static final Logger logger = LoggerFactory
 			.getLogger(SymmetryListener.class);
@@ -64,34 +64,43 @@ public void actionPerformed(ActionEvent ae) {
 			logger.error("Currently not displaying a symmetry!");
 
 		try {
-			if (cmd.equals("Repeats Superposition")) {
-				MultipleAlignmentJmol j = SymmetryDisplay.displayRepeats(symm);
-				String s = SymmetryDisplay.printSymmetryAxes(symm, false);
-				j.evalString(s);
-				j.evalString("save STATE state_1");
+			switch (cmd) {
+				case "Repeats Superposition": {
+					MultipleAlignmentJmol j = SymmetryDisplay.displayRepeats(symm);
+					String s = SymmetryDisplay.printSymmetryAxes(symm, false);
+					j.evalString(s);
+					j.evalString("save STATE state_1");
 
 
-			} else if (cmd.equals("Multiple Structure Alignment")) {
-				MultipleAlignmentJmol j = SymmetryDisplay.displayFull(symm);
-				String s = SymmetryDisplay.printSymmetryAxes(symm);
-				j.evalString(s);
-				j.evalString("save STATE state_1");
+					break;
+				}
+				case "Multiple Structure Alignment": {
+					MultipleAlignmentJmol j = SymmetryDisplay.displayFull(symm);
+					String s = SymmetryDisplay.printSymmetryAxes(symm);
+					j.evalString(s);
+					j.evalString("save STATE state_1");
 
-			} else if (cmd.equals("Optimal Self Alignment")) {
-				Atom[] cloned = StructureTools.cloneAtomArray(symm.getAtoms());
-				AbstractAlignmentJmol jmol = StructureAlignmentDisplay.display(
-						symm.getSelfAlignment(), symm.getAtoms(), cloned);
-				RotationAxis axis = new RotationAxis(symm.getSelfAlignment());
-				jmol.evalString(axis.getJmolScript(symm.getAtoms()));
-				jmol.setTitle(SymmetryDisplay.getSymmTitle(symm));
+					break;
+				}
+				case "Optimal Self Alignment":
+					Atom[] cloned = StructureTools.cloneAtomArray(symm.getAtoms());
+					AbstractAlignmentJmol jmol = StructureAlignmentDisplay.display(
+							symm.getSelfAlignment(), symm.getAtoms(), cloned);
+					RotationAxis axis = new RotationAxis(symm.getSelfAlignment());
+					jmol.evalString(axis.getJmolScript(symm.getAtoms()));
+					jmol.setTitle(SymmetryDisplay.getSymmTitle(symm));
 
-			} else if (cmd.equals("Show Symmetry Group")) {
-				String script = SymmetryDisplay.printSymmetryGroup(symm);
-				jmol.evalString(script);
+					break;
+				case "Show Symmetry Group":
+					String script = SymmetryDisplay.printSymmetryGroup(symm);
+					jmol.evalString(script);
 
-			} else if (cmd.equals("Show Symmetry Axes")) {
-				String s = SymmetryDisplay.printSymmetryAxes(symm);
-				jmol.evalString(s);
+					break;
+				case "Show Symmetry Axes": {
+					String s = SymmetryDisplay.printSymmetryAxes(symm);
+					jmol.evalString(s);
+					break;
+				}
 			}
 
 		} catch (Exception e) {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java
index 428635c78b..608c8b69ff 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java
@@ -39,10 +39,10 @@
  *
  */
 public class JmolSymmetryScriptGeneratorH extends JmolSymmetryScriptGenerator {
-	private static double AXIS_SCALE_FACTOR = 1.2;
-	private static double SIDE_CHAIN_EXTENSION = 6.0;
-	private HelixAxisAligner helixAxisAligner = null;
-	private String name = "";
+	private static final double AXIS_SCALE_FACTOR = 1.2;
+	private static final double SIDE_CHAIN_EXTENSION = 6.0;
+	private HelixAxisAligner helixAxisAligner;
+	private String name;
 	private String defaultColoring = "";
 	private boolean onTheFly = false;
 
@@ -416,16 +416,12 @@ public String colorBySubunit() {
 			   colors[half+i] = temp;
 			}
 		}
-		Map<Color4f, List<String>> colorMap = new HashMap<Color4f, List<String>>();
+		Map<Color4f, List<String>> colorMap = new HashMap<>();
 
 		for (int i = 0; i < orbits.size(); i++) {
 				for (Integer j: orbits.get(i)) {
 					Color4f c = colors[i];
-					List<String> ids = colorMap.get(c);
-					if (ids == null) {
-						ids = new ArrayList<String>();
-						colorMap.put(c,  ids);
-					}
+					List<String> ids = colorMap.computeIfAbsent(c, k -> new ArrayList<>());
 					String id = getChainSpecification(modelNumbers, chainIds, j);
 					ids.add(id);
 				}
@@ -448,15 +444,11 @@ public String colorBySequenceCluster() {
 		int clusters = Collections.max(seqClusterIds) + 1;
 		Color[] col = ColorBrewer.BrBG.getColorPalette(clusters);
 		Color4f[] colors = ColorConverter.convertColor4f(col);
-		Map<Color4f, List<String>> colorMap = new HashMap<Color4f, List<String>>();
+		Map<Color4f, List<String>> colorMap = new HashMap<>();
 
 		for (int i = 0; i < n; i++) {
 			Color4f c = colors[seqClusterIds.get(i)];
-			List<String> ids = colorMap.get(c);
-			if (ids == null) {
-				ids = new ArrayList<String>();
-				colorMap.put(c,  ids);
-			}
+			List<String> ids = colorMap.computeIfAbsent(c, k -> new ArrayList<>());
 			String id = getChainSpecification(modelNumbers, chainIds, i);
 			ids.add(id);
 
@@ -481,7 +473,7 @@ public String colorBySymmetry() {
 		List<Integer> clusterIds = subunits.getClusterIds();
 		int clusterCount = Collections.max(clusterIds) + 1;
 
-		Map<Color4f, List<String>> colorMap = new HashMap<Color4f, List<String>>();
+		Map<Color4f, List<String>> colorMap = new HashMap<>();
 
 		int maxLen = 0;
 		for (List<Integer> unit: units) {
@@ -502,11 +494,7 @@ public String colorBySymmetry() {
 					Color4f c = new Color4f(colors[count]);
 					count++;
 					c.scale(scale);
-					List<String> ids = colorMap.get(c);
-					if (ids == null) {
-						ids = new ArrayList<String>();
-						colorMap.put(c,  ids);
-					}
+					List<String> ids = colorMap.computeIfAbsent(c, k -> new ArrayList<>());
 					String id = getChainSpecification(modelNumbers, chainIds, subunit);
 					ids.add(id);
 				}
@@ -579,7 +567,7 @@ private List<Point3d> extendUnitCenters(List<Point3d> points) {
 //		System.out.println("XZRadius: " + radius);
 
 
-		List<Point3d> ePoints = new ArrayList<Point3d>(points.size());
+		List<Point3d> ePoints = new ArrayList<>(points.size());
 		for (Point3d p: points) {
 			Point3d q = new Point3d(p);
 			transformation.transform(q);
@@ -597,7 +585,7 @@ private List<Point3d> interiorCenters(List<Point3d> points) {
 		Matrix4d transformation = helixAxisAligner.getTransformation();
 		Matrix4d reversetransformation = helixAxisAligner.getReverseTransformation();
 
-		List<Point3d> ePoints = new ArrayList<Point3d>(points.size());
+		List<Point3d> ePoints = new ArrayList<>(points.size());
 		for (Point3d p: points) {
 			Point3d q = new Point3d(p);
 			transformation.transform(q);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
index 1a4f8a7301..8c968eb7c0 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
@@ -41,15 +41,15 @@
  *
  */
 public abstract class JmolSymmetryScriptGeneratorPointGroup extends JmolSymmetryScriptGenerator {
-	private static String N_FOLD_AXIS_COLOR = "red";
-	private static String TWO_FOLD_AXIS_COLOR = "deepskyblue";
-	private static String THREE_FOLD_AXIS_COLOR = "lime";
-	private static double AXIS_SCALE_FACTOR = 1.2;
+	private static final String N_FOLD_AXIS_COLOR = "red";
+	private static final String TWO_FOLD_AXIS_COLOR = "deepskyblue";
+	private static final String THREE_FOLD_AXIS_COLOR = "lime";
+	private static final double AXIS_SCALE_FACTOR = 1.2;
 
-	private RotationAxisAligner rotationAxisAligner = null;
-	private RotationGroup rotationGroup = null;
+	private RotationAxisAligner rotationAxisAligner;
+	private RotationGroup rotationGroup;
 	private Polyhedron polyhedron = null;
-	private String name = "";
+	private String name;
 	private String defaultColoring = "";
 	private boolean onTheFly = true;
 
@@ -298,15 +298,14 @@ public String colorBySubunit() {
 		List<List<Integer>> orbits = rotationAxisAligner.getOrbits();
 		int fold = rotationGroup.getRotation(0).getFold();
 
-		Color[] col = null;
-		Color4f[] colors = null;
+		Color[] col;
+		Color4f[] colors;
 		if (fold > 1) {
 			col = ColorBrewer.Spectral.getColorPalette(2*fold);
-			colors = ColorConverter.convertColor4f(col);
 		} else {
 			col = ColorBrewer.Spectral.getColorPalette(orbits.size());
-			colors = ColorConverter.convertColor4f(col);
 		}
+		colors = ColorConverter.convertColor4f(col);
 		int half = colors.length/2;
 		for (int i = 0; i < half; i++) {
 			if (i % 2 != 0) {
@@ -315,7 +314,7 @@ public String colorBySubunit() {
 			   colors[half+i] = temp;
 			}
 		}
-		Map<Color4f, List<String>> colorMap = new HashMap<Color4f, List<String>>();
+		Map<Color4f, List<String>> colorMap = new HashMap<>();
 
 		for (int i = 0; i < orbits.size(); i++) {
 			for (int j = 0; j < fold; j++) {
@@ -330,11 +329,7 @@ public String colorBySubunit() {
 				}
 				int subunit = orbits.get(i).get(j);
 				Color4f c = colors[colorIndex];
-				List<String> ids = colorMap.get(c);
-				if (ids == null) {
-					ids = new ArrayList<String>();
-					colorMap.put(c,  ids);
-				}
+				List<String> ids = colorMap.computeIfAbsent(c, k -> new ArrayList<>());
 				String id = getChainSpecification(modelNumbers, chainIds, subunit);
 				ids.add(id);
 			}
@@ -356,15 +351,11 @@ public String colorBySequenceCluster() {
 		int clusters = Collections.max(seqClusterIds) + 1;
 		Color[] col = ColorBrewer.BrBG.getColorPalette(clusters);
 		Color4f[] colors = ColorConverter.convertColor4f(col);
-		Map<Color4f, List<String>> colorMap = new HashMap<Color4f, List<String>>();
+		Map<Color4f, List<String>> colorMap = new HashMap<>();
 
 		for (int i = 0; i < n; i++) {
 			Color4f c = colors[seqClusterIds.get(i)];
-			List<String> ids = colorMap.get(c);
-			if (ids == null) {
-				ids = new ArrayList<String>();
-				colorMap.put(c,  ids);
-			}
+			List<String> ids = colorMap.computeIfAbsent(c, k -> new ArrayList<>());
 			String id = getChainSpecification(modelNumbers, chainIds, i);
 			ids.add(id);
 
@@ -388,7 +379,7 @@ public String colorBySymmetry() {
 		int n = subunits.getSubunitCount();
 		int fold = rotationGroup.getRotation(0).getFold();
 
-		Map<Color4f, List<String>> colorMap = new HashMap<Color4f, List<String>>();
+		Map<Color4f, List<String>> colorMap = new HashMap<>();
 
 		// Simple Cn symmetry
 		if (pointGroup.startsWith("C") && n == fold) {
@@ -396,7 +387,7 @@ public String colorBySymmetry() {
 			// complex cases
 		} else if ((pointGroup.startsWith("D") && orbits.size() > 2) ||
 				pointGroup.equals("T")|| pointGroup.equals("O") || pointGroup.equals("I")) {
-			int nColor = 0;
+			int nColor;
 			if (orbits.size() % 2 == 0) {
 				nColor = orbits.size()/2;
 			} else {
@@ -412,11 +403,7 @@ public String colorBySymmetry() {
 					colorIndex = orbits.size() - 1 - i;
 				}
 				Color4f c = colors[colorIndex];
-				List<String> ids = colorMap.get(c);
-				if (ids == null) {
-					ids = new ArrayList<String>();
-					colorMap.put(c,  ids);
-				}
+				List<String> ids = colorMap.computeIfAbsent(c, k -> new ArrayList<>());
 				for (int subunit: orbits.get(i)) {
 					String id = getChainSpecification(modelNumbers, chainIds, subunit);
 					ids.add(id);
@@ -429,11 +416,7 @@ public String colorBySymmetry() {
 
 			for (int i = 0; i < orbits.size(); i++) {
 				Color4f c = new Color4f(colors[i]);
-				List<String> ids = colorMap.get(c);
-				if (ids == null) {
-					ids = new ArrayList<String>();
-					colorMap.put(c,  ids);
-				}
+				List<String> ids = colorMap.computeIfAbsent(c, k -> new ArrayList<>());
 				List<Integer> orbit = orbits.get(i);
 				for (int j = 0; j < orbit.size(); j++) {
 					String id = getChainSpecification(modelNumbers, chainIds, orbit.get(j));
@@ -531,20 +514,16 @@ private Map<Color4f, List<String>> getCnColorMap() {
 
 		int fold = rotationGroup.getRotation(0).getFold();
 
-		Map<Color4f, List<String>> colorMap = new HashMap<Color4f, List<String>>();
+		Map<Color4f, List<String>> colorMap = new HashMap<>();
 		Color4f[] colors = getSymmetryColors(fold);
 
 		for (List<Integer> orbit: orbits) {
 			for (int i = 0; i < fold; i++) {
 				int subunit = orbit.get(i);
-				String id = null;
+				String id;
 				id = getChainSpecification(modelNumbers, chainIds, subunit);
 				Color4f c = colors[i];
-				List<String> ids = colorMap.get(c);
-				if (ids == null) {
-					ids = new ArrayList<String>();
-					colorMap.put(c, ids);
-				}
+				List<String> ids = colorMap.computeIfAbsent(c, k -> new ArrayList<>());
 				ids.add(id);
 			}
 		}
@@ -580,8 +559,8 @@ private Color4f getPolyhedronColor() {
 	 */
 	private Color4f[] getSymmetryColors(int nColors) {
 		String pointGroup = rotationGroup.getPointGroup();
-		Color[] col = null;
-		Color4f[] colors = null;
+		Color[] col;
+		Color4f[] colors;
 		if (pointGroup.equals("C1")) {
 			col = ColorBrewer.Greys.getColorPalette(nColors);
 			colors = ColorConverter.convertColor4f(col);
@@ -638,7 +617,7 @@ private String drawInertiaAxes() {
 			s.append(" off;");
 		}
 		return s.toString();
-	};
+	}
 
 	private String drawSymmetryAxes() {
 		StringBuilder s = new StringBuilder();
@@ -649,8 +628,8 @@ private String drawSymmetryAxes() {
 		}
 
 		float diameter = 0.5f;
-		double radius = 0;
-		String color = "";
+		double radius;
+		String color;
 
 		List<Rotation> axes = getUniqueAxes();
 
@@ -933,7 +912,7 @@ private static Vector3d[] getC2PolygonVertices(Vector3d axis, Vector3d reference
 		// in reverse order, draw reflected half of arc (1/6 of full circle)
 		// don't draw first and last element, since the are already part of the previous arc
 		for (int i = k; i < 2*k-2; i++) {
-			axisAngle.angle = (f/2*k + i + 1.5) * 2 * Math.PI/(f*k);
+			axisAngle.angle = (f/2.0*k + i + 1.5) * 2 * Math.PI/(f*k);
 			vectors[i] = new Vector3d(ref);
 			m.set(axisAngle);
 			// make sure matrix element m33 is 1.0. It's 0 on Linux.
@@ -947,7 +926,7 @@ private static Vector3d[] getC2PolygonVertices(Vector3d axis, Vector3d reference
 
 
 	private List<Rotation> getUniqueAxes() {
-		List<Rotation> uniqueRotations = new ArrayList<Rotation>();
+		List<Rotation> uniqueRotations = new ArrayList<>();
 
 		for (int i = 0, n = rotationGroup.getOrder(); i < n; i++) {
 			Rotation rotationI = rotationGroup.getRotation(i);
diff --git a/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/JmolViewerImplTest.java b/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/JmolViewerImplTest.java
index 727cbc137d..7bf2cebab9 100644
--- a/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/JmolViewerImplTest.java
+++ b/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/JmolViewerImplTest.java
@@ -36,11 +36,11 @@ public class JmolViewerImplTest {
 
 
 	@Before
-	public void setUp() throws Exception {
+	public void setUp() {
 	}
 
 	@After
-	public void tearDown() throws Exception {
+	public void tearDown() {
 	}
 
 	@Test
diff --git a/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/RenderStyleTest.java b/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/RenderStyleTest.java
index b26b3b6431..1c99583faa 100644
--- a/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/RenderStyleTest.java
+++ b/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/RenderStyleTest.java
@@ -34,11 +34,11 @@ public class RenderStyleTest {
 
 
 	@Before
-	public void setUp() throws Exception {
+	public void setUp() {
 	}
 
 	@After
-	public void tearDown() throws Exception {
+	public void tearDown() {
 	}
 
 	@Test
diff --git a/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/StructureViewerTest.java b/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/StructureViewerTest.java
index f954b27b20..0c29bbd0f7 100644
--- a/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/StructureViewerTest.java
+++ b/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/StructureViewerTest.java
@@ -37,11 +37,11 @@ public class StructureViewerTest {
 
 
 	@Before
-	public void setUp() throws Exception {
+	public void setUp() {
 	}
 
 	@After
-	public void tearDown() throws Exception {
+	public void tearDown() {
 	}
 
 	/**
@@ -178,7 +178,7 @@ public void testSetZoom() {
 	   // fail("The test case is a prototype.");
 	}
 
-	public class StructureViewerImpl implements StructureViewer {
+	public static class StructureViewerImpl implements StructureViewer {
 
 		@Override
 		public void setStructure(Structure structure) {
diff --git a/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/TestAtomInfo.java b/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/TestAtomInfo.java
index 9d271a873c..a36c8e0f14 100644
--- a/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/TestAtomInfo.java
+++ b/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/TestAtomInfo.java
@@ -34,7 +34,7 @@ public void testAtomInfoConversion(){
 		String s1 = "[MET]508:A.CA/1 #3918";
 
 		AtomInfo aa = AtomInfo.fromString(s1);
-		Assert.assertTrue(aa.getAtomName().equals("CA"));
+        Assert.assertEquals("CA", aa.getAtomName());
 		Assert.assertEquals(aa.getChainId(), "A");
 		Assert.assertEquals(aa.getModelNumber(), 1);
 		Assert.assertEquals(aa.getResidueName(), "MET");
diff --git a/biojava-structure/src/main/java/demo/DemoCE.java b/biojava-structure/src/main/java/demo/DemoCE.java
index 5d7859db4f..47a70913c0 100644
--- a/biojava-structure/src/main/java/demo/DemoCE.java
+++ b/biojava-structure/src/main/java/demo/DemoCE.java
@@ -55,8 +55,8 @@ public static void main(String[] args){
 
 		AtomCache cache = new AtomCache();
 
-		Structure structure1 = null;
-		Structure structure2 = null;
+		Structure structure1;
+		Structure structure2;
 
 		try {
 
@@ -110,7 +110,7 @@ private static void printScores(AFPChain afpChain) {
 		System.out.println("RMSD      :\t" + String.format("%.2f",afpChain.getTotalRmsdOpt() )+ "\t The RMSD of the alignment");
 		System.out.println("Z-score   :\t" + afpChain.getProbability() + "\t The Z-score of the alignment (CE)");
 		System.out.println("TM-score  :\t" + String.format("%.2f",afpChain.getTMScore()) + "\t The TM-score of the alignment.");
-		System.out.println("");
+		System.out.println();
 		System.out.println("Other scores:");
 		System.out.println("Identity  :\t" + String.format("%.2f",afpChain.getIdentity())   + "\t The percent of residues that are sequence-identical in the alignment.");
 		System.out.println("Similarity:\t" + String.format("%.2f",afpChain.getSimilarity()) + "\t The percent of residues in the alignment that are sequence-similar.");
diff --git a/biojava-structure/src/main/java/demo/DemoFATCAT.java b/biojava-structure/src/main/java/demo/DemoFATCAT.java
index d24473d98a..ad7b0a5b43 100644
--- a/biojava-structure/src/main/java/demo/DemoFATCAT.java
+++ b/biojava-structure/src/main/java/demo/DemoFATCAT.java
@@ -49,8 +49,8 @@ public static void main(String[] args){
 
 		AtomCache cache = new AtomCache();
 
-		Structure structure1 = null;
-		Structure structure2 = null;
+		Structure structure1;
+		Structure structure2;
 
 		try {
 
diff --git a/biojava-structure/src/main/java/demo/DemoMmtfReader.java b/biojava-structure/src/main/java/demo/DemoMmtfReader.java
index 0dc4b76ab1..a5dacae622 100644
--- a/biojava-structure/src/main/java/demo/DemoMmtfReader.java
+++ b/biojava-structure/src/main/java/demo/DemoMmtfReader.java
@@ -37,9 +37,8 @@ public class DemoMmtfReader {
 	 * Main function to run the demo
 	 * @param args no args to specify
 	 * @throws IOException
-	 * @throws StructureException
-	 */
-	public static void main(String[] args) throws IOException, StructureException {
+     */
+	public static void main(String[] args) throws IOException {
 		Structure structure = MmtfActions.readFromWeb("4cup");
 		System.out.println(structure.getChains().size());
 	}
diff --git a/biojava-structure/src/main/java/demo/DemoMultipleMC.java b/biojava-structure/src/main/java/demo/DemoMultipleMC.java
index 4ca84f0174..37979e28ea 100644
--- a/biojava-structure/src/main/java/demo/DemoMultipleMC.java
+++ b/biojava-structure/src/main/java/demo/DemoMultipleMC.java
@@ -48,7 +48,7 @@
  */
 public class DemoMultipleMC {
 
-	public static void main(String[] args) throws IOException, StructureException, InterruptedException, ExecutionException {
+	public static void main(String[] args) throws IOException, StructureException {
 
 		//Specify the structures to align
 		//ASP-proteinases (CEMC paper)
@@ -92,9 +92,9 @@ public static void main(String[] args) throws IOException, StructureException, I
 
 		//Load the CA atoms of the structures
 		AtomCache cache = new AtomCache();
-		List<Atom[]> atomArrays = new ArrayList<Atom[]>();
+		List<Atom[]> atomArrays = new ArrayList<>();
 
-		List<StructureIdentifier> ids = new ArrayList<StructureIdentifier>();
+		List<StructureIdentifier> ids = new ArrayList<>();
 		for (String name:names)	{
 			StructureIdentifier id = new StructureName(name);
 			ids.add(id);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/AminoAcid.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/AminoAcid.java
index 1877a84c16..ecc76c1dfa 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/AminoAcid.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/AminoAcid.java
@@ -52,44 +52,44 @@ public interface AminoAcid extends Group {
 	 * Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
 	 *
 	 */
-	public static final String ATOMRECORD = "ATOM";
+    String ATOMRECORD = "ATOM";
 
 	/**
 	 * Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
 	 *
 	 */
-	public static final String SEQRESRECORD = "SEQRES";
+    String SEQRESRECORD = "SEQRES";
 
 	/**
 	 * Get N atom.
 	 *
 	 * @return an Atom object or null if N atom does not exist
 	 */
-	public Atom getN()    ;
+    Atom getN()    ;
 
 	/**
 	 * Get CA atom.
 	 * @return an Atom object or null if CA atom does not exist
 	 */
-	public Atom getCA()   ;
+    Atom getCA()   ;
 
 	/**
 	 * Get C atom.
 	 * @return an Atom object or null if C atom does not exist
 	 */
-	public Atom getC()    ;
+    Atom getC()    ;
 
 	/**
 	 * Get O atom.
 	 * @return an Atom object or null if O atom does not exist
 	 */
-	public Atom getO()    ;
+    Atom getO()    ;
 
 	/**
 	 * Get CB atom.
 	 * @return an Atom object or null if CB atom does not exist
 	 */
-	public Atom getCB()   ;
+    Atom getCB()   ;
 
 	/**
 	 * Returns the name of the AA, in single letter code.
@@ -97,7 +97,7 @@ public interface AminoAcid extends Group {
 	 * @return a Character object representing the amino type value
 	 * @see #setAminoType
 	 */
-	public  Character getAminoType() ;
+    Character getAminoType() ;
 
 	/**
 	 * Set the name of the AA, in single letter code .
@@ -105,7 +105,7 @@ public interface AminoAcid extends Group {
 	 * @param aa  a Character object specifying the amino type value
 	 * @see #getAminoType
 	 */
-	public void setAminoType(Character aa) ;
+    void setAminoType(Character aa) ;
 
 	/**
 	 * Allows to distinguish between amino acids that are provided
@@ -113,7 +113,7 @@ public interface AminoAcid extends Group {
 	 * @param recordName either ATOMRECORD or SEQRESRECORD
 	 * @see #getRecordType()
 	 */
-	public void setRecordType(String recordName);
+    void setRecordType(String recordName);
 
 	/**
 	 * Allows to distinguish between amino acids that are provided
@@ -121,6 +121,6 @@ public interface AminoAcid extends Group {
 	 * @return the origin of this amino acid (ATOM or SEQRES records)
 	 * @see #setRecordType(String)
 	 */
-	public String getRecordType();
+    String getRecordType();
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
index 7b1c722bd9..23a401e0d0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
@@ -48,7 +48,7 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @param s  a trimmed String specifying the name value
 	 * @see #getName
 	 */
-	public void   setName(String s);
+    void   setName(String s);
 
 	/**
 	 * Get atom name, e.g. "CA".
@@ -57,42 +57,42 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @return a trimmed String representing the name value
 	 * @see #setName
 	 */
-	public String getName();
+    String getName();
 
 	/**
 	 * Set element of the atom name, e.g. {@link Element#Fe}
 	 * @param e  an Element enumeration
 	 * @see #getElement
 	 */
-	public void   setElement(Element e);
+    void   setElement(Element e);
 
 	/**
 	 * Get element of the atom, e.g. {@link Element#Ca}
 	 * @return an Element enumeration
 	 * @see #setElement
 	 */
-	public Element getElement();
+    Element getElement();
 
 	/**
 	 * Set PDB atom number.
 	 * @param i  an int specifying the PDBserial value
 	 * @see #getPDBserial
 	 */
-	public void setPDBserial(int i) ;
+    void setPDBserial(int i) ;
 
 	/**
 	 * Get PDB atom number.
 	 * @return an int representing the PDBserial value
 	 * @see #setPDBserial
 	 */
-	public int  getPDBserial() ;
+    int  getPDBserial() ;
 
 	/**
 	 * Set the coordinates.
 	 * @param c  an array of doubles specifying the coords value
 	 * @see #getCoords
 	 */
-	public void    setCoords(double[] c);
+    void    setCoords(double[] c);
 
 	/**
 	 * Get the coordinates.
@@ -100,7 +100,7 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @see #setCoords
 	 * @see #getCoordsAsPoint3d()
 	 */
-	public double[] getCoords() ;
+    double[] getCoords() ;
 
 	/**
 	 * Get the coordinates.
@@ -110,56 +110,56 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @return a reference to the Point3d coordinates
 	 * @see #getCoords()
 	 */
-	public Point3d getCoordsAsPoint3d();
+    Point3d getCoordsAsPoint3d();
 
 	/**
 	 * Set the X coordinate.
 	 * @param x  a double
 	 * @see #getX()
 	 */
-	public void setX(double x);
+    void setX(double x);
 
 	/**
 	 * Set the Y coordinate.
 	 * @param y  a double
 	 * @see #getY()
 	 */
-	public void setY(double y);
+    void setY(double y);
 
 	/**
 	 * Set the Z coordinate.
 	 * @param z  a double
 	 * @see #getZ()
 	 */
-	public void setZ(double z);
+    void setZ(double z);
 
 	/**
 	 * Get coordinate X.
 	 * @return a double
 	 * @see #setX(double)
 	 */
-	public double getX() ;
+    double getX() ;
 
 	/**
 	 * Get coordinate Y.
 	 * @return a double
 	 * @see #setY(double)
 	 */
-	public double getY() ;
+    double getY() ;
 
 	/**
 	 * Get coordinate Z.
 	 * @return a double
 	 * @see #setZ(double)
 	 */
-	public double getZ() ;
+    double getZ() ;
 
 	/**
 	 * Set alternate Location.
 	 * @param c  a Character object specifying the alt loc value
 	 * @see #getAltLoc
 	 */
-	public void setAltLoc(Character c);
+    void setAltLoc(Character c);
 
 	/**
 	 * Get alternate Location.
@@ -167,41 +167,41 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * is represented by ' ' (space character, ascii 32).
 	 * @see #setAltLoc
 	 */
-	public Character getAltLoc();
+    Character getAltLoc();
 
 	/**
 	 * Set occupancy.
 	 * @param occupancy  a float specifying the occupancy value
 	 * @see #getOccupancy
 	 */
-	public void setOccupancy(float occupancy) ;
+    void setOccupancy(float occupancy) ;
 
 	/**
 	 * Get occupancy.
 	 * @return a float representing the occupancy value
 	 * @see #setOccupancy
 	 */
-	public float getOccupancy();
+    float getOccupancy();
 
 	/**
 	 * Set temp factor .
 	 * @param temp  a float specifying the temp factor value
 	 * @see #getTempFactor
 	 */
-	public void   setTempFactor(float temp) ;
+    void   setTempFactor(float temp) ;
 
 	/**
 	 * Get temp factor.
 	 * @return a float representing the temp factor value
 	 * @see #setTempFactor
 	 */
-	public float getTempFactor() ;
+    float getTempFactor() ;
 
 	/**
 	 * Return an identical copy of this  object .
 	 * @return  an identical copy of this  object
 	 */
-	public Object clone();
+    Object clone();
 
 	/**
 	 * Set the back-reference to its parent Group.
@@ -209,7 +209,7 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @see #getGroup()
 	 */
 
-	public void setGroup(Group parent);
+    void setGroup(Group parent);
 
 	/**
 	 * Return the parent Group of the Atom.
@@ -217,27 +217,27 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @return Group the parent Group of the Atom, or null
 	 * @see #setGroup(Group)
 	 */
-	public Group getGroup();
+    Group getGroup();
 
 	/**
 	 * Add a bond
 	 * @param bond to be added
 	 * @see #getBonds()
 	 */
-	public void addBond(Bond bond);
+    void addBond(Bond bond);
 
 	/**
 	 * Get all {@link Bond}s this atom is part of.
 	 *
 	 * @return a list of {@link Bond}s or null if no bonds exist for this Atom
 	 */
-	public List<Bond> getBonds();
+    List<Bond> getBonds();
 
 	/**
 	 * Sets the bonds
 	 * @param bonds
 	 */
-	public void setBonds(List<Bond> bonds);
+    void setBonds(List<Bond> bonds);
 
 
 	/** Test if another atom has a bond to this atom
@@ -245,19 +245,19 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @param other
 	 * @return
 	 */
-	public boolean hasBond(Atom other);
+    boolean hasBond(Atom other);
 
 	/**
 	 * Get the charge of this atom
 	 *
 	 * @return a the integer charge.
 	 */
-	public short getCharge();
+    short getCharge();
 
 	/**
 	 * Set the charge of this atom
 	 *
 	 * @return void.
 	 */
-	public void setCharge(short charge);
+    void setCharge(short charge);
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomIterator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomIterator.java
index 20c0bde011..090c0f92df 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomIterator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomIterator.java
@@ -43,7 +43,7 @@ public class AtomIterator implements Iterator<Atom> {
 
 	private Group     group         ;
 	private int current_atom_pos    ;
-	private GroupIterator groupiter ;
+	private final GroupIterator groupiter ;
 
 	/**
 	 * Constructs an AtomIterator object over all models
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java
index b6c806417e..5330f3fe54 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java
@@ -61,54 +61,46 @@ public class AtomPositionMap {
 
 	private static final Logger logger = LoggerFactory.getLogger(AtomPositionMap.class);
 
-	private HashMap<ResidueNumber, Integer> hashMap;
-	private TreeMap<ResidueNumber, Integer> treeMap;
+	private final HashMap<ResidueNumber, Integer> hashMap;
+	private final TreeMap<ResidueNumber, Integer> treeMap;
 
 
 	/**
 	 * Used as a Predicate to indicate whether a particular Atom should be mapped
 	 */
-	public static interface GroupMatcher {
+	public interface GroupMatcher {
 		boolean matches(Group group);
 	}
 
 	/**
 	 * Matches CA atoms of protein groups
 	 */
-	public static final GroupMatcher AMINO_ACID_MATCHER = new GroupMatcher() {
-		@Override
-		public boolean matches(Group group) {
-			if( group == null )
-				return false;
-			ChemComp chem = group.getChemComp();
-			if(chem == null)
-				return false;
-			// Get polymer type
-			PolymerType polyType = chem.getPolymerType();
-			if( polyType == null) {
-				ResidueType type = chem.getResidueType();
-				if(type != null ) {
-					polyType = type.getPolymerType();
-				}
-			}
-			if( polyType == null ) {
-				return false;
+	public static final GroupMatcher AMINO_ACID_MATCHER = group -> {
+		if( group == null )
+			return false;
+		ChemComp chem = group.getChemComp();
+		if(chem == null)
+			return false;
+		// Get polymer type
+		PolymerType polyType = chem.getPolymerType();
+		if( polyType == null) {
+			ResidueType type = chem.getResidueType();
+			if(type != null ) {
+				polyType = type.getPolymerType();
 			}
-
-			return PolymerType.PROTEIN_ONLY.contains(polyType)
-					&& group.hasAtom(StructureTools.CA_ATOM_NAME);
 		}
+		if( polyType == null ) {
+			return false;
+		}
+
+		return PolymerType.PROTEIN_ONLY.contains(polyType)
+				&& group.hasAtom(StructureTools.CA_ATOM_NAME);
 	};
 
 	/**
 	 * Matches all atoms
 	 */
-	public static final GroupMatcher ANYTHING_MATCHER = new GroupMatcher() {
-		@Override
-		public boolean matches(Group group) {
-			return true;
-		}
-	};
+	public static final GroupMatcher ANYTHING_MATCHER = group -> true;
 
 	/**
 	 * A map that is sorted by its values. Used for the treemap
@@ -123,7 +115,7 @@ public boolean matches(Group group) {
 	private static class ValueComparator<T, V extends Comparable<V>> implements Comparator<T>, Serializable {
 	private static final long serialVersionUID = 1;
 
-		private Map<T, V> map;
+		private final Map<T, V> map;
 
 		public ValueComparator(Map<T, V> map) {
 			this.map = map;
@@ -153,7 +145,7 @@ public AtomPositionMap(Atom[] atoms) {
 	 * @param atoms
 	 */
 	public AtomPositionMap(Atom[] atoms, GroupMatcher matcher) {
-		hashMap = new HashMap<ResidueNumber, Integer>();
+		hashMap = new HashMap<>();
 		for (int i = 0; i < atoms.length; i++) {
 			Group group = atoms[i].getGroup();
 			ResidueNumber rn = group.getResidueNumber();
@@ -163,8 +155,8 @@ public AtomPositionMap(Atom[] atoms, GroupMatcher matcher) {
 				}
 			}
 		}
-		Comparator<ResidueNumber> vc = new ValueComparator<ResidueNumber, Integer>(hashMap);
-		treeMap = new TreeMap<ResidueNumber, Integer>(vc);
+		Comparator<ResidueNumber> vc = new ValueComparator<>(hashMap);
+		treeMap = new TreeMap<>(vc);
 		treeMap.putAll(hashMap);
 	}
 
@@ -341,7 +333,7 @@ public List<ResidueRangeAndLength> getRanges() {
 		String currentChain = "";
 		ResidueNumber first = null;
 		ResidueNumber prev = null;
-		List<ResidueRangeAndLength> ranges = new ArrayList<ResidueRangeAndLength>();
+		List<ResidueRangeAndLength> ranges = new ArrayList<>();
 		for (ResidueNumber rn : treeMap.keySet()) {
 			if (!rn.getChainName().equals(currentChain)) {
 				if (first != null) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
index b0d7253507..df2eefaf47 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
@@ -22,6 +22,7 @@
 package org.biojava.nbio.structure;
 
 import java.io.Serializable;
+import java.util.Objects;
 
 /**
  * Describes author attributes for author information in a PDB file.
@@ -59,10 +60,10 @@ public boolean equals(Object obj) {
 			return false;
 		}
 		final Author other = (Author) obj;
-		if ((this.surname == null) ? (other.surname != null) : !this.surname.equals(other.surname)) {
+		if (!Objects.equals(this.surname, other.surname)) {
 			return false;
 		}
-		return !((this.initials == null) ? (other.initials != null) : !this.initials.equals(other.initials));
+		return !(!Objects.equals(this.initials, other.initials));
 	}
 
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
index 365948f059..42c7e4116c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
@@ -31,8 +31,8 @@ public class BioAssemblyIdentifier implements StructureIdentifier {
 
 	private static final long serialVersionUID = -356206725119993449L;
 
-	private String pdbCode;
-	private int biolNr;
+	private final String pdbCode;
+	private final int biolNr;
 
 	public static final Pattern BIO_NAME_PATTERN = Pattern.compile("^(?:BIO:)([0-9][a-z0-9]{3})(?::([0-9]+))?$", Pattern.CASE_INSENSITIVE);
 
@@ -74,12 +74,12 @@ public Structure loadStructure(AtomCache cache) throws StructureException,
 	}
 
 	@Override
-	public SubstructureIdentifier toCanonical() throws StructureException {
-		return new SubstructureIdentifier(pdbCode, new ArrayList<ResidueRange>());
+	public SubstructureIdentifier toCanonical() {
+		return new SubstructureIdentifier(pdbCode, new ArrayList<>());
 	}
 
 	@Override
-	public Structure reduce(Structure input) throws StructureException {
+	public Structure reduce(Structure input) {
 		// Should be the full structure
 		return input;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java
index 7af10c23e0..8e27a2438c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java
@@ -39,7 +39,7 @@ public interface Bond extends Serializable {
 	 * @see #getAtomB()
 	 * @return one of the two atoms in this bond
 	 */
-	public Atom getAtomA();
+    Atom getAtomA();
 
 	/**
 	 * Gets atom 'B' of this bond. There is no meaning to which atom is 'A' and
@@ -49,7 +49,7 @@ public interface Bond extends Serializable {
 	 * @see #getAtomA()
 	 * @return one of the two atoms in this bond
 	 */
-	public Atom getAtomB();
+    Atom getAtomB();
 
 	/**
 	 * A utility method to get the other atom in a bond, given one of its atoms.
@@ -66,7 +66,7 @@ public interface Bond extends Serializable {
 	 *             if the passed atom is not in this bond
 	 * @return the atom in this bond that was not passed as an argument
 	 */
-	public Atom getOther(Atom exclude);
+    Atom getOther(Atom exclude);
 
 	/**
 	 * Gets the bond order of this bond. A return value of '1' corresponds to a
@@ -74,7 +74,7 @@ public interface Bond extends Serializable {
 	 *
 	 * @return this bond's bond order
 	 */
-	public int getBondOrder();
+    int getBondOrder();
 
 	/**
 	 * Gets the distance between the two atoms of this bond.
@@ -85,5 +85,5 @@ public interface Bond extends Serializable {
 	 *
 	 * @return the distance between the two atoms of this bond.
 	 */
-	public double getLength();
+    double getLength();
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java
index b467a7272e..ac2aa20125 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java
@@ -33,9 +33,9 @@
 public class BondImpl implements Bond {
 
 	private static final long serialVersionUID = 8836120946858134380L;
-	private Atom atomA;
-	private Atom atomB;
-	private int bondOrder;
+	private final Atom atomA;
+	private final Atom atomB;
+	private final int bondOrder;
 
 	/**
 	 * Constructs a new bond from a pair of atoms and the bond order of the bond
@@ -90,7 +90,7 @@ public BondImpl(Atom atomA, Atom atomB, int bondOrder, boolean addSelfToAtoms) {
 	private void addSelfToAtoms() {
 		List<Bond> bonds = atomA.getBonds();
 		if (bonds==null) {
-			bonds = new ArrayList<Bond>(AtomImpl.BONDS_INITIAL_CAPACITY);
+			bonds = new ArrayList<>(AtomImpl.BONDS_INITIAL_CAPACITY);
 			atomA.setBonds(bonds);
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java
index 9b3f752092..a569fb3fe2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java
@@ -26,5 +26,5 @@
  * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
  */
 public enum BondType {
-	UNDEFINED, COVALENT, IONIC, HBOND, VANDERWAALS, HYDROPHOBIC, METAL, PLANAR, ATOM_PLANE;
+	UNDEFINED, COVALENT, IONIC, HBOND, VANDERWAALS, HYDROPHOBIC, METAL, PLANAR, ATOM_PLANE
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
index b6fde44843..6bd5c47faa 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -339,8 +339,8 @@ public static final double getPsi(AminoAcid a, AminoAcid b)
 	 * @return true if ...
 	 */
 	public static final boolean isConnected(AminoAcid a, AminoAcid b) {
-		Atom C = null ;
-		Atom N = null;
+		Atom C;
+		Atom N;
 
 		C = a.getC();
 		N = b.getN();
@@ -422,7 +422,7 @@ public static final void rotate(Group group, double[][] rotationmatrix)
 		}
 		AtomIterator iter = new AtomIterator(group) ;
 		while (iter.hasNext()) {
-			Atom atom = null ;
+			Atom atom;
 
 			atom = iter.next() ;
 			rotate(atom,rotationmatrix);
@@ -651,7 +651,7 @@ public static final void plus(Structure s, Matrix matrix){
 		Atom oldAtom = null;
 		Atom rotOldAtom = null;
 		while (iter.hasNext()) {
-			Atom atom = null ;
+			Atom atom;
 
 			atom = iter.next() ;
 			try {
@@ -700,7 +700,7 @@ public static final void shift(Structure structure, Atom a ){
 
 		AtomIterator iter = new AtomIterator(structure) ;
 		while (iter.hasNext() ) {
-			Atom atom = null ;
+			Atom atom;
 
 			atom = iter.next()  ;
 
@@ -746,7 +746,7 @@ public static final void shift(Group group , Atom a ){
 
 		AtomIterator iter = new AtomIterator(group) ;
 		while (iter.hasNext() ) {
-			Atom atom = null ;
+			Atom atom;
 
 			atom = iter.next()  ;
 
@@ -947,11 +947,8 @@ public static final Atom[] centerAtoms(Atom[] atomSet)
 	 *
 	 * @param atomSet
 	 *            a set of Atoms
-	 * @return an Atom representing the Centroid of the set of atoms
-	 * @throws StructureException
-	 * */
-	public static final Atom[] centerAtoms(Atom[] atomSet, Atom centroid)
-			throws StructureException {
+	 * @return an Atom representing the Centroid of the set of atoms */
+	public static final Atom[] centerAtoms(Atom[] atomSet, Atom centroid) {
 
 		Atom shiftVector = getCenterVector(atomSet, centroid);
 
@@ -974,10 +971,8 @@ public static final Atom[] centerAtoms(Atom[] atomSet, Atom centroid)
 	 *            the amino acid for which a "virtual" CB atom should be
 	 *            calculated
 	 * @return a "virtual" CB atom
-	 * @throws StructureException
-	 */
-	public static final Atom createVirtualCBAtom(AminoAcid amino)
-			throws StructureException{
+     */
+	public static final Atom createVirtualCBAtom(AminoAcid amino) {
 
 		AminoAcid  ala = StandardAminoAcid.getAminoAcid("ALA");
 		Atom aN  = ala.getN();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
index 150d806995..3c694acc4c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
@@ -423,13 +423,13 @@ public interface Chain extends Serializable {
 	 *
 	 * @return true if there are only solvent molecules in this chain.
 	 */
-	public boolean isWaterOnly();
+    boolean isWaterOnly();
 
 	/**  Returns true if the given chain is composed of non-polymeric (including water) groups only.
 	 *
 	 * @return true if only non-polymeric groups in this chain.
 	 */
-	public boolean isPureNonPolymer();
+    boolean isPureNonPolymer();
 
 	/**
 	 * Get the predominant {@link GroupType} for a given Chain, following these
@@ -448,7 +448,7 @@ public interface Chain extends Serializable {
 	 *
 	 * @return
 	 */
-	public GroupType getPredominantGroupType();
+    GroupType getPredominantGroupType();
 
 	/**
 	 * Tell whether given chain is a protein chain
@@ -456,7 +456,7 @@ public interface Chain extends Serializable {
 	 * @return true if protein, false if nucleotide or ligand
 	 * @see #getPredominantGroupType()
 	 */
-	public  boolean isProtein();
+    boolean isProtein();
 
 	/**
 	 * Tell whether given chain is DNA or RNA
@@ -464,5 +464,5 @@ public interface Chain extends Serializable {
 	 * @return true if nucleic acid, false if protein or ligand
 	 * @see #getPredominantGroupType()
 	 */
-	public  boolean isNucleicAcid();
+    boolean isNucleicAcid();
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java
index 9400333aba..c763b5767e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java
@@ -66,7 +66,7 @@ public class ChainImpl implements Chain {
 	private EntityInfo entity;
 	private Structure parent;
 
-	private Map<String, Integer> pdbResnumMap;
+	private final Map<String, Integer> pdbResnumMap;
 	private String asymId; // the 'internal' chain identifier as used in mmCIF files
 
 
@@ -348,7 +348,7 @@ public Group[] getGroupsByPDB(ResidueNumber start, ResidueNumber end, boolean ig
 			throws StructureException {
 		// Short-circut for include all groups
 		if(start == null && end == null) {
-			return groups.toArray(new Group[groups.size()]);
+			return groups.toArray(new Group[0]);
 		}
 
 
@@ -415,7 +415,7 @@ public Group[] getGroupsByPDB(ResidueNumber start, ResidueNumber end, boolean ig
 
 		//not checking if the end has been found in this case...
 
-		return retlst.toArray(new Group[retlst.size()] );
+		return retlst.toArray(new Group[0]);
 	}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/DBRef.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/DBRef.java
index b4c397c544..8e27c687e1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/DBRef.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/DBRef.java
@@ -156,13 +156,13 @@ public String toString(){
 			for (Method m : methods) {
 				String name = m.getName();
 
-				if (name.substring(0, 3).equals("get")) {
+				if (name.startsWith("get")) {
 					if (name.equals("getClass")) {
 						continue;
 					}
 					Object o = m.invoke(this);
 					if (o != null) {
-						buf.append(name.substring(3, name.length()));
+						buf.append(name.substring(3));
 						buf.append(": ").append(o).append(" ");
 					}
 				}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
index 6afeb2a9b8..f2e8206824 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
@@ -159,24 +159,24 @@ public enum Element {
 	 */
 	R(104, 0, 105, 0.0f, 0.0f, 0, 0, 4, 1, 0, 0.000f, -1, 3, null, 0.00f, ElementType.UNKNOWN); // this is an R-group
 	// should these be declared final?
-	private int atomicNumber;
-	private int period;
+	private final int atomicNumber;
+	private final int period;
 	//private int hillOrder;
-	private float VDWRadius; // in Angstroms
-	private float covalentRadius; // in Angstroms
-	private int valenceElectronCount;
-	private int minimumValence;
-	private int maximumValence;
-	private int commonValence;
-	private int maximumCovalentValence;
-	private float atomicMass;
-	private int coreElectronCount;
-	private int oxidationState;
-	private int[] allOxidationStates;
+	private final float VDWRadius; // in Angstroms
+	private final float covalentRadius; // in Angstroms
+	private final int valenceElectronCount;
+	private final int minimumValence;
+	private final int maximumValence;
+	private final int commonValence;
+	private final int maximumCovalentValence;
+	private final float atomicMass;
+	private final int coreElectronCount;
+	private final int oxidationState;
+	private final int[] allOxidationStates;
 	// Pauling electronegativity: http://en.wikipedia.org/wiki/Electronegativity
-	private float paulingElectronegativity;
+	private final float paulingElectronegativity;
 	// Element type: http://www.ptable.com/
-	private ElementType elementType;
+	private final ElementType elementType;
 	//private static final Element[] hillOrderIndex;
 
 //
@@ -191,12 +191,12 @@ public enum Element {
 	private static final Map<String,Element> allElements ;
 
 	static {
-		allElements = new HashMap<String,Element>();
+		allElements = new HashMap<>();
 		for (Element e : Element.values()){
 			allElements.put(e.toString().toLowerCase(), e);
 		}
 	}
-	private Element(int atomicNumber,
+	Element(int atomicNumber,
 			int period,
 			int hillOrder,
 			float VDWRadius,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ElementType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ElementType.java
index 41abfd33c6..ea1f3f5e01 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ElementType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ElementType.java
@@ -48,9 +48,9 @@ public enum ElementType {
 	POST_TRANSITION_METAL(true),
 	UNKNOWN(false);
 
-	private boolean metal;
+	private final boolean metal;
 
-	private ElementType(boolean metal) {
+	ElementType(boolean metal) {
 		this.metal = metal;
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java
index cc52262b12..cf6dd2ec74 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java
@@ -77,7 +77,7 @@ public class EntityInfo implements Serializable {
 	 * Initialised lazily upon call to {@link #getAlignedResIndex(Group, Chain)}
 	 * Keys are asym_ids of chains, values maps of residue numbers to indices.
 	 */
-	private Map<String, Map<ResidueNumber,Integer>> chains2pdbResNums2ResSerials;
+	private final Map<String, Map<ResidueNumber,Integer>> chains2pdbResNums2ResSerials;
 
 	private String refChainId;
 	private String description = null;
@@ -159,11 +159,11 @@ public EntityInfo (EntityInfo c) {
 		this.title = c.title;
 
 		if (c.synonyms!=null) {
-			this.synonyms = new ArrayList<String>();
+			this.synonyms = new ArrayList<>();
 			synonyms.addAll(c.synonyms);
 		}
 		if (c.ecNums!=null) {
-			this.ecNums = new ArrayList<String>();
+			this.ecNums = new ArrayList<>();
 			ecNums.addAll(c.ecNums);
 		}
 
@@ -244,7 +244,7 @@ public Chain getRepresentative() {
 			chainIds.add(chain.getId());
 		}
 
-		Collections.sort(chainIds, String.CASE_INSENSITIVE_ORDER);
+		chainIds.sort(String.CASE_INSENSITIVE_ORDER);
 
 		for (Chain chain:chains) {
 			if (chain.getId().equals(chainIds.get(0))) {
@@ -380,7 +380,7 @@ private void initResSerialsMap(Chain c) {
 			return;
 		}
 
-		Map<ResidueNumber,Integer> resNums2ResSerials = new HashMap<ResidueNumber, Integer>();
+		Map<ResidueNumber,Integer> resNums2ResSerials = new HashMap<>();
 		chains2pdbResNums2ResSerials.put(c.getId(), resNums2ResSerials);
 
 		for (int i=0;i<c.getSeqResGroups().size();i++) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
index 9abf52b423..f72aa66ecd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
@@ -64,7 +64,7 @@ public enum EntityType {
 	/**
 	 * @param entType the type of the Entity
 	 */
-	private EntityType(String entType) {
+    EntityType(String entType) {
 
 		this.setEntityType(entType);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ExperimentalTechnique.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ExperimentalTechnique.java
index 65fc455d26..6a2631b9e5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ExperimentalTechnique.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ExperimentalTechnique.java
@@ -59,11 +59,11 @@ public enum ExperimentalTechnique {
 	 private static final HashMap<String, ExperimentalTechnique> expTechStr2Value = initExpTechStr2Value();
 
 
-	 private String name;
-	 private boolean isCrystallographic;
-	 private boolean isNmr;
+	 private final String name;
+	 private final boolean isCrystallographic;
+	 private final boolean isNmr;
 
-	 private ExperimentalTechnique(String name, boolean isXtallographic, boolean isNmr) {
+	 ExperimentalTechnique(String name, boolean isXtallographic, boolean isNmr) {
 		 this.name = name;
 		 this.isCrystallographic = isXtallographic;
 		 this.isNmr = isNmr;
@@ -71,7 +71,7 @@ private ExperimentalTechnique(String name, boolean isXtallographic, boolean isNm
 
 
 	 private static HashMap<String, ExperimentalTechnique> initExpTechStr2Value() {
-		HashMap<String, ExperimentalTechnique> expTechStr2Value = new HashMap<String, ExperimentalTechnique>();
+		HashMap<String, ExperimentalTechnique> expTechStr2Value = new HashMap<>();
 		for(ExperimentalTechnique exp:ExperimentalTechnique.values()) {
 			expTechStr2Value.put(exp.getName(), exp);
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java
index f2bc5a506a..5240d7295a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java
@@ -55,27 +55,27 @@
 public interface Group extends Serializable {
 
 	/** Group property key for secondary structure annotation */
-	public static final String SEC_STRUC = "secstruc";
+    String SEC_STRUC = "secstruc";
 
 	/**
 	 * Get number of atoms.
 	 * @return number of atoms of this Group
 	 */
-	public int size();
+    int size();
 
 	/**
 	 * Return true or false, depending if this group has 3D coordinates or not.
 	 *
 	 * @return true if Group has 3D coordinates
 	 */
-	public boolean has3D ();
+    boolean has3D();
 
 	/**
 	 * Flag if group has 3D data .
 	 *
 	 * @param flag  true to set flag that this Group has 3D coordinates
 	 */
-	public void setPDBFlag(boolean flag);
+    void setPDBFlag(boolean flag);
 
 	/**
 	 * Get Type of group, one of {@link GroupType#AMINOACID}, {@link GroupType#HETATM}
@@ -83,14 +83,14 @@ public interface Group extends Serializable {
 	 *
 	 * @return a String representing the type value
 	 */
-	public GroupType getType();
+    GroupType getType();
 
 	/**
 	 * Add an atom to this group.
 	 *
 	 * @param atom  an Atom object
 	 */
-	public void addAtom(Atom atom);
+    void addAtom(Atom atom);
 
 	/**
 	 * Get list of atoms.
@@ -98,7 +98,7 @@ public interface Group extends Serializable {
 	 * @return a List object representing the atoms
 	 * @see #setAtoms(List)
 	 */
-	public List<Atom> getAtoms() ;
+    List<Atom> getAtoms() ;
 
 
 	/**
@@ -106,13 +106,13 @@ public interface Group extends Serializable {
 	 * @see Atom
 	 * @param atoms a list of atoms
 	 */
-	public void setAtoms(List<Atom> atoms);
+    void setAtoms(List<Atom> atoms);
 
 	/**
 	 * Remove all atoms from this group.
 	 *
 	 */
-	public void clearAtoms();
+    void clearAtoms();
 
 	/**
 	 * Get an atom given its PDB name.
@@ -125,7 +125,7 @@ public interface Group extends Serializable {
 	 * @param name  a trimmed String representing the atom's PDB name, e.g. "CA"
 	 * @return an Atom object or null if no such atom exists within this group
 	 */
-	public Atom getAtom(String name) ;
+    Atom getAtom(String name) ;
 	
 	/**
 	 * Get at atom by position.
@@ -133,7 +133,7 @@ public interface Group extends Serializable {
 	 * @param position  an int
 	 * @return an Atom object or null if no Atom exists for given position
 	 */
-	public Atom getAtom(int position) ;
+    Atom getAtom(int position) ;
 
 	/**
 	 * Tell whether a particular atom exists within this group.
@@ -143,7 +143,7 @@ public interface Group extends Serializable {
 	 * @param name  a trimmed String representing the atom's PDB name, e.g. "CA"
 	 * @return true if Atom with name exists within this group
 	 */
-	public boolean hasAtom(String name);
+    boolean hasAtom(String name);
 
 	/**
 	 * Get the PDB 3-letter name for this group. (e.g. ALA)
@@ -151,7 +151,7 @@ public interface Group extends Serializable {
 	 * @return a String representing the PDBName value
 	 * @see #setPDBName
 	 */
-	public String getPDBName();
+    String getPDBName();
 
 	/**
 	 * Set the PDB 3-letter name for this group. (e.g. ALA)
@@ -159,7 +159,7 @@ public interface Group extends Serializable {
 	 * @param s  a String specifying the PDBName value
 	 * @see #getPDBName
 	 */
-	public void setPDBName(String s) ;
+    void setPDBName(String s) ;
 
 
 	/**
@@ -183,7 +183,7 @@ public interface Group extends Serializable {
 	 * @return true if all Atoms required for an AminoAcid are available (N, CA, C, O)
 	 * @see #getType
 	 */
-	public boolean hasAminoAtoms() ;
+    boolean hasAminoAtoms() ;
 
 
 	/**
@@ -191,7 +191,7 @@ public interface Group extends Serializable {
 	 *
 	 * @return true if a polymeric group
 	 */
-	public boolean isPolymeric();
+    boolean isPolymeric();
 
 
 	/**
@@ -199,7 +199,7 @@ public interface Group extends Serializable {
 	 *
 	 * @return true if an amino acid
 	 */
-	public boolean isAminoAcid();
+    boolean isAminoAcid();
 
 
 	/**
@@ -207,7 +207,7 @@ public interface Group extends Serializable {
 	 *
 	 * @return true if a nucleotide
 	 */
-	public boolean isNucleotide();
+    boolean isNucleotide();
 
 
 
@@ -220,7 +220,7 @@ public interface Group extends Serializable {
 	 * @param properties  a Map object specifying the properties value
 	 * @see #getProperties
 	 */
-	public void setProperties(Map<String,Object> properties) ;
+    void setProperties(Map<String, Object> properties) ;
 
 	/**
 	 * Return properties.
@@ -228,7 +228,7 @@ public interface Group extends Serializable {
 	 *
 	 * @return a HashMap object representing the properties value
 	 */
-	public Map<String,Object> getProperties() ;
+    Map<String,Object> getProperties() ;
 
 	/**
 	 * Set a single property .
@@ -237,7 +237,7 @@ public interface Group extends Serializable {
 	 * @param value  an Object
 	 * @see #getProperty
 	 */
-	public void setProperty(String key, Object value) ;
+    void setProperty(String key, Object value) ;
 
 	/**
 	 * Get a single property .
@@ -246,21 +246,21 @@ public interface Group extends Serializable {
 	 * @return an Object
 	 * @see #setProperty
 	 */
-	public Object getProperty(String key) ;
+    Object getProperty(String key) ;
 
 	/**
 	 * Get an Atom Iterator.
 	 *
 	 * @return an Iterator object
 	 */
-	public Iterator<Atom> iterator() ;
+    Iterator<Atom> iterator() ;
 
 
 	/**
 	 * Returns and identical copy of this Group object .
 	 * @return  and identical copy of this Group object
 	 */
-	public Object clone();
+    Object clone();
 
 	/**
 	 * Sets the back-reference to its parent Chain.
@@ -268,7 +268,7 @@ public interface Group extends Serializable {
 	 * @see #getChain()
 	 * @since 3.0
 	 */
-	public void setChain(Chain chain);
+    void setChain(Chain chain);
 
 	/**
 	 * Returns the parent Chain of the Group.
@@ -277,7 +277,7 @@ public interface Group extends Serializable {
 	 * @see #setChain(Chain)
 	 * @since 3.0
 	 */
-	public Chain getChain() ;
+    Chain getChain() ;
 
 	/**
 	 * Returns a dynamically created ResidueNumber for the group - this
@@ -286,7 +286,7 @@ public interface Group extends Serializable {
 	 * @return ResidueNumber for the group.
 	 * @since 3.0
 	 */
-	public ResidueNumber getResidueNumber();
+    ResidueNumber getResidueNumber();
 
 
 	/**
@@ -294,7 +294,7 @@ public interface Group extends Serializable {
 	 *
 	 * @param residueNumber the PDB residueNumber
 	 */
-	public void setResidueNumber(ResidueNumber residueNumber);
+    void setResidueNumber(ResidueNumber residueNumber);
 
 	/**
 	 * Utility method to temporarily set a chainID for a group, if a parent chain object does not exist yet.
@@ -304,7 +304,7 @@ public interface Group extends Serializable {
 	 * @param residueNumber
 	 * @param iCode
 	 */
-	public void setResidueNumber(String chainId, Integer residueNumber, Character iCode);
+    void setResidueNumber(String chainId, Integer residueNumber, Character iCode);
 
 	/**
 	 * Utility method for returning the chainId of the Group or null if no
@@ -314,21 +314,21 @@ public interface Group extends Serializable {
 	 * @since 3.0
 	 * @return  the ID of the chain
 	 */
-	public String getChainId();
+    String getChainId();
 
 	/**
 	 * Set the Chemical Component that closer describes this group.
 	 *
 	 * @param cc the chemical component
 	 */
-	public void setChemComp(ChemComp cc);
+    void setChemComp(ChemComp cc);
 
 	/**
 	 * Get the chemical component that closer describes this group. If the information does not exist yet, fetches the information from PDB web site.
 	 *
 	 * @return the Chemical Component definition for this Group.
 	 */
-	public ChemComp getChemComp();
+    ChemComp getChemComp();
 
 
 	/**
@@ -337,7 +337,7 @@ public interface Group extends Serializable {
 	 * @return boolean flag if there are alternate locations.
 	 * @see #getAltLocs()
 	 */
-	public boolean hasAltLoc();
+    boolean hasAltLoc();
 
 
 	/**
@@ -363,14 +363,14 @@ public interface Group extends Serializable {
 	 *
 	 * @return List of other groups that are on alternate locations
 	 */
-	public List<Group> getAltLocs();
+    List<Group> getAltLocs();
 
 	/**
 	 * Add a group that is an alternate location for this group.
 	 *
 	 * @param g the altloc group to add
 	 */
-	public void addAltLoc(Group g);
+    void addAltLoc(Group g);
 
 	/**
 	 * Determines if this group is water.
@@ -378,7 +378,7 @@ public interface Group extends Serializable {
 	 * @see GroupType#WATERNAMES
 	 * @return true if it's water, false otherwise.
 	 */
-	public boolean isWater();
+    boolean isWater();
 
 	/**
 	 * Gets the alternate location group to this group that has the alt-loc character code passed.
@@ -386,7 +386,7 @@ public interface Group extends Serializable {
 	 * @param altLoc the alternate location code of the group desired
 	 * @return the alternate location group if found, or null otherwise
 	 */
-	public Group getAltLocGroup(Character altLoc);
+    Group getAltLocGroup(Character altLoc);
 
 
 	/**
@@ -394,13 +394,13 @@ public interface Group extends Serializable {
 	 * all internal Collection objects to the required size.
 	 *
 	 */
-	public void trimToSize();
+    void trimToSize();
 
 	/**
 	 * Function to get the Group as an MDL molblock
 	 * @return the string of the MDL molblock
 	 */
-	public String toSDF();
+    String toSDF();
 
 	/**
 	 * Tells whether the group is annotated as HETATM in the file.
@@ -408,7 +408,7 @@ public interface Group extends Serializable {
 	 * polymeric group is in a ligand chain or not.
 	 * @return
 	 */
-	public boolean isHetAtomInFile();
+    boolean isHetAtomInFile();
 
 	/**
 	 * Sets the field isHetAtomInFile which is intented only for
@@ -416,5 +416,5 @@ public interface Group extends Serializable {
 	 * or in a polymeric chain.
 	 * @param isHetAtomInFile
 	 */
-	public void setHetAtomInFile(boolean isHetAtomInFile);
+    void setHetAtomInFile(boolean isHetAtomInFile);
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupIterator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupIterator.java
index a0e3c5be8b..4fa6a80a18 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupIterator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupIterator.java
@@ -38,7 +38,7 @@
 
 public class GroupIterator implements Iterator<Group> {
 
-	private Structure structure   ;
+	private final Structure structure   ;
 	private int current_model_pos ;
 	private int current_chain_pos ;
 	private int current_group_pos ;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupType.java
index 234813ef42..0e9ef84860 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupType.java
@@ -58,7 +58,7 @@ public enum GroupType {
 
 	private final String name;
 	private final Set<ResidueType> types;
-	private GroupType(String name,Set<ResidueType> types) {
+	GroupType(String name, Set<ResidueType> types) {
 		this.name = name;
 		this.types = types;
 	}
@@ -95,7 +95,7 @@ public Set<ResidueType> getResidueTypes() {
 	 * @return
 	 */
 	private static Set<ResidueType> matchPolymerTypes(Set<PolymerType> allowedTypes) {
-		Set<ResidueType> matched = new HashSet<ResidueType>();
+		Set<ResidueType> matched = new HashSet<>();
 		for(ResidueType restype : ResidueType.values()) {
 			if(allowedTypes.contains(restype.polymerType)) {
 				matched.add(restype);
@@ -109,7 +109,7 @@ private static Set<ResidueType> matchPolymerTypes(Set<PolymerType> allowedTypes)
 	 * @return
 	 */
 	private static Set<ResidueType> getHetatmTypes() {
-		Set<ResidueType> unmatched = new HashSet<ResidueType>();
+		Set<ResidueType> unmatched = new HashSet<>();
 		for(ResidueType restype : ResidueType.values()) {
 			if(!AMINOACID.getResidueTypes().contains(restype) &&
 					!NUCLEOTIDE.getResidueTypes().contains(restype) ) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
index 037dcb2b0b..b52b9b7c23 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
@@ -87,7 +87,7 @@ public enum PerformanceBehavior {
 
 	}
 
-	private static PerformanceBehavior performanceBehavior=PerformanceBehavior.LESS_MEMORY_SLOWER_PERFORMANCE;
+	private static final PerformanceBehavior performanceBehavior=PerformanceBehavior.LESS_MEMORY_SLOWER_PERFORMANCE;
 
 	private Map<String,Atom> atomNameLookup;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/JournalArticle.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/JournalArticle.java
index ff92f608f6..3723136daa 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/JournalArticle.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/JournalArticle.java
@@ -32,8 +32,8 @@
 public class JournalArticle implements Serializable {
 
 	private static final long serialVersionUID = 5062668226159515468L;
-	private List<Author> authorList = new ArrayList<Author>();
-	private List<Author> editorList = new ArrayList<Author>();
+	private List<Author> authorList = new ArrayList<>();
+	private List<Author> editorList = new ArrayList<>();
 	private String title = "";
 	private String ref = "";
 	private String journalName = "";
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Model.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Model.java
index 36cce008cb..4ff903814a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Model.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Model.java
@@ -41,9 +41,9 @@ public class Model implements Serializable {
 
 	private static final Logger logger = LoggerFactory.getLogger(Model.class);
 
-	private List<Chain> polyChains;
-	private List<Chain> nonPolyChains;
-	private List<Chain> waterChains;
+	private final List<Chain> polyChains;
+	private final List<Chain> nonPolyChains;
+	private final List<Chain> waterChains;
 
 	public Model(){
 		polyChains = new ArrayList<>();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java
index 42e4662689..0a82563f07 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java
@@ -59,7 +59,7 @@ public class Mutator{
 	List<String> supportedAtoms;
 
 	public Mutator(){
-		supportedAtoms = new ArrayList<String>();
+		supportedAtoms = new ArrayList<>();
 		supportedAtoms.add("N");
 		supportedAtoms.add("CA");
 		supportedAtoms.add("C");
@@ -138,10 +138,8 @@ public Structure  mutate(Structure struc, String chainId, String pdbResnum, Stri
 	 * @param oldAmino
 	 * @param newType
 	 * @return a new, mutated, residue
-	 * @throws PDBParseException
 	 */
-	public AminoAcid mutateResidue(AminoAcid oldAmino, String newType)
-	throws PDBParseException {
+	public AminoAcid mutateResidue(AminoAcid oldAmino, String newType) {
 
 		AminoAcid newgroup = new AminoAcidImpl();
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
index dbcc0f794c..04223ae778 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
@@ -73,7 +73,7 @@ public class PDBHeader implements PDBRecord {
 	private Long id;
 	public static final String newline = System.getProperty("line.separator");
 
-	private DateFormat dateFormat;
+	private final DateFormat dateFormat;
 
 	private Map<Integer,BioAssemblyInfo> bioAssemblies ;
 
@@ -90,7 +90,7 @@ public PDBHeader(){
 		rFree = DEFAULT_RFREE;
 		rWork = DEFAULT_RFREE;
 
-		bioAssemblies = new LinkedHashMap<Integer, BioAssemblyInfo>();
+		bioAssemblies = new LinkedHashMap<>();
 		crystallographicInfo = new PDBCrystallographicInfo();
 
 	}
@@ -111,22 +111,20 @@ public String toString(){
 			for (Method m : methods) {
 				String name = m.getName();
 
-				if (name.substring(0, 3).equals("get")) {
+				if (name.startsWith("get")) {
 					if (name.equals("getClass")) {
 						continue;
 					}
 					Object o = m.invoke(this);
 					if (o != null) {
-						buf.append(name.substring(3, name.length()));
+						buf.append(name.substring(3));
 						buf.append(": ").append(o).append(" ");
 					}
 				}
 			}
 		} catch (ClassNotFoundException e) {
 			logger.error("Exception caught while creating toString  ",e);
-		} catch (InvocationTargetException e) {
-			logger.error("Exception caught while creating toString ",e);
-		} catch (IllegalAccessException e) {
+		} catch (InvocationTargetException | IllegalAccessException e) {
 			logger.error("Exception caught while creating toString ",e);
 		}
 
@@ -408,7 +406,7 @@ public boolean equals(PDBHeader other){
 			for (Method m : methods) {
 				String name = m.getName();
 
-				if (name.substring(0, 3).equals("get")) {
+				if (name.startsWith("get")) {
 					if (name.equals("getClass")) {
 						continue;
 					}
@@ -432,13 +430,7 @@ public boolean equals(PDBHeader other){
 					}
 				}
 			}
-		} catch (ClassNotFoundException e) {
-			logger.error("Exception caught while comparing PDBHeader objects ",e);
-			return false;
-		} catch (InvocationTargetException e) {
-			logger.error("Exception caught while comparing PDBHeader objects ",e);
-			return false;
-		} catch (IllegalAccessException e) {
+		} catch (ClassNotFoundException | IllegalAccessException | InvocationTargetException e) {
 			logger.error("Exception caught while comparing PDBHeader objects ",e);
 			return false;
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBRecord.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBRecord.java
index eb3b2b3e5a..0850c1b62c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBRecord.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBRecord.java
@@ -34,13 +34,13 @@ public interface PDBRecord extends Serializable {
 	 *
 	 * @return a String providing a PDB file like representation of the record.
 	 */
-	public String toPDB();
+    String toPDB();
 
 
 	/** Appends a PDB file like representation of this record to the provided StringBuffer.
 	 *
 	 */
-	public void toPDB(StringBuffer buf);
+    void toPDB(StringBuffer buf);
 
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java
index dfb95eab8e..d22558d903 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java
@@ -87,7 +87,7 @@ public class PDBStatus {
 	 *
 	 */
 	//TODO Use SoftReferences to allow garbage collection
-	private static Map<String, Map<String, String>> recordsCache= new Hashtable<String, Map<String, String>>();
+	private static final Map<String, Map<String, String>> recordsCache= new Hashtable<>();
 
 	/**
 	 * Represents the status of PDB IDs. 'OBSOLETE' and 'CURRENT' are the most
@@ -291,7 +291,7 @@ public static List<String> getReplacement(String oldPdbId, boolean recurse, bool
 		}
 
 		// If we're current, just return
-		LinkedList<String> results = new LinkedList<String>();
+		LinkedList<String> results = new LinkedList<>();
 		switch(status) {
 			case CURRENT:
 				results.add(oldPdbId);
@@ -313,12 +313,7 @@ public static List<String> getReplacement(String oldPdbId, boolean recurse, bool
 				}
 
 				String[] replacements = replacementStr.split(" ");
-				Arrays.sort(replacements, new Comparator<String>() {
-					@Override
-					public int compare(String o1, String o2) {
-						return o2.compareToIgnoreCase(o1);
-					}
-				});
+				Arrays.sort(replacements, (o1, o2) -> o2.compareToIgnoreCase(o1));
 				for(String replacement : replacements) {
 
 					// Return the replacement.
@@ -328,7 +323,7 @@ public int compare(String o1, String o2) {
 					}
 					else {
 						if(includeObsolete) {
-							mergeReversed(results,Arrays.asList(replacement));
+							mergeReversed(results, Collections.singletonList(replacement));
 						} else {
 							// check status of replacement
 							Status replacementStatus = getStatus(replacement);
@@ -339,7 +334,7 @@ public int compare(String o1, String o2) {
 								case CURRENT:
 								default:
 									// include it
-									mergeReversed(results,Arrays.asList(replacement));
+									mergeReversed(results, Collections.singletonList(replacement));
 							}
 						}
 					}
@@ -371,12 +366,7 @@ public int compare(String o1, String o2) {
 				results.add(oldPdbId);
 
 				String[] replacements = replacementStr.split(" ");
-				Arrays.sort(replacements, new Comparator<String>() {
-					@Override
-					public int compare(String o1, String o2) {
-						return o2.compareToIgnoreCase(o1);
-					}
-				});
+				Arrays.sort(replacements, (o1, o2) -> o2.compareToIgnoreCase(o1));
 				for(String replacement : replacements) {
 
 					// Return the replacement.
@@ -385,7 +375,7 @@ public int compare(String o1, String o2) {
 						mergeReversed(results,others);
 					}
 					else {
-						mergeReversed(results,Arrays.asList(replacement));
+						mergeReversed(results, Collections.singletonList(replacement));
 					}
 				}
 
@@ -482,7 +472,7 @@ public static List<String> getReplaces(String newPdbId, boolean recurse) {
 		String replacedList = attrs.get("replaces"); //space-delimited list
 		if(replacedList == null) {
 			// no replaces value; assume root
-			return new ArrayList<String>();
+			return new ArrayList<>();
 		}
 		String[] directDescendents = replacedList.split("\\s");
 
@@ -490,7 +480,7 @@ public static List<String> getReplaces(String newPdbId, boolean recurse) {
 		if(recurse) {
 			// Note: Assumes a proper directed acyclic graph of revisions
 			// Cycles will cause infinite loops.
-			List<String> allDescendents = new LinkedList<String>();
+			List<String> allDescendents = new LinkedList<>();
 			for(String replaced : directDescendents) {
 				List<String> roots = PDBStatus.getReplaces(replaced, recurse);
 				mergeReversed(allDescendents,roots);
@@ -536,7 +526,7 @@ public static void clearCache() {
 	 */
 	private static List<Map<String, String>> getStatusIdRecords(String[] pdbIDs) {
 
-		List<Map<String,String>> result = new ArrayList<Map<String,String>>(pdbIDs.length);
+		List<Map<String,String>> result = new ArrayList<>(pdbIDs.length);
 
 		String serverName = System.getProperty(PDB_SERVER_PROPERTY);
 
@@ -598,13 +588,7 @@ private static List<Map<String, String>> getStatusIdRecords(String[] pdbIDs) {
 			result.addAll(handler.getRecords());
 
 			// TODO should throw these forward and let the caller log
-		} catch (IOException e){
-			logger.error("Problem getting status for {} from PDB server. Error: {}", Arrays.toString(pdbIDs), e.getMessage());
-			return null;
-		} catch (SAXException e) {
-			logger.error("Problem getting status for {} from PDB server. Error: {}", Arrays.toString(pdbIDs), e.getMessage());
-			return null;
-		} catch (ParserConfigurationException e) {
+		} catch (IOException | ParserConfigurationException | SAXException e){
 			logger.error("Problem getting status for {} from PDB server. Error: {}", Arrays.toString(pdbIDs), e.getMessage());
 			return null;
 		}
@@ -619,10 +603,10 @@ private static List<Map<String, String>> getStatusIdRecords(String[] pdbIDs) {
 	 *
 	 */
 	private static class PDBStatusXMLHandler extends DefaultHandler {
-		private List<Map<String,String>> records;
+		private final List<Map<String,String>> records;
 
 		public PDBStatusXMLHandler() {
-			records = new ArrayList<Map<String,String>>();
+			records = new ArrayList<>();
 		}
 
 		/**
@@ -630,17 +614,16 @@ public PDBStatusXMLHandler() {
 		 * @param localName
 		 * @param qName
 		 * @param attributes
-		 * @throws SAXException
 		 * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)
 		 */
 		@Override
 		public void startElement(String uri, String localName, String qName,
-		                         Attributes attributes) throws SAXException {
+		                         Attributes attributes) {
 			//System.out.format("Starting element: uri='%s' localName='%s' qName='%s'\n", uri, localName, qName);
 			if(qName.equals("record")) {
 				//Convert attributes into a Map, as it should have been.
 				//Important since SAX reuses Attributes objects for different calls
-				Map<String,String> attrMap = new HashMap<String,String>(attributes.getLength()*2);
+				Map<String,String> attrMap = new HashMap<>(attributes.getLength() * 2);
 				for(int i=0;i<attributes.getLength();i++) {
 					attrMap.put(attributes.getQName(i), attributes.getValue(i));
 				}
@@ -673,7 +656,7 @@ public List<Map<String, String>> getRecords() {
 
 	public static SortedSet<String> getCurrentPDBIds() throws IOException {
 
-		SortedSet<String> allPDBs = new TreeSet<String>();
+		SortedSet<String> allPDBs = new TreeSet<>();
 		String serverName = System.getProperty(PDB_SERVER_PROPERTY);
 
 		if ( serverName == null)
@@ -692,7 +675,7 @@ public static SortedSet<String> getCurrentPDBIds() throws IOException {
 			BufferedReader reader = new BufferedReader(
 					new InputStreamReader(stream));
 
-			String line = null;
+			String line;
 
 			while ((line = reader.readLine()) != null) {
 				int index = line.lastIndexOf("structureId=");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PassthroughIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PassthroughIdentifier.java
index a1793e2816..2a7c654919 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/PassthroughIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/PassthroughIdentifier.java
@@ -34,7 +34,7 @@ public class PassthroughIdentifier implements StructureIdentifier {
 
 	private static final long serialVersionUID = -2773111624414448950L;
 
-	private String identifier;
+	private final String identifier;
 	public PassthroughIdentifier(String identifier) {
 		this.identifier = identifier;
 	}
@@ -48,11 +48,11 @@ public String getIdentifier() {
 	 */
 	@Override
 	public SubstructureIdentifier toCanonical() {
-		return new SubstructureIdentifier(null, new ArrayList<ResidueRange>());
+		return new SubstructureIdentifier(null, new ArrayList<>());
 	}
 
 	@Override
-	public Structure reduce(Structure input) throws StructureException {
+	public Structure reduce(Structure input) {
 		return input;
 	}
 	/**
@@ -60,8 +60,7 @@ public Structure reduce(Structure input) throws StructureException {
 	 * @return null
 	 */
 	@Override
-	public Structure loadStructure(AtomCache cache) throws StructureException,
-			IOException {
+	public Structure loadStructure(AtomCache cache) {
 		return null;
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueNumber.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueNumber.java
index 46dfb9c4d3..544d1bc350 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueNumber.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueNumber.java
@@ -177,7 +177,7 @@ public String toString() {
 	public String toPDB() {
 		String insCodeS ;
 		if ( insCode != null)
-			insCodeS = insCode+"";
+			insCodeS = String.valueOf(insCode);
 		else insCodeS = " ";
 		return String.format("%s%4d%-2s", chainName, seqNum, insCodeS);
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRange.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRange.java
index 79dbedbdfc..713289de7d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRange.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRange.java
@@ -90,7 +90,7 @@ public static ResidueRange parse(String s) {
 		Matcher matcher = RANGE_REGEX.matcher(s);
 		if (matcher.matches()) {
 			ResidueNumber start = null, end = null;
-			String chain = null;
+			String chain;
 			try {
 				chain = matcher.group(1);
 				if (matcher.group(2) != null) {
@@ -137,7 +137,7 @@ public static List<ResidueRange> parseMultiple(String s) {
 		}
 
 		String[] parts = s.split(",");
-		List<ResidueRange> list = new ArrayList<ResidueRange>(parts.length);
+		List<ResidueRange> list = new ArrayList<>(parts.length);
 		for (String part : parts) {
 			list.add(parse(part));
 		}
@@ -152,6 +152,10 @@ public ResidueRange(String chainName, String start, String end) {
 		this.end.setChainName(chainName);
 	}
 
+	public ResidueRange(String chainName) {
+		this(chainName, (ResidueNumber)null, null);
+	}
+
 	public ResidueRange(String chainName, ResidueNumber start, ResidueNumber end) {
 		this.chainName = chainName;
 		this.start = start;
@@ -257,7 +261,7 @@ public Iterator<ResidueNumber> iterator(final AtomPositionMap map) {
 		final Iterator<Entry<ResidueNumber, Integer>> entryIt = map.getNavMap().entrySet().iterator();
 		if(! entryIt.hasNext()) {
 			// empty iterator
-			return Arrays.asList(new ResidueNumber[0]).iterator();
+			return Collections.emptyIterator(); //Arrays.asList(new ResidueNumber[0]).iterator();
 		}
 		// Peek at upcoming entry
 
@@ -352,7 +356,7 @@ public static Iterator<ResidueNumber> multiIterator(AtomPositionMap map, List<?
 	}
 
 	public static List<ResidueRange> parseMultiple(List<String> ranges) {
-		List<ResidueRange> rrs = new ArrayList<ResidueRange>(ranges.size());
+		List<ResidueRange> rrs = new ArrayList<>(ranges.size());
 		for (String range : ranges) {
 			ResidueRange rr = ResidueRange.parse(range);
 			if (rr != null) rrs.add(rr);
@@ -361,7 +365,7 @@ public static List<ResidueRange> parseMultiple(List<String> ranges) {
 	}
 
 	public static List<String> toStrings(List<? extends ResidueRange> ranges) {
-		List<String> list = new ArrayList<String>(ranges.size());
+		List<String> list = new ArrayList<>(ranges.size());
 		for (ResidueRange range : ranges) {
 			list.add(range.toString());
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java
index a8988aada4..f93670e532 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java
@@ -129,7 +129,7 @@ public static ResidueRangeAndLength parse(String s, AtomPositionMap map) {
 
 
 	public static List<ResidueRangeAndLength> parseMultiple(List<String> ranges, AtomPositionMap map) {
-		List<ResidueRangeAndLength> rrs = new ArrayList<ResidueRangeAndLength>(ranges.size());
+		List<ResidueRangeAndLength> rrs = new ArrayList<>(ranges.size());
 		for (String range : ranges) {
 			ResidueRangeAndLength rr = ResidueRangeAndLength.parse(range, map);
 			if (rr != null) rrs.add(rr);
@@ -145,7 +145,7 @@ public static List<ResidueRangeAndLength> parseMultiple(List<String> ranges, Ato
 	 */
 	public static List<ResidueRangeAndLength> parseMultiple(String s, AtomPositionMap map) {
 		String[] parts = s.split(",");
-		List<ResidueRangeAndLength> list = new ArrayList<ResidueRangeAndLength>(parts.length);
+		List<ResidueRangeAndLength> list = new ArrayList<>(parts.length);
 		for (String part : parts) {
 			list.add(parse(part, map));
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/SeqMisMatch.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/SeqMisMatch.java
index 9e90a22b7c..0e7fc278b1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/SeqMisMatch.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/SeqMisMatch.java
@@ -25,33 +25,33 @@
  */
 public interface SeqMisMatch {
 
-	public Integer getSeqNum() ;
+	Integer getSeqNum() ;
 
-	public void setSeqNum(Integer seqNum) ;
+	void setSeqNum(Integer seqNum) ;
 
-	public String getOrigGroup() ;
+	String getOrigGroup() ;
 
-	public void setOrigGroup(String origGroup);
+	void setOrigGroup(String origGroup);
 
-	public String getPdbGroup() ;
+	String getPdbGroup() ;
 
-	public void setPdbGroup(String pdbGroup) ;
+	void setPdbGroup(String pdbGroup) ;
 
-	public String getDetails() ;
+	String getDetails() ;
 
-	public void setDetails(String details);
-	public String getUniProtId() ;
+	void setDetails(String details);
+	String getUniProtId() ;
 
-	public void setUniProtId(String uniProtId) ;
+	void setUniProtId(String uniProtId) ;
 
-	public String getInsCode() ;
+	String getInsCode() ;
 
-	public void setInsCode(String insCode) ;
+	void setInsCode(String insCode) ;
 
-	public String getPdbResNum() ;
+	String getPdbResNum() ;
 
-	public void setPdbResNum(String pdbResNum) ;
+	void setPdbResNum(String pdbResNum) ;
 
 	@Override
-	public String toString();
+    String toString();
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/SeqMisMatchImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/SeqMisMatchImpl.java
index 755f951421..21b2033adc 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/SeqMisMatchImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/SeqMisMatchImpl.java
@@ -109,7 +109,7 @@ public void setPdbResNum(String pdbResNum) {
 
 	@Override
 	public String toString() {
-		StringBuffer  s = new StringBuffer();
+		StringBuilder s = new StringBuilder();
 
 		s.append("SeqMisMatchImpl{");
 		s.append("seqNum=" );
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java
index 3e1464cc2a..8a0dfc839c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java
@@ -23,6 +23,7 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Locale;
+import java.util.Objects;
 
 /**
  * Holds the data of sites presented in PDB files. <br/>
@@ -42,7 +43,7 @@ public class Site implements PDBRecord, Comparable<Site> {
 	private static final String lineEnd = System.getProperty("line.separator");
 
 	private String siteID = "";
-	private List<Group> groups = new ArrayList<Group>();
+	private List<Group> groups = new ArrayList<>();
 	//variables for REMARK 800
 	private String evCode = "";
 	private String description = "";
@@ -233,16 +234,16 @@ public boolean equals(Object obj) {
 			return false;
 		}
 		final Site other = (Site) obj;
-		if ((this.siteID == null) ? (other.siteID != null) : !this.siteID.equals(other.siteID)) {
+		if (!Objects.equals(this.siteID, other.siteID)) {
 			return false;
 		}
-		if (this.groups != other.groups && (this.groups == null || !this.groups.equals(other.groups))) {
+		if (!Objects.equals(this.groups, other.groups)) {
 			return false;
 		}
-		if ((this.evCode == null) ? (other.evCode != null) : !this.evCode.equals(other.evCode)) {
+		if (!Objects.equals(this.evCode, other.evCode)) {
 			return false;
 		}
-		if ((this.description == null) ? (other.description != null) : !this.description.equals(other.description)) {
+		if (!Objects.equals(this.description, other.description)) {
 			return false;
 		}
 		return true;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StandardAminoAcid.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StandardAminoAcid.java
index d52d358385..a4b17c6c94 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StandardAminoAcid.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StandardAminoAcid.java
@@ -43,7 +43,7 @@ public final class StandardAminoAcid {
 
 	private static final String STANDARD_AMINOS_FILE = "org/biojava/nbio/structure/standardaminos.pdb.gz";
 
-	static private Map<String,AminoAcid> aminoAcids;
+	static private final Map<String,AminoAcid> aminoAcids;
 
 	/**
 	 * Cannot be instantiated.
@@ -64,7 +64,7 @@ private StandardAminoAcid() {
 	 * @author Tamas Horvath provided the standard amino acids
 	 */
 	static {
-		aminoAcids = new HashMap<String,AminoAcid>();
+		aminoAcids = new HashMap<>();
 
 
 		InputStream fileStream = StandardAminoAcid.class.getClassLoader().getResourceAsStream(STANDARD_AMINOS_FILE);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureException.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureException.java
index 46c16fd503..c69bc77197 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureException.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureException.java
@@ -33,7 +33,7 @@
 
 public class StructureException extends Exception {
 
-	public static final long serialVersionUID = 62946250941673093l;
+	public static final long serialVersionUID = 62946250941673093L;
 	/**
 	 * Constructs a StructureException object.
 	 *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
index a90bc6db8c..ee331abe8c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
@@ -281,16 +281,16 @@ public static void setPdbPath(String pathToPDBFiles){
 	}
 
 
-	public static enum StructureFiletype {
+	public enum StructureFiletype {
 		PDB( (new PDBFileReader()).getExtensions()),
 		CIF( new MMCIFFileReader().getExtensions()),
-		UNKNOWN(Collections.<String>emptyList());
+		UNKNOWN(Collections.emptyList());
 
-		private List<String> extensions;
+		private final List<String> extensions;
 		/**
 		 * @param extensions List of supported extensions, including leading period
 		 */
-		private StructureFiletype(List<String> extensions) {
+		StructureFiletype(List<String> extensions) {
 			this.extensions = extensions;
 		}
 		/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
index 39664983be..336f350dad 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
@@ -145,7 +145,7 @@ public Structure clone() {
 
 		// go through each chain and clone chain
 		for (int i=0;i<nrModels();i++){
-			List<Chain> cloned_model = new ArrayList<Chain>();
+			List<Chain> cloned_model = new ArrayList<>();
 
 			for (int j=0;j<size(i);j++){
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
index 9ba8170ab5..7043e264fe 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -26,16 +26,7 @@
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
 
 import javax.vecmath.Point3d;
 
@@ -168,7 +159,7 @@ public class StructureTools {
 	private static final Set<Element> hBondDonorAcceptors;
 
 	static {
-		nucleotides30 = new HashMap<String, Character>();
+		nucleotides30 = new HashMap<>();
 		nucleotides30.put("DA", 'A');
 		nucleotides30.put("DC", 'C');
 		nucleotides30.put("DG", 'G');
@@ -212,14 +203,14 @@ public class StructureTools {
 		// store nucleic acids (C, G, A, T, U, and I), and
 		// the modified versions of nucleic acids (+C, +G, +A, +T, +U, and +I),
 		// and
-		nucleotides23 = new HashMap<String, Character>();
+		nucleotides23 = new HashMap<>();
 		String[] names = { "C", "G", "A", "T", "U", "I", "+C", "+G", "+A",
 				"+T", "+U", "+I" };
 		for (String n : names) {
 			nucleotides23.put(n, n.charAt(n.length() - 1));
 		}
 
-		aminoAcids = new HashMap<String, Character>();
+		aminoAcids = new HashMap<>();
 		aminoAcids.put("GLY", 'G');
 		aminoAcids.put("ALA", 'A');
 		aminoAcids.put("VAL", 'V');
@@ -251,7 +242,7 @@ public class StructureTools {
 		aminoAcids.put("PYH", 'O');
 		aminoAcids.put("PYL", 'O');
 
-		hBondDonorAcceptors = new HashSet<Element>();
+		hBondDonorAcceptors = new HashSet<>();
 		hBondDonorAcceptors.add(Element.N);
 		hBondDonorAcceptors.add(Element.O);
 		hBondDonorAcceptors.add(Element.S);
@@ -314,10 +305,10 @@ public static final int getNrGroups(Structure s) {
 	public static final Atom[] getAtomArray(Structure s, String[] atomNames) {
 		List<Chain> chains = s.getModel(0);
 
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		extractAtoms(atomNames, chains, atoms);
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 
 	}
 
@@ -340,13 +331,13 @@ public static final Atom[] getAtomArray(Structure s, String[] atomNames) {
 	public static final Atom[] getAtomArrayAllModels(Structure s,
 			String[] atomNames) {
 
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		for (int i = 0; i < s.nrModels(); i++) {
 			List<Chain> chains = s.getModel(i);
 			extractAtoms(atomNames, chains, atoms);
 		}
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 
 	}
 
@@ -358,14 +349,14 @@ public static final Atom[] getAtomArrayAllModels(Structure s,
 	 * @return all atom array
 	 */
 	public static final Atom[] getAllAtomArray(Structure s) {
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		AtomIterator iter = new AtomIterator(s);
 		while (iter.hasNext()) {
 			Atom a = iter.next();
 			atoms.add(a);
 		}
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 	}
 	/**
 	 * Convert all atoms of the structure (specified model) into an Atom array
@@ -375,14 +366,14 @@ public static final Atom[] getAllAtomArray(Structure s) {
 	 * @return all atom array
 	 */
 	public static final Atom[] getAllAtomArray(Structure s, int model) {
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		AtomIterator iter = new AtomIterator(s,model);
 		while (iter.hasNext()) {
 			Atom a = iter.next();
 			atoms.add(a);
 		}
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 
 	}
 
@@ -395,16 +386,14 @@ public static final Atom[] getAllAtomArray(Structure s, int model) {
 	 * @return all atom array
 	 */
 	public static final Atom[] getAllAtomArray(Chain c) {
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		for (Group g : c.getAtomGroups()) {
 			if (g.isWater())
 				continue;
-			for (Atom a : g.getAtoms()) {
-				atoms.add(a);
-			}
+			atoms.addAll(g.getAtoms());
 		}
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 	}
 
 	/**
@@ -417,8 +406,8 @@ public static final Atom[] getAllAtomArray(Chain c) {
 	 * @return
 	 */
 	public static List<Group> getUnalignedGroups(Atom[] ca) {
-		Set<Chain> chains = new HashSet<Chain>();
-		Set<Group> caGroups = new HashSet<Group>();
+		Set<Chain> chains = new HashSet<>();
+		Set<Group> caGroups = new HashSet<>();
 
 		// Create list of all chains in this structure
 		Structure s = null;
@@ -433,9 +422,7 @@ public static List<Group> getUnalignedGroups(Atom[] ca) {
 		}
 		if (s != null) {
 			// Add all chains from the structure
-			for (Chain c : s.getChains(0)) {
-				chains.add(c);
-			}
+			chains.addAll(s.getChains(0));
 		}
 
 		// Add groups and chains from ca
@@ -452,7 +439,7 @@ public static List<Group> getUnalignedGroups(Atom[] ca) {
 		}
 
 		// Iterate through all chains, finding groups not in ca
-		List<Group> unadded = new ArrayList<Group>();
+		List<Group> unadded = new ArrayList<>();
 		for (Chain c : chains) {
 			for (Group g : c.getAtomGroups()) {
 				if (!caGroups.contains(g)) {
@@ -690,7 +677,7 @@ public static final Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, in
 		return getAllNonHAtomArray(s, hetAtoms, iter);
 	}
 	private static final Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, AtomIterator iter) {
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		while (iter.hasNext()) {
 			Atom a = iter.next();
@@ -707,7 +694,7 @@ private static final Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, A
 
 			atoms.add(a);
 		}
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 	}
 
 	/**
@@ -720,7 +707,7 @@ private static final Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, A
 	 * @return
 	 */
 	public static final Atom[] getAllNonHAtomArray(Chain c, boolean hetAtoms) {
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		for (Group g : c.getAtomGroups()) {
 			if (g.isWater())
@@ -736,7 +723,7 @@ public static final Atom[] getAllNonHAtomArray(Chain c, boolean hetAtoms) {
 				atoms.add(a);
 			}
 		}
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 	}
 
 	/**
@@ -749,7 +736,7 @@ public static final Atom[] getAllNonHAtomArray(Chain c, boolean hetAtoms) {
 	 * @return
 	 */
 	public static final Point3d[] getAllNonHCoordsArray(Chain c, boolean hetAtoms) {
-		List<Point3d> atoms = new ArrayList<Point3d>();
+		List<Point3d> atoms = new ArrayList<>();
 
 		for (Group g : c.getAtomGroups()) {
 			if (g.isWater())
@@ -765,7 +752,7 @@ public static final Point3d[] getAllNonHCoordsArray(Chain c, boolean hetAtoms) {
 				atoms.add(a.getCoordsAsPoint3d());
 			}
 		}
-		return atoms.toArray(new Point3d[atoms.size()]);
+		return atoms.toArray(new Point3d[0]);
 	}
 
 	/**
@@ -785,7 +772,7 @@ private static void extractAtoms(String[] atomNames, List<Chain> chains,
 			for (Group g : c.getAtomGroups()) {
 
 				// a temp container for the atoms of this group
-				List<Atom> thisGroupAtoms = new ArrayList<Atom>();
+				List<Atom> thisGroupAtoms = new ArrayList<>();
 				// flag to check if this group contains all the requested atoms.
 				boolean thisGroupAllAtoms = true;
 				for (String atomName : atomNames) {
@@ -800,9 +787,7 @@ private static void extractAtoms(String[] atomNames, List<Chain> chains,
 				}
 				if (thisGroupAllAtoms) {
 					// add the atoms of this group to the array.
-					for (Atom a : thisGroupAtoms) {
-						atoms.add(a);
-					}
+					atoms.addAll(thisGroupAtoms);
 				}
 
 			}
@@ -824,12 +809,12 @@ private static void extractAtoms(String[] atomNames, List<Chain> chains,
 	 */
 	public static final Atom[] getAtomArray(Chain c, String[] atomNames) {
 
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		for (Group g : c.getAtomGroups()) {
 
 			// a temp container for the atoms of this group
-			List<Atom> thisGroupAtoms = new ArrayList<Atom>();
+			List<Atom> thisGroupAtoms = new ArrayList<>();
 			// flag to check if this group contains all the requested atoms.
 			boolean thisGroupAllAtoms = true;
 			for (String atomName : atomNames) {
@@ -848,13 +833,11 @@ public static final Atom[] getAtomArray(Chain c, String[] atomNames) {
 
 			if (thisGroupAllAtoms) {
 				// add the atoms of this group to the array.
-				for (Atom a : thisGroupAtoms) {
-					atoms.add(a);
-				}
+				atoms.addAll(thisGroupAtoms);
 			}
 
 		}
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 
 	}
 
@@ -868,7 +851,7 @@ public static final Atom[] getAtomArray(Chain c, String[] atomNames) {
 	 * @see #getRepresentativeAtomArray(Chain)
 	 */
 	public static final Atom[] getAtomCAArray(Chain c) {
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		for (Group g : c.getAtomGroups()) {
 			if (g.hasAtom(CA_ATOM_NAME)
@@ -877,7 +860,7 @@ public static final Atom[] getAtomCAArray(Chain c) {
 			}
 		}
 
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 	}
 
 	/**
@@ -895,7 +878,7 @@ public static final Atom[] getAtomCAArray(Chain c) {
 	 * @since Biojava 4.1.0
 	 */
 	public static final Atom[] getRepresentativeAtomArray(Chain c) {
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		for (Group g : c.getAtomGroups()) {
 
@@ -916,7 +899,7 @@ public static final Atom[] getRepresentativeAtomArray(Chain c) {
 			}
 		}
 
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 
 	}
 
@@ -933,7 +916,7 @@ public static final Atom[] getRepresentativeAtomArray(Chain c) {
 	public static final Atom[] cloneAtomArray(Atom[] ca) {
 		Atom[] newCA = new Atom[ca.length];
 
-		List<Chain> model = new ArrayList<Chain>();
+		List<Chain> model = new ArrayList<>();
 		int apos = -1;
 		for (Atom a : ca) {
 			apos++;
@@ -979,7 +962,7 @@ public static final Atom[] cloneAtomArray(Atom[] ca) {
 	public static Group[] cloneGroups(Atom[] ca) {
 		Group[] newGroup = new Group[ca.length];
 
-		List<Chain> model = new ArrayList<Chain>();
+		List<Chain> model = new ArrayList<>();
 		int apos = -1;
 		for (Atom a : ca) {
 			apos++;
@@ -1087,7 +1070,7 @@ public static Atom[] duplicateCA2(Atom[] ca2) {
 	 */
 	public static Atom[] getAtomCAArray(Structure s) {
 
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		for (Chain c : s.getChains()) {
 			for (Group g : c.getAtomGroups()) {
@@ -1098,7 +1081,7 @@ public static Atom[] getAtomCAArray(Structure s) {
 			}
 		}
 
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 	}
 
 	/**
@@ -1118,16 +1101,14 @@ public static Atom[] getAtomCAArray(Structure s) {
 	 */
 	public static Atom[] getRepresentativeAtomArray(Structure s) {
 
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		for (Chain c : s.getChains()) {
 			Atom[] chainAtoms = getRepresentativeAtomArray(c);
-			for (Atom a : chainAtoms) {
-				atoms.add(a);
-			}
+			atoms.addAll(Arrays.asList(chainAtoms));
 		}
 
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 	}
 
 	/**
@@ -1140,7 +1121,7 @@ public static Atom[] getRepresentativeAtomArray(Structure s) {
 	 */
 	public static Atom[] getBackboneAtomArray(Structure s) {
 
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		for (Chain c : s.getChains()) {
 			for (Group g : c.getAtomGroups()) {
@@ -1195,7 +1176,7 @@ public static Atom[] getBackboneAtomArray(Structure s) {
 
 		}
 
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 	}
 
 	/**
@@ -1313,7 +1294,7 @@ public static Structure getReducedStructure(Structure s,
 
 		}
 
-		Chain c = null;
+		Chain c;
 		try {
 			c = s.getChainByPDB(chainId);
 		} catch (StructureException e) {
@@ -1404,7 +1385,7 @@ public static AtomContactSet getAtomsInContact(Chain chain,
 			String[] atomNames, double cutoff) {
 		Grid grid = new Grid(cutoff);
 
-		Atom[] atoms = null;
+		Atom[] atoms;
 		if (atomNames == null) {
 			atoms = getAllNonHAtomArray(chain, false);
 		} else {
@@ -1433,7 +1414,7 @@ public static AtomContactSet getAtomsInContact(Chain chain,
 	 * @return
 	 */
 	public static AtomContactSet getAtomsInContact(Chain chain, double cutoff) {
-		return getAtomsInContact(chain, (String[]) null, cutoff);
+		return getAtomsInContact(chain, null, cutoff);
 	}
 
 	/**
@@ -1502,8 +1483,8 @@ public static AtomContactSet getRepresentativeAtomsInContact(Chain chain,
 	public static AtomContactSet getAtomsInContact(Chain chain1, Chain chain2,
 			String[] atomNames, double cutoff, boolean hetAtoms) {
 		Grid grid = new Grid(cutoff);
-		Atom[] atoms1 = null;
-		Atom[] atoms2 = null;
+		Atom[] atoms1;
+		Atom[] atoms2;
 		if (atomNames == null) {
 			atoms1 = getAllNonHAtomArray(chain1, hetAtoms);
 			atoms2 = getAllNonHAtomArray(chain2, hetAtoms);
@@ -1565,12 +1546,12 @@ public static Map<Group, Double> getGroupDistancesWithinShell(
 		// for speed, we avoid calculating square roots
 		radius = radius * radius;
 
-		Map<Group, Double> distances = new HashMap<Group, Double>();
+		Map<Group, Double> distances = new HashMap<>();
 
 		// we only need this if we're averaging distances
 		// note that we can't use group.getAtoms().size() because some the
 		// group's atoms be outside the shell
-		Map<Group, Integer> atomCounts = new HashMap<Group, Integer>();
+		Map<Group, Integer> atomCounts = new HashMap<>();
 
 		for (Chain chain : structure.getChains()) {
 			groupLoop: for (Group chainGroup : chain.getAtomGroups()) {
@@ -1627,9 +1608,7 @@ public static Map<Group, Double> getGroupDistancesWithinShell(
 			}
 		} else {
 			// in this case we used getDistanceFast
-			for (Map.Entry<Group, Double> entry : distances.entrySet()) {
-				distances.put(entry.getKey(), Math.sqrt(entry.getValue()));
-			}
+			distances.replaceAll((k, v) -> Math.sqrt(v));
 		}
 
 		return distances;
@@ -1644,7 +1623,7 @@ public static Set<Group> getGroupsWithinShell(Structure structure,
 		// which returns the square of a distance.
 		distance = distance * distance;
 
-		Set<Group> returnSet = new LinkedHashSet<Group>();
+		Set<Group> returnSet = new LinkedHashSet<>();
 		for (Chain chain : structure.getChains()) {
 			groupLoop: for (Group chainGroup : chain.getAtomGroups()) {
 				if (!includeWater && chainGroup.isWater())
@@ -1691,9 +1670,9 @@ public static Set<Group> getGroupsWithinShell(Structure structure,
 	public static Set<Group> getGroupsWithinShell(Structure structure,
 			Group group, double distance, boolean includeWater) {
 
-		Set<Group> returnList = new LinkedHashSet<Group>();
+		Set<Group> returnList = new LinkedHashSet<>();
 
-		Set<ResidueNumber> excludeGroups = new HashSet<ResidueNumber>();
+		Set<ResidueNumber> excludeGroups = new HashSet<>();
 		excludeGroups.add(group.getResidueNumber());
 		for (Atom atom : group.getAtoms()) {
 			Set<Group> set = getGroupsWithinShell(structure, atom,
@@ -1742,7 +1721,7 @@ public static Structure removeModels(Structure s) {
 	 */
 	public static List<Group> filterLigands(List<Group> allGroups) {
 
-		List<Group> groups = new ArrayList<Group>();
+		List<Group> groups = new ArrayList<>();
 		for (Group g : allGroups) {
 
 			if ( g.isPolymeric())
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
index da9c1e1dee..924bc9d66c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
@@ -100,7 +100,7 @@ public SubstructureIdentifier(String id) {
 
 			this.ranges = ResidueRange.parseMultiple(rangeStr);
 		} else {
-			this.ranges = new LinkedList<ResidueRange>();
+			this.ranges = new LinkedList<>();
 		}
 	}
 
@@ -199,7 +199,7 @@ public Structure reduce(Structure s) throws StructureException {
 		for( int modelNr=0;modelNr<s.nrModels();modelNr++) {
 
 			// Construct new model
-			newS.addModel(new ArrayList<Chain>());
+			newS.addModel(new ArrayList<>());
 
 			if(getResidueRanges().isEmpty()) {
 				// Include all residues
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
index 653683ee0f..f48927ec32 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
@@ -116,7 +116,7 @@ public SubstructureIdentifier toCanonical() {
 			if(params.containsKey(RESIDUES_PARAM)) {
 				ranges = ResidueRange.parseMultiple(params.get(RESIDUES_PARAM));
 			} else if(params.containsKey(CHAINID_PARAM)) {
-				ranges = Arrays.asList(new ResidueRange(params.get(CHAINID_PARAM),(ResidueNumber)null,(ResidueNumber)null));
+				ranges = Collections.singletonList(new ResidueRange(params.get(CHAINID_PARAM)));
 			}
 		} catch (UnsupportedEncodingException e) {
 			logger.error("Unable to decode URL "+url,e);
@@ -137,7 +137,7 @@ public Structure reduce(Structure input) throws StructureException {
 	 * @return null
 	 */
 	@Override
-	public Structure loadStructure(AtomCache cache) throws StructureException,
+	public Structure loadStructure(AtomCache cache) throws
 			IOException {
 		StructureFiletype format = StructureFiletype.UNKNOWN;
 
@@ -217,7 +217,7 @@ public static String guessPDBID(String name) {
 	 * @throws UnsupportedEncodingException
 	 */
 	private static Map<String,String> parseQuery(URL url) throws UnsupportedEncodingException {
-		Map<String,String> params = new LinkedHashMap<String, String>();
+		Map<String,String> params = new LinkedHashMap<>();
 		String query = url.getQuery();
 		if( query == null || query.isEmpty()) {
 			// empty query
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
index 57ff697730..ab6fade89e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
@@ -250,8 +250,7 @@ public static Group[] twistOptimized(AFPChain afpChain, Atom[] ca1,
 	 */
 	// orig name: transPdb
 	private static void transformOrigPDB(int n, int[] res1, int[] res2,
-			Atom[] ca1, Atom[] ca2, AFPChain afpChain, int blockNr)
-			throws StructureException {
+			Atom[] ca1, Atom[] ca2, AFPChain afpChain, int blockNr) {
 		logger.debug(
 				"transforming original coordinates {} len1: {} res1: {} len2: {} res2: {}",
 				n, ca1.length, res1.length, ca2.length, res2.length);
@@ -297,7 +296,7 @@ private static void transformOrigPDB(int n, int[] res1, int[] res2,
 	private static Atom[] getAtoms(Atom[] ca, int[] positions, int length,
 			boolean clone) {
 
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 		for (int i = 0; i < length; i++) {
 			int p = positions[i];
 			Atom a;
@@ -309,7 +308,7 @@ private static Atom[] getAtoms(Atom[] ca, int[] positions, int length,
 			}
 			atoms.add(a);
 		}
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 	}
 
 	/**
@@ -321,15 +320,14 @@ private static Atom[] getAtoms(Atom[] ca, int[] positions, int length,
 	 * @param r2
 	 */
 	// orig name: modifyCod
-	private static void cloneAtomRange(Atom[] p1, Atom[] p2, int r1, int r2)
-			throws StructureException {
+	private static void cloneAtomRange(Atom[] p1, Atom[] p2, int r1, int r2) {
 
 		logger.debug("modifyCod from: {} to: {}", r1, r2);
 
 		// special clone method, can;t use StructureTools.cloneCAArray, since we
 		// access the data
 		// slightly differently here.
-		List<Chain> model = new ArrayList<Chain>();
+		List<Chain> model = new ArrayList<>();
 		for (int i = r1; i < r2; i++) {
 
 			Group g = p2[i].getGroup();
@@ -369,7 +367,7 @@ private static void cloneAtomRange(Atom[] p1, Atom[] p2, int r1, int r2)
 	 * @return rmsd of CAs
 	 */
 	private static double calCaRmsd(Atom[] ca1, Atom[] pro, int resn,
-			int[] res1, int[] res2) throws StructureException {
+			int[] res1, int[] res2) {
 
 		Atom[] cod1 = getAtoms(ca1, res1, resn, false);
 		Atom[] cod2 = getAtoms(pro, res2, resn, false);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java
index 3a6150da3b..d4c4ef3947 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java
@@ -65,7 +65,7 @@ public static void cluster(AlternativeAlignment[] aligs, int cutoff){
 			List remainList = new ArrayList();
 			List currentCluster = new ArrayList();
 
-			currentCluster.add( new Integer(i));
+			currentCluster.add(i);
 			excludeList.add(a);
 
 			int j=-1;
@@ -94,7 +94,7 @@ public static void cluster(AlternativeAlignment[] aligs, int cutoff){
 				//		" l1:"+ idxA.length + " l2:" + idxB.length + " perpos:" + perpos);
 
 				if ( perpos > cutoff){
-					currentCluster.add(new Integer(j));
+					currentCluster.add(j);
 					excludeList.add(b);
 				} else {
 					remainList.add(b);
@@ -115,11 +115,10 @@ public static void cluster(AlternativeAlignment[] aligs, int cutoff){
 			cpos++;
 			//System.out.println("cluster "+cpos+":");
 			List cluster = (List) iter.next();
-			Iterator iter2 = cluster.iterator();
-			while (iter2.hasNext()){
-				Integer i = (Integer) iter2.next();
+			for (Object o : cluster) {
+				Integer i = (Integer) o;
 
-				AlternativeAlignment alig = aligs[i.intValue()];
+				AlternativeAlignment alig = aligs[i];
 				alig.setCluster(cpos);
 				//System.out.println( " ("+ aligs[i.intValue()]+")");
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/FarmJob.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/FarmJob.java
index fa749f2127..71f9ea8736 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/FarmJob.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/FarmJob.java
@@ -80,7 +80,7 @@ public void setParams(FarmJobParameters params) {
 
 	public void addAlignmentProgressListener(AlignmentProgressListener listener){
 		if (progressListeners == null)
-			progressListeners = new ArrayList<AlignmentProgressListener>();
+			progressListeners = new ArrayList<>();
 
 		progressListeners.add(listener);
 	}
@@ -172,7 +172,7 @@ public void run(){
 			System.setProperty(UserConfiguration.PDB_CACHE_DIR,path);
 		}
 		// declare SCOP to be locally cached, but fetching new stuff from remote
-		ScopDatabase scop = null;
+		ScopDatabase scop;
 		try {
 			scop = new CachedRemoteScopInstallation(true);
 		} catch (IOException e) {
@@ -181,7 +181,7 @@ public void run(){
 		ScopFactory.setScopDatabase(scop);
 
 		String username = params.getUsername();
-		jobs = new ArrayList<FarmJobRunnable>();
+		jobs = new ArrayList<>();
 		for ( int i = 0 ; i < params.getThreads();i++){
 			logger.info("starting thread #{}", (i+1));
 			FarmJobRunnable runner = new FarmJobRunnable(params);
@@ -232,14 +232,14 @@ public void printHelp(){
 		System.out.println("-------------------");
 
 		System.out.println("FarmJob accepts the following parameters:");
-		System.out.println("");
+		System.out.println();
 		System.out.println(" Mandatory:");
 		System.out.println("   -pdbFilePath (mandatory) Path to the directory in your file system that contains the PDB files.");
 
 		System.out.println("   provide either -time or -nrAlignments. If both are provided the job stops as soon as any of the criteria has been reached.");
 		System.out.println("   -time maximum number of time to run (in seconds). -1 means no time limit, but run -nrAlignment arguments. Default: " + FarmJobParameters.DEFAULT_JOB_TIME );
 		System.out.println("   -nrAlignments number of alignments to calculate. Default: " + FarmJobParameters.DEFAULT_NR_ALIGNMENTS) ;
-		System.out.println("");
+		System.out.println();
 		System.out.println(" Optional: ");
 		System.out.println("   -threads number of parallel threads to calculate alignments. Should be nr. of available CPUs. Default: " + FarmJobParameters.DEFAULT_NR_THREADS);
 		System.out.println("   -server the location of the server URL to talk to. Default : " + FarmJobParameters.DEFAULT_SERVER_URL);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java
index 636c2ce7a3..6af2a2a1e8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java
@@ -192,7 +192,7 @@ public void setResultFile(File resultList) {
 
 	public void run(){
 
-		File outFileF = null;
+		File outFileF;
 		SynchronizedOutFile out ;
 
 		try {
@@ -257,12 +257,7 @@ public void run(){
 			}
 
 			out.flush();
-		} catch (IOException e){
-			logger.error("Error while loading representative structure {}", name1, e);
-			interrupt();
-			cleanup();
-			return;
-		} catch (StructureException e) {
+		} catch (IOException | StructureException e){
 			logger.error("Error while loading representative structure {}", name1, e);
 			interrupt();
 			cleanup();
@@ -270,7 +265,7 @@ public void run(){
 		}
 
 
-		int nrJobs = 0;
+        int nrJobs = 0;
 		DomainProvider domainProvider;
 		try {
 			domainProvider = DomainProviderFactory.getDomainProvider();
@@ -301,12 +296,7 @@ public void run(){
 				}
 
 			}
-		} catch(IOException e) {
-			logger.error("Error while fetching representative domains", e);
-			interrupt();
-			cleanup();
-			return;
-		} catch (StructureException e) {
+		} catch(IOException | StructureException e) {
 			logger.error("Error while fetching representative domains", e);
 			interrupt();
 			cleanup();
@@ -314,7 +304,7 @@ public void run(){
 		}
 
 
-		ThreadPoolExecutor  pool = ConcurrencyTools.getThreadPool();
+        ThreadPoolExecutor  pool = ConcurrencyTools.getThreadPool();
 		logger.info("{}", pool.getPoolSize());
 
 		long startTime = System.currentTimeMillis();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultipleStructureAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultipleStructureAligner.java
index 964e280935..18e814caac 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultipleStructureAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultipleStructureAligner.java
@@ -45,7 +45,7 @@ public interface MultipleStructureAligner{
 	 * @throws StructureException
 	 * @see #align(List,Object)
 	 */
-	public MultipleAlignment align(List<Atom[]> atomArrays) throws StructureException;
+    MultipleAlignment align(List<Atom[]> atomArrays) throws StructureException;
 
 	/**
 	 * Run an alignment and also send a bean containing the parameters.
@@ -55,33 +55,33 @@ public interface MultipleStructureAligner{
 	 * @throws StructureException
 	 * @see #align(List)
 	 */
-	public MultipleAlignment align(List<Atom[]> atomArrays, Object params) throws StructureException;
+    MultipleAlignment align(List<Atom[]> atomArrays, Object params) throws StructureException;
 
 	/**
 	 * Return the parameters of this algorithm instance.
 	 *
 	 * @return The returned Object will be a Java bean.
 	 */
-	public ConfigStrucAligParams getParameters();
+    ConfigStrucAligParams getParameters();
 
 	/**
 	 * Set the parameters for this algorithm to use.
 	 *
 	 * @param parameters
 	 */
-	public void setParameters(ConfigStrucAligParams parameters);
+    void setParameters(ConfigStrucAligParams parameters);
 
 	/**
 	 * Get the name of this Algorithm.
 	 *
 	 * @return String name of the algorithm
 	 */
-	public String getAlgorithmName();
+    String getAlgorithmName();
 
 	/**
 	 * Get the Version information for this Algorithm.
 	 *
 	 * @return String version of the algorithm
 	 */
-	public String getVersion();
+    String getVersion();
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java
index 8851d863e1..36fb609a58 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StrucAligParameters.java
@@ -121,19 +121,19 @@ private void setDefault() {
 	}
 	@Override
 	public String toString() {
-		StringBuffer buf = new StringBuffer();
+		StringBuilder buf = new StringBuilder();
 		String t = " ";
 
-		Object[] params = new Object[]{new Integer(initialK) ,new Integer(seedFragmentLength),
-				new Float(seedRmsdCutoff),
-				new Integer(fragmentLength),
-				new Integer(diagonalDistance), new Integer(diagonalDistance2), new Float(fragmentMiniDistance),
-				new Integer(angleDiff),
-				new Float(fragCompat), new Integer(maxrefine),
-				new Boolean(reduceInitialFragments), new Double(joinRMSCutoff), new Boolean(joinPlo),
-				new Boolean(doAngleCheck), new Boolean(doDistanceCheck), new Boolean(doRMSCheck),
-				new Boolean(doDensityCheck), new Float(densityCutoff), new Float(create_co), new Integer(maxIter),
-				new Float(gapOpen), new Float(gapExtension), new Integer(permutationSize), new Float(evalCutoff)};
+		Object[] params = new Object[]{initialK, seedFragmentLength,
+				seedRmsdCutoff,
+				fragmentLength,
+				diagonalDistance, diagonalDistance2, fragmentMiniDistance,
+				angleDiff,
+				fragCompat, maxrefine,
+				reduceInitialFragments, joinRMSCutoff, joinPlo,
+				doAngleCheck, doDistanceCheck, doRMSCheck,
+				doDensityCheck, densityCutoff, create_co, maxIter,
+				gapOpen, gapExtension, permutationSize, evalCutoff};
 
 		for (int i=0 ; i< params.length ; i++){
 			buf.append(params[i]);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructureAlignment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructureAlignment.java
index 8dd138218e..70ff290286 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructureAlignment.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructureAlignment.java
@@ -35,7 +35,7 @@ public interface StructureAlignment {
 	 * @return the afpChain object that contains the alignment.
 	 * @throws StructureException
 	 */
-	public AFPChain align(Atom[] ca1, Atom[] ca2) throws StructureException;
+    AFPChain align(Atom[] ca1, Atom[] ca2) throws StructureException;
 
 	/** run an alignment and also send a bean containing the parameters.
 	 *
@@ -45,29 +45,29 @@ public interface StructureAlignment {
 	 * @return the afpChain object that contains the alignment.
 	 * @throws StructureException
 	 */
-	public AFPChain align(Atom[] ca1, Atom[] ca2, Object params) throws StructureException;
+    AFPChain align(Atom[] ca1, Atom[] ca2, Object params) throws StructureException;
 
 	/** Return the paramers for this algorithm.
 	 *
 	 * @return The returned object will be a Java bean.
 	 */
-	public ConfigStrucAligParams getParameters();
+    ConfigStrucAligParams getParameters();
 
 	/** Set the default parameters for this algorithm to use
 	 *
 	 * @param parameters
 	 */
-	public void setParameters(ConfigStrucAligParams parameters);
+    void setParameters(ConfigStrucAligParams parameters);
 
 	/** Get the name of the Algorithm
 	 *
 	 * @return the name of the algorithm
 	 */
-	public String getAlgorithmName();
+    String getAlgorithmName();
 
 	/** Get the Version information for this Algorithm.
 	 *
 	 * @return the version of the algorithm
 	 */
-	public String getVersion();
+    String getVersion();
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructureAlignmentFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructureAlignmentFactory.java
index a31012cf25..17d6f2c001 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructureAlignmentFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructureAlignmentFactory.java
@@ -38,7 +38,7 @@ public class StructureAlignmentFactory {
 
 	private final static Logger logger = LoggerFactory.getLogger(StructureAlignmentFactory.class);
 
-	private static List<StructureAlignment> algorithms = new ArrayList<StructureAlignment>();
+	private static final List<StructureAlignment> algorithms = new ArrayList<>();
 
 	static {
 		algorithms.add( new CeMain() );
@@ -111,13 +111,7 @@ public static StructureAlignment getAlgorithm(String name) throws StructureExcep
 					@SuppressWarnings("unchecked")
 					Class<StructureAlignment> c = (Class<StructureAlignment>) Class.forName(algo.getClass().getName());
 					return c.newInstance();
-				} catch (ClassNotFoundException e){
-					logger.error("Exception: ", e);
-					return null;
-				} catch (IllegalAccessException e){
-					logger.error("Exception: ", e);
-					return null;
-				} catch (InstantiationException e){
+				} catch (ClassNotFoundException | InstantiationException | IllegalAccessException e){
 					logger.error("Exception: ", e);
 					return null;
 				}
@@ -130,18 +124,18 @@ public static StructureAlignment getAlgorithm(String name) throws StructureExcep
 	}
 
 	public static StructureAlignment[] getAllAlgorithms(){
-		return algorithms.toArray(new StructureAlignment[algorithms.size()]);
+		return algorithms.toArray(new StructureAlignment[0]);
 	}
 
 	public static String[] getAllAlgorithmNames(){
 		StructureAlignment[] algos = getAllAlgorithms();
-		List<String> names = new ArrayList<String>();
+		List<String> names = new ArrayList<>();
 
 		for (StructureAlignment alg : algos){
 			names.add(alg.getAlgorithmName());
 		}
 
-		return names.toArray(new String[names.size()]);
+		return names.toArray(new String[0]);
 	}
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
index fabe4c9bc6..a196c8e022 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
@@ -143,7 +143,7 @@ public class StructurePairAligner {
 	StrucAligParameters params;
 	FragmentPair[] fragPairs;
 
-	List<AlignmentProgressListener> listeners = new ArrayList<AlignmentProgressListener>();
+	List<AlignmentProgressListener> listeners = new ArrayList<>();
 
 	public StructurePairAligner() {
 		super();
@@ -444,7 +444,7 @@ public void align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)
 		Atom unitvector = new AtomImpl();
 		unitvector.setCoords(utmp[0]);
 
-		List<FragmentPair> fragments = new ArrayList<FragmentPair>();
+		List<FragmentPair> fragments = new ArrayList<>();
 
 		for (int i = 0; i < rows; i++) {
 
@@ -500,7 +500,7 @@ public void align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)
 		notifyFragmentListeners(fragments);
 
 		FragmentPair[] fp = fragments
-				.toArray(new FragmentPair[fragments.size()]);
+				.toArray(new FragmentPair[0]);
 		setFragmentPairs(fp);
 
 		logger.debug(" got # fragment pairs: {}", fp.length);
@@ -536,7 +536,7 @@ public void align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)
 
 		logger.debug("step 3 - refine alignments");
 
-		List<AlternativeAlignment> aas = new ArrayList<AlternativeAlignment>();
+		List<AlternativeAlignment> aas = new ArrayList<>();
 		for (int i = 0; i < frags.length; i++) {
 			JointFragments f = frags[i];
 			AlternativeAlignment a = new AlternativeAlignment();
@@ -562,10 +562,10 @@ public void align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)
 
 		// sort the alternative alignments
 		Comparator<AlternativeAlignment> comp = new AltAligComparator();
-		Collections.sort(aas, comp);
+		aas.sort(comp);
 		Collections.reverse(aas);
 
-		alts = aas.toArray(new AlternativeAlignment[aas.size()]);
+		alts = aas.toArray(new AlternativeAlignment[0]);
 		// do final numbering of alternative solutions
 		int aanbr = 0;
 		for (AlternativeAlignment a : alts) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
index 2ffdbae748..8c196cb65f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
@@ -82,7 +82,7 @@ public abstract class AbstractUserArgumentProcessor implements UserArgumentProce
 
 	protected StartupParameters params ;
 
-	public static final List<String> mandatoryArgs= new ArrayList<String>();
+	public static final List<String> mandatoryArgs= new ArrayList<>();
 
 	protected AbstractUserArgumentProcessor(){
 		params = getStartupParametersInstance();
@@ -303,7 +303,7 @@ private void runDbSearch(AtomCache cache, String searchFile,
 		System.out.println("will use " + useNrCPUs + " CPUs.");
 
 		PDBFileReader reader = new PDBFileReader();
-		Structure structure1 = null ;
+		Structure structure1;
 		try {
 			structure1 = reader.getStructure(searchFile);
 		} catch (IOException e) {
@@ -351,7 +351,7 @@ private void runAlignPairs(AtomCache cache, String alignPairs,
 			String legend = getDbSearchLegend();
 			out.write(legend + newline );
 			System.out.println(legend);
-			String line = null;
+			String line;
 			while ( (line = is.readLine()) != null){
 				if ( line.startsWith("#"))
 					continue;
@@ -431,8 +431,8 @@ private void runPairwise() throws ConfigurationException{
 
 		// first load two example structures
 
-		Structure structure1 = null;
-		Structure structure2 = null;
+		Structure structure1;
+		Structure structure2;
 
 		String path = params.getPdbFilePath();
 
@@ -546,22 +546,7 @@ private void runPairwise() throws ConfigurationException{
 				System.out.println(afpChain.toCE(ca1, ca2));
 			}
 
-		} catch (IOException e) {
-			e.printStackTrace();
-			System.exit(1); return;
-		} catch (ClassNotFoundException e) {
-			e.printStackTrace();
-			System.exit(1); return;
-		} catch (NoSuchMethodException e) {
-			e.printStackTrace();
-			System.exit(1); return;
-		} catch (InvocationTargetException e) {
-			e.printStackTrace();
-			System.exit(1); return;
-		} catch (IllegalAccessException e) {
-			e.printStackTrace();
-			System.exit(1); return;
-		} catch (StructureException e) {
+		} catch (IOException | StructureException | IllegalAccessException | InvocationTargetException | NoSuchMethodException | ClassNotFoundException e) {
 			e.printStackTrace();
 			System.exit(1); return;
 		}
@@ -734,7 +719,7 @@ public String getDbSearchResult(AFPChain afpChain){
 
 	@Override
 	public String printHelp() {
-		StringBuffer buf = new StringBuffer();
+		StringBuilder buf = new StringBuilder();
 		StructureAlignment alg = getAlgorithm();
 
 		buf.append("-------------------").append(newline);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECPParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECPParameters.java
index 146be22a3b..f2aaa8e939 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECPParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECPParameters.java
@@ -32,14 +32,14 @@ public class CECPParameters extends CeParameters {
 
 	public static final int DEFAULT_MIN_CP_LENGTH = 5; //The minimum block length for CPs. Blocks shorter than this will be ignored.
 
-	public static enum DuplicationHint {
+	public enum DuplicationHint {
 		SHORTER("Shorter of the two"),
 		LEFT("Left"),
 		RIGHT("Right");
 
 
-		private String name;
-		private DuplicationHint(String name) {
+		private final String name;
+		DuplicationHint(String name) {
 			this.name = name;
 		}
 		@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
index e70efd5183..cf730bbdaa 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
@@ -118,7 +118,7 @@ public CECalculator(CeParameters params){
 		dist1= new double[0][0];
 		dist2= new double[0][0];
 		this.params = params;
-		matrixListeners = new ArrayList<MatrixListener>();
+		matrixListeners = new ArrayList<>();
 
 	}
 
@@ -139,7 +139,7 @@ public AFPChain extractFragments(AFPChain afpChain,
 		afpChain.setCa1Length(nse1);
 		afpChain.setCa2Length(nse2);
 
-		int traceMaxSize=nse1<nse2?nse1:nse2;
+		int traceMaxSize= Math.min(nse1, nse2);
 
 		f1 = new int[nse1];
 		f2 = new int[nse2];
@@ -259,9 +259,8 @@ public AFPChain extractFragments(AFPChain afpChain,
 	 * @param ca2 The CA of the second residue
 	 * @return The distance between the two fragments, according to the selected
 	 * scoring strategy. Lower distances are better alignments.
-	 * @throws StructureException
 	 */
-	private double getDistanceWithSidechain(Atom ca1, Atom ca2) throws StructureException {
+	private double getDistanceWithSidechain(Atom ca1, Atom ca2) {
 
 		if ( params.getScoringStrategy() == CeParameters.ScoringStrategy.CA_SCORING) {
 
@@ -447,7 +446,7 @@ public void traceFragmentMatrix( AFPChain afpChain,
 
 		//System.out.println("nse1 :" +nse1 + " nse2: " + nse2);
 
-		int traceMaxSize=nse1<nse2?nse1:nse2;
+		int traceMaxSize= Math.min(nse1, nse2);
 
 		bestTrace1 = new int [traceMaxSize];
 		bestTrace2 = new int [traceMaxSize];
@@ -477,10 +476,10 @@ public void traceFragmentMatrix( AFPChain afpChain,
 
 		nTraces =0;
 		long tracesLimit=(long)5e7;
-		double score =-1;
-		double score0 = -1;
-		double score1 = -1 ;
-		double score2 = -1;
+		double score;
+		double score0;
+		double score1;
+		double score2;
 
 		int mse1;
 		int mse2;
@@ -580,7 +579,7 @@ public void traceFragmentMatrix( AFPChain afpChain,
 
 								nTrace++;
 								boolean isTraceUp=true;
-								int traceIndex_=0;
+								int traceIndex_;
 
 								traceLoop:
 									while(nTrace>0) {
@@ -806,7 +805,7 @@ protected double getScore2(int jse1, int jse2, double[][] traceScore, int traceI
 			((nTrace>1?traceScore[nTrace-2][traceIndex[nTrace-1]]:score0)
 		 *a[nTrace-1]+score1*(a[nTrace]-a[nTrace-1]))/a[nTrace];
 		 */
-		double val = 0;
+		double val;
 		if ( nTrace>1)
 			val =traceScore[nTrace-2][traceIndex[nTrace-1]];
 		else
@@ -940,7 +939,7 @@ private void checkBestTraces( AFPChain afpChain,
 		int winSize = params.getWinSize();
 		int nse1 = ca1.length;
 		int nse2 = ca2.length;
-		int traceMaxSize=nse1<nse2?nse1:nse2;
+		int traceMaxSize= Math.min(nse1, nse2);
 		int idir;
 
 
@@ -998,7 +997,7 @@ private void checkBestTraces( AFPChain afpChain,
 		bestTraceLen=new int [traceMaxSize];
 
 
-		int strLen=0;
+		int strLen;
 
 		int jt;
 		strLen=0;
@@ -1143,7 +1142,7 @@ private void checkBestTraces( AFPChain afpChain,
 		}
 
 		// start to convert CE internal datastructure to generic AFPChain one...
-		List<AFP> afpSet = new ArrayList<AFP>();
+		List<AFP> afpSet = new ArrayList<>();
 		for (int afp=0;afp<nBestTrace;afp++){
 			// fill in data from nBestTrace into AFP
 
@@ -1253,7 +1252,7 @@ private void setStrBuf(Atom[] strBuf, int i, Atom[] ca, int j) {
 		int pos = 0;
 		String atomName = ca[j].getName();
 
-		Atom a = null;
+		Atom a;
 
 			a= parent.getAtom(atomName);
 			if ( a != null){
@@ -1555,7 +1554,7 @@ public static double[][] updateMatrixWithSequenceConservation(double[][] max, At
 
 				short aaScore = substMatrix.getValue(ac1,ac2);
 
-				double weightedScore = (aaScore / internalScale) * params.getSeqWeight();
+				double weightedScore = (((double)aaScore) / internalScale) * params.getSeqWeight();
 
 
 				val += weightedScore;
@@ -1609,7 +1608,7 @@ private double dpAlign(int nSeq1, int nSeq2, double gapI, double gapE,
 		// isGlobal1,isGlobal2 are always false...
 
 		int i, j, is, js, iMax, jMax, k;
-		boolean ge=(gapE!=0.0?true:false);
+		boolean ge=(gapE != 0.0);
 		double sum, sum_ret, sum_brk;
 
 		boolean[][] brk_flg=new boolean [nSeq1][nSeq2];
@@ -1850,7 +1849,7 @@ private double dpAlign(int nSeq1, int nSeq2, double gapI, double gapE,
 	}
 
 
-	private void rot_mol(Atom[] caA, Atom[] caB, int nse2, Matrix m , Atom shift) throws StructureException{
+	private void rot_mol(Atom[] caA, Atom[] caB, int nse2, Matrix m , Atom shift) {
 
 		for(int l=0; l<nse2; l++) {
 			Atom a = caA[l];
@@ -1919,11 +1918,10 @@ public double calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen,
 	 * @param length the number of atoms to copy
 	 * @param clone If true, preform a deep copy, cloning the underlying Groups
 	 * @return An array with the first length items of ca, possibly cloning the Atoms.
-	 * @throws StructureException
 	 */
-	private Atom[] getAtoms(Atom[] ca,  int length, boolean clone) throws StructureException{
+	private Atom[] getAtoms(Atom[] ca,  int length, boolean clone) {
 
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 		for ( int i = 0 ; i < length ; i++){
 
 			Atom a;
@@ -1936,7 +1934,7 @@ private Atom[] getAtoms(Atom[] ca,  int length, boolean clone) throws StructureE
 			}
 			atoms.add(a);
 		}
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 	}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
index 2d7e76cf77..d040ddc229 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
@@ -54,7 +54,7 @@
  *
  */
 public class CeCPMain extends CeMain {
-	private static boolean debug = false;
+	private static final boolean debug = false;
 
 	public static final String algorithmName = "jCE Circular Permutation";
 
@@ -84,7 +84,7 @@ public String getVersion() {
 		return CeCPMain.version;
 	}
 
-	public static void main(String[] args) throws ConfigurationException {
+	public static void main(String[] args) {
 		CeCPUserArgumentProcessor processor = new CeCPUserArgumentProcessor(); //Responsible for creating a CeCPMain instance
 		processor.process(args);
 	}
@@ -354,7 +354,7 @@ public static AFPChain filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCal
 
 
 		int firstRes = nStart; // start res number after trimming
-		int lastRes = nStart+ca2len;  // last res number after trimming
+		int lastRes;  // last res number after trimming
 		if(nStart >= ca2len || cEnd < ca2len) { // no circular permutation
 			firstRes=nStart;
 			lastRes=cEnd;
@@ -415,8 +415,8 @@ public static AFPChain filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCal
 
 		// Fix numbering:
 		// First, split up the atoms into left and right blocks
-		List< ResiduePair > left = new ArrayList<ResiduePair>(); // residues from left of duplication
-		List< ResiduePair > right = new ArrayList<ResiduePair>(); // residues from right of duplication
+		List< ResiduePair > left = new ArrayList<>(); // residues from left of duplication
+		List< ResiduePair > right = new ArrayList<>(); // residues from right of duplication
 
 		for(int i=0;i<optLen[0];i++) {
 			if( optAln[0][1][i] >= firstRes && optAln[0][1][i] <= lastRes ) { // not trimmed
@@ -432,7 +432,7 @@ public static AFPChain filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCal
 		alignLen = 0;
 
 		// Now we don't care about left/right, so just call them "blocks"
-		List<List<ResiduePair>> blocks = new ArrayList<List<ResiduePair>>(2);
+		List<List<ResiduePair>> blocks = new ArrayList<>(2);
 		if( !left.isEmpty() ) {
 			blocks.add(left);
 			alignLen += left.size();
@@ -756,7 +756,7 @@ private static CutPoint calculateCutPoint(int[] block,int nStart, int cEnd,
 	// requires additional dependencies biojava-structure-gui and JmolApplet
 	// TODO dmyersturnbull: This should probably be in structure-gui
 	@SuppressWarnings("unused")
-	private static void displayAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException, StructureException {
+	private static void displayAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException {
 		Atom[] ca1clone = StructureTools.cloneAtomArray(ca1);
 		Atom[] ca2clone = StructureTools.cloneAtomArray(ca2);
 		if (! GuiWrapper.isGuiModuleInstalled()) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPUserArgumentProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPUserArgumentProcessor.java
index 1897c96fe2..a437033d5a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPUserArgumentProcessor.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPUserArgumentProcessor.java
@@ -29,7 +29,7 @@
 
 public class CeCPUserArgumentProcessor extends CeUserArgumentProcessor {
 
-	protected class CeCPStartupParams extends CeStartupParams {
+	protected static class CeCPStartupParams extends CeStartupParams {
 		protected DuplicationHint duplicationHint;
 		protected Integer minCPLength;
 
@@ -67,7 +67,7 @@ public String toString() {
 
 	@Override
 	protected StartupParameters getStartupParametersInstance() {
-		return  new CeCPStartupParams();
+		return new CeCPStartupParams();
 	}
 	@Override
 	public StructureAlignment getAlgorithm() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
index 8610b10d0b..5a4c8b69ec 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
@@ -117,7 +117,7 @@ public CeCalculatorEnhanced(CeParameters params){
 		dist1= new double[0][0];
 		dist2= new double[0][0];
 		this.params = params;
-		matrixListeners = new ArrayList<MatrixListener>();
+		matrixListeners = new ArrayList<>();
 
 	}
 
@@ -138,7 +138,7 @@ public AFPChain extractFragments(AFPChain afpChain,
 		afpChain.setCa1Length(nse1);
 		afpChain.setCa2Length(nse2);
 
-		int traceMaxSize=nse1<nse2?nse1:nse2;
+		int traceMaxSize= Math.min(nse1, nse2);
 
 		f1 = new int[nse1];
 		f2 = new int[nse2];
@@ -258,9 +258,8 @@ public AFPChain extractFragments(AFPChain afpChain,
 	 * @param ca2 The CA of the second residue
 	 * @return The distance between the two fragments, according to the selected
 	 * scoring strategy. Lower distances are better alignments.
-	 * @throws StructureException
 	 */
-	private double getDistanceWithSidechain(Atom ca1, Atom ca2) throws StructureException {
+	private double getDistanceWithSidechain(Atom ca1, Atom ca2) {
 
 		if ( params.getScoringStrategy() == CeParameters.ScoringStrategy.CA_SCORING) {
 
@@ -446,7 +445,7 @@ public void traceFragmentMatrix( AFPChain afpChain,
 
 		//System.out.println("nse1 :" +nse1 + " nse2: " + nse2);
 
-		int traceMaxSize=nse1<nse2?nse1:nse2;
+		int traceMaxSize= Math.min(nse1, nse2);
 
 		bestTrace1 = new int [traceMaxSize];
 		bestTrace2 = new int [traceMaxSize];
@@ -476,10 +475,10 @@ public void traceFragmentMatrix( AFPChain afpChain,
 
 		nTraces =0;
 		long tracesLimit=(long)5e7;
-		double score =-1;
-		double score0 = -1;
-		double score1 = -1 ;
-		double score2 = -1;
+		double score;
+		double score0;
+		double score1;
+		double score2;
 
 		int mse1;
 		int mse2;
@@ -579,7 +578,7 @@ public void traceFragmentMatrix( AFPChain afpChain,
 
 								nTrace++;
 								boolean isTraceUp=true;
-								int traceIndex_=0;
+								int traceIndex_;
 
 								traceLoop:
 									while(nTrace>0) {
@@ -805,7 +804,7 @@ protected double getScore2(int jse1, int jse2, double[][] traceScore, int traceI
 			((nTrace>1?traceScore[nTrace-2][traceIndex[nTrace-1]]:score0)
 		 *a[nTrace-1]+score1*(a[nTrace]-a[nTrace-1]))/a[nTrace];
 		 */
-		double val = 0;
+		double val;
 		if ( nTrace>1)
 			val =traceScore[nTrace-2][traceIndex[nTrace-1]];
 		else
@@ -937,7 +936,7 @@ private void checkBestTraces( AFPChain afpChain,
 		int winSize = params.getWinSize();
 		int nse1 = ca1.length;
 		int nse2 = ca2.length;
-		int traceMaxSize=nse1<nse2?nse1:nse2;
+		int traceMaxSize= Math.min(nse1, nse2);
 		int idir;
 
 
@@ -995,7 +994,7 @@ private void checkBestTraces( AFPChain afpChain,
 		bestTraceLen=new int [traceMaxSize];
 
 
-		int strLen=0;
+		int strLen;
 
 		int jt;
 		strLen=0;
@@ -1135,7 +1134,7 @@ private void checkBestTraces( AFPChain afpChain,
 		}
 
 		// start to convert CE internal datastructure to generic AFPChain one...
-		List<AFP> afpSet = new ArrayList<AFP>();
+		List<AFP> afpSet = new ArrayList<>();
 		for (int afp=0;afp<nBestTrace;afp++){
 			// fill in data from nBestTrace into AFP
 
@@ -1244,7 +1243,7 @@ private void setStrBuf(Atom[] strBuf, int i, Atom[] ca, int j) {
 		int pos = 0;
 		String atomName = ca[j].getName();
 
-		Atom a = null;
+		Atom a;
 
 		a= parent.getAtom(atomName);
 		if ( a != null){
@@ -1552,16 +1551,15 @@ public static double[][] updateMatrixWithSequenceConservation(double[][] max, At
 
 				AminoAcidCompound ac1 =
 						set.getCompoundForString(a1.getGroup().getChemComp().getOne_letter_code());
+				if (ac1 == null) continue;
+
 				AminoAcidCompound ac2 =
 						set.getCompoundForString(a2.getGroup().getChemComp().getOne_letter_code());
-
-
-				if ( ac1 == null || ac2 == null)
-					continue;
+				if (ac2 == null) continue;
 
 				short aaScore = substMatrix.getValue(ac1,ac2);
 
-				double weightedScore = (aaScore / internalScale) * params.getSeqWeight();
+				double weightedScore = (((double)aaScore) / internalScale) * params.getSeqWeight();
 
 
 				val += weightedScore;
@@ -1604,7 +1602,7 @@ private double dpAlign(int nSeq1, int nSeq2, double gapI, double gapE,
 		// i.e. we do local alignments by default
 
 		int i, j, iStart, jStart, iMax, jMax, k;
-		boolean hasGapExtensionPenalty=(gapE!=0.0?true:false);
+		boolean hasGapExtensionPenalty=(gapE != 0.0);
 		double  sum_ret, sum_brk;
 
 		boolean[][] brk_flg=new boolean [nSeq1][nSeq2];
@@ -1920,7 +1918,7 @@ private String getTraceBack(int[][] tracebackMatrix1,
 
 	}
 
-	private void rot_mol(Atom[] caA, Atom[] caB, int nse2, Matrix m , Atom shift) throws StructureException{
+	private void rot_mol(Atom[] caA, Atom[] caB, int nse2, Matrix m , Atom shift) {
 
 
 
@@ -2010,11 +2008,10 @@ public double calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTrans
 	 * @param length the number of atoms to copy
 	 * @param clone If true, preform a deep copy, cloning the underlying Groups
 	 * @return An array with the first length items of ca, possibly cloning the Atoms.
-	 * @throws StructureException
 	 */
-	private Atom[] getAtoms(Atom[] ca,  int length, boolean clone) throws StructureException{
+	private Atom[] getAtoms(Atom[] ca,  int length, boolean clone) {
 
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 		for ( int i = 0 ; i < length ; i++){
 
 			Atom a;
@@ -2027,7 +2024,7 @@ private Atom[] getAtoms(Atom[] ca,  int length, boolean clone) throws StructureE
 			}
 			atoms.add(a);
 		}
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 	}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
index 70f4acb64f..e9bb7fd501 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
@@ -75,7 +75,7 @@ public CeMain(){
 	 * -pdbFilePath /tmp -autoFetch -printCE -pdb1 1cnv -pdb2 3cna
 	 *
 	 */
-	public static void main(String[] args) throws Exception {
+	public static void main(String[] args) {
 		CeUserArgumentProcessor processor = new CeUserArgumentProcessor(); //Responsible for creating a CeMain instance
 		processor.process(args);
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
index 8383acf585..7253a7be9c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
@@ -46,7 +46,7 @@ public class CeParameters implements ConfigStrucAligParams  {
 	protected double rmsdThrJoin;
 	protected double maxOptRMSD;
 
-	public static enum ScoringStrategy {
+	public enum ScoringStrategy {
 		CA_SCORING("CA only"),
 		SIDE_CHAIN_SCORING("Sidechain orientation"),
 		SIDE_CHAIN_ANGLE_SCORING("Angle between sidechains"),
@@ -54,8 +54,8 @@ public static enum ScoringStrategy {
 		SEQUENCE_CONSERVATION("Sequence Conservation");
 		public static ScoringStrategy DEFAULT_SCORING_STRATEGY = CA_SCORING;
 
-		private String name;
-		private ScoringStrategy(String name) {
+		private final String name;
+		ScoringStrategy(String name) {
 			this.name = name;
 		}
 		@Override
@@ -205,7 +205,7 @@ public Integer getMaxGapSize() {
 
 	@Override
 	public List<String> getUserConfigHelp() {
-		List<String> params =new ArrayList<String>();
+		List<String> params = new ArrayList<>();
 		String helpMaxGap = "This parameter configures the maximum gap size G, that is applied during the AFP extension. The larger the value, the longer the calculation time can become, Default value is 30. Set to 0 for no limit. " ;
 		//String helpRmsdThr = "This configures the RMSD threshold applied during the trace of the fragment matrix.";
 		String helpWinSize = "This configures the fragment size m of Aligned Fragment Pairs (AFPs).";
@@ -222,7 +222,7 @@ public List<String> getUserConfigHelp() {
 
 	@Override
 	public List<String> getUserConfigParameters() {
-		List<String> params = new ArrayList<String>();
+		List<String> params = new ArrayList<>();
 		params.add("MaxGapSize");
 		//params.add("RmsdThr");
 		params.add("WinSize");
@@ -236,7 +236,7 @@ public List<String> getUserConfigParameters() {
 
 	@Override
 	public List<String> getUserConfigParameterNames(){
-		List<String> params = new ArrayList<String>();
+		List<String> params = new ArrayList<>();
 		params.add("max. gap size G (during AFP extension).");
 		//params.add("RMSD threshold during trace of the fragment matrix.");
 		params.add("fragment size m");
@@ -250,7 +250,7 @@ public List<String> getUserConfigParameterNames(){
 	@Override
 	@SuppressWarnings("rawtypes")
 	public List<Class> getUserConfigTypes() {
-		List<Class> params = new ArrayList<Class>();
+		List<Class> params = new ArrayList<>();
 		params.add(Integer.class);
 		//params.add(Double.class);
 		params.add(Integer.class);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeSideChainMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeSideChainMain.java
index f74793e7f4..6d3a366dee 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeSideChainMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeSideChainMain.java
@@ -44,7 +44,7 @@ public CeSideChainMain(){
 		}
 	}
 
-	public static void main(String[] args) throws ConfigurationException {
+	public static void main(String[] args) {
 		CeSideChainUserArgumentProcessor processor = new CeSideChainUserArgumentProcessor();
 		processor.process(args);
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/ConfigStrucAligParams.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/ConfigStrucAligParams.java
index a22323fe25..3af1ca3321 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/ConfigStrucAligParams.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/ConfigStrucAligParams.java
@@ -31,31 +31,31 @@ public interface ConfigStrucAligParams {
 	 *
 	 * @return list of parameters
 	 */
-	public List<String> getUserConfigParameters();
+    List<String> getUserConfigParameters();
 
 	/** The labels to be displayed to the user for each parameter
 	 *
 	 * @return list of parameter names
 	 */
-	public List<String> getUserConfigParameterNames();
+    List<String> getUserConfigParameterNames();
 
 	/** Get the data types of the parameters
 	 *
 	 * @return list of parameter classes
 	 */
 	@SuppressWarnings("rawtypes")
-	public List<Class> getUserConfigTypes();
+    List<Class> getUserConfigTypes();
 
 
 	/** The help text for each of these parameters.
 	 *
 	 * @return help strings
 	 */
-	public List<String> getUserConfigHelp();
+    List<String> getUserConfigHelp();
 
 
 	/** Set the parameters to the default.
 	 *
 	 */
-	public void reset();
+    void reset();
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/GuiWrapper.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/GuiWrapper.java
index 687d2e625f..df7d98ad66 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/GuiWrapper.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/GuiWrapper.java
@@ -69,8 +69,8 @@ public static Object display(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
 
 		Class c = Class.forName(strucAlignmentDisplay);
 
-		Method display = c.getMethod("display", new Class[]{AFPChain.class, Atom[].class,
-				Atom[].class});
+		Method display = c.getMethod("display", AFPChain.class, Atom[].class,
+				Atom[].class);
 
 		Object structureAlignmentJmol = display.invoke(null, afpChain,ca1,ca2);
 
@@ -87,7 +87,7 @@ public static void showAlignmentImage(AFPChain afpChain, Atom[] ca1,
 		Class abstractAligJmolC = Class.forName(abstractAligJmol);
 
 		Class c = Class.forName(displayAFP);
-		Method show = c.getMethod("showAlignmentPanel", new Class[] {AFPChain.class, Atom[].class, Atom[].class, abstractAligJmolC});
+		Method show = c.getMethod("showAlignmentPanel", AFPChain.class, Atom[].class, Atom[].class, abstractAligJmolC);
 
 		show.invoke(null,afpChain, ca1, ca2, jmol);
 	}
@@ -104,7 +104,7 @@ public static void showStructure(Structure structure)
 
 		Object strucAligJ = structureAlignmentJmol.newInstance();
 
-		Method setS = structureAlignmentJmol.getMethod("setStructure", new Class[] {Structure.class});
+		Method setS = structureAlignmentJmol.getMethod("setStructure", Structure.class);
 
 		setS.invoke(strucAligJ,structure);
 	}
@@ -129,7 +129,7 @@ public static Structure getAlignedStructure(Atom[] ca1, Atom[] ca2)
 		Class<?> structureAlignmentJmol = Class.forName(strucAligJmol);
 
 		Class<?> c = Class.forName(displayAFP);
-		Method show = c.getMethod("getAlignedStructure", new Class[] { Atom[].class, Atom[].class});
+		Method show = c.getMethod("getAlignedStructure", Atom[].class, Atom[].class);
 
 		Structure s = (Structure) show.invoke(null, ca1, ca2);
 
@@ -143,7 +143,7 @@ public static JPanel getScaleableMatrixPanel(Matrix m)
 
 		Class<?> scaleMatrixPanelC = Class.forName(scaleMatrixPanel);
 
-		Method setMatrix = scaleMatrixPanelC.getMethod("setMatrix", new Class[] { Matrix.class});
+		Method setMatrix = scaleMatrixPanelC.getMethod("setMatrix", Matrix.class);
 
 		JPanel panel = (JPanel) scaleMatrixPanelC.newInstance();
 
@@ -161,7 +161,7 @@ public static Atom[] getAtomArray(Atom[] ca, List<Group> hetatoms, List<Group> n
 		Class structureAlignmentJmol = Class.forName(strucAligJmol);
 
 		Class c = Class.forName(displayAFP);
-		Method show = c.getMethod("getAtomArray", new Class[] { Atom[].class, List.class, List.class});
+		Method show = c.getMethod("getAtomArray", Atom[].class, List.class, List.class);
 
 		Atom[] atoms = (Atom[]) show.invoke(null, ca, hetatoms, nucs);
 
@@ -185,7 +185,7 @@ public static void showDBResults(StartupParameters params) {
 			Class<?> c = Class.forName(tableClass);
 			Object table = c.newInstance();
 
-			Method show = c.getMethod("show", new Class[]{File.class, UserConfiguration.class });
+			Method show = c.getMethod("show", File.class, UserConfiguration.class);
 
 			show.invoke(table, new File(params.getShowDBresult()),config);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/MatrixListener.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/MatrixListener.java
index 618f688265..1010a95bcc 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/MatrixListener.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/MatrixListener.java
@@ -24,7 +24,7 @@
 
 public interface MatrixListener {
 
-	public double[][] matrixInOptimizer(double[][] max);
+	double[][] matrixInOptimizer(double[][] max);
 
-	public boolean[][] initializeBreakFlag(boolean[][] brkFlag);
+	boolean[][] initializeBreakFlag(boolean[][] brkFlag);
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java
index b10e09fbfd..ac00b171ad 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java
@@ -34,10 +34,7 @@
 import org.biojava.nbio.structure.jama.Matrix;
 
 import java.lang.reflect.InvocationTargetException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.Scanner;
+import java.util.*;
 
 /**
  * A wrapper for {@link CeMain} which sets default parameters to be appropriate for finding
@@ -126,15 +123,11 @@ private static <T> void permuteArray(T[] arr, int cp) {
 					"Permutation point ("+cp+") must be between -ca2.length and ca2.length-1" );
 		}
 
-		List<T> temp = new ArrayList<T>(cp);
+		List<T> temp = new ArrayList<>(cp);
 
 		// shift residues left
-		for(int i=0;i<cp;i++) {
-			temp.add(arr[i]);
-		}
-		for(int j=cp;j<arr.length;j++) {
-			arr[j-cp]=arr[j];
-		}
+		temp.addAll(Arrays.asList(arr).subList(0, cp));
+        System.arraycopy(arr, cp, arr, cp - cp, arr.length - cp);
 		for(int i=0;i<cp;i++) {
 			arr[arr.length-cp+i] = temp.get(i);
 		}
@@ -333,7 +326,7 @@ private static void permuteOptAln(AFPChain afpChain, int cp)
 		int[] optLen = afpChain.getOptLen();
 
 		// the processed alignment
-		List<List<List<Integer>>> blocks = new ArrayList<List<List<Integer>>>(afpChain.getBlockNum()*2);
+		List<List<List<Integer>>> blocks = new ArrayList<>(afpChain.getBlockNum() * 2);
 
 		//Update residue indices
 		// newi = (oldi-cp) % N
@@ -342,9 +335,9 @@ private static void permuteOptAln(AFPChain afpChain, int cp)
 				continue;
 
 			// set up storage for the current block
-			List<List<Integer>> currBlock = new ArrayList<List<Integer>>(2);
-			currBlock.add( new ArrayList<Integer>());
-			currBlock.add( new ArrayList<Integer>());
+			List<List<Integer>> currBlock = new ArrayList<>(2);
+			currBlock.add(new ArrayList<>());
+			currBlock.add(new ArrayList<>());
 			blocks.add(currBlock);
 
 			// pos = 0 case
@@ -356,9 +349,9 @@ private static void permuteOptAln(AFPChain afpChain, int cp)
 				//this happens when the new alignment crosses the protein terminus
 				if( optAln[block][1][pos-1]+cp<ca2len &&
 						optAln[block][1][pos]+cp >= ca2len) {
-					currBlock = new ArrayList<List<Integer>>(2);
-					currBlock.add( new ArrayList<Integer>());
-					currBlock.add( new ArrayList<Integer>());
+					currBlock = new ArrayList<>(2);
+					currBlock.add(new ArrayList<>());
+					currBlock.add(new ArrayList<>());
 					blocks.add(currBlock);
 				}
 				currBlock.get(0).add( optAln[block][0][pos] );
@@ -651,9 +644,8 @@ public static void main(String[] args){
 	 * @throws NoSuchMethodException
 	 * @throws InvocationTargetException
 	 * @throws IllegalAccessException
-	 * @throws StructureException
 	 */
-	private static void displayAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException, StructureException {
+	private static void displayAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException {
 		Atom[] ca1clone = StructureTools.cloneAtomArray(ca1);
 		Atom[] ca2clone = StructureTools.cloneAtomArray(ca2);
 		if (! GuiWrapper.isGuiModuleInstalled()) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/UserArgumentProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/UserArgumentProcessor.java
index db5e720e5b..f1ded24d04 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/UserArgumentProcessor.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/UserArgumentProcessor.java
@@ -29,11 +29,11 @@ public interface UserArgumentProcessor {
 	 *
 	 * @param argv
 	 */
-	public void process(String[] argv) throws ConfigurationException;
+    void process(String[] argv);
 
 	/**
 	 * Print help about the arguments
 	 * @return
 	 */
-	public String printHelp();
+    String printHelp();
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobParameters.java
index 0415ce0439..3ab4dcae93 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobParameters.java
@@ -29,7 +29,7 @@ public class FarmJobParameters {
 	public static final int DEFAULT_NR_ALIGNMENTS = -1;
 	public static final int DEFAULT_NR_THREADS = 1;
 	public static final String DEFAULT_SERVER_URL;
-	private static ResourceManager resourceManager;
+	private static final ResourceManager resourceManager;
 	static {
 		resourceManager = ResourceManager.getResourceManager("jfatcat");
 		DEFAULT_SERVER_URL = resourceManager.getString("server.url");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java
index d592cc014d..cd7a2332f0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java
@@ -70,7 +70,7 @@ public class FarmJobRunnable implements Runnable {
 	private static final String JFATCAT_NAME            = "jfatcat.name";
 	private static final String JFATCAT_VERSION         = "jfatcat.version";
 
-	private static ResourceManager resourceManager = ResourceManager.getResourceManager("jfatcat");
+	private static final ResourceManager resourceManager = ResourceManager.getResourceManager("jfatcat");
 
 
 	//private static DateFormat dateFormat = new SimpleDateFormat("MMMM dd, yyyy h:mm a",Locale.US);
@@ -95,10 +95,10 @@ public class FarmJobRunnable implements Runnable {
 	List<AlignmentProgressListener> progressListeners;
 	CountProgressListener counter ;
 
-	String userName = null;
+	String userName;
 	protected AtomCache cache;
 
-	boolean verbose = false; // TODO dmyersturnbull: we should probably remove this in favor of SLF4J
+	boolean verbose; // TODO dmyersturnbull: we should probably remove this in favor of SLF4J
 	String version = null;
 
 	private static final String alignURL = "/align/";
@@ -155,7 +155,7 @@ public FarmJobRunnable(FarmJobParameters params){
 	public void addAlignmentProgressListener(AlignmentProgressListener listener){
 
 		if (progressListeners == null)
-			progressListeners = new ArrayList<AlignmentProgressListener>();
+			progressListeners = new ArrayList<>();
 
 		progressListeners.add(listener);
 	}
@@ -228,7 +228,7 @@ public void run() {
 			}
 			SortedSet<PdbPair> alignmentPairs = msg.getPairs();
 			logger.debug("{}: Server responded with {} pairs.", userName, alignmentPairs.size());
-			List<String> results = new ArrayList<String>();
+			List<String> results = new ArrayList<>();
 
 			String algorithmName = msg.getMethod();
 			if ( version == null) {
@@ -470,7 +470,7 @@ private void printMemory() {
 	private StructureAlignment getAlgorithm(String algorithmName) throws StructureException {
 
 
-		StructureAlignment algorithm    = null;
+		StructureAlignment algorithm;
 
 		if ( algorithmName == null){
 
@@ -531,7 +531,7 @@ protected PdbPairsMessage getAlignmentPairsFromServer() {
 		if ( maxNrAlignments < nrPairs )
 			nrPairs = maxNrAlignments;
 
-		SortedSet<PdbPair> allPairs = new TreeSet<PdbPair>();
+		SortedSet<PdbPair> allPairs = new TreeSet<>();
 
 		PdbPairsMessage msg = null;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
index 92c4577115..afb83ad348 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
@@ -44,7 +44,7 @@
 public class JFatCatClient {
 	private final static Logger logger = LoggerFactory.getLogger(JFatCatClient.class);
 
-	private static ResourceManager resourceManager = ResourceManager.getResourceManager("jfatcat");
+	private static final ResourceManager resourceManager = ResourceManager.getResourceManager("jfatcat");
 
 	private static final String serverAPPEND    = "show?name1=%s&name2=%s";
 
@@ -60,13 +60,13 @@ public class JFatCatClient {
 
 	private static final String serverPositionInQueue =  "queuePosition?method=%s&name1=%s&name2=%s";
 
-	private static Random generator;
+	private static final Random generator;
 
-	private static String newline = System.getProperty("line.separator");
+	private static final String newline = System.getProperty("line.separator");
 
-	private static String KILL_JOB = "KILL_JOB";
+	private static final String KILL_JOB = "KILL_JOB";
 
-	private static String COME_BACK_LATER = "COME_BACK_LATER";
+	private static final String COME_BACK_LATER = "COME_BACK_LATER";
 
 	static {
 
@@ -113,7 +113,7 @@ public static boolean hasPrecalculatedResult(String serverLocation, String metho
 
 			InputStream stream = URLConnectionTools.getInputStream(url,timeout);
 
-			String xml = null;
+			String xml;
 
 			if ( stream != null) {
 
@@ -146,7 +146,7 @@ public int getPositionInQueue(String serverLocation, String method, String name1
 
 			InputStream stream = URLConnectionTools.getInputStream(url,timeout);
 
-			String xml = null;
+			String xml;
 
 			if ( stream != null) {
 
@@ -198,9 +198,7 @@ public static AFPChain getAFPChainFromServer(String serverLocation , String meth
 				return null;
 			}
 			// TODO dmyersturnbull: method should throw; we shouldn't catch here
-		} catch (IOException e){
-			logger.error("error in JFatCatClient: getAFPChainFromServer",e);
-		} catch (StructureException e) {
+		} catch (IOException | StructureException e){
 			logger.error("error in JFatCatClient: getAFPChainFromServer",e);
 		}
 		return null;
@@ -211,7 +209,7 @@ public static String convertStreamToString(InputStream stream){
 		BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
 		StringBuilder sb = new StringBuilder();
 
-		String line = null;
+		String line;
 		try {
 			while ((line = reader.readLine()) != null) {
 				sb.append(line).append(newline);
@@ -354,7 +352,7 @@ public static final PdbPairsMessage getPdbPairs(String url,int nrPair, String us
 		// we are very tolerant with requesting a set of pairs, since we probably depend on getting it to get work started...
 		// 1 min...
 		InputStream stream = URLConnectionTools.getInputStream(serverUrl,timeout);
-		String xml = null;
+		String xml;
 
 		if ( stream != null) {
 
@@ -374,7 +372,7 @@ public static final PdbPairsMessage getPdbPairs(String url,int nrPair, String us
 
 
 	public static final SortedSet<String> getRepresentatives(String serverLocation, int cutoff){
-		SortedSet<String> representatives = new TreeSet<String>();
+		SortedSet<String> representatives = new TreeSet<>();
 
 		String representURL = serverLocation + representAPPEND;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
index 4c682e624f..ceb8dfb0b0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
@@ -94,7 +94,7 @@ public enum Source {
 		FILE,
 		ECOD,
 		BIO,
-	};
+	}
 
 	private Source mySource = null;
 
@@ -340,7 +340,7 @@ private boolean initFromFile() {
 	}
 
 	private static Set<String> getChainNames(SubstructureIdentifier si) {
-		Set<String> chains = new TreeSet<String>();
+		Set<String> chains = new TreeSet<>();
 		List<ResidueRange> ranges = si.getResidueRanges();
 		for(ResidueRange range : ranges) {
 			String chainName = range.getChainName();
@@ -626,7 +626,7 @@ public int compareTo(StructureName o) {
 	 * @return The best match for name among the domains of scopDB, or null if none match.
 	 */
 	public static ScopDomain guessScopDomain(String name, ScopDatabase scopDB) {
-		List<ScopDomain> matches = new LinkedList<ScopDomain>();
+		List<ScopDomain> matches = new LinkedList<>();
 
 		// Try exact match first
 		ScopDomain domain = scopDB.getDomainByScopID(name);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/events/AlignmentProgressListener.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/events/AlignmentProgressListener.java
index b8c898d251..0abbf6728c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/events/AlignmentProgressListener.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/events/AlignmentProgressListener.java
@@ -22,17 +22,17 @@
 
 public interface AlignmentProgressListener {
 
-	public void alignmentStarted(String name1, String name2);
+	void alignmentStarted(String name1, String name2);
 
-	public void alignmentEnded();
+	void alignmentEnded();
 
-	public void logStatus(String message);
+	void logStatus(String message);
 
-	public void downloadingStructures(String name);
+	void downloadingStructures(String name);
 
-	public void requestingAlignmentsFromServer(int nrAlignments);
+	void requestingAlignmentsFromServer(int nrAlignments);
 
-	public void sentResultsToServer(int nrAlignments,String serverMessage);
+	void sentResultsToServer(int nrAlignments, String serverMessage);
 
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java
index 6a5aa6dc93..ae3acd965e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java
@@ -60,7 +60,7 @@ public class FatCat
 	 *
 	 * @param argv
 	 */
-	public static void main(String[] argv) throws ConfigurationException {
+	public static void main(String[] argv) {
 		FatCatUserArgumentProcessor processor = new FatCatUserArgumentProcessor();
 		processor.process(argv);
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatUserArgumentProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatUserArgumentProcessor.java
index 69a25b9283..e047d876c9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatUserArgumentProcessor.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatUserArgumentProcessor.java
@@ -36,7 +36,7 @@
 public class FatCatUserArgumentProcessor extends AbstractUserArgumentProcessor {
 	Logger logger = LoggerFactory.getLogger(FatCatUserArgumentProcessor.class);
 
-	protected class FatCatStartupParams extends StartupParameters {
+	protected static class FatCatStartupParams extends StartupParameters {
 		int fragLen;
 		Double rmsdCut;
 		double disCut;
@@ -91,7 +91,7 @@ protected StartupParameters getStartupParametersInstance() {
 
 	@Override
 	public StructureAlignment getAlgorithm() {
-		StructureAlignment algorithm = null;
+		StructureAlignment algorithm;
 		if ( params != null && ((FatCatStartupParams)params).isFlexible()) {
 			logger.info("running flexible alignment");
 			algorithm = new FatCatFlexible();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
index 3fd3400800..92dd9a08e4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
@@ -49,7 +49,7 @@ public static final  void extractAFPChains(FatCatParameters params, AFPChain afp
 
 
 
-		List<AFP> afpSet = new ArrayList<AFP>();
+		List<AFP> afpSet = new ArrayList<>();
 		afpChain.setAfpSet(afpSet);
 
 		if ( debug )
@@ -61,7 +61,7 @@ public static final  void extractAFPChains(FatCatParameters params, AFPChain afp
 		@SuppressWarnings("unused")
 		int n0, n, n1, n2;
 		double  filter1;
-		double rmsd = 0;
+		double rmsd;
 
 		Matrix r = new Matrix(3,3);
 		Atom   t = new AtomImpl();
@@ -78,15 +78,12 @@ public static final  void extractAFPChains(FatCatParameters params, AFPChain afp
 		int     add = sparse + 1; //if add > 1, use sparse sampling
 		n0 = n = n1 = n2 = 0;
 
-		int minLen = 0;
+		int minLen;
 
 		int prot1Length = ca1.length;
 		int prot2Length = ca2.length;
 
-		if(prot1Length < prot2Length)
-			minLen = prot1Length;
-		else
-			minLen = prot2Length;
+        minLen = Math.min(prot1Length, prot2Length);
 		afpChain.setMinLen(minLen);
 
 		afpChain.setBlockResList(new int[maxTra+1][2][minLen]);
@@ -150,7 +147,7 @@ public static final  void extractAFPChains(FatCatParameters params, AFPChain afp
 	private static final double getEnd2EndDistance(Atom[] ca1, Atom[] ca2, int p1b, int p1e, int p2b, int p2e)
 	{
 
-		double min = 99;
+		double min;
 			double dist1 = Calc.getDistance(ca1[p1b], ca1[p1e]);
 			double dist2 = Calc.getDistance(ca2[p2b], ca2[p2e]);
 			min = dist1 - dist2;
@@ -169,8 +166,8 @@ private static final double getEnd2EndDistance(Atom[] ca1, Atom[] ca2, int p1b,
 
 	private static final  boolean filterTerminal(Atom[] ca1, Atom[] ca2, int p1b, int p1e, int p2b, int p2e, int fragLen, int minLen)
 	{
-		int     d1 = (p1b < p2b)?p1b:p2b;
-		int     d2 = (ca1.length - p1e) < (ca2.length - p2e)?(ca1.length - p1e):(ca2.length - p2e);
+		int     d1 = Math.min(p1b, p2b);
+		int     d2 = Math.min((ca1.length - p1e), (ca2.length - p2e));
 		int     d3 = d1 + d2 + fragLen; //maximum alignment length from current AFP
 
 
@@ -182,7 +179,7 @@ private static final  boolean filterTerminal(Atom[] ca1, Atom[] ca2, int p1b, in
 	}
 
 	private static final double getRmsd(Atom[] ca1, Atom[] ca2, int fragLen,
-			int p1, int p2, Matrix m, Atom t) throws StructureException {
+			int p1, int p2, Matrix m, Atom t) {
 
 
 		double rmsd = 99.9;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
index 0f9c2254d9..db9a385b0c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
@@ -94,7 +94,7 @@ public static void doChainAfp(FatCatParameters params, AFPChain afpChain,Atom[]
 		//transformation, calculated at DoChainAfp, be used in List extraction
 
 		//forward: calculate the score matrix
-		boolean isConnected = false;
+		boolean isConnected;
 		int     i, j, j0,  n;
 		double  stmp;
 
@@ -247,14 +247,14 @@ private  static int getCompatibleAfps(int afp, int[] list, FatCatParameters para
 		a3 = i1 - f;
 		a2 = a3 - c;
 		a1 = i1 - G;
-		a2 = a2>0?a2:0;
-		a1 = a1>0?a1:0;
+		a2 = Math.max(a2, 0);
+		a1 = Math.max(a1, 0);
 
 		b3 = j1 - f;
 		b2 = b3 - c;
 		b1 = j1 - G;
-		b2 = (b2 > 0)?b2:0;
-		b1 = (b1 > 0)?b1:0;
+		b2 = Math.max(b2, 0);
+		b1 = Math.max(b1, 0);
 
 		int[][] afpAftIndex = afpChain.getAfpAftIndex();
 		int[][] afpBefIndex = afpChain.getAfpBefIndex();
@@ -309,8 +309,8 @@ public static boolean afpPairConn(int afp1, int afp2,  FatCatParameters params,
 
 	{
 
-		Double conn = afpChain.getConn();
-		Double dvar = afpChain.getDVar();
+		Double conn;
+		Double dvar;
 
 		double misScore = params.getMisScore();
 		double maxPenalty = params.getMaxPenalty();
@@ -383,7 +383,7 @@ private static int calcMismatch(AFP afp1, AFP afp2)
 	{
 		int     l1 = afp1.getP1() - afp2.getP1() - afp2.getFragLen();
 		int     l2 = afp1.getP2() - afp2.getP2() - afp2.getFragLen();
-		return (l1 > l2?l2:l1);
+		return (Math.min(l1, l2));
 	}
 
 	/**
@@ -446,7 +446,7 @@ private static void traceBack(int[] pre, int currafp0, int twist, FatCatParamete
 		int minLen = afpChain.getMinLen();
 		List<AFP> afpSet = afpChain.getAfpSet();
 
-		int afpChainLen = 0;
+		int afpChainLen;
 
 		//trace-back from currafp (maxsco)
 		int[]     afpchain    = new int[minLen];
@@ -611,7 +611,7 @@ private static void traceBack(int[] pre, int currafp0, int twist, FatCatParamete
 
 		afpChain.setBlockSize(blockSize);
 		afpChain.setBlockRmsd(blockRmsd);
-		int blockNum = afpChain.getBlockNum();
+		int blockNum;
 		blockNum = ++bk;
 		if ( debug)
 			System.err.println("AFPChainser setBlockNUm:" + blockNum);
@@ -698,7 +698,7 @@ private static double getRmsd(int focusResn, int[] focusRes1, int[] focusRes2, A
 	 * @param catmp1
 	 * @return
 	 */
-	private static double getRmsd(Atom[] catmp1, Atom[] catmp2) throws StructureException{
+	private static double getRmsd(Atom[] catmp1, Atom[] catmp2) {
 
 		Matrix4d trans = SuperPositions.superpose(Calc.atomsToPoints(catmp1),
 				Calc.atomsToPoints(catmp2));
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java
index 9752c4cc7f..f701268c9f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java
@@ -72,7 +72,7 @@ public static void optimizeAln(FatCatParameters params, AFPChain afpChain,Atom[]
 
 		List<AFP> afpSet = afpChain.getAfpSet();
 
-		int optLength         = afpChain.getOptLength();
+		int optLength;
 		int[] afpChainList    = afpChain.getAfpChainList();
 		int[] block2Afp       = afpChain.getBlock2Afp();
 		int[] blockSize       = afpChain.getBlockSize();
@@ -241,7 +241,7 @@ public static void updateScore(FatCatParameters params, AFPChain afpChain)
 					blockScore[i] += afpSet.get(bknow).getScore() + conn;
 					g1 = afpSet.get(bknow).getP1() - afpSet.get(bkold).getP1() - afpSet.get(bkold).getFragLen();
 					g2 = afpSet.get(bknow).getP2() - afpSet.get(bkold).getP2() - afpSet.get(bkold).getFragLen();
-					blockGap[i] += (g1 > g2)?g1:g2;
+					blockGap[i] += Math.max(g1, g2);
 				}
 				bkold = bknow;
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.java
index 5f940ec6a1..a4242e5c85 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.java
@@ -203,7 +203,7 @@ private static void deleteBlock(FatCatParameters params, AFPChain afpChain,Atom[
 				e2 = ca2.length;
 			}
 			if(blockSize[i] > 1)    continue;
-			len = (e1 - b1) < (e2 - b2)?(e1 - b1):(e2 - b2);
+			len = Math.min((e1 - b1), (e2 - b2));
 			//if(i == blockNum - 1) blockNum --;
 			if(len < 2 * fragLen)   {
 				for(j = i; j < blockNum - 1; j ++)      {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java
index 760b196bd5..bee2eb4df5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java
@@ -366,7 +366,7 @@ public void setSparse(int sparse)
 
 	@Override
 	public List<String> getUserConfigHelp() {
-		List<String> params = new ArrayList<String>();
+		List<String> params = new ArrayList<>();
 		String fragLen = "The length of the fragments.";
 		String rmsdCutHelp = "The RMSD cutoff to be used during AFP detection.";
 		String disCutHelp = "The distance cutoff used when calculate the connectivity of AFP pairs";
@@ -382,7 +382,7 @@ public List<String> getUserConfigHelp() {
 
 	@Override
 	public List<String> getUserConfigParameterNames() {
-		List<String> params = new ArrayList<String>();
+		List<String> params = new ArrayList<>();
 		params.add("Fragment Length");
 		params.add("RMSD Cutoff");
 		params.add("AFP Distance Cutoff");
@@ -393,7 +393,7 @@ public List<String> getUserConfigParameterNames() {
 
 	@Override
 	public List<String> getUserConfigParameters() {
-		List<String> params = new ArrayList<String>();
+		List<String> params = new ArrayList<>();
 		params.add("FragLen");
 		params.add("RmsdCut");
 		params.add("DisCut");
@@ -406,7 +406,7 @@ public List<String> getUserConfigParameters() {
 	@SuppressWarnings({  "rawtypes" })
 	public List<Class> getUserConfigTypes() {
 
-		List<Class> params = new ArrayList<Class>();
+		List<Class> params = new ArrayList<>();
 		params.add(Integer.class);
 		params.add(Double.class);
 		params.add(Double.class);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/SigEva.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/SigEva.java
index d111e55fd6..b16477c96b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/SigEva.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/SigEva.java
@@ -169,9 +169,9 @@ private double calSigAll(int twist, int sparse, int len1, int len2, double score
 			else    getPara(5, len);        //flexible-FATCAT
 		}
 		else if(sparse == 3)    { //sparse sampling = 3
-			if(twist == 0)  getPara(8, len); //rigid-FATCAT
-			else    getPara(8, len); //flexible-FATCAT
-		}
+            //flexible-FATCAT
+            getPara(8, len); //rigid-FATCAT
+        }
 		else if(sparse == 1)    { //sparse sampling = 1
 			if(twist == 0)  getPara(6, len); //rigid-FATCAT
 			else    getPara(7, len); //flexible-FATCAT
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
index 89685fcbbd..96aa0217af 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
@@ -76,7 +76,7 @@ public class StructureAlignmentOptimizer
 	 */
 
 	public StructureAlignmentOptimizer(int b1, int end1, Atom[] c1, int b2, int end2, Atom[] c2,
-			int iniLen, int[][] iniSet) throws StructureException{
+			int iniLen, int[][] iniSet) {
 
 		//System.err.println("optimizing range:" + b1 + "-" + end1 + "("+ (end1-b1) + ") b2:  " + b2 + "-" + end2+ "("+ (end2-b2) + ") iniLen " + iniLen);
 		//System.out.println("ca1: " + c1.length + " ca2: " + c2.length);
@@ -111,7 +111,7 @@ public StructureAlignmentOptimizer(int b1, int end1, Atom[] c1, int b2, int end2
 
 
 		//initial equivalent sets
-		maxLen = (len1 < len2)?len1:len2;
+		maxLen = Math.min(len1, len2);
 
 		equSet = new int[2][maxLen];
 		for(int i = 0; i < iniLen; i ++)    {
@@ -232,9 +232,7 @@ private void setParameters()
 	/**
 	 * superimpose two structures according to the equivalent residues
 	 */
-	private void superimposeBySet ()
-	throws StructureException
-	{
+	private void superimposeBySet () {
 
 		//extract the coordinations of equivalent residues
 		Atom[] tmp1 = new Atom[equLen];
@@ -289,8 +287,8 @@ private void optimize(int maxi) throws StructureException
 		long optStart = System.currentTimeMillis();
 		if ( debug)
 			System.out.println("Optimizing up to " + maxi + " iterations.. ");
-		boolean ifstop = true;;
-		int     i, alnLen;
+		boolean ifstop;
+        int     i, alnLen;
 		alnLen = 0;
 
 		int[][]     alnList =  new int[2][maxLen];
@@ -334,8 +332,7 @@ private void optimize(int maxi) throws StructureException
 	//              Sij = Dc^2 - Dij^2 if Dij <= Dc
 	//                    0            else
 	//--------------------------------------------------------------------------------------------------------
-	private void calMatrix() throws StructureException
-	{
+	private void calMatrix() {
 		int     i, j;
 		double  dis;
 		for(i = 0; i < pro1Len; i ++)   {
@@ -388,7 +385,7 @@ private boolean defineEquPos(int alnLen, int[][] alnList)
 		//if (debug)
 		//   System.out.println(String.format(" OPT: new equLen %d rmsd %f", equLen, rmsd));
 
-		boolean     ifstop = false;
+		boolean     ifstop;
 
 //      if (debug) {
 //         System.out.print(" OPT: rmsd diff: " + Math.abs(rmsd - rmsdOld) + " equLens: " + equLenOld + ":"+ equLen);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/AlignUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/AlignUtils.java
index eb90288595..48a05d122a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/AlignUtils.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/AlignUtils.java
@@ -95,9 +95,7 @@ public static Atom[] getFragmentNoClone(Atom[] caall, int pos, int fragmentLengt
 
 		Atom[] tmp = new Atom[fragmentLength];
 
-		for (int i=0;i< fragmentLength;i++){
-			tmp[i] = caall[i+pos];
-		}
+        if (fragmentLength >= 0) System.arraycopy(caall, 0 + pos, tmp, 0, fragmentLength);
 		return tmp;
 
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java
index 862e7d8d50..659ebd1780 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java
@@ -40,7 +40,7 @@ public class JointFragments {
 
 		List<int[]> idxlist;
 		public JointFragments(){
-			idxlist = new ArrayList<int[]>();
+			idxlist = new ArrayList<>();
 			rms = 999;
 		}
 
@@ -49,11 +49,7 @@ public JointFragments(){
 		 * Each int[] stores the residue numbers of several equivalent residues.
 		 */
 		public void setIdxlist(List<int[]> idxs) {
-			Iterator<int[]> iter = idxs.iterator();
-			while (iter.hasNext()){
-				int[] e = iter.next();
-				idxlist.add(e);
-			}
+			idxlist.addAll(idxs);
 		}
 
 
@@ -77,16 +73,14 @@ public void add(int p1, int p2,int start,int end){
 				int[] e = new int[] {p1+k,p2+k};
 
 				// check if already known ...
-				Iterator<int[]> iter = idxlist.iterator();
-				while (iter.hasNext()){
-					int[] kno = iter.next();
-					if ((kno[0] == e[0]) && ( kno[1] == e[1])){
+				for (int[] kno : idxlist) {
+					if ((kno[0] == e[0]) && (kno[1] == e[1])) {
 						System.err.println("already known index pair, not adding a 2nd time." + e[0] + " " + e[1]);
 						return;
 					}
 				}
 				idxlist.add(e);
-				Collections.sort(idxlist, new IdxComparator());
+				idxlist.sort(new IdxComparator());
 			}
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFP.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFP.java
index 7156d25c76..5cf9ca4b11 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFP.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFP.java
@@ -56,7 +56,7 @@ public String toString(){
 		// Bioinformatics, 24, pp. 872-873  (2008)
 
 
-		StringBuffer buf = new StringBuffer();
+		StringBuilder buf = new StringBuilder();
 		buf.append("AFP: p1:");
 		buf.append(p1);
 		buf.append(" p2: ");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
index 38844a0963..877ee8f4bf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
@@ -179,7 +179,7 @@ public AFPChain(AFPChain o) {
 		this.alignScoreUpdate = o.alignScoreUpdate;
 		this.afpChainTwiNum = o.afpChainTwiNum;
 		this.minLen = o.minLen;
-		this.afpSet = new ArrayList<AFP>(o.afpSet);
+		this.afpSet = new ArrayList<>(o.afpSet);
 		this.afpIndex = o.afpIndex == null? null: o.afpIndex.clone();
 		this.afpAftIndex = o.afpAftIndex == null? null: o.afpAftIndex.clone();
 		this.afpBefIndex = o.afpBefIndex == null? null: o.afpBefIndex.clone();
@@ -231,8 +231,8 @@ public AFPChain(AFPChain o) {
 		this.ca1Length = o.ca1Length;
 		this.ca2Length = o.ca2Length;
 		this.maxTra = o.maxTra;
-		this.conn = new Double(o.conn);
-		this.dvar = new Double(o.dvar);
+		this.conn = o.conn;
+		this.dvar = o.dvar;
 		this.probability = o.probability;
 		this.identity = o.identity;
 		this.similarity = o.similarity;
@@ -358,7 +358,7 @@ public String toString(){
 		//int lB = ca2Length;
 		//int distance = lA + lB - 2 * getNrEQR();
 
-		StringBuffer str = new StringBuffer("");
+		StringBuilder str = new StringBuilder();
 		str.append("EQR:");
 		str.append(getNrEQR());
 
@@ -439,15 +439,15 @@ private void init(){
 
 		blockResSize = new int[maxTra+1];
 
-		afpSet = new ArrayList<AFP>();
+		afpSet = new ArrayList<>();
 		totalLenIni = totalLenOpt = 0;
 		totalRmsdIni = totalRmsdOpt = 0.0;
 
 		afpChainTwiNum = 0;
 		alignScore = 0;
 		alignScoreUpdate = 0;
-		conn = new Double(0);
-		dvar = new Double(0);
+		conn = (double) 0;
+		dvar = (double) 0;
 		calculationTime = 0;
 
 		similarity = -1;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AfpChainWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AfpChainWriter.java
index ce527bc586..ace0f58b00 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AfpChainWriter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AfpChainWriter.java
@@ -45,7 +45,7 @@ public class AfpChainWriter
 
 	public static final String newline = System.getProperty("line.separator");
 
-	private static int LINELENGTH = 70;
+	private static final int LINELENGTH = 70;
 
 	public static String toFatCat(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
 	{
@@ -248,8 +248,7 @@ public static String toFatCatCore(
 		//System.out.println(alnseq1.length + " " + alnseq1.toString());
 
 		while((alnLength - t) > 0)      {
-			if(alnLength - t > linelen)     len = linelen;
-			else    len = alnLength - t;
+            len = Math.min(alnLength - t, linelen);
 
 			if ( ap >= ca1.length)
 				break;
@@ -295,12 +294,11 @@ public static String toFatCatCore(
 						if ( showAlignmentBlock && block > -1 ) {
 							a += "<span class=\"alignmentBlock1"+block+"\">" + c1 + "</span>";
 							b += "<span class=\"alignmentBlock2"+block+"\">" + c2 + "</span>";
-							c += "<span class=\"m\">" + cl + "</span>";
 						} else {
 							a += getPrefix(c1, c2, 0, block, false).toString() + c1 + "</span>";
 							b += getPrefix(c1, c2, 1, block, false).toString() + c2 + "</span>";
-							c += "<span class=\"m\">" + cl + "</span>";
 						}
+						c += "<span class=\"m\">" + cl + "</span>";
 
 					} else if ( c1 != '-' && c2 != '-') {
 
@@ -330,10 +328,7 @@ public static String toFatCatCore(
 			}
 
 			txt.append(newline);
-			if ( longHeader )
-				txt.append(String.format("%14s", " "));
-			else
-				txt.append(String.format("%14s", " "));
+			txt.append(String.format("%14s", " "));
 
 			if (  longHeader ) {
 				for(k = 10; k <= len; k += 10)
@@ -589,7 +584,7 @@ public static String toPrettyAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2
 					formatStartingText(p1,p2,header1,header2,footer1,footer2,ca1,ca2);
 				} else {
 					// check for gapped region
-					int lmax = (p1 - p1b - 1)>(p2 - p2b - 1)?(p1 - p1b - 1):(p2 - p2b - 1);
+					int lmax = Math.max((p1 - p1b - 1), (p2 - p2b - 1));
 					for(k = 0; k < lmax; k ++)      {
 
 
@@ -715,15 +710,13 @@ private static void formatGappedRegion(Atom[] ca1, Atom[] ca2, StringBuffer txt,
 			//alnseq1[len] = '-';
 			if (  formatHTML){
 				alnseq1.append("<span class=\"qg\">-</span>");
-				header1.append(" ");
-				header2.append(" ");
 
 
 			} else {
 				alnseq1.append('-');
-				header1.append(" ");
-				header2.append(" ");
 			}
+			header1.append(" ");
+			header2.append(" ");
 
 		}
 		else {
@@ -742,13 +735,11 @@ private static void formatGappedRegion(Atom[] ca1, Atom[] ca2, StringBuffer txt,
 			//alnseq2[len] = '-';
 			if ( formatHTML){
 				alnseq2.append("<span class=\"qg\">-</span>");
-				footer1.append(" ");
-				footer2.append(" ");
 			} else {
 				alnseq2.append('-');
-				footer1.append(" ");
-				footer2.append(" ");
 			}
+			footer1.append(" ");
+			footer2.append(" ");
 
 		}
 		else  {
@@ -833,10 +824,8 @@ private static void formatPosition(int pos1, Atom[] ca, int len, StringWriter he
 			//System.out.println(len + " p1:" + tmp + " = " + pos1 + " " + " " + display + " " + ignoreH1);
 			if ( ! ignoreH1) {
 				header1.append(String.format("%-13s",display ));
-				header2.append("|");
-			} else {
-				header2.append("|");
 			}
+			header2.append("|");
 
 		} else if ( hasInsertionCode){
 			Character insCode = g.getResidueNumber().getInsCode();
@@ -991,22 +980,16 @@ private static boolean doLenCheck(int len, StringBuffer txt, StringWriter header
 				alnsymb.getBuffer().replace(0, lens, "");
 
 
-
-				header1.getBuffer().replace(0, LINELENGTH, "");
-				header2.getBuffer().replace(0, LINELENGTH , "");
-				footer1.getBuffer().replace(0, LINELENGTH, "");
-				footer2.getBuffer().replace(0, LINELENGTH, "");
-				block.getBuffer().replace(0, LINELENGTH, "");
 			} else {
 				alnseq1.getBuffer().replace(0, LINELENGTH, "");
 				alnseq2.getBuffer().replace(0, LINELENGTH, "");
 				alnsymb.getBuffer().replace(0, LINELENGTH, "");
-				header1.getBuffer().replace(0, LINELENGTH, "");
-				header2.getBuffer().replace(0, LINELENGTH , "");
-				footer1.getBuffer().replace(0, LINELENGTH, "");
-				footer2.getBuffer().replace(0, LINELENGTH, "");
-				block.getBuffer().replace(0, LINELENGTH, "");
 			}
+			header1.getBuffer().replace(0, LINELENGTH, "");
+			header2.getBuffer().replace(0, LINELENGTH , "");
+			footer1.getBuffer().replace(0, LINELENGTH, "");
+			footer2.getBuffer().replace(0, LINELENGTH, "");
+			block.getBuffer().replace(0, LINELENGTH, "");
 			StringBuffer buf = header1.getBuffer();
 			for ( int i=0;i<buf.length();i++){
 				char c = buf.charAt(i);
@@ -1058,7 +1041,7 @@ private static char getOneLetter(Group g){
 
 	public static String toDBSearchResult(AFPChain afpChain)
 	{
-		StringBuffer str = new StringBuffer();
+		StringBuilder str = new StringBuilder();
 
 		str.append(afpChain.getName1());
 		str.append("\t");
@@ -1098,7 +1081,7 @@ public static String toRotMat(AFPChain afpChain)
 		int blockNum = afpChain.getBlockNum();
 		Atom[] blockShiftVector = afpChain.getBlockShiftVector();
 
-		StringBuffer txt = new StringBuffer();
+		StringBuilder txt = new StringBuilder();
 
 		if ( blockRotationMatrix == null || blockRotationMatrix.length < 1)
 			return "";
@@ -1169,7 +1152,7 @@ public static String toCE(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
 
 
 
-		StringBuffer txt = new StringBuffer();
+		StringBuilder txt = new StringBuilder();
 
 		txt.append("Chain 1: ");
 		txt.append(name1);
@@ -1199,8 +1182,7 @@ public static String toCE(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
 		int     k, len;
 
 		while((alnLength - t) > 0)      {
-			if(alnLength - t > linelen)     len = linelen;
-			else    len = alnLength - t;
+            len = Math.min(alnLength - t, linelen);
 
 
 			//System.err.println("t,len:"+t+":"+len);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/AbstractScoresCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/AbstractScoresCache.java
index b1ae2bf543..72b69ba7d1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/AbstractScoresCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/AbstractScoresCache.java
@@ -35,7 +35,7 @@
  */
 public abstract class AbstractScoresCache implements ScoresCache {
 
-	private Map<String,Double> scores = null;
+	private Map<String,Double> scores;
 
 	protected AbstractScoresCache() {
 		scores = null;
@@ -48,7 +48,7 @@ protected AbstractScoresCache(AbstractScoresCache cache) {
 	@Override
 	public void putScore(String property, Double score) {
 		if(scores == null) {
-			scores = new TreeMap<String, Double>();
+			scores = new TreeMap<>();
 		}
 		scores.put(property, score);
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
index 8e79653de6..e7be69a09f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
@@ -45,7 +45,7 @@ public interface Block extends ScoresCache {
 	 *
 	 * @return Block identical copy of this object.
 	 */
-	public Block clone();
+    Block clone();
 
 	/**
 	 * Set the back-reference to its parent BlockSet.
@@ -54,7 +54,7 @@ public interface Block extends ScoresCache {
 	 *            the parent BlockSet.
 	 * @see #getBlockSet()
 	 */
-	public void setBlockSet(BlockSet parent);
+    void setBlockSet(BlockSet parent);
 
 	/**
 	 * Returns the parent BlockSet of the Block. Returns null if there is no
@@ -63,7 +63,7 @@ public interface Block extends ScoresCache {
 	 * @return BlockSet the parent BlockSet of the Block, or null.
 	 * @see #setBlockSet(BlockSet)
 	 */
-	public BlockSet getBlockSet();
+    BlockSet getBlockSet();
 
 	/**
 	 * Returns the double List containing the aligned residues for each
@@ -74,7 +74,7 @@ public interface Block extends ScoresCache {
 	 * @return List a double List of aligned residues for each structure.
 	 * @see #setAlignRes()
 	 */
-	public List<List<Integer>> getAlignRes();
+    List<List<Integer>> getAlignRes();
 
 	/**
 	 * Set the double List containing the aligned residues for each structure.
@@ -83,7 +83,7 @@ public interface Block extends ScoresCache {
 	 *            a double List of Integers with the aligned residues.
 	 * @see #getAlignRes()
 	 */
-	public void setAlignRes(List<List<Integer>> alignRes);
+    void setAlignRes(List<List<Integer>> alignRes);
 
 	/**
 	 * Returns the total number of aligned positions (columns) in the Block.
@@ -92,7 +92,7 @@ public interface Block extends ScoresCache {
 	 * @see #getCoreLength();
 	 * @see #size()
 	 */
-	public int length();
+    int length();
 
 	/**
 	 * Returns the number of aligned structures (rows) in the Block.
@@ -101,7 +101,7 @@ public interface Block extends ScoresCache {
 	 * @see #length()
 	 * @see #getCoreLength()
 	 */
-	public int size();
+    int size();
 
 	/**
 	 * Returns the number of aligned positions (columns) without gaps in the
@@ -112,7 +112,7 @@ public interface Block extends ScoresCache {
 	 * @see #length()
 	 * @see #size()
 	 */
-	public int getCoreLength();
+    int getCoreLength();
 
 	/**
 	 * Returns the number of non null positions (residues) of each structure in
@@ -120,7 +120,7 @@ public interface Block extends ScoresCache {
 	 *
 	 * @return List of residue counts for each structure
 	 */
-	public List<Integer> getAlignResCounts();
+    List<Integer> getAlignResCounts();
 
 	/**
 	 * Calculates and returns the first position of the specified structure in
@@ -132,7 +132,7 @@ public interface Block extends ScoresCache {
 	 *
 	 * @return the first non null aligned position of the structure
 	 */
-	public int getStartIndex(int str);
+    int getStartIndex(int str);
 
 	/**
 	 * Calculates and returns the first residue of the specified structure in
@@ -144,7 +144,7 @@ public interface Block extends ScoresCache {
 	 *
 	 * @return the first non null aligned residue of the structure
 	 */
-	public int getStartResidue(int str);
+    int getStartResidue(int str);
 
 	/**
 	 * Calculates and returns the last position of the specified structure in
@@ -156,7 +156,7 @@ public interface Block extends ScoresCache {
 	 *
 	 * @return the last non null aligned position of the structure
 	 */
-	public int getFinalIndex(int str);
+    int getFinalIndex(int str);
 
 	/**
 	 * Calculates and returns the last residue of the specified structure in the
@@ -168,12 +168,12 @@ public interface Block extends ScoresCache {
 	 *
 	 * @return the last non null aligned residue of the structure
 	 */
-	public int getFinalResidue(int str);
+    int getFinalResidue(int str);
 
 	/**
 	 * Clear scores and other properties which depend on the specific alignment.
 	 * This frees memory and ensures consistency of the cached variables.
 	 */
-	public void clear();
+    void clear();
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
index 402aa5984e..0ab5aa64a9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
@@ -80,9 +80,9 @@ public BlockImpl(BlockImpl b) {
 		this.alignRes = null;
 		if (b.alignRes != null) {
 			// Make a deep copy of everything
-			alignRes = new ArrayList<List<Integer>>();
+			alignRes = new ArrayList<>();
 			for (int k = 0; k < b.size(); k++) {
-				alignRes.add(new ArrayList<Integer>(b.alignRes.get(k)));
+				alignRes.add(new ArrayList<>(b.alignRes.get(k)));
 			}
 		}
 	}
@@ -188,7 +188,7 @@ public List<Integer> getAlignResCounts() {
 		if (alignResCounts != null)
 			return alignResCounts;
 
-		alignResCounts = new ArrayList<Integer>(size());
+		alignResCounts = new ArrayList<>(size());
 		for (int s = 0; s < size(); s++) {
 			int count = 0;
 			for (int r = 0; r < length(); r++) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java
index 4fdf318c61..aa531a8f01 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java
@@ -55,7 +55,7 @@ public interface BlockSet extends ScoresCache {
 	 *
 	 * @return BlockSet identical copy of this object.
 	 */
-	public BlockSet clone();
+    BlockSet clone();
 
 	/**
 	 * Returns the parent MultipleAlignment of the BlockSet.
@@ -65,7 +65,7 @@ public interface BlockSet extends ScoresCache {
 	 * or null.
 	 * @see #setMultipleAlignment(MultipleAlignment)
 	 */
-	public MultipleAlignment getMultipleAlignment();
+    MultipleAlignment getMultipleAlignment();
 
 	/**
 	 * Set the back-reference to its parent MultipleAlignment.
@@ -77,7 +77,7 @@ public interface BlockSet extends ScoresCache {
 	 * @param parent the parent MultipleAlignment.
 	 * @see #getMultipleAlignment()
 	 */
-	public void setMultipleAlignment(MultipleAlignment parent);
+    void setMultipleAlignment(MultipleAlignment parent);
 
 	/**
 	 * Returns the List of alignment Blocks of the BlockSet.
@@ -86,7 +86,7 @@ public interface BlockSet extends ScoresCache {
 	 *
 	 * @see #setBlocks(List)
 	 */
-	public List<Block> getBlocks();
+    List<Block> getBlocks();
 
 	/**
 	 * Set the List of alignment Blocks of the BlockSet.
@@ -96,7 +96,7 @@ public interface BlockSet extends ScoresCache {
 	 * @param blocks List of alignment Blocks.
 	 * @see #getBlocks()
 	 */
-	public void setBlocks(List<Block> blocks);
+    void setBlocks(List<Block> blocks);
 
 	/**
 	 * Returns a transformation matrix for each structure giving the
@@ -104,7 +104,7 @@ public interface BlockSet extends ScoresCache {
 	 *
 	 * @return the 3D superimposition information of the alignment
 	 */
-	public List<Matrix4d> getTransformations();
+    List<Matrix4d> getTransformations();
 
 	/**
 	 * Set a new superposition for the structures.
@@ -113,7 +113,7 @@ public interface BlockSet extends ScoresCache {
 	 *
 	 * @param matrices
 	 */
-	public void setTransformations(List<Matrix4d> transformations);
+    void setTransformations(List<Matrix4d> transformations);
 
 	/**
 	 * Returns the total number of aligned residues (columns) in the alignment:
@@ -123,7 +123,7 @@ public interface BlockSet extends ScoresCache {
 	 * @see #getCoreLength()
 	 * @see #size()
 	 */
-	public int length();
+    int length();
 
 	/**
 	 * Returns the number of aligned residues (columns) without gaps in the
@@ -133,7 +133,7 @@ public interface BlockSet extends ScoresCache {
 	 * @see #length()
 	 * @see #size()
 	 */
-	public int getCoreLength();
+    int getCoreLength();
 
 	/**
 	 * Returns the number of non null positions (residues) of each structure in
@@ -141,7 +141,7 @@ public interface BlockSet extends ScoresCache {
 	 *
 	 * @return List of residue counts for each structure
 	 */
-	public List<Integer> getAlignResCounts();
+    List<Integer> getAlignResCounts();
 
 	/**
 	 * Returns the number of aligned structures in the BlockSet.
@@ -150,7 +150,7 @@ public interface BlockSet extends ScoresCache {
 	 * @see #length()
 	 * @see #getCoreLength()
 	 */
-	public int size();
+    int size();
 
 	/**
 	 * Clear scores and other properties which depend on the specific
@@ -158,5 +158,5 @@ public interface BlockSet extends ScoresCache {
 	 * variables.<p>
 	 * Recursively clears the memeber Blocks.
 	 */
-	public void clear();
+    void clear();
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
index c817853634..6b2bbfad86 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
@@ -88,7 +88,7 @@ public BlockSetImpl(BlockSetImpl bs) {
 		this.pose = null;
 		if (bs.pose != null) {
 			// Make a deep copy of everything
-			this.pose = new ArrayList<Matrix4d>();
+			this.pose = new ArrayList<>();
 			for (Matrix4d trans : bs.pose) {
 				Matrix4d newTrans = (Matrix4d) trans.clone();
 				pose.add(newTrans);
@@ -98,7 +98,7 @@ public BlockSetImpl(BlockSetImpl bs) {
 		blocks = null;
 		if (bs.blocks != null) {
 			// Make a deep copy of everything
-			this.blocks = new ArrayList<Block>();
+			this.blocks = new ArrayList<>();
 			for (Block b : bs.blocks) {
 				Block newB = b.clone();
 				newB.setBlockSet(this);
@@ -143,7 +143,7 @@ public void setMultipleAlignment(MultipleAlignment parent) {
 	@Override
 	public List<Block> getBlocks() {
 		if (blocks == null)
-			blocks = new ArrayList<Block>();
+			blocks = new ArrayList<>();
 		return blocks;
 	}
 
@@ -232,7 +232,7 @@ public List<Integer> getAlignResCounts() {
 		if (alignResCounts != null)
 			return alignResCounts;
 
-		alignResCounts = new ArrayList<Integer>(size());
+		alignResCounts = new ArrayList<>(size());
 		for (int s = 0; s < size(); s++)
 			alignResCounts.add(0);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignment.java
index 1b167caace..b4130a3498 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignment.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignment.java
@@ -53,7 +53,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 *
 	 * @return MultipleAlignment identical copy of this object.
 	 */
-	public MultipleAlignment clone();
+    MultipleAlignment clone();
 
 	/**
 	 * Returns the parent Ensemble of the MultipleAlignment. Returns null if
@@ -63,7 +63,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 *         BlockSet, or null.
 	 * @see #setEnsemble(MultipleAlignmentEnsemble)
 	 */
-	public MultipleAlignmentEnsemble getEnsemble();
+    MultipleAlignmentEnsemble getEnsemble();
 
 	/**
 	 * Set the back-reference to its parent Ensemble.
@@ -76,7 +76,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 *            the parent MultipleAlignmentEnsemble.
 	 * @see #getEnsemble()
 	 */
-	public void setEnsemble(MultipleAlignmentEnsemble parent);
+    void setEnsemble(MultipleAlignmentEnsemble parent);
 
 	/**
 	 * Returns the BlockSet List of the multiple structure alignment.
@@ -87,7 +87,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 * @see #getBlocks()
 	 * @see #setBlockSets(List)
 	 */
-	public List<BlockSet> getBlockSets();
+    List<BlockSet> getBlockSets();
 
 	/**
 	 * Returns the BlockSet with the specified index of the MultipleAlignment.
@@ -100,7 +100,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 * @see #getBlocks()
 	 * @see #getBlockSets()
 	 */
-	public BlockSet getBlockSet(int index);
+    BlockSet getBlockSet(int index);
 
 	/**
 	 * Sets the List of BlockSet List of the specified alignment.
@@ -109,7 +109,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 *            the List of BlockSets that describe the aligned residues.
 	 * @see #getBlockSets()
 	 */
-	public void setBlockSets(List<BlockSet> blockSets);
+    void setBlockSets(List<BlockSet> blockSets);
 
 	/**
 	 * Convenience method to get a List of all Blocks from all BlockSets.
@@ -119,7 +119,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 * @return List of Blocks
 	 * @see #getBlockSets()
 	 */
-	public List<Block> getBlocks();
+    List<Block> getBlocks();
 
 	/**
 	 * Returns the Block with the specified index of the MultipleAlignment.
@@ -132,7 +132,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 * @see #getBlocks()
 	 * @see #getBlockSets()
 	 */
-	public Block getBlock(int index);
+    Block getBlock(int index);
 
 	/**
 	 * Returns the array of Atoms for each structure from its parent Ensemble.
@@ -142,7 +142,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 * @return List of Atom arrays
 	 * @see #getEnsemble()
 	 */
-	public List<Atom[]> getAtomArrays();
+    List<Atom[]> getAtomArrays();
 
 	/**
 	 * Returns the StructureIdentifier associated with the structure index from
@@ -152,7 +152,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 * @return StructureIdentifier
 	 * @see #getEnsemble()
 	 */
-	public StructureIdentifier getStructureIdentifier(int index);
+    StructureIdentifier getStructureIdentifier(int index);
 
 	/**
 	 * Returns the number of aligned structures in the MultipleAlignment.
@@ -161,7 +161,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 * @see #length()
 	 * @see #getCoreLength()
 	 */
-	public int size();
+    int size();
 
 	/**
 	 * Returns the total number of aligned residues (columns) in the multiple
@@ -171,7 +171,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 * @see #getCoreLength()
 	 * @see #size()
 	 */
-	public int length();
+    int length();
 
 	/**
 	 * Returns the number of aligned residues (columns) without gaps in the
@@ -181,7 +181,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 * @see #length()
 	 * @see #size()
 	 */
-	public int getCoreLength();
+    int getCoreLength();
 
 	/**
 	 * Returns the number of non null positions (residues) of each structure in
@@ -189,7 +189,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 *
 	 * @return List of residue counts for each structure
 	 */
-	public List<Integer> getAlignResCounts();
+    List<Integer> getAlignResCounts();
 
 	/**
 	 * Returns the coverage of the alignment for each structure in the
@@ -197,7 +197,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 *
 	 * @return List coverage for each structure
 	 */
-	public List<Double> getCoverages();
+    List<Double> getCoverages();
 
 	/**
 	 * Clear scores and other properties which depend on the specific alignment.
@@ -205,7 +205,7 @@ public interface MultipleAlignment extends ScoresCache {
 	 * <p>
 	 * Recursively clears member BlockSets.
 	 */
-	public void clear();
+    void clear();
 
 	/**
 	 * Return a summary of the MultipleAlignment, containing the structures, the
@@ -215,6 +215,6 @@ public interface MultipleAlignment extends ScoresCache {
 	 * @return String header summary of the MultipleAlignment
 	 */
 	@Override
-	public String toString();
+    String toString();
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java
index d6358a825d..24a52d1562 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java
@@ -49,7 +49,7 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 *
 	 * @return MultipleAlignmentEnsemble identical copy of this object.
 	 */
-	public MultipleAlignmentEnsemble clone();
+    MultipleAlignmentEnsemble clone();
 
 	/**
 	 * Returns the name of the multiple structure alignment algorithm that
@@ -58,7 +58,7 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * @return String name of the algorithm.
 	 * @see #setAlgorithmName(String)
 	 */
-	public String getAlgorithmName();
+    String getAlgorithmName();
 
 	/**
 	 * Set the name of the multiple structure alignment algorithm that created
@@ -67,7 +67,7 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * @param algorithmName name of the algorithm.
 	 * @see #getAlgorithmName()
 	 */
-	public void setAlgorithmName(String algorithmName);
+    void setAlgorithmName(String algorithmName);
 
 	/**
 	 * Returns the version of the algorithm used to generate the
@@ -76,7 +76,7 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * @return String version of the algorithm.
 	 * @see #setVersion(String)
 	 */
-	public String getVersion();
+    String getVersion();
 
 	/**
 	 * Sets the version of the algorithm used to generate the MultipleAlignment
@@ -85,7 +85,7 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * @param version the version of the algorithm.
 	 * @see #getVersion()
 	 */
-	public void setVersion(String version);
+    void setVersion(String version);
 
 	/**
 	 * Returns a List containing the names of the structures aligned
@@ -98,7 +98,7 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * @see #setStructureIdentifiers(List)
 	 * @see #getAtomArrays()
 	 */
-	public List<StructureIdentifier> getStructureIdentifiers();
+    List<StructureIdentifier> getStructureIdentifiers();
 
 	/**
 	 * Set the List containing the names of the structures aligned
@@ -109,7 +109,7 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * @see #getStructureIdentifiers()
 	 * @see #setAtomArrays(List)
 	 */
-	public void setStructureIdentifiers(List<StructureIdentifier> structureIdentifiers);
+    void setStructureIdentifiers(List<StructureIdentifier> structureIdentifiers);
 
 	/**
 	 * Get an array of representative atoms for each structure (CA atoms for
@@ -126,7 +126,7 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * @return List of Atom[].
 	 * @see #setAtomArrays(List)
 	 */
-	public List<Atom[]> getAtomArrays();
+    List<Atom[]> getAtomArrays();
 
 	/**
 	 * Sets the List of Atom arrays. Every structure has an Atom array
@@ -140,7 +140,7 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * @see #getAtomArrays()
 	 * @see #setStructureIdentifiers(List)
 	 */
-	public void setAtomArrays(List<Atom[]> atomArrays);
+    void setAtomArrays(List<Atom[]> atomArrays);
 
 	/**
 	 * Returns the List containing the interatomic distance Matrix of each
@@ -149,7 +149,7 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * @return List of Matrix interatomic distance matrices.
 	 * @see #updateDistanceMatrix()
 	 */
-	public List<Matrix> getDistanceMatrix();
+    List<Matrix> getDistanceMatrix();
 
 	/**
 	 * Returns the List of MultipleAlignments in the ensemble.
@@ -157,7 +157,7 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * @return List of MultipleAlignment in the ensemble.
 	 * @see #setMultipleAlignments()
 	 */
-	public List<MultipleAlignment> getMultipleAlignments();
+    List<MultipleAlignment> getMultipleAlignments();
 
 	/**
 	 * Returns the MultipleAlignments at the specified index
@@ -167,7 +167,7 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * @return MultipleAlignment at the index in the ensemble.
 	 * @see #setMultipleAlignments()
 	 */
-	public MultipleAlignment getMultipleAlignment(int index);
+    MultipleAlignment getMultipleAlignment(int index);
 
 	/**
 	 * Set the List of MultipleAlignments in the ensemble.
@@ -176,7 +176,7 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * ensemble.
 	 * @see #addMultipleAlignment(MultipleAlignment)
 	 */
-	public void setMultipleAlignments(List<MultipleAlignment> alignments);
+    void setMultipleAlignments(List<MultipleAlignment> alignments);
 
 	/**
 	 * Add a new MultipleAlignment to the end of the ensemble and set its
@@ -184,7 +184,7 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 *
 	 * @param alignment
 	 */
-	public void addMultipleAlignment(MultipleAlignment alignment);
+    void addMultipleAlignment(MultipleAlignment alignment);
 
 	/**
 	 * Returns the number of aligned structures in the MultipleAlignments.
@@ -193,19 +193,19 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * @see #getStructureIdentifiers()
 	 * @see #getAtomArrays()
 	 */
-	public int size();
+    int size();
 
 	/**
 	 * Returns the io time for this object, in milliseconds.
 	 * @return long creation time, or null if unset
 	 */
-	public Long getIoTime();
+    Long getIoTime();
 
 	/**
 	 * Set the IO time to load this object
 	 * @param millis
 	 */
-	public void setIoTime(Long millis);
+    void setIoTime(Long millis);
 
 	/**
 	 * Returns the running time of the structure alignment calculation, in
@@ -214,14 +214,14 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * @return long running time of the calculation, or null if unset
 	 * @see #getIoTime()
 	 */
-	public Long getCalculationTime();
+    Long getCalculationTime();
 
 	/**
 	 * Set the running time spent to calculate this alignment.
 	 *
 	 * @param millis
 	 */
-	public void setCalculationTime(Long millis);
+    void setCalculationTime(Long millis);
 
 	/**
 	 * Clear scores and other properties which depend on the specific
@@ -229,5 +229,5 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * variables.<p>
 	 * Recursively clears the member MultipleAlignments.
 	 */
-	public void clear();
+    void clear();
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
index 04b31447b0..4445821ab1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
@@ -24,6 +24,7 @@
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 import javax.vecmath.Matrix4d;
@@ -115,7 +116,7 @@ public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e) {
 		distanceMatrix = null;
 		if (e.distanceMatrix != null) {
 			// Make a deep copy of everything
-			distanceMatrix = new ArrayList<Matrix>();
+			distanceMatrix = new ArrayList<>();
 			for (Matrix mat : e.distanceMatrix) {
 				distanceMatrix.add((Matrix) mat.clone());
 			}
@@ -124,7 +125,7 @@ public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e) {
 		multipleAlignments = null;
 		if (e.multipleAlignments != null) {
 			// Make a deep copy of everything
-			multipleAlignments = new ArrayList<MultipleAlignment>();
+			multipleAlignments = new ArrayList<>();
 			for (MultipleAlignment msa : e.multipleAlignments) {
 				MultipleAlignment newMSA = msa.clone();
 				newMSA.setEnsemble(this);
@@ -133,10 +134,10 @@ public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e) {
 		}
 
 		if (e.atomArrays != null) {
-			atomArrays = new ArrayList<Atom[]>(e.atomArrays);
+			atomArrays = new ArrayList<>(e.atomArrays);
 		}
 		if (e.structureIdentifiers != null) {
-			structureIdentifiers = new ArrayList<StructureIdentifier>(
+			structureIdentifiers = new ArrayList<>(
 					e.structureIdentifiers);
 		}
 	}
@@ -163,7 +164,7 @@ public MultipleAlignmentEnsembleImpl(AFPChain afp, Atom[] ca1, Atom[] ca2,
 		atomArrays = Arrays.asList(ca1, ca2);
 		if (afp.getName1() != null && !afp.getName1().isEmpty() &&
 				afp.getName2() != null && !afp.getName2().isEmpty()) {
-			structureIdentifiers = Arrays.<StructureIdentifier> asList(
+			structureIdentifiers = Arrays.asList(
 					new StructureName(afp.getName1()),
 					new StructureName(afp.getName2()));
 		}
@@ -172,7 +173,7 @@ public MultipleAlignmentEnsembleImpl(AFPChain afp, Atom[] ca1, Atom[] ca2,
 		calculationTime = afp.getCalculationTime();
 
 		MultipleAlignment msa = new MultipleAlignmentImpl(this);
-		setMultipleAlignments(Arrays.asList(msa));
+		setMultipleAlignments(Collections.singletonList(msa));
 
 		// Convert the rotation and translation to a Matrix4D and set it
 		Matrix4d ident = new Matrix4d();
@@ -184,19 +185,17 @@ public MultipleAlignmentEnsembleImpl(AFPChain afp, Atom[] ca1, Atom[] ca2,
 		if (flexible) {
 			for (int bs = 0; bs < afp.getBlockNum(); bs++) {
 				BlockSet blockSet = new BlockSetImpl(msa);
-				Matrix4d blockTr = null;
+				Matrix4d blockTr;
 				try {
 					blockTr = Calc.getTransformation(rot[bs], shift[bs]);
-				} catch (IndexOutOfBoundsException e) {
-					blockTr = ident;
-				} catch (NullPointerException e) {
+				} catch (IndexOutOfBoundsException | NullPointerException e) {
 					blockTr = ident;
 				}
 				blockSet.setTransformations(Arrays.asList(ident, blockTr));
 				Block block = new BlockImpl(blockSet);
-				block.setAlignRes(new ArrayList<List<Integer>>());
-				block.getAlignRes().add(new ArrayList<Integer>());
-				block.getAlignRes().add(new ArrayList<Integer>());
+				block.setAlignRes(new ArrayList<>());
+				block.getAlignRes().add(new ArrayList<>());
+				block.getAlignRes().add(new ArrayList<>());
 
 				// Set the transformation of the BlockSet
 				Matrix rotB = afp.getBlockRotationMatrix()[bs];
@@ -213,20 +212,18 @@ public MultipleAlignmentEnsembleImpl(AFPChain afp, Atom[] ca1, Atom[] ca2,
 		} // Create a Block for every block in AFPChain if not flexible
 		else {
 			BlockSet blockSet = new BlockSetImpl(msa);
-			Matrix4d blockTr = null;
+			Matrix4d blockTr;
 			try {
 				blockTr = Calc.getTransformation(rot[0], shift[0]);
-			} catch (IndexOutOfBoundsException e) {
-				blockTr = ident;
-			} catch (NullPointerException e) {
+			} catch (IndexOutOfBoundsException | NullPointerException e) {
 				blockTr = ident;
 			}
 			blockSet.setTransformations(Arrays.asList(ident, blockTr));
 			for (int bs = 0; bs < afp.getBlockNum(); bs++) {
 				Block block = new BlockImpl(blockSet);
-				block.setAlignRes(new ArrayList<List<Integer>>());
-				block.getAlignRes().add(new ArrayList<Integer>());
-				block.getAlignRes().add(new ArrayList<Integer>());
+				block.setAlignRes(new ArrayList<>());
+				block.getAlignRes().add(new ArrayList<>());
+				block.getAlignRes().add(new ArrayList<>());
 
 				// Convert the optimal alignment to a Block
 				for (int i = 0; i < afp.getOptAln()[bs][0].length; i++) {
@@ -303,9 +300,7 @@ public List<Atom[]> getAtomArrays() {
 		if (atomArrays == null) {
 			try {
 				updateAtomArrays();
-			} catch (IOException e) {
-				throw new NullPointerException(e.getMessage());
-			} catch (StructureException e) {
+			} catch (IOException | StructureException e) {
 				throw new NullPointerException(e.getMessage());
 			}
 		}
@@ -326,7 +321,7 @@ public void setAtomArrays(List<Atom[]> atomArrays) {
 	 */
 	public void updateAtomArrays() throws IOException, StructureException {
 		AtomCache cache = new AtomCache();
-		atomArrays = new ArrayList<Atom[]>();
+		atomArrays = new ArrayList<>();
 		for (StructureIdentifier name : getStructureIdentifiers()) {
 			Atom[] array = cache.getRepresentativeAtoms(name);
 			atomArrays.add(array);
@@ -346,7 +341,7 @@ public List<Matrix> getDistanceMatrix() {
 	public void updateDistanceMatrix() {
 
 		// Reset the distance Matrix variable
-		distanceMatrix = new ArrayList<Matrix>();
+		distanceMatrix = new ArrayList<>();
 
 		for (int s = 0; s < size(); s++) {
 			Atom[] ca = atomArrays.get(s);
@@ -359,7 +354,7 @@ public void updateDistanceMatrix() {
 	public List<MultipleAlignment> getMultipleAlignments() {
 
 		if (multipleAlignments == null) {
-			multipleAlignments = new ArrayList<MultipleAlignment>();
+			multipleAlignments = new ArrayList<>();
 		}
 		return multipleAlignments;
 	}
@@ -377,7 +372,7 @@ public void setMultipleAlignments(List<MultipleAlignment> alignments) {
 	@Override
 	public void addMultipleAlignment(MultipleAlignment alignment) {
 		if (multipleAlignments == null) {
-			multipleAlignments = new ArrayList<MultipleAlignment>();
+			multipleAlignments = new ArrayList<>();
 		}
 		multipleAlignments.add(alignment);
 		alignment.setEnsemble(this);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
index e2131449fd..d2ccafb320 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
@@ -99,7 +99,7 @@ public MultipleAlignmentImpl(MultipleAlignmentImpl ma) {
 		blockSets = null;
 		if (ma.blockSets != null) {
 			// Make a deep copy of everything
-			this.blockSets = new ArrayList<BlockSet>();
+			this.blockSets = new ArrayList<>();
 			for (BlockSet bs : ma.blockSets) {
 				BlockSet newBS = bs.clone();
 				newBS.setMultipleAlignment(this);
@@ -126,7 +126,7 @@ public MultipleAlignmentImpl clone() {
 
 	@Override
 	public String toString() {
-		List<String> ids = new ArrayList<String>(parent
+		List<String> ids = new ArrayList<>(parent
 				.getStructureIdentifiers().size());
 		for (StructureIdentifier i : parent.getStructureIdentifiers()) {
 			ids.add(i.getIdentifier());
@@ -146,13 +146,13 @@ public String toString() {
 	@Override
 	public List<BlockSet> getBlockSets() {
 		if (blockSets == null)
-			blockSets = new ArrayList<BlockSet>();
+			blockSets = new ArrayList<>();
 		return blockSets;
 	}
 
 	@Override
 	public List<Block> getBlocks() {
-		List<Block> blocks = new ArrayList<Block>();
+		List<Block> blocks = new ArrayList<>();
 		for (BlockSet bs : getBlockSets()) {
 			blocks.addAll(bs.getBlocks());
 		}
@@ -262,7 +262,7 @@ public List<Integer> getAlignResCounts() {
 		if (alignResCounts != null)
 			return alignResCounts;
 
-		alignResCounts = new ArrayList<Integer>(size());
+		alignResCounts = new ArrayList<>(size());
 		for (int s = 0; s < size(); s++)
 			alignResCounts.add(0);
 
@@ -281,7 +281,7 @@ public List<Double> getCoverages() {
 			return coverages;
 
 		List<Integer> counts = getAlignResCounts();
-		coverages = new ArrayList<Double>(size());
+		coverages = new ArrayList<>(size());
 		for (int s = 0; s < size(); s++)
 			coverages.add(counts.get(s)
 					/ (double) getAtomArrays().get(s).length);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/ScoresCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/ScoresCache.java
index bca1af269f..c96bbf416d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/ScoresCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/ScoresCache.java
@@ -51,7 +51,7 @@ public interface ScoresCache {
 	 * in headers. Example names found in: {@link MultipleAlignmentScorer}.
 	 * @param score Value of the score
 	 */
-	public void putScore(String property, Double score);
+    void putScore(String property, Double score);
 
 	/**
 	 * Get the value for a particular score. Scores which return null
@@ -61,12 +61,12 @@ public interface ScoresCache {
 	 * @param property Name of the score to fetch
 	 * @return Value of the score, or null if it is not set.
 	 */
-	public Double getScore(String property);
+    Double getScore(String property);
 
 	/**
 	 * Get a collection of all scores that have been set.
 	 *
 	 * @return Set of all score names
 	 */
-	public Set<String> getScores();
+    Set<String> getScores();
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
index dcc843d791..ce50208f14 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
@@ -124,16 +124,16 @@ private MultipleAlignment generateSeed(List<Atom[]> atomArrays)
 		int size = atomArrays.size();
 
 		//List to store the all-to-all alignments
-		List<List<AFPChain>> afpAlignments = new ArrayList<List<AFPChain>>();
+		List<List<AFPChain>> afpAlignments = new ArrayList<>();
 		for (int i=0; i<size; i++){
-			afpAlignments.add(new ArrayList<AFPChain>());
+			afpAlignments.add(new ArrayList<>());
 			for (int j=0; j<size; j++)
 				afpAlignments.get(i).add(null);
 		}
 
 		int threads = params.getNrThreads();
 		ExecutorService executor = Executors.newFixedThreadPool(threads);
-		List<Future<AFPChain>> afpFuture = new ArrayList<Future<AFPChain>>();
+		List<Future<AFPChain>> afpFuture = new ArrayList<>();
 
 		//Create all the possible protein pairwise combinations
 		//(N*(N-1)/2) and call the pairwise alignment algorithm
@@ -184,7 +184,7 @@ private static int chooseReferenceRMSD(List<List<AFPChain>> afpAlignments){
 
 		int size = afpAlignments.size();
 
-		List<Double> RMSDs = new ArrayList<Double>();
+		List<Double> RMSDs = new ArrayList<>();
 		for (int i=0; i<afpAlignments.size(); i++){
 			double rmsd=0.0;
 			for (int j=0; j<size; j++){
@@ -216,22 +216,21 @@ private static int chooseReferenceRMSD(List<List<AFPChain>> afpAlignments){
 	 * @param ref index of the reference structure
 	 * @param flexible uses BlockSets if true, uses Blocks otherwise
 	 * @return MultipleAlignment seed alignment
-	 * @throws StructureException
 	 */
 	private static MultipleAlignment combineReferenceAlignments(
 			List<AFPChain> afpList, List<Atom[]> atomArrays,
-			int ref, boolean flexible) throws StructureException {
+			int ref, boolean flexible) {
 
 		int size = atomArrays.size();
-		int length = 0;  //the number of residues of the reference structure
+		int length;  //the number of residues of the reference structure
 		if (ref==0) length = afpList.get(1).getCa1Length();
 		else length = afpList.get(0).getCa2Length();
-		SortedSet<Integer> flexibleBoundaries = new TreeSet<Integer>();
+		SortedSet<Integer> flexibleBoundaries = new TreeSet<>();
 
 		//Stores the equivalencies of all the structures as a double List
-		List<List<Integer>> equivalencies = new ArrayList<List<Integer>>();
+		List<List<Integer>> equivalencies = new ArrayList<>();
 		for (int str=0; str<size; str++){
-			equivalencies.add(new ArrayList<Integer>());
+			equivalencies.add(new ArrayList<>());
 			for (int res=0; res<length; res++){
 				if (str==ref) equivalencies.get(str).add(res);  //identity
 				else equivalencies.get(str).add(null);
@@ -305,10 +304,10 @@ else if (str<ref){
 				if (lastB.getAlignRes() == null){
 					//Initialize the aligned residues list
 					List<List<Integer>> alnRes =
-							new ArrayList<List<Integer>>(size);
+							new ArrayList<>(size);
 
 					for (int k=0; k<size; k++) {
-						alnRes.add(new ArrayList<Integer>());
+						alnRes.add(new ArrayList<>());
 					}
 					lastB.setAlignRes(alnRes);
 				}
@@ -335,9 +334,7 @@ public MultipleAlignment align(List<Atom[]> atomArrays, Object parameters)
 		//Generate the seed alignment and optimize it
 		try {
 			result = generateSeed(atomArrays);
-		} catch (InterruptedException e) {
-			logger.warn("Seed generation failed.",e);
-		} catch (ExecutionException e) {
+		} catch (InterruptedException | ExecutionException e) {
 			logger.warn("Seed generation failed.",e);
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
index 0845c61300..b1f6ced268 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -67,28 +67,28 @@ public class MultipleMcOptimizer implements Callable<MultipleAlignment> {
 	private static final Logger logger = LoggerFactory
 			.getLogger(MultipleMcOptimizer.class);
 
-	private Random rnd;
-	private MultipleSuperimposer imposer;
+	private final Random rnd;
+	private final MultipleSuperimposer imposer;
 
 	// Optimization parameters
-	private int Rmin; // number of aligned structures without a gap
-	private int Lmin; // Minimum alignment length of a Block
-	private int convergenceSteps; // Steps without score change before stopping
-	private double C; // Probability function constant
+	private final int Rmin; // number of aligned structures without a gap
+	private final int Lmin; // Minimum alignment length of a Block
+	private final int convergenceSteps; // Steps without score change before stopping
+	private final double C; // Probability function constant
 
 	// Score function parameters - they are defined by the user
-	private double Gopen; // Penalty for opening gap
-	private double Gextend; // Penalty for extending gaps
-	private double dCutoff; // max allowed residue distance
+	private final double Gopen; // Penalty for opening gap
+	private final double Gextend; // Penalty for extending gaps
+	private final double dCutoff; // max allowed residue distance
 
 	// Alignment Information
 	private MultipleAlignment msa; // Alignment to optimize
 	private List<SortedSet<Integer>> freePool; // unaligned residues
-	private List<Atom[]> atomArrays;
+	private final List<Atom[]> atomArrays;
 
 	// Alignment Properties
-	private int size; // number of structures in the alignment
-	private int blockNr; // the number of Blocks in the alignment
+	private final int size; // number of structures in the alignment
+	private final int blockNr; // the number of Blocks in the alignment
 	private double mcScore; // Optimization score, objective function
 
 	// Variables that store the history of the optimization - slower if on
@@ -125,7 +125,7 @@ public MultipleMcOptimizer(MultipleAlignment seedAln,
 		imposer = new CoreSuperimposer(reference);
 
 		if (params.getConvergenceSteps() == 0) {
-			List<Integer> lens = new ArrayList<Integer>();
+			List<Integer> lens = new ArrayList<>();
 			for (int i = 0; i < size; i++)
 				lens.add(atomArrays.get(i).length);
 			convergenceSteps = Collections.min(lens) * size;
@@ -142,8 +142,8 @@ public MultipleMcOptimizer(MultipleAlignment seedAln,
 		Lmin = params.getMinBlockLen();
 
 		// Delete all shorter than Lmin blocks, and empty blocksets
-		List<Block> toDelete = new ArrayList<Block>();
-		List<BlockSet> emptyBs = new ArrayList<BlockSet>();
+		List<Block> toDelete = new ArrayList<>();
+		List<BlockSet> emptyBs = new ArrayList<>();
 
 		for (Block b : msa.getBlocks()) {
 			if (b.getCoreLength() < Lmin) {
@@ -183,12 +183,12 @@ public MultipleAlignment call() throws Exception {
 	private void initialize() throws StructureException {
 
 		// Initialize alignment variables
-		freePool = new ArrayList<SortedSet<Integer>>();
-		List<List<Integer>> aligned = new ArrayList<List<Integer>>();
+		freePool = new ArrayList<>();
+		List<List<Integer>> aligned = new ArrayList<>();
 
 		// Generate freePool residues from the ones not aligned
 		for (int i = 0; i < size; i++) {
-			List<Integer> residues = new ArrayList<Integer>();
+			List<Integer> residues = new ArrayList<>();
 			for (BlockSet bs : msa.getBlockSets()) {
 				for (Block b : bs.getBlocks()) {
 					for (int l = 0; l < b.length(); l++) {
@@ -199,7 +199,7 @@ private void initialize() throws StructureException {
 				}
 			}
 			aligned.add(residues);
-			freePool.add(new TreeSet<Integer>());
+			freePool.add(new TreeSet<>());
 		}
 
 		// Add any residue not aligned to the free pool for every structure
@@ -219,9 +219,9 @@ private void initialize() throws StructureException {
 
 		// Initialize the history variables
 		if (history) {
-			lengthHistory = new ArrayList<Integer>();
-			rmsdHistory = new ArrayList<Double>();
-			scoreHistory = new ArrayList<Double>();
+			lengthHistory = new ArrayList<>();
+			rmsdHistory = new ArrayList<>();
+			scoreHistory = new ArrayList<>();
 		}
 	}
 
@@ -249,11 +249,10 @@ public MultipleAlignment optimize() throws StructureException {
 
 			// Save the state of the system
 			MultipleAlignment lastMSA = msa.clone();
-			List<SortedSet<Integer>> lastFreePool = new ArrayList<SortedSet<Integer>>();
+			List<SortedSet<Integer>> lastFreePool = new ArrayList<>();
 			for (int k = 0; k < size; k++) {
-				SortedSet<Integer> p = new TreeSet<Integer>();
-				for (Integer l : freePool.get(k))
-					p.add(l);
+				SortedSet<Integer> p = new TreeSet<>();
+				p.addAll(freePool.get(k));
 				lastFreePool.add(p);
 			}
 			double lastScore = mcScore;
@@ -349,10 +348,10 @@ private boolean checkGaps() {
 
 		boolean shrinkedAny = false;
 
-		List<List<Integer>> shrinkColumns = new ArrayList<List<Integer>>();
+		List<List<Integer>> shrinkColumns = new ArrayList<>();
 		// Loop for each Block
 		for (Block b : msa.getBlocks()) {
-			List<Integer> shrinkCol = new ArrayList<Integer>();
+			List<Integer> shrinkCol = new ArrayList<>();
 			// Loop for each column in the Block
 			for (int res = 0; res < b.length(); res++) {
 				int gapCount = 0;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcParameters.java
index a49d9febc3..d70ce9ceff 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcParameters.java
@@ -54,7 +54,7 @@ public MultipleMcParameters(){
 	@Override
 	public List<String> getUserConfigParameters() {
 
-		List<String> params = new ArrayList<String>();
+		List<String> params = new ArrayList<>();
 		params.add("RandomSeed");
 		params.add("MinBlockLen");
 		params.add("MinAlignedStructures");
@@ -69,7 +69,7 @@ public List<String> getUserConfigParameters() {
 	@Override
 	public List<String> getUserConfigParameterNames() {
 
-		List<String> params = new ArrayList<String>();
+		List<String> params = new ArrayList<>();
 		params.add("Random Seed");
 		params.add("Minimum Block Length");
 		params.add("Minimum Structures per Column");
@@ -85,7 +85,7 @@ public List<String> getUserConfigParameterNames() {
 	@SuppressWarnings("rawtypes")
 	public List<Class> getUserConfigTypes() {
 
-		List<Class> params = new ArrayList<Class>();
+		List<Class> params = new ArrayList<>();
 		params.add(Integer.class);
 		params.add(Integer.class);
 		params.add(Integer.class);
@@ -100,7 +100,7 @@ public List<Class> getUserConfigTypes() {
 	@Override
 	public List<String> getUserConfigHelp() {
 
-		List<String> params =new ArrayList<String>();
+		List<String> params = new ArrayList<>();
 		String randomSeed =
 				"Random seed for the optimizer random number generator.";
 		String minBlockLen =
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java
index 097615a554..19cb367441 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java
@@ -54,7 +54,7 @@
  */
 public class CoreSuperimposer implements MultipleSuperimposer {
 
-	private int reference;
+	private final int reference;
 
 	/**
 	 * Default Constructor.
@@ -79,8 +79,7 @@ public CoreSuperimposer(int reference) {
 	}
 
 	@Override
-	public void superimpose(MultipleAlignment alignment)
-			throws StructureException {
+	public void superimpose(MultipleAlignment alignment) {
 
 		//Check for inconsistencies in the alignment
 		if(alignment.getEnsemble() == null) {
@@ -111,7 +110,7 @@ public void superimpose(MultipleAlignment alignment)
 
 			//Block transformations
 			List<Matrix4d> transforms =
-					new ArrayList<Matrix4d>(atomArrays.size());
+					new ArrayList<>(atomArrays.size());
 
 			//Loop through structures
 			for (int i=0; i<atomArrays.size(); i++){
@@ -127,8 +126,8 @@ public void superimpose(MultipleAlignment alignment)
 				Atom[] ref = atomArrays.get(reference);
 				Atom[] curr = atomArrays.get(i);
 
-				List<Atom> atomSet1 = new ArrayList<Atom>();
-				List<Atom> atomSet2 = new ArrayList<Atom>();
+				List<Atom> atomSet1 = new ArrayList<>();
+				List<Atom> atomSet2 = new ArrayList<>();
 
 				for( Block blk : bs.getBlocks() ) {
 
@@ -156,8 +155,8 @@ public void superimpose(MultipleAlignment alignment)
 						atomSet2.add(curr[pos2]);
 					}
 				}
-				Atom[] array1 = atomSet1.toArray(new Atom[atomSet1.size()]);
-				Atom[] array2 = atomSet2.toArray(new Atom[atomSet2.size()]);
+				Atom[] array1 = atomSet1.toArray(new Atom[0]);
+				Atom[] array2 = atomSet2.toArray(new Atom[0]);
 
 				array2 = StructureTools.cloneAtomArray(array2);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.java
index ad5b1dd83f..d3fe14ba20 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.java
@@ -69,7 +69,7 @@ public static List<Atom[]> getRotatedAtoms(MultipleAlignment multAln)
 								+ atomArrays.get(i).length);
 		}
 
-		List<Atom[]> rotatedAtoms = new ArrayList<Atom[]>();
+		List<Atom[]> rotatedAtoms = new ArrayList<>();
 
 		// TODO implement independent BlockSet superposition of the structure
 		List<Matrix4d> transf = multAln.getBlockSet(0).getTransformations();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
index 1422348e6d..82ff77eff3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
@@ -66,7 +66,7 @@ public static void calculateScores(MultipleAlignment alignment)
 		alignment.putScore(RMSD, getRMSD(trans));
 
 		// Put AvgTM-Score
-		List<Integer> lengths = new ArrayList<Integer>(alignment.size());
+		List<Integer> lengths = new ArrayList<>(alignment.size());
 		for (Atom[] atoms : alignment.getAtomArrays()) {
 			lengths.add(atoms.length);
 		}
@@ -237,7 +237,7 @@ public static double getAvgTMScore(MultipleAlignment alignment)
 
 		List<Atom[]> trans = MultipleAlignmentTools.transformAtoms(alignment);
 
-		List<Integer> lengths = new ArrayList<Integer>(alignment.size());
+		List<Integer> lengths = new ArrayList<>(alignment.size());
 		for (Atom[] atoms : alignment.getAtomArrays()) {
 			lengths.add(atoms.length);
 		}
@@ -314,7 +314,7 @@ public static double getRefTMScore(MultipleAlignment alignment, int ref)
 
 		List<Atom[]> trans = MultipleAlignmentTools.transformAtoms(alignment);
 
-		List<Integer> lengths = new ArrayList<Integer>(alignment.size());
+		List<Integer> lengths = new ArrayList<>(alignment.size());
 		for (Atom[] atoms : alignment.getAtomArrays()) {
 			lengths.add(atoms.length);
 		}
@@ -440,11 +440,9 @@ public static double getMCScore(MultipleAlignment alignment,
 	 * @param A
 	 *            the distance cutoff penalization
 	 * @return the value of the score
-	 * @throws StructureException
 	 */
 	private static double getMCScore(List<Atom[]> trans, double d0,
-			double gapOpen, double gapExtension, double A)
-			throws StructureException {
+			double gapOpen, double gapExtension, double A) {
 
 		int size = trans.size();
 		int length = trans.get(0).length;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
index d790eec19c..68b07632b0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
@@ -108,7 +108,7 @@ public static List<String> getSequenceAlignment(
 			MultipleAlignment alignment, final List<Integer> mapSeqToStruct) {
 
 		// Initialize sequence variables
-		List<String> alnSequences = new ArrayList<String>();
+		List<String> alnSequences = new ArrayList<>();
 		for (int str = 0; str < alignment.size(); str++)
 			alnSequences.add("");
 		mapSeqToStruct.clear();
@@ -116,15 +116,15 @@ public static List<String> getSequenceAlignment(
 		int globalPos = -1;
 
 		// Initialize helper variables in constucting the sequence alignment
-		List<SortedSet<Integer>> freePool = new ArrayList<SortedSet<Integer>>();
-		List<SortedSet<Integer>> blockStarts = new ArrayList<SortedSet<Integer>>();
-		List<List<Integer>> aligned = new ArrayList<List<Integer>>();
+		List<SortedSet<Integer>> freePool = new ArrayList<>();
+		List<SortedSet<Integer>> blockStarts = new ArrayList<>();
+		List<List<Integer>> aligned = new ArrayList<>();
 
 		// Generate freePool residues from the ones not aligned
 		for (int i = 0; i < alignment.size(); i++) {
-			List<Integer> residues = new ArrayList<Integer>();
-			freePool.add(new TreeSet<Integer>());
-			blockStarts.add(new TreeSet<Integer>());
+			List<Integer> residues = new ArrayList<>();
+			freePool.add(new TreeSet<>());
+			blockStarts.add(new TreeSet<>());
 			for (BlockSet bs : alignment.getBlockSets()) {
 				for (Block b : bs.getBlocks()) {
 					boolean first = true;
@@ -314,7 +314,7 @@ public static List<String> getSequenceAlignment(
 	 *         for each aligned residue.
 	 */
 	public static List<String> getSequenceAlignment(MultipleAlignment msa) {
-		return getSequenceAlignment(msa, new ArrayList<Integer>());
+		return getSequenceAlignment(msa, new ArrayList<>());
 	}
 
 	/**
@@ -346,7 +346,7 @@ public static List<String> getBlockSequenceAlignment(
 			MultipleAlignment alignment, List<Integer> mapSeqToStruct) {
 
 		// Initialize sequence variables
-		List<String> alnSequences = new ArrayList<String>();
+		List<String> alnSequences = new ArrayList<>();
 		for (int str = 0; str < alignment.size(); str++)
 			alnSequences.add("");
 		mapSeqToStruct.clear();
@@ -471,7 +471,7 @@ else if (previousPos[str] + 1 == residue) {
 	 *         for each aligned residue.
 	 */
 	public static List<String> getBlockSequenceAlignment(MultipleAlignment ma) {
-		return getBlockSequenceAlignment(ma, new ArrayList<Integer>());
+		return getBlockSequenceAlignment(ma, new ArrayList<>());
 	}
 
 	/**
@@ -661,7 +661,7 @@ public static List<Atom[]> transformAtoms(MultipleAlignment alignment) {
 		}
 
 		List<Atom[]> atomArrays = alignment.getAtomArrays();
-		List<Atom[]> transformed = new ArrayList<Atom[]>(atomArrays.size());
+		List<Atom[]> transformed = new ArrayList<>(atomArrays.size());
 
 		// Loop through structures
 		for (int i = 0; i < atomArrays.size(); i++) {
@@ -729,7 +729,7 @@ public static List<Atom[]> transformAtoms(MultipleAlignment alignment) {
 	 */
 	public static List<Integer> getCorePositions(Block block) {
 
-		List<Integer> corePositions = new ArrayList<Integer>();
+		List<Integer> corePositions = new ArrayList<>();
 
 		for (int col = 0; col < block.length(); col++) {
 			boolean core = true;
@@ -755,28 +755,25 @@ public static List<Integer> getCorePositions(Block block) {
 	 *            Index of the row to be sorted
 	 */
 	public static void sortBlocks(List<Block> blocks, final int sortedIndex) {
-		Collections.sort(blocks, new Comparator<Block>() {
-			@Override
-			public int compare(Block o1, Block o2) {
-				// Compare the first non-null residue of each block
-				List<Integer> alignres1 = o1.getAlignRes().get(sortedIndex);
-				List<Integer> alignres2 = o2.getAlignRes().get(sortedIndex);
-				Integer res1 = null;
-				Integer res2 = null;
-				for (Integer r : alignres1) {
-					if (r != null) {
-						res1 = r;
-						break;
-					}
+		blocks.sort((o1, o2) -> {
+			// Compare the first non-null residue of each block
+			List<Integer> alignres1 = o1.getAlignRes().get(sortedIndex);
+			List<Integer> alignres2 = o2.getAlignRes().get(sortedIndex);
+			Integer res1 = null;
+			Integer res2 = null;
+			for (Integer r : alignres1) {
+				if (r != null) {
+					res1 = r;
+					break;
 				}
-				for (Integer r : alignres2) {
-					if (r != null) {
-						res2 = r;
-						break;
-					}
+			}
+			for (Integer r : alignres2) {
+				if (r != null) {
+					res2 = r;
+					break;
 				}
-				return res1.compareTo(res2);
 			}
+			return res1.compareTo(res2);
 		});
 	}
 
@@ -800,9 +797,9 @@ public static MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> toPr
 							+ "the structures aligned are not proteins");
 		}
 
-		MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> msa = new MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound>();
+		MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> msa = new MultipleSequenceAlignment<>();
 
-		Map<String, Integer> uniqueID = new HashMap<String, Integer>();
+		Map<String, Integer> uniqueID = new HashMap<>();
 		List<String> seqs = getSequenceAlignment(msta);
 		for (int i = 0; i < msta.size(); i++) {
 			// Make sure the identifiers are unique (required by AccessionID)
@@ -845,10 +842,8 @@ public static Structure toMultimodelStructure(MultipleAlignment multAln, List<At
 	 * @param atomArrays an array of Atoms for every aligned structure
 	 * @return a structure object containing a set of models,
 	 * 			one for each input array of Atoms.
-	 * @throws StructureException
 	 */
-	public static final Structure getAlignedStructure(List<Atom[]> atomArrays)
-			throws StructureException {
+	public static final Structure getAlignedStructure(List<Atom[]> atomArrays) {
 
 		Structure s = new StructureImpl();
 		for (int i=0; i<atomArrays.size(); i++){
@@ -875,7 +870,7 @@ public static Matrix getRMSDMatrix(MultipleAlignment msa) {
 			for (int j = i; j < msa.size(); j++) {
 				if (i == j)
 					rmsdMat.set(i, j, 0.0);
-				List<Atom[]> compared = new ArrayList<Atom[]>();
+				List<Atom[]> compared = new ArrayList<>();
 				compared.add(superposed.get(i));
 				compared.add(superposed.get(j));
 				double rmsd = MultipleAlignmentScorer.getRMSD(compared);
@@ -918,10 +913,9 @@ public static Phylogeny getKimuraTree(MultipleAlignment msta)
 	 *            MultipleAlignment of protein structures
 	 * @return Phylogeny phylogenetic tree
 	 * @throws CompoundNotFoundException
-	 * @throws IOException
 	 */
 	public static Phylogeny getHSDMTree(MultipleAlignment msta)
-			throws CompoundNotFoundException, IOException {
+			throws CompoundNotFoundException {
 		MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> msa = MultipleAlignmentTools
 				.toProteinMSA(msta);
 		BasicSymmetricalDistanceMatrix distmat = (BasicSymmetricalDistanceMatrix) DistanceMatrixCalculator
@@ -947,7 +941,7 @@ public static Phylogeny getStructuralTree(MultipleAlignment msta) {
 		BasicSymmetricalDistanceMatrix rmsdDist = (BasicSymmetricalDistanceMatrix) DistanceMatrixCalculator
 				.structuralDistance(rmsdMat, 1, 5, 0.4);
 		// Set the identifiers of the matrix
-		Map<String, Integer> alreadySeen = new HashMap<String, Integer>();
+		Map<String, Integer> alreadySeen = new HashMap<>();
 		for (int i = 0; i < msta.size(); i++) {
 			// Make sure the identifiers are unique
 			String id = msta.getStructureIdentifier(i).toString();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
index d20a884a62..15c83accff 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
@@ -93,7 +93,7 @@ public static String toFatCat(MultipleAlignment alignment) {
 		fatcat.append(alignment.toString() + "\n\n");
 
 		// Get the alignment sequences and the mapping
-		List<Integer> mapSeqToStruct = new ArrayList<Integer>();
+		List<Integer> mapSeqToStruct = new ArrayList<>();
 		List<String> alnSequences = MultipleAlignmentTools
 				.getSequenceAlignment(alignment, mapSeqToStruct);
 
@@ -197,7 +197,7 @@ public static String toAlignedResidues(MultipleAlignment multAln) {
 	 */
 	public static String toTransformMatrices(MultipleAlignment alignment) {
 
-		StringBuffer txt = new StringBuffer();
+		StringBuilder txt = new StringBuilder();
 
 		for (int bs = 0; bs < alignment.getBlockSets().size(); bs++) {
 
@@ -360,11 +360,11 @@ public static String to3DFormat(MultipleAlignment alignment,
 				String tPDB = templateAtoms[tRes].toPDB();
 
 				// merge the two records into 3D format
-				str.append(qPDB.substring(0, 30)); // up through coordinates
-				str.append(tPDB.substring(30, 54)); // coordinates
-				str.append(tPDB.substring(22, 27)); // residue number
+				str.append(qPDB, 0, 30); // up through coordinates
+				str.append(tPDB, 30, 54); // coordinates
+				str.append(tPDB, 22, 27); // residue number
 				str.append(' ');
-				str.append(tPDB.substring(17, 20));
+				str.append(tPDB, 17, 20);
 				str.append('\n');
 			}
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.java
index 81f95243f1..c6068e1365 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.java
@@ -58,8 +58,7 @@ public interface MultipleSuperimposer {
 	 *  		atoms to align (via the {@link MultipleAlignment#getEnsemble()
 	 *  		ensemble}).
 	 *
-	 * @throws StructureException
 	 */
-	public void superimpose(MultipleAlignment alignment)
-			throws StructureException;
+    void superimpose(MultipleAlignment alignment)
+	;
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java
index 0285f8a90d..a11fcdef4b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java
@@ -52,7 +52,7 @@
  */
 public class ReferenceSuperimposer implements MultipleSuperimposer {
 
-	private int reference;
+	private final int reference;
 
 	/**
 	 * Default Constructor.
@@ -77,8 +77,7 @@ public ReferenceSuperimposer(int reference) {
 	}
 
 	@Override
-	public void superimpose(MultipleAlignment alignment)
-			throws StructureException {
+	public void superimpose(MultipleAlignment alignment) {
 
 		//Check for inconsistencies in the alignment
 		if(alignment.getEnsemble() == null) {
@@ -109,7 +108,7 @@ public void superimpose(MultipleAlignment alignment)
 
 			//Block transformations
 			List<Matrix4d> transforms =
-					new ArrayList<Matrix4d>(atomArrays.size());
+					new ArrayList<>(atomArrays.size());
 
 			//Loop through structures
 			for (int i=0; i<atomArrays.size(); i++){
@@ -125,8 +124,8 @@ public void superimpose(MultipleAlignment alignment)
 				Atom[] ref = atomArrays.get(reference);
 				Atom[] curr = atomArrays.get(i);
 
-				List<Atom> atomSet1 = new ArrayList<Atom>();
-				List<Atom> atomSet2 = new ArrayList<Atom>();
+				List<Atom> atomSet1 = new ArrayList<>();
+				List<Atom> atomSet2 = new ArrayList<>();
 
 				for( Block blk : bs.getBlocks() ) {
 					if( blk.size() != atomArrays.size()) {
@@ -145,8 +144,8 @@ public void superimpose(MultipleAlignment alignment)
 						atomSet2.add(curr[pos2]);
 					}
 				}
-				Atom[] array1 = atomSet1.toArray(new Atom[atomSet1.size()]);
-				Atom[] array2 = atomSet2.toArray(new Atom[atomSet2.size()]);
+				Atom[] array1 = atomSet1.toArray(new Atom[0]);
+				Atom[] array2 = atomSet2.toArray(new Atom[0]);
 
 				array2 = StructureTools.cloneAtomArray(array2);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AligNPE.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AligNPE.java
index b1ef23788c..da23009c0d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AligNPE.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AligNPE.java
@@ -61,7 +61,7 @@ public static Alignable align_NPE(Matrix sim,StrucAligParameters params){
 		for (int i = 0; i < rows; i++) {
 			for (int j = 0; j < cols; j++) {
 
-				int e=0;
+				int e;
 				//if ( ( i < rows) &&
 				//        ( j < cols)) {
 					//TODO: the ALIGFACTOR calc should be hidden in Gotoh!!
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Alignable.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Alignable.java
index a243cc4f54..ff6893c1c8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Alignable.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Alignable.java
@@ -26,22 +26,22 @@
 import org.biojava.nbio.structure.align.helper.IndexPair;
 
 public interface Alignable {
-	public int getRows();
-	public int getCols();
-	public AligMatEl[][] getAligMat();
-	public void setAligMat(AligMatEl[][] alignmentMatrix);
-	public float getGapExtCol();
-	public void setGapExtCol(float penalty);
-	public float getGapExtRow();
-	public void setGapExtRow(float penalty);
-	public float getGapOpenCol();
-	public void setGapOpenCol(float penalty);
-	public float getGapOpenRow();
-	public void setGapOpenRow(float penalty);
-	public void setScore(float score);
-	public float getScore();
-	public int getPathSize();
-	public void setPathSize(int pathSize);
-	public void setPath(IndexPair[] path);
-	public IndexPair[] getPath();
+	int getRows();
+	int getCols();
+	AligMatEl[][] getAligMat();
+	void setAligMat(AligMatEl[][] alignmentMatrix);
+	float getGapExtCol();
+	void setGapExtCol(float penalty);
+	float getGapExtRow();
+	void setGapExtRow(float penalty);
+	float getGapOpenCol();
+	void setGapOpenCol(float penalty);
+	float getGapOpenRow();
+	void setGapOpenRow(float penalty);
+	void setScore(float score);
+	float getScore();
+	int getPathSize();
+	void setPathSize(int pathSize);
+	void setPath(IndexPair[] path);
+	IndexPair[] getPath();
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlignmentResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlignmentResult.java
index bfa720e183..ebd0e2ec09 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlignmentResult.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlignmentResult.java
@@ -48,7 +48,7 @@ public class AlignmentResult implements Serializable
 
 	@Override
 public String toString(){
-		StringBuffer buf = new StringBuffer();
+		StringBuilder buf = new StringBuilder();
 		buf.append(pdb1);
 		buf.append("_");
 		buf.append(chain1);
@@ -166,7 +166,7 @@ public void setIoTime(long ioTime)
 		this.ioTime = ioTime;
 	}
 	public void serialize (File output)
-	throws FileNotFoundException, IOException{
+	throws IOException{
 		// save alignment result:
 
 		FileOutputStream outStream = new FileOutputStream(output);
@@ -177,7 +177,7 @@ public void serialize (File output)
 	}
 
 	public static AlignmentResult deserialize(File output)
-	throws FileNotFoundException, IOException, ClassNotFoundException{
+	throws IOException, ClassNotFoundException{
 		FileInputStream fin = new FileInputStream(output);
 		ObjectInputStream objIn = new ObjectInputStream(fin);
 		AlignmentResult result = (AlignmentResult) objIn.readObject();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
index f6f3073ab7..c9dab3c084 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
@@ -67,17 +67,17 @@ public class AlternativeAlignment implements Serializable{
 	//short[] alig1;
 	//short[] alig2;
 
-	private int nfrags;
-	private Atom center;
-	private Matrix rot;
-	private Atom tr;
+	private final int nfrags;
+	private final Atom center;
+	private final Matrix rot;
+	private final Atom tr;
 
 
 	// the scores...
 	private int gaps0;
 	private int eqr0;
-	private int rms0;
-	private int joined;
+	private final int rms0;
+	private final int joined;
 	private int percId;
 	private int cluster;
 	private float score;
@@ -133,7 +133,7 @@ public String toString(){
 		d2.setMaximumIntegerDigits(3);
 		d2.setMinimumFractionDigits(2);
 		d2.setMaximumFractionDigits(2);
-		StringBuffer s = new StringBuffer();
+		StringBuilder s = new StringBuilder();
 		s.append("#" + getAltAligNumber() +
 				" cluster:" + cluster +
 				" eqr:" + getEqr() +
@@ -345,11 +345,11 @@ public static Matrix getDistanceMatrix(Atom[] ca1, Atom[]ca2){
 		return out;
 	}
 
-	private Alignable getInitalStrCompAlignment(
+	private static Alignable getInitalStrCompAlignment(
 			Atom[] ca1,
-			Atom[]ca2,
+			Atom[] ca2,
 			StrucAligParameters params
-			){
+	){
 
 		int rows = ca1.length;
 		int cols = ca2.length;
@@ -383,11 +383,8 @@ private Alignable getInitalStrCompAlignment(
 				aligmat[0][j] = new AligMatEl();
 
 				Atom b1 = ca2[j];
-				double d = 999;
-
-				d = Calc.getDistance(a1,b1);
-
 
+				double d = Calc.getDistance(a1,b1);
 				AligMatEl e = new AligMatEl();
 				if (d > co) {
 					e.setValue(0);
@@ -497,7 +494,7 @@ public void refine(StrucAligParameters params,Atom[]ca1,Atom[]ca2) throws Struct
 		int maxiter = params.getMaxIter();
 		for (int iter = 0 ; iter< maxiter; iter++){
 
-			float  subscore = 0.0f;
+			float  subscore;
 
 			rotateShiftAtoms(ca3);
 
@@ -581,12 +578,8 @@ public void refine(StrucAligParameters params,Atom[]ca1,Atom[]ca2) throws Struct
 				// now we join the two solutions
 				if ( subpathsize > permsize){
 					IndexPair[] wholepath = new IndexPair[pathsize+subpathsize];
-					for ( int t=0; t < pathsize; t++){
-						wholepath[t] = path[t];
-					}
-					for ( int t=0 ; t < subpathsize; t++){
-						wholepath[t+pathsize] = subpath[t];
-					}
+                    System.arraycopy(path, 0, wholepath, 0, pathsize);
+                    System.arraycopy(subpath, 0, wholepath, 0 + pathsize, subpathsize);
 					pathsize += subpathsize;
 					path = wholepath;
 					ali.setPath(path);
@@ -760,12 +753,11 @@ public void calculateSuperpositionByIdx(Atom[] ca1, Atom[] ca2)throws StructureE
 	 * @param idx1 idx positions in set1
 	 * @param idx2 idx positions in set2
 	 * @param getRMS a flag if the RMS should be calculated
-	 * @throws StructureException
 	 */
 
 
 
-	private void super_pos_alig(Atom[]ca1,Atom[]ca2,int[] idx1, int[] idx2, boolean getRMS) throws StructureException{
+	private void super_pos_alig(Atom[]ca1,Atom[]ca2,int[] idx1, int[] idx2, boolean getRMS) {
 
 		//System.out.println("superpos alig ");
 		Atom[] ca1subset = new Atom[idx1.length];
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
index ac8fdaa563..4dc944ee9c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
@@ -118,7 +118,7 @@ public JointFragments[] approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] frag
 													 StrucAligParameters params) throws StructureException {
 
 		//the final list of joined fragments stores as apairs
-		List<JointFragments> fll = new ArrayList<JointFragments>();
+		List<JointFragments> fll = new ArrayList<>();
 
 		FragmentPair[] tmpfidx = new FragmentPair[fraglst.length];
 		for ( int i=0 ; i < fraglst.length; i++){
@@ -200,16 +200,16 @@ public JointFragments[] approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] frag
 
 
 		Comparator<JointFragments> comp = new JointFragmentsComparator();
-		Collections.sort(fll,comp);
+		fll.sort(comp);
 		Collections.reverse(fll);
 		int m = Math.min(params.getMaxrefine(),fll.size());
-		List<JointFragments> retlst = new ArrayList<JointFragments>();
+		List<JointFragments> retlst = new ArrayList<>();
 		for ( int i = 0 ; i < m ; i++){
 			JointFragments jf = fll.get(i);
 			retlst.add(jf);
 		}
 
-		return retlst.toArray(new JointFragments[retlst.size()]);
+		return retlst.toArray(new JointFragments[0]);
 
 	}
 
@@ -244,9 +244,8 @@ private boolean densityCheckOk(Atom[] aa1, Atom[] aa2, List<int[]> idxlist,
 	 * @param ca1subset
 	 * @param ca2subset
 	 * @return a double
-	 * @throws StructureException
 	 */
-	private double getDensity(Atom[] ca1subset, Atom[] ca2subset ) throws StructureException{
+	private double getDensity(Atom[] ca1subset, Atom[] ca2subset ) {
 
 		Atom centroid1 =  Calc.getCentroid(ca1subset);
 		Atom centroid2 = Calc.getCentroid(ca2subset);
@@ -297,7 +296,7 @@ public static double getRMS(Atom[] ca1, Atom[]ca2,JointFragments frag) throws St
 		//      now svd ftmp and check if the rms is < X ...
 		AlternativeAlignment ali = new AlternativeAlignment();
 		ali.apairs_from_idxlst(frag);
-		double rms = 999;
+		double rms;
 
 		int[] idx1 = ali.getIdx1();
 		int[] idx2 = ali.getIdx2();
@@ -323,7 +322,7 @@ public static double getRMS(Atom[] ca1, Atom[]ca2,JointFragments frag) throws St
 
 	public boolean angleCheckOk(FragmentPair a, FragmentPair b, float distcutoff){
 
-		double dist = -999;
+		double dist;
 
 		Atom v1 = a.getUnitv();
 		Atom v2 = b.getUnitv();
@@ -372,7 +371,7 @@ public JointFragments[] frag_pairwise_compat(FragmentPair[] fraglst, int angleDi
 		int[] used = new int[n];
 
 		//the final list of joined fragments stores as apairs
-		List<JointFragments> fll = new ArrayList<JointFragments>();
+		List<JointFragments> fll = new ArrayList<>();
 
 		double adiff = angleDiff * Math.PI / 180d;
 		logger.debug("addiff" + adiff);
@@ -440,16 +439,16 @@ public JointFragments[] frag_pairwise_compat(FragmentPair[] fraglst, int angleDi
 
 
 		Comparator<JointFragments> comp = new JointFragmentsComparator();
-		Collections.sort(fll,comp);
+		fll.sort(comp);
 		Collections.reverse(fll);
 		int m = Math.min(maxRefine,fll.size());
-		List<JointFragments> retlst = new ArrayList<JointFragments>();
+		List<JointFragments> retlst = new ArrayList<>();
 		for ( int i = 0 ; i < m ; i++){
 			JointFragments jf = fll.get(i);
 			retlst.add(jf);
 		}
 
-		return retlst.toArray(new JointFragments[retlst.size()]);
+		return retlst.toArray(new JointFragments[0]);
 
 	}
 
@@ -555,11 +554,7 @@ else if ( s1 < s2){
 			return -1;
 		}
 		else{
-			if ( rms1 < rms2)
-				return 1;
-			if ( rms1 > rms2)
-				return -1;
-			return 0;
+			return Double.compare(rms2, rms1);
 		}
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java
index d0b9752519..83ed3ffaae 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java
@@ -209,7 +209,7 @@ private void setPath(){
 
 		int  n;
 		IndexPair[] backId = new IndexPair[a.getRows()+1+a.getCols()+1];
-		List<IndexPair> path = new ArrayList<IndexPair>();
+		List<IndexPair> path = new ArrayList<>();
 
 		backId[0] = new IndexPair((short)(a.getRows()),(short)(a.getCols()));
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java
index 355c76ea15..295820deed 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java
@@ -94,13 +94,13 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 		List<SubunitCluster> c2 = SubunitClusterer.cluster(s2, cParams).getClusters();
 
 		// STEP 2: match each subunit cluster between groups O(N^2*L^2) - inter
-		Map<Integer, Integer> clusterMap = new HashMap<Integer, Integer>();
+		Map<Integer, Integer> clusterMap = new HashMap<>();
 		for (int i = 0; i < c1.size(); i++) {
 			for (int j = 0; j < c2.size(); j++) {
 
-				if (clusterMap.keySet().contains(i))
+				if (clusterMap.containsKey(i))
 					break;
-				if (clusterMap.values().contains(j))
+				if (clusterMap.containsValue(j))
 					continue;
 
 				// Use structural alignment to match the subunit clusters
@@ -114,38 +114,40 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 		result.setClusters(c1);
 
 		// STEP 3: Align the assemblies for each cluster match O(N^2*L)
-		for (int globalKey : clusterMap.keySet()) {
+		for (Entry<Integer, Integer> e : clusterMap.entrySet()) {
+			int globalKey = e.getKey();
 
 			// Obtain the clusters
 			SubunitCluster clust1 = c1.get(globalKey);
-			SubunitCluster clust2 = c2.get(clusterMap.get(globalKey));
+			SubunitCluster clust2 = c2.get(e.getValue());
 
 			// Take a cluster match as reference
 			int index1 = 0;
 			int index2 = clust1.size() - clust2.size();
-			Map<Integer, Integer> subunitMap = new HashMap<Integer, Integer>();
+			Map<Integer, Integer> subunitMap = new HashMap<>();
 			subunitMap.put(index1, index2);
 
 			// Map cluster id to their subunit matching
-			Map<Integer, Map<Integer, Integer>> clustSubunitMap = new HashMap<Integer, Map<Integer, Integer>>();
+			Map<Integer, Map<Integer, Integer>> clustSubunitMap = new HashMap<>();
 			clustSubunitMap.put(globalKey, subunitMap);
 
 			// Change order of key set so that globalKey is first
-			List<Integer> keySet = new ArrayList<Integer>(clusterMap.keySet());
+			List<Integer> keySet = new ArrayList<>(clusterMap.keySet());
 			keySet.remove((Integer) globalKey);
 			keySet.add(0, globalKey);
 
-			for (int key : clusterMap.keySet()) {
+			for (Entry<Integer, Integer> entry : clusterMap.entrySet()) {
+				int key = entry.getKey();
 
 				// Recover subunitMap if it is the reference, new one otherwise
 				if (key == globalKey)
 					subunitMap = clustSubunitMap.get(key);
 				else
-					subunitMap = new HashMap<Integer, Integer>();
+					subunitMap = new HashMap<>();
 
 				// Obtain the clusters of each subunit group
 				clust1 = c1.get(key);
-				clust2 = c2.get(clusterMap.get(key));
+				clust2 = c2.get(entry.getValue());
 
 				// Get the initial subunit indices of each group
 				index1 = 0;
@@ -154,9 +156,9 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 				for (int i = 0; i < index2; i++) {
 					for (int j = index2; j < clust1.size(); j++) {
 
-						if (subunitMap.keySet().contains(i))
+						if (subunitMap.containsKey(i))
 							break;
-						if (subunitMap.values().contains(j))
+						if (subunitMap.containsValue(j))
 							continue;
 
 						// Obtain cumulative transformation matrix
@@ -224,20 +226,20 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 			logger.info("Cluster Subunit Map: " + clustSubunitMap.toString());
 
 			// Unfold the nested map into subunit map and alignment
-			subunitMap = new HashMap<Integer, Integer>();
-			List<Integer> alignRes1 = new ArrayList<Integer>();
-			List<Integer> alignRes2 = new ArrayList<Integer>();
-			List<Atom> atomArray1 = new ArrayList<Atom>();
-			List<Atom> atomArray2 = new ArrayList<Atom>();
+			subunitMap = new HashMap<>();
+			List<Integer> alignRes1 = new ArrayList<>();
+			List<Integer> alignRes2 = new ArrayList<>();
+			List<Atom> atomArray1 = new ArrayList<>();
+			List<Atom> atomArray2 = new ArrayList<>();
 
-			for (int key : clustSubunitMap.keySet()) {
+			for (Entry<Integer, Map<Integer, Integer>> entry : clustSubunitMap.entrySet()) {
 
 				// Obtain the cluster and the alignment in it
-				SubunitCluster cluster = c1.get(key);
+				SubunitCluster cluster = c1.get(entry.getKey());
 				List<List<Integer>> clusterEqrs = cluster
 						.getMultipleAlignment().getBlock(0).getAlignRes();
 
-				for (Entry<Integer, Integer> pair : clustSubunitMap.get(key)
+				for (Entry<Integer, Integer> pair : entry.getValue()
 						.entrySet()) {
 
 					int i = pair.getKey();
@@ -267,14 +269,13 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 			MultipleAlignment msa = new MultipleAlignmentImpl();
 			msa.setEnsemble(new MultipleAlignmentEnsembleImpl());
 			msa.getEnsemble().setAtomArrays(
-					Arrays.asList(new Atom[][] {
-							atomArray1.toArray(new Atom[atomArray1.size()]),
-							atomArray2.toArray(new Atom[atomArray2.size()]) }));
+					Arrays.asList(atomArray1.toArray(new Atom[0]),
+							atomArray2.toArray(new Atom[0])));
 
 			// Fill in the alignment information
 			BlockSet bs = new BlockSetImpl(msa);
 			Block b = new BlockImpl(bs);
-			List<List<Integer>> alignRes = new ArrayList<List<Integer>>(2);
+			List<List<Integer>> alignRes = new ArrayList<>(2);
 			alignRes.add(alignRes1);
 			alignRes.add(alignRes2);
 			b.setAlignRes(alignRes);
@@ -324,17 +325,17 @@ private static Pair<Atom[]> getAlignedAtomsForClusterSubunitMap(
 			List<SubunitCluster> clusters,
 			Map<Integer, Map<Integer, Integer>> clusterSubunitMap) {
 
-		List<Atom> atomArray1 = new ArrayList<Atom>();
-		List<Atom> atomArray2 = new ArrayList<Atom>();
+		List<Atom> atomArray1 = new ArrayList<>();
+		List<Atom> atomArray2 = new ArrayList<>();
 
 		// For each cluster of subunits
-		for (int key : clusterSubunitMap.keySet()) {
+		for (Entry<Integer, Map<Integer, Integer>> entry : clusterSubunitMap.entrySet()) {
 
 			// Obtain the cluster and the alignment in it
-			SubunitCluster cluster = clusters.get(key);
+			SubunitCluster cluster = clusters.get(entry.getKey());
 
 			// For each subunit matching in the cluster
-			for (Entry<Integer, Integer> pair : clusterSubunitMap.get(key)
+			for (Entry<Integer, Integer> pair : entry.getValue()
 					.entrySet()) {
 
 				int i = pair.getKey();
@@ -348,9 +349,9 @@ private static Pair<Atom[]> getAlignedAtomsForClusterSubunitMap(
 			}
 
 		}
-		return new Pair<Atom[]>(
-				atomArray1.toArray(new Atom[atomArray1.size()]),
-				atomArray2.toArray(new Atom[atomArray2.size()]));
+		return new Pair<>(
+				atomArray1.toArray(new Atom[0]),
+				atomArray2.toArray(new Atom[0]));
 	}
 
 	/**
@@ -364,12 +365,10 @@ private static Pair<Atom[]> getAlignedAtomsForClusterSubunitMap(
 	 * @param clusterSubunitMap
 	 *            map from cluster id to subunit matching
 	 * @return transformation matrix
-	 * @throws StructureException
 	 */
 	private static Matrix4d getTransformForClusterSubunitMap(
 			List<SubunitCluster> clusters,
-			Map<Integer, Map<Integer, Integer>> clusterSubunitMap)
-			throws StructureException {
+			Map<Integer, Map<Integer, Integer>> clusterSubunitMap) {
 
 		Pair<Atom[]> pair = getAlignedAtomsForClusterSubunitMap(clusters,
 				clusterSubunitMap);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
index 68b0b4a4da..086928bc72 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
@@ -47,8 +47,8 @@ public class QsAlignResult {
 
 	private List<SubunitCluster> clusters;
 
-	private List<Subunit> subunits1;
-	private List<Subunit> subunits2;
+	private final List<Subunit> subunits1;
+	private final List<Subunit> subunits2;
 
 	private Map<Integer, Integer> subunitMap;
 	private MultipleAlignment alignment;
@@ -234,7 +234,7 @@ public void setAlignment(MultipleAlignment alignment) {
 	 */
 	public List<Subunit> getAlignedSubunits1() {
 
-		List<Subunit> aligned = new ArrayList<Subunit>(subunitMap.size());
+		List<Subunit> aligned = new ArrayList<>(subunitMap.size());
 
 		for (Integer key : subunitMap.keySet())
 			aligned.add(subunits1.get(key));
@@ -250,10 +250,10 @@ public List<Subunit> getAlignedSubunits1() {
 	 */
 	public List<Subunit> getAlignedSubunits2() {
 
-		List<Subunit> aligned = new ArrayList<Subunit>(subunitMap.size());
+		List<Subunit> aligned = new ArrayList<>(subunitMap.size());
 
-		for (Integer key : subunitMap.keySet())
-			aligned.add(subunits2.get(subunitMap.get(key)));
+		for (Integer integer : subunitMap.values())
+			aligned.add(subunits2.get(integer));
 
 		return aligned;
 	}
@@ -295,10 +295,10 @@ public String toString() {
 				+ ", length="
 				+ length()
 				+ ", Aligned 1: "
-				+ getAlignedSubunits1().stream().map(s -> s.getName())
+				+ getAlignedSubunits1().stream().map(Subunit::getName)
 						.collect(Collectors.toList())
 				+ ", Aligned 2: "
-				+ getAlignedSubunits2().stream().map(s -> s.getName())
+				+ getAlignedSubunits2().stream().map(Subunit::getName)
 						.collect(Collectors.toList()) + "]";
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsRelation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsRelation.java
index e07ca0fff3..d289cee72a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsRelation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsRelation.java
@@ -71,5 +71,5 @@ public enum QsRelation {
 	 * {@link #EQUIVALENT}, {@link #PARTIAL_COMPLETE} or
 	 * {@link #PARTIAL_INCOMPLETE}.
 	 */
-	DIFFERENT;
+	DIFFERENT
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3DParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3DParameters.java
index 986bf3a8d3..74b8b891d5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3DParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3DParameters.java
@@ -42,7 +42,7 @@ public SmithWaterman3DParameters() {
 
 	@Override
 	public List<String> getUserConfigHelp() {
-		List<String> params = new ArrayList<String>();
+		List<String> params = new ArrayList<>();
 		params.add("The Gap open penalty");
 		params.add("The Gap extension penalty");
 		params.add("The maximum RMSD of superposition allowed");
@@ -54,7 +54,7 @@ public List<String> getUserConfigHelp() {
 
 	@Override
 	public List<String> getUserConfigParameterNames() {
-		List<String> params = new ArrayList<String>();
+		List<String> params = new ArrayList<>();
 		params.add("Gap Open");
 		params.add("Gap Extension");
 		params.add("Maximum RMSD");
@@ -65,7 +65,7 @@ public List<String> getUserConfigParameterNames() {
 
 	@Override
 	public List<String> getUserConfigParameters() {
-		List<String> params = new ArrayList<String>();
+		List<String> params = new ArrayList<>();
 		params.add("GapOpen");
 		params.add("GapExtend");
 		params.add("MaxRmsd");
@@ -77,7 +77,7 @@ public List<String> getUserConfigParameters() {
 	@Override
 	@SuppressWarnings("rawtypes")
 	public List<Class> getUserConfigTypes() {
-		List<Class> params = new ArrayList<Class>();
+		List<Class> params = new ArrayList<>();
 		params.add(Short.class);
 		params.add(Short.class);
 		params.add(Double.class);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java
index 1a0597fd07..bba233c390 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java
@@ -112,8 +112,8 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object parameters)
 		String seq1 = StructureTools.convertAtomsToSeq(ca1);
 		String seq2 = StructureTools.convertAtomsToSeq(ca2);
 
-		ProteinSequence s1 = null;
-		ProteinSequence s2 = null;
+		ProteinSequence s1;
+		ProteinSequence s2;
 
 		try {
 			s1 = new ProteinSequence(seq1);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
index cdde7480a3..6f53fd69c3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
@@ -60,11 +60,11 @@ public class AFPAlignmentDisplay
 			{-2,-3,-4,-2,-2,-3,-4,-4,-3,-2,-3,-2,-3,-3,-3,-2,-1,1,2,11,-4},
 			{-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,1}};
 
-	private static Character[] aa1 = new Character[]{  'G',   'A',   'P',   'C',   'T',   'S','D',   'N',   'E',   'Q',   'K',   'H',   'R', 'V',   'I',   'L',   'M',   'F',   'Y',   'W', '-'};
+	private static final Character[] aa1 = new Character[]{  'G',   'A',   'P',   'C',   'T',   'S','D',   'N',   'E',   'Q',   'K',   'H',   'R', 'V',   'I',   'L',   'M',   'F',   'Y',   'W', '-'};
 
 	private static final List<Character> aa1List = Arrays.asList(aa1);
 
-	public static Matrix getRotMax(AFPChain afpChain,Atom[] ca1,Atom[] ca2) throws StructureException{
+	public static Matrix getRotMax(AFPChain afpChain,Atom[] ca1,Atom[] ca2) {
 
 		Atom[] a1 = getAlignedAtoms1(afpChain,ca1);
 		Atom[] a2 = getAlignedAtoms2(afpChain,ca2);
@@ -76,7 +76,7 @@ public static Matrix getRotMax(AFPChain afpChain,Atom[] ca1,Atom[] ca2) throws S
 
 	}
 
-	public static Atom getTranslation(AFPChain afpChain,Atom[] ca1,Atom[] ca2) throws StructureException{
+	public static Atom getTranslation(AFPChain afpChain,Atom[] ca1,Atom[] ca2) {
 
 
 		Atom[] a1 = getAlignedAtoms1(afpChain,ca1);
@@ -90,7 +90,7 @@ public static Atom getTranslation(AFPChain afpChain,Atom[] ca1,Atom[] ca2) throw
 	}
 
 	public static Atom[] getAlignedAtoms1(AFPChain afpChain,Atom[] ca1){
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		int blockNum = afpChain.getBlockNum();
 
@@ -107,11 +107,11 @@ public static Atom[] getAlignedAtoms1(AFPChain afpChain,Atom[] ca1){
 			}
 
 		}
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 	}
 	public static Atom[] getAlignedAtoms2(AFPChain afpChain,Atom[] ca2){
 
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 
 		int blockNum = afpChain.getBlockNum();
 
@@ -128,7 +128,7 @@ public static Atom[] getAlignedAtoms2(AFPChain afpChain,Atom[] ca2){
 			}
 
 		}
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 	}
 
 
@@ -233,7 +233,7 @@ public static void getAlign(AFPChain afpChain,Atom[] ca1,Atom[] ca2, boolean sho
 					continue;
 				}
 				if(len > 0)     {
-					lmax = (p1 - p1b - 1)>(p2 - p2b - 1)?(p1 - p1b - 1):(p2 - p2b - 1);
+					lmax = Math.max((p1 - p1b - 1), (p2 - p2b - 1));
 					for(k = 0; k < lmax; k ++)      {
 						if(k >= (p1 - p1b - 1)) alnseq1[len] = '-';
 						else {
@@ -329,7 +329,7 @@ public static Map<String,Double> calcIdSimilarity(char[] seq1, char[] seq2, int
 
 		if ( seq1 == null || seq2 == null){
 			logger.warn("Can't calc %ID for an empty alignment! ");
-			Map<String, Double> m = new HashMap<String, Double>();
+			Map<String, Double> m = new HashMap<>();
 			m.put("similarity", similarity);
 			m.put("identity", identity);
 			return m;
@@ -369,7 +369,7 @@ public static Map<String,Double> calcIdSimilarity(char[] seq1, char[] seq2, int
 			similarity = (similarity) / eqr;
 			identity = identity/eqr;
 		}
-		Map<String, Double> m = new HashMap<String, Double>();
+		Map<String, Double> m = new HashMap<>();
 		m.put("similarity", similarity);
 		m.put("identity", identity);
 
@@ -400,7 +400,7 @@ public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1,
 
 		Group[] twistedGroups = AlignmentTools.prepareGroupsForDisplay(afpChain,ca1, ca2);
 
-		List<Atom> twistedAs = new ArrayList<Atom>();
+		List<Atom> twistedAs = new ArrayList<>();
 
 		for ( Group g: twistedGroups){
 			if ( g == null )
@@ -410,23 +410,23 @@ public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1,
 			Atom a = g.getAtom(0);
 			twistedAs.add(a);
 		}
-		Atom[] twistedAtoms = twistedAs.toArray(new Atom[twistedAs.size()]);
+		Atom[] twistedAtoms = twistedAs.toArray(new Atom[0]);
 
-		List<Group> hetatms  = new ArrayList<Group>();
-		List<Group> nucs1    = new ArrayList<Group>();
+		List<Group> hetatms  = new ArrayList<>();
+		List<Group> nucs1    = new ArrayList<>();
 		Group g1 = ca1[0].getGroup();
-		Chain c1 = null;
+		Chain c1;
 		if ( g1 != null) {
 			c1 = g1.getChain();
 			if ( c1 != null){
-				hetatms = c1.getAtomGroups(GroupType.HETATM);;
+				hetatms = c1.getAtomGroups(GroupType.HETATM);
 				nucs1  = c1.getAtomGroups(GroupType.NUCLEOTIDE);
 			}
 		}
-		List<Group> hetatms2 = new ArrayList<Group>();
-		List<Group> nucs2    = new ArrayList<Group>();
+		List<Group> hetatms2 = new ArrayList<>();
+		List<Group> nucs2    = new ArrayList<>();
 		Group g2 = ca2[0].getGroup();
-		Chain c2 = null;
+		Chain c2;
 		if ( g2 != null){
 			c2 = g2.getChain();
 			if ( c2 != null){
@@ -467,7 +467,7 @@ public static int getBlockNrForAlignPos(AFPChain afpChain, int aligPos){
 
 				if (len != 0) {
 					// check for gapped region
-					int lmax = (p1 - p1b - 1)>(p2 - p2b - 1)?(p1 - p1b - 1):(p2 - p2b - 1);
+					int lmax = Math.max((p1 - p1b - 1), (p2 - p2b - 1));
 					for(int k = 0; k < lmax; k ++)      {
 						len++;
 					}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
index f7660e2097..0a7ea5ea13 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -157,7 +157,7 @@ public static boolean isSequentialAlignment(AFPChain afpChain, boolean checkWith
 	 * @throws StructureException If afpChain is not one-to-one
 	 */
 	public static Map<Integer, Integer> alignmentAsMap(AFPChain afpChain) throws StructureException {
-		Map<Integer,Integer> map = new HashMap<Integer,Integer>();
+		Map<Integer,Integer> map = new HashMap<>();
 
 		if( afpChain.getAlnLength() < 1 ) {
 			return map;
@@ -189,7 +189,7 @@ public static Map<Integer, Integer> alignmentAsMap(AFPChain afpChain) throws Str
 	 *  function is undefined for that input.
 	 */
 	public static <T> Map<T,T> applyAlignment(Map<T, T> alignmentMap, int k) {
-		return applyAlignment(alignmentMap, new IdentityMap<T>(), k);
+		return applyAlignment(alignmentMap, new IdentityMap<>(), k);
 	}
 
 	/**
@@ -223,11 +223,11 @@ public static <S,T> Map<S,T> applyAlignment(Map<S, T> alignmentMap, Map<T,S> ide
 
 		if(k<0) throw new IllegalArgumentException("k must be positive");
 		if(k==1) {
-			return new HashMap<S,T>(alignmentMap);
+			return new HashMap<>(alignmentMap);
 		}
 		// Convert to lists to establish a fixed order
-		List<S> preimage = new ArrayList<S>(alignmentMap.keySet()); // currently unmodified
-		List<S> image = new ArrayList<S>(preimage);
+		List<S> preimage = new ArrayList<>(alignmentMap.keySet()); // currently unmodified
+		List<S> image = new ArrayList<>(preimage);
 
 		for(int n=1;n<k;n++) {
 			// apply alignment
@@ -241,7 +241,7 @@ public static <S,T> Map<S,T> applyAlignment(Map<S, T> alignmentMap, Map<T,S> ide
 
 
 
-		Map<S, T> imageMap = new HashMap<S,T>(alignmentMap.size());
+		Map<S, T> imageMap = new HashMap<>(alignmentMap.size());
 
 		//TODO handle nulls consistently.
 		// assure that all the residues in the domain are valid keys
@@ -282,7 +282,7 @@ public static <S,T> Map<S,T> applyAlignment(Map<S, T> alignmentMap, Map<T,S> ide
 	 */
 	public static int getSymmetryOrder(Map<Integer, Integer> alignment,
 									   final int maxSymmetry, final float minimumMetricChange) {
-		return getSymmetryOrder(alignment, new IdentityMap<Integer>(), maxSymmetry, minimumMetricChange);
+		return getSymmetryOrder(alignment, new IdentityMap<>(), maxSymmetry, minimumMetricChange);
 	}
 	/**
 	 * Tries to detect symmetry in an alignment.
@@ -321,8 +321,8 @@ public static int getSymmetryOrder(Map<Integer, Integer> alignment,
 	 */
 	public static int getSymmetryOrder(Map<Integer, Integer> alignment, Map<Integer,Integer> identity,
 									   final int maxSymmetry, final float minimumMetricChange) {
-		List<Integer> preimage = new ArrayList<Integer>(alignment.keySet()); // currently unmodified
-		List<Integer> image = new ArrayList<Integer>(preimage);
+		List<Integer> preimage = new ArrayList<>(alignment.keySet()); // currently unmodified
+		List<Integer> image = new ArrayList<>(preimage);
 
 		int bestSymmetry = 1;
 		double bestMetric = Double.POSITIVE_INFINITY; //lower is better
@@ -443,10 +443,10 @@ public static int getSymmetryOrder(AFPChain afpChain, int maxSymmetry, float min
 	 */
 	public static Map<Integer, Integer> guessSequentialAlignment(
 			Map<Integer,Integer> alignment, boolean inverseAlignment) {
-		Map<Integer,Integer> identity = new HashMap<Integer,Integer>();
+		Map<Integer,Integer> identity = new HashMap<>();
 
-		SortedSet<Integer> aligned1 = new TreeSet<Integer>();
-		SortedSet<Integer> aligned2 = new TreeSet<Integer>();
+		SortedSet<Integer> aligned1 = new TreeSet<>();
+		SortedSet<Integer> aligned2 = new TreeSet<>();
 
 		for(Entry<Integer,Integer> pair : alignment.entrySet()) {
 			aligned1.add(pair.getKey());
@@ -480,18 +480,18 @@ public static Map<Integer, Integer> guessSequentialAlignment(
 	public static List<List<List<Integer>>> getOptAlnAsList(AFPChain afpChain) {
 		int[][][] optAln = afpChain.getOptAln();
 		int[] optLen = afpChain.getOptLen();
-		List<List<List<Integer>>> blocks = new ArrayList<List<List<Integer>>>(afpChain.getBlockNum());
+		List<List<List<Integer>>> blocks = new ArrayList<>(afpChain.getBlockNum());
 		for(int blockNum=0;blockNum<afpChain.getBlockNum();blockNum++) {
 			//TODO could improve speed an memory by wrapping the arrays with
 			// an unmodifiable list, similar to Arrays.asList(...) but with the
 			// correct size parameter.
-			List<Integer> align1 = new ArrayList<Integer>(optLen[blockNum]);
-			List<Integer> align2 = new ArrayList<Integer>(optLen[blockNum]);
+			List<Integer> align1 = new ArrayList<>(optLen[blockNum]);
+			List<Integer> align2 = new ArrayList<>(optLen[blockNum]);
 			for(int pos=0;pos<optLen[blockNum];pos++) {
 				align1.add(optAln[blockNum][0][pos]);
 				align2.add(optAln[blockNum][1][pos]);
 			}
-			List<List<Integer>> block = new ArrayList<List<Integer>>(2);
+			List<List<Integer>> block = new ArrayList<>(2);
 			block.add(align1);
 			block.add(align2);
 			blocks.add(block);
@@ -559,13 +559,12 @@ public boolean containsKey(Object key) {
 	 *  Must be the same length as aligned1.
 	 * @return An AFPChain representing the alignment. Many properties may be
 	 *  null or another default.
-	 * @throws StructureException if an error occured during superposition
 	 * @throws IllegalArgumentException if aligned1 and aligned2 have different
 	 *  lengths
 	 * @see AlignmentTools#replaceOptAln(AFPChain, Atom[], Atom[], Map)
 	 */
 	public static AFPChain createAFPChain(Atom[] ca1, Atom[] ca2,
-										  ResidueNumber[] aligned1, ResidueNumber[] aligned2 ) throws StructureException {
+										  ResidueNumber[] aligned1, ResidueNumber[] aligned2 ) {
 		//input validation
 		int alnLen = aligned1.length;
 		if(alnLen != aligned2.length) {
@@ -627,7 +626,7 @@ public static AFPChain splitBlocksByTopology(AFPChain a, Atom[] ca1, Atom[] ca2)
 
 		// Determine block lengths
 		// Split blocks if residue indices don't increase monotonically
-		List<Integer> newBlkLen = new ArrayList<Integer>();
+		List<Integer> newBlkLen = new ArrayList<>();
 		boolean blockChanged = false;
 		for(int blk=0;blk<blockNum;blk++) {
 			int currLen=1;
@@ -655,7 +654,7 @@ public static AFPChain splitBlocksByTopology(AFPChain a, Atom[] ca1, Atom[] ca2)
 		}
 
 		// Split blocks
-		List<int[][]> blocks = new ArrayList<int[][]>( newBlkLen.size() );
+		List<int[][]> blocks = new ArrayList<>(newBlkLen.size());
 
 		int oldBlk = 0;
 		int pos = 0;
@@ -758,7 +757,7 @@ public static AFPChain replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
 		// increasing monotonically.
 		Integer[] res1 = alignment.keySet().toArray(new Integer[0]);
 		Arrays.sort(res1);
-		List<Integer> blockLens = new ArrayList<Integer>(2);
+		List<Integer> blockLens = new ArrayList<>(2);
 		int optLength = 0;
 		Integer lastRes = alignment.get(res1[0]);
 		int blkLen = lastRes==null?0:1;
@@ -989,17 +988,17 @@ public static Object resizeArray (Object oldArray, int newSize) {
 	 */
 	public static <S,T> String toConciseAlignmentString(Map<S,T> alignment, Map<T,S> identity) {
 		// Clone input to prevent changes
-		Map<S,T> alig = new HashMap<S,T>(alignment);
+		Map<S,T> alig = new HashMap<>(alignment);
 
 		// Generate inverse alignment
-		Map<S,List<S>> inverse = new HashMap<S,List<S>>();
+		Map<S,List<S>> inverse = new HashMap<>();
 		for(Entry<S,T> e: alig.entrySet()) {
 			S val = identity.get(e.getValue());
 			if( inverse.containsKey(val) ) {
 				List<S> l = inverse.get(val);
 				l.add(e.getKey());
 			} else {
-				List<S> l = new ArrayList<S>();
+				List<S> l = new ArrayList<>();
 				l.add(e.getKey());
 				inverse.put(val,l);
 			}
@@ -1051,14 +1050,14 @@ public static <S,T> String toConciseAlignmentString(Map<S,T> alignment, Map<T,S>
 	 * @see #toConciseAlignmentString(Map, Map)
 	 */
 	public static <T> String toConciseAlignmentString(Map<T, T> alignment) {
-		return toConciseAlignmentString(alignment, new IdentityMap<T>());
+		return toConciseAlignmentString(alignment, new IdentityMap<>());
 	}
 
 	/**
 	 * @see #toConciseAlignmentString(Map, Map)
 	 */
 	public static Map<Integer, Integer> fromConciseAlignmentString(String string) {
-		Map<Integer, Integer> map = new HashMap<Integer, Integer>();
+		Map<Integer, Integer> map = new HashMap<>();
 		boolean matches = true;
 		while (matches) {
 			Pattern pattern = Pattern.compile("(\\d+)>(\\d+)");
@@ -1101,14 +1100,10 @@ public static int[] calculateBlockGap(int[][][] optAln){
 					//If one of the positions or both are not contiguous increment the number of gaps
 					if (optAln[i][0][j] > last1+1 || optAln[i][1][j] > last2+1){
 						gaps++;
-						last1 = optAln[i][0][j];
-						last2 = optAln[i][1][j];
 					}
 					//Otherwise just set the last position to the current one
-					else{
-						last1 = optAln[i][0][j];
-						last2 = optAln[i][1][j];
-					}
+					last1 = optAln[i][0][j];
+					last2 = optAln[i][1][j];
 				}
 			}
 			blockGap[i] = gaps;
@@ -1201,7 +1196,7 @@ public static void alignmentToSIF(Writer out,AFPChain afpChain,
 	 */
 	public static final List<Chain> getAlignedModel(Atom[] ca){
 
-		List<Chain> model = new ArrayList<Chain>();
+		List<Chain> model = new ArrayList<>();
 		for ( Atom a: ca){
 
 			Group g = a.getGroup();
@@ -1236,9 +1231,8 @@ public static final List<Chain> getAlignedModel(Atom[] ca){
 	 * @param ca1
 	 * @param ca2
 	 * @return a structure object containing two models, one for each set of Atoms.
-	 * @throws StructureException
 	 */
-	public static final Structure getAlignedStructure(Atom[] ca1, Atom[] ca2) throws StructureException{
+	public static final Structure getAlignedStructure(Atom[] ca1, Atom[] ca2) {
 
 		/* Previous implementation commented
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index 4b7ba3f0fc..728c211add 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -92,7 +92,7 @@ public class AtomCache {
 	private String cachePath;
 
 	// make sure IDs are loaded uniquely
-	private Collection<String> currentlyLoading = Collections.synchronizedCollection(new TreeSet<String>());
+	private final Collection<String> currentlyLoading = Collections.synchronizedCollection(new TreeSet<>());
 
 	private String path;
 
@@ -188,7 +188,7 @@ public Atom[] getAtoms(String name) throws IOException, StructureException {
 	}
 	public Atom[] getAtoms(StructureIdentifier name) throws IOException, StructureException {
 
-		Atom[] atoms = null;
+		Atom[] atoms;
 
 		// System.out.println("loading " + name);
 		Structure s = getStructure(name);
@@ -217,7 +217,7 @@ public Atom[] getRepresentativeAtoms(String name) throws IOException, StructureE
 
 	public Atom[] getRepresentativeAtoms(StructureIdentifier name) throws IOException, StructureException {
 
-		Atom[] atoms = null;
+		Atom[] atoms;
 
 		Structure s = getStructure(name);
 
@@ -911,7 +911,7 @@ private Structure loadStructureFromMmtfByPdbId(String pdbId) throws IOException
 		return structure;
 	}
 
-	protected Structure loadStructureFromCifByPdbId(String pdbId) throws IOException, StructureException {
+	protected Structure loadStructureFromCifByPdbId(String pdbId) throws IOException {
 
 		logger.debug("Loading structure {} from mmCIF file {}.", pdbId, path);
 		Structure s;
@@ -930,7 +930,7 @@ protected Structure loadStructureFromCifByPdbId(String pdbId) throws IOException
 		return s;
 	}
 
-	protected Structure loadStructureFromPdbByPdbId(String pdbId) throws IOException, StructureException {
+	protected Structure loadStructureFromPdbByPdbId(String pdbId) throws IOException {
 
 		logger.debug("Loading structure {} from PDB file {}.", pdbId, path);
 		Structure s;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java
index 97566c86b3..c4697356e3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java
@@ -100,14 +100,14 @@ public static String[] configureBean(Object bean, String[] args)
 			throw new ConfigurationException("Couldn't get information for target bean " + ex.getMessage());
 		}
 
-		Map<String,PropertyDescriptor> propertiesByName = new HashMap<String, PropertyDescriptor>();
+		Map<String,PropertyDescriptor> propertiesByName = new HashMap<>();
 		for (PropertyDescriptor pd : bi.getPropertyDescriptors() ) {
 			propertiesByName.put(pd.getName(), pd);
 		}
 
-		List<String> anonArgs = new ArrayList<String>();
-		Map<PropertyDescriptor,List<String>> arrayProps = new HashMap<PropertyDescriptor, List<String>>();
-		Set<PropertyDescriptor> usedProps = new HashSet<PropertyDescriptor>();
+		List<String> anonArgs = new ArrayList<>();
+		Map<PropertyDescriptor,List<String>> arrayProps = new HashMap<>();
+		Set<PropertyDescriptor> usedProps = new HashSet<>();
 
 		boolean stdInUsed = false;
 		boolean stdOutUsed = false;
@@ -125,7 +125,7 @@ public static String[] configureBean(Object bean, String[] args)
 
 				boolean arrayMode = false;
 				Object propVal = null;
-				Class propType = null;
+				Class propType;
 
 				if (pd == null) {
 					if (arg.startsWith("-no")) {
@@ -274,20 +274,14 @@ else if( val.equalsIgnoreCase("false") || val.equalsIgnoreCase("f"))
 				//System.out.println("setting to: " + propVal + " " + propVal.getClass().getName());
 
 				if (arrayMode) {
-					List valList = arrayProps.get(pd);
-					if (valList == null) {
-						valList = new ArrayList();
-						arrayProps.put(pd, valList);
-					}
+					List valList = arrayProps.computeIfAbsent(pd, k -> new ArrayList());
 					valList.add(propVal);
 				} else {
 					if (usedProps.contains(pd)) {
 						throw new ConfigurationException("Multiple values supplied for " + pd.getName());
 					}
 					try {
-						pd.getWriteMethod().invoke(bean, new Object[] {propVal});
-					} catch (InvocationTargetException ex) {
-						throw new ConfigurationException("Error configuring '" + pd.getName() + "'");
+						pd.getWriteMethod().invoke(bean, propVal);
 					} catch (Exception ex) {
 						throw new ConfigurationException("Error configuring '" + pd.getName() + "'");
 					}
@@ -317,15 +311,13 @@ else if( val.equalsIgnoreCase("false") || val.equalsIgnoreCase("f"))
 				valArray = vals.toArray((Object[]) Array.newInstance(compType, vals.size()));
 			}
 			try {
-				pd.getWriteMethod().invoke(bean, new Object[] {valArray});
-			} catch (InvocationTargetException ex) {
-				throw new ConfigurationException("Error configuring '" + pd.getName() + "'");
+				pd.getWriteMethod().invoke(bean, valArray);
 			} catch (Exception ex) {
 				throw new ConfigurationException("Error configuring '" + pd.getName() + "'");
 			}
 		}
 
-		return anonArgs.toArray(new String[anonArgs.size()]);
+		return anonArgs.toArray(new String[0]);
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CollectionTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CollectionTools.java
index 45b7f38e56..5490f2d76d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CollectionTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CollectionTools.java
@@ -48,7 +48,7 @@ public static double[] toDoubleArray(Collection<Number> l) {
 	}
 
 	public static Object randomPick(Collection<Number> col) {
-		Object[] objs = col.toArray(new Object[col.size()]);
+		Object[] objs = col.toArray(new Object[0]);
 		return objs[(int) Math.floor(Math.random() * objs.length)];
 	}
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/SynchronizedOutFile.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/SynchronizedOutFile.java
index 9d05773c25..7160005bca 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/SynchronizedOutFile.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/SynchronizedOutFile.java
@@ -33,7 +33,7 @@ public class SynchronizedOutFile {
 	int ARR_SIZE=100;
 	Integer counter;
 
-	boolean useGzipCompression = false;
+	boolean useGzipCompression;
 
 
 	/** Create a thread safe wrapper for writing to this file, the file will be gzip compressed.
@@ -62,7 +62,7 @@ public SynchronizedOutFile(File f, boolean gzipCompress) throws FileNotFoundExce
 	 *
 	 * @param f
 	 */
-	public SynchronizedOutFile(File f) throws FileNotFoundException, IOException{
+	public SynchronizedOutFile(File f) throws IOException{
 
 		this(f,false);
 
@@ -98,7 +98,7 @@ private void writeArr() throws IOException{
 
 
 		OutputStream out = null;
-		FileOutputStream fileOutputStream=null;
+		FileOutputStream fileOutputStream;
 		try {
 			//This is less code-redundant
 			fileOutputStream = new FileOutputStream(file, true);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java
index 9794bf3f1f..8def86cfad 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java
@@ -123,7 +123,7 @@ public static InputStream getInputStream(URL url) throws IOException
 	 * @throws IOException due to an error opening the URL
 	 */
 	public static InputStream getInputStream(URL url, boolean acceptGzipEncoding, int timeout) throws IOException {
-		InputStream inStream = null ;
+		InputStream inStream;
 		URLConnection huc = URLConnectionTools.openURLConnection(url,timeout);
 
 		if ( acceptGzipEncoding) huc.setRequestProperty("Accept-Encoding", "gzip");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
index e23f8e6db1..021c461c1e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
@@ -63,7 +63,7 @@ public class UserConfiguration
 
 	private String fileFormat;
 
-	private static AtomicBoolean warningShown = new AtomicBoolean(false);
+	private static final AtomicBoolean warningShown = new AtomicBoolean(false);
 
 
 	/**
@@ -103,7 +103,7 @@ public UserConfiguration(){
 
 	private String initPdbFilePath() {
 
-		String path = null;
+		String path;
 
 		String propertyName = PDB_DIR;
 
@@ -174,7 +174,7 @@ private String initPdbFilePath() {
 
 	private String initCacheFilePath() {
 
-		String path = null;
+		String path;
 
 		String propertyName = PDB_CACHE_DIR;
 
@@ -320,8 +320,8 @@ public XMLWriter toXML(XMLWriter xw)
 		if (! pdbFilePath.equals(tempdir))
 			xw.attribute("path", pdbFilePath);
 
-		xw.attribute("fetchBehavior", fetchBehavior+"");
-		xw.attribute("obsoleteBehavior", obsoleteBehavior+"");
+		xw.attribute("fetchBehavior", String.valueOf(fetchBehavior));
+		xw.attribute("obsoleteBehavior", String.valueOf(obsoleteBehavior));
 		xw.attribute("fileFormat", fileFormat);
 		xw.closeTag("PDBFILEPATH");
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainFlipper.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainFlipper.java
index 5ace60fc8f..c1640aecf2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainFlipper.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainFlipper.java
@@ -40,7 +40,7 @@ public class AFPChainFlipper {
 	 * @param o ... the original AFPCHain that should be flipped
 	 * @return a cloned AFPCHain which the positions of name1 and name2 flipped.
 	 */
-	public static AFPChain flipChain(AFPChain o) throws StructureException{
+	public static AFPChain flipChain(AFPChain o) {
 
 		AFPChain n = new AFPChain(o.getAlgorithmName());
 		n.setVersion(o.getVersion());
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java
index f8be1609c8..10b973cb0f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java
@@ -237,11 +237,11 @@ public static void printXMLHeader(PrettyXMLWriter xml, AFPChain afpChain) throws
 		xml.attribute("name2", afpChain.getName2());
 		xml.attribute("method", afpChain.getAlgorithmName());
 		xml.attribute("version" , afpChain.getVersion());
-		xml.attribute("alnLength", afpChain.getAlnLength() + "");
-		xml.attribute("blockNum", afpChain.getBlockNum() + "");
-		xml.attribute("gapLen", afpChain.getGapLen() + "");
-		xml.attribute("optLength", afpChain.getOptLength() + "");
-		xml.attribute("totalLenIni", afpChain.getTotalLenIni() + "");
+		xml.attribute("alnLength", String.valueOf(afpChain.getAlnLength()));
+		xml.attribute("blockNum", String.valueOf(afpChain.getBlockNum()));
+		xml.attribute("gapLen", String.valueOf(afpChain.getGapLen()));
+		xml.attribute("optLength", String.valueOf(afpChain.getOptLength()));
+		xml.attribute("totalLenIni", String.valueOf(afpChain.getTotalLenIni()));
 
 		xml.attribute("alignScore", String.format("%5.2f", afpChain.getAlignScore() ).trim());
 		xml.attribute("chainRmsd",  String.format("%5.2f", afpChain.getChainRmsd() ).trim());
@@ -250,13 +250,13 @@ public static void printXMLHeader(PrettyXMLWriter xml, AFPChain afpChain) throws
 		xml.attribute("probability", String.format("%.2e", afpChain.getProbability() ).trim());
 		xml.attribute("similarity", String.format("%5.4f", afpChain.getSimilarity() ).trim());
 
-		xml.attribute("similarity1", afpChain.getCoverage1() + "");
-		xml.attribute("similarity2", afpChain.getCoverage2() + "");
+		xml.attribute("similarity1", String.valueOf(afpChain.getCoverage1()));
+		xml.attribute("similarity2", String.valueOf(afpChain.getCoverage2()));
 		xml.attribute("totalRmsdIni", String.format("%5.2f",afpChain.getTotalRmsdIni() ).trim());
 		xml.attribute("totalRmsdOpt", String.format("%5.2f",afpChain.getTotalRmsdOpt() ).trim());
-		xml.attribute("ca1Length", afpChain.getCa1Length()+"");
-		xml.attribute("ca2Length", afpChain.getCa2Length()+"");
-		xml.attribute("afpNum",afpChain.getAfpSet().size()+"");
+		xml.attribute("ca1Length", String.valueOf(afpChain.getCa1Length()));
+		xml.attribute("ca2Length", String.valueOf(afpChain.getCa2Length()));
+		xml.attribute("afpNum", String.valueOf(afpChain.getAfpSet().size()));
 		xml.attribute("alignScoreUpdate",String.format("%5.2f",afpChain.getAlignScoreUpdate()).trim());
 		xml.attribute("time", String.format("%d",afpChain.getCalculationTime()));
 		if ( afpChain.getTMScore() != -1){
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java
index 0827134bbe..aa98063e4d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java
@@ -223,7 +223,7 @@ public static void rebuildAFPChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2){
 	}
 
 	public static AFPChain[] parseMultiXML(String xml) throws IOException {
-		List<AFPChain> afpChains = new ArrayList<AFPChain>();
+		List<AFPChain> afpChains = new ArrayList<>();
 
 		try
 		{
@@ -273,7 +273,7 @@ public static AFPChain[] parseMultiXML(String xml) throws IOException {
 
 				a.setAlignScore(Double.parseDouble(getAttribute(rootElement,"alignScore")));
 				a.setChainRmsd(Double.parseDouble(getAttribute(rootElement,"chainRmsd")));
-				Double identity = Double.parseDouble(getAttribute(rootElement,"identity"));
+				double identity = Double.parseDouble(getAttribute(rootElement,"identity"));
 				a.setIdentity(identity);
 
 				a.setNormAlignScore(Double.parseDouble(getAttribute(rootElement,"normAlignScore")));
@@ -298,7 +298,7 @@ public static AFPChain[] parseMultiXML(String xml) throws IOException {
 				}
 
 				String calcTimeS = getAttribute(rootElement,"time");
-				Long calcTime = -1L;
+				long calcTime = -1L;
 				if ( calcTimeS != null){
 
 					try {
@@ -316,7 +316,7 @@ public static AFPChain[] parseMultiXML(String xml) throws IOException {
 				a.setBlockShiftVector(blockShiftVector);
 
 				int afpNum = Integer.parseInt(getAttribute(rootElement,"afpNum"));
-				List<AFP> afpSet = new ArrayList<AFP>();
+				List<AFP> afpSet = new ArrayList<>();
 				for (int afp=0;afp<afpNum;afp++){
 					afpSet.add( new AFP());
 				}
@@ -361,7 +361,7 @@ public static AFPChain[] parseMultiXML(String xml) throws IOException {
 			e.printStackTrace();
 		}
 
-		return afpChains.toArray(new AFPChain[afpChains.size()]);
+		return afpChains.toArray(new AFPChain[0]);
 	}
 
 
@@ -421,23 +421,24 @@ private static  void processBlock(Node block, AFPChain a, int minLength){
 			if(!eqr.hasAttributes()) continue;
 
 
-			if ( eqr.getNodeName().equals("eqr")) {
-				nrEqr++;
-				NamedNodeMap atts = eqr.getAttributes();
+			switch (eqr.getNodeName()) {
+				case "eqr":
+					nrEqr++;
+					NamedNodeMap atts = eqr.getAttributes();
 
-				int eqrNr = Integer.parseInt(atts.getNamedItem("eqrNr").getTextContent());
+					int eqrNr = Integer.parseInt(atts.getNamedItem("eqrNr").getTextContent());
 
-				String pdbres1 = atts.getNamedItem("pdbres1").getTextContent();
-				String chain1 = atts.getNamedItem("chain1").getTextContent();
-				String pdbres2 = atts.getNamedItem("pdbres2").getTextContent();
-				String chain2 = atts.getNamedItem("chain2").getTextContent();
+					String pdbres1 = atts.getNamedItem("pdbres1").getTextContent();
+					String chain1 = atts.getNamedItem("chain1").getTextContent();
+					String pdbres2 = atts.getNamedItem("pdbres2").getTextContent();
+					String chain2 = atts.getNamedItem("chain2").getTextContent();
 
-				//System.out.println(blockNr + " " + eqrNr + " " + chain1+" " + pdbres1 + ":" + chain2 + " " + pdbres2);
+					//System.out.println(blockNr + " " + eqrNr + " " + chain1+" " + pdbres1 + ":" + chain2 + " " + pdbres2);
 
-				pdbAln[blockNr][0][eqrNr] = chain1+":"+pdbres1;
-				pdbAln[blockNr][1][eqrNr] = chain2+":"+pdbres2;
+					pdbAln[blockNr][0][eqrNr] = chain1 + ":" + pdbres1;
+					pdbAln[blockNr][1][eqrNr] = chain2 + ":" + pdbres2;
 
-				//  A WORK AROUND FOR THE PROBLEM THAT WE DON:T HAVE PDBs LOADED AT THIS TIME...
+					//  A WORK AROUND FOR THE PROBLEM THAT WE DON:T HAVE PDBs LOADED AT THIS TIME...
 
 				/* int pos1 = getPositionForPDBresunm(pdbres1,chain1,ca1);
 				int pos2 = getPositionForPDBresunm(pdbres2,chain2,ca2);
@@ -445,30 +446,33 @@ private static  void processBlock(Node block, AFPChain a, int minLength){
 				optAln[blockNr][0][eqrNr] = pos1;
 				optAln[blockNr][1][eqrNr] = pos2;
 				 */
-			} else if ( eqr.getNodeName().equals("matrix")){
-				// process Matrix
-				Matrix m = new Matrix(3,3);
-
-				for (int i =1 ; i <= 3 ; i++){
-					for (int j =1 ; j <= 3 ; j++){
-						String att = getAttribute(eqr, "mat" +i + j);
-						double val = Double.parseDouble(att);
-						m.set(i-1,j-1,val);
-
+					break;
+				case "matrix":
+					// process Matrix
+					Matrix m = new Matrix(3, 3);
+
+					for (int i = 1; i <= 3; i++) {
+						for (int j = 1; j <= 3; j++) {
+							String att = getAttribute(eqr, "mat" + i + j);
+							double val = Double.parseDouble(att);
+							m.set(i - 1, j - 1, val);
+
+						}
 					}
-				}
-				ms[blockNr] = m;
-
-			} else if ( eqr.getNodeName().equals("shift")){
-				Atom shift = new AtomImpl();
-				double x = Double.parseDouble(getAttribute(eqr, "x"));
-				double y = Double.parseDouble(getAttribute(eqr, "y"));
-				double z = Double.parseDouble(getAttribute(eqr, "z"));
-				shift.setX(x);
-				shift.setY(y);
-				shift.setZ(z);
-				shifts[blockNr] = shift;
-
+					ms[blockNr] = m;
+
+					break;
+				case "shift":
+					Atom shift = new AtomImpl();
+					double x = Double.parseDouble(getAttribute(eqr, "x"));
+					double y = Double.parseDouble(getAttribute(eqr, "y"));
+					double z = Double.parseDouble(getAttribute(eqr, "z"));
+					shift.setX(x);
+					shift.setY(y);
+					shift.setZ(z);
+					shifts[blockNr] = shift;
+
+					break;
 			}
 
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLConverter.java
index 1b9fe49ae5..84c53f1c39 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLConverter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLConverter.java
@@ -104,7 +104,7 @@ public synchronized static void printXMLblock(PrettyXMLWriter xml,
 
 			xml.openTag("eqr"+pos);
 			for (int str=0; str<alignment.size(); str++){
-				xml.attribute("str"+(str+1),alignment.get(str).get(pos)+"");
+				xml.attribute("str"+(str+1), String.valueOf(alignment.get(str).get(pos)));
 			}
 			xml.closeTag("eqr"+pos);
 		}
@@ -122,7 +122,7 @@ public synchronized static void printXMLmatrix4d(PrettyXMLWriter xml,
 		for (int x=0;x<4;x++){
 			for (int y=0;y<4;y++){
 				String key = "mat"+(x+1)+(y+1);
-				String value = transform.getElement(x,y)+"";
+				String value = String.valueOf(transform.getElement(x, y));
 				xml.attribute(key,value);
 			}
 		}
@@ -138,7 +138,7 @@ public synchronized static void printXMLscoresCache(PrettyXMLWriter xml,
 		//We need a new tag for every score, we don't know their names
 		for (String score:cache.getScores()){
 			xml.openTag(score);
-			String value = cache.getScore(score)+"";
+			String value = String.valueOf(cache.getScore(score));
 			xml.attribute("value", value);
 			xml.closeTag(score);
 		}
@@ -151,8 +151,8 @@ public synchronized static void printXMLheader(PrettyXMLWriter xml,
 		//Creation properties
 		xml.attribute("Algorithm", ensemble.getAlgorithmName());
 		xml.attribute("Version", ensemble.getVersion());
-		xml.attribute("IOTime", ensemble.getIoTime()+"");
-		xml.attribute("CalculationTime", ensemble.getCalculationTime()+"");
+		xml.attribute("IOTime", String.valueOf(ensemble.getIoTime()));
+		xml.attribute("CalculationTime", String.valueOf(ensemble.getCalculationTime()));
 
 		//Structure Identifiers
 		xml.openTag("Structures");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java
index 5d7b6fb3ad..1e174584b3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java
@@ -77,7 +77,7 @@ public static List<MultipleAlignmentEnsemble> parseXMLfile(String xml)
 			throws ParserConfigurationException, SAXException, IOException {
 
 		List<MultipleAlignmentEnsemble> ensembles =
-				new ArrayList<MultipleAlignmentEnsemble>();
+				new ArrayList<>();
 
 		//Convert string to XML document
 		DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
@@ -113,14 +113,16 @@ public static MultipleAlignmentEnsemble parseEnsemble(Node root){
 		for (int i=0; i<children.getLength(); i++) {
 
 			Node child = children.item(i);
-			if (child.getNodeName().equals("MultipleAlignment")){
-				parseMultipleAlignment(child, ensemble);
-			}
-			else if (child.getNodeName().equals("Structures")){
-				parseStructures(child, ensemble);
-			}
-			else if (child.getNodeName().equals("ScoresCache")){
-				parseScoresCache(child, ensemble);
+			switch (child.getNodeName()) {
+				case "MultipleAlignment":
+					parseMultipleAlignment(child, ensemble);
+					break;
+				case "Structures":
+					parseStructures(child, ensemble);
+					break;
+				case "ScoresCache":
+					parseScoresCache(child, ensemble);
+					break;
 			}
 		}
 
@@ -150,22 +152,24 @@ else if (child.getNodeName().equals("ScoresCache")){
 	public static BlockSet parseBlockSet(Node root, MultipleAlignment msa) {
 
 		BlockSet bs = new BlockSetImpl(msa);
-		List<Matrix4d> transforms = new ArrayList<Matrix4d>();
+		List<Matrix4d> transforms = new ArrayList<>();
 		NodeList children = root.getChildNodes();
 
 		for (int i=0; i<children.getLength(); i++) {
 
 			Node child = children.item(i);
 
-			if (child.getNodeName().equals("Block")){
-				parseBlock(child, bs);
-			}
-			else if (child.getNodeName().equals("Matrix4d")){
-				Matrix4d t = parseMatrix4d(child);
-				transforms.add(t);
-			}
-			else if (child.getNodeName().equals("ScoresCache")){
-				parseScoresCache(child, bs);
+			switch (child.getNodeName()) {
+				case "Block":
+					parseBlock(child, bs);
+					break;
+				case "Matrix4d":
+					Matrix4d t = parseMatrix4d(child);
+					transforms.add(t);
+					break;
+				case "ScoresCache":
+					parseScoresCache(child, bs);
+					break;
 			}
 		}
 		//Because if it is 0 means that there were no transformations
@@ -178,7 +182,7 @@ else if (child.getNodeName().equals("ScoresCache")){
 	public static Block parseBlock(Node root, BlockSet blockSet) {
 
 		Block b = new BlockImpl(blockSet);
-		List<List<Integer>> alignRes = new ArrayList<List<Integer>>();
+		List<List<Integer>> alignRes = new ArrayList<>();
 		b.setAlignRes(alignRes);
 		NodeList children = root.getChildNodes();
 
@@ -195,7 +199,7 @@ public static Block parseBlock(Node root, BlockSet blockSet) {
 				while (node!=null){
 
 					if (alignRes.size() < str) {
-						alignRes.add(new ArrayList<Integer>());
+						alignRes.add(new ArrayList<>());
 					}
 
 					String residue = node.getTextContent();
@@ -276,7 +280,7 @@ public static void parseHeader(Node node,
 	public static void parseStructures(Node root,
 			MultipleAlignmentEnsemble ensemble) {
 
-		List<StructureIdentifier> names = new ArrayList<StructureIdentifier>();
+		List<StructureIdentifier> names = new ArrayList<>();
 		ensemble.setStructureIdentifiers(names);
 
 		NamedNodeMap atts = root.getAttributes();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.java
index 433e053a3c..afcc4f95ac 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.java
@@ -44,7 +44,7 @@ public class PdbPairXMLConverter {
 	public static final String DEFAULT_METHOD_NAME = FatCatRigid.algorithmName;
 
 	public static PdbPairsMessage convertXMLtoPairs(String xml) {
-		SortedSet<PdbPair>  pairs = new TreeSet<PdbPair>();
+		SortedSet<PdbPair>  pairs = new TreeSet<>();
 		PdbPairsMessage message = new PdbPairsMessage();
 		try
 		{
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairsMessage.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairsMessage.java
index 170ee5ff47..6aa415a8d9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairsMessage.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairsMessage.java
@@ -40,7 +40,7 @@ public PdbPairsMessage(){
 
 		method = PdbPairXMLConverter.DEFAULT_METHOD_NAME;
 
-		pairs = new TreeSet<PdbPair>();
+		pairs = new TreeSet<>();
 
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/RepresentativeXMLConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/RepresentativeXMLConverter.java
index dccec37fb3..db0ce1331b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/RepresentativeXMLConverter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/RepresentativeXMLConverter.java
@@ -60,7 +60,7 @@ public static final String toXML(SortedSet<String> representatives){
 	}
 
 	public static final SortedSet<String> fromXML(String xml){
-		SortedSet<String> representatives = new TreeSet<String>();
+		SortedSet<String> representatives = new TreeSet<>();
 		try {
 			DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
 			DocumentBuilder db = factory.newDocumentBuilder();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
index 19ece0ab72..493ab25733 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
@@ -86,8 +86,8 @@ public class AsaCalculator {
 
 	private class AsaCalcWorker implements Runnable {
 
-		private int i;
-		private double[] asas;
+		private final int i;
+		private final double[] asas;
 
 		public AsaCalcWorker(int i, double[] asas) {
 			this.i = i;
@@ -101,11 +101,11 @@ public void run() {
 	}
 
 
-	private Point3d[] atomCoords;
-	private Atom[] atoms;
-	private double[] radii;
-	private double probe;
-	private int nThreads;
+	private final Point3d[] atomCoords;
+	private final Atom[] atoms;
+	private final double[] radii;
+	private final double probe;
+	private final int nThreads;
 	private Point3d[] spherePoints;
 	private double cons;
 	private int[][] neighborIndices;
@@ -243,7 +243,7 @@ public GroupAsa[] getGroupAsas() {
 			}
 		}
 
-		return asas.values().toArray(new GroupAsa[asas.size()]);
+		return asas.values().toArray(new GroupAsa[0]);
 	}
 
 	/**
@@ -347,7 +347,7 @@ void setUseSpatialHashingForNeighbors(boolean useSpatialHashingForNeighbors) {
 	 * @param nSpherePoints the number of points to be used in generating the spherical dot-density
 	 * @return
 	 */
-	private Point3d[] generateSpherePoints(int nSpherePoints) {
+	private static Point3d[] generateSpherePoints(int nSpherePoints) {
 		Point3d[] points = new Point3d[nSpherePoints];
 		double inc = Math.PI * (3.0 - Math.sqrt(5.0));
 		double offset = 2.0 / nSpherePoints;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/GroupAsa.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/GroupAsa.java
index 05d34b8d21..431405d62c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/GroupAsa.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/GroupAsa.java
@@ -44,7 +44,7 @@ public class GroupAsa implements Serializable {
 
 	private static HashMap<Character,Double>  initTriPeptAsas() {
 		// ASA in extended tripeptide conformation (GLY-X-GLY) from Miller et al JMB 1987 (for calculation of relative ASAs)
-		HashMap<Character,Double> map = new HashMap<Character,Double>();
+		HashMap<Character,Double> map = new HashMap<>();
 		map.put('A', 113.0);
 		map.put('R', 241.0);
 		map.put('N', 158.0);
@@ -71,7 +71,7 @@ private static HashMap<Character,Double>  initTriPeptAsas() {
 
 
 
-	private Group g;
+	private final Group g;
 
 	/**
 	 * ASA of uncomplexed residue
@@ -223,14 +223,10 @@ public Object clone() {
 		GroupAsa n = new GroupAsa(this.g);
 		n.setAsaC(this.getAsaC());
 		n.setAsaU(this.getAsaU());
-		n.atomAsaUs = new ArrayList<Double>(this.atomAsaUs.size());
-		n.atomAsaCs = new ArrayList<Double>(this.atomAsaCs.size());
-		for (int i=0;i<this.atomAsaUs.size();i++) {
-			n.atomAsaUs.add(this.atomAsaUs.get(i));
-		}
-		for (int i=0;i<this.atomAsaCs.size();i++) {
-			n.atomAsaCs.add(this.atomAsaCs.get(i));
-		}
+		n.atomAsaUs = new ArrayList<>(this.atomAsaUs.size());
+		n.atomAsaCs = new ArrayList<>(this.atomAsaCs.size());
+        n.atomAsaUs.addAll(this.atomAsaUs);
+        n.atomAsaCs.addAll(this.atomAsaCs);
 
 		return n;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java
index 6427447d75..386003b903 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java
@@ -70,7 +70,7 @@
 public class BasePairParameters implements Serializable {
 
 	private static final long serialVersionUID = 6214502385L;
-	private static Logger log = LoggerFactory.getLogger(BasePairParameters.class);
+	private static final Logger log = LoggerFactory.getLogger(BasePairParameters.class);
 
 	// See URL http://ndbserver.rutgers.edu/ndbmodule/archives/reports/tsukuba/Table1.html
 	// and the paper cited at the top of this class (also as Table 1).
@@ -145,9 +145,9 @@ public class BasePairParameters implements Serializable {
 	}
 
 	protected Structure structure;
-	protected boolean canonical = true;
-	protected boolean useRNA = false;
-	protected boolean nonredundant = false;
+	protected boolean canonical;
+	protected boolean useRNA;
+	protected boolean nonredundant;
 	protected double[] pairParameters;
 
 	// this is the main data that the user wants to get back out from the procedure.
@@ -227,12 +227,12 @@ public BasePairParameters analyze() {
 			lastStep = currentStep;
 			currentStep = this.basePairReferenceFrame(pairs.get(i));
 			referenceFrames.add((Matrix4d)currentStep.clone());
-			for (int j = 0; j < 6; j++) pairingParameters[i][j] = pairParameters[j];
+			System.arraycopy(pairParameters, 0, pairingParameters[i], 0, 6);
 			if (i != 0) {
 				lastStep.invert();
 				lastStep.mul(currentStep);
 				double[] sparms = calculateTp(lastStep);
-				for (int j = 0; j < 6; j++) stepParameters[i][j] = sparms[j];
+				System.arraycopy(sparms, 0, stepParameters[i], 0, 6);
 			}
 		}
 		return this;
@@ -509,7 +509,7 @@ public List<Pair<Group>> findPairs(List<Chain> chains) {
 							if (a == null) valid = false;
 						}
 						if (valid) {
-							result.add(new Pair<Group>(g1, g2));
+							result.add(new Pair<>(g1, g2));
 							pairingNames.add((useRNA ? BASE_LIST_RNA[type1]+ BASE_LIST_RNA[type2] : BASE_LIST_DNA[type1]+ BASE_LIST_DNA[type2]));
 							pairSequence += c.getAtomSequence().charAt(index1 + k);
 						} else if (pairSequence.length() != 0 && pairSequence.charAt(pairSequence.length()-1) != ' ') pairSequence += ' ';
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathCategory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathCategory.java
index 4aabdc04b7..dfdd74d65f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathCategory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathCategory.java
@@ -47,26 +47,27 @@ public enum CathCategory {
 	static final String lut = "CATHSOLID";
 
 	public static CathCategory fromString(String type) {
-		if ( type.equals("C") ) {
-			return Class;
-		} else if ( type.equals("A") ) {
-			return Architecture;
-		} else if ( type.equals("T") ) {
-			return Topolgy;
-		} else if ( type.equals("H") ) {
-			return Homology;
-		} else if ( type.equals("S") ) {
-			return SequenceFamily;
-		} else if ( type.equals("O") ) {
-			return OrthologousSequenceFamily;
-		} else if ( type.equals("L") ) {
-			return LikeSequenceFamily;
-		} else if ( type.equals("I") ) {
-			return IdenticalSequenceFamily;
+        switch (type) {
+            case "C":
+                return Class;
+            case "A":
+                return Architecture;
+            case "T":
+                return Topolgy;
+            case "H":
+                return Homology;
+            case "S":
+                return SequenceFamily;
+            case "O":
+                return OrthologousSequenceFamily;
+            case "L":
+                return LikeSequenceFamily;
+            case "I":
+                return IdenticalSequenceFamily;
 //        } else if ( type.equals("D") ) {
-		} else {
-			return DomainCounter;
-		}
+            default:
+                return DomainCounter;
+        }
 	}
 
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathDatabase.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathDatabase.java
index 351af83e52..65aa6f41bb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathDatabase.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathDatabase.java
@@ -35,21 +35,21 @@ public interface CathDatabase {
 	 *
 	 * @return CATH version
 	 */
-	public String getCathVersion();
+    String getCathVersion();
 
 	/** Return the CathNode for a node ID.
 	 *
 	 * @param nodeId
 	 * @return CATH node
 	 */
-	public CathNode getCathNode(String nodeId);
+    CathNode getCathNode(String nodeId);
 
 	/** Return list of CATH descriptions for node representatives at a CATH category (e.g. "T").
 	 *
 	 * @param category
 	 * @return CATH descriptions
 	 */
-	public List<CathDomain> getByCategory(CathCategory category);
+    List<CathDomain> getByCategory(CathCategory category);
 
 	/** Return list of CATH descriptions whose CATH codes (e.g. 1.4.6.10) start with the query.
 	 * This is currently redundant with getDescriptionsByNodeId.
@@ -57,63 +57,63 @@ public interface CathDatabase {
 	 * @param query
 	 * @return CATH descriptions
 	 */
-	public List<CathDomain> filterByCathCode(String query);
+    List<CathDomain> filterByCathCode(String query);
 
 	/** Return the CATH sub-tree for a particular domain.
 	 *
 	 * @param domain
 	 * @return CATH sub-tree
 	 */
-	public List<CathNode> getTree(CathDomain domain);
+    List<CathNode> getTree(CathDomain domain);
 
 	/** Return list of CATH domains whose node name (e.g. Orthogonal Bundle) starts with the query.
 	 *
 	 * @param query
 	 * @return CATH domains
 	 */
-	public List<CathDomain> filterByNodeName(String query);
+    List<CathDomain> filterByNodeName(String query);
 
 	/** Return list of CATH descriptions whose descriptions (name field) starts with the query.
 	 *
 	 * @param query
 	 * @return CATH descriptions
 	 */
-	public List<CathDomain> filterByDescription(String query);
+    List<CathDomain> filterByDescription(String query);
 
 	/** Return CATH description for node representative by node ID.
 	 *
 	 * @param nodeId
 	 * @return CATH description
 	 */
-	public CathDomain getDescriptionByNodeId(String nodeId);
+    CathDomain getDescriptionByNodeId(String nodeId);
 
 	/** Return all CATH domains for a PDB ID.
 	 *
 	 * @param pdbId
 	 * @return CATH domains
 	 */
-	public List<CathDomain> getDomainsForPdb(String pdbId);
+    List<CathDomain> getDomainsForPdb(String pdbId);
 
 	/** Return CATH domain for CATH domain ID.
 	 *
 	 * @param cathId
 	 * @return CATH domain
 	 */
-	public CathDomain getDomainByCathId(String cathId);
+    CathDomain getDomainByCathId(String cathId);
 
 	/** Return CATH description for CATH domain ID.
 	 *
 	 * @param cathId
 	 * @return
 	 */
-	public CathDomain getDescriptionByCathId(String cathId);
+    CathDomain getDescriptionByCathId(String cathId);
 
 	/** Return all CATH domains for a particular CATH node.
 	 *
 	 * @param nodeId
 	 * @return
 	 */
-	public List<CathDomain> getDomainsByNodeId(String nodeId);
+    List<CathDomain> getDomainsByNodeId(String nodeId);
 
-	public List<CathFragment> getFragmentsByPdbId(String pdbId);
+	List<CathFragment> getFragmentsByPdbId(String pdbId);
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathDomain.java
index b4d0efaa89..891b9ec1bc 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathDomain.java
@@ -176,7 +176,7 @@ public String getThePdbId() {
 	 */
 	public String getPdbIdAndChain() {
 		return domainName.substring(0, 4) +
-				(!domainName.substring(4, 5).equals("0") ? "." + domainName.substring(4, 5) : "");
+				(!domainName.startsWith("0", 4) ? "." + domainName.substring(4, 5) : "");
 	}
 
 	public Integer getDomainId() {
@@ -280,10 +280,10 @@ public void setCATH(String cathCode) {
 	}
 
 	public String getCATH() {
-		return Integer.toString(getClassId()) + "." +
-				Integer.toString(getArchitectureId()) + "." +
-				Integer.toString(getTopologyId()) + "." +
-				Integer.toString(getHomologyId());
+		return getClassId() + "." +
+				getArchitectureId() + "." +
+				getTopologyId() + "." +
+				getHomologyId();
 	}
 
 	public void setSOLID(String cathCode) {
@@ -296,11 +296,11 @@ public void setSOLID(String cathCode) {
 	}
 
 	public String getSOILD() {
-		return Integer.toString(getSequenceFamilyId()) + "." +
-				Integer.toString(getOrthologousSequenceFamilyId()) + "." +
-				Integer.toString(getLikeSequenceFamilyId()) + "." +
-				Integer.toString(getIdenticalSequenceFamilyId()) + "." +
-				Integer.toString(getDomainCounter());
+		return getSequenceFamilyId() + "." +
+				getOrthologousSequenceFamilyId() + "." +
+				getLikeSequenceFamilyId() + "." +
+				getIdenticalSequenceFamilyId() + "." +
+				getDomainCounter();
 	}
 
 	public Integer getClassificationId(CathCategory cathCategory) {
@@ -422,7 +422,7 @@ public String toString() {
 	 * Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
 	 */
 	public Set<String> getChains() {
-		Set<String> chains = new HashSet<String>();
+		Set<String> chains = new HashSet<>();
 		List<ResidueRange> rrs = toCanonical().getResidueRanges();
 		for (ResidueRange rr : rrs) chains.add(rr.getChainName());
 		return chains;
@@ -435,7 +435,7 @@ public String getIdentifier() {
 
 	@Override
 	public SubstructureIdentifier toCanonical() {
-		List<ResidueRange> ranges = new ArrayList<ResidueRange>();
+		List<ResidueRange> ranges = new ArrayList<>();
 		String chain = String.valueOf(getDomainName().charAt(getDomainName().length() - 3));
 		for (CathSegment segment : this.getSegments()) {
 			ranges.add(new ResidueRange(chain, segment.getStart(), segment.getStop()));
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java
index 77fe36fd8e..55407aa93a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java
@@ -45,7 +45,7 @@ public class CathFactory {
 
 	private static CathDatabase cath;
 
-	private static Map<String, CathDatabase> versions = new HashMap<String, CathDatabase>();
+	private static final Map<String, CathDatabase> versions = new HashMap<>();
 
 	/**
 	 * Sets the default (singleton) CathDatabase.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
index 45914f6208..ea2f7cbb00 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
@@ -56,8 +56,8 @@ public class CathInstallation implements CathDatabase{
 	public static final String CATH_DOWNLOAD_ALL_RELEASES_DIR        = "all-releases";
 	public static final String CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR = "cath-classification-data";
 
-	public static final String NEWLINE = System.getProperty("line.separator");;
-	public static final String FILESPLIT = System.getProperty("file.separator");;
+	public static final String NEWLINE = System.getProperty("line.separator");
+	public static final String FILESPLIT = System.getProperty("file.separator");
 
 
 	private String cathVersion;
@@ -74,9 +74,9 @@ public class CathInstallation implements CathDatabase{
 	private final boolean useCathDomainDescriptionFile;
 	private final boolean parseCathFragments;
 
-	private Map<String, List<CathDomain>> pdbMap;
-	private Map<String, CathDomain> domainMap;
-	private Map<String, CathNode> cathTree;
+	private final Map<String, List<CathDomain>> pdbMap;
+	private final Map<String, CathDomain> domainMap;
+	private final Map<String, CathNode> cathTree;
 	private Map<String, List<CathFragment>> fragmentMap;
 
 
@@ -95,11 +95,11 @@ public CathInstallation(String cacheLocation, boolean usingCDDF, boolean parseCF
 		cathVersion = DEFAULT_VERSION;
 		cathDownloadUrl = CATH_DOWNLOAD_URL;
 
-		pdbMap = new HashMap<String, List<CathDomain>>();
-		domainMap = new HashMap<String ,CathDomain>();
-		cathTree = new HashMap<String, CathNode>();
+		pdbMap = new HashMap<>();
+		domainMap = new HashMap<>();
+		cathTree = new HashMap<>();
 
-		if (parseCathFragments) fragmentMap = new HashMap<String,List<CathFragment>>();
+		if (parseCathFragments) fragmentMap = new HashMap<>();
 
 	}
 
@@ -205,10 +205,10 @@ public List<CathDomain> getByCategory(CathCategory category) {
 			ensureDomallInstalled();
 		}
 		ensureNodeListInstalled();
-		List<CathDomain> matches = new ArrayList<CathDomain>();
+		List<CathDomain> matches = new ArrayList<>();
 		CathNode node;
-		for ( String nodeId : cathTree.keySet() ) {
-			if ( (node = cathTree.get(nodeId)).getCategory() == category ) {
+		for (CathNode cathNode : cathTree.values()) {
+			if ( (node = cathNode).getCategory() == category ) {
 				matches.add( domainMap.get( node.getRepresentative() ) );
 			}
 		}
@@ -222,10 +222,10 @@ public List<CathDomain> filterByCathCode(String query) {
 		} else {
 			ensureDomallInstalled();
 		}
-		List<CathDomain> matches = new ArrayList<CathDomain>();
-		for ( String k : domainMap.keySet() ) {
-			if ( domainMap.get(k).getCATH().startsWith(query) ) {
-				matches.add( domainMap.get(k) );
+		List<CathDomain> matches = new ArrayList<>();
+		for (CathDomain cathDomain : domainMap.values()) {
+			if (cathDomain.getCATH().startsWith(query) ) {
+				matches.add(cathDomain);
 			}
 		}
 		return matches;
@@ -234,7 +234,7 @@ public List<CathDomain> filterByCathCode(String query) {
 	@Override
 	public List<CathNode> getTree(CathDomain domain) {
 		CathNode node = getCathNode( domain.getCATH() );
-		List<CathNode> tree = new ArrayList<CathNode>();
+		List<CathNode> tree = new ArrayList<>();
 		while (node != null) {
 			node = getCathNode( node.getParentId() );
 			if (node != null) tree.add(node);
@@ -246,14 +246,14 @@ public List<CathNode> getTree(CathDomain domain) {
 	@Override
 	public List<CathDomain> filterByNodeName(String query) {
 		ensureNodeListInstalled();
-		List<CathNode> matchingNodes = new ArrayList<CathNode>();
+		List<CathNode> matchingNodes = new ArrayList<>();
 		CathNode node;
-		for ( String nodeId : cathTree.keySet() ) {
-			if ( (node = cathTree.get(nodeId) ).getDescription().startsWith(query) ) {
+		for (CathNode cathNode : cathTree.values()) {
+			if ( (node = cathNode).getDescription().startsWith(query) ) {
 				matchingNodes.add(node);
 			}
 		}
-		List<CathDomain> matches = new ArrayList<CathDomain>();
+		List<CathDomain> matches = new ArrayList<>();
 		for (CathNode n : matchingNodes) {
 			matches.addAll(getDomainsByNodeId(n.getNodeId()));
 		}
@@ -267,10 +267,10 @@ public List<CathDomain> filterByDescription(String query) {
 		} else {
 			ensureDomallInstalled();
 		}
-		List<CathDomain> matches = new ArrayList<CathDomain>();
-		for ( String k : domainMap.keySet() ) {
-			if ( domainMap.get(k).getName().startsWith(query) ) {
-				matches.add( domainMap.get(k) );
+		List<CathDomain> matches = new ArrayList<>();
+		for (CathDomain cathDomain : domainMap.values()) {
+			if (cathDomain.getName().startsWith(query) ) {
+				matches.add(cathDomain);
 			}
 		}
 		return matches;
@@ -326,10 +326,9 @@ public List<CathDomain> getDomainsByNodeId(String nodeId) {
 		} else {
 			ensureDomallInstalled();
 		}
-		List<CathDomain> domains = new ArrayList<CathDomain>();
-		for (String domainName : domainMap.keySet()) {
-			CathDomain description = domainMap.get(domainName);
-			if ( description.getCATH().startsWith(nodeId) ) {
+		List<CathDomain> domains = new ArrayList<>();
+		for (CathDomain description : domainMap.values()) {
+            if ( description.getCATH().startsWith(nodeId) ) {
 				domains.add(description);
 			}
 		}
@@ -364,7 +363,7 @@ private void parseCathDomainList(BufferedReader bufferedReader) throws IOExcepti
 			if ( pdbMap.containsKey(pdbId)){
 				domainList = pdbMap.get(pdbId);
 			} else {
-				domainList = new ArrayList<CathDomain>();
+				domainList = new ArrayList<>();
 				pdbMap.put(pdbId,domainList);
 			}
 
@@ -445,7 +444,7 @@ private void parseCathDomainDescriptionFile(BufferedReader bufferedReader) throw
 			} else if ( line.startsWith("DSEQS") ) {
 				seqs = seqs.append( line.substring(10) );
 			} else if ( line.startsWith("NSEGMENTS") ) {
-				segments = new ArrayList<CathSegment>();
+				segments = new ArrayList<>();
 			} else if ( line.startsWith("SEGMENT") ) {
 				segment = new CathSegment();
 				sseqh = new StringBuilder();
@@ -482,7 +481,7 @@ private void parseCathDomainDescriptionFile(BufferedReader bufferedReader) throw
 				if ( pdbMap.containsKey(pdbId)){
 					domainList = pdbMap.get(pdbId);
 				} else {
-					domainList = new ArrayList<CathDomain>();
+					domainList = new ArrayList<>();
 					pdbMap.put(pdbId,domainList);
 				}
 
@@ -547,15 +546,15 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{
 			if ( line.length() == 0 ) continue;
 			String[] token = line.split("\\s+");
 			String chainId = token[0];
-			Integer numberOfDomains = Integer.parseInt( token[1].substring(1) );
-			Integer numberOfFragments = Integer.parseInt( token[2].substring(1) );
+			int numberOfDomains = Integer.parseInt( token[1].substring(1) );
+			int numberOfFragments = Integer.parseInt( token[2].substring(1) );
 			int domIdx = 3;
 			int segIdx;
-			Integer sstop;
-			Integer sstart;
-			Integer fstart;
-			Integer fstop;
-			Integer flength;
+			int sstop;
+			int sstart;
+			int fstart;
+			int fstop;
+			int flength;
 			for (int i=1; i<=numberOfDomains; i++) {
 				DecimalFormat df = new DecimalFormat("00");
 				String domainId;
@@ -575,14 +574,14 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{
 					domain = domainMap.get(domainId);
 				}
 
-				Integer numberOfSegments = Integer.parseInt( token[domIdx] );
+				int numberOfSegments = Integer.parseInt( token[domIdx] );
 
 				if ( domain == null ) {
 					domIdx += 6*numberOfSegments + 1;
 					continue;
 				}
 
-				List<CathSegment> segments = new ArrayList<CathSegment>(numberOfSegments);
+				List<CathSegment> segments = new ArrayList<>(numberOfSegments);
 				segIdx = 1; // Offset from domIdx.
 				for (int j=1; j<=numberOfSegments; j++) {
 					CathSegment segment = new CathSegment();
@@ -609,7 +608,7 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{
 				domIdx += 6*numberOfSegments + 1;
 			}
 			if (parseCathFragments) {
-			List<CathFragment> fragments = new ArrayList<CathFragment>(numberOfFragments);
+			List<CathFragment> fragments = new ArrayList<>(numberOfFragments);
 				for (int i=1; i<=numberOfFragments; i++) {
 					CathFragment fragment = new CathFragment();
 					fragment.setFragmentId(i);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/Subunit.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/Subunit.java
index 58b4845213..5aef2b6357 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/Subunit.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/Subunit.java
@@ -43,11 +43,11 @@ public class Subunit {
 
 	// Optional fields for Subunit annotation
 	private String name;
-	private Structure structure;
-	private StructureIdentifier identifier;
+	private final Structure structure;
+	private final StructureIdentifier identifier;
 
 	// Required fields for Subunit definition
-	private Atom[] reprAtoms;
+	private final Atom[] reprAtoms;
 	private ProteinSequence sequence = null;
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
index d73d747cb6..9ea7474b5f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
@@ -49,7 +49,6 @@
 import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
 import org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer;
-import org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
 import org.biojava.nbio.structure.symmetry.internal.CESymmParameters;
 import org.biojava.nbio.structure.symmetry.internal.CeSymm;
@@ -80,7 +79,7 @@ public class SubunitCluster {
 
 	private List<Subunit> subunits = new ArrayList<>();
 	private List<List<Integer>> subunitEQR = new ArrayList<>();
-	private int representative = -1;
+	private int representative;
 
 	private SubunitClustererMethod method = SubunitClustererMethod.SEQUENCE;
 	private boolean pseudoStoichiometric = false;
@@ -679,9 +678,9 @@ public boolean divideInternally(SubunitClustererParameters clusterParams)
 		}
 
 		// Divide the Subunits in their repeats
-		List<Subunit> newSubunits = new ArrayList<Subunit>(subunits.size()
+		List<Subunit> newSubunits = new ArrayList<>(subunits.size()
 				* columns.size());
-		List<List<Integer>> newSubunitEQR = new ArrayList<List<Integer>>(
+		List<List<Integer>> newSubunitEQR = new ArrayList<>(
 				subunits.size() * columns.size());
 
 		for (int s = 0; s < subunits.size(); s++) {
@@ -700,7 +699,7 @@ public boolean divideInternally(SubunitClustererParameters clusterParams)
 						.get(s).getStructure()));
 
 				// Recalculate equivalent residues
-				List<Integer> eqr = new ArrayList<Integer>();
+				List<Integer> eqr = new ArrayList<>();
 				for (int p = 0; p < columns.get(r).size(); p++) {
 					eqr.add(subunitEQR.get(s).get(columns.get(r).get(p))
 							- start);
@@ -795,7 +794,7 @@ public MultipleAlignment getMultipleAlignment() throws StructureException {
 		MultipleAlignment msa = new MultipleAlignmentImpl();
 		msa.setEnsemble(new MultipleAlignmentEnsembleImpl());
 		msa.getEnsemble().setAtomArrays(
-				subunits.stream().map(s -> s.getRepresentativeAtoms())
+				subunits.stream().map(Subunit::getRepresentativeAtoms)
 						.collect(Collectors.toList()));
 
 		// Fill in the alignment information
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java
index 7060037bfc..7071a028ad 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java
@@ -66,7 +66,7 @@ public static List<Subunit> extractSubunits(Structure structure,
 			int absMinLen, double fraction, int minLen) {
 
 		// The extracted subunit container
-		List<Subunit> subunits = new ArrayList<Subunit>();
+		List<Subunit> subunits = new ArrayList<>();
 
 		for (Chain c : structure.getPolyChains()) {
 			// Only take protein chains
@@ -107,7 +107,7 @@ private static int calcAdjustedMinimumSequenceLength(
 		int minLength = Integer.MAX_VALUE;
 
 		// Extract the length List, the min and the max
-		List<Integer> lengths = new ArrayList<Integer>();
+		List<Integer> lengths = new ArrayList<>();
 		for (int i = 0; i < subunits.size(); i++) {
 			if (subunits.get(i).size() >= absMinLen) {
 				maxLength = Math.max(subunits.get(i).size(), maxLength);
@@ -123,7 +123,7 @@ private static int calcAdjustedMinimumSequenceLength(
 			return adjustedMinimumSequenceLength;
 
 		// Calculate the median of the lengths
-		double median = 0;
+		double median;
 		Collections.sort(lengths);
 		if (lengths.size() % 2 == 1) {
 			int middle = (lengths.size() - 1) / 2;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomContactSet.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomContactSet.java
index e1297faec9..ab9d1c2fa0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomContactSet.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomContactSet.java
@@ -37,12 +37,12 @@ public class AtomContactSet implements Serializable, Iterable<AtomContact> {
 
 	private static final long serialVersionUID = 1L;
 
-	private HashMap<Pair<AtomIdentifier>, AtomContact> contacts;
-	private double cutoff;
+	private final HashMap<Pair<AtomIdentifier>, AtomContact> contacts;
+	private final double cutoff;
 
 	public AtomContactSet(double cutoff) {
 		this.cutoff = cutoff;
-		this.contacts = new HashMap<Pair<AtomIdentifier>,AtomContact>();
+		this.contacts = new HashMap<>();
 	}
 
 	public void add(AtomContact contact) {
@@ -62,7 +62,7 @@ public boolean hasContact(Atom atom1, Atom atom2) {
 	}
 
 	public boolean hasContact(AtomIdentifier atomId1, AtomIdentifier atomId2) {
-		return contacts.containsKey(new Pair<AtomIdentifier>(atomId1,atomId2));
+		return contacts.containsKey(new Pair<>(atomId1, atomId2));
 	}
 
 	/**
@@ -72,9 +72,9 @@ public boolean hasContact(AtomIdentifier atomId1, AtomIdentifier atomId2) {
 	 * @return
 	 */
 	public AtomContact getContact(Atom atom1, Atom atom2) {
-		return contacts.get(new Pair<AtomIdentifier>(
-				new AtomIdentifier(atom1.getPDBserial(),atom1.getGroup().getChainId()),
-				new AtomIdentifier(atom2.getPDBserial(),atom2.getGroup().getChainId()) ));
+		return contacts.get(new Pair<>(
+				new AtomIdentifier(atom1.getPDBserial(), atom1.getGroup().getChainId()),
+				new AtomIdentifier(atom2.getPDBserial(), atom2.getGroup().getChainId())));
 	}
 
 	public int size() {
@@ -86,12 +86,13 @@ public Iterator<AtomContact> iterator() {
 		return contacts.values().iterator();
 	}
 
-	private Pair<AtomIdentifier> getAtomIdPairFromContact(AtomContact contact) {
-		Pair<AtomIdentifier> pair = new Pair<AtomIdentifier>(
-				new AtomIdentifier(contact.getPair().getFirst().getPDBserial(),contact.getPair().getFirst().getGroup().getChainId()),
-				new AtomIdentifier(contact.getPair().getSecond().getPDBserial(),contact.getPair().getSecond().getGroup().getChainId()));
-
-		return pair;
+	private static Pair<AtomIdentifier> getAtomIdPairFromContact(AtomContact contact) {
+		Pair<Atom> pair = contact.getPair();
+		Atom a = pair.getFirst();
+		Atom b = pair.getSecond();
+		return new Pair<>(
+				new AtomIdentifier(a.getPDBserial(), a.getGroup().getChainId()),
+				new AtomIdentifier(b.getPDBserial(), b.getGroup().getChainId()));
 	}
 
 	/**
@@ -132,7 +133,7 @@ public List<AtomContact> getContactsWithinDistance(double distance) {
 					String.format("%.2f", distance)+" is larger than contacts' distance cutoff "+
 					String.format("%.2f", cutoff));
 
-		List<AtomContact> list = new ArrayList<AtomContact>();
+		List<AtomContact> list = new ArrayList<>();
 		for (AtomContact contact:this.contacts.values()) {
 			if (contact.getDistance()<distance) {
 				list.add(contact);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java
index cdc124ad86..9a9b9a613e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java
@@ -139,7 +139,7 @@ public BoundingBox(BoundingBox[] boxes) {
 
 	}
 
-	private class Bound implements Comparable<Bound> {
+	private static class Bound implements Comparable<Bound> {
 		int cardinal;
 		double value;
 		public Bound(int cardinal,double value) {
@@ -181,8 +181,8 @@ public boolean overlaps(BoundingBox o, double cutoff) {
 
 	private boolean areOverlapping(double imin, double imax, double jmin, double jmax, double cutoff) {
 
-		Bound[] bounds = {new Bound(0,imin), new Bound(1,imax),
-				new Bound(2,jmin), new Bound(3,jmax)};
+		Bound[] bounds = {new Bound(0, imin), new Bound(1, imax),
+                new Bound(2, jmin), new Bound(3, jmax)};
 
 		Arrays.sort(bounds);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Contact.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Contact.java
index 1a3c169ce2..1ca67c981b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Contact.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Contact.java
@@ -31,9 +31,9 @@ public class Contact implements Serializable {
 
 	private static final long serialVersionUID = 5059569852079048728L;
 
-	private int i;
-	private int j;
-	private double distance;
+	private final int i;
+	private final int j;
+	private final double distance;
 
 	public Contact(int i, int j, double distance) {
 		this.i = i;
@@ -42,7 +42,7 @@ public Contact(int i, int j, double distance) {
 	}
 
 	public Pair<Integer> getIndexPair() {
-		return new Pair<Integer>(i,j);
+		return new Pair<>(i, j);
 	}
 
 	public int getI() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java
index 0047385ab2..9fa884df10 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java
@@ -65,8 +65,8 @@ public class Grid {
 
 	private GridCell[][][] cells;
 
-	private double cutoff;
-	private int cellSize;
+	private final double cutoff;
+	private final int cellSize;
 
 	private Point3d[] iAtoms;
 	private Point3d[] jAtoms;
@@ -386,12 +386,12 @@ public AtomContactSet getAtomContacts() {
 
 		if (jAtomObjects == null) {
 			for (Contact cont : list) {
-				contacts.add(new AtomContact(new Pair<Atom>(iAtomObjects[cont.getI()],iAtomObjects[cont.getJ()]),cont.getDistance()));
+				contacts.add(new AtomContact(new Pair<>(iAtomObjects[cont.getI()], iAtomObjects[cont.getJ()]),cont.getDistance()));
 			}
 
 		} else {
 			for (Contact cont : list) {
-				contacts.add(new AtomContact(new Pair<Atom>(iAtomObjects[cont.getI()],jAtomObjects[cont.getJ()]),cont.getDistance()));
+				contacts.add(new AtomContact(new Pair<>(iAtomObjects[cont.getI()], jAtomObjects[cont.getJ()]),cont.getDistance()));
 			}
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java
index 5123831ec6..f025ac5fda 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java
@@ -35,13 +35,13 @@
 public class GridCell {
 
 
-	private Grid grid;
-	private ArrayList<Integer> iIndices;
-	private ArrayList<Integer> jIndices;
+	private final Grid grid;
+	private final ArrayList<Integer> iIndices;
+	private final ArrayList<Integer> jIndices;
 
 	public GridCell(Grid parent){
-		iIndices = new ArrayList<Integer>();
-		jIndices = new ArrayList<Integer>();
+		iIndices = new ArrayList<>();
+		jIndices = new ArrayList<>();
 		this.grid = parent;
 	}
 
@@ -70,7 +70,7 @@ public int getNumJindices() {
 	 */
 	public List<Contact> getContactsWithinCell(){
 
-		List<Contact> contacts = new ArrayList<Contact>();
+		List<Contact> contacts = new ArrayList<>();
 
 		Point3d[] iAtoms = grid.getIAtoms();
 		Point3d[] jAtoms = grid.getJAtoms();
@@ -110,7 +110,7 @@ public List<Contact> getContactsWithinCell(){
 	 */
 	public List<Contact> getContactsToOtherCell(GridCell otherCell){
 
-		List<Contact> contacts = new ArrayList<Contact>();
+		List<Contact> contacts = new ArrayList<>();
 
 		Point3d[] iAtoms = grid.getIAtoms();
 		Point3d[] jAtoms = grid.getJAtoms();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java
index 16c0eb08c5..8740f8bdf9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java
@@ -38,10 +38,10 @@ public class GroupContact implements Serializable {
 
 	private Pair<Group> pair;
 
-	private List<AtomContact> atomContacts;
+	private final List<AtomContact> atomContacts;
 
 	public GroupContact() {
-		atomContacts = new ArrayList<AtomContact>();
+		atomContacts = new ArrayList<>();
 	}
 
 	public void addAtomContact(AtomContact atomContact) {
@@ -82,7 +82,7 @@ public List<AtomContact> getAtomContacts() {
 	 */
 	public List<AtomContact> getContactsWithinDistance(double distance) {
 
-		List<AtomContact> list = new ArrayList<AtomContact>();
+		List<AtomContact> list = new ArrayList<>();
 		for (AtomContact contact:this.atomContacts) {
 			if (contact.getDistance()<distance) {
 				list.add(contact);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContactSet.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContactSet.java
index 625766b46b..ed9e1a2d73 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContactSet.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContactSet.java
@@ -40,10 +40,10 @@ public class GroupContactSet implements Serializable, Iterable<GroupContact>{
 
 	private static final long serialVersionUID = 1L;
 
-	private HashMap<Pair<ResidueIdentifier>, GroupContact> contacts;
+	private final HashMap<Pair<ResidueIdentifier>, GroupContact> contacts;
 
 	public GroupContactSet() {
-		contacts = new HashMap<Pair<ResidueIdentifier>, GroupContact>();
+		contacts = new HashMap<>();
 	}
 
 	/**
@@ -52,7 +52,7 @@ public GroupContactSet() {
 	 * @param atomContacts
 	 */
 	public GroupContactSet(AtomContactSet atomContacts) {
-		contacts = new HashMap<Pair<ResidueIdentifier>, GroupContact>();
+		contacts = new HashMap<>();
 		atoms2groups(atomContacts);
 	}
 
@@ -69,8 +69,8 @@ private void atoms2groups(AtomContactSet atomContacts) {
 			// we skip the self-residue contacts
 			if (iResidue.equals(jResidue)) continue;
 
-			Pair<Group> residuePair = new Pair<Group> (iResidue, jResidue);
-			Pair<ResidueIdentifier> pair = new Pair<ResidueIdentifier>(new ResidueIdentifier(iResidue), new ResidueIdentifier(jResidue));
+			Pair<Group> residuePair = new Pair<>(iResidue, jResidue);
+			Pair<ResidueIdentifier> pair = new Pair<>(new ResidueIdentifier(iResidue), new ResidueIdentifier(jResidue));
 
 			if (!contacts.containsKey(pair)) {
 
@@ -114,7 +114,7 @@ public boolean hasContact(Group group1, Group group2) {
 	 * @return
 	 */
 	public boolean hasContact(ResidueNumber resNumber1, ResidueNumber resNumber2) {
-		return contacts.containsKey(new Pair<ResidueNumber>(resNumber1, resNumber2));
+		return contacts.containsKey(new Pair<>(resNumber1, resNumber2));
 	}
 
 	/**
@@ -128,7 +128,7 @@ public boolean hasContact(ResidueNumber resNumber1, ResidueNumber resNumber2) {
 	 */
 	public boolean hasContact(ResidueIdentifier resId1, ResidueIdentifier resId2) {
 
-		return contacts.containsKey(new Pair<ResidueIdentifier>(resId1, resId2));
+		return contacts.containsKey(new Pair<>(resId1, resId2));
 	}
 
 	/**
@@ -139,7 +139,7 @@ public boolean hasContact(ResidueIdentifier resId1, ResidueIdentifier resId2) {
 	 */
 	public GroupContact getContact(Group group1, Group group2) {
 		return contacts.get(
-				new Pair<ResidueNumber>(group1.getResidueNumber(),group2.getResidueNumber()));
+				new Pair<>(group1.getResidueNumber(), group2.getResidueNumber()));
 	}
 
 	public int size() {
@@ -152,9 +152,9 @@ public Iterator<GroupContact> iterator() {
 	}
 
 	private Pair<ResidueIdentifier> getResIdPairFromContact(GroupContact groupContact) {
-		return new Pair<ResidueIdentifier>(
+		return new Pair<>(
 				new ResidueIdentifier(groupContact.getPair().getFirst()),
-				new ResidueIdentifier(groupContact.getPair().getSecond()) );
+				new ResidueIdentifier(groupContact.getPair().getSecond()));
 
 	}
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Pair.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Pair.java
index 88f7d01b17..23a2cac4aa 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Pair.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Pair.java
@@ -35,8 +35,8 @@ public final class Pair<T> implements Serializable {
 
 	private static final long serialVersionUID = 1L;
 
-	private T first;
-	private T second;
+	private final T first;
+	private final T second;
 
 	/**
 	 * Creates a <code>Pair</code> from the specified elements.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
index e9150fcfbe..e2d3183db7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
@@ -285,12 +285,8 @@ protected Atom[] getAtomsForAsa(int cofactorSizeToUse) {
 		Atom[] atoms2 = getSecondAtomsForAsa(cofactorSizeToUse);
 
 		Atom[] atoms = new Atom[atoms1.length+atoms2.length];
-		for (int i=0;i<atoms1.length;i++) {
-			atoms[i] = atoms1[i];
-		}
-		for (int i=0;i<atoms2.length;i++) {
-			atoms[i+atoms1.length] = atoms2[i];
-		}
+		System.arraycopy(atoms1, 0, atoms, 0, atoms1.length);
+		System.arraycopy(atoms2, 0, atoms, 0 + atoms1.length, atoms2.length);
 
 		return atoms;
 	}
@@ -321,7 +317,7 @@ private static final Atom[] getAllNonHAtomArray(Atom[] m, int minSizeHetAtomToIn
 			atoms.add(a);
 
 		}
-		return atoms.toArray(new Atom[atoms.size()]);
+		return atoms.toArray(new Atom[0]);
 	}
 
 	/**
@@ -458,8 +454,8 @@ public GroupAsa getSecondGroupAsa(ResidueNumber resNum) {
 	 */
 	public Pair<List<Group>> getCoreResidues(double bsaToAsaCutoff, double minAsaForSurface) {
 
-		List<Group> core1 = new ArrayList<Group>();
-		List<Group> core2 = new ArrayList<Group>();
+		List<Group> core1 = new ArrayList<>();
+		List<Group> core2 = new ArrayList<>();
 
 		for (GroupAsa groupAsa:groupAsas1.values()) {
 
@@ -482,7 +478,7 @@ public Pair<List<Group>> getCoreResidues(double bsaToAsaCutoff, double minAsaFor
 			}
 		}
 
-		return new Pair<List<Group>>(core1, core2);
+		return new Pair<>(core1, core2);
 	}
 
 	/**
@@ -494,8 +490,8 @@ public Pair<List<Group>> getCoreResidues(double bsaToAsaCutoff, double minAsaFor
 	 */
 	public Pair<List<Group>> getRimResidues(double bsaToAsaCutoff, double minAsaForSurface) {
 
-		List<Group> rim1 = new ArrayList<Group>();
-		List<Group> rim2 = new ArrayList<Group>();
+		List<Group> rim1 = new ArrayList<>();
+		List<Group> rim2 = new ArrayList<>();
 
 		for (GroupAsa groupAsa:groupAsas1.values()) {
 
@@ -518,7 +514,7 @@ public Pair<List<Group>> getRimResidues(double bsaToAsaCutoff, double minAsaForS
 			}
 		}
 
-		return new Pair<List<Group>>(rim1, rim2);
+		return new Pair<>(rim1, rim2);
 	}
 
 	/**
@@ -529,8 +525,8 @@ public Pair<List<Group>> getRimResidues(double bsaToAsaCutoff, double minAsaForS
 	 */
 	public Pair<List<Group>> getInterfacingResidues(double minAsaForSurface) {
 
-		List<Group> interf1 = new ArrayList<Group>();
-		List<Group> interf2 = new ArrayList<Group>();
+		List<Group> interf1 = new ArrayList<>();
+		List<Group> interf2 = new ArrayList<>();
 
 		for (GroupAsa groupAsa:groupAsas1.values()) {
 
@@ -545,7 +541,7 @@ public Pair<List<Group>> getInterfacingResidues(double minAsaForSurface) {
 			}
 		}
 
-		return new Pair<List<Group>>(interf1, interf2);
+		return new Pair<>(interf1, interf2);
 	}
 
 	/**
@@ -554,8 +550,8 @@ public Pair<List<Group>> getInterfacingResidues(double minAsaForSurface) {
 	 * @return
 	 */
 	public Pair<List<Group>> getSurfaceResidues(double minAsaForSurface) {
-		List<Group> surf1 = new ArrayList<Group>();
-		List<Group> surf2 = new ArrayList<Group>();
+		List<Group> surf1 = new ArrayList<>();
+		List<Group> surf2 = new ArrayList<>();
 
 		for (GroupAsa groupAsa:groupAsas1.values()) {
 
@@ -570,7 +566,7 @@ public Pair<List<Group>> getSurfaceResidues(double minAsaForSurface) {
 			}
 		}
 
-		return new Pair<List<Group>>(surf1, surf2);
+		return new Pair<>(surf1, surf2);
 	}
 
 	public StructureInterfaceCluster getCluster() {
@@ -619,8 +615,8 @@ public double getContactOverlapScore(StructureInterface other, boolean invert) {
 			return 0;
 		}
 
-		Pair<EntityInfo> thisCompounds = new Pair<EntityInfo>(thisChains.getFirst().getEntityInfo(), thisChains.getSecond().getEntityInfo());
-		Pair<EntityInfo> otherCompounds = new Pair<EntityInfo>(otherChains.getFirst().getEntityInfo(), otherChains.getSecond().getEntityInfo());
+		Pair<EntityInfo> thisCompounds = new Pair<>(thisChains.getFirst().getEntityInfo(), thisChains.getSecond().getEntityInfo());
+		Pair<EntityInfo> otherCompounds = new Pair<>(otherChains.getFirst().getEntityInfo(), otherChains.getSecond().getEntityInfo());
 
 		if ( (  (thisCompounds.getFirst() == otherCompounds.getFirst()) &&
 				(thisCompounds.getSecond() == otherCompounds.getSecond())   )  ||
@@ -633,8 +629,8 @@ public double getContactOverlapScore(StructureInterface other, boolean invert) {
 
 			for (GroupContact thisContact:thisContacts) {
 
-				ResidueIdentifier first = null;
-				ResidueIdentifier second = null;
+				ResidueIdentifier first;
+				ResidueIdentifier second;
 
 				if (!invert) {
 					first = new ResidueIdentifier(thisContact.getPair().getFirst());
@@ -691,7 +687,7 @@ public Pair<Chain> getParentChains() {
 			return null;
 		}
 
-		return new Pair<Chain>(firstMol[0].getGroup().getChain(), secondMol[0].getGroup().getChain());
+		return new Pair<>(firstMol[0].getGroup().getChain(), secondMol[0].getGroup().getChain());
 	}
 
 	/**
@@ -704,7 +700,7 @@ public Pair<EntityInfo> getParentCompounds() {
 			logger.warn("Could not find parents chains, compounds will be null");
 			return null;
 		}
-		return new Pair<EntityInfo>(chains.getFirst().getEntityInfo(), chains.getSecond().getEntityInfo());
+		return new Pair<>(chains.getFirst().getEntityInfo(), chains.getSecond().getEntityInfo());
 	}
 
 	private Structure getParentStructure() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceCluster.java
index 5b1699bf8a..8743cdff9a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceCluster.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceCluster.java
@@ -40,7 +40,7 @@ public class StructureInterfaceCluster implements Serializable {
 
 
 	public StructureInterfaceCluster() {
-		this.members = new ArrayList<StructureInterface>();
+		this.members = new ArrayList<>();
 	}
 
 	public List<StructureInterface> getMembers() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
index 8bc0b627d0..8211c61688 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
@@ -74,7 +74,7 @@ public class StructureInterfaceList implements Serializable, Iterable<StructureI
 
 	private static final long serialVersionUID = 1L;
 
-	private List<StructureInterface> list;
+	private final List<StructureInterface> list;
 
 	private List<StructureInterfaceCluster> clusters = null;
 	private List<StructureInterfaceCluster> clustersNcs = null;
@@ -164,11 +164,12 @@ public void calcAsas(int nSpherePoints, int nThreads, int cofactorSizeToUse) {
 		long start = System.currentTimeMillis();
 
 		// we only need to calculate ASA for that subset (any translation of those will have same values)
-		for (String molecId:uniqAsaChains.keySet()) {
+		for (Map.Entry<String, Atom[]> entry : uniqAsaChains.entrySet()) {
+            String molecId = entry.getKey();
 
-			logger.debug("Calculating uncomplexed ASA for molecId {}, with {} atoms", molecId, uniqAsaChains.get(molecId).length);
+            logger.debug("Calculating uncomplexed ASA for molecId {}, with {} atoms", molecId, entry.getValue().length);
 
-			AsaCalculator asaCalc = new AsaCalculator(uniqAsaChains.get(molecId),
+			AsaCalculator asaCalc = new AsaCalculator(entry.getValue(),
 					AsaCalculator.DEFAULT_PROBE_SIZE, nSpherePoints, nThreads);
 
 			double[] atomAsas = asaCalc.calculateAsas();
@@ -398,9 +399,9 @@ public List<StructureInterfaceCluster> getClusters(double contactOverlapScoreClu
 		SingleLinkageClusterer slc = new SingleLinkageClusterer(matrix, true);
 
 		Map<Integer, Set<Integer>> clusteredIndices = slc.getClusters(contactOverlapScoreClusterCutoff);
-		for (int clusterIdx:clusteredIndices.keySet()) {
+		for (Set<Integer> integers : clusteredIndices.values()) {
 			List<StructureInterface> members = new ArrayList<>();
-			for (int idx:clusteredIndices.get(clusterIdx)) {
+			for (int idx: integers) {
 				members.add(list.get(idx));
 			}
 			StructureInterfaceCluster cluster = new StructureInterfaceCluster();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/AssignmentXMLSerializer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/AssignmentXMLSerializer.java
index d6a75c6560..8f29abedee 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/AssignmentXMLSerializer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/AssignmentXMLSerializer.java
@@ -55,7 +55,7 @@ public class AssignmentXMLSerializer {
 	}
 
 	public AssignmentXMLSerializer(){
-		assignments = new HashMap<String, String>();
+		assignments = new HashMap<>();
 
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/DomainProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/DomainProvider.java
index 044aaba4a5..c736af4eb3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/DomainProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/DomainProvider.java
@@ -37,7 +37,7 @@ public interface DomainProvider {
 	 * @throws IOException For IO errors getting the domains
 	 * @throws StructureException For errors converting name to a valid identifier
 	 */
-	public SortedSet<String> getDomainNames(String name) throws IOException, StructureException;
+    SortedSet<String> getDomainNames(String name) throws IOException, StructureException;
 	/**
 	 * Get the full list of representative domains for the PDB.
 	 *
@@ -46,5 +46,5 @@ public interface DomainProvider {
 	 * @return A full list of all representative domains recognized by this provider
 	 * @throws IOException For IO errors getting the representatives
 	 */
-	public SortedSet<String> getRepresentativeDomains() throws IOException;
+    SortedSet<String> getRepresentativeDomains() throws IOException;
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java
index adb7f2f6bf..a333ff6fe9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java
@@ -46,8 +46,8 @@ public class PDBDomainProvider implements DomainProvider{
 	public static final String DEFAULT_PDB_HOST = "http://www.rcsb.org";
 	public static final String DEFAULT_PDB_API_URL = DEFAULT_PDB_HOST + "/pdb/rest/";
 
-	private String base;
-	private int cutoff;
+	private final String base;
+	private final int cutoff;
 
 	/**
 	 */
@@ -95,11 +95,11 @@ private SortedSet<String> requestRepresentativeDomains(String url) {
 
 			//System.out.println(url);
 
-			final SortedSet<String> results = new TreeSet<String>();
+			final SortedSet<String> results = new TreeSet<>();
 			DefaultHandler handler = new DefaultHandler() {
 				@Override
 				public void startElement(String uri, String localName,String qName,
-						Attributes attributes) throws SAXException {
+						Attributes attributes) {
 
 					//System.out.println("Start Element :" + qName);
 
@@ -111,13 +111,7 @@ public void startElement(String uri, String localName,String qName,
 			};
 			handleRestRequest(url,handler);
 			return results;
-		} catch (MalformedURLException e) {
-			e.printStackTrace();
-		} catch (IOException e) {
-			e.printStackTrace();
-		} catch (SAXException e) {
-			e.printStackTrace();
-		} catch (ParserConfigurationException e) {
+		} catch (ParserConfigurationException | SAXException | IOException e) {
 			e.printStackTrace();
 		}
 		return null;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java
index fe3f6b6beb..2b108bf41e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java
@@ -35,8 +35,8 @@
 public class PDPDomain implements StructureIdentifier {
 	private static final long serialVersionUID = 6894463080739943026L;
 
-	private String identifier;
-	private SubstructureIdentifier canonical;
+	private final String identifier;
+	private final SubstructureIdentifier canonical;
 
 	public static final Pattern PDP_NAME_PATTERN = Pattern.compile("^(?:PDP:)([0-9][a-z0-9]{3})(\\w)(\\w)$",Pattern.CASE_INSENSITIVE);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPProvider.java
index d621373bb1..79e91bc835 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPProvider.java
@@ -48,7 +48,7 @@ public interface PDPProvider {
 	 * @return Set of domain names, e.g. "PDP:4HHBAa"
 	 * @throws IOException
 	 */
-	public SortedSet<String> getPDPDomainNamesForPDB(String pdbId) throws IOException;
+    SortedSet<String> getPDPDomainNamesForPDB(String pdbId) throws IOException;
 	/**
 	 * Get the structure for a particular PDP domain
 	 * @param pdpDomainName PDP identifier, e.g. "PDP:4HHBAa"
@@ -57,7 +57,7 @@ public interface PDPProvider {
 	 * @throws IOException For IO errors, e.g. when parsing PDP information
 	 * @throws StructureException For errors creating the structure
 	 */
-	public Structure getDomain(String pdpDomainName, AtomCache cache) throws IOException, StructureException;
+    Structure getDomain(String pdpDomainName, AtomCache cache) throws IOException, StructureException;
 	/**
 	 * Get a StructureIdentifier representing the specified PDP domain.
 	 *
@@ -65,5 +65,5 @@ public interface PDPProvider {
 	 * @return a PDPDomain representing this domain name
 	 * @throws IOException
 	 */
-	public PDPDomain getPDPDomain(String pdpDomainName) throws IOException;
+    PDPDomain getPDPDomain(String pdpDomainName) throws IOException;
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java
index 5d5aaaefd6..9e8eda55e7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java
@@ -24,10 +24,7 @@
 import java.io.InputStream;
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.util.List;
-import java.util.Map;
-import java.util.SortedSet;
-import java.util.TreeSet;
+import java.util.*;
 
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.client.JFatCatClient;
@@ -58,7 +55,7 @@ public class RemoteDomainProvider extends SerializableCache<String,SortedSet<Str
 	ScopDatabase scop;
 	PDPProvider pdp;
 
-	private static String CACHE_FILE_NAME = "remotedomaincache.ser";
+	private static final String CACHE_FILE_NAME = "remotedomaincache.ser";
 
 
 	public RemoteDomainProvider(){
@@ -95,7 +92,7 @@ public RemoteDomainProvider(boolean cache) throws IOException{
 	 *
 	 */
 	private void loadRepresentativeDomainAssignments() throws IOException {
-		AssignmentXMLSerializer results = null;
+		AssignmentXMLSerializer results;
 		try {
 			URL u = new URL(url + "getRepresentativeDomains");
 			logger.info("Fetching {}",u);
@@ -105,19 +102,16 @@ private void loadRepresentativeDomainAssignments() throws IOException {
 
 			Map<String,String> data = results.getAssignments();
 			logger.info("got {} ranges from server.",data.size());
-			for (String key: data.keySet()){
-				String range = data.get(key);
+			for (Map.Entry<String, String> entry : data.entrySet()){
+				String range = entry.getValue();
 
 				// work around list in results;
 
 				String[] spl = range.split(",");
-				SortedSet<String> value = new TreeSet<String>();
+				SortedSet<String> value = new TreeSet<>();
 
-				for (String s : spl){
-					value.add(s);
-
-				}
-				serializedCache.put(key, value);
+                value.addAll(Arrays.asList(spl));
+				serializedCache.put(entry.getKey(), value);
 			}
 
 		} catch (MalformedURLException e){
@@ -150,7 +144,7 @@ public SortedSet<String> getDomainNames(String name) throws IOException, Structu
 			cache(name,data);
 			return data;
 		} else {
-			SortedSet<String> r = new TreeSet<String>();
+			SortedSet<String> r = new TreeSet<>();
 			for ( ScopDomain d: scopDomains){
 				StructureName s = new StructureName(d.getScopId());
 
@@ -176,7 +170,7 @@ public SortedSet<String> getDomainNames(String name) throws IOException, Structu
 	private SortedSet<String> getPDPDomains(StructureName n) throws IOException, StructureException {
 		SortedSet<String> pdpDomains = pdp.getPDPDomainNamesForPDB(n.getPdbId());
 
-		SortedSet<String> r = new TreeSet<String>();
+		SortedSet<String> r = new TreeSet<>();
 		String chainID = n.getChainId();
 		for ( String s : pdpDomains){
 			StructureName d = new StructureName(s);
@@ -213,7 +207,7 @@ public void flushCache() {
 	public SortedSet<String> getRepresentativeDomains() throws IOException {
 
 		String url = "http://source.rcsb.org/jfatcatserver/domains/getRepresentativeDomainNames";
-		SortedSet<String> domainRanges = null;
+		SortedSet<String> domainRanges;
 		try {
 			URL u = new URL(url);
 			logger.info("Fetching {}",url);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
index d45a0285bd..30882691f9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
@@ -28,11 +28,7 @@
 import java.io.InputStream;
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.SortedSet;
-import java.util.TreeSet;
+import java.util.*;
 
 import org.biojava.nbio.structure.ResidueRange;
 import org.biojava.nbio.structure.Structure;
@@ -59,7 +55,7 @@ public class RemotePDPProvider extends SerializableCache<String,SortedSet<String
 
 	String server = DEFAULT_SERVER;
 
-	private static String CACHE_FILE_NAME = "remotepdpdomaindefs.ser";
+	private static final String CACHE_FILE_NAME = "remotepdpdomaindefs.ser";
 
 
 	public static void main(String[] args) throws IOException, StructureException{
@@ -111,7 +107,7 @@ public RemotePDPProvider(boolean useCache) throws IOException {
 	 */
 	private void loadRepresentativeDomains() throws IOException {
 
-		AssignmentXMLSerializer results = null;
+		AssignmentXMLSerializer results;
 		try {
 			URL u = new URL(server + "getRepresentativePDPDomains");
 			logger.info("Fetching {}",u);
@@ -121,19 +117,16 @@ private void loadRepresentativeDomains() throws IOException {
 
 			Map<String,String> data = results.getAssignments();
 			logger.info("got {} domain ranges for PDP domains from server.",data.size());
-			for (String key: data.keySet()){
-				String range = data.get(key);
+			for (Map.Entry<String, String> entry : data.entrySet()){
+				String range = entry.getValue();
 
 				// work around list in results;
 
 				String[] spl = range.split(",");
-				SortedSet<String> value = new TreeSet<String>();
+				SortedSet<String> value = new TreeSet<>();
 
-				for (String s : spl){
-					value.add(s);
-
-				}
-				serializedCache.put(key, value);
+                value.addAll(Arrays.asList(spl));
+				serializedCache.put(entry.getKey(), value);
 			}
 
 		} catch (MalformedURLException e){
@@ -200,7 +193,7 @@ public PDPDomain getPDPDomain(String pdpDomainName) throws IOException{
 		}
 
 		String pdbId = null;
-		List<ResidueRange> ranges = new ArrayList<ResidueRange>();
+		List<ResidueRange> ranges = new ArrayList<>();
 		for(String domainRange : domainRanges) {
 			SubstructureIdentifier strucId = new SubstructureIdentifier(domainRange);
 			if(pdbId == null) {
@@ -244,7 +237,7 @@ private boolean checkDomainRanges(SortedSet<String> domainRanges) {
 	 */
 	@Override
 	public SortedSet<String> getPDPDomainNamesForPDB(String pdbId) throws IOException{
-		SortedSet<String> results = null;
+		SortedSet<String> results;
 		try {
 			URL u = new URL(server + "getPDPDomainNamesForPDB?pdbId="+pdbId);
 			logger.info("Fetching {}",u);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/SerializableCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/SerializableCache.java
index b653b73d52..7377f82a7f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/SerializableCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/SerializableCache.java
@@ -117,7 +117,7 @@ public Map<K,V> reloadFromFile() {
 
 		File f = getCacheFile();
 
-		serializedCache = new HashMap<K,V>();
+		serializedCache = new HashMap<>();
 
 		// has never been cached here before
 		if( ! f.exists()) {
@@ -133,13 +133,10 @@ public Map<K,V> reloadFromFile() {
 			ObjectInputStream ois = new ObjectInputStream(fis);
 			serializedCache = (HashMap<K,V>) ois.readObject();
 			ois.close();
-		} catch (IOException e){
+		} catch (IOException | ClassNotFoundException e){
 			// TODO shouldn't this be thrown forward?
 			logger.error("Exception caught while reading serialized file",e);
 			return null;
-		} catch (ClassNotFoundException e) {
-			logger.error("Exception caught while reading serialized file",e);
-			return null;
 		}
 
 		//if ( debug )
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java
index 9c80bc8b3a..345e849c74 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java
@@ -28,7 +28,7 @@
 public class ClusterDomains {
 
 
-	static private boolean verbose = CutDomain.verbose;
+	static private final boolean verbose = CutDomain.verbose;
 
 	private static int ndom;
 	public static List<Domain> cluster(List<Domain> domains, PDPDistanceMatrix pdpDistMatrix){
@@ -43,7 +43,7 @@ public static List<Domain> cluster(List<Domain> domains, PDPDistanceMatrix pdpDi
 		int Sim = -1;
 		int Sjm = -1;
 
-		long total_max_contacts = 0;
+		long total_max_contacts;
 
 		double maximum_values = PDPParameters.CUT_OFF_VALUE1S;
 		double maximum_valuem = PDPParameters.CUT_OFF_VALUE1M;
@@ -226,7 +226,7 @@ private static List<Domain> combine(List<Domain> domains,int Si, int Sj, double
 		if ( verbose)
 			System.out.println("  +++  combining domains " + Si + " " + Sj);
 
-		List<Domain> newdoms = new ArrayList<Domain>();
+		List<Domain> newdoms = new ArrayList<>();
 
 		//int ndom = domains.size();
 		for(int i=0;i<domains.get(Sj).nseg;i++) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Cut.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Cut.java
index 38bace0f14..a845ce1304 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Cut.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Cut.java
@@ -28,7 +28,7 @@ public class Cut {
 
 	static boolean verbose = CutDomain.verbose;
 
-	public int cut( Atom[] ca, Domain dom, CutValues val, int[][] dist, PDPDistanceMatrix pdpMatrix) {
+	public static int cut(Atom[] ca, Domain dom, CutValues val, int[][] dist, PDPDistanceMatrix pdpMatrix) {
 
 		int nclose = pdpMatrix.getNclose();
 
@@ -59,7 +59,7 @@ public int cut( Atom[] ca, Domain dom, CutValues val, int[][] dist, PDPDistanceM
 
 		List<Segment> segments = dom.getSegments();
 
-		java.util.Collections.sort(segments, new SegmentComparator());
+		segments.sort(new SegmentComparator());
 
 		if ( verbose)
 			System.out.println("  ---  Cut.cut " + dom + " ");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/CutDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/CutDomain.java
index 839fdec1c4..d16bfe6c30 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/CutDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/CutDomain.java
@@ -43,7 +43,7 @@ public CutDomain(Atom[]ca, PDPDistanceMatrix pdpMatrix){
 
 		ndom = 0;
 
-		domains = new ArrayList<Domain>();
+		domains = new ArrayList<>();
 
 	}
 
@@ -69,7 +69,7 @@ public  void cutDomain(Domain dom, CutSites cut_sites, PDPDistanceMatrix pdpMatr
 
 		Cut cut = new Cut();
 
-		site = cut.cut(ca,dom,val, dist, pdpMatrix);
+		site = Cut.cut(ca,dom,val, dist, pdpMatrix);
 		if ( verbose )
 		System.out.println("  S ... site " + dom + " : site: " + site + " val : " + val);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Domain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Domain.java
index 878ec29686..c721fc5349 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Domain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Domain.java
@@ -48,7 +48,7 @@ public class Domain implements Comparable<Domain>, Serializable{
 	int nseg;
 	double score;
 
-	List<Segment>segments = new ArrayList<Segment>();
+	List<Segment>segments = new ArrayList<>();
 
 	public Domain(){
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java
index be3ff6a987..1bdad14a7c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java
@@ -30,7 +30,7 @@ public class GetDistanceMatrix {
 	 *
 	 * @param protein
 	 */
-	public  PDPDistanceMatrix getDistanceMatrix(Atom[] protein) throws StructureException{
+	public  PDPDistanceMatrix getDistanceMatrix(Atom[] protein) {
 		int[][] dist = new int[protein.length+3][protein.length+3];
 		int i,j;
 		double d,dt1,dt2,dt3,dt4;
@@ -69,7 +69,7 @@ public  PDPDistanceMatrix getDistanceMatrix(Atom[] protein) throws StructureExce
 					d+= distance*distance;
 				}
 				else if(hasCbeta1 && ! hasCbeta2) {
-					double distance = 999;
+					double distance;
 
 					distance = Calc.getDistance(cb1, ca2);
 					d += distance * distance;
@@ -157,7 +157,7 @@ else if(i>3&&j<protein.length-3) {
 
 
 	private Atom getCBeta(Group g1) {
-		Atom cb = null;
+		Atom cb;
 
 
 		cb = g1.getAtom("CB");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDatabase.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDatabase.java
index d9170766b7..bc6b28d482 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDatabase.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDatabase.java
@@ -34,7 +34,7 @@ public interface EcodDatabase {
 	 * @return version
 	 * @throws IOException
 	 */
-	public String getVersion() throws IOException;
+    String getVersion() throws IOException;
 
 	/**
 	 * Get a particular ECOD domain by the domain ID (e.g. "e4hhbA1")
@@ -42,7 +42,7 @@ public interface EcodDatabase {
 	 * @return
 	 * @throws IOException
 	 */
-	public EcodDomain getDomainsById(String ecodId) throws IOException;
+    EcodDomain getDomainsById(String ecodId) throws IOException;
 
 	/**
 	 * Get a list of all ECOD domains for a particular PDB ID
@@ -50,7 +50,7 @@ public interface EcodDatabase {
 	 * @return the list of domains, or null if no matching domains were found
 	 * @throws IOException
 	 */
-	public List<EcodDomain> getDomainsForPdb(String pdbId) throws IOException;
+    List<EcodDomain> getDomainsForPdb(String pdbId) throws IOException;
 
 	/**
 	 * Get a list of domains within a particular level of the hierarchy
@@ -59,12 +59,12 @@ public interface EcodDatabase {
 	 * @return
 	 * @throws IOException
 	 */
-	public List<EcodDomain> filterByHierarchy(String hierarchy) throws IOException;
+    List<EcodDomain> filterByHierarchy(String hierarchy) throws IOException;
 
 	/**
 	 * Get all ECOD domains
 	 * @return
 	 * @throws IOException
 	 */
-	public List<EcodDomain> getAllDomains() throws IOException;
+    List<EcodDomain> getAllDomains() throws IOException;
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java
index 55ce880ec2..d09a906343 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java
@@ -150,13 +150,13 @@ public EcodDomain(EcodDomain o) {
 		this.tGroupName = o.tGroupName;
 		this.fGroupName = o.fGroupName;
 		this.assemblyId = o.assemblyId;
-		this.ligands = new HashSet<String>(o.ligands);
+		this.ligands = new HashSet<>(o.ligands);
 	}
 
 
 
 	@Override
-	protected Object clone() throws CloneNotSupportedException {
+	protected Object clone() {
 		return new EcodDomain(this);
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
index 89791c59e1..1ecf094845 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
@@ -49,8 +49,8 @@ public class EcodFactory {
 
 	public static final String DEFAULT_VERSION = EcodInstallation.DEFAULT_VERSION;
 
-	private static Map<String, SoftReference<EcodDatabase>> versionedEcodDBs =
-			Collections.synchronizedMap(new HashMap<String, SoftReference<EcodDatabase>>());
+	private static final Map<String, SoftReference<EcodDatabase>> versionedEcodDBs =
+			Collections.synchronizedMap(new HashMap<>());
 	private static String defaultVersion = EcodInstallation.DEFAULT_VERSION;
 
 	/**
@@ -79,13 +79,13 @@ public static EcodDatabase getEcodDatabase(String version) {
 				logger.debug("Creating new {}, version {}",EcodInstallation.class.getSimpleName(),version);
 				String cacheDir = new UserConfiguration().getCacheFilePath();
 				ecod = new EcodInstallation(cacheDir, version);
-				versionedEcodDBs.put(version.toLowerCase(), new SoftReference<EcodDatabase>(ecod));
+				versionedEcodDBs.put(version.toLowerCase(), new SoftReference<>(ecod));
 
 				// If the parsed version differed from that requested, add that too
 				// Note that getVersion() may trigger file parsing
 				try {
 					if( ! versionedEcodDBs.containsKey(ecod.getVersion().toLowerCase()) ) {
-						versionedEcodDBs.put(ecod.getVersion().toLowerCase(),new SoftReference<EcodDatabase>(ecod));
+						versionedEcodDBs.put(ecod.getVersion().toLowerCase(), new SoftReference<>(ecod));
 					}
 				} catch (IOException e) {
 					// For parsing errors, just use the requested version
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
index 836d19f107..e229da576e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
@@ -77,12 +77,12 @@ public class EcodInstallation implements EcodDatabase {
 
 
 	private String cacheLocation;
-	private String requestedVersion; // version requested, e.g. "latest". Used for the paths
+	private final String requestedVersion; // version requested, e.g. "latest". Used for the paths
 	private String parsedVersion; // actual version parsed
 
 	// lock to prevent multiple threads from downloading simultaneously
 	// Should hold the lock when reading/writing allDomains or domainMap
-	private ReadWriteLock domainsFileLock;
+	private final ReadWriteLock domainsFileLock;
 	private List<EcodDomain> allDomains;
 	private Map<String,List<EcodDomain>> domainMap;//PDB ID -> domains, lazily constructed from allDomains
 
@@ -148,7 +148,7 @@ public List<EcodDomain> getDomainsForPdb(String pdbId) throws IOException {
 				return null;
 			}
 			// Deep clone
-			List<EcodDomain> clonedDoms = new ArrayList<EcodDomain>(doms.size());
+			List<EcodDomain> clonedDoms = new ArrayList<>(doms.size());
 			for(EcodDomain d : doms) {
 				clonedDoms.add( new EcodDomain(d) );
 			}
@@ -173,7 +173,7 @@ public List<EcodDomain> filterByHierarchy(String hierarchy) throws IOException {
 		Integer hGroup = xhtGroup.length>1 ? Integer.parseInt(xhtGroup[1]) : null;
 		Integer tGroup = xhtGroup.length>2 ? Integer.parseInt(xhtGroup[2]) : null;
 
-		List<EcodDomain> filtered = new ArrayList<EcodDomain>();
+		List<EcodDomain> filtered = new ArrayList<>();
 		for(EcodDomain d: getAllDomains()) {
 			boolean match = true;
 			if(xhtGroup.length>0) {
@@ -477,7 +477,7 @@ private void indexDomains() throws IOException {
 			}
 
 			// Leave enough space for all PDBs as of 2015
-			domainMap = new HashMap<String, List<EcodDomain>>((int) (150000/.85),.85f);
+			domainMap = new HashMap<>((int) (150000 / .85), .85f);
 
 			// Index with domainMap
 			for(EcodDomain d : allDomains) {
@@ -496,7 +496,7 @@ private void indexDomains() throws IOException {
 				if( domainMap.containsKey(pdbId) ) {
 					currDomains = domainMap.get(pdbId);
 				} else {
-					currDomains = new LinkedList<EcodDomain>();
+					currDomains = new LinkedList<>();
 					domainMap.put(pdbId,currDomains);
 				}
 				currDomains.add(d);
@@ -574,7 +574,7 @@ public EcodParser(BufferedReader reader) throws IOException {
 		private void parse(BufferedReader in) throws IOException {
 			try {
 				// Allocate plenty of space for ECOD as of 2015
-				ArrayList<EcodDomain> domainsList = new ArrayList<EcodDomain>(500000);
+				ArrayList<EcodDomain> domainsList = new ArrayList<>(500000);
 
 				Pattern versionRE = Pattern.compile("^\\s*#.*ECOD\\s*version\\s+(\\S+).*");
 				Pattern commentRE = Pattern.compile("^\\s*#.*");
@@ -692,12 +692,12 @@ private void parse(BufferedReader in) throws IOException {
 									}
 
 									String ligandStr = fields[i++];
-									Set<String> ligands = null;
+									Set<String> ligands;
 									if( ligandStr.equals("NO_LIGANDS_4A") || ligandStr.isEmpty() ) {
 										ligands = Collections.emptySet();
 									} else {
 										String[] ligSplit = ligandStr.split(",");
-										ligands = new LinkedHashSet<String>(ligSplit.length);
+										ligands = new LinkedHashSet<>(ligSplit.length);
 										for(String s : ligSplit) {
 											ligands.add(s.intern());
 										}
@@ -767,7 +767,7 @@ public String getVersion() {
 
 	@Override
 	public String toString() {
-		String version = null;
+		String version;
 		try {
 			version = getVersion();
 		} catch (IOException e) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
index 7d638bce65..10d6d224a2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
@@ -46,19 +46,19 @@
  */
 public class MomentsOfInertia {
 
-	private List<Point3d> points = new ArrayList<Point3d>();
-	private List<Double> masses = new ArrayList<Double>();
+	private final List<Point3d> points = new ArrayList<>();
+	private final List<Double> masses = new ArrayList<>();
 
 	private boolean modified = true;
 
 	private double[] principalMomentsOfInertia = new double[3];
-	private Vector3d[] principalAxes = new Vector3d[3];
+	private final Vector3d[] principalAxes = new Vector3d[3];
 
-	private Matrix3d orientation = new Matrix3d();
+	private final Matrix3d orientation = new Matrix3d();
 
 	public enum SymmetryClass {
 		LINEAR, PROLATE, OBLATE, SYMMETRIC, ASYMMETRIC
-	};
+	}
 
 	/** Creates a new empty instance of MomentsOfInertia */
 	public MomentsOfInertia() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPosition.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPosition.java
index f6b0d2dfb3..9fa91ad0ba 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPosition.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPosition.java
@@ -51,7 +51,7 @@ public interface SuperPosition {
 	 * @return transformation matrix as a Matrix4d to superpose moved onto fixed
 	 *         point arrays
 	 */
-	public Matrix4d superpose(Point3d[] fixed, Point3d[] moved);
+    Matrix4d superpose(Point3d[] fixed, Point3d[] moved);
 
 	/**
 	 * Transform an array of points so that the coordinates of its points
@@ -71,7 +71,7 @@ public interface SuperPosition {
 	 * @return transformation matrix as a Matrix4d to superpose moved onto fixed
 	 *         point arrays
 	 */
-	public Matrix4d superposeAndTransform(Point3d[] fixed, Point3d[] moved);
+    Matrix4d superposeAndTransform(Point3d[] fixed, Point3d[] moved);
 
 	/**
 	 * Calculate the RMSD between two arrays of equivalent points that are not
@@ -94,6 +94,6 @@ public interface SuperPosition {
 	 * @return the minimum RMSD between the equivalent point arrays (after
 	 *         superposition)
 	 */
-	public double getRmsd(Point3d[] x, Point3d[] y);
+    double getRmsd(Point3d[] x, Point3d[] y);
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
index a3d5728f19..8b7c2a65dc 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
@@ -126,8 +126,8 @@ public final class SuperPositionQCP extends SuperPositionAbstract {
 	private Point3d ytrans;
 
 	private double e0;
-	private Matrix3d rotmat = new Matrix3d();
-	private Matrix4d transformation = new Matrix4d();
+	private final Matrix3d rotmat = new Matrix3d();
+	private final Matrix4d transformation = new Matrix4d();
 	private double rmsd = 0;
 	private double Sxy, Sxz, Syx, Syz, Szx, Szy;
 	private double SxxpSyy, Szz, mxEigenV, SyzmSzy, SxzmSzx, SxymSyx;
@@ -135,7 +135,7 @@ public final class SuperPositionQCP extends SuperPositionAbstract {
 	private double Syy, Sxx, SyzpSzy;
 	private boolean rmsdCalculated = false;
 	private boolean transformationCalculated = false;
-	private boolean centered = false;
+	private final boolean centered = false;
 
 	/**
 	 * Default constructor for the quaternion based superposition algorithm.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
index bb92724aa4..ad28c5550b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
@@ -81,8 +81,8 @@ public class BondMaker {
 	 */
 	private static final double MAX_NUCLEOTIDE_BOND_LENGTH = 2.1;
 
-	private Structure structure;
-	private FileParsingParameters params;
+	private final Structure structure;
+	private final FileParsingParameters params;
 
 	public BondMaker(Structure structure, FileParsingParameters params) {
 		this.structure = structure;
@@ -169,7 +169,7 @@ private void formIntraResidueBonds() {
 						continue;
 					}
 					// Now add support for altLocGroup
-					List<Group> totList = new ArrayList<Group>();
+					List<Group> totList = new ArrayList<>();
 					totList.add(mainGroup);
 					totList.addAll(mainGroup.getAltLocs());
 
@@ -203,7 +203,7 @@ private void formIntraResidueBonds() {
 	 * @param maxAllowedLength max length, if atoms distance above this length no bond will be added. If negative no check on distance is performed.
 	 * @param bondOrder the bond order to be set in the created bond(s)
 	 */
-	private void formBondAltlocAware(Group g1, String name1, Group g2, String name2, double maxAllowedLength, int bondOrder) {
+	private static void formBondAltlocAware(Group g1, String name1, Group g2, String name2, double maxAllowedLength, int bondOrder) {
 		List<Atom> a1s = getAtoms(g1, name1);
 		List<Atom> a2s = getAtoms(g2, name2);
 
@@ -247,7 +247,7 @@ private void formBondAltlocAware(Group g1, String name1, Group g2, String name2,
 	 * @param name the atom name
 	 * @return list of all atoms, or empty list if no atoms with the name
 	 */
-	private List<Atom> getAtoms(Group g, String name) {
+	private static List<Atom> getAtoms(Group g, String name) {
 		List<Atom> atoms = new ArrayList<>();
 		List<Group> groupsWithAltLocs = new ArrayList<>();
 		groupsWithAltLocs.add(g);
@@ -410,8 +410,8 @@ public void formBondsFromStructConn(List<StructConn> structConn) {
 			String altLocStr1 = altLoc1.isEmpty()? "" : "(alt loc "+altLoc1+")";
 			String altLocStr2 = altLoc2.isEmpty()? "" : "(alt loc "+altLoc2+")";
 
-			Map<Integer,Atom> a1 = null;
-			Map<Integer,Atom> a2 = null;
+			Map<Integer,Atom> a1;
+			Map<Integer,Atom> a2;
 
 			try {
 				a1 = getAtomFromRecord(atomName1, altLoc1, resName1, chainId1, seqId1, insCode1);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/CAConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/CAConverter.java
index 4ffc5f1883..5b65b011d4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/CAConverter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/CAConverter.java
@@ -42,7 +42,7 @@ public class CAConverter {
 	 * @since Biojava 4.1.0
 	 */
 	public static List<Chain> getRepresentativeAtomsOnly(List<Chain> chains){
-		List<Chain> newChains = new ArrayList<Chain>();
+		List<Chain> newChains = new ArrayList<>();
 
 		for (Chain chain : chains){
 			Chain newChain = getRepresentativeAtomsOnly(chain);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java
index c77f28d1a7..d6fed972c8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java
@@ -102,7 +102,7 @@ public static List<EntityInfo> findPolyEntities(List<List<Chain>> polyModels) {
 	 */
 	private static List<EntityInfo> findUniqueEntities(TreeMap<String,EntityInfo> chainIds2entities) {
 
-		List<EntityInfo> list = new ArrayList<EntityInfo>();
+		List<EntityInfo> list = new ArrayList<>();
 
 		for (EntityInfo cluster:chainIds2entities.values()) {
 			boolean present = false;
@@ -131,12 +131,7 @@ public static void createPurelyNonPolyEntities(List<List<Chain>> nonPolyModels,
 		// let's find first the max entity id to assign entity ids to the newly found entities
 		int maxMolId = 0;
 		if (!entities.isEmpty()) {
-			maxMolId = Collections.max(entities, new Comparator<EntityInfo>() {
-				@Override
-				public int compare(EntityInfo o1, EntityInfo o2) {
-					return new Integer(o1.getMolId()).compareTo(o2.getMolId());
-				}
-			}).getMolId();
+			maxMolId = Collections.max(entities, (o1, o2) -> new Integer(o1.getMolId()).compareTo(o2.getMolId())).getMolId();
 		}
 		// we go one over the max
 		int molId = maxMolId + 1;
@@ -200,7 +195,7 @@ private static boolean areResNumbersAligned(Chain c1, Chain c2) {
 		// different kind of chain: we won't try to align them
 		if (isC1prot != isC2prot ) return false;
 
-		List<Group> c1AtomGroups = null;
+		List<Group> c1AtomGroups;
 		if (isC1prot) {
 			c1AtomGroups = c1.getAtomGroups(GroupType.AMINOACID);
 		}
@@ -240,11 +235,11 @@ private static TreeMap<String,EntityInfo> findEntitiesFromAlignment(List<List<Ch
 
 
 
-		TreeMap<String, EntityInfo> chainIds2entities = new TreeMap<String,EntityInfo>();
+		TreeMap<String, EntityInfo> chainIds2entities = new TreeMap<>();
 
 		if (polyModels.isEmpty()) return chainIds2entities;
 
-		Set<Integer> polyChainIndices = new TreeSet<Integer>();
+		Set<Integer> polyChainIndices = new TreeSet<>();
 		for (int i=0;i<polyModels.get(0).size();i++) {
 			polyChainIndices.add(i);
 		}
@@ -261,16 +256,16 @@ private static TreeMap<String,EntityInfo> findEntitiesFromAlignment(List<List<Ch
 					Chain c1 = polyModels.get(0).get(i);
 					Chain c2 = polyModels.get(0).get(j);
 
-					Map<Integer,Integer> positionIndex1 = new HashMap<Integer, Integer>();
-					Map<Integer,Integer> positionIndex2 = new HashMap<Integer, Integer>();
+					Map<Integer,Integer> positionIndex1 = new HashMap<>();
+					Map<Integer,Integer> positionIndex2 = new HashMap<>();
 					// here we use false, which means that X will be used for unknown compounds
 					String str1 = SeqRes2AtomAligner.getFullAtomSequence(c1.getAtomGroups(), positionIndex1, false);
 					String str2 = SeqRes2AtomAligner.getFullAtomSequence(c2.getAtomGroups(), positionIndex2, false);
 
-					int seq1Length = 0;
-					int seq2Length = 0;
+					int seq1Length;
+					int seq2Length;
 
-					SequencePair<?,?> pair = null;
+					SequencePair<?,?> pair;
 					if (isProteinSequence(str1) && isProteinSequence(str2)) {
 						ProteinSequence s1 = getProteinSequence(str1);
 						ProteinSequence s2 = getProteinSequence(str2);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
index 6c6506504c..e2e28a77db 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
@@ -85,8 +85,8 @@ public static AFPChain cpFastaToAfpChain(String first, String second, Structure
 	public static AFPChain cpFastaToAfpChain(File fastaFile, Structure structure, int cpSite) throws IOException, StructureException {
 		InputStream inStream = new FileInputStream(fastaFile);
 		SequenceCreatorInterface<AminoAcidCompound> creator = new CasePreservingProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet());
-		SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound> headerParser = new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>();
-		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(inStream, headerParser, creator);
+		SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound> headerParser = new GenericFastaHeaderParser<>();
+		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(inStream, headerParser, creator);
 		LinkedHashMap<String, ProteinSequence> sequences = fastaReader.process();
 		inStream.close();
 		Iterator<ProteinSequence> iter = sequences.values().iterator();
@@ -196,8 +196,8 @@ public static AFPChain fastaFileToAfpChain(File fastaFile, Structure structure1,
 		InputStream inStream = new FileInputStream(fastaFile);
 		SequenceCreatorInterface<AminoAcidCompound> creator = new CasePreservingProteinSequenceCreator(
 				AminoAcidCompoundSet.getAminoAcidCompoundSet());
-		SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound> headerParser = new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>();
-		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+		SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound> headerParser = new GenericFastaHeaderParser<>();
+		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
 				inStream, headerParser, creator);
 		LinkedHashMap<String, ProteinSequence> sequences = fastaReader.process();
 		inStream.close();
@@ -236,8 +236,8 @@ public static AFPChain fastaToAfpChain(Map<String, ProteinSequence> sequences, S
 			throw new IllegalArgumentException("A structure is null");
 		}
 
-		List<ProteinSequence> seqs = new ArrayList<ProteinSequence>();
-		List<String> names = new ArrayList<String>(2);
+		List<ProteinSequence> seqs = new ArrayList<>();
+		List<String> names = new ArrayList<>(2);
 		for (Map.Entry<String, ProteinSequence> entry : sequences.entrySet()) {
 			seqs.add(entry.getValue());
 			names.add(entry.getKey());
@@ -321,7 +321,7 @@ public static AFPChain fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>,
 				sb1.append(a.getBase());
 			}
 			ProteinSequence seq2 = new ProteinSequence(sb2.toString());
-			LinkedHashMap<String, ProteinSequence> map = new LinkedHashMap<String, ProteinSequence>();
+			LinkedHashMap<String, ProteinSequence> map = new LinkedHashMap<>();
 			map.put(structure1.getName(), seq1);
 			map.put(structure2.getName(), seq2);
 			return fastaToAfpChain(map, structure1, structure2);
@@ -349,8 +349,8 @@ private static AFPChain buildAlignment(Atom[] ca1, Atom[] ca2, ResidueNumber[] r
 
 		// remove any gap
 		// this includes the ones introduced by the nullifying above
-		List<ResidueNumber> alignedResiduesList1 = new ArrayList<ResidueNumber>();
-		List<ResidueNumber> alignedResiduesList2 = new ArrayList<ResidueNumber>();
+		List<ResidueNumber> alignedResiduesList1 = new ArrayList<>();
+		List<ResidueNumber> alignedResiduesList2 = new ArrayList<>();
 		for (int i = 0; i < residues1.length; i++) {
 			if (residues1[i] != null && residues2[i] != null) {
 				alignedResiduesList1.add(residues1[i]);
@@ -358,8 +358,8 @@ private static AFPChain buildAlignment(Atom[] ca1, Atom[] ca2, ResidueNumber[] r
 			}
 		}
 
-		ResidueNumber[] alignedResidues1 = alignedResiduesList1.toArray(new ResidueNumber[alignedResiduesList1.size()]);
-		ResidueNumber[] alignedResidues2 = alignedResiduesList2.toArray(new ResidueNumber[alignedResiduesList2.size()]);
+		ResidueNumber[] alignedResidues1 = alignedResiduesList1.toArray(new ResidueNumber[0]);
+		ResidueNumber[] alignedResidues2 = alignedResiduesList2.toArray(new ResidueNumber[0]);
 
 		AFPChain afpChain = AlignmentTools.createAFPChain(ca1, ca2, alignedResidues1, alignedResidues2);
 		afpChain.setAlgorithmName("unknown");
@@ -379,7 +379,7 @@ private static AFPChain buildAlignment(Atom[] ca1, Atom[] ca2, ResidueNumber[] r
 	 * @param sequence Make sure <em>not</em> to use {@link ProteinSequence#getSequenceAsString()} for this, as it won't preserve upper- and lower-case
 	 */
 	public static List<Object> getAlignedUserCollection(String sequence) {
-		List<Object> aligned = new ArrayList<Object>(sequence.length());
+		List<Object> aligned = new ArrayList<>(sequence.length());
 		for (char c : sequence.toCharArray()) {
 			aligned.add(Character.isUpperCase(c));
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaStructureParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaStructureParser.java
index 29baf9d825..7507d7df8d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaStructureParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaStructureParser.java
@@ -57,8 +57,8 @@
 public class FastaStructureParser {
 
 	// inputs
-	private FastaReader<ProteinSequence, AminoAcidCompound> reader;
-	private AtomCache cache;
+	private final FastaReader<ProteinSequence, AminoAcidCompound> reader;
+	private final AtomCache cache;
 
 	// cache processed data
 	private String[] accessions;
@@ -71,7 +71,7 @@ public FastaStructureParser(InputStream is,
 			SequenceCreatorInterface<AminoAcidCompound> sequenceCreator,
 			AtomCache cache)
 	{
-		this(new FastaReader<ProteinSequence, AminoAcidCompound>(
+		this(new FastaReader<>(
 				is, headerParser, sequenceCreator),cache);
 	}
 
@@ -80,7 +80,7 @@ public FastaStructureParser(File file,
 			SequenceCreatorInterface<AminoAcidCompound> sequenceCreator,
 			AtomCache cache) throws FileNotFoundException
 	{
-		this(new FastaReader<ProteinSequence, AminoAcidCompound>(
+		this(new FastaReader<>(
 				file, headerParser, sequenceCreator), cache);
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java
index 1b4ce20b58..1f5f9da245 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java
@@ -58,7 +58,7 @@ public class FileConvert {
 
 
 
-	private Structure structure ;
+	private final Structure structure ;
 
 	private boolean printConnections;
 
@@ -231,7 +231,7 @@ public String toPDB() {
 				}
 
 			}
-			if (nonPolyGroupsExist) str.append(String.format("%-80s","TER")).append(newline);;
+			if (nonPolyGroupsExist) str.append(String.format("%-80s","TER")).append(newline);
 
 			boolean waterGroupsExist = false;
 			for (Chain chain : waterChains) {
@@ -248,7 +248,7 @@ public String toPDB() {
 				}
 
 			}
-			if (waterGroupsExist) str.append(String.format("%-80s","TER")).append(newline);;
+			if (waterGroupsExist) str.append(String.format("%-80s","TER")).append(newline);
 
 
 			if ( nrModels>1) {
@@ -271,7 +271,7 @@ private static void toPDB(Group g, StringBuffer str) {
 		int groupsize  = g.size();
 
 		for ( int atompos = 0 ; atompos < groupsize; atompos++) {
-			Atom a = null ;
+			Atom a;
 
 			a = g.getAtom(atompos);
 			if ( a == null)
@@ -390,7 +390,7 @@ public static void toPDB(Atom a, StringBuffer str, String chainID) {
 
 		GroupType type = g.getType() ;
 
-		String record = "" ;
+		String record;
 		if ( type.equals(GroupType.HETATM) ) {
 			record = "HETATM";
 		} else {
@@ -411,7 +411,7 @@ record = "ATOM  ";
 		if ( altLoc == null)
 			altLoc = ' ';
 
-		String resseq = "" ;
+		String resseq;
 		if ( hasInsertionCode(pdbcode) )
 			resseq     = String.format("%5s",pdbcode);
 		else
@@ -426,7 +426,7 @@ record = "ATOM  ";
 
 		String leftResName = String.format("%3s",resName);
 
-		StringBuffer s = new StringBuffer();
+		StringBuilder s = new StringBuilder();
 		s.append(record);
 		s.append(serial);
 		s.append(" ");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java
index bbc277b89f..6350a3551f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java
@@ -59,10 +59,10 @@ private String getCtab(Group thisGroup){
 				if(atoms.indexOf(otherAtom)>=atoms.indexOf(a)){
 					continue;
 				}
-				if(atoms.indexOf(otherAtom)<0){
+				if(!atoms.contains(otherAtom)){
 					continue;
 				}
-				if(atoms.indexOf(a)<0){
+				if(!atoms.contains(a)){
 					continue;
 				}
 				numBonds++;
@@ -130,7 +130,7 @@ private Object getCharges(Group thisGroup) {
 
 	private static List<Number> getAtomCharges(Group group) {
 		// The list to store the answer
-		List<Number> outArr = new ArrayList<Number>();
+		List<Number> outArr = new ArrayList<>();
 		// Get the atom charge Information
 		for(Atom a: group.getAtoms()){
 			outArr.add(a.getCharge());
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
index 61735ecfa6..6ec299ef90 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
@@ -68,7 +68,7 @@ public abstract class LocalPDBDirectory implements StructureIOFile {
 	 * @author Spencer Bliven
 	 * @see LocalPDBDirectory#setObsoleteBehavior(ObsoleteBehavior)
 	 */
-	public static enum ObsoleteBehavior {
+	public enum ObsoleteBehavior {
 		/** Fetch the most recent version of the PDB entry. */
 		FETCH_CURRENT,
 		/** Fetch the obsolete entry from the PDB archives. */
@@ -84,7 +84,7 @@ public static enum ObsoleteBehavior {
 	 * @author Spencer Bliven
 	 *
 	 */
-	public static enum FetchBehavior {
+	public enum FetchBehavior {
 		/** Never fetch from the server; Throw errors for missing files */
 		LOCAL_ONLY,
 		/** Fetch missing files from the server. Don't check for outdated files */
@@ -133,14 +133,14 @@ public static enum FetchBehavior {
 	public static final long MIN_PDB_FILE_SIZE = 40;  // Empty gzip files are 20bytes. Add a few more for buffer.
 
 	private File path;
-	private List<String> extensions;
+	private final List<String> extensions;
 
 	/**
 	 * The server name, prefixed by the protocol string (http:// or ftp://).
 	 * Note that we don't support file stamp retrieving for ftp protocol, thus some of the
 	 * fetch modes will not work properly with ftp protocol
 	 */
-	private String serverName;
+	private final String serverName;
 
 	private FileParsingParameters params;
 
@@ -163,7 +163,7 @@ public static enum FetchBehavior {
 	 * @param path Path to the PDB file directory
 	 */
 	public LocalPDBDirectory(String path) {
-		extensions    = new ArrayList<String>();
+		extensions    = new ArrayList<>();
 
 		params = new FileParsingParameters();
 
@@ -526,7 +526,7 @@ private File downloadStructure(String pdbId, String pathOnServer, boolean obsole
 
 		URL url = new URL(ftp);
 
-		Date serverFileDate = null;
+		Date serverFileDate;
 		if (existingFile!=null) {
 
 			serverFileDate = getLastModifiedTime(url);
@@ -611,7 +611,7 @@ private Date getLastModifiedTime(URL url) {
 	 */
 	protected File getDir(String pdbId, boolean obsolete) {
 
-		File dir = null;
+		File dir;
 
 		if (obsolete) {
 			// obsolete is always split
@@ -644,7 +644,7 @@ public File getLocalFile(String pdbId) throws IOException {
 		// Search directories:
 		// 1) LOCAL_MMCIF_SPLIT_DIR/<middle>/(pdb)?<pdbId>.<ext>
 		// 2) LOCAL_MMCIF_ALL_DIR/<middle>/(pdb)?<pdbId>.<ext>
-		LinkedList<File> searchdirs = new LinkedList<File>();
+		LinkedList<File> searchdirs = new LinkedList<>();
 		String middle = pdbId.substring(1,3).toLowerCase();
 
 		File splitdir = new File(splitDirPath, middle);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java
index 22462bafe1..678b011370 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java
@@ -41,10 +41,10 @@ public class PDBBioAssemblyParser {
 	//private static final Logger logger = LoggerFactory.getLogger(PDBBioAssemblyParser.class);
 
 	private Integer currentBioMolecule = null;
-	private List<String> currentChainIDs = new ArrayList<String>();
+	private final List<String> currentChainIDs = new ArrayList<>();
 	private Matrix currentMatrix = null;
 	private double[] shift = null;
-	private Map<Integer,BioAssemblyInfo> transformationMap = new HashMap<Integer, BioAssemblyInfo>();
+	private final Map<Integer,BioAssemblyInfo> transformationMap = new HashMap<>();
 	private int modelNumber = 1;
 
 	private List<BiologicalAssemblyTransformation> transformations;
@@ -159,7 +159,7 @@ private void addToCurrentChainList(String line) {
 	}
 
 	private void initialize() {
-		transformations = new ArrayList<BiologicalAssemblyTransformation>();
+		transformations = new ArrayList<>();
 		currentMatrix = Matrix.identity(3,3);
 		currentBioMolecule = null;
 		shift = new double[3];
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
index 41014e1ec4..91fbe32045 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -158,34 +158,34 @@ public class PDBFileParser  {
 	//(pdb_COMPOUND_handler for example)
 	private boolean isLegacyFormat = false;
 
-	private boolean blankChainIdsPresent = false;
+	private boolean blankChainIdsPresent;
 
 	// for re-creating the biological assembly
 	private PDBBioAssemblyParser bioAssemblyParser = null;
 
 	private PDBHeader pdbHeader;
-	private PDBCrystallographicInfo crystallographicInfo;
+	private final PDBCrystallographicInfo crystallographicInfo;
 	private JournalArticle journalArticle;
 	private List<Map<String, Integer>> connects ;
-	private List<Map<String,String>> helixList;
-	private List<Map<String,String>> strandList;
-	private List<Map<String,String>> turnList;
+	private final List<Map<String,String>> helixList;
+	private final List<Map<String,String>> strandList;
+	private final List<Map<String,String>> turnList;
 
 	private int lengthCheck ;
 
 	private boolean isLastCompndLine = false;
 	private boolean isLastSourceLine = false;
 	private EntityInfo current_compound;
-	private List<EntityInfo> entities = new ArrayList<EntityInfo>();
-	private HashMap<Integer,List<String>> compoundMolIds2chainIds = new HashMap<Integer, List<String>>();
-	private List<String> compndLines = new ArrayList<String>();
-	private List<String> sourceLines = new ArrayList<String>();
-	private List<String> journalLines = new ArrayList<String>();
-	private List<DBRef> dbrefs;
-	private Map<String, Site> siteMap = new LinkedHashMap<String, Site>();
-	private Map<String, List<ResidueNumber>> siteToResidueMap = new LinkedHashMap<String, List<ResidueNumber>>();
+	private List<EntityInfo> entities = new ArrayList<>();
+	private final HashMap<Integer,List<String>> compoundMolIds2chainIds = new HashMap<>();
+	private final List<String> compndLines = new ArrayList<>();
+	private final List<String> sourceLines = new ArrayList<>();
+	private final List<String> journalLines = new ArrayList<>();
+	private final List<DBRef> dbrefs;
+	private Map<String, Site> siteMap;
+	private final Map<String, List<ResidueNumber>> siteToResidueMap = new LinkedHashMap<>();
 
-	private List<SSBondImpl> ssbonds = new ArrayList<>();
+	private final List<SSBondImpl> ssbonds = new ArrayList<>();
 
 	// for storing LINK until we have all the atoms parsed
 	private List<LinkRecord> linkRecords;
@@ -199,31 +199,31 @@ public class PDBFileParser  {
 	private String continuationField;
 	private String continuationString;
 
-	private DateFormat dateFormat;
+	private final DateFormat dateFormat;
 
 	// for rfree parsing
 	private float rfreeStandardLine = -1;
 	private float rfreeNoCutoffLine = -1;
 
-	private static  final List<String> compndFieldValues = new ArrayList<String>(
+	private static  final List<String> compndFieldValues = new ArrayList<>(
 			Arrays.asList(
 					"MOL_ID:", "MOLECULE:", "CHAIN:", "SYNONYM:",
 					"EC:", "FRAGMENT:", "ENGINEERED:", "MUTATION:",
 					"BIOLOGICAL_UNIT:", "OTHER_DETAILS:"
-					));
+			));
 
 
-	private static final List<String> ignoreCompndFieldValues = new ArrayList<String>(
+	private static final List<String> ignoreCompndFieldValues = new ArrayList<>(
 			Arrays.asList(
-					"HETEROGEN:","ENGINEEREED:","FRAGMENT,",
-					"MUTANT:","SYNTHETIC:"
-					));
+					"HETEROGEN:", "ENGINEEREED:", "FRAGMENT,",
+					"MUTANT:", "SYNTHETIC:"
+			));
 	// ENGINEEREED in pdb219d
 
-	private static final List<String> sourceFieldValues = new ArrayList<String>(
+	private static final List<String> sourceFieldValues = new ArrayList<>(
 			Arrays.asList("ENGINEERED:", "MOL_ID:", "SYNTHETIC:", "FRAGMENT:",
 					"ORGANISM_SCIENTIFIC:", "ORGANISM_COMMON:",
-					"ORGANISM_TAXID:","STRAIN:",
+					"ORGANISM_TAXID:", "STRAIN:",
 					"VARIANT:", "CELL_LINE:", "ATCC:", "ORGAN:", "TISSUE:",
 					"CELL:", "ORGANELLE:", "SECRETION:", "GENE:",
 					"CELLULAR_LOCATION:", "EXPRESSION_SYSTEM:",
@@ -272,14 +272,14 @@ public PDBFileParser() {
 
 		pdbHeader 	  = new PDBHeader();
 		crystallographicInfo = new PDBCrystallographicInfo();
-		connects      = new ArrayList<Map<String,Integer>>() ;
+		connects      = new ArrayList<>() ;
 
 
-		helixList     = new ArrayList<Map<String,String>>();
-		strandList    = new ArrayList<Map<String,String>>();
-		turnList      = new ArrayList<Map<String,String>>();
+		helixList     = new ArrayList<>();
+		strandList    = new ArrayList<>();
+		turnList      = new ArrayList<>();
 		current_compound = null;
-		dbrefs        = new ArrayList<DBRef>();
+		dbrefs        = new ArrayList<>();
 		siteMap = null;
 		dateFormat = new SimpleDateFormat("dd-MMM-yy", Locale.US);
 		atomCount = 0;
@@ -292,7 +292,7 @@ public PDBFileParser() {
 		loadMaxAtoms = params.getMaxAtoms();
 		atomCAThreshold = params.getAtomCaThreshold();
 
-		linkRecords = new ArrayList<LinkRecord>();
+		linkRecords = new ArrayList<>();
 
 		blankChainIdsPresent = false;
 
@@ -344,9 +344,9 @@ private Group getNewGroup(String recordName,Character aminoCode1, String aminoCo
 	 */
 	private void pdb_HEADER_Handler(String line) {
 
-		String classification  = null;
-		String deposition_date = null;
-		String pdbCode         = null;
+		String classification;
+		String deposition_date;
+		String pdbCode;
 
 		int len = line.trim().length();
 		if(len > 10) {
@@ -474,7 +474,7 @@ private void pdb_HELIX_Handler(String line){
 		//System.out.println(initResName + " " + initChainId + " " + initSeqNum + " " + initICode + " " +
 		//        endResName + " " + endChainId + " " + endSeqNum + " " + endICode);
 
-		Map<String,String> m = new HashMap<String,String>();
+		Map<String,String> m = new HashMap<>();
 
 		m.put("initResName",initResName);
 		m.put("initChainId", initChainId);
@@ -561,7 +561,7 @@ private void pdb_SHEET_Handler( String line){
 		//System.out.println(initResName + " " + initChainId + " " + initSeqNum + " " + initICode + " " +
 		//        endResName + " " + endChainId + " " + endSeqNum + " " + endICode);
 
-		Map<String,String> m = new HashMap<String,String>();
+		Map<String,String> m = new HashMap<>();
 
 		m.put("initResName",initResName);
 		m.put("initChainId", initChainId);
@@ -626,7 +626,7 @@ private void pdb_TURN_Handler( String line){
 		//System.out.println(initResName + " " + initChainId + " " + initSeqNum + " " + initICode + " " +
 		//        endResName + " " + endChainId + " " + endSeqNum + " " + endICode);
 
-		Map<String,String> m = new HashMap<String,String>();
+		Map<String,String> m = new HashMap<>();
 
 		m.put("initResName",initResName);
 		m.put("initChainId", initChainId);
@@ -769,7 +769,7 @@ private void pdb_SEQRES_Handler(String line) {
 
 		StringTokenizer subSequenceResidues = new StringTokenizer(subSequence);
 
-		Character aminoCode1 = null;
+		Character aminoCode1;
 		if (! recordName.equals(AminoAcid.SEQRESRECORD)) {
 			// should not have been called
 			return;
@@ -847,7 +847,7 @@ private void pdb_TITLE_Handler(String line) {
 		if ( line.length() > 79)
 			title = line.substring(10,80).trim();
 		else
-			title = line.substring(10,line.length()).trim();
+			title = line.substring(10).trim();
 
 		String t = pdbHeader.getTitle();
 		if ( (t != null) && (! t.equals("")) ){
@@ -890,10 +890,8 @@ private void pdb_JRNL_Handler(String line) {
 			logger.debug("trimming legacy PDB id from end of JRNL section line");
 
 			line = line.substring(0, line.length() - 8);
-			journalLines.add(line);
-		} else {
-			journalLines.add(line);
 		}
+		journalLines.add(line);
 	}
 
 	/**
@@ -926,7 +924,7 @@ private void pdb_COMPND_Handler(String line) {
 			line = line.substring(0, 72);
 		}
 
-		line = line.substring(10, line.length());
+		line = line.substring(10);
 
 
 		String[] fieldList = line.trim().split("\\s+");
@@ -1014,7 +1012,7 @@ private void compndValueSetter(String field, String value) {
 
 			int i = -1;
 			try {
-				i = Integer.valueOf(value);
+				i = Integer.parseInt(value);
 			} catch (NumberFormatException e){
 				logger.warn("Value '{}' does not look like a number, while trying to parse COMPND MOL_ID line.",value);
 			}
@@ -1048,7 +1046,7 @@ private void compndValueSetter(String field, String value) {
 		if (field.equals("CHAIN:")) {
 			//System.out.println(value);
 			StringTokenizer chainTokens = new StringTokenizer(value, ",");
-			List<String> chains = new ArrayList<String>();
+			List<String> chains = new ArrayList<>();
 
 			while (chainTokens.hasMoreTokens()) {
 				String chainID = chainTokens.nextToken().trim();
@@ -1063,7 +1061,7 @@ private void compndValueSetter(String field, String value) {
 		if (field.equals("SYNONYM:")) {
 
 			StringTokenizer synonyms = new StringTokenizer(value, ",");
-			List<String> names = new ArrayList<String>();
+			List<String> names = new ArrayList<>();
 
 			while (synonyms.hasMoreTokens()) {
 				names.add(synonyms.nextToken());
@@ -1076,7 +1074,7 @@ private void compndValueSetter(String field, String value) {
 		if (field.equals("EC:")) {
 
 			StringTokenizer ecNumTokens = new StringTokenizer(value, ",");
-			List<String> ecNums = new ArrayList<String>();
+			List<String> ecNums = new ArrayList<>();
 
 			while (ecNumTokens.hasMoreTokens()) {
 				ecNums.add(ecNumTokens.nextToken());
@@ -1153,7 +1151,7 @@ private void pdb_SOURCE_Handler(String line) {
 			line = line.substring(0, 79);
 		}
 
-		line = line.substring(10, line.length());
+		line = line.substring(10);
 
 		logger.debug("LINE: >" + line + "<");
 
@@ -1252,7 +1250,7 @@ private void sourceValueSetter(String field, String value) {
 		if (field.equals("MOL_ID:")) {
 
 			try {
-				current_compound = entities.get(Integer.valueOf(value) - 1);
+				current_compound = entities.get(Integer.parseInt(value) - 1);
 			} catch (NumberFormatException e){
 				logger.info("could not process SOURCE MOL_ID record correctly:" + e.getMessage());
 				return;
@@ -1262,70 +1260,103 @@ private void sourceValueSetter(String field, String value) {
 			//			System.out.println("[sourceValueSetter] Fetching compound " + value + " " + current_compound.getMolId());
 
 		}
-		if (field.equals("SYNTHETIC:")) {
-			current_compound.setSynthetic(value);
-		} else if (field.equals("FRAGMENT:")) {
-			current_compound.setFragment(value);
-		} else if (field.equals("ORGANISM_SCIENTIFIC:")) {
-			current_compound.setOrganismScientific(value);
-		} else if (field.equals("ORGANISM_TAXID:")) {
-			current_compound.setOrganismTaxId(value);
-		} else if (field.equals("ORGANISM_COMMON:")) {
-			current_compound.setOrganismCommon(value);
-		} else if (field.equals("STRAIN:")) {
-			current_compound.setStrain(value);
-		} else if (field.equals("VARIANT:")) {
-			current_compound.setVariant(value);
-		} else if (field.equals("CELL_LINE:")) {
-			current_compound.setCellLine(value);
-		} else if (field.equals("ATCC:")) {
-			current_compound.setAtcc(value);
-		} else if (field.equals("ORGAN:")) {
-			current_compound.setOrgan(value);
-		} else if (field.equals("TISSUE:")) {
-			current_compound.setTissue(value);
-		} else if (field.equals("CELL:")) {
-			current_compound.setCell(value);
-		} else if (field.equals("ORGANELLE:")) {
-			current_compound.setOrganelle(value);
-		} else if (field.equals("SECRETION:")) {
-			current_compound.setSecretion(value);
-		} else if (field.equals("GENE:")) {
-			current_compound.setGene(value);
-		} else if (field.equals("CELLULAR_LOCATION:")) {
-			current_compound.setCellularLocation(value);
-		} else if (field.equals("EXPRESSION_SYSTEM:")) {
-			current_compound.setExpressionSystem(value);
-		} else if (field.equals("EXPRESSION_SYSTEM_TAXID:")) {
-			current_compound.setExpressionSystemTaxId(value);
-		} else if (field.equals("EXPRESSION_SYSTEM_STRAIN:")) {
-			current_compound.setExpressionSystemStrain(value);
-		} else if (field.equals("EXPRESSION_SYSTEM_VARIANT:")) {
-			current_compound.setExpressionSystemVariant(value);
-		} else if (field.equals("EXPRESSION_SYSTEM_CELL_LINE:")) {
-			current_compound.setExpressionSystemCellLine(value);
-		} else if (field.equals("EXPRESSION_SYSTEM_ATCC_NUMBER:")) {
-			current_compound.setExpressionSystemAtccNumber(value);
-		} else if (field.equals("EXPRESSION_SYSTEM_ORGAN:")) {
-			current_compound.setExpressionSystemOrgan(value);
-		} else if (field.equals("EXPRESSION_SYSTEM_TISSUE:")) {
-			current_compound.setExpressionSystemTissue(value);
-		} else if (field.equals("EXPRESSION_SYSTEM_CELL:")) {
-			current_compound.setExpressionSystemCell(value);
-		} else if (field.equals("EXPRESSION_SYSTEM_ORGANELLE:")) {
-			current_compound.setExpressionSystemOrganelle(value);
-		} else if (field.equals("EXPRESSION_SYSTEM_CELLULAR_LOCATION:")) {
-			current_compound.setExpressionSystemCellularLocation(value);
-		} else if (field.equals("EXPRESSION_SYSTEM_VECTOR_TYPE:")) {
-			current_compound.setExpressionSystemVectorType(value);
-		} else if (field.equals("EXPRESSION_SYSTEM_VECTOR:")) {
-			current_compound.setExpressionSystemVector(value);
-		} else if (field.equals("EXPRESSION_SYSTEM_PLASMID:")) {
-			current_compound.setExpressionSystemPlasmid(value);
-		} else if (field.equals("EXPRESSION_SYSTEM_GENE:")) {
-			current_compound.setExpressionSystemGene(value);
-		} else if (field.equals("OTHER_DETAILS:")) {
-			current_compound.setExpressionSystemOtherDetails(value);
+		switch (field) {
+			case "SYNTHETIC:":
+				current_compound.setSynthetic(value);
+				break;
+			case "FRAGMENT:":
+				current_compound.setFragment(value);
+				break;
+			case "ORGANISM_SCIENTIFIC:":
+				current_compound.setOrganismScientific(value);
+				break;
+			case "ORGANISM_TAXID:":
+				current_compound.setOrganismTaxId(value);
+				break;
+			case "ORGANISM_COMMON:":
+				current_compound.setOrganismCommon(value);
+				break;
+			case "STRAIN:":
+				current_compound.setStrain(value);
+				break;
+			case "VARIANT:":
+				current_compound.setVariant(value);
+				break;
+			case "CELL_LINE:":
+				current_compound.setCellLine(value);
+				break;
+			case "ATCC:":
+				current_compound.setAtcc(value);
+				break;
+			case "ORGAN:":
+				current_compound.setOrgan(value);
+				break;
+			case "TISSUE:":
+				current_compound.setTissue(value);
+				break;
+			case "CELL:":
+				current_compound.setCell(value);
+				break;
+			case "ORGANELLE:":
+				current_compound.setOrganelle(value);
+				break;
+			case "SECRETION:":
+				current_compound.setSecretion(value);
+				break;
+			case "GENE:":
+				current_compound.setGene(value);
+				break;
+			case "CELLULAR_LOCATION:":
+				current_compound.setCellularLocation(value);
+				break;
+			case "EXPRESSION_SYSTEM:":
+				current_compound.setExpressionSystem(value);
+				break;
+			case "EXPRESSION_SYSTEM_TAXID:":
+				current_compound.setExpressionSystemTaxId(value);
+				break;
+			case "EXPRESSION_SYSTEM_STRAIN:":
+				current_compound.setExpressionSystemStrain(value);
+				break;
+			case "EXPRESSION_SYSTEM_VARIANT:":
+				current_compound.setExpressionSystemVariant(value);
+				break;
+			case "EXPRESSION_SYSTEM_CELL_LINE:":
+				current_compound.setExpressionSystemCellLine(value);
+				break;
+			case "EXPRESSION_SYSTEM_ATCC_NUMBER:":
+				current_compound.setExpressionSystemAtccNumber(value);
+				break;
+			case "EXPRESSION_SYSTEM_ORGAN:":
+				current_compound.setExpressionSystemOrgan(value);
+				break;
+			case "EXPRESSION_SYSTEM_TISSUE:":
+				current_compound.setExpressionSystemTissue(value);
+				break;
+			case "EXPRESSION_SYSTEM_CELL:":
+				current_compound.setExpressionSystemCell(value);
+				break;
+			case "EXPRESSION_SYSTEM_ORGANELLE:":
+				current_compound.setExpressionSystemOrganelle(value);
+				break;
+			case "EXPRESSION_SYSTEM_CELLULAR_LOCATION:":
+				current_compound.setExpressionSystemCellularLocation(value);
+				break;
+			case "EXPRESSION_SYSTEM_VECTOR_TYPE:":
+				current_compound.setExpressionSystemVectorType(value);
+				break;
+			case "EXPRESSION_SYSTEM_VECTOR:":
+				current_compound.setExpressionSystemVector(value);
+				break;
+			case "EXPRESSION_SYSTEM_PLASMID:":
+				current_compound.setExpressionSystemPlasmid(value);
+				break;
+			case "EXPRESSION_SYSTEM_GENE:":
+				current_compound.setExpressionSystemGene(value);
+				break;
+			case "OTHER_DETAILS:":
+				current_compound.setExpressionSystemOtherDetails(value);
+				break;
 		}
 
 	}
@@ -1363,7 +1394,7 @@ private void pdb_REMARK_Handler(String line) {
 			// a) take the '(NO CUTOFF)' value if the only one available (shelx software, e.g. 1x7q)
 			// b) don't take it if also a line without '(NO CUTOFF)' is present (CNX software, e.g. 3lak)
 
-			Pattern pR = Pattern.compile("^REMARK   3   FREE R VALUE\\s+(?:\\(NO CUTOFF\\))?\\s+:\\s+(\\d?\\.\\d+).*");
+			Pattern pR = Pattern.compile("^REMARK   3 {3}FREE R VALUE\\s+(?:\\(NO CUTOFF\\))?\\s+:\\s+(\\d?\\.\\d+).**");
 			Matcher mR = pR.matcher(line);
 			if (mR.matches()) {
 				try {
@@ -1372,7 +1403,7 @@ private void pdb_REMARK_Handler(String line) {
 					logger.info("Rfree value "+mR.group(1)+" does not look like a number, will ignore it");
 				}
 			}
-			pR = Pattern.compile("^REMARK   3   FREE R VALUE\\s+:\\s+(\\d?\\.\\d+).*");
+			pR = Pattern.compile("^REMARK   3 {3}FREE R VALUE\\s+:\\s+(\\d?\\.\\d+).**");
 			mR = pR.matcher(line);
 			if (mR.matches()) {
 				try {
@@ -1386,7 +1417,7 @@ private void pdb_REMARK_Handler(String line) {
 		// note: if more than 1 value present (occurring in hybrid experimental technique entries, e.g. 3ins, 4n9m)
 		// then last one encountered will be taken
 		} else if (line.startsWith("REMARK   3   RESOLUTION RANGE HIGH")){
-			Pattern pR = Pattern.compile("^REMARK   3   RESOLUTION RANGE HIGH \\(ANGSTROMS\\) :\\s+(\\d+\\.\\d+).*");
+			Pattern pR = Pattern.compile("^REMARK   3 {3}RESOLUTION RANGE HIGH \\(ANGSTROMS\\) :\\s+(\\d+\\.\\d+).**");
 			Matcher mR = pR.matcher(line);
 			if (mR.matches()) {
 				try {
@@ -1480,7 +1511,7 @@ private void pdb_CRYST1_Handler(String line) {
 		float alpha;
 		float beta;
 		float gamma;
-		String spaceGroup = "";
+		String spaceGroup;
 
 		try {
 			a = Float.parseFloat(line.substring(6,15).trim());
@@ -1498,7 +1529,7 @@ private void pdb_CRYST1_Handler(String line) {
 			spaceGroup = line.substring(55,66).trim();
 		} else {
 			// for not-so-well formatted files, e.g. phenix-produced ones: they lack a Z value
-			spaceGroup = line.substring(55,line.length()).trim();
+			spaceGroup = line.substring(55).trim();
 		}
 
 		CrystalCell xtalCell = new CrystalCell();
@@ -1575,7 +1606,7 @@ private void pdb_MTRIXn_Handler(String line) {
 
 			if (ncsOperators==null) {
 				// we initialise on first pass
-				ncsOperators = new ArrayList<Matrix4d>();
+				ncsOperators = new ArrayList<>();
 			}
 
 			if (currentNcsOp==null) {
@@ -1717,7 +1748,7 @@ private void  pdb_ATOM_Handler(String line)	{
 		startOfMolecule = false;
 
 
-		Character altLoc   = new Character(line.substring (16, 17).charAt(0));
+		Character altLoc   = line.substring(16, 17).charAt(0);
 		Group altGroup = null;
 
 
@@ -1965,7 +1996,7 @@ private Group getCorrectAltLocGroup( Character altLoc,
 			Group altLocG = (Group) currentGroup.clone();
 			// drop atoms from cloned group...
 			// https://redmine.open-bio.org/issues/3307
-			altLocG.setAtoms(new ArrayList<Atom>());
+			altLocG.setAtoms(new ArrayList<>());
 			altLocG.getAltLocs().clear();
 			currentGroup.addAltLoc(altLocG);
 			return altLocG;
@@ -2005,12 +2036,12 @@ private Integer conect_helper (String line,int start,int end) {
 		if (line.length() < end) return null;
 
 		String sbond = line.substring(start,end).trim();
-		int bond  = -1 ;
+		int bond;
 		Integer b = null ;
 
 		if ( ! sbond.equals("")) {
 			bond = Integer.parseInt(sbond);
-			b = new Integer(bond);
+			b = bond;
 		}
 
 		return b ;
@@ -2066,8 +2097,8 @@ private void pdb_CONECT_Handler(String line) {
 
 			//System.out.println(atomserial+ " "+ bond1 +" "+bond2+ " " +bond3+" "+bond4+" "+
 			//		   hyd1+" "+hyd2 +" "+salt1+" "+hyd3+" "+hyd4+" "+salt2);
-			HashMap<String, Integer> cons = new HashMap<String, Integer>();
-			cons.put("atomserial",new Integer(atomserial));
+			HashMap<String, Integer> cons = new HashMap<>();
+			cons.put("atomserial", atomserial);
 
 			if ( bond1 != null) cons.put("bond1",bond1);
 			if ( bond2 != null) cons.put("bond2",bond2);
@@ -2370,7 +2401,7 @@ private void pdb_SITE_Handler(String line){
 
 		//if the siteResidues doesn't yet exist, make a new one.
 		if (siteResidues == null || ! siteToResidueMap.containsKey(siteID.trim())){
-			siteResidues = new ArrayList<ResidueNumber>();
+			siteResidues = new ArrayList<>();
 			siteToResidueMap.put(siteID.trim(), siteResidues);
 
 			logger.debug(String.format("New Site made: %s %s", siteID,  siteResidues));
@@ -2384,7 +2415,7 @@ private void pdb_SITE_Handler(String line){
 		//line = 'SITE     1 AC1  6 ARG H 221A LYS H 224  HOH H 403  HOH H 460'
 		//line.substring(18) = 'ARG H 221A LYS H 224  HOH H 403  HOH H 460'
 		line = line.substring(18);
-		String groupString = null;
+		String groupString;
 		//groupString = 'ARG H 221A'
 		//keep iterating through chunks of 10 characters - these are the groups in the siteResidues
 		while (!(groupString = line.substring(0, 10)).equals("          ")) {
@@ -2434,8 +2465,8 @@ private void pdb_SITE_Handler(String line){
 		}
 
 		logger.debug("Current SiteMap (contains "+ siteToResidueMap.keySet().size() + " sites):");
-		for (String key : siteToResidueMap.keySet()) {
-			logger.debug(key + " : " + siteToResidueMap.get(key));
+		for (Map.Entry<String, List<ResidueNumber>> entry : siteToResidueMap.entrySet()) {
+			logger.debug(entry.getKey() + " : " + entry.getValue());
 		}
 
 	}
@@ -2462,7 +2493,7 @@ private void pdb_REMARK_800_Handler(String line){
 
 				//if the siteResidues doesn't yet exist, make a new one.
 				if (site == null || !siteID.equals(site.getSiteID())) {
-					site = new Site(siteID, new ArrayList<Group>());
+					site = new Site(siteID, new ArrayList<>());
 					siteMap.put(site.getSiteID(), site);
 
 					logger.debug("New Site made: " + site);
@@ -2585,10 +2616,10 @@ public  Structure parsePDBFile(BufferedReader buf)
 		startOfMolecule = true;
 		startOfModel = true;
 
-		seqResChains  = new ArrayList<Chain>();
-		siteMap = new LinkedHashMap<String, Site>();
+		seqResChains  = new ArrayList<>();
+		siteMap = new LinkedHashMap<>();
 		pdbHeader     = new PDBHeader();
-		connects      = new ArrayList<Map<String,Integer>>();
+		connects      = new ArrayList<>();
 		previousContinuationField = "";
 		continuationField = "";
 		continuationString = "";
@@ -2605,14 +2636,14 @@ public  Structure parsePDBFile(BufferedReader buf)
 		lengthCheck = -1;
 		atomCount = 0;
 		atomOverflow = false;
-		linkRecords = new ArrayList<LinkRecord>();
+		linkRecords = new ArrayList<>();
 		siteToResidueMap.clear();
 
 		blankChainIdsPresent = false;
 
 		parseCAonly = params.isParseCAOnly();
 
-		String line = null;
+		String line;
 
 		while ((line = buf.readLine()) != null) {
 
@@ -2633,7 +2664,7 @@ public  Structure parsePDBFile(BufferedReader buf)
 				continue;
 			}
 
-			String recordName = null;
+			String recordName;
 			if (line.length()<6)
 				recordName = line.trim();
 			else
@@ -2683,9 +2714,17 @@ else if (recordName.equals("SSBOND"))
 				else if (recordName.equals("LINK"))
 					pdb_LINK_Handler(line);
 				else if ( params.isParseSecStruc()) {
-					if ( recordName.equals("HELIX") ) pdb_HELIX_Handler (  line ) ;
-					else if (recordName.equals("SHEET")) pdb_SHEET_Handler(line ) ;
-					else if (recordName.equals("TURN")) pdb_TURN_Handler(   line ) ;
+					switch (recordName) {
+						case "HELIX":
+							pdb_HELIX_Handler(line);
+							break;
+						case "SHEET":
+							pdb_SHEET_Handler(line);
+							break;
+						case "TURN":
+							pdb_TURN_Handler(line);
+							break;
+					}
 				}
 			} catch (StringIndexOutOfBoundsException | NullPointerException ex) {
 				logger.info("Unable to parse [" + line + "]");
@@ -2858,7 +2897,7 @@ private void triggerEndFileChecks(){
 
 		if (ncsOperators !=null && ncsOperators.size()>0) {
 			crystallographicInfo.setNcsOperators(
-				ncsOperators.toArray(new Matrix4d[ncsOperators.size()]));
+				ncsOperators.toArray(new Matrix4d[0]));
 		}
 
 
@@ -3249,10 +3288,10 @@ private void linkSitesToGroups() {
 			return;
 		}
 
-		List<Site> sites = null;
+		List<Site> sites;
 		//check that there are chains with which to associate the groups
 		if (structure.getChains().isEmpty()) {
-			sites = new ArrayList<Site>(siteMap.values());
+			sites = new ArrayList<>(siteMap.values());
 			logger.info("No chains to link Site Groups with - Sites will not be present in the Structure");
 			return;
 		}
@@ -3266,9 +3305,9 @@ private void linkSitesToGroups() {
 
 		//so we have chains - associate the siteResidues-related groups with the ones
 		//already in in the chains
-		for (String key : siteMap.keySet()) {
-			Site currentSite = siteMap.get(key);
-			List<ResidueNumber> linkedGroups = siteToResidueMap.get(key);
+		for (Map.Entry<String, Site> entry : siteMap.entrySet()) {
+			Site currentSite = entry.getValue();
+			List<ResidueNumber> linkedGroups = siteToResidueMap.get(entry.getKey());
 			if ( linkedGroups == null)
 				continue;
 			for (ResidueNumber residueNumber : linkedGroups) {
@@ -3279,7 +3318,7 @@ private void linkSitesToGroups() {
 				//                    String resNum = resNum.getSeqNum().toString();
 				//                    System.out.println("resNum: '" + resNum + "'");
 
-				Group linkedGroup = null;
+				Group linkedGroup;
 				try {
 					//TODO: implement findGroup(ResidueNumber resNum)
 					linkedGroup = structure.findGroup(chain, pdbCode);
@@ -3295,7 +3334,7 @@ private void linkSitesToGroups() {
 
 		//System.out.println("SITEMAP: " + siteMap);
 
-		sites = new ArrayList<Site>(siteMap.values());
+		sites = new ArrayList<>(siteMap.values());
 		structure.setSites(sites);
 		//System.out.println("STRUCTURE SITES: " + structure.getSites().size());
 		//            for (Site site : structure.getSites()) {
@@ -3321,14 +3360,14 @@ private void buildjournalArticle() {
 		//        JRNL        REFN                   ISSN 1529-2908
 		//        JRNL        PMID   17351618
 		//        JRNL        DOI    10.1038/NI1450
-		StringBuffer auth = new StringBuffer();
-		StringBuffer titl = new StringBuffer();
-		StringBuffer edit = new StringBuffer();
-		StringBuffer ref = new StringBuffer();
-		StringBuffer publ = new StringBuffer();
-		StringBuffer refn = new StringBuffer();
-		StringBuffer pmid = new StringBuffer();
-		StringBuffer doi = new StringBuffer();
+		StringBuilder auth = new StringBuilder();
+		StringBuilder titl = new StringBuilder();
+		StringBuilder edit = new StringBuilder();
+		StringBuilder ref = new StringBuilder();
+		StringBuilder publ = new StringBuilder();
+		StringBuilder refn = new StringBuilder();
+		StringBuilder pmid = new StringBuilder();
+		StringBuilder doi = new StringBuilder();
 
 		for (String line : journalLines) {
 			if ( line.length() < 19 ) {
@@ -3339,7 +3378,7 @@ private void buildjournalArticle() {
 			String subField = line.substring(12, 16);
 			//            System.out.println("'" + subField + "'");
 			if (subField.equals("AUTH")) {
-				auth.append(line.substring(19, line.length()).trim());
+				auth.append(line.substring(19).trim());
 
 				logger.debug("AUTH '" + auth.toString() + "'");
 
@@ -3347,26 +3386,26 @@ private void buildjournalArticle() {
 			if (subField.equals("TITL")) {
 				//add a space to the end of a line so that when wrapped the
 				//words on the join won't be concatenated
-				titl.append(line.substring(19, line.length()).trim()).append(" ");
+				titl.append(line.substring(19).trim()).append(" ");
 
 				logger.debug("TITL '" + titl.toString() + "'");
 
 			}
 			if (subField.equals("EDIT")) {
-				edit.append(line.substring(19, line.length()).trim());
+				edit.append(line.substring(19).trim());
 
 				logger.debug("EDIT '" + edit.toString() + "'");
 
 			}
 			//        JRNL        REF    NAT.IMMUNOL.                  V.   8   430 2007
 			if (subField.equals("REF ")) {
-				ref.append(line.substring(19, line.length()).trim()).append(" ");
+				ref.append(line.substring(19).trim()).append(" ");
 
 				logger.debug("REF '" + ref.toString() + "'");
 
 			}
 			if (subField.equals("PUBL")) {
-				publ.append(line.substring(19, line.length()).trim()).append(" ");
+				publ.append(line.substring(19).trim()).append(" ");
 
 				logger.debug("PUBL '" + publ.toString() + "'");
 
@@ -3377,21 +3416,21 @@ private void buildjournalArticle() {
 					logger.info("can not process Journal REFN line: " + line);
 					continue;
 				}
-				refn.append(line.substring(35, line.length()).trim());
+				refn.append(line.substring(35).trim());
 
 				logger.debug("REFN '" + refn.toString() + "'");
 
 			}
 			//        JRNL        PMID   17351618
 			if (subField.equals("PMID")) {
-				pmid.append(line.substring(19, line.length()).trim());
+				pmid.append(line.substring(19).trim());
 
 				logger.debug("PMID '" + pmid.toString() + "'");
 
 			}
 			//        JRNL        DOI    10.1038/NI1450
 			if (subField.equals("DOI ")) {
-				doi.append(line.substring(19, line.length()).trim());
+				doi.append(line.substring(19).trim());
 
 				logger.debug("DOI '" + doi.toString() + "'");
 
@@ -3423,7 +3462,7 @@ private void buildjournalArticle() {
 	}
 
 	//inner class to deal with all the journal info
-	private class JournalParser {
+	private static class JournalParser {
 
 		private String journalName;
 		private String volume;
@@ -3497,7 +3536,7 @@ public JournalParser(String ref) {
 
 			if (!dateString.equals("    ")) {
 				try {
-					publicationDate = Integer.valueOf(dateString);
+					publicationDate = Integer.parseInt(dateString);
 				} catch (NumberFormatException nfe) {
 					logger.info(dateString + " is not a valid integer for a date in JRNL sub-section REF line 1");
 				}
@@ -3546,7 +3585,7 @@ private String getVolume() {
 	}
 
 	private List<Author> authorBuilder(String authorString) {
-		ArrayList<Author> authorList = new ArrayList<Author>();
+		ArrayList<Author> authorList = new ArrayList<>();
 
 		if (authorString.equals("")) {
 			return authorList;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBParseException.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBParseException.java
index 150201027f..4b0c6d11b2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBParseException.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBParseException.java
@@ -28,7 +28,7 @@
  */
 
 public class PDBParseException extends Exception{
-	public static final long serialVersionUID = 219047230178423923l;
+	public static final long serialVersionUID = 219047230178423923L;
 	/**
 	 * Constructs a PDBParseException object.
 	 *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SandboxStyleStructureProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SandboxStyleStructureProvider.java
index 6dc3b9a1f0..84bce020b6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SandboxStyleStructureProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SandboxStyleStructureProvider.java
@@ -187,7 +187,7 @@ public List<String> getAllPDBIDs() throws IOException{
 
 		String[] dirName = f.list();
 
-		List<String>pdbIds = new ArrayList<String>();
+		List<String>pdbIds = new ArrayList<>();
 		for (String dir : dirName) {
 			File d2= new File(f,dir);
 			if ( ! d2.isDirectory())
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java
index 580a8af158..fc2ca86a54 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java
@@ -82,7 +82,7 @@ public class SeqRes2AtomAligner {
 
 
 
-	private String alignmentString;
+	private final String alignmentString;
 
 	public SeqRes2AtomAligner(){
 		logger.debug("initialising SeqRes2AtomAligner");
@@ -103,12 +103,9 @@ public String getAlignmentString() {
 	 */
 	public static Chain getMatchingAtomRes(Chain seqRes, List<Chain> atomList, boolean useChainId)
 	{
-		Iterator<Chain> iter = atomList.iterator();
-		while(iter.hasNext()){
-			Chain atomChain = iter.next();
-
-			String atomChainId = null;
-			String seqResChainId = null;
+		for (Chain atomChain : atomList) {
+			String atomChainId;
+			String seqResChainId;
 			if (useChainId) {
 				atomChainId = atomChain.getId();
 				seqResChainId = seqRes.getId();
@@ -118,7 +115,7 @@ public static Chain getMatchingAtomRes(Chain seqRes, List<Chain> atomList, boole
 
 			}
 
-			if ( atomChainId.equals(seqResChainId)){
+			if (atomChainId.equals(seqResChainId)) {
 				return atomChain;
 			}
 
@@ -189,13 +186,12 @@ public void mapSeqresRecords(Chain atomRes, Chain seqRes) {
 				logger.debug("SEQRES chain {} is a nucleotide chain ({} nucleotides), aligning nucleotides...", seqRes.getId(), numNucleotidesSeqres);
 
 				alignNucleotideChains(seqRes,atomRes);
-				return;
 			} else {
 
 				logger.debug("SEQRES chain {} contains {} amino acids and {} nucleotides, ignoring...", seqRes.getId(),numAminosSeqres,numNucleotidesSeqres);
 
-				return;
 			}
+			return;
 		}
 
 		if ( atomRes.getAtomGroups(GroupType.AMINOACID).size() < 1) {
@@ -367,7 +363,7 @@ private List<Group> trySimpleMatch(List<Group> seqResGroups,List<Group> atmResGr
 	 */
 	public static String getFullAtomSequence(List<Group> groups, Map<Integer, Integer> positionIndex, boolean isNucleotideChain){
 
-		StringBuffer sequence = new StringBuffer() ;
+		StringBuilder sequence = new StringBuilder() ;
 		int seqIndex = 0; // track sequence.length()
 		for ( int i=0 ; i< groups.size(); i++){
 			Group g = groups.get(i);
@@ -453,8 +449,8 @@ public static String getFullAtomSequence(List<Group> groups, Map<Integer, Intege
 
 	private boolean alignNucleotideGroups(List<Group> seqRes, List<Group> atomRes) {
 
-		Map<Integer,Integer> seqresIndexPosition = new HashMap<Integer, Integer>();
-		Map<Integer,Integer> atomIndexPosition   = new HashMap<Integer, Integer>();
+		Map<Integer,Integer> seqresIndexPosition = new HashMap<>();
+		Map<Integer,Integer> atomIndexPosition   = new HashMap<>();
 
 		String seq1 = getFullAtomSequence(seqRes, seqresIndexPosition, true);
 		//
@@ -531,7 +527,7 @@ private boolean alignNucleotideGroups(List<Group> seqRes, List<Group> atomRes) {
 	}
 
 	private Sequence<NucleotideCompound> getNucleotideSequence(String seq) {
-		Sequence<NucleotideCompound> s = null;
+		Sequence<NucleotideCompound> s;
 
 		// first we try DNA, then RNA, them hybrid
 
@@ -573,8 +569,8 @@ private Sequence<NucleotideCompound> getNucleotideSequence(String seq) {
 	 */
 	private boolean alignProteinChains(List<Group> seqRes, List<Group> atomRes) {
 
-		Map<Integer,Integer> seqresIndexPosition = new HashMap<Integer, Integer>();
-		Map<Integer,Integer> atomIndexPosition   = new HashMap<Integer, Integer>();
+		Map<Integer,Integer> seqresIndexPosition = new HashMap<>();
+		Map<Integer,Integer> atomIndexPosition   = new HashMap<>();
 
 		String seq1 = getFullAtomSequence(seqRes, seqresIndexPosition, false);
 		//
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureIOFile.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureIOFile.java
index 91e22b8b3c..294566f9e3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureIOFile.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureIOFile.java
@@ -42,13 +42,13 @@ public interface StructureIOFile extends StructureProvider {
 	 * called only in the constructor of the implementing class.
 	 * @param ext  a String ...
 	 */
-	public void addExtension(String ext);
+    void addExtension(String ext);
 
 	/**
 	 * Returns a list of extensions supported by this class
 	 * @return a (potentially empty) list of strings
 	 */
-	public List<String> getExtensions();
+    List<String> getExtensions();
 
 	/**
 	 * Open filename and return a Structure object.
@@ -59,7 +59,7 @@ public interface StructureIOFile extends StructureProvider {
 	 * @return a Structure object
 	 * @throws IOException ...
 	 */
-	public Structure getStructure(String filename) throws IOException ;
+    Structure getStructure(String filename) throws IOException ;
 
 	/**
 	 * Read file from File and returns
@@ -69,5 +69,5 @@ public interface StructureIOFile extends StructureProvider {
 	 * @return a Structure object
 	 * @throws IOException ...
 	 */
-	public Structure getStructure(File file) throws IOException ;
+    Structure getStructure(File file) throws IOException ;
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
index 3c884bbc2d..585f790e00 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
@@ -119,7 +119,7 @@ public static ProteinSequence getProteinSequenceForStructure(Structure struct, M
 
 		for(Chain chain : struct.getChains()) {
 			List<Group> groups = chain.getAtomGroups();
-			Map<Integer,Integer> chainIndexPosition = new HashMap<Integer, Integer>();
+			Map<Integer,Integer> chainIndexPosition = new HashMap<>();
 			int prevLen = seqStr.length();
 
 			// get the sequence for this chain
@@ -128,9 +128,9 @@ public static ProteinSequence getProteinSequenceForStructure(Structure struct, M
 
 
 			// fix up the position to include previous chains, and map the value back to a Group
-			for(Integer seqIndex : chainIndexPosition.keySet()) {
-				Integer groupIndex = chainIndexPosition.get(seqIndex);
-				groupIndexPosition.put(prevLen + seqIndex, groups.get(groupIndex));
+			for(Map.Entry<Integer, Integer> entry : chainIndexPosition.entrySet()) {
+				Integer groupIndex = entry.getValue();
+				groupIndexPosition.put(prevLen + entry.getKey(), groups.get(groupIndex));
 			}
 		}
 
@@ -163,7 +163,7 @@ public static ProteinSequence getProteinSequenceForStructure(Structure struct, M
 	public static ResidueNumber[] matchSequenceToStructure(ProteinSequence seq, Structure struct) {
 
 		//1. Create ProteinSequence for struct while remembering to which group each residue corresponds
-		Map<Integer,Group> atomIndexPosition   = new HashMap<Integer, Group>();
+		Map<Integer,Group> atomIndexPosition   = new HashMap<>();
 
 		ProteinSequence structSeq = getProteinSequenceForStructure(struct,atomIndexPosition);
 
@@ -172,14 +172,14 @@ public static ResidueNumber[] matchSequenceToStructure(ProteinSequence seq, Stru
 		// Identity substitution matrix with +1 for match, -1 for mismatch
 		// TODO
 		SubstitutionMatrix<AminoAcidCompound> matrix =
-			new SimpleSubstitutionMatrix<AminoAcidCompound>(
-					AminoAcidCompoundSet.getAminoAcidCompoundSet(),
-					(short)1, (short)-1 );
-		matrix = new SimpleSubstitutionMatrix<AminoAcidCompound>(
+				new SimpleSubstitutionMatrix<>(
+						AminoAcidCompoundSet.getAminoAcidCompoundSet(),
+						(short) 1, (short) -1);
+		matrix = new SimpleSubstitutionMatrix<>(
 				AminoAcidCompoundSet.getAminoAcidCompoundSet(),
 				new InputStreamReader(
 						SimpleSubstitutionMatrix.class.getResourceAsStream("/matrices/blosum100.txt")),
-		"blosum100");
+				"blosum100");
 		SequencePair<ProteinSequence, AminoAcidCompound> pair =
 			Alignments.getPairwiseAlignment(seq, structSeq,
 					PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(), matrix);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java
index 66e2b6be04..90f987056b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java
@@ -144,7 +144,7 @@ class CifFileConsumerImpl implements CifFileConsumer<Structure> {
     private Map<String, String> asymId2authorId;
     private Matrix4d parsedScaleMatrix;
 
-    private FileParsingParameters params;
+    private final FileParsingParameters params;
 
     public CifFileConsumerImpl(FileParsingParameters params) {
         this.params = params;
@@ -1260,14 +1260,15 @@ public void finish() {
             seqMisMatches.add(seqMisMatch);
         }
 
-        for (String chainId : misMatchMap.keySet()){
+        for (Map.Entry<String, List<SeqMisMatch>> entry : misMatchMap.entrySet()){
+            String chainId = entry.getKey();
             Chain chain = structure.getPolyChainByPDB(chainId);
             if (chain == null) {
                 logger.warn("Could not set mismatches for chain with author id {}", chainId);
                 continue;
             }
 
-            chain.setSeqMisMatches(misMatchMap.get(chainId));
+            chain.setSeqMisMatches(entry.getValue());
         }
     }
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java
index b2b3222d58..4cb3e397c4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java
@@ -132,7 +132,7 @@ public static void downloadFile() throws IOException {
 	}
 
 
-	private static  void downloadFileFromRemote(URL remoteURL, File localFile) throws FileNotFoundException, IOException{
+	private static  void downloadFileFromRemote(URL remoteURL, File localFile) throws IOException{
 		logger.info("Downloading " + remoteURL + " to: " + localFile);
 		FileOutputStream out = new FileOutputStream(localFile);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java
index 87f6408e86..64b29ad38b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java
@@ -40,7 +40,7 @@ public class ChemCompGroupFactory {
 
 	private static ChemCompProvider chemCompProvider = new DownloadChemCompProvider();
 
-	private static SoftHashMap<String, ChemComp> cache = new SoftHashMap<String, ChemComp>(0);
+	private static final SoftHashMap<String, ChemComp> cache = new SoftHashMap<>(0);
 
 	public static ChemComp getChemComp(String recordName){
 
@@ -98,7 +98,7 @@ public static Group getGroupFromChemCompDictionary(String recordName) {
 		// make sure we work with upper case records
 		recordName = recordName.toUpperCase().trim();
 
-		Group g = null;
+		Group g;
 
 
 		ChemComp cc =  getChemComp(recordName);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemicalComponentDictionary.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemicalComponentDictionary.java
index 19c97f9aed..79ec004df5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemicalComponentDictionary.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemicalComponentDictionary.java
@@ -36,14 +36,14 @@
  */
 public class ChemicalComponentDictionary {
 
-	private Map<String, ChemComp> dictionary;
-	private Map<String,String> replaces;
-	private Map<String,String> isreplacedby;
+	private final Map<String, ChemComp> dictionary;
+	private final Map<String,String> replaces;
+	private final Map<String,String> isreplacedby;
 
 	public ChemicalComponentDictionary(){
-		dictionary = new HashMap<String, ChemComp>();
-		replaces   = new HashMap<String, String>();
-		isreplacedby = new HashMap<String, String>();
+		dictionary = new HashMap<>();
+		replaces   = new HashMap<>();
+		isreplacedby = new HashMap<>();
 	}
 
 	public boolean isReplaced(ChemComp c){
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
index 86355e40b6..00fc056555 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
@@ -87,7 +87,7 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 	// flags to make sure there is only one thread running that is loading the dictionary
 	static AtomicBoolean loading = new AtomicBoolean(false);
 
-	static final List<String> protectedIDs = new ArrayList<String> ();
+	static final List<String> protectedIDs = new ArrayList<>();
 	static {
 		protectedIDs.add("CON");
 		protectedIDs.add("PRN");
@@ -151,13 +151,7 @@ public void checkDoFirstInstall(){
 		} else {
 			// file exists.. did it get extracted?
 
-			FilenameFilter filter =new FilenameFilter() {
-
-				@Override
-				public boolean accept(File dir, String file) {
-					return file.endsWith(".cif.gz");
-				}
-			};
+			FilenameFilter filter = (dir1, file) -> file.endsWith(".cif.gz");
 			String[] files = dir.list(filter);
 			if ( files.length < 500) {
 				// not all did get unpacked
@@ -182,9 +176,9 @@ private void split() throws IOException {
 		int counter = 0;
 		InputStreamProvider prov = new InputStreamProvider();
 
-		try( BufferedReader buf = new BufferedReader (new InputStreamReader (prov.getInputStream(f)));
-				) {
-			String line = null;
+		try( BufferedReader buf = new BufferedReader (new InputStreamReader (prov.getInputStream(f)))
+		) {
+			String line;
 			line = buf.readLine ();
 			StringWriter writer = new StringWriter();
 
@@ -404,8 +398,8 @@ private static boolean downloadChemCompRecord(String recordName) {
 			URLConnection uconn = URLConnectionTools.openURLConnection(url);
 
 			try( PrintWriter pw = new PrintWriter(new GZIPOutputStream(new FileOutputStream(newFile)));
-					BufferedReader fileBuffer = new BufferedReader(new InputStreamReader(uconn.getInputStream()));
-					) {
+					BufferedReader fileBuffer = new BufferedReader(new InputStreamReader(uconn.getInputStream()))
+			) {
 
 				String line;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
index 14fdac7d3e..182250f427 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
@@ -497,7 +497,7 @@ public static List<AtomSite> convertChainToAtomSites(Chain c, int model, String
 	 * @return
 	 */
 	public static List<AtomSite> convertStructureToAtomSites(Structure s) {
-		List<AtomSite> list = new ArrayList<AtomSite>();
+		List<AtomSite> list = new ArrayList<>();
 
 		for (int m=0;m<s.nrModels();m++) {
 			for (Chain c:s.getChains(m)) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMcifConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMcifConsumer.java
index 9284c2ad31..b65cbb253c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMcifConsumer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMcifConsumer.java
@@ -37,63 +37,63 @@ public interface MMcifConsumer {
 	/** called at start of document
 	 *
 	 */
-	public void documentStart();
+    void documentStart();
 
 	/** called at end of document
 	 *
 	 */
-	public void documentEnd();
+    void documentEnd();
 
 
 	/** A new AtomSite record has been read. Contains the Atom data
 	 *
 	 * @param atom
 	 */
-	public void newAtomSite(AtomSite atom);
-	public void newEntity(Entity entity);
-	public void newEntityPoly(EntityPoly entityPoly);
-	public void newEntityPolySeq(EntityPolySeq epolseq);
-	public void newStructAsym(StructAsym sasym);
-	public void setStruct(Struct struct);
-	public void newDatabasePDBrev(DatabasePDBrev dbrev);
-	public void newDatabasePDBrevRecord(DatabasePdbrevRecord dbrev);
-	public void newDatabasePDBremark(DatabasePDBremark remark);
-	public void newExptl(Exptl exptl);
-	public void newCell(Cell cell);
-	public void newSymmetry(Symmetry symmetry);
-	public void newStructNcsOper(StructNcsOper sNcsOper);
-	public void newAtomSites(AtomSites atomSites);
-	public void newStructRef(StructRef sref);
-	public void newStructRefSeq(StructRefSeq sref);
-	public void newStructRefSeqDif(StructRefSeqDif sref);
-	public void newStructSite(StructSite sref);
-	public void newStructSiteGen(StructSiteGen sref);
-	public void newPdbxAuditRevisionHistory(PdbxAuditRevisionHistory history);
-	public void newPdbxDatabaseStatus(PdbxDatabaseStatus status);
-	public void newPdbxPolySeqScheme(PdbxPolySeqScheme ppss);
-	public void newPdbxNonPolyScheme(PdbxNonPolyScheme ppss);
-	public void newPdbxEntityNonPoly(PdbxEntityNonPoly pen);
-	public void newStructKeywords(StructKeywords kw);
-	public void newRefine(Refine r);
-	public void newChemComp(ChemComp c);
-	public void newChemCompDescriptor(ChemCompDescriptor ccd);
-	public void newPdbxStructOperList(PdbxStructOperList structOper);
-	public void newPdbxStrucAssembly(PdbxStructAssembly strucAssembly);
-	public void newPdbxStrucAssemblyGen(PdbxStructAssemblyGen strucAssembly);
-	public void newChemCompAtom(ChemCompAtom atom);
-	public void newPdbxChemCompIndentifier(PdbxChemCompIdentifier id);
-	public void newChemCompBond(ChemCompBond bond);
-	public void newPdbxChemCompDescriptor(PdbxChemCompDescriptor desc);
-	public void newEntitySrcGen(EntitySrcGen entitySrcGen);
-	public void newEntitySrcNat(EntitySrcNat entitySrcNat);
-	public void newEntitySrcSyn(EntitySrcSyn entitySrcSyn);
-	public void newStructConn(StructConn structConn);
+    void newAtomSite(AtomSite atom);
+	void newEntity(Entity entity);
+	void newEntityPoly(EntityPoly entityPoly);
+	void newEntityPolySeq(EntityPolySeq epolseq);
+	void newStructAsym(StructAsym sasym);
+	void setStruct(Struct struct);
+	void newDatabasePDBrev(DatabasePDBrev dbrev);
+	void newDatabasePDBrevRecord(DatabasePdbrevRecord dbrev);
+	void newDatabasePDBremark(DatabasePDBremark remark);
+	void newExptl(Exptl exptl);
+	void newCell(Cell cell);
+	void newSymmetry(Symmetry symmetry);
+	void newStructNcsOper(StructNcsOper sNcsOper);
+	void newAtomSites(AtomSites atomSites);
+	void newStructRef(StructRef sref);
+	void newStructRefSeq(StructRefSeq sref);
+	void newStructRefSeqDif(StructRefSeqDif sref);
+	void newStructSite(StructSite sref);
+	void newStructSiteGen(StructSiteGen sref);
+	void newPdbxAuditRevisionHistory(PdbxAuditRevisionHistory history);
+	void newPdbxDatabaseStatus(PdbxDatabaseStatus status);
+	void newPdbxPolySeqScheme(PdbxPolySeqScheme ppss);
+	void newPdbxNonPolyScheme(PdbxNonPolyScheme ppss);
+	void newPdbxEntityNonPoly(PdbxEntityNonPoly pen);
+	void newStructKeywords(StructKeywords kw);
+	void newRefine(Refine r);
+	void newChemComp(ChemComp c);
+	void newChemCompDescriptor(ChemCompDescriptor ccd);
+	void newPdbxStructOperList(PdbxStructOperList structOper);
+	void newPdbxStrucAssembly(PdbxStructAssembly strucAssembly);
+	void newPdbxStrucAssemblyGen(PdbxStructAssemblyGen strucAssembly);
+	void newChemCompAtom(ChemCompAtom atom);
+	void newPdbxChemCompIndentifier(PdbxChemCompIdentifier id);
+	void newChemCompBond(ChemCompBond bond);
+	void newPdbxChemCompDescriptor(PdbxChemCompDescriptor desc);
+	void newEntitySrcGen(EntitySrcGen entitySrcGen);
+	void newEntitySrcNat(EntitySrcNat entitySrcNat);
+	void newEntitySrcSyn(EntitySrcSyn entitySrcSyn);
+	void newStructConn(StructConn structConn);
 
 	/** AuditAuthor contains the info from the PDB-AUTHOR records.
 	 *
 	 * @param aa
 	 */
-	public void newAuditAuthor(AuditAuthor aa);
+    void newAuditAuthor(AuditAuthor aa);
 
 	/** This method is called if no particular handler for the provided cif category
 	 * has been implemented so far.
@@ -101,10 +101,10 @@ public interface MMcifConsumer {
 	 * @param loopFields the fields of this category.
 	 * @param lineData the data that is being provided.
 	 */
-	public void newGenericData(String category, List<String> loopFields, List<String> lineData);
+    void newGenericData(String category, List<String> loopFields, List<String> lineData);
 
-	public void setFileParsingParameters(FileParsingParameters params);
-	public FileParsingParameters getFileParsingParameters();
+	void setFileParsingParameters(FileParsingParameters params);
+	FileParsingParameters getFileParsingParameters();
 
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMcifParser.java
index e20a35d87c..a6c8655ece 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMcifParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMcifParser.java
@@ -36,31 +36,31 @@ public interface MMcifParser {
 	 *
 	 * @param consumer a consumer object.
 	 */
-	public void addMMcifConsumer(MMcifConsumer consumer);
+    void addMMcifConsumer(MMcifConsumer consumer);
 
 	/** Remove all consumers from the parser.
 	 *
 	 */
-	public void clearConsumers();
+    void clearConsumers();
 
 	/** remove a single consumer from the parser
 	 *
 	 * @param consumer
 	 */
-	public void removeMMcifConsumer(MMcifConsumer consumer);
+    void removeMMcifConsumer(MMcifConsumer consumer);
 
 
 	/** Start the actual parsing. The parser will trigger events that are defined by the MMcifConsumer class.
 	 *
 	 * @param buf a BufferedReader.
 	 */
-	public void parse(BufferedReader buf) throws IOException;
+    void parse(BufferedReader buf) throws IOException;
 
 	/** Start the actual parsing. The parser will trigger events that are defined by the MMcifConsumer class.
 	 *
 	 * @param inStream InputStream to parse from.
 	 */
-	public void parse(InputStream inStream) throws IOException;
+    void parse(InputStream inStream) throws IOException;
 
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java
index dbb91bd71f..4438de1470 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java
@@ -255,14 +255,9 @@ public void newGenericData(String category, List<String> loopFields, List<String
 		d.setLowerLimit(Float.parseFloat(lineData.get(2)));
 		d.setUpperLimit(Float.parseFloat(lineData.get(3)));
 
-		List<MetalBondDistance> defs = definitions.get(d.getAtomType1());
+        List<MetalBondDistance> defs = definitions.computeIfAbsent(d.getAtomType1(), k -> new ArrayList<>());
 
-		if ( defs == null){
-			defs = new ArrayList<>();
-			definitions.put(d.getAtomType1(),defs);
-		}
-
-		defs.add(d);
+        defs.add(d);
 
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
index b0cdecdc14..5279083e25 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
@@ -352,7 +352,7 @@ public void newAtomSite(AtomSite atom) {
 
 		boolean isHetAtomInFile = false;
 
-		Character aminoCode1 = null;
+		Character aminoCode1;
 		if ( recordName.equals("ATOM") )
 			aminoCode1 = StructureTools.get1LetterCodeAmino(groupCode3);
 		else {
@@ -399,7 +399,7 @@ public void newAtomSite(AtomSite atom) {
 
 			// we came to the beginning of a new NMR model
 			allModels.add(currentModel);
-			currentModel = new ArrayList<Chain>();
+			currentModel = new ArrayList<>();
 			currentChain = null;
 			currentGroup = null;
 		}
@@ -569,9 +569,9 @@ private Atom convertAtom(AtomSite atom){
 
 		String alt = atom.getLabel_alt_id();
 		if (( alt != null ) && ( alt.length() > 0) && (! alt.equals("."))){
-			a.setAltLoc(new Character(alt.charAt(0)));
+			a.setAltLoc(alt.charAt(0));
 		} else {
-			a.setAltLoc(new Character(' '));
+			a.setAltLoc(' ');
 		}
 
 		Element element = Element.R;
@@ -630,7 +630,7 @@ private Group getCorrectAltLocGroup( Character altLoc,
 			Group altLocG = (Group) currentGroup.clone();
 			// drop atoms from cloned group...
 			// https://redmine.open-bio.org/issues/3307
-			altLocG.setAtoms(new ArrayList<Atom>());
+			altLocG.setAtoms(new ArrayList<>());
 			altLocG.getAltLocs().clear();
 			currentGroup.addAltLoc(altLocG);
 			return altLocG;
@@ -658,27 +658,27 @@ public void documentStart() {
 		currentNmrModelNumber 	= null;
 		//atomCount     		= 0;
 
-		allModels     = new ArrayList<List<Chain>>();
-		currentModel  = new ArrayList<Chain>();
-		entities      = new ArrayList<Entity>();
+		allModels     = new ArrayList<>();
+		currentModel  = new ArrayList<>();
+		entities      = new ArrayList<>();
 		entityPolys   = new ArrayList<>();
-		strucRefs     = new ArrayList<StructRef>();
-		seqResChains  = new ArrayList<Chain>();
-		entityChains  = new ArrayList<Chain>();
-		structAsyms   = new ArrayList<StructAsym>();
+		strucRefs     = new ArrayList<>();
+		seqResChains  = new ArrayList<>();
+		entityChains  = new ArrayList<>();
+		structAsyms   = new ArrayList<>();
 
-		asymId2entityId = new HashMap<String,String>();
+		asymId2entityId = new HashMap<>();
 		asymId2authorId = new HashMap<>();
-		structOpers   = new ArrayList<PdbxStructOperList>();
-		strucAssemblies = new ArrayList<PdbxStructAssembly>();
-		strucAssemblyGens = new ArrayList<PdbxStructAssemblyGen>();
-		entitySrcGens = new ArrayList<EntitySrcGen>();
-		entitySrcNats = new ArrayList<EntitySrcNat>();
-		entitySrcSyns = new ArrayList<EntitySrcSyn>();
-		structConn = new ArrayList<StructConn>();
-		structNcsOper = new ArrayList<StructNcsOper>();
-		sequenceDifs = new ArrayList<StructRefSeqDif>();
-		structSiteGens = new ArrayList<StructSiteGen>();
+		structOpers   = new ArrayList<>();
+		strucAssemblies = new ArrayList<>();
+		strucAssemblyGens = new ArrayList<>();
+		entitySrcGens = new ArrayList<>();
+		entitySrcNats = new ArrayList<>();
+		entitySrcSyns = new ArrayList<>();
+		structConn = new ArrayList<>();
+		structNcsOper = new ArrayList<>();
+		sequenceDifs = new ArrayList<>();
+		structSiteGens = new ArrayList<>();
 	}
 
 
@@ -791,11 +791,11 @@ public void documentEnd() {
 
 			// the more detailed mapping of chains to rotation operations happens in StructureIO...
 
-			Map<Integer,BioAssemblyInfo> bioAssemblies = new LinkedHashMap<Integer, BioAssemblyInfo>();
+			Map<Integer,BioAssemblyInfo> bioAssemblies = new LinkedHashMap<>();
 
 			for ( PdbxStructAssembly psa : strucAssemblies){
 
-				List<PdbxStructAssemblyGen> psags = new ArrayList<PdbxStructAssemblyGen>(1);
+				List<PdbxStructAssemblyGen> psags = new ArrayList<>(1);
 
 				for ( PdbxStructAssemblyGen psag: strucAssemblyGens ) {
 					if ( psag.getAssembly_id().equals(psa.getId())) {
@@ -853,7 +853,7 @@ public void documentEnd() {
 		setCrystallographicInfoMetadata();
 
 
-		Map<String,List<SeqMisMatch>> misMatchMap = new HashMap<String, List<SeqMisMatch>>();
+		Map<String,List<SeqMisMatch>> misMatchMap = new HashMap<>();
 		for (StructRefSeqDif sdif : sequenceDifs) {
 			SeqMisMatch misMatch = new SeqMisMatchImpl();
 			misMatch.setDetails(sdif.getDetails());
@@ -869,16 +869,13 @@ public void documentEnd() {
 			misMatch.setSeqNum(sdif.getSeq_num());
 
 
-			List<SeqMisMatch> mms = misMatchMap.get(sdif.getPdbx_pdb_strand_id());
-			if ( mms == null) {
-				mms = new ArrayList<SeqMisMatch>();
-				misMatchMap.put(sdif.getPdbx_pdb_strand_id(),mms);
-			}
+			List<SeqMisMatch> mms = misMatchMap.computeIfAbsent(sdif.getPdbx_pdb_strand_id(), k -> new ArrayList<>());
 			mms.add(misMatch);
 
 		}
 
-		for (String chainId : misMatchMap.keySet()){
+		for (Map.Entry<String, List<SeqMisMatch>> entry : misMatchMap.entrySet()){
+			String chainId = entry.getKey();
 
 			Chain chain = structure.getPolyChainByPDB(chainId);
 
@@ -887,7 +884,7 @@ public void documentEnd() {
 				continue;
 			}
 
-			chain.setSeqMisMatches(misMatchMap.get(chainId));
+			chain.setSeqMisMatches(entry.getValue());
 
 
 		}
@@ -1070,7 +1067,7 @@ private void alignSeqRes() {
 				//map the atoms to the seqres...
 
 				// we need to first clone the seqres so that they stay independent for different models
-				List<Group> seqResGroups = new ArrayList<Group>();
+				List<Group> seqResGroups = new ArrayList<>();
 				for (int i=0;i<seqResChain.getAtomGroups().size();i++) {
 					seqResGroups.add((Group)seqResChain.getAtomGroups().get(i).clone());
 				}
@@ -1281,7 +1278,7 @@ private void initMaps() {
 
 	private void setStructNcsOps() {
 
-		ArrayList<Matrix4d> ncsOperators = new ArrayList<Matrix4d>();
+		ArrayList<Matrix4d> ncsOperators = new ArrayList<>();
 
 		for (StructNcsOper sNcsOper:structNcsOper) {
 
@@ -1322,7 +1319,7 @@ private void setStructNcsOps() {
 		// we only set it if not empty, otherwise remains null
 		if (ncsOperators.size()>0) {
 			structure.getCrystallographicInfo().setNcsOperators(
-					ncsOperators.toArray(new Matrix4d[ncsOperators.size()]));
+					ncsOperators.toArray(new Matrix4d[0]));
 		}
 	}
 
@@ -1362,7 +1359,7 @@ public void newDatabasePDBrevRecord(DatabasePdbrevRecord record) {
 
 		List<DatabasePdbrevRecord> revRecords = header.getRevisionRecords();
 		if ( revRecords == null) {
-			revRecords = new ArrayList<DatabasePdbrevRecord>();
+			revRecords = new ArrayList<>();
 			header.setRevisionRecords(revRecords);
 		}
 		revRecords.add(record);
@@ -1491,7 +1488,7 @@ public void newDatabasePDBremark(DatabasePDBremark remark) {
 				// line contains ANGSTROM info...
 				String resolution = line.substring(i-5,i).trim();
 				// convert string to float
-				float res = 99 ;
+				float res;
 				try {
 					res = Float.parseFloat(resolution);
 
@@ -1573,8 +1570,8 @@ public void newAuditAuthor(AuditAuthor aa){
 
 		String name =  aa.getName();
 
-		StringBuffer famName = new StringBuffer();
-		StringBuffer initials = new StringBuffer();
+		StringBuilder famName = new StringBuilder();
+		StringBuilder initials = new StringBuilder();
 		boolean afterComma = false;
 		for ( char c: name.toCharArray()) {
 			if ( c == ' ')
@@ -1590,7 +1587,7 @@ public void newAuditAuthor(AuditAuthor aa){
 				famName.append(c);
 		}
 
-		StringBuffer newaa = new StringBuffer();
+		StringBuilder newaa = new StringBuilder();
 		newaa.append(initials);
 		newaa.append(famName);
 
@@ -1757,14 +1754,14 @@ public void newStructRefSeq(StructRefSeq sref) {
 			return;
 		}
 
-		Character begin_ins_code = ' ';
+		char begin_ins_code = ' ';
 		if (sref.getPdbx_seq_align_beg_ins_code() != null ) {
-		    begin_ins_code = new Character(sref.getPdbx_seq_align_beg_ins_code().charAt(0));
+		    begin_ins_code = sref.getPdbx_seq_align_beg_ins_code().charAt(0);
 		}
 
-		Character end_ins_code = ' ';
+		char end_ins_code = ' ';
 		if (sref.getPdbx_seq_align_end_ins_code() != null) {
-		    end_ins_code = new Character(sref.getPdbx_seq_align_end_ins_code().charAt(0));
+		    end_ins_code = sref.getPdbx_seq_align_end_ins_code().charAt(0);
 		}
 
 		if (begin_ins_code == '?')
@@ -1782,14 +1779,14 @@ public void newStructRefSeq(StructRefSeq sref) {
 		int dbseqbegin = Integer.parseInt(sref.getDb_align_beg());
 		int dbseqend   = Integer.parseInt(sref.getDb_align_end());
 
-		Character db_begin_in_code = ' ';
+		char db_begin_in_code = ' ';
 		if (sref.getPdbx_db_align_beg_ins_code() != null) {
-		    db_begin_in_code = new Character(sref.getPdbx_db_align_beg_ins_code().charAt(0));
+		    db_begin_in_code = sref.getPdbx_db_align_beg_ins_code().charAt(0);
 		}
 
-		Character db_end_in_code = ' ';
+		char db_end_in_code = ' ';
 		if (sref.getPdbx_db_align_end_ins_code() != null) {
-		    db_end_in_code = new Character(sref.getPdbx_db_align_end_ins_code().charAt(0));
+		    db_end_in_code = sref.getPdbx_db_align_end_ins_code().charAt(0);
 		}
 
 		if (db_begin_in_code == '?')
@@ -1807,7 +1804,7 @@ public void newStructRefSeq(StructRefSeq sref) {
 
 		List<DBRef> dbrefs = structure.getDBRefs();
 		if ( dbrefs == null)
-			dbrefs = new ArrayList<DBRef>();
+			dbrefs = new ArrayList<>();
 		dbrefs.add(r);
 
 		logger.debug(r.toPDB());
@@ -2072,7 +2069,7 @@ public void newStructSite(StructSite structSite) {
 
 		// Simply implement the method.
 		List<Site> sites = structure.getSites();
-		if (sites == null) sites = new ArrayList<Site>();
+		if (sites == null) sites = new ArrayList<>();
 
 		Site site = null;
 		for (Site asite : sites) {
@@ -2096,7 +2093,7 @@ public void newStructSite(StructSite structSite) {
 	 */
 	private void addSites() {
 		List<Site> sites = structure.getSites();
-		if (sites == null) sites = new ArrayList<Site>();
+		if (sites == null) sites = new ArrayList<>();
 
 		for (StructSiteGen siteGen : structSiteGens) {
 				// For each StructSiteGen, find the residues involved, if they exist then
@@ -2150,7 +2147,7 @@ private void addSites() {
 					}
 
 					List<Group> groups = site.getGroups();
-					if (groups == null) groups = new ArrayList<Group>();
+					if (groups == null) groups = new ArrayList<>();
 
 					// Check the self-consistency of the residue reference from auth_seq_id and chain_id
 					if (!comp_id.equals(g.getPDBName())) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
index 7e9b23d3c2..6430db5e9c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
@@ -138,14 +138,14 @@ public class SimpleMMcifParser implements MMcifParser {
 	public static final String STRING_LIMIT = ";";
 
 
-	private List<MMcifConsumer> consumers ;
+	private final List<MMcifConsumer> consumers ;
 
 	private Struct struct ;
 
 	private static final Logger logger = LoggerFactory.getLogger(SimpleMMcifParser.class);
 
 	public SimpleMMcifParser(){
-		consumers = new ArrayList<MMcifConsumer>();
+		consumers = new ArrayList<>();
 		struct = null;
 	}
 
@@ -200,15 +200,15 @@ public void parse(BufferedReader buf)
 
 		// init container objects...
 		struct = new Struct();
-		String line = null;
+		String line;
 
 		boolean inLoop = false;
 		boolean inLoopData = false;
 
 
-		List<String> loopFields = new ArrayList<String>();
-		List<String> lineData   = new ArrayList<String>();
-		Set<String> loopWarnings = new HashSet<String>(); // used only to reduce logging statements
+		List<String> loopFields = new ArrayList<>();
+		List<String> lineData   = new ArrayList<>();
+		Set<String> loopWarnings = new HashSet<>(); // used only to reduce logging statements
 
 		String category = null;
 
@@ -288,7 +288,7 @@ public void parse(BufferedReader buf)
 						}
 						category = key.substring(0,pos);
 						String value = data.get(1);
-						loopFields.add(key.substring(pos+1,key.length()));
+						loopFields.add(key.substring(pos+1));
 						lineData.add(value);
 
 						logger.debug("Found data for category {}: {}", key, value);
@@ -382,7 +382,7 @@ public void parse(BufferedReader buf)
 					category = key.substring(0,pos);
 
 					String value = data.get(1);
-					loopFields.add(key.substring(pos+1,key.length()));
+					loopFields.add(key.substring(pos+1));
 					lineData.add(value);
 
 					logger.debug("Found data for category {}: {}", key, value);
@@ -413,7 +413,7 @@ private void resetBuffers(List<String> loopFields, List<String> lineData, Set<St
 
 	private List<String> processSingleLine(String line){
 
-		List<String> data = new ArrayList<String>();
+		List<String> data = new ArrayList<>();
 
 		if ( line.trim().length() == 0){
 			return data;
@@ -430,7 +430,7 @@ private List<String> processSingleLine(String line){
 
 		for (int i=0; i< line.length(); i++ ){
 
-			Character c = line.charAt(i);
+			char c = line.charAt(i);
 
 			Character nextC = null;
 			if (i < line.length() - 1)
@@ -539,7 +539,7 @@ private List<String> processLine(String line,
 
 		//System.out.println("XX processLine " + fieldLength + " " + line);
 		// go through the line and process each character
-		List<String> lineData = new ArrayList<String>();
+		List<String> lineData = new ArrayList<>();
 
 		boolean inString = false;
 
@@ -554,7 +554,7 @@ private List<String> processLine(String line,
 					if ( line.length() > 1)
 						bigWord = new StringBuilder(line.substring(1));
 					else
-						bigWord = new StringBuilder("");
+						bigWord = new StringBuilder();
 
 
 				} else {
@@ -571,9 +571,7 @@ private List<String> processLine(String line,
 
 					List<String> dat = processSingleLine(line);
 
-					for (String d : dat){
-						lineData.add(d);
-					}
+					lineData.addAll(dat);
 				}
 			}
 
@@ -616,258 +614,309 @@ private void endLineChecks(String category,List<String> loopFields, List<String>
 					lineData );
 		}
 
-		if ( category.equals("_entity")){
+		switch (category) {
+			case "_entity":
 
-			Entity e =  (Entity) buildObject(
-					Entity.class.getName(),
-					loopFields,lineData, loopWarnings);
-			triggerNewEntity(e);
+				Entity e = (Entity) buildObject(
+						Entity.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewEntity(e);
 
-		} else if (category.equals("_entity_poly")) {
-			EntityPoly ep = (EntityPoly) buildObject(EntityPoly.class.getName(), loopFields, lineData, loopWarnings);
-			triggerNewEntityPoly(ep);
+				break;
+			case "_entity_poly":
+				EntityPoly ep = (EntityPoly) buildObject(EntityPoly.class.getName(), loopFields, lineData, loopWarnings);
+				triggerNewEntityPoly(ep);
 
-		} else if ( category.equals("_struct")){
+				break;
+			case "_struct":
 
-			struct =  (Struct) buildObject(
-					Struct.class.getName(),
-					loopFields, lineData, loopWarnings);
+				struct = (Struct) buildObject(
+						Struct.class.getName(),
+						loopFields, lineData, loopWarnings);
 
-		} else if ( category.equals("_atom_site")){
+				break;
+			case "_atom_site":
 
-			AtomSite a = (AtomSite) buildObject(
-					AtomSite.class.getName(),
-					loopFields, lineData, loopWarnings);
-			triggerNewAtomSite(a);
+				AtomSite a = (AtomSite) buildObject(
+						AtomSite.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewAtomSite(a);
 
-		} else if ( category.equals("_database_PDB_rev")){
-			DatabasePDBrev dbrev = (DatabasePDBrev) buildObject(
-					DatabasePDBrev.class.getName(),
-					loopFields, lineData, loopWarnings);
+				break;
+			case "_database_PDB_rev": {
+				DatabasePDBrev dbrev = (DatabasePDBrev) buildObject(
+						DatabasePDBrev.class.getName(),
+						loopFields, lineData, loopWarnings);
 
-			triggerNewDatabasePDBrev(dbrev);
-
-		} else if ( category.equals("_database_PDB_rev_record")){
-			DatabasePdbrevRecord dbrev = (DatabasePdbrevRecord) buildObject(
-					DatabasePdbrevRecord.class.getName(),
-					loopFields, lineData, loopWarnings);
-
-			triggerNewDatabasePDBrevRecord(dbrev);
-
-	// MMCIF version 5 dates
-		} else if ( category.equals("_pdbx_audit_revision_history")) {
-			PdbxAuditRevisionHistory history = (PdbxAuditRevisionHistory) buildObject(
-					PdbxAuditRevisionHistory.class.getName(),
-					loopFields, lineData, loopWarnings);
-
-			triggerNewPdbxAuditRevisionHistory(history);
-
-	// MMCIF version 5 dates
-		} else if ( category.equals("_pdbx_database_status")) {
-			PdbxDatabaseStatus status = (PdbxDatabaseStatus) buildObject(
-					PdbxDatabaseStatus.class.getName(),
-					loopFields, lineData, loopWarnings);
-
-			triggerNewPdbxDatabaseStatus(status);
-
-		}else if (  category.equals("_database_PDB_remark")){
-			DatabasePDBremark remark = (DatabasePDBremark) buildObject(
-					DatabasePDBremark.class.getName(),
-					loopFields, lineData, loopWarnings);
-
-			triggerNewDatabasePDBremark(remark);
-
-		} else if ( category.equals("_exptl")){
-			Exptl exptl  = (Exptl) buildObject(
-					Exptl.class.getName(),
-					loopFields,lineData, loopWarnings);
-
-			triggerExptl(exptl);
-
-		} else if ( category.equals("_cell")){
-			Cell cell  = (Cell) buildObject(
-					Cell.class.getName(),
-					loopFields,lineData, loopWarnings);
-
-			triggerNewCell(cell);
-
-		} else if ( category.equals("_symmetry")){
-			Symmetry symmetry  = (Symmetry) buildObject(
-					Symmetry.class.getName(),
-					loopFields,lineData, loopWarnings);
-
-			triggerNewSymmetry(symmetry);
-		} else if ( category.equals("_struct_ncs_oper")) {
-
-			StructNcsOper sNcsOper = (StructNcsOper) buildObject(
-					StructNcsOper.class.getName(),
-					loopFields, lineData, loopWarnings);
-			triggerNewStructNcsOper(sNcsOper);
-		} else if ( category.equals("_atom_sites")) {
-
-			AtomSites atomSites = (AtomSites) buildObject(
-					AtomSites.class.getName(),
-					loopFields, lineData, loopWarnings);
-			triggerNewAtomSites(atomSites);
-
-		} else if ( category.equals("_struct_ref")){
-			StructRef sref  = (StructRef) buildObject(
-					StructRef.class.getName(),
-					loopFields,lineData, loopWarnings);
-
-			triggerNewStrucRef(sref);
-
-		} else if ( category.equals("_struct_ref_seq")){
-			StructRefSeq sref  = (StructRefSeq) buildObject(
-					StructRefSeq.class.getName(),
-					loopFields,lineData, loopWarnings);
-
-			triggerNewStrucRefSeq(sref);
-		} else if ( category.equals("_struct_ref_seq_dif")) {
-			StructRefSeqDif sref = (StructRefSeqDif) buildObject(
-					StructRefSeqDif.class.getName(),
-					loopFields, lineData, loopWarnings);
-
-			triggerNewStrucRefSeqDif(sref);
-		} else if ( category.equals("_struct_site_gen")) {
-			StructSiteGen sref = (StructSiteGen) buildObject(
-					StructSiteGen.class.getName(),
-					loopFields, lineData, loopWarnings);
-
-			triggerNewStructSiteGen(sref);
-		} else if ( category.equals("_struct_site")) {
-			StructSite sref = (StructSite) buildObject(
-					StructSite.class.getName(),
-					loopFields, lineData, loopWarnings);
-			triggerNewStructSite(sref);
-		} else if ( category.equals("_entity_poly_seq")){
-			EntityPolySeq exptl  = (EntityPolySeq) buildObject(
-					EntityPolySeq.class.getName(),
-					loopFields,lineData, loopWarnings);
-
-			triggerNewEntityPolySeq(exptl);
-		} else if ( category.equals("_entity_src_gen")){
-			EntitySrcGen entitySrcGen = (EntitySrcGen) buildObject(
-					EntitySrcGen.class.getName(),
-					loopFields,lineData, loopWarnings);
-			triggerNewEntitySrcGen(entitySrcGen);
-		} else if ( category.equals("_entity_src_nat")){
-			EntitySrcNat entitySrcNat = (EntitySrcNat) buildObject(
-					EntitySrcNat.class.getName(),
-					loopFields,lineData, loopWarnings);
-			triggerNewEntitySrcNat(entitySrcNat);
-		} else if ( category.equals("_pdbx_entity_src_syn")){
-			EntitySrcSyn entitySrcSyn = (EntitySrcSyn) buildObject(
-					EntitySrcSyn.class.getName(),
-					loopFields,lineData, loopWarnings);
-			triggerNewEntitySrcSyn(entitySrcSyn);
-		} else if ( category.equals("_struct_asym")){
-			StructAsym sasym  = (StructAsym) buildObject(
-					StructAsym.class.getName(),
-					loopFields,lineData, loopWarnings);
-
-			triggerNewStructAsym(sasym);
-
-		} else if ( category.equals("_pdbx_poly_seq_scheme")){
-			PdbxPolySeqScheme ppss  = (PdbxPolySeqScheme) buildObject(
-					PdbxPolySeqScheme.class.getName(),
-					loopFields,lineData, loopWarnings);
-
-			triggerNewPdbxPolySeqScheme(ppss);
-
-		} else if ( category.equals("_pdbx_nonpoly_scheme")){
-			PdbxNonPolyScheme ppss  = (PdbxNonPolyScheme) buildObject(
-					PdbxNonPolyScheme.class.getName(),
-					loopFields,lineData, loopWarnings);
-
-			triggerNewPdbxNonPolyScheme(ppss);
-
-		} else if ( category.equals("_pdbx_entity_nonpoly")){
-			PdbxEntityNonPoly pen = (PdbxEntityNonPoly) buildObject(
-					PdbxEntityNonPoly.class.getName(),
-					loopFields,lineData, loopWarnings
-					);
-			triggerNewPdbxEntityNonPoly(pen);
-		} else if ( category.equals("_struct_keywords")){
-			StructKeywords kw = (StructKeywords)buildObject(
-					StructKeywords.class.getName(),
-					loopFields,lineData, loopWarnings
-					);
-			triggerNewStructKeywords(kw);
-		} else if (category.equals("_refine")){
-			Refine r = (Refine)buildObject(
-					Refine.class.getName(),
-					loopFields,lineData, loopWarnings
-					);
-			triggerNewRefine(r);
-		} else if (category.equals("_chem_comp")){
-			ChemComp c = (ChemComp)buildObject(
-					ChemComp.class.getName(),
-					loopFields, lineData, loopWarnings
-					);
-			triggerNewChemComp(c);
-		} else if (category.equals("_audit_author")) {
-			AuditAuthor aa = (AuditAuthor)buildObject(
-					AuditAuthor.class.getName(),
-					loopFields, lineData, loopWarnings);
-			triggerNewAuditAuthor(aa);
-		} else if (category.equals("_pdbx_chem_comp_descriptor")) {
-			ChemCompDescriptor ccd = (ChemCompDescriptor) buildObject(
-					ChemCompDescriptor.class.getName(),
-					loopFields, lineData, loopWarnings);
-			triggerNewChemCompDescriptor(ccd);
-		} else if (category.equals("_pdbx_struct_oper_list")) {
-
-			PdbxStructOperList structOper = (PdbxStructOperList) buildObject(
-					PdbxStructOperList.class.getName(),
-					loopFields, lineData, loopWarnings
-					);
-			triggerNewPdbxStructOper(structOper);
-
-		} else if (category.equals("_pdbx_struct_assembly")) {
-			PdbxStructAssembly sa = (PdbxStructAssembly) buildObject(
-					PdbxStructAssembly.class.getName(),
-					loopFields, lineData, loopWarnings);
-			triggerNewPdbxStructAssembly(sa);
-
-		} else if (category.equals("_pdbx_struct_assembly_gen")) {
-			PdbxStructAssemblyGen sa = (PdbxStructAssemblyGen) buildObject(
-					PdbxStructAssemblyGen.class.getName(),
-					loopFields, lineData, loopWarnings);
-			triggerNewPdbxStructAssemblyGen(sa);
-		} else if ( category.equals("_chem_comp_atom")){
-			ChemCompAtom atom = (ChemCompAtom)buildObject(
-					ChemCompAtom.class.getName(),
-					loopFields,lineData, loopWarnings);
-			triggerNewChemCompAtom(atom);
-
-		}else if ( category.equals("_chem_comp_bond")){
-			ChemCompBond bond = (ChemCompBond)buildObject(
-					ChemCompBond.class.getName(),
-					loopFields,lineData, loopWarnings);
-			triggerNewChemCompBond(bond);
-		} else if ( category.equals("_pdbx_chem_comp_identifier")){
-			PdbxChemCompIdentifier id = (PdbxChemCompIdentifier)buildObject(
-					PdbxChemCompIdentifier.class.getName(),
-					loopFields,lineData, loopWarnings);
-			triggerNewPdbxChemCompIdentifier(id);
-		} else if ( category.equals("_pdbx_chem_comp_descriptor")){
-			PdbxChemCompDescriptor id = (PdbxChemCompDescriptor)buildObject(
-					PdbxChemCompDescriptor.class.getName(),
-					loopFields,lineData, loopWarnings);
-			triggerNewPdbxChemCompDescriptor(id);
-		} else if ( category.equals("_struct_conn")){
-			StructConn id = (StructConn)buildObject(
-					StructConn.class.getName(),
-					loopFields,lineData, loopWarnings);
-			triggerNewStructConn(id);
+				triggerNewDatabasePDBrev(dbrev);
 
-		} else {
+				break;
+			}
+			case "_database_PDB_rev_record": {
+				DatabasePdbrevRecord dbrev = (DatabasePdbrevRecord) buildObject(
+						DatabasePdbrevRecord.class.getName(),
+						loopFields, lineData, loopWarnings);
+
+				triggerNewDatabasePDBrevRecord(dbrev);
+
+				// MMCIF version 5 dates
+				break;
+			}
+			case "_pdbx_audit_revision_history":
+				PdbxAuditRevisionHistory history = (PdbxAuditRevisionHistory) buildObject(
+						PdbxAuditRevisionHistory.class.getName(),
+						loopFields, lineData, loopWarnings);
+
+				triggerNewPdbxAuditRevisionHistory(history);
+
+				// MMCIF version 5 dates
+				break;
+			case "_pdbx_database_status":
+				PdbxDatabaseStatus status = (PdbxDatabaseStatus) buildObject(
+						PdbxDatabaseStatus.class.getName(),
+						loopFields, lineData, loopWarnings);
+
+				triggerNewPdbxDatabaseStatus(status);
+
+				break;
+			case "_database_PDB_remark":
+				DatabasePDBremark remark = (DatabasePDBremark) buildObject(
+						DatabasePDBremark.class.getName(),
+						loopFields, lineData, loopWarnings);
+
+				triggerNewDatabasePDBremark(remark);
+
+				break;
+			case "_exptl": {
+				Exptl exptl = (Exptl) buildObject(
+						Exptl.class.getName(),
+						loopFields, lineData, loopWarnings);
+
+				triggerExptl(exptl);
+
+				break;
+			}
+			case "_cell":
+				Cell cell = (Cell) buildObject(
+						Cell.class.getName(),
+						loopFields, lineData, loopWarnings);
+
+				triggerNewCell(cell);
+
+				break;
+			case "_symmetry":
+				Symmetry symmetry = (Symmetry) buildObject(
+						Symmetry.class.getName(),
+						loopFields, lineData, loopWarnings);
+
+				triggerNewSymmetry(symmetry);
+				break;
+			case "_struct_ncs_oper":
+
+				StructNcsOper sNcsOper = (StructNcsOper) buildObject(
+						StructNcsOper.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewStructNcsOper(sNcsOper);
+				break;
+			case "_atom_sites":
+
+				AtomSites atomSites = (AtomSites) buildObject(
+						AtomSites.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewAtomSites(atomSites);
+
+				break;
+			case "_struct_ref": {
+				StructRef sref = (StructRef) buildObject(
+						StructRef.class.getName(),
+						loopFields, lineData, loopWarnings);
+
+				triggerNewStrucRef(sref);
+
+				break;
+			}
+			case "_struct_ref_seq": {
+				StructRefSeq sref = (StructRefSeq) buildObject(
+						StructRefSeq.class.getName(),
+						loopFields, lineData, loopWarnings);
+
+				triggerNewStrucRefSeq(sref);
+				break;
+			}
+			case "_struct_ref_seq_dif": {
+				StructRefSeqDif sref = (StructRefSeqDif) buildObject(
+						StructRefSeqDif.class.getName(),
+						loopFields, lineData, loopWarnings);
+
+				triggerNewStrucRefSeqDif(sref);
+				break;
+			}
+			case "_struct_site_gen": {
+				StructSiteGen sref = (StructSiteGen) buildObject(
+						StructSiteGen.class.getName(),
+						loopFields, lineData, loopWarnings);
 
-			logger.debug("Using a generic bean for category {}",category);
+				triggerNewStructSiteGen(sref);
+				break;
+			}
+			case "_struct_site": {
+				StructSite sref = (StructSite) buildObject(
+						StructSite.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewStructSite(sref);
+				break;
+			}
+			case "_entity_poly_seq": {
+				EntityPolySeq exptl = (EntityPolySeq) buildObject(
+						EntityPolySeq.class.getName(),
+						loopFields, lineData, loopWarnings);
+
+				triggerNewEntityPolySeq(exptl);
+				break;
+			}
+			case "_entity_src_gen":
+				EntitySrcGen entitySrcGen = (EntitySrcGen) buildObject(
+						EntitySrcGen.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewEntitySrcGen(entitySrcGen);
+				break;
+			case "_entity_src_nat":
+				EntitySrcNat entitySrcNat = (EntitySrcNat) buildObject(
+						EntitySrcNat.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewEntitySrcNat(entitySrcNat);
+				break;
+			case "_pdbx_entity_src_syn":
+				EntitySrcSyn entitySrcSyn = (EntitySrcSyn) buildObject(
+						EntitySrcSyn.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewEntitySrcSyn(entitySrcSyn);
+				break;
+			case "_struct_asym":
+				StructAsym sasym = (StructAsym) buildObject(
+						StructAsym.class.getName(),
+						loopFields, lineData, loopWarnings);
+
+				triggerNewStructAsym(sasym);
 
-			// trigger a generic bean that can deal with all missing data types...
-			triggerGeneric(category,loopFields,lineData);
+				break;
+			case "_pdbx_poly_seq_scheme": {
+				PdbxPolySeqScheme ppss = (PdbxPolySeqScheme) buildObject(
+						PdbxPolySeqScheme.class.getName(),
+						loopFields, lineData, loopWarnings);
+
+				triggerNewPdbxPolySeqScheme(ppss);
+
+				break;
+			}
+			case "_pdbx_nonpoly_scheme": {
+				PdbxNonPolyScheme ppss = (PdbxNonPolyScheme) buildObject(
+						PdbxNonPolyScheme.class.getName(),
+						loopFields, lineData, loopWarnings);
+
+				triggerNewPdbxNonPolyScheme(ppss);
+
+				break;
+			}
+			case "_pdbx_entity_nonpoly":
+				PdbxEntityNonPoly pen = (PdbxEntityNonPoly) buildObject(
+						PdbxEntityNonPoly.class.getName(),
+						loopFields, lineData, loopWarnings
+				);
+				triggerNewPdbxEntityNonPoly(pen);
+				break;
+			case "_struct_keywords":
+				StructKeywords kw = (StructKeywords) buildObject(
+						StructKeywords.class.getName(),
+						loopFields, lineData, loopWarnings
+				);
+				triggerNewStructKeywords(kw);
+				break;
+			case "_refine":
+				Refine r = (Refine) buildObject(
+						Refine.class.getName(),
+						loopFields, lineData, loopWarnings
+				);
+				triggerNewRefine(r);
+				break;
+			case "_chem_comp":
+				ChemComp c = (ChemComp) buildObject(
+						ChemComp.class.getName(),
+						loopFields, lineData, loopWarnings
+				);
+				triggerNewChemComp(c);
+				break;
+			case "_audit_author":
+				AuditAuthor aa = (AuditAuthor) buildObject(
+						AuditAuthor.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewAuditAuthor(aa);
+				break;
+			case "_pdbx_chem_comp_descriptor":
+				ChemCompDescriptor ccd = (ChemCompDescriptor) buildObject(
+						ChemCompDescriptor.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewChemCompDescriptor(ccd);
+				break;
+			case "_pdbx_struct_oper_list":
+
+				PdbxStructOperList structOper = (PdbxStructOperList) buildObject(
+						PdbxStructOperList.class.getName(),
+						loopFields, lineData, loopWarnings
+				);
+				triggerNewPdbxStructOper(structOper);
+
+				break;
+			case "_pdbx_struct_assembly": {
+				PdbxStructAssembly sa = (PdbxStructAssembly) buildObject(
+						PdbxStructAssembly.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewPdbxStructAssembly(sa);
+
+				break;
+			}
+			case "_pdbx_struct_assembly_gen": {
+				PdbxStructAssemblyGen sa = (PdbxStructAssemblyGen) buildObject(
+						PdbxStructAssemblyGen.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewPdbxStructAssemblyGen(sa);
+				break;
+			}
+			case "_chem_comp_atom":
+				ChemCompAtom atom = (ChemCompAtom) buildObject(
+						ChemCompAtom.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewChemCompAtom(atom);
+
+				break;
+			case "_chem_comp_bond":
+				ChemCompBond bond = (ChemCompBond) buildObject(
+						ChemCompBond.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewChemCompBond(bond);
+				break;
+			case "_pdbx_chem_comp_identifier": {
+				PdbxChemCompIdentifier id = (PdbxChemCompIdentifier) buildObject(
+						PdbxChemCompIdentifier.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewPdbxChemCompIdentifier(id);
+				break;
+			}
+			case "_struct_conn": {
+				StructConn id = (StructConn) buildObject(
+						StructConn.class.getName(),
+						loopFields, lineData, loopWarnings);
+				triggerNewStructConn(id);
+
+				break;
+			}
+			default:
+
+				logger.debug("Using a generic bean for category {}", category);
+
+				// trigger a generic bean that can deal with all missing data types...
+				triggerGeneric(category, loopFields, lineData);
+				break;
 		}
 
 
@@ -952,8 +1001,8 @@ public void triggerNewAtomSites(AtomSites atomSites) {
 	 */
 	private Object buildObject(String className, List<String> loopFields, List<String> lineData, Set<String> warnings) {
 
-		Object o = null;
-		Class<?> c = null;
+		Object o;
+		Class<?> c;
 
 		try {
 			// build up the Entity object from the line data...
@@ -973,7 +1022,7 @@ private Object buildObject(String className, List<String> loopFields, List<Strin
 		// let's build a map of all methods so that we can look up the setter methods later
 		Method[] methods = c.getMethods();
 
-		Map<String,Method> methodMap = new HashMap<String, Method>();
+		Map<String,Method> methodMap = new HashMap<>();
 		for (Method m : methods) {
 			methodMap.put(m.getName(),m);
 		}
@@ -1003,7 +1052,7 @@ private Object buildObject(String className, List<String> loopFields, List<Strin
 			// have more functionality than just setting the value (e.g. some setters in ChemComp)
 
 			// building up the setter method name: need to upper case the first letter, leave the rest untouched
-			String setterMethodName = "set" + field.getName().substring(0,1).toUpperCase() + field.getName().substring(1, field.getName().length());
+			String setterMethodName = "set" + field.getName().substring(0,1).toUpperCase() + field.getName().substring(1);
 
 			Method setter = methodMap.get(setterMethodName);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
index f06d294f78..57e4f7f622 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
@@ -33,7 +33,6 @@
 import java.nio.file.Paths;
 import java.nio.file.StandardCopyOption;
 import java.util.HashSet;
-import java.util.Map;
 import java.util.Set;
 import java.util.zip.GZIPInputStream;
 import java.util.zip.ZipEntry;
@@ -68,7 +67,7 @@ public class ZipChemCompProvider implements ChemCompProvider{
 	private boolean m_removeCif;
 
 	// Missing IDs from library that cannot be download added here to prevent delays.
-	private Set<String> unavailable = new HashSet<String>();
+	private final Set<String> unavailable = new HashSet<>();
 
 	/**
 	 * ZipChemCompProvider is a Chemical Component provider that stores chemical components
@@ -105,12 +104,9 @@ private void initializeZip() throws IOException {
 		if (!f.exists()) {
 			s_logger.info("Creating missing zip archive: " + m_zipFile.toString());
 			FileOutputStream fo = new FileOutputStream(f);
-			ZipOutputStream zip = new ZipOutputStream(new BufferedOutputStream(fo));
-			try {
+			try (ZipOutputStream zip = new ZipOutputStream(new BufferedOutputStream(fo))) {
 				zip.putNextEntry(new ZipEntry("chemcomp/"));
 				zip.closeEntry();
-			} finally {
-				zip.close();
 			}
 		}
 	}
@@ -219,11 +215,7 @@ static private File[] finder( String dirName, final String suffix){
 		}
 
 		final File dir = new File(dirName);
-		return dir.listFiles(new FilenameFilter() {
-			@Override
-			public boolean accept(File dir, String filename)
-			{ return filename.endsWith(suffix); }
-		} );
+		return dir.listFiles((dir1, filename) -> filename.endsWith(suffix));
 	}
 
 	/**
@@ -270,7 +262,7 @@ private synchronized ChemComp getFromZip(String recordName) {
 	 * @return true if successfully appended these files.
 	 */
 	private synchronized boolean addToZipFileSystem(Path zipFile, File[] files, Path pathWithinArchive) {
-		boolean ret = false;
+		boolean ret;
 
 		/* URIs in Java 7 cannot have spaces, must use Path instead
 		 * and so, cannot use the properties map to describe need to create
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java
index d1392f5117..5f66ade976 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java
@@ -62,7 +62,7 @@ public class ChemCompTools {
 	 */
 	static
 	{
-		Map<String, Character> foo = new HashMap<String, Character>();
+		Map<String, Character> foo = new HashMap<>();
 		foo.put("ALA", 'A');
 		foo.put("ASP", 'D');
 		foo.put("ASN", 'N');
@@ -87,7 +87,7 @@ public class ChemCompTools {
 		foo.put("VAL", 'V');
 		AMINO_ACID_LOOKUP_3TO1 = Collections.unmodifiableMap((Collections.synchronizedMap(foo)));
 
-		Map<Character, String> bar = new HashMap<Character, String>();
+		Map<Character, String> bar = new HashMap<>();
 		bar.put('A', "ALA");
 		bar.put('D', "ASP");
 		bar.put('N', "ASN");
@@ -112,7 +112,7 @@ public class ChemCompTools {
 		bar.put('V', "VAL");
 		AMINO_ACID_LOOKUP_1TO3 = Collections.unmodifiableMap(Collections.synchronizedMap(bar));
 
-		foo = new HashMap<String, Character>();
+		foo = new HashMap<>();
 		foo.put("DA",'A');
 		foo.put("DC",'C');
 		foo.put("DG",'G');
@@ -121,7 +121,7 @@ public class ChemCompTools {
 		foo.put("DT",'T');
 		DNA_LOOKUP_2TO1 = Collections.unmodifiableMap((Collections.synchronizedMap(foo)));
 
-		bar = new HashMap<Character, String>();
+		bar = new HashMap<>();
 		bar.put('A',"DA");
 		bar.put('C',"DC");
 		bar.put('G',"DG");
@@ -132,7 +132,7 @@ public class ChemCompTools {
 
 
 		// initialise standard chemical components
-		List<String> stdMonIds = new ArrayList<String>();
+		List<String> stdMonIds = new ArrayList<>();
 		stdMonIds.addAll(AMINO_ACID_LOOKUP_3TO1.keySet());
 		stdMonIds.addAll(DNA_LOOKUP_2TO1.keySet());
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/PolymerType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/PolymerType.java
index d7b4853cf0..1ab4dad31a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/PolymerType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/PolymerType.java
@@ -167,25 +167,25 @@ public static PolymerType polymerTypeFromString(String polymerType)
 	static {
 		Set<PolymerType> tmp;
 
-		tmp = new HashSet<PolymerType>();
+		tmp = new HashSet<>();
 		tmp.add(peptide);
 		PROTEIN_ONLY = Collections.unmodifiableSet(tmp);
 
-		tmp = new HashSet<PolymerType>();
+		tmp = new HashSet<>();
 		tmp.add(dna);
 		DNA_ONLY = Collections.unmodifiableSet(tmp);
 
-		tmp = new HashSet<PolymerType>();
+		tmp = new HashSet<>();
 		tmp.add(rna);
 		RNA_ONLY = Collections.unmodifiableSet(tmp);
 
-		tmp = new HashSet<PolymerType>();
+		tmp = new HashSet<>();
 		tmp.add(dna);
 		tmp.add(rna);
 		tmp.add(dnarna);
 		POLYNUCLEOTIDE_ONLY = Collections.unmodifiableSet(tmp);
 
-		ALL_POLYMER_TYPES = Collections.unmodifiableSet(new HashSet<PolymerType>(Arrays.asList(values())));
+		ALL_POLYMER_TYPES = Collections.unmodifiableSet(new HashSet<>(Arrays.asList(values())));
 	}
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/AbstractBean.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/AbstractBean.java
index 7dc7b869f5..07b83b782b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/AbstractBean.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/AbstractBean.java
@@ -41,7 +41,7 @@ public abstract class AbstractBean {
 	@Override
 	@SuppressWarnings({  "unchecked" })
 	public String toString(){
-		StringBuffer buf = new StringBuffer();
+		StringBuilder buf = new StringBuilder();
 		buf.append(this.getClass().getName()).append(": ");
 		/* disabled for the moment
 
@@ -61,14 +61,14 @@ public String toString(){
 				Method m = methods[i];
 
 				String name = m.getName();
-				if ( name.substring(0,3).equals("get")) {
+				if ( name.startsWith("get")) {
 
-					Object o  = m.invoke(this, new Object[]{});
+					Object o  = m.invoke(this);
 					if ( o instanceof String){
-						buf.append(name.substring(3, name.length())+": "+ o + " ");
+						buf.append(name.substring(3)+": "+ o + " ");
 					}
 					else if ( o instanceof List){
-						buf.append(name.substring(3, name.length())).append(": ");
+						buf.append(name.substring(3)).append(": ");
 
 						List<Object>lst = (List<Object>)o;
 						for (Object obj : lst){
@@ -86,9 +86,7 @@ else if ( o instanceof List){
 
 			}
 
-		} catch (InvocationTargetException e){
-			logger.error("Exception caught while producing toString",e);
-		} catch (IllegalAccessException e) {
+		} catch (InvocationTargetException | IllegalAccessException e){
 			logger.error("Exception caught while producing toString",e);
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemComp.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemComp.java
index cb38de1755..f30e3a6ff8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemComp.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemComp.java
@@ -67,11 +67,11 @@ public class ChemComp implements Serializable, Comparable<ChemComp>{
 	private String mon_nstd_flag;
 
 	@IgnoreField
-	private List<ChemCompDescriptor> descriptors = new ArrayList<ChemCompDescriptor>();
+	private List<ChemCompDescriptor> descriptors = new ArrayList<>();
 	@IgnoreField
-	private List<ChemCompBond> bonds = new ArrayList<ChemCompBond>();
+	private List<ChemCompBond> bonds = new ArrayList<>();
 	@IgnoreField
-	private List<ChemCompAtom> atoms = new ArrayList<ChemCompAtom>();
+	private List<ChemCompAtom> atoms = new ArrayList<>();
 
 	// and some derived data for easier processing...
 	@IgnoreField
@@ -83,7 +83,7 @@ public class ChemComp implements Serializable, Comparable<ChemComp>{
 
 	@Override
 	public String toString(){
-		StringBuffer buf = new StringBuffer("ChemComp ");
+		StringBuilder buf = new StringBuilder("ChemComp ");
 		buf.append(id);
 		buf.append(" ");
 		buf.append(one_letter_code);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemCompBond.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemCompBond.java
index cd49d3b116..be33fed0f3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemCompBond.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemCompBond.java
@@ -116,18 +116,19 @@ public void setPdbx_ordinal(String pdbx_ordinal) {
 	 *         the value is non-numeric or unknown.
 	 */
 	public int getNumericalBondOrder() {
-		if (value_order.equals("SING")) {
-			return 1;
-		} else if (value_order.equals("DOUB")) {
-			return 2;
-		} else if (value_order.equals("TRIP")) {
-			return 3;
-		} else if (value_order.equals("QUAD")) {
-			return 4;
-		} else {
-			logger.error("Unknown or non-numeric value for value_order: "
-					+ value_order);
-			return -1;
-		}
+        switch (value_order) {
+            case "SING":
+                return 1;
+            case "DOUB":
+                return 2;
+            case "TRIP":
+                return 3;
+            case "QUAD":
+                return 4;
+            default:
+                logger.error("Unknown or non-numeric value for value_order: "
+                        + value_order);
+                return -1;
+        }
 	}
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/DatabasePDBrev.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/DatabasePDBrev.java
index ef884327e3..d57c98b90d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/DatabasePDBrev.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/DatabasePDBrev.java
@@ -31,7 +31,7 @@ public class DatabasePDBrev {
 
 	@Override
 	public String toString(){
-		StringBuffer buf = new StringBuffer();
+		StringBuilder buf = new StringBuilder();
 		buf.append("DatabasePDBrev ");
 		buf.append("mod_type :");
 		buf.append(mod_type);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Entity.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Entity.java
index cae779dee2..3256a41dcd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Entity.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Entity.java
@@ -41,7 +41,7 @@ public class Entity {
 
 	@Override
 	public String toString(){
-		StringBuffer buf = new StringBuffer();
+		StringBuilder buf = new StringBuilder();
 
 	buf.append("Entity - id:").append(id);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
index 7c7c24e9ec..f15a639c2c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
@@ -80,7 +80,7 @@ public class MmtfStructureReader implements StructureAdapterInterface, Serializa
 	private static final Logger logger = LoggerFactory.getLogger(MmtfStructureReader.class);
 
 	/** The structure. */
-	private Structure structure;
+	private final Structure structure;
 
 	/** The model number. */
 	private int modelNumber;
@@ -99,19 +99,19 @@ public class MmtfStructureReader implements StructureAdapterInterface, Serializa
 	private int atomCounter;
 
 	/** The list of EntityInformation */
-	private List<EntityInfo> entityInfoList;
+	private final List<EntityInfo> entityInfoList;
 
 	/** All the chains */
-	private List<Chain> chainList;
+	private final List<Chain> chainList;
 
 	/** All the chains as a list of maps */
-	private List<Map<String,Chain>> chainMap;
+	private final List<Map<String,Chain>> chainMap;
 
 	private List<double[]> transformList;
 
 	private int bioassIndex;
 
-	private Map<String,String> chainSequenceMap;
+	private final Map<String,String> chainSequenceMap;
 
 	/**
 	 * Instantiates a new bio java structure decoder.
@@ -177,7 +177,7 @@ public void initStructure(int totalNumBonds, int totalNumAtoms, int totalNumGrou
 	public void setModelInfo(int inputModelNumber,
 			int chainCount) {
 		modelNumber = inputModelNumber;
-		structure.addModel(new ArrayList<Chain>(chainCount));
+		structure.addModel(new ArrayList<>(chainCount));
 		chainMap.add(new HashMap<>());
 	}
 
@@ -293,7 +293,7 @@ public void setAtomInfo(String atomName,
 			altGroup = getCorrectAltLocGroup(alternativeLocationId);
 			atom.setAltLoc(alternativeLocationId);
 		} else {
-			atom.setAltLoc(Character.valueOf(' '));
+			atom.setAltLoc(' ');
 		}
 		atom.setX(x);
 		atom.setY(y);
@@ -395,7 +395,7 @@ private Group getCorrectAltLocGroup(Character altLoc) {
 		Group altLocG = (Group) group.clone();
 		// drop atoms from cloned group...
 		// https://redmine.open-bio.org/issues/3307
-		altLocG.setAtoms(new ArrayList<Atom>());
+		altLocG.setAtoms(new ArrayList<>());
 		altLocG.getAltLocs().clear();
 		group.addAltLoc(altLocG);
 		return altLocG;
@@ -458,19 +458,19 @@ public void setBioAssemblyTrans(int bioAssemblyId, int[] inputChainIndices, doub
 		}
 		else{
 			bioAssInfo = new  BioAssemblyInfo();
-			bioAssInfo.setTransforms(new ArrayList<BiologicalAssemblyTransformation>());
+			bioAssInfo.setTransforms(new ArrayList<>());
 			bioAssemblies.put(bioAssemblyId, bioAssInfo);
 			bioAssInfo.setId(bioAssemblyId);
 		}
 
 		for(int currChainIndex : inputChainIndices){
 			BiologicalAssemblyTransformation bioAssTrans = new BiologicalAssemblyTransformation();
-			Integer transId = transformList.indexOf(inputTransform)+1;
+			int transId = transformList.indexOf(inputTransform)+1;
 			if(transId==0){
 				transformList.add(inputTransform);
 				transId = transformList.indexOf(inputTransform)+1;
 			}
-			bioAssTrans.setId(transId.toString());
+			bioAssTrans.setId(Integer.toString(transId));
 			// If it actually has an index - if it doesn't it is because the chain has no density.
 			if (currChainIndex!=-1){
 				bioAssTrans.setChainId(chainList.get(currChainIndex).getId());
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java
index dbc14ebbe4..568fe15c8d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java
@@ -48,7 +48,7 @@
  */
 public class MmtfStructureWriter {
 
-	private StructureAdapterInterface mmtfDecoderInterface;
+	private final StructureAdapterInterface mmtfDecoderInterface;
 
 	/**
 	 * Pass data from Biojava structure  to another generic output type. Loops through the data
@@ -102,14 +102,14 @@ public MmtfStructureWriter(Structure structure, StructureAdapterInterface dataTr
 					if (chemComp.getOne_letter_code().length()==1){
 						singleLetterCode = chemComp.getOne_letter_code().charAt(0);
 					}
-					mmtfDecoderInterface.setGroupInfo(group.getPDBName(), group.getResidueNumber().getSeqNum(), insCode.charValue(),
+					mmtfDecoderInterface.setGroupInfo(group.getPDBName(), group.getResidueNumber().getSeqNum(), insCode,
 							chemComp.getType().toUpperCase(), atomsInGroup.size(), MmtfUtils.getNumBondsInGroup(atomsInGroup), singleLetterCode,
 							sequenceGroups.indexOf(group), MmtfUtils.getSecStructType(group));
 					for (Atom atom : atomsInGroup){
 						char altLoc = MmtfStructure.UNAVAILABLE_CHAR_VALUE;
 						if(atom.getAltLoc()!=null){
-							if(atom.getAltLoc().charValue()!=' '){
-								altLoc=atom.getAltLoc().charValue();
+							if(atom.getAltLoc() !=' '){
+								altLoc= atom.getAltLoc();
 							}
 						}
 						mmtfDecoderInterface.setAtomInfo(atom.getName(), atom.getPDBserial(), altLoc, (float) atom.getX(),
@@ -138,7 +138,7 @@ private void addBonds(Atom atom, List<Atom> atomsInGroup, List<Atom> allAtoms) {
 			// Now set the bonding information.
 			Atom other = bond.getOther(atom);
 			// If both atoms are in the group
-			if (atomsInGroup.indexOf(other)!=-1){
+			if (atomsInGroup.contains(other)){
 				Integer firstBondIndex = atomsInGroup.indexOf(atom);
 				Integer secondBondIndex = atomsInGroup.indexOf(other);
 				// Don't add the same bond twice
@@ -149,8 +149,8 @@ private void addBonds(Atom atom, List<Atom> atomsInGroup, List<Atom> allAtoms) {
 			}
 			// Otherwise it's an inter group bond - so add it here
 			else {
-				Integer firstBondIndex = allAtoms.indexOf(atom);
-				Integer secondBondIndex = allAtoms.indexOf(other);
+				int firstBondIndex = allAtoms.indexOf(atom);
+				int secondBondIndex = allAtoms.indexOf(other);
 				if(firstBondIndex>secondBondIndex){
 					// Don't add the same bond twice
 					int bondOrder = bond.getBondOrder();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
index bbd34c9610..59b0b45742 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
@@ -310,8 +310,8 @@ public static int getNumGroups(Structure structure) {
 	 * @return the atoms for the input Biojava Group
 	 */
 	public static List<Atom> getAtomsForGroup(Group inputGroup) {
-		Set<Atom> uniqueAtoms = new HashSet<Atom>();
-		List<Atom> theseAtoms = new ArrayList<Atom>();
+		Set<Atom> uniqueAtoms = new HashSet<>();
+		List<Atom> theseAtoms = new ArrayList<>();
 		for(Atom a: inputGroup.getAtoms()){
 			theseAtoms.add(a);
 			uniqueAtoms.add(a);
@@ -343,9 +343,9 @@ public static int getNumBondsInGroup(List<Atom> atomsInGroup) {
 				// Now set the bonding information.
 				Atom other = bond.getOther(atom);
 				// If both atoms are in the group
-				if (atomsInGroup.indexOf(other)!=-1){
-					Integer firstBondIndex = atomsInGroup.indexOf(atom);
-					Integer secondBondIndex = atomsInGroup.indexOf(other);
+				if (atomsInGroup.contains(other)){
+					int firstBondIndex = atomsInGroup.indexOf(atom);
+					int secondBondIndex = atomsInGroup.indexOf(other);
 					// Don't add the same bond twice
 					if (firstBondIndex<secondBondIndex){
 						bondCounter++;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java
index 84cd9ae138..9dae6e5091 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java
@@ -121,7 +121,7 @@ public static SiftsChainToUniprotMapping load(boolean useOnlyLocal) throws IOExc
 	protected static SiftsChainToUniprotMapping build() throws IOException {
 		SiftsChainToUniprotMapping sifts = new SiftsChainToUniprotMapping();
 		BufferedReader br = new BufferedReader(new FileReader(DEFAULT_FILE));
-		String line = "";
+		String line;
 		while ((line = br.readLine()) != null) {
 			if (line.isEmpty() || line.startsWith("#") || line.startsWith("PDB")) continue;
 			String[] parts = line.split("\t");
@@ -147,8 +147,8 @@ private static void download() throws IOException {
 
 		logger.info("Downloading {} to {}",DEFAULT_URL.toString(),DEFAULT_FILE);
 
-		InputStream in = null;
-		OutputStream out = null;
+		InputStream in;
+		OutputStream out;
 
 		in = new GZIPInputStream(DEFAULT_URL.openStream());
 		out = new FileOutputStream(DEFAULT_FILE);
@@ -156,9 +156,9 @@ private static void download() throws IOException {
 
 	}
 
-	private Map<String, SiftsChainEntry> byChainId = new HashMap<String, SiftsChainEntry>();
+	private final Map<String, SiftsChainEntry> byChainId = new HashMap<>();
 
-	private Map<String, SiftsChainEntry> byUniProtId = new HashMap<String, SiftsChainEntry>();
+	private final Map<String, SiftsChainEntry> byUniProtId = new HashMap<>();
 
 	private SiftsChainToUniprotMapping() {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsEntity.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsEntity.java
index 34b2ba1bc4..20e1008859 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsEntity.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsEntity.java
@@ -46,7 +46,7 @@ public SiftsEntity(){
 	public SiftsEntity(String type, String entityId) {
 		this.type = type;
 		this.entityId = entityId;
-		segments = new ArrayList<SiftsSegment>();
+		segments = new ArrayList<>();
 	}
 
 	public void addSegment(SiftsSegment s) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsSegment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsSegment.java
index 1594228a05..e582a3881a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsSegment.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsSegment.java
@@ -49,7 +49,7 @@ public SiftsSegment(String segId, String start, String end) {
 		this.segId = segId;
 		this.start = start;
 		this.end = end;
-		residues = new ArrayList<SiftsResidue>();
+		residues = new ArrayList<>();
 	}
 
 	public String getSegId() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java
index a563aca4ff..05e1784dc9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java
@@ -51,7 +51,7 @@ public class SiftsXMLParser {
 
 	static boolean debug = false;
 	public SiftsXMLParser(){
-		entities = new ArrayList<SiftsEntity>();
+		entities = new ArrayList<>();
 	}
 
 	public List<SiftsEntity> getEntities(){
@@ -60,7 +60,7 @@ public List<SiftsEntity> getEntities(){
 
 
 	public void parseXmlFile(InputStream is){
-		entities = new ArrayList<SiftsEntity>();
+		entities = new ArrayList<>();
 
 		//get the factory
 		DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
@@ -75,12 +75,8 @@ public void parseXmlFile(InputStream is){
 
 			parseDocument();
 
-		}catch(ParserConfigurationException pce) {
+		}catch(ParserConfigurationException | IOException | SAXException pce) {
 			pce.printStackTrace();
-		}catch(SAXException se) {
-			se.printStackTrace();
-		}catch(IOException ioe) {
-			ioe.printStackTrace();
 		}
 	}
 
@@ -269,7 +265,7 @@ private String getTextValue(Element ele, String tagName) {
 		}
 
 	private List<String> getTextValues(Element ele, String tagName) {
-		List<String>values = new ArrayList<String>();
+		List<String>values = new ArrayList<>();
 		NodeList nl = ele.getElementsByTagName(tagName);
 		if(nl != null && nl.getLength() > 0) {
 			for ( int i = 0 ;i < nl.getLength() ; i ++) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/util/PDBTemporaryStorageUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/util/PDBTemporaryStorageUtils.java
index 7ca25d24bc..1ab75c40a9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/util/PDBTemporaryStorageUtils.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/util/PDBTemporaryStorageUtils.java
@@ -40,22 +40,22 @@ public class PDBTemporaryStorageUtils {
 	 * @author Ulysse Carion
 	 */
 	public static class LinkRecord {
-		private String name1;
-		private String altLoc1;
-		private String resName1;
-		private String chainID1;
-		private String resSeq1;
-		private String iCode1;
-
-		private String name2;
-		private String altLoc2;
-		private String resName2;
-		private String chainID2;
-		private String resSeq2;
-		private String iCode2;
-
-		private String sym1;
-		private String sym2;
+		private final String name1;
+		private final String altLoc1;
+		private final String resName1;
+		private final String chainID1;
+		private final String resSeq1;
+		private final String iCode1;
+
+		private final String name2;
+		private final String altLoc2;
+		private final String resName2;
+		private final String chainID2;
+		private final String resSeq2;
+		private final String iCode2;
+
+		private final String sym1;
+		private final String sym2;
 
 		public LinkRecord(String name1, String altLoc1, String resName1,
 				String chainID1, String resSeq1, String iCode1, String name2,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/CholeskyDecomposition.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/CholeskyDecomposition.java
index 0a57710d3e..8e157da9a3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/CholeskyDecomposition.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/CholeskyDecomposition.java
@@ -32,7 +32,7 @@ be queried by the isSPD() method.
 
 public class CholeskyDecomposition implements java.io.Serializable {
 
-	 static final long serialVersionUID = 224348942390823l;
+	 static final long serialVersionUID = 224348942390823L;
 
 /* ------------------------
 	Class variables
@@ -41,12 +41,12 @@ public class CholeskyDecomposition implements java.io.Serializable {
 	/** Array for internal storage of decomposition.
 	@serial internal array storage.
 	*/
-	private double[][] L;
+	private final double[][] L;
 
 	/** Row and column dimension (square matrix).
 	@serial matrix dimension.
 	*/
-	private int n;
+	private final int n;
 
 	/** Symmetric and positive definite flag.
 	@serial is symmetric and positive definite flag.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/EigenvalueDecomposition.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/EigenvalueDecomposition.java
index 13665270cf..96d67edae2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/EigenvalueDecomposition.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/EigenvalueDecomposition.java
@@ -51,7 +51,7 @@ public class EigenvalueDecomposition implements java.io.Serializable {
 /** Row and column dimension (square matrix).
 	@serial matrix dimension.
 	*/
-	private int n;
+	private final int n;
 
 	/** Symmetry flag.
 	@serial internal symmetry flag.
@@ -61,12 +61,13 @@ public class EigenvalueDecomposition implements java.io.Serializable {
 	/** Arrays for internal storage of eigenvalues.
 	@serial internal storage of eigenvalues.
 	*/
-	private double[] d, e;
+	private final double[] d;
+    private final double[] e;
 
 	/** Array for internal storage of eigenvectors.
 	@serial internal storage of eigenvectors.
 	*/
-	private double[][] V;
+	private final double[][] V;
 
 	/** Array for internal storage of nonsymmetric Hessenberg form.
 	@serial internal storage of nonsymmetric Hessenberg form.
@@ -91,9 +92,7 @@ private void tred2 () {
 	//  Auto. Comp., Vol.ii-Linear Algebra, and the corresponding
 	//  Fortran subroutine in EISPACK.
 
-		for (int j = 0; j < n; j++) {
-			d[j] = V[n-1][j];
-		}
+        if (n >= 0) System.arraycopy(V[n - 1], 0, d, 0, n);
 
 		// Householder reduction to tridiagonal form.
 
@@ -208,9 +207,7 @@ private void tql2 () {
 	//  Auto. Comp., Vol.ii-Linear Algebra, and the corresponding
 	//  Fortran subroutine in EISPACK.
 
-		for (int i = 1; i < n; i++) {
-			e[i-1] = e[i];
-		}
+        if (n - 1 >= 0) System.arraycopy(e, 1, e, 0, n - 1);
 		e[n-1] = 0.0;
 
 		double f = 0.0;
@@ -855,9 +852,7 @@ private void hqr2 () {
 
 		for (int i = 0; i < nn; i++) {
 			if (i < low || i > high) {
-				for (int j = i; j < nn; j++) {
-					V[i][j] = H[i][j];
-				}
+                System.arraycopy(H[i], i, V[i], i, nn - i);
 			}
 		}
 
@@ -900,9 +895,7 @@ public EigenvalueDecomposition (Matrix Arg) {
 
 		if (issymmetric) {
 			for (int i = 0; i < n; i++) {
-				for (int j = 0; j < n; j++) {
-					V[i][j] = A[i][j];
-				}
+                System.arraycopy(A[i], 0, V[i], 0, n);
 			}
 
 			// Tridiagonalize.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/LUDecomposition.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/LUDecomposition.java
index 00f5d302ec..b9a2b7791e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/LUDecomposition.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/LUDecomposition.java
@@ -35,7 +35,7 @@ linear equations.  This will fail if isNonsingular() returns false.
 
 public class LUDecomposition implements java.io.Serializable {
 
-	 static final long serialVersionUID = 9271028462937843l;
+	 static final long serialVersionUID = 9271028462937843L;
 
 /* ------------------------
 	Class variables
@@ -44,19 +44,21 @@ public class LUDecomposition implements java.io.Serializable {
 	/** Array for internal storage of decomposition.
 	@serial internal array storage.
 	*/
-	private double[][] LU;
+	private final double[][] LU;
 
 	/** Row and column dimensions, and pivot sign.
 	@serial column dimension.
 	@serial row dimension.
 	@serial pivot sign.
 	*/
-	private int m, n, pivsign;
+	private final int m;
+        private final int n;
+        private int pivsign;
 
 	/** Internal storage of pivot vector.
 	@serial pivot vector.
 	*/
-	private int[] piv;
+	private final int[] piv;
 
 /* ------------------------
 	Constructor
@@ -254,9 +256,7 @@ public Matrix getU () {
 
 	public int[] getPivot () {
 		int[] p = new int[m];
-		for (int i = 0; i < m; i++) {
-			p[i] = piv[i];
-		}
+		if (m >= 0) System.arraycopy(piv, 0, p, 0, m);
 		return p;
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
index 15bd130b99..1df157ee5a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
@@ -80,7 +80,7 @@
 
 public class Matrix implements Cloneable, java.io.Serializable {
 
-	 static final long serialVersionUID = 8492558293015348719l;
+	 static final long serialVersionUID = 8492558293015348719L;
 
 
 /* ------------------------
@@ -90,13 +90,14 @@ public class Matrix implements Cloneable, java.io.Serializable {
 	/** Array for internal storage of elements.
 	@serial internal array storage.
 	*/
-	private double[][] A;
+	private final double[][] A;
 
 	/** Row and column dimensions.
 	@serial row dimension.
 	@serial column dimension.
 	*/
-	private int m, n;
+	private final int m;
+    private final int n;
 
 /* ------------------------
 	Constructors
@@ -199,9 +200,7 @@ public static Matrix constructWithCopy(double[][] A) {
 				throw new IllegalArgumentException
 					("All rows must have the same length.");
 			}
-			for (int j = 0; j < n; j++) {
-				C[i][j] = A[i][j];
-			}
+			System.arraycopy(A[i], 0, C[i], 0, n);
 		}
 		return X;
 	}
@@ -214,9 +213,7 @@ public Matrix copy () {
 		Matrix X = new Matrix(m,n);
 		double[][] C = X.getArray();
 		for (int i = 0; i < m; i++) {
-			for (int j = 0; j < n; j++) {
-				C[i][j] = A[i][j];
-			}
+			if (n >= 0) System.arraycopy(A[i], 0, C[i], 0, n);
 		}
 		return X;
 	}
@@ -244,9 +241,7 @@ public double[][] getArray () {
 	public double[][] getArrayCopy () {
 		double[][] C = new double[m][n];
 		for (int i = 0; i < m; i++) {
-			for (int j = 0; j < n; j++) {
-				C[i][j] = A[i][j];
-			}
+			if (n >= 0) System.arraycopy(A[i], 0, C[i], 0, n);
 		}
 		return C;
 	}
@@ -272,9 +267,7 @@ public double[] getColumnPackedCopy () {
 	public double[] getRowPackedCopy () {
 		double[] vals = new double[m*n];
 		for (int i = 0; i < m; i++) {
-			for (int j = 0; j < n; j++) {
-				vals[i*n+j] = A[i][j];
-			}
+			if (n >= 0) System.arraycopy(A[i], 0, vals, i * n + 0, n);
 		}
 		return vals;
 	}
@@ -320,9 +313,7 @@ public Matrix getMatrix (int i0, int i1, int j0, int j1) {
 		double[][] B = X.getArray();
 		try {
 			for (int i = i0; i <= i1; i++) {
-				for (int j = j0; j <= j1; j++) {
-					B[i-i0][j-j0] = A[i][j];
-				}
+				if (j1 + 1 - j0 >= 0) System.arraycopy(A[i], j0, B[i - i0], j0 - j0, j1 + 1 - j0);
 			}
 		} catch(ArrayIndexOutOfBoundsException e) {
 			throw new ArrayIndexOutOfBoundsException("Submatrix indices");
@@ -388,9 +379,7 @@ public Matrix getMatrix (int[] r, int j0, int j1) {
 		double[][] B = X.getArray();
 		try {
 			for (int i = 0; i < r.length; i++) {
-				for (int j = j0; j <= j1; j++) {
-					B[i][j-j0] = A[r[i]][j];
-				}
+				if (j1 + 1 - j0 >= 0) System.arraycopy(A[r[i]], j0, B[i], j0 - j0, j1 + 1 - j0);
 			}
 		} catch(ArrayIndexOutOfBoundsException e) {
 			throw new ArrayIndexOutOfBoundsException("Submatrix indices");
@@ -1050,7 +1039,7 @@ public static Matrix read (BufferedReader input) throws java.io.IOException {
 		int n = v.size();  // Now we've got the number of columns!
 		double[] row = new double[n];
 		for (int j=0; j<n; j++)  // extract the elements of the 1st row.
-			row[j]=((Double)v.elementAt(j)).doubleValue();
+			row[j]= (Double) v.elementAt(j);
 		v.removeAllElements();
 		v.addElement(row);  // Start storing rows instead of columns.
 		while (tokenizer.nextToken() == StreamTokenizer.TT_WORD) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/QRDecomposition.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/QRDecomposition.java
index daf2d16a72..3babc45cc6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/QRDecomposition.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/QRDecomposition.java
@@ -36,7 +36,7 @@ of simultaneous linear equations.  This will fail if isFullRank()
 
 public class QRDecomposition implements java.io.Serializable {
 
-	 static final long serialVersionUID = 10293720387423l;
+	 static final long serialVersionUID = 10293720387423L;
 
 /* ------------------------
 	Class variables
@@ -45,18 +45,19 @@ public class QRDecomposition implements java.io.Serializable {
 	/** Array for internal storage of decomposition.
 	@serial internal array storage.
 	*/
-	private double[][] QR;
+	private final double[][] QR;
 
 	/** Row and column dimensions.
 	@serial column dimension.
 	@serial row dimension.
 	*/
-	private int m, n;
+	private final int m;
+    private final int n;
 
 	/** Array for internal storage of diagonal of R.
 	@serial diagonal of R.
 	*/
-	private double[] Rdiag;
+	private final double[] Rdiag;
 
 /* ------------------------
 	Constructor
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/SingularValueDecomposition.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/SingularValueDecomposition.java
index e1e1a399f3..67a8f35a35 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/SingularValueDecomposition.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/SingularValueDecomposition.java
@@ -36,7 +36,7 @@
 
 public class SingularValueDecomposition implements java.io.Serializable {
 
-	 static final long serialVersionUID = 640239472093534756l;
+	 static final long serialVersionUID = 640239472093534756L;
 
 /* ------------------------
 	Class variables
@@ -46,18 +46,20 @@ public class SingularValueDecomposition implements java.io.Serializable {
 	@serial internal storage of U.
 	@serial internal storage of V.
 	*/
-	private double[][] U, V;
+	private final double[][] U;
+        private final double[][] V;
 
 	/** Array for internal storage of singular values.
 	@serial internal storage of singular values.
 	*/
-	private double[] s;
+	private final double[] s;
 
 	/** Row and column dimensions.
 	@serial row dimension.
 	@serial column dimension.
 	*/
-	private int m, n;
+	private final int m;
+        private final int n;
 
 /* ------------------------
 	Constructor
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SparseSquareMatrix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SparseSquareMatrix.java
index 2574d1f386..ea875230b7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SparseSquareMatrix.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SparseSquareMatrix.java
@@ -50,7 +50,7 @@ public class SparseSquareMatrix implements Serializable {
 	private static final long serialVersionUID = -5217767192992868955L;
 
 	private final int N;           // N-by-N matrix
-	private SparseVector[] rows;   // the rows, each row is a sparse vector
+	private final SparseVector[] rows;   // the rows, each row is a sparse vector
 
 	/** initialize an N-by-N matrix of all 0s
 	 *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SparseVector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SparseVector.java
index 124b44d1c2..4ea38f4545 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SparseVector.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SparseVector.java
@@ -45,7 +45,7 @@ public class SparseVector implements Serializable{
 
 	private final int N;             // length
 
-	private SymbolTable<Integer, Double> symbolTable;  // the vector, represented by index-value pairs
+	private final SymbolTable<Integer, Double> symbolTable;  // the vector, represented by index-value pairs
 
 
 	/** Constructor. initialize the all 0s vector of length N
@@ -54,7 +54,7 @@ public class SparseVector implements Serializable{
 	 */
 	public SparseVector(int N) {
 		this.N  = N;
-		this.symbolTable = new SymbolTable<Integer, Double>();
+		this.symbolTable = new SymbolTable<>();
 	}
 
 	/** Setter method (should it be renamed to set?)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java
index 39d7926d9f..8f4b90b426 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java
@@ -63,13 +63,13 @@ public class SymbolTable<Key extends Comparable<Key>, Value> implements Iterable
 	 */
 	private static final long serialVersionUID = -4417561575046471931L;
 
-	private TreeMap<Key, Value> st;
+	private final TreeMap<Key, Value> st;
 
 	/**
 	 * Create an empty symbol table.
 	 */
 	public SymbolTable() {
-		st = new TreeMap<Key, Value>();
+		st = new TreeMap<>();
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
index 9cd5d72d10..bff90ac251 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
@@ -68,7 +68,7 @@ private static List<String> parseSubExpression(String expression) throws Illegal
 		tmp = tmp.replace(")", "");
 
 		// separate the operators
-		List<String> components = null;
+		List<String> components;
 		try {
 			components = Arrays.asList(tmp.split(","));
 		} catch (Exception e) {
@@ -76,7 +76,7 @@ private static List<String> parseSubExpression(String expression) throws Illegal
 		}
 
 		// expand ranges if present, i.e. 1-60 -> 1, 2, 3, ..., 60
-		List<String> operators = new ArrayList<String>();
+		List<String> operators = new ArrayList<>();
 		for (String component : components) {
 			if (component.contains("-")) {
 				operators.addAll(expandRange(component));
@@ -94,8 +94,8 @@ private static List<String> parseSubExpression(String expression) throws Illegal
 	 * @throws IllegalArgumentException
 	 */
 	private static List<String> expandRange(String expression) throws IllegalArgumentException {
-		int first = 0;
-		int last = 0;
+		int first;
+		int last;
 		try {
 			String[] range = expression.split("-");
 			first = Integer.parseInt(range[0]);
@@ -104,7 +104,7 @@ private static List<String> expandRange(String expression) throws IllegalArgumen
 			throw new IllegalArgumentException("Invalid range specification in oper_expression: " + expression);
 		}
 
-		List<String> expandedExpression = new ArrayList<String>(last-first+1);
+		List<String> expandedExpression = new ArrayList<>(last - first + 1);
 		for (int i = first; i <= last; i++) {
 			expandedExpression.add(String.valueOf(i));
 		}
@@ -114,7 +114,7 @@ private static List<String> expandRange(String expression) throws IllegalArgumen
 	public static List<OrderedPair<String>> parseBinaryOperatorExpression(String expression)
 			throws IllegalArgumentException {
 		// split operator expression, i.e. (1,2,3)(4,5) into two subexpressions
-		String[] subExpressions = null;
+		String[] subExpressions;
 		try {
 			subExpressions = expression.split("\\)\\(");
 		} catch (Exception e) {
@@ -127,7 +127,7 @@ public static List<OrderedPair<String>> parseBinaryOperatorExpression(String exp
 		List<String> rightSide = parseSubExpression(subExpressions[1]);
 
 		// form the cartesian product of the two lists
-		CartesianProduct<String> product = new CartesianProduct<String>(leftSide, rightSide);
+		CartesianProduct<String> product = new CartesianProduct<>(leftSide, rightSide);
 		return product.getOrderedPairs();
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
index 502730dcf3..457a639d6c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
@@ -65,7 +65,7 @@ public class BiologicalAssemblyBuilder {
 	 */
 	private Map<String, Matrix4d> allTransformations;
 
-	private List<String> modelIndex = new ArrayList<>();
+	private final List<String> modelIndex = new ArrayList<>();
 
 	public BiologicalAssemblyBuilder(){
 		init();
@@ -164,16 +164,13 @@ public Structure rebuildQuaternaryStructure(Structure asymUnit, List<BiologicalA
 	 */
 	private void orderTransformationsByChainId(Structure asymUnit, List<BiologicalAssemblyTransformation> transformations) {
 		final List<String> chainIds = getChainIds(asymUnit);
-		Collections.sort(transformations, new Comparator<BiologicalAssemblyTransformation>() {
-			@Override
-			public int compare(BiologicalAssemblyTransformation t1, BiologicalAssemblyTransformation t2) {
-				// set sort order only if the two ids are identical
-				if (t1.getId().equals(t2.getId())) {
-					 return chainIds.indexOf(t1.getChainId()) - chainIds.indexOf(t2.getChainId());
-				} else {
-					return t1.getId().compareTo(t2.getId());
-				}
-		    }
+		transformations.sort((t1, t2) -> {
+			// set sort order only if the two ids are identical
+			if (t1.getId().equals(t2.getId())) {
+				return chainIds.indexOf(t1.getChainId()) - chainIds.indexOf(t2.getChainId());
+			} else {
+				return t1.getId().compareTo(t2.getId());
+			}
 		});
 	}
 
@@ -184,7 +181,7 @@ public int compare(BiologicalAssemblyTransformation t1, BiologicalAssemblyTransf
 	 * @return
 	 */
 	private List<String> getChainIds(Structure asymUnit) {
-		List<String> chainIds = new ArrayList<String>();
+		List<String> chainIds = new ArrayList<>();
 		for ( Chain c : asymUnit.getChains()){
 			String intChainID = c.getId();
 			chainIds.add(intChainID);
@@ -300,7 +297,7 @@ private ArrayList<BiologicalAssemblyTransformation> getBioUnitTransformationsLis
 		for ( PdbxStructAssemblyGen psag : psags){
 			if ( psag.getAssembly_id().equals(assemblyId)) {
 
-				List<String>asymIds= Arrays.asList(psag.getAsym_id_list().split(","));
+				String[] asymIds= psag.getAsym_id_list().split(",");
 
 				operatorResolver.parseOperatorExpressionString(psag.getOper_expression());
 
@@ -332,7 +329,7 @@ private ArrayList<BiologicalAssemblyTransformation> getBioUnitTransformationsLis
 	}
 
 	private ArrayList<BiologicalAssemblyTransformation> getBioUnitTransformationsListUnaryOperators(String assemblyId, List<PdbxStructAssemblyGen> psags) {
-		ArrayList<BiologicalAssemblyTransformation> transformations = new ArrayList<BiologicalAssemblyTransformation>();
+		ArrayList<BiologicalAssemblyTransformation> transformations = new ArrayList<>();
 
 
 		for ( PdbxStructAssemblyGen psag : psags){
@@ -341,7 +338,7 @@ private ArrayList<BiologicalAssemblyTransformation> getBioUnitTransformationsLis
 				operatorResolver.parseOperatorExpressionString(psag.getOper_expression());
 				List<String> operators = operatorResolver.getUnaryOperators();
 
-				List<String>asymIds= Arrays.asList(psag.getAsym_id_list().split(","));
+				String[] asymIds= psag.getAsym_id_list().split(",");
 
 				// apply unary operators to the specified chains
 				for (String chainId : asymIds) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java
index cf5a7a1ea4..8a57be4dac 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java
@@ -236,7 +236,7 @@ public static BiologicalAssemblyTransformation fromXML(String xml)
 	public static List<BiologicalAssemblyTransformation> fromMultiXML(String xml) throws ParserConfigurationException, SAXException, IOException{
 
 
-		List<BiologicalAssemblyTransformation> transformations = new ArrayList<BiologicalAssemblyTransformation>();
+		List<BiologicalAssemblyTransformation> transformations = new ArrayList<>();
 
 		// read the XML of a string and returns a ModelTransformationmatrix
 		DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
@@ -247,7 +247,7 @@ public static List<BiologicalAssemblyTransformation> fromMultiXML(String xml) th
 		Document doc = db.parse(inStream);
 
 		// normalize text representation
-		doc.getDocumentElement().normalize();;
+		doc.getDocumentElement().normalize();
 
 		NodeList listOfTransforms = doc.getElementsByTagName("transformation");
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/CartesianProduct.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/CartesianProduct.java
index da6853a6fb..5011f8cca2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/CartesianProduct.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/CartesianProduct.java
@@ -43,8 +43,8 @@
  */
 public class CartesianProduct<T> {
 
-	private List<T> list1 = Collections.emptyList();
-	private List<T> list2 = Collections.emptyList();
+	private List<T> list1;
+	private List<T> list2;
 
 	/**
 	 * Class constructor specifying the two lists of a cartesian product.
@@ -60,11 +60,11 @@ public CartesianProduct(List<T> list1, List<T> list2) {
 	 * @return the list of ordered pairs
 	 */
 	public List<OrderedPair<T>> getOrderedPairs() {
-		List<OrderedPair<T>> pairs = new ArrayList<OrderedPair<T>>(list1.size()*list2.size());
+		List<OrderedPair<T>> pairs = new ArrayList<>(list1.size() * list2.size());
 
 		for (T element1: list1) {
 			for (T element2: list2) {
-				pairs.add(new OrderedPair<T>(element1, element2));
+				pairs.add(new OrderedPair<>(element1, element2));
 			}
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/GetRepresentatives.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/GetRepresentatives.java
index c3bbf1b907..5b4ccd0b6b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/GetRepresentatives.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/GetRepresentatives.java
@@ -39,11 +39,11 @@
  */
 public class GetRepresentatives {
 
-	private static String clusterUrl = "http://www.rcsb.org/pdb/rest/representatives?cluster=";
-	private static String allUrl = "http://www.rcsb.org/pdb/rest/getCurrent/";
+	private static final String clusterUrl = "http://www.rcsb.org/pdb/rest/representatives?cluster=";
+	private static final String allUrl = "http://www.rcsb.org/pdb/rest/getCurrent/";
 
 	// available sequence clusters
-	private static List<Integer> seqIdentities = Arrays.asList(30, 40, 50, 70, 90, 95, 100);
+	private static final List<Integer> seqIdentities = Arrays.asList(30, 40, 50, 70, 90, 95, 100);
 
 
 	/**
@@ -54,7 +54,7 @@ public class GetRepresentatives {
 	 * @return PdbChainKey set of representatives
 	 */
 	public static SortedSet<StructureName> getRepresentatives(int sequenceIdentity) {
-		SortedSet<StructureName> representatives = new TreeSet<StructureName>();
+		SortedSet<StructureName> representatives = new TreeSet<>();
 
 		if (!seqIdentities.contains(sequenceIdentity)) {
 			System.err.println("Error: representative chains are not available for %sequence identity: "
@@ -69,7 +69,7 @@ public static SortedSet<StructureName> getRepresentatives(int sequenceIdentity)
 
 			InputStream stream = URLConnectionTools.getInputStream(u, 60000);
 
-			String xml = null;
+			String xml;
 
 			if (stream != null) {
 				xml = JFatCatClient.convertStreamToString(stream);
@@ -95,7 +95,7 @@ public static SortedSet<StructureName> getRepresentatives(int sequenceIdentity)
 	 * @return PdbChainKey set of all PDB IDs.
 	 */
 	public static SortedSet<String> getAll() {
-		SortedSet<String> representatives = new TreeSet<String>();
+		SortedSet<String> representatives = new TreeSet<>();
 
 		try {
 
@@ -107,7 +107,7 @@ public static SortedSet<String> getAll() {
 				BufferedReader reader = new BufferedReader(
 						new InputStreamReader(stream));
 
-				String line = null;
+				String line;
 
 				while ((line = reader.readLine()) != null) {
 					int index = line.lastIndexOf("structureId=");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/PdbIdLists.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/PdbIdLists.java
index 78f1ea8c9e..94b4df0b23 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/PdbIdLists.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/PdbIdLists.java
@@ -226,7 +226,7 @@ public static Set<String> postQuery(String xml)
 
 		InputStream in =  doPOST(u,encodedXML);
 
-		Set<String> pdbIds = new TreeSet<String>();
+		Set<String> pdbIds = new TreeSet<>();
 
 
 		try (BufferedReader rd = new BufferedReader(new InputStreamReader(in))) {
@@ -237,7 +237,6 @@ public static Set<String> postQuery(String xml)
 				pdbIds.add(line);
 
 			}
-			rd.close();
 		}
 
 
@@ -275,7 +274,7 @@ public static InputStream doPOST(URL url, String data)
 		// Get the response
 		return conn.getInputStream();
 
-	};
+	}
 
 	public static void main(String[] args){
 		try {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBDescription.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBDescription.java
index 6c738697c9..e6eb75bddf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBDescription.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBDescription.java
@@ -39,10 +39,10 @@ public class RCSBDescription {
 
 	private String pdbId;
 
-	private List<RCSBPolymer> polymers;
+	private final List<RCSBPolymer> polymers;
 
 	public RCSBDescription() {
-		polymers = new ArrayList<RCSBPolymer>();
+		polymers = new ArrayList<>();
 	}
 
 	public void addPolymer(RCSBPolymer polymer) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBDescriptionFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBDescriptionFactory.java
index f181a39e6b..8c1f75e40f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBDescriptionFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBDescriptionFactory.java
@@ -86,7 +86,7 @@ public static RCSBDescription get(InputStream stream) {
 
 		// now get polymers
 		data = structureIdE.getChildNodes();
-		Element polymerE = null;
+		Element polymerE;
 		for (int i = 0; i < data.getLength(); i++) {
 			if (data.item(i).getNodeType() != 1) continue;
 			polymerE = (Element) data.item(i);
@@ -121,7 +121,7 @@ public static RCSBDescription get(String pdbId) {
 	private static RCSBMacromolecule makeMolecule(Element moleculeE) {
 		RCSBMacromolecule molecule = new RCSBMacromolecule();
 		molecule.setName(moleculeE.getAttribute("name"));
-		Element element = null;
+		Element element;
 		NodeList data = moleculeE.getChildNodes();
 		for (int i = 0; i < data.getLength(); i++) {
 			if (data.item(i).getNodeType() != 1) continue;
@@ -141,28 +141,35 @@ private static RCSBPolymer makePolymer(Element polymerE) {
 		polymer.setWeight(ReadUtils.toDouble(polymerE.getAttribute("weight")));
 		polymer.setType(ReadUtils.toStr(polymerE.getAttribute("type")));
 
-		Element element = null;
+		Element element;
 		NodeList data = polymerE.getChildNodes();
 		for (int i = 0; i < data.getLength(); i++) {
 			if (data.item(i).getNodeType() != 1) continue;
 			element = (Element) data.item(i);
-			if (element.getNodeName().equals("chain")) {
-				parseChains(polymer, element.getAttribute("id"));
-			} else if (element.getNodeName().equals("Taxonomy")) {
-				String name = element.getAttribute("name");
-				int id = ReadUtils.toInt(element.getAttribute("id"));
-				RCSBTaxonomy taxonomy = new RCSBTaxonomy(name, id);
-				polymer.setTaxonomy(taxonomy);
-			} else if (element.getNodeName().equals("macroMolecule")) {
-				RCSBMacromolecule molecule = makeMolecule(element);
-				polymer.setMolecule(molecule);
-			} else if (element.getNodeName().equals("polymerDescription")) {
-				polymer.setDescription(element.getAttribute("description"));
-			} else if (element.getNodeName().equals("enzClass")) {
-				polymer.setEnzClass(element.getAttribute("ec"));
-			} else if (element.getNodeName().equals("synonym")) {
-				parseSynonyms(polymer, element.getAttribute("name"));
-			}
+            switch (element.getNodeName()) {
+                case "chain":
+                    parseChains(polymer, element.getAttribute("id"));
+                    break;
+                case "Taxonomy":
+                    String name = element.getAttribute("name");
+                    int id = ReadUtils.toInt(element.getAttribute("id"));
+                    RCSBTaxonomy taxonomy = new RCSBTaxonomy(name, id);
+                    polymer.setTaxonomy(taxonomy);
+                    break;
+                case "macroMolecule":
+                    RCSBMacromolecule molecule = makeMolecule(element);
+                    polymer.setMolecule(molecule);
+                    break;
+                case "polymerDescription":
+                    polymer.setDescription(element.getAttribute("description"));
+                    break;
+                case "enzClass":
+                    polymer.setEnzClass(element.getAttribute("ec"));
+                    break;
+                case "synonym":
+                    parseSynonyms(polymer, element.getAttribute("name"));
+                    break;
+            }
 		}
 		return polymer;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBLigands.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBLigands.java
index 2b06448fd0..e8d92c1683 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBLigands.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBLigands.java
@@ -39,10 +39,10 @@ public class RCSBLigands {
 
 	private String pdbId;
 
-	private List<RCSBLigand> ligands;
+	private final List<RCSBLigand> ligands;
 
 	public RCSBLigands() {
-		ligands = new ArrayList<RCSBLigand>();
+		ligands = new ArrayList<>();
 	}
 
 	public void addLigand(RCSBLigand ligand) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBLigandsFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBLigandsFactory.java
index 723bbfac5a..49e5a93ac0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBLigandsFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBLigandsFactory.java
@@ -96,7 +96,7 @@ public static List<RCSBLigand> getFromHeteroAtomIds(InputStream stream) {
 			return null;
 		}
 
-		List<RCSBLigand> ligands = new ArrayList<RCSBLigand>();
+		List<RCSBLigand> ligands = new ArrayList<>();
 
 		// first get the ligandInfo
 		Element structureIdE = null;
@@ -110,7 +110,7 @@ public static List<RCSBLigand> getFromHeteroAtomIds(InputStream stream) {
 
 		// now get individual ligands
 		data = structureIdE.getChildNodes();
-		Element ligandE = null;
+		Element ligandE;
 		for (int i = 0; i < data.getLength(); i++) {
 			if (data.item(i).getNodeType() != 1) continue;
 			ligandE = (Element) data.item(i);
@@ -187,7 +187,7 @@ public static RCSBLigands getFromPdbId(InputStream stream) {
 
 		// now get individual ligands
 		data = structureIdE.getChildNodes();
-		Element ligandE = null;
+		Element ligandE;
 		for (int i = 0; i < data.getLength(); i++) {
 			if (data.item(i).getNodeType() != 1) continue;
 			ligandE = (Element) data.item(i);
@@ -239,9 +239,9 @@ public static List<RCSBLigands> getFromPdbIds(InputStream stream) {
 
 		// first we have to handle the element "ligandsInEntry", which is not present if we have only 1 structure
 
-		List<RCSBLigands> ligandsList = new ArrayList<RCSBLigands>();
+		List<RCSBLigands> ligandsList = new ArrayList<>();
 
-		Element structureIdE = null;
+		Element structureIdE;
 
 		for (int k = 0; k < dataaa.getLength(); k++) {
 
@@ -263,7 +263,7 @@ public static List<RCSBLigands> getFromPdbIds(InputStream stream) {
 
 				// now get individual ligands
 				data = ligandIdE.getChildNodes();
-				Element ligandE = null;
+				Element ligandE;
 				for (int i = 0; i < data.getLength(); i++) {
 					if (data.item(i).getNodeType() != 1) continue;
 					ligandE = (Element) data.item(i);
@@ -343,21 +343,27 @@ private static RCSBLigand makeLigand(Element ligandE) {
 		ligand.setId(ligandE.getAttribute("chemicalID"));
 		ligand.setType(ligandE.getAttribute("type"));
 		ligand.setWeight(ReadUtils.toDouble(ligandE.getAttribute("molecularWeight")));
-		Element element = null;
+		Element element;
 		NodeList data = ligandE.getChildNodes();
 		for (int i = 0; i < data.getLength(); i++) {
 			if (data.item(i).getNodeType() != 1) continue;
 			element = (Element) data.item(i);
-			if (element.getNodeName().equals("chemicalName")) {
-				ligand.setName(element.getTextContent());
-			} else if (element.getNodeName().equals("formula")) {
-				ligand.setFormula(element.getTextContent());
-			} else if (element.getNodeName().equals("InChIKey")) {
-				ligand.setInChIKey(element.getTextContent());
-			} else if (element.getNodeName().equals("InChI")) {
-				ligand.setInChI(element.getTextContent());
-			} else if (element.getNodeName().equals("smiles")) {
-				ligand.setSmiles(element.getTextContent());
+			switch (element.getNodeName()) {
+				case "chemicalName":
+					ligand.setName(element.getTextContent());
+					break;
+				case "formula":
+					ligand.setFormula(element.getTextContent());
+					break;
+				case "InChIKey":
+					ligand.setInChIKey(element.getTextContent());
+					break;
+				case "InChI":
+					ligand.setInChI(element.getTextContent());
+					break;
+				case "smiles":
+					ligand.setSmiles(element.getTextContent());
+					break;
 			}
 		}
 		return ligand;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBMacromolecule.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBMacromolecule.java
index 5ab13502fa..31be20a33d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBMacromolecule.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBMacromolecule.java
@@ -37,11 +37,11 @@
  */
 public class RCSBMacromolecule {
 
-	private List<String> accessions;
+	private final List<String> accessions;
 	private String name;
 
 	public RCSBMacromolecule() {
-		accessions = new ArrayList<String>();
+		accessions = new ArrayList<>();
 	}
 
 	public List<String> getAccessions() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBPolymer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBPolymer.java
index 1d3113e73b..f3cbfcf34f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBPolymer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBPolymer.java
@@ -37,7 +37,7 @@
  */
 public class RCSBPolymer {
 
-	private List<Character> chains;
+	private final List<Character> chains;
 
 	private String description;
 
@@ -49,7 +49,7 @@ public class RCSBPolymer {
 
 	private RCSBMacromolecule molecule;
 
-	private List<String> synonyms;
+	private final List<String> synonyms;
 
 	private RCSBTaxonomy taxonomy;
 
@@ -58,8 +58,8 @@ public class RCSBPolymer {
 	private Double weight;
 
 	public RCSBPolymer() {
-		chains = new ArrayList<Character>();
-		synonyms = new ArrayList<String>();
+		chains = new ArrayList<>();
+		synonyms = new ArrayList<>();
 	}
 
 	public List<Character> getChains() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBUpdates.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBUpdates.java
index b4860b2cf1..b14f1efbc8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBUpdates.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBUpdates.java
@@ -44,12 +44,12 @@ public class RCSBUpdates {
 	 */
 	public Map<String,String[]> getUpdates() throws IOException{
 
-		Map<String,String[]> outMap = new HashMap<String, String[]>();
+		Map<String,String[]> outMap = new HashMap<>();
 		// A list of files to get
 		String[] newStringList = {"added.models","added.nmr","added.pdb","added.sf","modified.cs","modified.models",
 				"modified.nmr","modified.pdb","modified.sf","obsolete.cs","obsolete.models","obsolete.nmr","obsolete.pdb","obsolete.sf"};
 		for(String fileName: newStringList){
-			String[] thisList = readURL(baseURL+""+fileName);
+			String[] thisList = readURL(baseURL + fileName);
 			outMap.put(fileName, thisList);
 		}
 		return outMap;
@@ -64,7 +64,7 @@ public Map<String,String[]> getUpdates() throws IOException{
 	 * @throws IOException
 	 */
 	private String[] readURL(String urlIn) throws IOException{
-		List<String> outList = new ArrayList<String>();
+		List<String> outList = new ArrayList<>();
 		// create a url object
 		URL url = new URL(urlIn);
 
@@ -84,6 +84,6 @@ private String[] readURL(String urlIn) throws IOException{
 
 		}
 
-		return outList.toArray(new String[outList.size()]);
+		return outList.toArray(new String[0]);
 	}
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/ReadUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/ReadUtils.java
index 27efb2e36d..e3d0ab4e6a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/ReadUtils.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/ReadUtils.java
@@ -70,8 +70,8 @@ static NodeList getNodes(InputStream stream) throws IOException {
 			documentBuilderFactorySet = true;
 		}
 		DocumentBuilderFactory builderFactory = DocumentBuilderFactory.newInstance();
-		DocumentBuilder builder = null;
-		Document document = null;
+		DocumentBuilder builder;
+		Document document;
 		try {
 			builder = builderFactory.newDocumentBuilder();
 		} catch (ParserConfigurationException e) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/Astral.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/Astral.java
index d7c1ebe5d5..6d875a2ef4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/Astral.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/Astral.java
@@ -59,7 +59,7 @@ public class Astral {
 	 * @author dmyersturnbull
 	 *
 	 */
-	public static enum AstralSet {
+	public enum AstralSet {
 		FORTY_175("1.75_40", "http://scop.berkeley.edu/downloads/scopseq-1.75/astral-scopdom-seqres-gd-sel-gs-bib-40-1.75.fa"),
 		NINETY_FIVE_175("1.75_95", "http://scop.berkeley.edu/downloads/scopseq-1.75/astral-scopdom-seqres-gd-sel-gs-bib-95-1.75.fa"),
 		FORTY_175A("1.75A_40", "http://scop.berkeley.edu/downloads/scopeseq-2.01/astral-scopedom-seqres-gd-sel-gs-bib-40-2.01.fa"),
@@ -72,8 +72,8 @@ public static enum AstralSet {
 		NINETY_FIVE_202("2.02_95", "http://scop.berkeley.edu/downloads/scopeseq-2.02/astral-scopedom-seqres-gd-sel-gs-bib-95-2.02.fa"),
 		FORTY_203("2.03_40", "http://scop.berkeley.edu/downloads/scopeseq-2.03/astral-scopedom-seqres-gd-sel-gs-bib-40-2.03.fa"),
 		NINETY_FIVE_203("2.03_95", "http://scop.berkeley.edu/downloads/scopeseq-2.03/astral-scopedom-seqres-gd-sel-gs-bib-95-2.03.fa");
-		private String id;
-		private String url;
+		private final String id;
+		private final String url;
 
 		public static AstralSet parse(String str) {
 			for (AstralSet c : AstralSet.class.getEnumConstants()) {
@@ -101,7 +101,7 @@ public String toString() {
 		}
 	}
 
-	private static Map<String, SoftReference<Astral>> instances = new HashMap<String, SoftReference<Astral>>();
+	private static final Map<String, SoftReference<Astral>> instances = new HashMap<>();
 
 	private static final Logger logger = LoggerFactory.getLogger(Astral.class);
 
@@ -116,7 +116,7 @@ public static Set<String> getRepresentatives(AstralSet cutoff) {
 			return instances.get(cutoff.getId()).get().getNames();
 		}
 		Astral astral = new Astral(cutoff);
-		instances.put(cutoff.getId(), new SoftReference<Astral>(astral));
+		instances.put(cutoff.getId(), new SoftReference<>(astral));
 		return astral.getNames();
 	}
 
@@ -203,8 +203,8 @@ public LinkedHashMap<Integer, String> getFailedLines() {
 	 * Parses the FASTA file opened by reader.
 	 */
 	private void init(Reader reader) {
-		names = new TreeSet<String>();
-		failedLines = new LinkedHashMap<Integer,String>();
+		names = new TreeSet<>();
+		failedLines = new LinkedHashMap<>();
 
 		BufferedReader br = null;
 
@@ -214,7 +214,7 @@ private void init(Reader reader) {
 
 			logger.info("Reading ASTRAL file...");
 
-			String line = "";
+			String line;
 			int i = 0;
 			while ((line = br.readLine()) != null) {
 				if (line.startsWith(">")) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.java
index f0aab86b95..598a99d513 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.java
@@ -45,7 +45,7 @@ public class BerkeleyScopInstallation extends ScopInstallation {
 	 * A map from SCOP version names which the Berkeley server offers as a
 	 * download to an array of equivalent deprecated SCOP version names.
 	 */
-	public static final Map<String,String[]> EQUIVALENT_VERSIONS = new HashMap<String,String[]>();
+	public static final Map<String,String[]> EQUIVALENT_VERSIONS = new HashMap<>();
 
 	static {
 		EQUIVALENT_VERSIONS.put("2.01", new String[] {"1.75A"});
@@ -62,7 +62,7 @@ public BerkeleyScopInstallation() {
 	}
 
 	private static class BerkeleyScopMirror extends ScopMirror {
-		private String rootURL;
+		private final String rootURL;
 		public BerkeleyScopMirror(String url) {
 			super(url);
 			rootURL = url;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/CachedRemoteScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/CachedRemoteScopInstallation.java
index 5f7ca94589..8c2c49df91 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/CachedRemoteScopInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/CachedRemoteScopInstallation.java
@@ -64,7 +64,7 @@ public CachedRemoteScopInstallation(boolean useCache) throws IOException {
 
 		proxy = new RemoteScopInstallation();
 
-		scopDescriptionCache = new SerializableCache<Integer,ScopDescription>("scopDescriptionCache.ser");
+		scopDescriptionCache = new SerializableCache<>("scopDescriptionCache.ser");
 
 		if ( ! useCache) {
 			logger.warn(getClass().getSimpleName() + " disabling cache");
@@ -85,7 +85,7 @@ public CachedRemoteScopInstallation(boolean useCache) throws IOException {
 	 */
 	private void loadRepresentativeDomains() throws IOException {
 
-		URL u = null;
+		URL u;
 		try {
 			u = new URL(RemoteScopInstallation.DEFAULT_SERVER + "getRepresentativeScopDomains");
 		} catch (MalformedURLException e) {
@@ -212,7 +212,7 @@ public void flushCache() {
 
 	@Override
 	public List<String> getComments(int sunid) {
-		return new ArrayList<String>(1);
+		return new ArrayList<>(1);
 	}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopCategory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopCategory.java
index c60e2c06e5..e140bb5d7e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopCategory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopCategory.java
@@ -41,20 +41,22 @@ public enum ScopCategory implements Serializable
 	Class,Fold, Superfamily,  Family, Domain, Species, Px;
 
 	public static ScopCategory fromString(String type){
-		if ( type.equals("cl"))
-			return Class;
-		else if ( type.equals("cf"))
-			return Fold;
-		else if ( type.equals("sf"))
-			return Superfamily;
-		else if ( type.equals("fa"))
-			return Family;
-		else if ( type.equals("dm"))
-			return Domain;
-		else if ( type.equals("sp"))
-			return Species;
-		else
-			return Px;
+        switch (type) {
+            case "cl":
+                return Class;
+            case "cf":
+                return Fold;
+            case "sf":
+                return Superfamily;
+            case "fa":
+                return Family;
+            case "dm":
+                return Domain;
+            case "sp":
+                return Species;
+            default:
+                return Px;
+        }
 	}
 
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDatabase.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDatabase.java
index ee3706cc76..6999069bee 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDatabase.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDatabase.java
@@ -35,21 +35,21 @@ public interface ScopDatabase {
 	 * @param category e.g. "superfamily"
 	 * @return all records of this type
 	 */
-	public abstract List<ScopDescription> getByCategory(ScopCategory category);
+    List<ScopDescription> getByCategory(ScopCategory category);
 
 	/** Get all scop descriptions that start with a classification ID, e.g. b.1.18
 	 *
 	 * @param query
 	 * @return list of scop descriptions
 	 */
-	public abstract List<ScopDescription> filterByClassificationId(String query);
+    List<ScopDescription> filterByClassificationId(String query);
 
 	/** get the SCOP sub-tree for a particular domain.
 	 *
 	 * @param domain
 	 * @return list of ScopNodes providing the path to this domain
 	 */
-	public abstract List<ScopNode> getTree(ScopDomain domain);
+    List<ScopNode> getTree(ScopDomain domain);
 
 
 	/** search through SCOP and filter based on domain name
@@ -57,28 +57,28 @@ public interface ScopDatabase {
 	 * @param query a (part) of a name
 	 * @return list of matchin ScopDomains
 	 */
-	public abstract List<ScopDomain> filterByDomainName(String query);
+    List<ScopDomain> filterByDomainName(String query);
 
 	/** Get all scop descriptions that start with a certain name. e.g. Globin
 	 *
 	 * @param query
 	 * @return list of scop descriptions
 	 */
-	public abstract List<ScopDescription> filterByDescription(String query);
+    List<ScopDescription> filterByDescription(String query);
 
 	/** Return the SCOP description for a node in the hierarchy by its "sunid" id.
 	 *
 	 * @param sunid
 	 * @return a ScopDescription object
 	 */
-	public abstract ScopDescription getScopDescriptionBySunid(int sunid);
+    ScopDescription getScopDescriptionBySunid(int sunid);
 
 	/** Get a list of ScopDomains that have been assigned to a PDB ID
 	 *
 	 * @param pdbId the PDB entry
 	 * @return a list of ScopDomains
 	 */
-	public abstract List<ScopDomain> getDomainsForPDB(String pdbId);
+    List<ScopDomain> getDomainsForPDB(String pdbId);
 
 	/** get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
 	 *
@@ -86,40 +86,40 @@ public interface ScopDatabase {
 	 * @param scopId e.g. d2bq6a1
 	 * @return a ScopDomain or null if no domain with the particular ID could be found
 	 */
-	public abstract ScopDomain getDomainByScopID(String scopId);
+    ScopDomain getDomainByScopID(String scopId);
 
 	/** Access a particular ScopNode. The scopNode then allows to traverse through the scop hierarchy...
 	 *
 	 * @param sunid the scop unique id
 	 * @return a ScopNode that matches this sunid
 	 */
-	public abstract ScopNode getScopNode(int sunid);
+    ScopNode getScopNode(int sunid);
 
 	/** Returns the SCOP version
 	 *
 	 * @return version of SCOP
 	 */
 
-	public abstract String getScopVersion();
+    String getScopVersion();
 
 	/**
 	 * Sets the scop version used.
 	 * @param version
 	 * @throws UnsupportedOperationException If the version cannot be changed
 	 */
-	public abstract void setScopVersion(String version);
+    void setScopVersion(String version);
 
 	/** Get a SCOP domain by its sunid
 	 *
 	 * @param sunid the scop unique id
 	 * @return a list of scop domains that match this sunid
 	 */
-	public abstract List<ScopDomain> getScopDomainsBySunid(Integer sunid);
+    List<ScopDomain> getScopDomainsBySunid(Integer sunid);
 
 	/**
 	 * Get comments about a SCOP domain by its sunid
 	 * @param sunid
 	 * @return
 	 */
-	public abstract List<String> getComments(int sunid);
+    List<String> getComments(int sunid);
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDescription.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDescription.java
index b85845ce2c..07d2704af3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDescription.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDescription.java
@@ -55,7 +55,7 @@ public class ScopDescription implements Serializable,Cloneable{
 	public String toString(){
 		StringBuilder buf = new StringBuilder();
 
-		buf.append(String.valueOf(sunID));
+		buf.append(sunID);
 		buf.append("\t");
 		buf.append(category);
 		buf.append("\t");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java
index 121498f03d..23de56d73b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java
@@ -90,23 +90,23 @@ public String toString() {
 		buf.append("\t") ;
 		buf.append(classificationId);
 		buf.append("\t") ;
-		buf.append(String.valueOf(sunid));
+		buf.append(sunid);
 		buf.append("\t") ;
 
 		buf.append("cl=");
-		buf.append(String.valueOf(classId));
+		buf.append(classId);
 		buf.append(",cf=");
-		buf.append(String.valueOf(foldId));
+		buf.append(foldId);
 		buf.append(",sf=");
-		buf.append(String.valueOf(superfamilyId));
+		buf.append(superfamilyId);
 		buf.append(",fa=");
-		buf.append(String.valueOf(familyId));
+		buf.append(familyId);
 		buf.append(",dm=");
-		buf.append(String.valueOf(domainId));
+		buf.append(domainId);
 		buf.append(",sp=");
-		buf.append(String.valueOf(speciesId));
+		buf.append(speciesId);
 		buf.append(",px=");
-		buf.append(String.valueOf(px));
+		buf.append(px);
 
 
 		return buf.toString();
@@ -214,7 +214,7 @@ protected Object clone() throws CloneNotSupportedException {
 	 * Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
 	 */
 	public Set<String> getChains() {
-		Set<String> chains = new HashSet<String>();
+		Set<String> chains = new HashSet<>();
 		List<ResidueRange> rrs = ResidueRange.parseMultiple(getRanges());
 		for (ResidueRange rr : rrs) chains.add(rr.getChainName());
 		return chains;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java
index 15363bd3e7..bf591b65be 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java
@@ -83,7 +83,7 @@ public class ScopFactory {
 	public static final String LATEST_VERSION = VERSION_2_0_7;
 
 	// Hold one instance for each version
-	private static Map<String,ScopDatabase> versionedScopDBs = new HashMap<String, ScopDatabase>();
+	private static final Map<String,ScopDatabase> versionedScopDBs = new HashMap<>();
 	private static String defaultVersion = LATEST_VERSION;
 
 	/**
@@ -147,7 +147,6 @@ public static ScopDatabase getSCOP(String version, boolean forceLocalData){
 				versionedScopDBs.put(version,berkeley);
 				return berkeley;
 			}
-			return scop;
 		} else {
 			// Use a remote installation
 			if( scop == null ) {
@@ -156,8 +155,8 @@ public static ScopDatabase getSCOP(String version, boolean forceLocalData){
 				scop.setScopVersion(version);
 				versionedScopDBs.put(version,scop);
 			}
-			return scop;
 		}
+		return scop;
 	}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
index bb65b81341..d295cfdc7c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
@@ -82,15 +82,15 @@ public class ScopInstallation implements LocalScopDatabase {
 
 	private String cacheLocation ;
 
-	private AtomicBoolean installedCla;
-	private AtomicBoolean installedDes;
-	private AtomicBoolean installedHie;
-	private AtomicBoolean installedCom;
+	private final AtomicBoolean installedCla;
+	private final AtomicBoolean installedDes;
+	private final AtomicBoolean installedHie;
+	private final AtomicBoolean installedCom;
 
 	private Map<Integer, List<String>> commentsMap;
-	private Map<String, List<ScopDomain>> domainMap;
-	private Map<Integer, ScopDescription> sunidMap;
-	private Map<Integer, ScopNode> scopTree;
+	private final Map<String, List<ScopDomain>> domainMap;
+	private final Map<Integer, ScopDescription> sunidMap;
+	private final Map<Integer, ScopNode> scopTree;
 
 
 	/**
@@ -112,12 +112,12 @@ public ScopInstallation(String cacheLocation){
 		installedCom.set(false);
 
 		scopVersion = DEFAULT_VERSION;
-		mirrors = new ArrayList<ScopMirror>(1);
+		mirrors = new ArrayList<>(1);
 
-		domainMap = new HashMap<String, List<ScopDomain>>();
+		domainMap = new HashMap<>();
 
-		sunidMap  = new HashMap<Integer, ScopDescription>();
-		scopTree  = new TreeMap<Integer, ScopNode>();
+		sunidMap  = new HashMap<>();
+		scopTree  = new TreeMap<>();
 
 	}
 
@@ -178,10 +178,9 @@ public List<ScopDescription> getByCategory(ScopCategory category){
 			throw new ScopIOException(e);
 		}
 
-		List<ScopDescription> matches = new ArrayList<ScopDescription>();
-		for (Integer i : sunidMap.keySet()){
-			ScopDescription sc = sunidMap.get(i);
-			if ( sc.getCategory().equals(category))
+		List<ScopDescription> matches = new ArrayList<>();
+		for (ScopDescription sc : sunidMap.values()){
+            if ( sc.getCategory().equals(category))
 
 				try {
 					matches.add((ScopDescription)sc.clone());
@@ -205,12 +204,11 @@ public List<ScopDescription> filterByClassificationId(String query){
 			throw new ScopIOException(e);
 		}
 
-		List<ScopDescription> matches = new ArrayList<ScopDescription>();
-		for (Integer i : sunidMap.keySet()){
-			ScopDescription sc = sunidMap.get(i);
+		List<ScopDescription> matches = new ArrayList<>();
+		for (ScopDescription sc : sunidMap.values()){
 
 
-			if( sc.getClassificationId().startsWith(query)){
+            if( sc.getClassificationId().startsWith(query)){
 				matches.add(sc);
 			}
 		}
@@ -227,7 +225,7 @@ public List<ScopNode> getTree(ScopDomain domain){
 		ScopNode node = getScopNode(domain.getSunid());
 
 
-		List<ScopNode> tree = new ArrayList<ScopNode>();
+		List<ScopNode> tree = new ArrayList<>();
 		while (node != null){
 
 			//System.out.println("This node: sunid:" + node.getSunid() );
@@ -246,7 +244,7 @@ public List<ScopNode> getTree(ScopDomain domain){
 	@Override
 	public List<ScopDomain> filterByDomainName(String query) {
 
-		List<ScopDomain > domains = new ArrayList<ScopDomain>();
+		List<ScopDomain > domains = new ArrayList<>();
 		if (query.length() <5){
 			return domains;
 		}
@@ -281,11 +279,10 @@ public List<ScopDescription> filterByDescription(String query) throws ScopIOExce
 		}
 
 		query = query.toLowerCase();
-		List<ScopDescription> matches = new ArrayList<ScopDescription>();
-		for (Integer i : sunidMap.keySet()){
-			ScopDescription sc = sunidMap.get(i);
+		List<ScopDescription> matches = new ArrayList<>();
+		for (ScopDescription sc : sunidMap.values()){
 
-			if( sc.getDescription().toLowerCase().startsWith(query)){
+            if( sc.getDescription().toLowerCase().startsWith(query)){
 				matches.add(sc);
 			}
 		}
@@ -321,7 +318,7 @@ public  List<ScopDomain> getDomainsForPDB(String pdbId) {
 
 		List<ScopDomain> doms = domainMap.get(pdbId.toLowerCase());
 
-		List<ScopDomain> retdoms = new ArrayList<ScopDomain>();
+		List<ScopDomain> retdoms = new ArrayList<>();
 
 		if ( doms == null)
 			return retdoms;
@@ -428,7 +425,7 @@ private void parseHierarchy(BufferedReader buffer) throws IOException {
 			String children = spl[2];
 			String[] childIds = children.split(",");
 
-			List<Integer> chis = new ArrayList<Integer>();
+			List<Integer> chis = new ArrayList<>();
 
 			for ( String id : childIds){
 				if ( id.equals("-"))
@@ -472,7 +469,7 @@ private void parseComments() throws IOException{
 
 	private void parseComments(BufferedReader buffer) throws IOException {
 
-		commentsMap = new HashMap<Integer,List<String>>();
+		commentsMap = new HashMap<>();
 
 		int counter = 0;
 		String line;
@@ -481,10 +478,10 @@ private void parseComments(BufferedReader buffer) throws IOException {
 			String[] parts = line.split("!");
 			int sunId = Integer.parseInt(parts[0].trim());
 			if (parts.length == 1) {
-				commentsMap.put(sunId, new ArrayList<String>(1));
+				commentsMap.put(sunId, new ArrayList<>(1));
 				continue;
 			}
-			List<String> comments = new ArrayList<String>(parts.length - 1);
+			List<String> comments = new ArrayList<>(parts.length - 1);
 			for (int i = 1; i < parts.length; i++) {
 				String trimmed = parts[i].trim();
 				if( !trimmed.isEmpty() ) {
@@ -499,7 +496,7 @@ private void parseComments(BufferedReader buffer) throws IOException {
 	}
 
 	private void parseDescriptions(BufferedReader buffer) throws IOException {
-		String line = null;
+		String line;
 
 		int counter = 0;
 		while ((line = buffer.readLine ()) != null) {
@@ -536,7 +533,7 @@ private void parseDescriptions(BufferedReader buffer) throws IOException {
 
 
 	private void parseClassification(BufferedReader buffer) throws IOException {
-		String line = null;
+		String line;
 
 		int counter = 0;
 		while ((line = buffer.readLine ()) != null) {
@@ -594,7 +591,7 @@ private void parseClassification(BufferedReader buffer) throws IOException {
 			if ( domainMap.containsKey(pdbId)){
 				domainList = domainMap.get(pdbId);
 			} else {
-				domainList = new ArrayList<ScopDomain>();
+				domainList = new ArrayList<>();
 				domainMap.put(pdbId,domainList);
 			}
 
@@ -637,7 +634,7 @@ private List<String> extractRanges(String range) {
 		return ranges;
 	}
 
-	protected void downloadClaFile() throws FileNotFoundException, IOException{
+	protected void downloadClaFile() throws IOException{
 		if(mirrors.size()<1) {
 			initScopURLs();
 		}
@@ -658,7 +655,7 @@ protected void downloadClaFile() throws FileNotFoundException, IOException{
 		throw new IOException("Unable to download SCOP .cla file",exception);
 	}
 
-	protected void downloadDesFile() throws FileNotFoundException, IOException{
+	protected void downloadDesFile() throws IOException{
 		if(mirrors.size()<1) {
 			initScopURLs();
 		}
@@ -701,7 +698,7 @@ protected void downloadHieFile() throws IOException{
 
 	}
 
-	protected void downloadComFile() throws FileNotFoundException, IOException{
+	protected void downloadComFile() throws IOException{
 		if(mirrors.size()<1) {
 			initScopURLs();
 		}
@@ -836,10 +833,10 @@ public List<ScopDomain> getScopDomainsBySunid(Integer sunid)
 			throw new ScopIOException(e);
 		}
 
-		List<ScopDomain> domains = new ArrayList<ScopDomain>();
+		List<ScopDomain> domains = new ArrayList<>();
 
-		for (String pdbId: domainMap.keySet()){
-			for (ScopDomain d : domainMap.get(pdbId)){
+		for (List<ScopDomain> scopDomains : domainMap.values()){
+			for (ScopDomain d : scopDomains){
 				try {
 					if ( d.getPx() == sunid) {
 						domains.add((ScopDomain)d.clone());
@@ -874,7 +871,7 @@ public List<String> getComments(int sunid) {
 		} catch (IOException e) {
 			throw new ScopIOException(e);
 		}
-		if (!commentsMap.containsKey(sunid)) return new ArrayList<String>(1);
+		if (!commentsMap.containsKey(sunid)) return new ArrayList<>(1);
 		return commentsMap.get(sunid);
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ListStringWrapper.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ListStringWrapper.java
index 574052b86b..6f8b4e5174 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ListStringWrapper.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ListStringWrapper.java
@@ -60,7 +60,7 @@ public class ListStringWrapper implements Serializable{
 	}
 
 	public ListStringWrapper(){
-		data = new ArrayList<String>();
+		data = new ArrayList<>();
 	}
 
 	public List<String> getData() {
@@ -95,7 +95,7 @@ public  String toXML(){
 
 	public static ListStringWrapper fromXML(String xml){
 
-		ListStringWrapper job = null;
+		ListStringWrapper job;
 
 		try {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDescriptions.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDescriptions.java
index 8d618f710e..a175add7c2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDescriptions.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDescriptions.java
@@ -92,7 +92,7 @@ public  String toXML(){
 
 	public static ScopDescriptions fromXML(String xml){
 
-		ScopDescriptions job = null;
+		ScopDescriptions job;
 
 		try {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDomains.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDomains.java
index c9e8f8422b..f648d0ed3c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDomains.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDomains.java
@@ -93,7 +93,7 @@ public  String toXML(){
 
 	public static ScopDomains fromXML(String xml){
 
-		ScopDomains job = null;
+		ScopDomains job;
 
 		try {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopNodes.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopNodes.java
index 70e9965a5b..57277bb54a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopNodes.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopNodes.java
@@ -92,7 +92,7 @@ public  String toXML(){
 
 	public static ScopNodes fromXML(String xml){
 
-		ScopNodes job = null;
+		ScopNodes job;
 
 		try {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/TreeSetStringWrapper.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/TreeSetStringWrapper.java
index 004b81c069..6f3123e364 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/TreeSetStringWrapper.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/TreeSetStringWrapper.java
@@ -59,7 +59,7 @@ public class TreeSetStringWrapper implements Serializable{
 	}
 
 	public TreeSetStringWrapper(){
-		data = new TreeSet<String>();
+		data = new TreeSet<>();
 	}
 
 	public TreeSet<String> getData() {
@@ -94,7 +94,7 @@ public  String toXML(){
 
 	public static TreeSetStringWrapper fromXML(String xml){
 
-		TreeSetStringWrapper job = null;
+		TreeSetStringWrapper job;
 
 		try {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/XMLUtil.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/XMLUtil.java
index 8061e6ef6e..f206813b41 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/XMLUtil.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/XMLUtil.java
@@ -112,7 +112,7 @@ public static String getScopDescriptionXML(ScopDescription desc){
 
 	public static ScopDescription getScopDescriptionFromXML(String xml){
 
-		ScopDescription job = null;
+		ScopDescription job;
 
 		try {
 
@@ -186,7 +186,7 @@ public static String getCommentsXML(List<String> comments ){
 	}
 	public static List<String> getCommentsFromXML(String xml){
 
-		List<String> comments = null;
+		List<String> comments;
 
 		try {
 
@@ -227,7 +227,7 @@ public static String getScopNodeXML(ScopNode scopNode){
 	}
 
 	public static ScopNode getScopNodeFromXML(String xml){
-		ScopNode job = null;
+		ScopNode job;
 
 		try {
 
@@ -273,7 +273,7 @@ public static String getScopDomainXML(ScopDomain domain){
 	}
 
 	public static ScopDomain getScopDomainFromXML(String xml){
-		ScopDomain job = null;
+		ScopDomain job;
 
 		try {
 
@@ -321,7 +321,7 @@ public static String getDomainsXML(SortedSet<Domain> domains){
 	@SuppressWarnings("unchecked")
 	public static SortedSet<Domain> getDomainsFromXML(String xml) {
 
-		SortedSet<Domain> domains = null;
+		SortedSet<Domain> domains;
 		try {
 
 			Unmarshaller un = jaxbContextDomains.createUnmarshaller();
@@ -364,7 +364,7 @@ public static String getDomainRangesXML(SortedSet<String> domainRanges){
 	}
 
 	public static SortedSet<String> getDomainRangesFromXML(String xml){
-		SortedSet<String> domains = null;
+		SortedSet<String> domains;
 		try {
 
 			Unmarshaller un = jaxbContextStringSortedSet.createUnmarshaller();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java
index 04e35fe14d..39791b56e7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java
@@ -40,7 +40,7 @@ public enum BridgeType {
 	public final Character type;
 	public final String name;
 
-	private BridgeType(String name, Character stype) {
+	BridgeType(String name, Character stype) {
 		this.name = name;
 		this.type = stype;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java
index 519aef812d..fb5db72895 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java
@@ -152,7 +152,7 @@ private static List<SecStrucState> generalParse(BufferedReader reader,
 		String startLine = "  #  RESIDUE AA STRUCTURE BP1 BP2  ACC";
 		String line;
 
-		List<SecStrucState> secstruc = new ArrayList<SecStrucState>();
+		List<SecStrucState> secstruc = new ArrayList<>();
 
 		//Find the first line of the DSSP output
 		while((line = reader.readLine()) != null) {
@@ -185,14 +185,14 @@ private static List<SecStrucState> generalParse(BufferedReader reader,
 				String bp = line.substring(25,29).trim();
 				if (bp != "") {
 					BetaBridge bb = new BetaBridge(
-							index, Integer.valueOf(bp), BridgeType.parallel);
+							index, Integer.parseInt(bp), BridgeType.parallel);
 					ss.addBridge(bb);
 				} else logger.warn("Unable to parse beta Bridge for resn "+index);
 
 				bp = line.substring(29,33).trim();
 				if (bp != "") {
 					BetaBridge bb = new BetaBridge(
-							index, Integer.valueOf(bp), BridgeType.parallel);
+							index, Integer.parseInt(bp), BridgeType.parallel);
 					ss.addBridge(bb);
 				} else logger.warn("Unable to parse beta Bridge for resn "+index);
 
@@ -212,7 +212,7 @@ private static List<SecStrucState> generalParse(BufferedReader reader,
 
 					int partner = Integer.parseInt(p[0]);
 					if (partner != 0) partner += index;
-					double energy = Double.valueOf(p[1]) * 1000.0;
+					double energy = Double.parseDouble(p[1]) * 1000.0;
 
 					switch(i){
 					case 0:
@@ -236,15 +236,15 @@ private static List<SecStrucState> generalParse(BufferedReader reader,
 
 				//Angle properties
 				String val = line.substring(91,97).trim();
-				if (val != "") ss.setKappa(Float.valueOf(val));
+				if (val != "") ss.setKappa(Float.parseFloat(val));
 				else logger.warn("Unable to parse kappa for resn "+index);
 
 				val = line.substring(103,109).trim();
-				if (val != "") ss.setPhi(Float.valueOf(val));
+				if (val != "") ss.setPhi(Float.parseFloat(val));
 				else logger.warn("Unable to parse phi for resn "+index);
 
 				val = line.substring(109,116).trim();
-				if (val != "") ss.setPsi(Float.valueOf(val));
+				if (val != "") ss.setPsi(Float.parseFloat(val));
 				else logger.warn("Unable to parse psi for resn "+index);
 
 				if (assign) parent.setProperty(Group.SEC_STRUC, ss);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java
index 4696f3dc43..0034bbd293 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java
@@ -103,8 +103,8 @@ public class SecStrucCalc {
 	private AtomContactSet contactSet;
 	private Map<ResidueNumber, Integer> indResMap;
 	public SecStrucCalc(){
-		ladders = new ArrayList<Ladder>();
-		bridges = new ArrayList<BetaBridge>();
+		ladders = new ArrayList<>();
+		bridges = new ArrayList<>();
 	}
 
 
@@ -119,11 +119,11 @@ public SecStrucCalc(){
 	public List<SecStrucState> calculate(Structure s, boolean assign)
 			throws StructureException {
 
-		List<SecStrucState> secstruc = new ArrayList<SecStrucState>();
+		List<SecStrucState> secstruc = new ArrayList<>();
 		for(int i=0; i<s.nrModels(); i++) {
 			// Reinitialise the global vars
-			ladders = new ArrayList<Ladder>();
-			bridges = new ArrayList<BetaBridge>();
+			ladders = new ArrayList<>();
+			bridges = new ArrayList<>();
 			groups = initGroupArray(s, i);
 			// Initialise the contact set for this structure
 			initContactSet();
@@ -423,7 +423,7 @@ private boolean shouldExtendLadder(Ladder ladder, BetaBridge b) {
 	private void findBridges() {
 		// Get the interator of contacts
 		Iterator<AtomContact> myIter = contactSet.iterator();
-		List<Pair<Integer>> outList = new ArrayList<Pair<Integer>>();
+		List<Pair<Integer>> outList = new ArrayList<>();
 
 		// Now iterate through this
 		while(myIter.hasNext()){
@@ -460,29 +460,22 @@ private void findBridges() {
 				continue;
 			}
 
-			Pair<Integer> thisPair = new Pair<Integer>(i,j);
+			Pair<Integer> thisPair = new Pair<>(i, j);
 			outList.add(thisPair);
 		}
 		//
-		Collections.sort(outList, new Comparator<Pair<Integer>>() {
-			@Override
-			public int compare(Pair<Integer> o1, Pair<Integer> o2) {
-				if(o1.getFirst()<o2.getFirst()){
+		outList.sort((o1, o2) -> {
+			if (o1.getFirst() < o2.getFirst()) {
+				return -1;
+			} else if (o1.getFirst() > o2.getFirst()) {
+				return +1;
+			} else {
+				if (o1.getSecond() < o2.getSecond()) {
 					return -1;
-				}
-				else if(o1.getFirst()>o2.getFirst()){
-					return +1;
-				}
-				else{
-					if(o1.getSecond()<o2.getSecond()){
-						return -1;
-					}
-					else if(o1.getSecond()>o2.getSecond()){
-						return 1;
-					}
-					else{
-						return 0;
-					}
+				} else if (o1.getSecond() > o2.getSecond()) {
+					return 1;
+				} else {
+					return 0;
 				}
 			}
 		});
@@ -601,7 +594,7 @@ public String toString() {
 	 */
 	public String printDSSP() {
 
-		StringBuffer buf = new StringBuffer();
+		StringBuilder buf = new StringBuilder();
 		String nl = System.getProperty("line.separator");
 
 		//Header Line
@@ -634,11 +627,11 @@ public String printDSSP() {
 	 */
 	public String printHelixSummary() {
 
-		StringBuffer g = new StringBuffer(); //3-10 helix
-		StringBuffer h = new StringBuffer(); //alpha helix
-		StringBuffer i = new StringBuffer(); //pi-helix
-		StringBuffer ss = new StringBuffer(); //SS summary
-		StringBuffer aa = new StringBuffer(); //AA one-letter
+		StringBuilder g = new StringBuilder(); //3-10 helix
+		StringBuilder h = new StringBuilder(); //alpha helix
+		StringBuilder i = new StringBuilder(); //pi-helix
+		StringBuilder ss = new StringBuilder(); //SS summary
+		StringBuilder aa = new StringBuilder(); //AA one-letter
 		String nl = System.getProperty("line.separator");
 
 		g.append(	"3 turn: ");
@@ -668,7 +661,7 @@ public String printHelixSummary() {
 	 */
 	public String printFASTA() {
 
-		StringBuffer buf = new StringBuffer();
+		StringBuilder buf = new StringBuilder();
 		String nl = System.getProperty("line.separator");
 		buf.append(">"+groups[0].getChain().getStructure().getIdentifier()+nl);
 
@@ -704,7 +697,7 @@ public boolean equals(Object o){
 	}
 
 	private static SecStrucGroup[] initGroupArray(Structure s, int modelId) {
-		List<SecStrucGroup> groupList = new ArrayList<SecStrucGroup>();
+		List<SecStrucGroup> groupList = new ArrayList<>();
 		//
 		for ( Chain c : s.getChains(modelId)){
 
@@ -742,7 +735,7 @@ private static SecStrucGroup[] initGroupArray(Structure s, int modelId) {
 			}
 
 		}
-		return groupList.toArray(new SecStrucGroup[groupList.size()]);
+		return groupList.toArray(new SecStrucGroup[0]);
 	}
 
 	/**
@@ -750,7 +743,7 @@ private static SecStrucGroup[] initGroupArray(Structure s, int modelId) {
 	 * missing in the PDB files as only few experimental methods allow
 	 * to resolve their location.
 	 */
-	private void calculateHAtoms() throws StructureException {
+	private void calculateHAtoms() {
 
 		for ( int i = 0 ; i < groups.length-1  ; i++) {
 
@@ -777,9 +770,7 @@ private void calculateHBonds() {
 		 * More efficient method for calculating C-Alpha pairs
 		 */
 		if (groups.length < 5) return;
-		Iterator<AtomContact> otu = contactSet.iterator();
-		while(otu.hasNext()){
-			AtomContact ac = otu.next();
+		for (AtomContact ac : contactSet) {
 			Pair<Atom> pair = ac.getPair();
 			Group g1 = pair.getFirst().getGroup();
 			Group g2 = pair.getSecond().getGroup();
@@ -787,9 +778,9 @@ private void calculateHBonds() {
 			int i = indResMap.get(g1.getResidueNumber());
 			int j = indResMap.get(g2.getResidueNumber());
 			// Now check this
-			checkAddHBond(i,j);
+			checkAddHBond(i, j);
 			//"backwards" hbonds are not allowed
-			if (j!=(i+1)) checkAddHBond(j,i);
+			if (j != (i + 1)) checkAddHBond(j, i);
 		}
 	}
 
@@ -808,7 +799,7 @@ private void checkAddHBond(int i, int j){
 
 		SecStrucGroup two = groups[j];
 
-		double energy = 0;
+		double energy;
 
 		try {
 			energy = calculateHBondEnergy(one,two);
@@ -816,7 +807,7 @@ private void checkAddHBond(int i, int j){
 			logger.warn("Energy calculation failed", e);
 			return;
 		}
-		logger.debug("Energy between positions ({},{}): ",i,j,energy);
+		logger.debug("Energy between positions ({},{}={}): ",i,j,energy);
 
 		trackHBondEnergy(i,j,energy);
 	}
@@ -842,32 +833,31 @@ private static double calculateHBondEnergy(SecStrucGroup one,
 		Atom O = two.getO();
 		Atom C = two.getC();
 
-		double dno = Calc.getDistance(O,N);
-		double dhc = Calc.getDistance(C,H);
-		double dho = Calc.getDistance(O,H);
-		double dnc = Calc.getDistance(C,N);
+		double dno = Calc.getDistance(O,N); if (dno < MINDIST) return HBONDLOWENERGY;
+		double dhc = Calc.getDistance(C,H); if (dhc < MINDIST) return HBONDLOWENERGY;
+		double dho = Calc.getDistance(O,H); if (dho < MINDIST) return HBONDLOWENERGY;
+		double dnc = Calc.getDistance(C,N); if (dnc < MINDIST) return HBONDLOWENERGY;
 
-		logger.debug(" cccc: {} {} {} {} O ({})..N ({}):{}  |  ho:{} - hc:{} + nc:{} - no:{}",
-				one.getResidueNumber(),one.getPDBName(),two.getResidueNumber(),two.getPDBName(),
-				O.getPDBserial(),N.getPDBserial(),dno,dho,dhc,dnc,dno);
+		if (logger.isDebugEnabled()) {
+			logger.debug(" cccc: {} {} {} {} O ({})..N ({}):{}  |  ho:{} - hc:{} + nc:{} - no:{}",
+					one.getResidueNumber(), one.getPDBName(), two.getResidueNumber(), two.getPDBName(),
+					O.getPDBserial(), N.getPDBserial(), dno, dho, dhc, dnc, dno);
+		}
 
 		//there seems to be a contact!
-		if ( (dno < MINDIST) || (dhc < MINDIST) ||
-				(dnc < MINDIST) || (dno < MINDIST)) {
-			return HBONDLOWENERGY;
-		}
 
 		double e1 = Q / dho - Q / dhc;
 		double e2 = Q / dnc - Q / dno;
 
 		double energy = e1 + e2;
 
-		logger.debug(" N ({}) O({}): {} : {} ",N.getPDBserial(),O.getPDBserial(),(float) dno,energy);
+		if (logger.isDebugEnabled()) {
+			logger.debug(" N ({}) O({}): {} : {} ", N.getPDBserial(), O.getPDBserial(), (float) dno, energy);
+		}
 
-		//Avoid too strong energy
-		if (energy > HBONDLOWENERGY) return energy;
+		//Avoid too strong energy?
+		return energy > HBONDLOWENERGY ? energy : HBONDLOWENERGY;
 
-		return HBONDLOWENERGY ;
 	}
 
 	/**
@@ -951,8 +941,8 @@ private void calculateTurns(){
 					getSecStrucState(i+turn).setTurn('<', turn);
 					//Bracketed residues get the helix number
 					for (int j=i+1; j<i+turn; j++){
-						Integer t = turn;
-						char helix = t.toString().charAt(0);
+						int t = turn;
+						char helix = Integer.toString(t).charAt(0);
 						getSecStrucState(j).setTurn(helix, turn);
 					}
 				}
@@ -1009,8 +999,7 @@ private boolean isBonded(int i, int j) {
 	 * 		2009/08/how-to-calculate-h-atoms-for-nitrogens.html
 	 */
 	@SuppressWarnings("unused")
-	private static Atom calc_H(Atom C, Atom N, Atom CA)
-			throws StructureException {
+	private static Atom calc_H(Atom C, Atom N, Atom CA) {
 
 		Atom nc  = Calc.subtract(N,C);
 		Atom nca = Calc.subtract(N,CA);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucElement.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucElement.java
index da0dbd5095..7c08b9100d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucElement.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucElement.java
@@ -37,9 +37,9 @@ public class SecStrucElement implements Serializable  {
 
 	private static final long serialVersionUID = -8485685793171396131L;
 
-	private SecStrucType type;
-	private ResidueRangeAndLength range;
-	private int index;
+	private final SecStrucType type;
+	private final ResidueRangeAndLength range;
+	private final int index;
 
 	/**
 	 * Create a new SSE object. The start and end residue numbers cannot be the
@@ -100,7 +100,7 @@ public int getLength() {
 	 * @return
 	 */
 	public String getId() {
-		return type.toString() + index + "";
+		return type.toString() + index;
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucGroup.java
index 0680d1b6e3..082a677b19 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucGroup.java
@@ -53,7 +53,7 @@ public SecStrucGroup() {
 	@Override
 	public String toString() {
 
-		StringBuffer str = new StringBuffer("SecStrucGroup ");
+		StringBuilder str = new StringBuilder("SecStrucGroup ");
 		str.append(residueNumber);
 		str.append(" ");
 		str.append(pdb_name);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java
index 8ba6193eed..1a9a673856 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java
@@ -53,7 +53,7 @@ public class SecStrucState extends SecStrucInfo {
 
 	// Symbols: starting '>', ending '<', or both 'X'.
 	// Number means bracketed n-turn residue without h-bond
-	private char[] turn;
+	private final char[] turn;
 	private boolean bend;
 
 	private BetaBridge bridge1;
@@ -226,7 +226,7 @@ public void setBridge2(BetaBridge bridge2) {
 
 	public String printDSSPline(int index) {
 
-		StringBuffer buf = new StringBuffer();
+		StringBuilder buf = new StringBuilder();
 
 		// #
 		if (index < 9)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
index e2d1efd6ab..93f248768c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
@@ -20,10 +20,7 @@
  */
 package org.biojava.nbio.structure.secstruc;
 
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
+import java.util.*;
 
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.GroupIterator;
@@ -50,7 +47,7 @@ public class SecStrucTools {
 	 */
 	public static List<SecStrucInfo> getSecStrucInfo(Structure s) {
 
-		List<SecStrucInfo> listSSI = new ArrayList<SecStrucInfo>();
+		List<SecStrucInfo> listSSI = new ArrayList<>();
 		GroupIterator iter = new GroupIterator(s);
 
 		while (iter.hasNext()) {
@@ -88,7 +85,7 @@ public static void assignSecStruc( Structure s,List<SecStrucInfo> listSSI){
 	 */
 	public static List<SecStrucElement> getSecStrucElements(Structure s) {
 
-		List<SecStrucElement> listSSE = new ArrayList<SecStrucElement>();
+		List<SecStrucElement> listSSE = new ArrayList<>();
 		GroupIterator iter = new GroupIterator(s);
 
 		// SecStruc information - initialize
@@ -99,7 +96,7 @@ public static List<SecStrucElement> getSecStrucElements(Structure s) {
 		int count = 0; // counts the number of residues in SSE
 
 		// Create a map for the IDs of the SSE in the structure
-		Map<SecStrucType, Integer> ids = new TreeMap<SecStrucType, Integer>();
+		Map<SecStrucType, Integer> ids = new EnumMap<>(SecStrucType.class);
 		for (SecStrucType t : SecStrucType.values())
 			ids.put(t, 1);
 
@@ -161,7 +158,7 @@ public static List<SecStrucElement> getSecStrucElements(Structure s) {
 	 */
 	public static List<SecStrucElement> getSecStrucElements(List<Group> groups) {
 
-		List<SecStrucElement> listSSE = new ArrayList<SecStrucElement>();
+		List<SecStrucElement> listSSE = new ArrayList<>();
 
 		// SecStruc information - initialize
 		SecStrucType type = SecStrucType.coil;
@@ -171,7 +168,7 @@ public static List<SecStrucElement> getSecStrucElements(List<Group> groups) {
 		int count = 0; // counts the number of residues in SSE
 
 		// Create a map for the IDs of the SSE in the structure
-		Map<SecStrucType, Integer> ids = new TreeMap<SecStrucType, Integer>();
+		Map<SecStrucType, Integer> ids = new EnumMap<>(SecStrucType.class);
 		for (SecStrucType t : SecStrucType.values())
 			ids.put(t, 1);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucType.java
index 0def2da13e..2633a384ee 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucType.java
@@ -45,7 +45,7 @@ public enum SecStrucType {
 	public final Character type;
 	public final String name;
 
-	private SecStrucType(String name, Character stype) {
+	SecStrucType(String name, Character stype) {
 		this.name = name;
 		this.type = stype;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java
index b76e844965..7a34d2e47b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java
@@ -42,18 +42,18 @@ public class HelixAxisAligner extends AxisAligner {
 	private static final Vector3d Y_AXIS = new Vector3d(0,1,0);
 	private static final Vector3d Z_AXIS = new Vector3d(0,0,1);
 
-	private QuatSymmetrySubunits subunits = null;
-	private HelixLayers helixLayers = null;
+	private QuatSymmetrySubunits subunits;
+	private HelixLayers helixLayers;
 
 	private Matrix4d transformationMatrix = new Matrix4d();
-	private Matrix4d reverseTransformationMatrix = new Matrix4d();
+	private final Matrix4d reverseTransformationMatrix = new Matrix4d();
 	private Vector3d referenceVector = new Vector3d();
 	private Vector3d principalRotationVector = new Vector3d();
 	private Vector3d[] principalAxesOfInertia = null;
 	private List<List<Integer>> alignedOrbits = null;
 
-	private Vector3d minBoundary = new Vector3d();
-	private Vector3d maxBoundary = new Vector3d();
+	private final Vector3d minBoundary = new Vector3d();
+	private final Vector3d maxBoundary = new Vector3d();
 	private double xzRadiusMax = Double.MIN_VALUE;
 
 	boolean modified = true;
@@ -276,7 +276,7 @@ public Point3d calcCenterOfRotation() {
 		}
 
 		// average over all midpoints to find best center of rotation
-		centerOfRotation.scale(1/(line.size()-2));
+		centerOfRotation.scale(1.0/(line.size()-2));
 		// since helix is aligned along the y-axis, with an origin at y = 0, place the center of rotation there
 		centerOfRotation.y = 0;
 		// transform center of rotation to the original coordinate frame
@@ -356,7 +356,7 @@ private Matrix4d reorientHelix(int index) {
 	 * @return list of orbits ordered by z-depth
 	 */
 	private void calcAlignedOrbits() {
-		Map<Double, List<Integer>> depthMap = new TreeMap<Double, List<Integer>>();
+		Map<Double, List<Integer>> depthMap = new TreeMap<>();
 		double[] depth = getSubunitZDepth();
 		alignedOrbits = calcOrbits();
 
@@ -378,13 +378,11 @@ private void calcAlignedOrbits() {
 
 		// now fill orbits back into list ordered by depth
 		alignedOrbits.clear();
-		for (List<Integer> orbit: depthMap.values()) {
-			// order subunit in a clockwise rotation around the z-axis
-			/// starting at the 12 O-clock position (+y position)
-			// TODO how should this be aligned??
-	//		alignWithReferenceAxis(orbit);
-			alignedOrbits.add(orbit);
-		}
+		// order subunit in a clockwise rotation around the z-axis
+		/// starting at the 12 O-clock position (+y position)
+		// TODO how should this be aligned??
+		//		alignWithReferenceAxis(orbit);
+		alignedOrbits.addAll(depthMap.values());
 	}
 
 
@@ -429,7 +427,7 @@ private void calcTransformationBySymmetryAxes() {
 	 * @param referenceVectors
 	 * @return
 	 */
-	private Matrix4d alignAxes(Vector3d[] axisVectors, Vector3d[] referenceVectors) {
+	private static Matrix4d alignAxes(Vector3d[] axisVectors, Vector3d[] referenceVectors) {
 		Matrix4d m1 = new Matrix4d();
 		AxisAngle4d a = new AxisAngle4d();
 		Vector3d axis = new Vector3d();
@@ -585,7 +583,7 @@ private double[] getSubunitZDepth() {
 	private List<List<Integer>> calcOrbits() {
 		int n = subunits.getSubunitCount();
 
-		List<List<Integer>> orbits = new ArrayList<List<Integer>>();
+		List<List<Integer>> orbits = new ArrayList<>();
 		for (int i = 0; i < n; i++) {
 			orbits.add(Collections.singletonList(i));
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java
index 30539a98ca..4f86920492 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java
@@ -42,18 +42,18 @@ public class RotationAxisAligner extends AxisAligner{
 	private static final Vector3d Y_AXIS = new Vector3d(0,1,0);
 	private static final Vector3d Z_AXIS = new Vector3d(0,0,1);
 
-	private QuatSymmetrySubunits subunits = null;
-	private RotationGroup rotationGroup = null;
+	private QuatSymmetrySubunits subunits;
+	private RotationGroup rotationGroup;
 
 	private Matrix4d transformationMatrix = new Matrix4d();
-	private Matrix4d reverseTransformationMatrix = new Matrix4d();
+	private final Matrix4d reverseTransformationMatrix = new Matrix4d();
 	private Vector3d referenceVector = new Vector3d();
 	private Vector3d principalRotationVector = new Vector3d();
 	private Vector3d[] principalAxesOfInertia = null;
 	 List<List<Integer>> alignedOrbits = null;
 
-	private Vector3d minBoundary = new Vector3d();
-	private Vector3d maxBoundary = new Vector3d();
+	private final Vector3d minBoundary = new Vector3d();
+	private final Vector3d maxBoundary = new Vector3d();
 	private double xyRadiusMax = Double.MIN_VALUE;
 
 	boolean modified = true;
@@ -236,7 +236,7 @@ private void run () {
 	 * @return list of orbits ordered by z-depth
 	 */
 	private void calcAlignedOrbits() {
-		Map<Double, List<Integer>> depthMap = new TreeMap<Double, List<Integer>>();
+		Map<Double, List<Integer>> depthMap = new TreeMap<>();
 		double[] depth = getSubunitZDepth();
 		alignedOrbits = calcOrbits();
 
@@ -539,7 +539,7 @@ private void calcZDirection() {
 	 *
 	 */
 	private List<List<Integer>> getOrbitsByXYWidth() {
-		Map<Double, List<Integer>> widthMap = new TreeMap<Double, List<Integer>>();
+		Map<Double, List<Integer>> widthMap = new TreeMap<>();
 		double[] width = getSubunitXYWidth();
 		List<List<Integer>> orbits = calcOrbits();
 
@@ -559,9 +559,7 @@ private List<List<Integer>> getOrbitsByXYWidth() {
 
 		// now fill orbits back into list ordered by width
 		orbits.clear();
-		for (List<Integer> orbit: widthMap.values()) {
-			orbits.add(orbit);
-		}
+        orbits.addAll(widthMap.values());
 		return orbits;
 	}
 
@@ -608,14 +606,14 @@ private List<List<Integer>> calcOrbits() {
 		int n = subunits.getSubunitCount();
 		int fold = rotationGroup.getRotation(0).getFold();
 
-		List<List<Integer>> orbits = new ArrayList<List<Integer>>();
+		List<List<Integer>> orbits = new ArrayList<>();
 		boolean[] used = new boolean[n];
 		Arrays.fill(used, false);
 
 		for (int i = 0; i < n; i++) {
 			if (! used[i]) {
 				// determine the equivalent subunits
-				List<Integer> orbit = new ArrayList<Integer>(fold);
+				List<Integer> orbit = new ArrayList<>(fold);
 				for (int j = 0; j < fold; j++) {
 					List<Integer> permutation = rotationGroup.getRotation(j).getPermutation();
 					orbit.add(permutation.get(i));
@@ -637,7 +635,7 @@ private List<Integer> deconvolute(List<Integer> orbit) {
 //		System.out.println("Permutation0: " + p0);
 //		System.out.println("Permutation1: " + p1);
 
-		List<Integer> inRotationOrder = new ArrayList<Integer>(orbit.size());
+		List<Integer> inRotationOrder = new ArrayList<>(orbit.size());
 		inRotationOrder.add(orbit.get(0));
 		for (int i = 1; i < orbit.size(); i++) {
 			int current = inRotationOrder.get(i-1);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java
index 90b3a3f6e1..0101c9d189 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java
@@ -39,12 +39,12 @@
  * @author Peter
  */
 public class C2RotationSolver implements QuatSymmetrySolver {
-	private QuatSymmetrySubunits subunits;
-	private QuatSymmetryParameters parameters;
+	private final QuatSymmetrySubunits subunits;
+	private final QuatSymmetryParameters parameters;
 	private Vector3d centroid = new Vector3d();
-	private Matrix4d centroidInverse = new Matrix4d();
+	private final Matrix4d centroidInverse = new Matrix4d();
 
-	private RotationGroup rotations = new RotationGroup();
+	private final RotationGroup rotations = new RotationGroup();
 
 
 	public C2RotationSolver(QuatSymmetrySubunits subunits, QuatSymmetryParameters parameters) {
@@ -155,7 +155,7 @@ private void combineWithTranslation(Matrix4d rotation) {
 
 	private Rotation createSymmetryOperation(List<Integer> permutation, Matrix4d transformation, AxisAngle4d axisAngle, int fold, QuatSymmetryScores scores) {
 		Rotation s = new Rotation();
-		s.setPermutation(new ArrayList<Integer>(permutation));
+		s.setPermutation(new ArrayList<>(permutation));
 		s.setTransformation(new Matrix4d(transformation));
 		s.setAxisAngle(new AxisAngle4d(axisAngle));
 		s.setFold(fold);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
index f62208aadf..1b306f2753 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
@@ -27,10 +27,10 @@
 import java.util.Map.Entry;
 
 public class HelicalRepeatUnit {
-	private QuatSymmetrySubunits subunits = null;
-	private List<Point3d> repeatUnitCenters = new ArrayList<Point3d>();
-	private List<Point3d[]> repeatUnits = new ArrayList<Point3d[]>();
-	private List<List<Integer>> repeatUnitIndices = new ArrayList<List<Integer>>();
+	private QuatSymmetrySubunits subunits;
+	private List<Point3d> repeatUnitCenters = new ArrayList<>();
+	private List<Point3d[]> repeatUnits = new ArrayList<>();
+	private final List<List<Integer>> repeatUnitIndices = new ArrayList<>();
 	private Map<Integer[], Integer> interactingNeighbors = Collections.emptyMap();
 
 public HelicalRepeatUnit(QuatSymmetrySubunits subunits) {
@@ -74,23 +74,23 @@ private void run() {
 private List<Point3d> calcRepeatUnitCenters() {
 
 	// TODO why do we use models here? it should not matter. Setting to 0 all
-	List<Integer> models = new ArrayList<Integer>(subunits.getSubunitCount());
+	List<Integer> models = new ArrayList<>(subunits.getSubunitCount());
 	for (int s = 0; s <subunits.getSubunitCount(); s++)
 		models.add(0);
-	Set<Integer> uniqueModels = new HashSet<Integer>(Arrays.asList(1));
+	Set<Integer> uniqueModels = new HashSet<>(Collections.singletonList(1));
 
 	int modelCount = uniqueModels.size();
 	List<Integer> folds = this.subunits.getFolds();
 	int maxFold = folds.get(folds.size()-1);
 
-	List<Point3d> repeatCenters = new ArrayList<Point3d>();
+	List<Point3d> repeatCenters = new ArrayList<>();
 	List<Point3d> centers = subunits.getCenters();
 
 //	if (modelCount == maxFold && subunits.getSubunitCount() > 3) {
 	if (maxFold%modelCount == 0 && modelCount > 1 && subunits.getSubunitCount() > 3) {
 //		System.out.println("calcRepeatUnitCenters case 1");
 		for (int i = 0; i < modelCount; i++) {
-			List<Integer> subunitIndices = new ArrayList<Integer>();
+			List<Integer> subunitIndices = new ArrayList<>();
 			Point3d p = new Point3d();
 			int count = 0;
 //			System.out.println("Models: " + models.size());
@@ -113,7 +113,7 @@ private List<Point3d> calcRepeatUnitCenters() {
 		// Case of 3B5U: A14, but seems to form (A2)*7 and symmetry related subunits don't have direct contact
 		List<Integer> sequenceClusterIds = subunits.getClusterIds();
 		for (int i = 0; i < subunits.getSubunitCount(); i++) {
-			List<Integer> subunitIndices = new ArrayList<Integer>(1);
+			List<Integer> subunitIndices = new ArrayList<>(1);
 			if (sequenceClusterIds.get(i) == 0) {
 				repeatCenters.add(new Point3d(centers.get(i)));
 //				System.out.println("Orig Repeat unit: " + centers.get(i));
@@ -135,23 +135,23 @@ private List<Point3d> calcRepeatUnitCenters() {
 private List<Point3d[]> calcRepeatUnits() {
 
 	// TODO why do we use models here? it should not matter. Setting to 0 all
-	List<Integer> models = new ArrayList<Integer>(
+	List<Integer> models = new ArrayList<>(
 			subunits.getSubunitCount());
 	for (int s = 0; s < subunits.getSubunitCount(); s++)
 		models.add(0);
-	Set<Integer> uniqueModels = new HashSet<Integer>(Arrays.asList(1));
+	Set<Integer> uniqueModels = new HashSet<>(Collections.singletonList(1));
 
 	int modelCount = uniqueModels.size();
 	List<Integer> folds = this.subunits.getFolds();
 	int maxFold = folds.get(folds.size()-1);
 
-	List<Point3d[]> repeatTraces = new ArrayList<Point3d[]>();
+	List<Point3d[]> repeatTraces = new ArrayList<>();
 	List<Point3d[]> traces = subunits.getTraces();
 
 //	if (modelCount == maxFold && subunitCount > 3) {
 	if (maxFold%modelCount == 0 && modelCount > 1 && subunits.getSubunitCount() > 3) {
 		for (int i = 0; i < modelCount; i++) {
-			List<Point3d> coords = new ArrayList<Point3d>();
+			List<Point3d> coords = new ArrayList<>();
 			for (int j = 0; j < models.size(); j++) {
 				if (models.get(j) == i) {
 					coords.addAll(Arrays.asList(traces.get(j)));
@@ -180,12 +180,12 @@ private List<Point3d[]> calcRepeatUnits() {
 }
 
 private Map<Integer[], Integer> findInteractingNeigbors() {
-	Map<Integer[], Integer>  contactMap = new HashMap<Integer[], Integer>();
+	Map<Integer[], Integer>  contactMap = new HashMap<>();
 
 	Map<Integer, List<Integer[]>> distanceMap = findClosestPairs(8);
 	for (List<Integer[]> pairs: distanceMap.values())
 	for (Integer[] pair: pairs) {
-		Integer contacts = calcContactNumber(repeatUnits.get(pair[0]), repeatUnits.get(pair[1]));
+		int contacts = calcContactNumber(repeatUnits.get(pair[0]), repeatUnits.get(pair[1]));
 //		System.out.println("contacts: " + pair[0] + "-" + pair[1] + ": " + contacts);
 		if (contacts > 0) {
 			contactMap.put(pair, contacts);
@@ -196,9 +196,9 @@ private Map<Integer[], Integer> findInteractingNeigbors() {
 }
 
 private Map<Integer, List<Integer[]>> findClosestPairs(int maxNeighbors) {
-	Map<Integer, List<Integer[]>>  reducedMap = new TreeMap<Integer, List<Integer[]>>();
+	Map<Integer, List<Integer[]>>  reducedMap = new TreeMap<>();
 
-	Map<Integer, List<Integer[]>>  distanceMap = new TreeMap<Integer, List<Integer[]>>();
+	Map<Integer, List<Integer[]>>  distanceMap = new TreeMap<>();
 	int nCenters = repeatUnitCenters.size();
 //	System.out.println("repeatUnitCenters: " + repeatUnitCenters);
 
@@ -212,7 +212,7 @@ private Map<Integer, List<Integer[]>> findClosestPairs(int maxNeighbors) {
 			List<Integer[]> pairs = distanceMap.get(intDist);
 			// save only one representative pair for each distance
 			if (pairs == null) {
-				pairs = new ArrayList<Integer[]>();
+				pairs = new ArrayList<>();
 			}
 			Integer[] pair = new Integer[2];
 			pair[0] = i;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java
index d25f14ec34..824e2e7300 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java
@@ -161,7 +161,7 @@ public String toString() {
 	}
 
 	public List<List<Integer>> getLayerLines() {
-		List<List<Integer>> layerLines = new ArrayList<List<Integer>>();
+		List<List<Integer>> layerLines = new ArrayList<>();
 
 		createLineSegments(permutation, layerLines);
 
@@ -170,7 +170,7 @@ public List<List<Integer>> getLayerLines() {
 //			System.out.println(lineSegment);
 //		}
 
-		int count = layerLines.size();
+		int count;
 
 		// iteratively join line segments
 		do {
@@ -192,7 +192,7 @@ private static void createLineSegments(List<Integer> permutation,
 			List<List<Integer>> layerLines) {
 		for (int i = 0; i < permutation.size(); i++) {
 			if (permutation.get(i) != -1 ) {
-				List<Integer> lineSegment = new ArrayList<Integer>();
+				List<Integer> lineSegment = new ArrayList<>();
 				lineSegment.add(i);
 				lineSegment.add(permutation.get(i));
 				layerLines.add(lineSegment);
@@ -225,10 +225,6 @@ private static void joinLineSegments(List<List<Integer>> layerLines) {
 	}
 
 	private static void trimEmptyLineSegments(List<List<Integer>> layerLines) {
-		for (Iterator<List<Integer>> iter = layerLines.iterator(); iter.hasNext();) {
-			if (iter.next().isEmpty()) {
-				iter.remove();
-			}
-		}
+		layerLines.removeIf(List::isEmpty);
 	}
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java
index 30d799b6f3..c17ab9f64d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java
@@ -25,11 +25,12 @@
 import javax.vecmath.Point3d;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 public class HelixExtender {
-	private QuatSymmetrySubunits subunits = null;
-	private Helix helix = null;
+	private QuatSymmetrySubunits subunits;
+	private Helix helix;
 
 	public HelixExtender(QuatSymmetrySubunits subunits, Helix helix) {
 		this.subunits = subunits;
@@ -40,7 +41,7 @@ public Point3d[] extendHelix(int steps) {
 		List<List<Integer>> layerLines = helix.getLayerLines();
 
 		// get list of subunit indices to be used for helix extension
-		List<Integer> indices = new ArrayList<Integer>();
+		List<Integer> indices = new ArrayList<>();
 		for (List<Integer> line: layerLines) {
 			if (steps < 0) {
 				indices.add(line.get(0));
@@ -50,7 +51,7 @@ public Point3d[] extendHelix(int steps) {
 		}
 		System.out.println("Extending subunits: " + indices);
 
-		List<Point3d> points = new ArrayList<Point3d>();
+		List<Point3d> points = new ArrayList<>();
 		Matrix4d transformation = helix.getTransformation();
 		for (int index: indices) {
 	    	Point3d[] trace = subunits.getTraces().get(index);
@@ -58,9 +59,7 @@ public Point3d[] extendHelix(int steps) {
 		    for (int i = 0; i < Math.abs(steps); i++) {
 		    	CalcPoint.transform(transformation, copy);
 		    }
-		    for (Point3d p: copy) {
-		    	points.add(p);
-		    }
+            points.addAll(Arrays.asList(copy));
 		}
 		return points.toArray(new Point3d[0]);
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixLayers.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixLayers.java
index a42958d062..527f324ecb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixLayers.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixLayers.java
@@ -29,7 +29,7 @@
  * @author Peter
  */
 public class HelixLayers {
-	private List<Helix> helices = new ArrayList<Helix>();
+	private final List<Helix> helices = new ArrayList<>();
 	private double symmetryDeviation = 0;
 
 	public int size() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
index 9576c248f6..ccb70c2a1f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
@@ -44,10 +44,10 @@ public class HelixSolver {
 	private static final Logger logger = LoggerFactory
 			.getLogger(HelixSolver.class);
 
-	private QuatSymmetrySubunits subunits = null;
-	private int fold = 1;
-	private HelixLayers helixLayers = new HelixLayers();
-	private QuatSymmetryParameters parameters = null;
+	private QuatSymmetrySubunits subunits;
+	private int fold;
+	private final HelixLayers helixLayers = new HelixLayers();
+	private QuatSymmetryParameters parameters;
 	boolean modified = true;
 
 	public HelixSolver(QuatSymmetrySubunits subunits, int fold,
@@ -73,7 +73,7 @@ private void solve() {
 		HelicalRepeatUnit unit = new HelicalRepeatUnit(subunits);
 		List<Point3d> repeatUnitCenters = unit.getRepeatUnitCenters();
 		List<Point3d[]> repeatUnits = unit.getRepeatUnits();
-		Set<List<Integer>> permutations = new HashSet<List<Integer>>();
+		Set<List<Integer>> permutations = new HashSet<>();
 
 		double minRise = parameters.getMinimumHelixRise() * fold; // for n-start
 																	// helix,
@@ -129,7 +129,7 @@ private void solve() {
 
 
 			// keep track of which subunits are permuted
-			Set<Integer> permSet = new HashSet<Integer>();
+			Set<Integer> permSet = new HashSet<>();
 			int count = 0;
 			boolean valid = true;
 			for (int i = 0; i < permutation.size(); i++) {
@@ -164,8 +164,8 @@ private void solve() {
 			}
 
 			// superpose all permuted subunits
-			List<Point3d> point1 = new ArrayList<Point3d>();
-			List<Point3d> point2 = new ArrayList<Point3d>();
+			List<Point3d> point1 = new ArrayList<>();
+			List<Point3d> point2 = new ArrayList<>();
 			List<Point3d> centers = subunits.getOriginalCenters();
 			for (int j = 0; j < permutation.size(); j++) {
 				if (permutation.get(j) != -1) {
@@ -355,7 +355,7 @@ private List<Integer> getPermutation(Matrix4d transformation) {
 		List<Point3d> centers = subunits.getOriginalCenters();
 		List<Integer> seqClusterId = subunits.getClusterIds();
 
-		List<Integer> permutations = new ArrayList<Integer>(centers.size());
+		List<Integer> permutations = new ArrayList<>(centers.size());
 		double[] dSqs = new double[centers.size()];
 		boolean[] used = new boolean[centers.size()];
 		Arrays.fill(used, false);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
index 8bbcb5a650..e1f4792410 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
@@ -32,7 +32,7 @@
  * @author Peter
  */
 public class PermutationGroup implements Iterable<List<Integer>> {
-	List<List<Integer>> permutations = new ArrayList<List<Integer>>();
+	List<List<Integer>> permutations = new ArrayList<>();
 
 	public void addPermutation(List<Integer> permutation) {
 		if (!permutations.contains(permutation)) {
@@ -60,13 +60,13 @@ public int getOrder() {
 	 */
 	public void completeGroup() {
 		// Copy initial set to allow permutations to grow
-		List<List<Integer>> gens = new ArrayList<List<Integer>>(permutations);
+		List<List<Integer>> gens = new ArrayList<>(permutations);
 		// Keep HashSet version of permutations for fast lookup.
-		Set<List<Integer>> known = new HashSet<List<Integer>>(permutations);
+		Set<List<Integer>> known = new HashSet<>(permutations);
 		//breadth-first search through the map of all members
-		List<List<Integer>> currentLevel = new ArrayList<List<Integer>>(permutations);
+		List<List<Integer>> currentLevel = new ArrayList<>(permutations);
 		while( currentLevel.size() > 0) {
-			List<List<Integer>> nextLevel = new ArrayList<List<Integer>>();
+			List<List<Integer>> nextLevel = new ArrayList<>();
 			for( List<Integer> p : currentLevel) {
 				for(List<Integer> gen : gens) {
 					List<Integer> y = combine(p,gen);
@@ -93,7 +93,7 @@ public String toString() {
 	}
 
 	public static List<Integer> combine(List<Integer> permutation1, List<Integer> permutation2) {
-		List<Integer> intermediate = new ArrayList<Integer>(permutation1.size());
+		List<Integer> intermediate = new ArrayList<>(permutation1.size());
 		for (int i = 0, n = permutation1.size(); i < n; i++) {
 			intermediate.add(permutation2.get(permutation1.get(i)));
 		}
@@ -101,7 +101,7 @@ public static List<Integer> combine(List<Integer> permutation1, List<Integer> pe
 	}
 
 	public static int getOrder(List<Integer> permutation) {
-		List<Integer> copy = new ArrayList<Integer>(permutation);
+		List<Integer> copy = new ArrayList<>(permutation);
 		for (int i = 0, n = permutation.size(); i < n; i++) {
 			copy = combine(copy, permutation);
 			if (copy.equals(permutation)) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
index 4b26906ffd..4a9642efc2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
@@ -463,7 +463,6 @@ private static Stoichiometry trimSubunitClusters(Stoichiometry globalComposition
 		Set<Integer> usedClusterIds =
 				usedSubunitIds.stream().
 					map(allSubunitClusterIds::get).
-					distinct().
 					collect(Collectors.toSet());
 
 		// for each used cluster, remove unused subunits
@@ -501,8 +500,8 @@ private static QuatSymmetryResults calcQuatSymmetry(Stoichiometry composition, Q
 		if (subunits.getSubunitCount() == 0)
 			return null;
 
-		RotationGroup rotationGroup = null;
-		SymmetryPerceptionMethod method = null;
+		RotationGroup rotationGroup;
+		SymmetryPerceptionMethod method;
 		if (subunits.getFolds().size() == 1) {
 			// no symmetry possible, create empty ("C1") rotation group
 			method = SymmetryPerceptionMethod.NO_ROTATION;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java
index cdc7341c4b..ba6b711643 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java
@@ -44,15 +44,15 @@ public class QuatSymmetryResults {
 	private Structure structure;
 
 	// Information about the clustering process
-	private Stoichiometry stoichiometry;
+	private final Stoichiometry stoichiometry;
 	private boolean local = false;
 
 	// Cached properties
-	private List<SubunitCluster> clusters;
-	private List<Subunit> subunits;
+	private final List<SubunitCluster> clusters;
+	private final List<Subunit> subunits;
 
 	// Information about the symmetry
-	private SymmetryPerceptionMethod method;
+	private final SymmetryPerceptionMethod method;
 	private HelixLayers helixLayers;
 	private RotationGroup rotationGroup = new RotationGroup();
 
@@ -72,7 +72,7 @@ public QuatSymmetryResults(Stoichiometry stoichiometry,
 		this.stoichiometry = stoichiometry;
 		this.clusters = stoichiometry.getClusters();
 
-		subunits = new ArrayList<Subunit>();
+		subunits = new ArrayList<>();
 		for (SubunitCluster c : clusters) {
 			subunits.addAll(c.getSubunits());
 		}
@@ -95,7 +95,7 @@ public QuatSymmetryResults(Stoichiometry stoichiometry,
 		this.stoichiometry = stoichiometry;
 		this.clusters = stoichiometry.getClusters();
 
-		subunits = new ArrayList<Subunit>();
+		subunits = new ArrayList<>();
 		for (SubunitCluster c : clusters) {
 			subunits.addAll(c.getSubunits());
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
index 27d16cd6fe..827a3f12fe 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
@@ -46,17 +46,17 @@
  */
 public class QuatSymmetrySubunits {
 
-	private List<Point3d[]> caCoords = new ArrayList<>();
-	private List<Point3d> originalCenters = new ArrayList<>();
-	private List<Point3d> centers = new ArrayList<>();
-	private List<Vector3d> unitVectors = new ArrayList<>();
+	private final List<Point3d[]> caCoords = new ArrayList<>();
+	private final List<Point3d> originalCenters = new ArrayList<>();
+	private final List<Point3d> centers = new ArrayList<>();
+	private final List<Vector3d> unitVectors = new ArrayList<>();
 
-	private List<Integer> folds = new ArrayList<>();
-	private List<Integer> clusterIds = new ArrayList<>();
-	private List<SubunitCluster> clusters;
+	private List<Integer> folds;
+	private final List<Integer> clusterIds = new ArrayList<>();
+	private final List<SubunitCluster> clusters;
 
 	private Point3d centroid;
-	private MomentsOfInertia momentsOfInertia = new MomentsOfInertia();
+	private final MomentsOfInertia momentsOfInertia = new MomentsOfInertia();
 
 	/**
 	 * Converts the List of {@link SubunitCluster} to a Subunit object.
@@ -83,7 +83,7 @@ public QuatSymmetrySubunits(List<SubunitCluster> clusters) {
 		}
 
 		// List number of members in each cluster
-		List<Integer> stoichiometries = clusters.stream().map(c -> c.size())
+		List<Integer> stoichiometries = clusters.stream().map(SubunitCluster::size)
 				.collect(Collectors.toList());
 		folds = SymmetryTools.getValidFolds(stoichiometries);
 	}
@@ -105,7 +105,7 @@ public List<Integer> getClusterIds() {
 	 */
 	public List<String> getChainIds() {
 
-		List<String> chains = new ArrayList<String>(getSubunitCount());
+		List<String> chains = new ArrayList<>(getSubunitCount());
 
 		// Loop through all subunits in the clusters and fill Lists
 		for (int c = 0; c < clusters.size(); c++) {
@@ -125,7 +125,7 @@ public List<String> getChainIds() {
 	 */
 	public List<Integer> getModelNumbers() {
 
-		List<Integer> models = new ArrayList<Integer>(getSubunitCount());
+		List<Integer> models = new ArrayList<>(getSubunitCount());
 
 		// Loop through all subunits in the clusters and fill Lists
 		for (int c = 0; c < clusters.size(); c++) {
@@ -224,8 +224,7 @@ private void calcOriginalCenters() {
 	}
 
 	private void calcCentroid() {
-		Point3d[] orig = originalCenters.toArray(new Point3d[originalCenters
-				.size()]);
+		Point3d[] orig = originalCenters.toArray(new Point3d[0]);
 		centroid = CalcPoint.centroid(orig);
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
index 9a13d35813..fd662fac3b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
@@ -35,7 +35,7 @@
  * @author Peter
  */
 public class RotationGroup implements Iterable<Rotation> {
-	private List<Rotation> rotations = new ArrayList<Rotation>();
+	private final List<Rotation> rotations = new ArrayList<>();
 	private int principalAxisIndex = 0;
 	private int higherOrderRotationAxis = 0;
 	private int twoFoldsPerpendicular = 0;
@@ -61,7 +61,7 @@ public void addRotation(Rotation rotation) {
 
 	public void setC1(int n) {
 		Rotation r = new Rotation();
-		List<Integer> permutation = new ArrayList<Integer>(n);
+		List<Integer> permutation = new ArrayList<>(n);
 		for (int i = 0; i < n; i++) {
 			permutation.add(i);
 		}
@@ -353,21 +353,18 @@ private void calcPointGroup() {
 	}
 
 	public void sortByFoldDecending() {
-		Collections.sort(rotations, new Comparator<Rotation>() {
-			@Override
-			public int compare(Rotation o1, Rotation o2) {
-				int delta = o1.getDirection() - o2.getDirection();
-				if (delta != 0) {
-					return delta;
-				}
-				delta = Math.round(Math.signum(o2.getFold() - o1.getFold()));
-				if (delta != 0) {
-					return delta;
-				}
-
-				delta = (int)(Math.signum(o1.getAxisAngle().angle - o2.getAxisAngle().angle));
+		rotations.sort((o1, o2) -> {
+			int delta = o1.getDirection() - o2.getDirection();
+			if (delta != 0) {
 				return delta;
 			}
+			delta = Math.round(Math.signum(o2.getFold() - o1.getFold()));
+			if (delta != 0) {
+				return delta;
+			}
+
+			delta = (int) (Math.signum(o1.getAxisAngle().angle - o2.getAxisAngle().angle));
+			return delta;
 		});
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
index d03c1d36da..8a29271e0f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
@@ -46,19 +46,19 @@
  * @author Peter
  */
 public class RotationSolver implements QuatSymmetrySolver {
-	private QuatSymmetrySubunits subunits = null;
-	private QuatSymmetryParameters parameters = null;
+	private QuatSymmetrySubunits subunits;
+	private QuatSymmetryParameters parameters;
 
 	private double distanceThreshold = 0.0f;
 	private DistanceBox<Integer> box = null;
 	private Vector3d centroid = new Vector3d();
-	private Matrix4d centroidInverse = new Matrix4d();
+	private final Matrix4d centroidInverse = new Matrix4d();
 	private Point3d[] originalCoords = null;
 	private Point3d[] transformedCoords = null;
 	// Cache whether a permutation is invalid (null) vs has been added to rotations
-	private Map<List<Integer>,Rotation> evaluatedPermutations = new HashMap<>();
+	private final Map<List<Integer>,Rotation> evaluatedPermutations = new HashMap<>();
 
-	private RotationGroup rotations = new RotationGroup();
+	private final RotationGroup rotations = new RotationGroup();
 
 	public RotationSolver(QuatSymmetrySubunits subunits, QuatSymmetryParameters parameters) {
 		if (subunits.getSubunitCount()== 2) {
@@ -280,7 +280,7 @@ private List<Double> getAngles() {
 			 n = 60;
 		}
 		List<Integer> folds = subunits.getFolds();
-		List<Double> angles = new ArrayList<Double>(folds.size()-1);
+		List<Double> angles = new ArrayList<>(folds.size() - 1);
 
 		// note this loop starts at 1, we do ignore 1-fold symmetry, which is the first entry
 		for (int fold: folds) {
@@ -356,7 +356,7 @@ private void combineWithTranslation(Matrix4d rotation) {
 
 	private static Rotation createSymmetryOperation(List<Integer> permutation, Matrix4d transformation, AxisAngle4d axisAngle, int fold, QuatSymmetryScores scores) {
 		Rotation s = new Rotation();
-		s.setPermutation(new ArrayList<Integer>(permutation));
+		s.setPermutation(new ArrayList<>(permutation));
 		s.setTransformation(new Matrix4d(transformation));
 		s.setAxisAngle(new AxisAngle4d(axisAngle));
 		s.setFold(fold);
@@ -367,7 +367,7 @@ private static Rotation createSymmetryOperation(List<Integer> permutation, Matri
 
 	private void setupDistanceBox() {
 		distanceThreshold = calcDistanceThreshold();
-		box = new DistanceBox<Integer>(distanceThreshold);
+		box = new DistanceBox<>(distanceThreshold);
 
 		for (int i = 0; i < originalCoords.length; i++) {
 			box.addPoint(originalCoords[i], i);
@@ -399,7 +399,7 @@ private double calcDistanceThreshold() {
 	 * @return A list mapping each subunit to the closest transformed subunit
 	 */
 	private List<Integer> getPermutation() {
-		List<Integer> permutation = new ArrayList<Integer>(transformedCoords.length);
+		List<Integer> permutation = new ArrayList<>(transformedCoords.length);
 		double sum = 0.0f;
 
 		for (Point3d t: transformedCoords) {
@@ -429,7 +429,7 @@ private List<Integer> getPermutation() {
 		}
 
 		// check uniqueness of indices
-		Set<Integer> set = new HashSet<Integer>(permutation);
+		Set<Integer> set = new HashSet<>(permutation);
 
 		// if size mismatch, clear permutation (its invalid)
 		if (set.size() != originalCoords.length) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SymmetryPerceptionMethod.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SymmetryPerceptionMethod.java
index ba17de700e..3876e49ac0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SymmetryPerceptionMethod.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SymmetryPerceptionMethod.java
@@ -31,5 +31,5 @@ public enum SymmetryPerceptionMethod {
 	NO_ROTATION,
 	C2_ROTATION,
 	ROTATION,
-	ROTO_TRANSLATION;
+	ROTO_TRANSLATION
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
index 04c53c00ce..dd5f7e1473 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
@@ -42,15 +42,15 @@
  * @author Peter
  */
 public class SystematicSolver implements QuatSymmetrySolver {
-	private QuatSymmetrySubunits subunits = null;
-	private QuatSymmetryParameters parameters = null;
+	private QuatSymmetrySubunits subunits;
+	private QuatSymmetryParameters parameters;
 
 	private Point3d[] originalCoords = null;
 	private Point3d[] transformedCoords = null;
-	private RotationGroup rotations = new RotationGroup();
+	private final RotationGroup rotations = new RotationGroup();
 	private Vector3d centroid = new Vector3d();
-	private Matrix4d centroidInverse = new Matrix4d();
-	private Set<List<Integer>> hashCodes = new HashSet<List<Integer>>();
+	private final Matrix4d centroidInverse = new Matrix4d();
+	private final Set<List<Integer>> hashCodes = new HashSet<>();
 
 	public SystematicSolver(QuatSymmetrySubunits subunits, QuatSymmetryParameters parameters) {
 		if (subunits.getSubunitCount()== 2) {
@@ -77,7 +77,7 @@ private void solve() {
 		// loop over all permutations
 		while (g.hasMore()) {
 			int[] perm = g.getNext();
-			List<Integer> permutation = new ArrayList<Integer>(perm.length);
+			List<Integer> permutation = new ArrayList<>(perm.length);
 			for (int j = 0; j < n; j++) {
 				permutation.add(perm[j]);
 			}
@@ -110,7 +110,7 @@ private void combineWithTranslation(Matrix4d rotation) {
 
 	private Rotation createSymmetryOperation(List<Integer> permutation, Matrix4d transformation, AxisAngle4d axisAngle, int fold, QuatSymmetryScores scores) {
 		Rotation s = new Rotation();
-		s.setPermutation(new ArrayList<Integer>(permutation));
+		s.setPermutation(new ArrayList<>(permutation));
 		s.setTransformation(new Matrix4d(transformation));
 		s.setAxisAngle(new AxisAngle4d(axisAngle));
 		s.setFold(fold);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java
index 37430260ca..7791aee231 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java
@@ -28,10 +28,10 @@
  * @author Peter
  */
 public class DistanceBox<T> {
-	private Map<Long, List<T>> map;
-	private Map<Long, List<T>> layerMap;
+	private final Map<Long, List<T>> map;
+	private final Map<Long, List<T>> layerMap;
 	private boolean modified;
-	private double inverseBinWidth;
+	private final double inverseBinWidth;
 	// relative locations of 26 boxes surrounding a box at (0, 0, 0)
 	private static final long[] offset = new long[] {
 		0 + ( 0 * 10000) + ( 0 * 1000000000L),
@@ -63,12 +63,12 @@ public class DistanceBox<T> {
 		1 + ( 1 * 10000) + ( 1 * 1000000000L)
 	};
 
-	private List<T> tempBox = new ArrayList<T>(offset.length);
+	private final List<T> tempBox = new ArrayList<>(offset.length);
 
 	/** Creates a new instance of DistanceBox */
 	public DistanceBox(double binWidth) {
-		map = new HashMap<Long, List<T>>();
-		layerMap = new HashMap<Long, List<T>>();
+		map = new HashMap<>();
+		layerMap = new HashMap<>();
 		this.inverseBinWidth = 1.0f/binWidth;
 		this.modified = true;
 	}
@@ -79,12 +79,7 @@ public void addPoint(Point3d point, T object) {
 		long k = (long) StrictMath.rint(point.z * inverseBinWidth);
 		long location = i + (j * 10000L) + (k * 1000000000L);
 
-		List<T> box = map.get(location);
-
-		if (box == null) {
-			box = new ArrayList<T>();
-			map.put(location, box);
-		}
+		List<T> box = map.computeIfAbsent(location, k1 -> new ArrayList<>());
 
 		box.add(object);
 		modified = true;
@@ -127,8 +122,8 @@ public List<T> getNeighbors(Point3d point) {
 	}
 
 	public List<T> getIntersection(DistanceBox<T> distanceBox) {
-		List<T> intersection = new ArrayList<T>();
-		HashSet<Long> checkedLocations = new HashSet<Long>();
+		List<T> intersection = new ArrayList<>();
+		HashSet<Long> checkedLocations = new HashSet<>();
 
 		for (Iterator<Long> iter = map.keySet().iterator(); iter.hasNext();) {
 			long location = iter.next();
@@ -165,13 +160,13 @@ private List<T> getBoxTwo(long location) {
 			}
 		}
 		// ensure that boxTwo has no empty element by copying from tempBox of defined size
-		List<T> boxTwo = null;
+		List<T> boxTwo;
 		if (tempBox.size() == 0) {
 			boxTwo = Collections.emptyList();
 		} else if (tempBox.size() == 1) {
 			boxTwo = Collections.singletonList(tempBox.get(0));
 		} else {
-			boxTwo = new ArrayList<T>(tempBox);
+			boxTwo = new ArrayList<>(tempBox);
 		}
 		return boxTwo;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.java
index 96b4758fc4..4ba6629de4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.java
@@ -31,7 +31,7 @@
  */
 // This would be better named HexacosichoronSampler, since it's sampling 4D space. -SB
 public final class IcosahedralSampler {
-	private static Quat4d quat = new Quat4d();
+	private static final Quat4d quat = new Quat4d();
 
 	// this class cannot be instantiated
 	private IcosahedralSampler() {
@@ -57,7 +57,7 @@ public static void getAxisAngle(int index, AxisAngle4d axisAngle) {
 	//	format quaternion
 	// The fifth column gives a weighting factor. Since the 600-cell is regular, all
 	// orientations cover an equal fraction of orientation space and have equal weight.
-	private static double[][] orientations = {
+	private static final double[][] orientations = {
 	{1.000000000f, 0.000000000f, 0.000000000f, 0.000000000f, 1.000000f},
 	{0.000000000f, 1.000000000f, 0.000000000f, 0.000000000f, 1.000000f},
 	{0.000000000f, 0.000000000f, 1.000000000f, 0.000000000f, 1.000000f},
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.java
index 7de37ee842..6712075b08 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.java
@@ -27,12 +27,12 @@
 
 
 public class Icosahedron implements Polyhedron {
-	private static int[] lineLoop1 = {4,0,1,2,3,4,5,1};
-	private static int[] lineLoop2 = {3,0,2};
-	private static int[] lineLoop3 = {0,5};
-	private static int[] lineLoop4 = {11,3,7,4,8,6,7,8,9,10,11,7};
-	private static int[] lineLoop5 = {6,11,2,10,1,9,6,10};
-	private static int[] lineLoop6 = {8,5,9};
+	private static final int[] lineLoop1 = {4,0,1,2,3,4,5,1};
+	private static final int[] lineLoop2 = {3,0,2};
+	private static final int[] lineLoop3 = {0,5};
+	private static final int[] lineLoop4 = {11,3,7,4,8,6,7,8,9,10,11,7};
+	private static final int[] lineLoop5 = {6,11,2,10,1,9,6,10};
+	private static final int[] lineLoop6 = {8,5,9};
 
 	private double circumscribedRadius = 1.0;
 
@@ -124,7 +124,7 @@ public Point3d[] getVertices() {
 		}
 
 		return icosahedron;
-	};
+	}
 
 	@Override
 	public List<int[]> getLineLoops() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java
index 6cc5842dda..b6e1b4f4c7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java
@@ -23,12 +23,13 @@
 import javax.vecmath.Matrix3d;
 import javax.vecmath.Point3d;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 
 public class Octahedron implements Polyhedron {
-	private static double TETRAHEDRAL_ANGLE = Math.acos(-1.0/3.0);
-	private static int[] lineLoop1 = {2,4,3,5,2,1,3,0,5,1,4,0,2};
+	private static final double TETRAHEDRAL_ANGLE = Math.acos(-1.0/3.0);
+	private static final int[] lineLoop1 = {2,4,3,5,2,1,3,0,5,1,4,0,2};
 	private double cirumscribedRadius = 1.0;
 
 	/**
@@ -108,11 +109,11 @@ public Point3d[] getVertices() {
 	    octahedron[5] = new Point3d(0, 0,  cirumscribedRadius);
 
 		return octahedron;
-	};
+	}
 
 	@Override
 	public List<int[]> getLineLoops() {
-		return Arrays.asList(lineLoop1);
+		return Collections.singletonList(lineLoop1);
 	}
 
 	public Point3d getC4Axis(double scale) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Polyhedron.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Polyhedron.java
index 286c784225..fcb015a7d1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Polyhedron.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Polyhedron.java
@@ -33,10 +33,10 @@
  */
 public interface Polyhedron {
 
-	public Point3d[] getVertices();
-	public List<int[]> getLineLoops();
-	public double getCirumscribedRadius();
-	public int getViewCount();
-	public String getViewName(int index);
-	public Matrix3d getViewMatrix(int index);
+	Point3d[] getVertices();
+	List<int[]> getLineLoops();
+	double getCirumscribedRadius();
+	int getViewCount();
+	String getViewName(int index);
+	Matrix3d getViewMatrix(int index);
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java
index 6b5d7edacf..dd33c96bea 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java
@@ -34,7 +34,7 @@
  *
  */
 public class Prism implements Polyhedron {
-	private int n = 3;
+	private int n;
 	private double circumscribedRadius = 1.0;
 	private double height = 1.0;
 
@@ -115,11 +115,11 @@ public Point3d[] getVertices() {
 		}
 
 		return polygon;
-	};
+	}
 
 	@Override
 	public List<int[]> getLineLoops() {
-		List<int[]> list = new ArrayList<int[]>();
+		List<int[]> list = new ArrayList<>();
 		int[] l1 = new int[2*n+2];
 		for (int i = 0; i < n; i++) {
 			l1[i] = i;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java
index 45d32828c3..e3794eed65 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java
@@ -27,14 +27,14 @@
 
 
 public class RectangularPrism implements Polyhedron {
-	private static int[] lineLoop1 = {0,1,2,3,0,4,5,6,7,4};
-	private static int[] lineLoop2 = {1,5};
-	private static int[] lineLoop3 = {2,6};
-	private static int[] lineLoop4 = {3,7};
-	private double length = 1.0;
-	private double width = 1.0;
-	private double height = 1.0;
-	private static String[] viewNames = {"Front", "Left", "Back", "Right", "Top", "Bottom"};
+	private static final int[] lineLoop1 = {0,1,2,3,0,4,5,6,7,4};
+	private static final int[] lineLoop2 = {1,5};
+	private static final int[] lineLoop3 = {2,6};
+	private static final int[] lineLoop4 = {3,7};
+	private double length;
+	private double width;
+	private double height;
+	private static final String[] viewNames = {"Front", "Left", "Back", "Right", "Top", "Bottom"};
 
 	public RectangularPrism(double length, double width, double height) {
 		this.length = length;
@@ -103,7 +103,7 @@ public Point3d[] getVertices() {
 		vertices[7] = new Point3d( x, -y, -z);
 
 		return vertices;
-	};
+	}
 
 	@Override
 	public List<int[]> getLineLoops() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SphereSampler.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SphereSampler.java
index e36e942d89..e953a94c47 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SphereSampler.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SphereSampler.java
@@ -32,7 +32,7 @@
  */
 class Permute {
 
-	private List<Point3i> triples = new ArrayList<Point3i>();
+	private final List<Point3i> triples = new ArrayList<>();
 
 	Permute(Point3i t) {
 		Point3i tmp = new Point3i();
@@ -98,7 +98,7 @@ public int size() {
 	public Point3i get(int i) {
 		return triples.get(i);
 	}
-};
+}
 
 /**
  * Sample possible orientations. An orientation can be represented as a
@@ -154,7 +154,7 @@ public final class SphereSampler {
 	static
 	{
 
-		List<Quat4d> myorientations = new ArrayList<Quat4d>();
+		List<Quat4d> myorientations = new ArrayList<>();
 
 		// 60 equally spaced grid points covering all quaternions
 		// This could be removed, since the 48-cell bcc lattice has lower angle error -SB
@@ -173,7 +173,7 @@ public final class SphereSampler {
 		// This is the c48u309 lattice from Karney 2006, with a max error of 10.07
 		// degrees.
 
-		List<Quat4d> grid = new ArrayList<Quat4d>();
+		List<Quat4d> grid = new ArrayList<>();
 		int ncell1 = 0;
 		for (int n = 0; n < nent; ++n) { // for each tuple (k,l,m) above
 			Permute p = new Permute(new Point3i(k[n], l[n], m[n]));
@@ -209,7 +209,7 @@ public final class SphereSampler {
 
 	// this class cannot be instantiated
 	private SphereSampler() {
-	};
+	}
 
 	public static int getSphereCount() {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java
index 7effd81cbe..c6a4d49594 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java
@@ -29,9 +29,9 @@
 
 
 public class Tetrahedron implements Polyhedron {
-	private static double TETRAHEDRAL_ANGLE = Math.acos(-1.0/3.0);
-	private static int[] lineLoop1 = {0,1,2,3,0,2};
-	private static int[] lineLoop2 = {1,3};
+	private static final double TETRAHEDRAL_ANGLE = Math.acos(-1.0/3.0);
+	private static final int[] lineLoop1 = {0,1,2,3,0,2};
+	private static final int[] lineLoop2 = {1,3};
 
 	private double circumscribedRadius = 1.0;
 
@@ -120,7 +120,7 @@ public  Point3d[] getVertices() {
 			m.transform(p);
 		}
 		return tetrahedron;
-	};
+	}
 
 	@Override
 	public List<int[]> getLineLoops() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java
index 96b41f48e9..52be30f224 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java
@@ -40,9 +40,9 @@
  */
 public class AngleOrderDetectorPlus implements OrderDetector {
 
-	private int maxOrder;
+	private final int maxOrder;
 	private final double error;
-	private boolean normalizeError;
+	private final boolean normalizeError;
 
 	/**
 	 * @param error
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java
index 863826103d..2548d7ef8d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java
@@ -51,12 +51,12 @@ public class CESymmParameters extends CeParameters {
 	private boolean gaps;
 	private int optimizationSteps;
 
-	public static enum OrderDetectorMethod {
+	public enum OrderDetectorMethod {
 		SEQUENCE_FUNCTION, GRAPH_COMPONENT, ANGLE, USER_INPUT;
 		public static final OrderDetectorMethod DEFAULT = SEQUENCE_FUNCTION;
 	}
 
-	public static enum RefineMethod {
+	public enum RefineMethod {
 		NOT_REFINED, SEQUENCE_FUNCTION, GRAPH_COMPONENT;
 		public static final RefineMethod DEFAULT = SEQUENCE_FUNCTION;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
index f81bd25dda..0403f71439 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
@@ -189,8 +189,8 @@ protected static CeSymmResult align(Atom[] atoms, CESymmParameters params)
 		CECalculator calculator = new CECalculator(params);
 		Matrix lastMatrix = null;
 
-		List<AFPChain> selfAlignments = new ArrayList<AFPChain>();
-		AFPChain optimalAFP = null;
+		List<AFPChain> selfAlignments = new ArrayList<>();
+		AFPChain optimalAFP;
 
 		// STEP 2: perform the self-alignments of the structure
 		int i = 0;
@@ -270,7 +270,7 @@ protected static CeSymmResult align(Atom[] atoms, CESymmParameters params)
 		// STEP 3: order detection & symmetry refinement, apply consistency
 		try {
 			// ORDER DETECTION
-			OrderDetector orderDetector = null;
+			OrderDetector orderDetector;
 			int order = 1;
 			switch (params.getOrderDetectorMethod()) {
 			case USER_INPUT:
@@ -424,7 +424,7 @@ public static CeSymmResult analyzeLevel(Atom[] atoms,
 			// STEP 5: symmetry alignment optimization
 			if (result.getParams().getOptimization()) {
 				try {
-					MultipleAlignment msa = result.getMultipleAlignment();
+					MultipleAlignment msa;
 					SymmOptimizer optimizer = new SymmOptimizer(result);
 					msa = optimizer.optimize();
 					result.setMultipleAlignment(msa);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
index 66df0f2658..21ae1ad30f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
@@ -30,7 +30,6 @@
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIdentifier;
 import org.biojava.nbio.structure.align.multiple.Block;
 import org.biojava.nbio.structure.align.multiple.BlockImpl;
 import org.biojava.nbio.structure.align.multiple.BlockSet;
@@ -74,9 +73,9 @@ public class CeSymmIterative {
 	private static final Logger logger = LoggerFactory
 			.getLogger(CeSymmIterative.class);
 
-	private CESymmParameters params;
-	private Graph<Integer, DefaultEdge> alignGraph; // cumulative
-	private List<CeSymmResult> levels; // symmetry at each level
+	private final CESymmParameters params;
+	private final Graph<Integer, DefaultEdge> alignGraph; // cumulative
+	private final List<CeSymmResult> levels; // symmetry at each level
 
 	/**
 	 * For the iterative algorithm to work properly the refinement and
@@ -88,8 +87,8 @@ public class CeSymmIterative {
 	 */
 	public CeSymmIterative(CESymmParameters param) {
 		params = param;
-		alignGraph = new SimpleGraph<Integer, DefaultEdge>(DefaultEdge.class);
-		levels = new ArrayList<CeSymmResult>();
+		alignGraph = new SimpleGraph<>(DefaultEdge.class);
+		levels = new ArrayList<>();
 	}
 
 	/**
@@ -218,21 +217,21 @@ private CeSymmResult reconstructSymmResult(Atom[] atoms)
 
 		// Initialize a new multiple alignment
 		MultipleAlignment msa = new MultipleAlignmentImpl();
-		msa.getEnsemble().setAtomArrays(new ArrayList<Atom[]>());
+		msa.getEnsemble().setAtomArrays(new ArrayList<>());
 		msa.getEnsemble().setStructureIdentifiers(
-				new ArrayList<StructureIdentifier>());
+				new ArrayList<>());
 		msa.getEnsemble().setAlgorithmName(CeSymm.algorithmName);
 		msa.getEnsemble().setVersion(CeSymm.version);
 
 		BlockSet bs = new BlockSetImpl(msa);
 		Block b = new BlockImpl(bs);
-		b.setAlignRes(new ArrayList<List<Integer>>());
+		b.setAlignRes(new ArrayList<>());
 
 		// Calculate the connected groups of the alignment graph
-		ConnectivityInspector<Integer, DefaultEdge> inspector = new ConnectivityInspector<Integer, DefaultEdge>(
+		ConnectivityInspector<Integer, DefaultEdge> inspector = new ConnectivityInspector<>(
 				alignGraph);
 		List<Set<Integer>> comps = inspector.connectedSets();
-		List<ResidueGroup> groups = new ArrayList<ResidueGroup>(comps.size());
+		List<ResidueGroup> groups = new ArrayList<>(comps.size());
 		for (Set<Integer> comp : comps)
 			groups.add(new ResidueGroup(comp));
 
@@ -241,7 +240,7 @@ private CeSymmResult reconstructSymmResult(Atom[] atoms)
 		for (CeSymmResult sr : levels)
 			order *= sr.getMultipleAlignment().size();
 		for (int su = 0; su < order; su++)
-			b.getAlignRes().add(new ArrayList<Integer>());
+			b.getAlignRes().add(new ArrayList<>());
 
 		// Construct the resulting MultipleAlignment from ResidueGroups
 		for (ResidueGroup group : groups) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java
index b88ad1e112..8376220e57 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java
@@ -22,6 +22,7 @@
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 import org.biojava.nbio.structure.Atom;
@@ -105,7 +106,7 @@ public List<StructureIdentifier> getRepeatsID() throws StructureException {
 		if (!isRefined())
 			return null;
 
-		List<StructureIdentifier> repeats = new ArrayList<StructureIdentifier>(
+		List<StructureIdentifier> repeats = new ArrayList<>(
 				numRepeats);
 
 		String pdbId = structureId.toCanonical().getPdbId();
@@ -120,7 +121,7 @@ public List<StructureIdentifier> getRepeatsID() throws StructureException {
 			ResidueRange range = new ResidueRange(res1.getChainName(), res1, res2);
 
 			StructureIdentifier id = new SubstructureIdentifier(pdbId,
-					Arrays.asList(range));
+                    Collections.singletonList(range));
 
 			repeats.add(id);
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java
index 822e62a8c2..0c77cfce07 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java
@@ -46,8 +46,7 @@
 public class GraphComponentOrderDetector implements OrderDetector {
 
 	@Override
-	public int calculateOrder(AFPChain selfAlignment, Atom[] ca)
-			throws RefinerFailedException {
+	public int calculateOrder(AFPChain selfAlignment, Atom[] ca) {
 
 		// Construct the alignment graph with jgrapht
 		Graph<Integer, DefaultEdge> graph = SymmetryTools
@@ -55,11 +54,11 @@ public int calculateOrder(AFPChain selfAlignment, Atom[] ca)
 
 		// Find the maximally connected components of the graph
 		ConnectivityInspector<Integer, DefaultEdge> inspector =
-				new ConnectivityInspector<Integer, DefaultEdge>(graph);
+				new ConnectivityInspector<>(graph);
 		List<Set<Integer>> components = inspector.connectedSets();
 
 		// The order maximizes the residues aligned
-		Map<Integer, Integer> counts = new HashMap<Integer, Integer>();
+		Map<Integer, Integer> counts = new HashMap<>();
 		for (Set<Integer> c : components) {
 			if (counts.containsKey(c.size()))
 				counts.put(c.size(), counts.get(c.size()) + c.size());
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java
index 6c7d44f6a7..e4a682b35a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java
@@ -63,12 +63,12 @@ public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms, int order)
 				.buildSymmetryGraph(selfAlignment);
 
 		// Find the maximally connected components of the graph
-		ConnectivityInspector<Integer, DefaultEdge> inspector = new ConnectivityInspector<Integer, DefaultEdge>(
+		ConnectivityInspector<Integer, DefaultEdge> inspector = new ConnectivityInspector<>(
 				graph);
 		List<Set<Integer>> components = inspector.connectedSets();
 
 		// Filter components with size != order, and transform to ResidueGroups
-		List<ResidueGroup> groups = new ArrayList<ResidueGroup>();
+		List<ResidueGroup> groups = new ArrayList<>();
 		for (Set<Integer> comp : components) {
 			if (comp.size() == order) {
 				ResidueGroup group = new ResidueGroup(comp);
@@ -103,7 +103,7 @@ public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms, int order)
 		}
 
 		// The compatibility score is the sum of rows of the matrix
-		List<Integer> rowScores = new ArrayList<Integer>(size);
+		List<Integer> rowScores = new ArrayList<>(size);
 		for (int i = 0; i < size; i++) {
 			GVector row = new GVector(size);
 			matrix.getRow(i, row);
@@ -113,9 +113,9 @@ public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms, int order)
 		}
 
 		// Refined multiple alignment Block as a result
-		List<List<Integer>> alignRes = new ArrayList<List<Integer>>(order);
+		List<List<Integer>> alignRes = new ArrayList<>(order);
 		for (int i = 0; i < order; i++)
-			alignRes.add(new ArrayList<Integer>());
+			alignRes.add(new ArrayList<>());
 
 		// Iterate until no more groups left to add (all groups score 0)
 		while (true) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/OrderDetector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/OrderDetector.java
index a33c3b575f..36e448e37c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/OrderDetector.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/OrderDetector.java
@@ -33,7 +33,7 @@
  */
 public interface OrderDetector {
 
-	public int calculateOrder(AFPChain afpChain, Atom[] ca)
+	int calculateOrder(AFPChain afpChain, Atom[] ca)
 			throws RefinerFailedException;
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java
index 2fb0b0e64e..a9e1bcdeb5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java
@@ -48,7 +48,7 @@ public class ResidueGroup {
 	 */
 	public ResidueGroup(Set<Integer> component) {
 		// Transform component into sorted List of residues
-		residues = new ArrayList<Integer>(component);
+		residues = new ArrayList<>(component);
 		Collections.sort(residues);
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionOrderDetector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionOrderDetector.java
index eb34659b5d..8a5e0aff81 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionOrderDetector.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionOrderDetector.java
@@ -56,7 +56,7 @@ public int calculateOrder(AFPChain afpChain, Atom[] ca)
 					AlignmentTools.alignmentAsMap(afpChain);
 
 			return AlignmentTools.getSymmetryOrder(alignment,
-					new AlignmentTools.IdentityMap<Integer>(),
+					new AlignmentTools.IdentityMap<>(),
 					maxSymmetry, minimumMetricChange);
 
 		} catch (StructureException e) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
index 9635debb05..8672f68b76 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
@@ -103,9 +103,8 @@ public static AFPChain refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
 	 * @param alignment The input alignment, as a map. This will be modified.
 	 * @param k Symmetry order. This can be guessed by {@link CeSymm#getSymmetryOrder(AFPChain)}
 	 * @return A modified map with the refined alignment
-	 * @throws StructureException
 	 */
-	public static Map<Integer, Integer> refineSymmetry(Map<Integer, Integer> alignment,int k) throws StructureException {
+	public static Map<Integer, Integer> refineSymmetry(Map<Integer, Integer> alignment,int k) {
 
 		// Store scores
 		Map<Integer, Double> scores = null;
@@ -117,8 +116,8 @@ public static Map<Integer, Integer> refineSymmetry(Map<Integer, Integer> alignme
 		//  2. f^K-1(x) is defined
 		//	3. score(f^K-1(x))>0
 
-		TreeSet<Integer> forwardLoops = new TreeSet<Integer>();
-		TreeSet<Integer> backwardLoops = new TreeSet<Integer>();
+		TreeSet<Integer> forwardLoops = new TreeSet<>();
+		TreeSet<Integer> backwardLoops = new TreeSet<>();
 
 
 		List<Integer> eligible = null;
@@ -184,9 +183,10 @@ public static Map<Integer, Integer> refineSymmetry(Map<Integer, Integer> alignme
 			if (scores.size() != virginScores.size()) {
 				System.out.println("Size missmatch");
 			} else {
-				for (Integer key : scores.keySet()) {
-					if (!virginScores.containsKey(key) || !scores.get(key).equals(virginScores.get(key))) {
-						System.out.format("Mismatch %d -> %f/%f%n", key, scores.get(key), virginScores.get(key));
+				for (Map.Entry<Integer, Double> entry : scores.entrySet()) {
+                    Integer key = entry.getKey();
+                    if (!virginScores.containsKey(key) || !entry.getValue().equals(virginScores.get(key))) {
+						System.out.format("Mismatch %d -> %f/%f%n", key, entry.getValue(), virginScores.get(key));
 					}
 				}
 			}
@@ -240,7 +240,7 @@ private static List<Integer> initializeEligible(Map<Integer, Integer> alignment,
 
 		// Assume all residues are eligible to start
 		if(eligible == null) {
-			eligible = new LinkedList<Integer>(alignment.keySet());
+			eligible = new LinkedList<>(alignment.keySet());
 		}
 
 		// Precalculate f^K-1(x)
@@ -334,8 +334,8 @@ private static List<Integer> initializeEligible(Map<Integer, Integer> alignment,
 	private static Map<Integer, Integer> applyAlignmentAndCheckCycles(Map<Integer, Integer> alignmentMap, int k, List<Integer> eligible) {
 
 		// Convert to lists to establish a fixed order (avoid concurrent modification)
-		List<Integer> preimage = new ArrayList<Integer>(alignmentMap.keySet()); // currently unmodified
-		List<Integer> image = new ArrayList<Integer>(preimage);
+		List<Integer> preimage = new ArrayList<>(alignmentMap.keySet()); // currently unmodified
+		List<Integer> image = new ArrayList<>(preimage);
 
 		for (int n = 1; n <= k; n++) {
 			// apply alignment
@@ -351,7 +351,7 @@ private static Map<Integer, Integer> applyAlignmentAndCheckCycles(Map<Integer, I
 			}
 		}
 
-		Map<Integer, Integer> imageMap = new HashMap<Integer, Integer>(alignmentMap.size());
+		Map<Integer, Integer> imageMap = new HashMap<>(alignmentMap.size());
 
 		// now populate with actual values
 		for (int i = 0; i < preimage.size(); i++) {
@@ -372,7 +372,7 @@ private static Map<Integer, Integer> applyAlignmentAndCheckCycles(Map<Integer, I
 	private static Map<Integer, Double> initializeScores(Map<Integer, Integer> alignment,
 			Map<Integer, Double> scores, int k) {
 		if(scores == null) {
-			scores = new HashMap<Integer, Double>(alignment.size());
+			scores = new HashMap<>(alignment.size());
 		} else {
 			scores.clear();
 		}
@@ -444,7 +444,7 @@ private static AFPChain partitionAFPchain(AFPChain afpChain,
 		int repeatLen = afpChain.getOptLength()/order;
 
 		//Extract all the residues considered in the first chain of the alignment
-		List<Integer> alignedRes = new ArrayList<Integer>();
+		List<Integer> alignedRes = new ArrayList<>();
 		for (int su=0; su<afpChain.getBlockNum(); su++){
 			for (int i=0; i<afpChain.getOptLen()[su]; i++){
 				alignedRes.add(afpChain.getOptAln()[su][0][i]);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
index ce4a1d69e7..67e1878675 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
@@ -64,24 +64,24 @@ public class SymmOptimizer {
 	private static final Logger logger = LoggerFactory
 			.getLogger(SymmOptimizer.class);
 
-	private Random rnd;
+	private final Random rnd;
 
 	// Optimization parameters
-	private int Rmin = 2; // min aligned repeats per column
-	private int Lmin; // min repeat length
+	private int Rmin; // min aligned repeats per column
+	private final int Lmin; // min repeat length
 	private int maxIter; // max iterations
 	private double C = 20; // probability of accept bad moves constant
 
 	// Score function parameters
 	private static final double Gopen = 20.0; // Penalty for opening gap
 	private static final double Gextend = 10.0; // Penalty for extending gaps
-	private double dCutoff;
+	private final double dCutoff;
 
 	// Alignment Information
-	private MultipleAlignment msa;
-	private SymmetryAxes axes;
-	private Atom[] atoms;
-	private int order;
+	private final MultipleAlignment msa;
+	private final SymmetryAxes axes;
+	private final Atom[] atoms;
+	private final int order;
 	private int length; // total alignment columns (block size)
 	private int repeatCore; // core length (without gaps)
 
@@ -146,21 +146,21 @@ private void initialize() throws StructureException, RefinerFailedException {
 					"Seed alignment too short: repeat core length < 1");
 
 		// Initialize the history variables
-		timeHistory = new ArrayList<Long>();
-		lengthHistory = new ArrayList<Integer>();
-		rmsdHistory = new ArrayList<Double>();
-		mcScoreHistory = new ArrayList<Double>();
-		tmScoreHistory = new ArrayList<Double>();
+		timeHistory = new ArrayList<>();
+		lengthHistory = new ArrayList<>();
+		rmsdHistory = new ArrayList<>();
+		mcScoreHistory = new ArrayList<>();
+		tmScoreHistory = new ArrayList<>();
 
 		C = 20 * order;
 
 		// Initialize alignment variables
 		block = msa.getBlock(0).getAlignRes();
-		freePool = new ArrayList<Integer>();
+		freePool = new ArrayList<>();
 		length = block.get(0).size();
 
 		// Store the residues aligned in the block
-		List<Integer> aligned = new ArrayList<Integer>();
+		List<Integer> aligned = new ArrayList<>();
 		for (int su = 0; su < order; su++)
 			aligned.addAll(block.get(su));
 
@@ -196,11 +196,11 @@ public MultipleAlignment optimize() throws StructureException,
 		initialize();
 
 		// Save the optimal alignment
-		List<List<Integer>> optBlock = new ArrayList<List<Integer>>();
-		List<Integer> optFreePool = new ArrayList<Integer>();
+		List<List<Integer>> optBlock = new ArrayList<>();
+		List<Integer> optFreePool = new ArrayList<>();
 		optFreePool.addAll(freePool);
 		for (int k = 0; k < order; k++) {
-			List<Integer> b = new ArrayList<Integer>();
+			List<Integer> b = new ArrayList<>();
 			b.addAll(block.get(k));
 			optBlock.add(b);
 		}
@@ -214,11 +214,11 @@ public MultipleAlignment optimize() throws StructureException,
 		while (i < maxIter && conv < stepsToConverge) {
 
 			// Save the state of the system
-			List<List<Integer>> lastBlock = new ArrayList<List<Integer>>();
-			List<Integer> lastFreePool = new ArrayList<Integer>();
+			List<List<Integer>> lastBlock = new ArrayList<>();
+			List<Integer> lastFreePool = new ArrayList<>();
 			lastFreePool.addAll(freePool);
 			for (int k = 0; k < order; k++) {
-				List<Integer> b = new ArrayList<Integer>();
+				List<Integer> b = new ArrayList<>();
 				b.addAll(block.get(k));
 				lastBlock.add(b);
 			}
@@ -281,11 +281,11 @@ public MultipleAlignment optimize() throws StructureException,
 
 			// Store as the optimal alignment if better
 			if (mcScore > optScore) {
-				optBlock = new ArrayList<List<Integer>>();
-				optFreePool = new ArrayList<Integer>();
+				optBlock = new ArrayList<>();
+				optFreePool = new ArrayList<>();
 				optFreePool.addAll(freePool);
 				for (int k = 0; k < order; k++) {
-					List<Integer> b = new ArrayList<Integer>();
+					List<Integer> b = new ArrayList<>();
 					b.addAll(block.get(k));
 					optBlock.add(b);
 				}
@@ -366,7 +366,7 @@ private void updateMultipleAlignment() throws StructureException,
 	 */
 	private boolean checkGaps() {
 
-		List<Integer> shrinkColumns = new ArrayList<Integer>();
+		List<Integer> shrinkColumns = new ArrayList<>();
 		// Loop for each column
 		for (int res = 0; res < length; res++) {
 			int gapCount = 0;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java
index fcf9ff29d0..cd8509e50b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java
@@ -75,8 +75,8 @@ public class SymmetryAxes {
 	 */
 	public static class Axis {
 		private Matrix4d operator;
-		private int order;
-		private SymmetryType symmType;
+		private final int order;
+		private final SymmetryType symmType;
 		private int level;
 		//private int indexInLevel;
 		private int firstRepeat;
@@ -261,7 +261,7 @@ public void updateAxis(Integer index, Matrix4d newAxis){
 	 * @return axes elementary axes of symmetry.
 	 */
 	public List<Matrix4d> getElementaryAxes(){
-		List<Matrix4d> ops = new ArrayList<Matrix4d>(getNumLevels());
+		List<Matrix4d> ops = new ArrayList<>(getNumLevels());
 		for(Axis axis : axes) {
 			ops.add(axis.getOperator());
 		}
@@ -541,7 +541,7 @@ private int getNumRepeats(int level) {
 	 * @return List of first Repeats of each index, sorted in ascending order
 	 */
 	public List<Integer> getFirstRepeats(int level) {
-		List<Integer> firstRepeats = new ArrayList<Integer>();
+		List<Integer> firstRepeats = new ArrayList<>();
 		int m = getNumRepeats(level+1); //size of the level
 		int d = axes.get(level).getOrder(); //degree of this level
 		int n = m*d; // number of repeats included in each axis
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryRefiner.java
index c21f51b30f..e16a72206a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryRefiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryRefiner.java
@@ -48,7 +48,7 @@ public interface SymmetryRefiner {
 	 * @throws RefinerFailedException
 	 * @throws StructureException
 	 */
-	public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms, int order)
+    MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms, int order)
 			throws RefinerFailedException, StructureException;
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ChainSignature.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ChainSignature.java
index e60a507bce..cf9c295a0a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ChainSignature.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ChainSignature.java
@@ -23,10 +23,10 @@
 import java.util.List;
 
 public class ChainSignature implements Comparable<ChainSignature> {
-	private int chainCount = 0;
-	private String representative = "";
+	private int chainCount;
+	private String representative;
 	private String compositionId = "";
-	private List<String> chainIds = null;
+	private List<String> chainIds;
 
 	public ChainSignature(String representative, int chainCount, List<String> chainIds) {
 		this.representative = representative;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.java
index 492e1485e1..5b3da7b27d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.java
@@ -26,10 +26,10 @@
 import java.util.Map.Entry;
 
 public class ProteinComplexSignature {
-	private BlastClustReader blastClust = null;
-	private String pdbId = "";
-	private List<String> chainIds = null;
-	private List<ChainSignature> chainSignatures = new ArrayList<ChainSignature>();
+	private BlastClustReader blastClust;
+	private String pdbId;
+	private List<String> chainIds;
+	private final List<ChainSignature> chainSignatures = new ArrayList<>();
 
 
 	public ProteinComplexSignature(String pdbId, List<String> chainIds, BlastClustReader blastClust) {
@@ -75,15 +75,15 @@ public int getSubunitTypeCount() {
 	private List<ChainSignature> getChainSignatures() {
 		String alpha = "ABCDEFGHIJKLMNOPQRSTUVWXYZ";
 
-		Map<String,Integer> mapCounts = new TreeMap<String,Integer>();
-		Map<String,List<String>> mapChainIds = new TreeMap<String, List<String>>();
+		Map<String,Integer> mapCounts = new TreeMap<>();
+		Map<String,List<String>> mapChainIds = new TreeMap<>();
 
 		for (String chainId: chainIds) {
 			String rep = blastClust.getRepresentativeChain(pdbId, chainId);
 			Integer value = mapCounts.get(rep);
 			if (value == null) {
 				mapCounts.put(rep, 1);
-				List<String> list = new ArrayList<String>();
+				List<String> list = new ArrayList<>();
 				list.add(chainId);
 				mapChainIds.put(rep, list);
 			} else {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java
index a0653c2055..d3ef8c2932 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java
@@ -38,8 +38,8 @@ public class BlastClustReader implements Serializable {
 
 	private static final Logger logger = LoggerFactory.getLogger(BlastClustReader.class);
 
-	private int sequenceIdentity = 0;
-	private List<List<String>> clusters = new ArrayList<>();
+	private int sequenceIdentity;
+	private final List<List<String>> clusters = new ArrayList<>();
 	// https://cdn.rcsb.org/resources/sequence/clusters/bc-95.out
 	private static final String coreUrl = "https://cdn.rcsb.org/resources/sequence/clusters/";
 
@@ -102,7 +102,7 @@ public List<List<String>> getPdbChainIdClusters(String pdbId) {
 		loadClusters(sequenceIdentity);
 		String pdbIdUpper = pdbId.toUpperCase();
 
-		List<List<String>> matches = new ArrayList<List<String>>();
+		List<List<String>> matches = new ArrayList<>();
 		for (List<String> cluster: clusters) {
 			for (String chainId: cluster) {
 				if (chainId.startsWith(pdbIdUpper)) {
@@ -117,14 +117,14 @@ public List<List<String>> getPdbChainIdClusters(String pdbId) {
 	public List<List<String>> getChainIdsInEntry(String pdbId) {
 		loadClusters(sequenceIdentity);
 
-		List<List<String>> matches = new ArrayList<List<String>>();
+		List<List<String>> matches = new ArrayList<>();
 		List<String> match = null;
 
 		for (List<String> cluster: clusters) {
 			for (String chainId: cluster) {
 				if (chainId.startsWith(pdbId)) {
 					if (match == null) {
-						match = new ArrayList<String>();
+						match = new ArrayList<>();
 					}
 					match.add(chainId.substring(5));
 				}
@@ -159,7 +159,7 @@ private void loadClusters(int sequenceIdentity) {
 			if (stream != null) {
 				BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
 
-				String line = null;
+				String line;
 				while ((line = reader.readLine()) != null) {
 					line = line.replaceAll("_", ".");
 					List<String> cluster = Arrays.asList(line.split(" "));
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PermutationGenerator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PermutationGenerator.java
index 5a8a778017..2a23cb5ab5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PermutationGenerator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PermutationGenerator.java
@@ -34,9 +34,9 @@ public class PermutationGenerator {
 // http://www.merriampark.com/perm.htm // The PermutationGenerator Java class systematically generates permutations. It relies on the fact that any set with n elements can be placed in one-to-one correspondence with the set {1, 2, 3, ..., n}. The algorithm is described by Kenneth H. Rosen, Discrete Mathematics and Its Applications, 2nd edition (NY: McGraw-Hill, 1991), pp. 282-284.
 
 
-	private int[] a;
+	private final int[] a;
 	private BigInteger numLeft;
-	private BigInteger total;
+	private final BigInteger total;
 
 	//-----------------------------------------------------------
 	// Constructor. WARNING: Don't make n too large.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PowerSet.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PowerSet.java
index 10b5652ea1..9a0f154d6d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PowerSet.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PowerSet.java
@@ -52,16 +52,16 @@ public PowerSet() {
 	 * @return the set of power Sets of the original Set
 	 */
 	public Set<Set<T>> powerSet(Set<T> originalSet) {
-		Set<Set<T>> sets = new LinkedHashSet<Set<T>>();
+		Set<Set<T>> sets = new LinkedHashSet<>();
 		if (originalSet.isEmpty()) {
-			sets.add(new LinkedHashSet<T>());
+			sets.add(new LinkedHashSet<>());
 			return sets;
 		}
-		List<T> list = new ArrayList<T>(originalSet);
+		List<T> list = new ArrayList<>(originalSet);
 		T head = list.get(0);
-		Set<T> rest = new LinkedHashSet<T>(list.subList(1, list.size()));
+		Set<T> rest = new LinkedHashSet<>(list.subList(1, list.size()));
 		for (Set<T> set : powerSet(rest)) {
-			Set<T> newSet = new LinkedHashSet<T>();
+			Set<T> newSet = new LinkedHashSet<>();
 			newSet.add(head);
 			newSet.addAll(set);
 			sets.add(newSet);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
index 3cac9be3f1..db5ebb04cf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
@@ -443,17 +443,17 @@ public static double getAngle(AFPChain afpChain, Atom[] ca1, Atom[] ca2) {
 	public static List<List<Integer>> buildSymmetryGraph(List<AFPChain> afps,
 			Atom[] atoms, boolean undirected) {
 
-		List<List<Integer>> graph = new ArrayList<List<Integer>>();
+		List<List<Integer>> graph = new ArrayList<>();
 
 		for (int n = 0; n < atoms.length; n++) {
-			graph.add(new ArrayList<Integer>());
+			graph.add(new ArrayList<>());
 		}
 
 		for (int k = 0; k < afps.size(); k++) {
 			for (int i = 0; i < afps.get(k).getOptAln().length; i++) {
 				for (int j = 0; j < afps.get(k).getOptAln()[i][0].length; j++) {
-					Integer res1 = afps.get(k).getOptAln()[i][0][j];
-					Integer res2 = afps.get(k).getOptAln()[i][1][j];
+					int res1 = afps.get(k).getOptAln()[i][0][j];
+					int res2 = afps.get(k).getOptAln()[i][1][j];
 					graph.get(res1).add(res2);
 					if (undirected)
 						graph.get(res2).add(res1);
@@ -476,7 +476,7 @@ public static List<List<Integer>> buildSymmetryGraph(List<AFPChain> afps,
 	public static Graph<Integer, DefaultEdge> buildSymmetryGraph(
 			AFPChain selfAlignment) {
 
-		Graph<Integer, DefaultEdge> graph = new SimpleGraph<Integer, DefaultEdge>(
+		Graph<Integer, DefaultEdge> graph = new SimpleGraph<>(
 				DefaultEdge.class);
 
 		for (int i = 0; i < selfAlignment.getOptAln().length; i++) {
@@ -512,13 +512,13 @@ public static List<Structure> divideStructure(CeSymmResult symmetry)
 		Atom[] atoms = symmetry.getAtoms();
 		Set<Group> allGroups = StructureTools.getAllGroupsFromSubset(atoms, GroupType.HETATM);
 		List<StructureIdentifier> repeatsId = symmetry.getRepeatsID();
-		List<Structure> repeats = new ArrayList<Structure>(order);
+		List<Structure> repeats = new ArrayList<>(order);
 
 		// Create new structure containing the repeat atoms
 		for (int i = 0; i < order; i++) {
 
 			Structure s = new StructureImpl();
-			s.addModel(new ArrayList<Chain>(1));
+			s.addModel(new ArrayList<>(1));
 			s.setStructureIdentifier(repeatsId.get(i));
 
 			Block align = symmetry.getMultipleAlignment().getBlock(0);
@@ -542,7 +542,7 @@ public static List<Structure> divideStructure(CeSymmResult symmetry)
 
 			List<Group> ligands = StructureTools.getLigandsByProximity(
 					allGroups,
-					repeat.toArray(new Atom[repeat.size()]),
+					repeat.toArray(new Atom[0]),
 					StructureTools.DEFAULT_LIGAND_PROXIMITY_CUTOFF);
 
 			logger.warn("Adding {} ligands to {}",ligands.size(), symmetry.getMultipleAlignment().getStructureIdentifier(i));
@@ -613,7 +613,7 @@ public static MultipleAlignment toRepeatsAlignment(CeSymmResult result)
 
 		MultipleAlignment repeats = newEnsemble.getMultipleAlignment(0);
 		Block block = repeats.getBlock(0);
-		List<Atom[]> atomArrays = new ArrayList<Atom[]>();
+		List<Atom[]> atomArrays = new ArrayList<>();
 
 		for (Structure s : repSt)
 			atomArrays.add(StructureTools.getRepresentativeAtomArray(s));
@@ -621,7 +621,7 @@ public static MultipleAlignment toRepeatsAlignment(CeSymmResult result)
 		newEnsemble.setAtomArrays(atomArrays);
 
 		for (int su = 0; su < block.size(); su++) {
-			Integer start = block.getStartResidue(su);
+			int start = block.getStartResidue(su);
 
 			// Normalize aligned residues
 			for (int res = 0; res < block.length(); res++) {
@@ -658,7 +658,7 @@ public static MultipleAlignment fromAFP(AFPChain symm, Atom[] atoms)
 
 		MultipleAlignmentEnsemble e = new MultipleAlignmentEnsembleImpl(symm,
 				atoms, atoms, false);
-		e.setAtomArrays(new ArrayList<Atom[]>());
+		e.setAtomArrays(new ArrayList<>());
 		StructureIdentifier name = null;
 		if (e.getStructureIdentifiers() != null) {
 			if (!e.getStructureIdentifiers().isEmpty())
@@ -667,12 +667,12 @@ public static MultipleAlignment fromAFP(AFPChain symm, Atom[] atoms)
 			name = atoms[0].getGroup().getChain().getStructure()
 					.getStructureIdentifier();
 
-		e.setStructureIdentifiers(new ArrayList<StructureIdentifier>());
+		e.setStructureIdentifiers(new ArrayList<>());
 
 		MultipleAlignment result = new MultipleAlignmentImpl();
 		BlockSet bs = new BlockSetImpl(result);
 		Block b = new BlockImpl(bs);
-		b.setAlignRes(new ArrayList<List<Integer>>());
+		b.setAlignRes(new ArrayList<>());
 
 		int order = symm.getBlockNum();
 		for (int su = 0; su < order; su++) {
@@ -737,7 +737,7 @@ public static QuatSymmetryResults getQuaternarySymmetry(CeSymmResult result)
 	 */
 	public static List<Group> getGroups(Atom[] rAtoms) {
 
-		List<Group> groups = new ArrayList<Group>(rAtoms.length);
+		List<Group> groups = new ArrayList<>(rAtoms.length);
 
 		for (Atom a : rAtoms) {
 			Group g = a.getGroup();
@@ -774,8 +774,8 @@ public static void updateSymmetryTransformation(SymmetryAxes axes,
 			for (int level = 0; level < axes.getNumLevels(); level++) {
 
 				// Calculate the aligned atom arrays to superimpose
-				List<Atom> list1 = new ArrayList<Atom>();
-				List<Atom> list2 = new ArrayList<Atom>();
+				List<Atom> list1 = new ArrayList<>();
+				List<Atom> list2 = new ArrayList<>();
 
 				for (int firstRepeat : axes.getFirstRepeats(level)) {
 
@@ -805,8 +805,8 @@ public static void updateSymmetryTransformation(SymmetryAxes axes,
 					}
 				}
 
-				Atom[] arr1 = list1.toArray(new Atom[list1.size()]);
-				Atom[] arr2 = list2.toArray(new Atom[list2.size()]);
+				Atom[] arr1 = list1.toArray(new Atom[0]);
+				Atom[] arr2 = list2.toArray(new Atom[0]);
 
 				// Calculate the new transformation information
 				if (arr1.length > 0 && arr2.length > 0) {
@@ -817,7 +817,7 @@ public static void updateSymmetryTransformation(SymmetryAxes axes,
 				}
 
 				// Get the transformations from the SymmetryAxes
-				List<Matrix4d> transformations = new ArrayList<Matrix4d>();
+				List<Matrix4d> transformations = new ArrayList<>();
 				for (int su = 0; su < msa.size(); su++) {
 					transformations.add(axes.getRepeatTransform(su));
 				}
@@ -866,7 +866,7 @@ public static Atom[] getRepresentativeAtoms(Structure structure) {
 		else {
 
 			// Get Atoms of all models
-			List<Atom> atomList = new ArrayList<Atom>();
+			List<Atom> atomList = new ArrayList<>();
 			for (int m = 0; m < structure.nrModels(); m++) {
 				for (Chain c : structure.getModel(m))
 					atomList.addAll(Arrays.asList(StructureTools
@@ -888,7 +888,7 @@ public static Atom[] getRepresentativeAtoms(Structure structure) {
 	 */
 	public static List<Integer> getValidFolds(List<Integer> stoichiometry) {
 
-		List<Integer> denominators = new ArrayList<Integer>();
+		List<Integer> denominators = new ArrayList<>();
 
 		if (stoichiometry.isEmpty())
 			return denominators;
@@ -896,7 +896,7 @@ public static List<Integer> getValidFolds(List<Integer> stoichiometry) {
 		int nChains = Collections.max(stoichiometry);
 
 		// Remove duplicate stoichiometries
-		Set<Integer> nominators = new TreeSet<Integer>(stoichiometry);
+		Set<Integer> nominators = new TreeSet<>(stoichiometry);
 
 		// find common denominators
 		for (int d = 1; d <= nChains; d++) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/ModelledSubgroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/ModelledSubgroup.java
index 310bb9e1af..19d5d307e0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/ModelledSubgroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/ModelledSubgroup.java
@@ -204,7 +204,7 @@ public class ModelledSubgroup {
 	 */
 	public List<AngleOutlier> getAngleOutlier() {
 		if (angleOutlier == null) {
-			angleOutlier = new ArrayList<AngleOutlier>();
+			angleOutlier = new ArrayList<>();
 		}
 		return this.angleOutlier;
 	}
@@ -233,7 +233,7 @@ public List<AngleOutlier> getAngleOutlier() {
 	 */
 	public List<Clash> getClash() {
 		if (clash == null) {
-			clash = new ArrayList<Clash>();
+			clash = new ArrayList<>();
 		}
 		return this.clash;
 	}
@@ -262,7 +262,7 @@ public List<Clash> getClash() {
 	 */
 	public List<BondOutlier> getBondOutlier() {
 		if (bondOutlier == null) {
-			bondOutlier = new ArrayList<BondOutlier>();
+			bondOutlier = new ArrayList<>();
 		}
 		return this.bondOutlier;
 	}
@@ -291,7 +291,7 @@ public List<BondOutlier> getBondOutlier() {
 	 */
 	public List<MogAngleOutlier> getMogAngleOutlier() {
 		if (mogAngleOutlier == null) {
-			mogAngleOutlier = new ArrayList<MogAngleOutlier>();
+			mogAngleOutlier = new ArrayList<>();
 		}
 		return this.mogAngleOutlier;
 	}
@@ -320,7 +320,7 @@ public List<MogAngleOutlier> getMogAngleOutlier() {
 	 */
 	public List<SymmClash> getSymmClash() {
 		if (symmClash == null) {
-			symmClash = new ArrayList<SymmClash>();
+			symmClash = new ArrayList<>();
 		}
 		return this.symmClash;
 	}
@@ -349,7 +349,7 @@ public List<SymmClash> getSymmClash() {
 	 */
 	public List<MogBondOutlier> getMogBondOutlier() {
 		if (mogBondOutlier == null) {
-			mogBondOutlier = new ArrayList<MogBondOutlier>();
+			mogBondOutlier = new ArrayList<>();
 		}
 		return this.mogBondOutlier;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/Programs.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/Programs.java
index afd4ac4876..f6bdb256f6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/Programs.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/Programs.java
@@ -86,7 +86,7 @@ public class Programs {
 	 */
 	public List<Program> getProgram() {
 		if (program == null) {
-			program = new ArrayList<Program>();
+			program = new ArrayList<>();
 		}
 		return this.program;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/WwPDBValidationInformation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/WwPDBValidationInformation.java
index 85585a9770..7bcf3a9a13 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/WwPDBValidationInformation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/WwPDBValidationInformation.java
@@ -122,7 +122,7 @@ public void setEntry(Entry value) {
 	 */
 	public List<ModelledSubgroup> getModelledSubgroup() {
 		if (modelledSubgroup == null) {
-			modelledSubgroup = new ArrayList<ModelledSubgroup>();
+			modelledSubgroup = new ArrayList<>();
 		}
 		return this.modelledSubgroup;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/BravaisLattice.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/BravaisLattice.java
index 02efe5be5a..7585053c02 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/BravaisLattice.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/BravaisLattice.java
@@ -38,12 +38,12 @@ public enum BravaisLattice {
 	HEXAGONAL    (6, "HEXAGONAL",    new CrystalCell(1.00,1.00,1.25, 90,90,120)),// a=b!=c, alpha=beta=90, gamma=120
 	CUBIC        (7, "CUBIC",        new CrystalCell(1.00,1.00,1.00, 90,90,90)); // a=b=c, alpha=beta=gamma=90
 
-	private static HashMap<String, BravaisLattice> name2bl = initname2bl();
-	private String name;
-	private int id;
-	private CrystalCell exampleUnitCell;
+	private static final HashMap<String, BravaisLattice> name2bl = initname2bl();
+	private final String name;
+	private final int id;
+	private final CrystalCell exampleUnitCell;
 
-	private BravaisLattice(int id, String name, CrystalCell exampleUnitCell) {
+	BravaisLattice(int id, String name, CrystalCell exampleUnitCell) {
 		this.name = name;
 		this.id = id;
 		this.exampleUnitCell = exampleUnitCell;
@@ -62,7 +62,7 @@ public CrystalCell getExampleUnitCell() {
 	}
 
 	private static HashMap<String,BravaisLattice> initname2bl(){
-		HashMap<String,BravaisLattice> name2bl = new HashMap<String, BravaisLattice>();
+		HashMap<String,BravaisLattice> name2bl = new HashMap<>();
 		for (BravaisLattice bl:BravaisLattice.values()) {
 			name2bl.put(bl.getName(), bl);
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalBuilder.java
index 2bc6806b77..6e4fc5394c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalBuilder.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalBuilder.java
@@ -78,10 +78,10 @@ public class CrystalBuilder {
 	 */
 	private static final boolean INCLUDE_HETATOMS = true;
 
-	private Structure structure;
-	private PDBCrystallographicInfo crystallographicInfo;
-	private int numPolyChainsAu;
-	private int numOperatorsSg;
+	private final Structure structure;
+	private final PDBCrystallographicInfo crystallographicInfo;
+	private final int numPolyChainsAu;
+	private final int numOperatorsSg;
 	private Map<String,Matrix4d> chainNcsOps = null;
 	private Map<String,String> chainOrigNames = null;
 
@@ -93,7 +93,7 @@ public class CrystalBuilder {
 	private Map<String,Map<Matrix4d,StructureInterface>> visitedNcsChainPairs = null;
 
 	private boolean searchBeyondAU;
-	private Matrix4d[] ops;
+	private final Matrix4d[] ops;
 
 	/**
 	 * Special constructor for NCS-aware CrystalBuilder.
@@ -256,7 +256,7 @@ private void calcInterfacesCrystal(StructureInterfaceList set, double cutoff) {
 
 		// initialising debugging vars
 		long start = -1;
-		long end = -1;
+		long end;
 		int trialCount = 0;
 		int skippedRedundant = 0;
 		int skippedAUsNoOverlap = 0;
@@ -264,7 +264,7 @@ private void calcInterfacesCrystal(StructureInterfaceList set, double cutoff) {
 		int skippedSelfEquivalent = 0;
 
 		// The bounding boxes of all AUs of the unit cell
-		UnitCellBoundingBox bbGrid = new UnitCellBoundingBox(numOperatorsSg, numPolyChainsAu);;
+		UnitCellBoundingBox bbGrid = new UnitCellBoundingBox(numOperatorsSg, numPolyChainsAu);
 		// we calculate all the bounds of each of the asym units, those will then be reused and translated
 		bbGrid.setBbs(structure, ops, INCLUDE_HETATOMS);
 
@@ -466,8 +466,7 @@ private StructureInterface findNcsRef(StructureInterface interf) {
 
 		// same original chain names
 		Optional<Matrix4d> matchDirect =
-				visitedNcsChainPairs.computeIfAbsent(matchChainIdsIJ, k-> new HashMap<>()).entrySet().stream().
-					map(r->r.getKey()).
+				visitedNcsChainPairs.computeIfAbsent(matchChainIdsIJ, k-> new HashMap<>()).keySet().stream().
 					filter(r->r.epsilonEquals(j2iNcsOrigin,0.01)).
 					findFirst();
 
@@ -477,8 +476,7 @@ private StructureInterface findNcsRef(StructureInterface interf) {
 		if(matchMatrix == null) {
 			// reversed original chain names with inverted transform
 			Optional<Matrix4d> matchInverse =
-					visitedNcsChainPairs.computeIfAbsent(matchChainIdsJI, k-> new HashMap<>()).entrySet().stream().
-					map(r->r.getKey()).
+					visitedNcsChainPairs.computeIfAbsent(matchChainIdsJI, k-> new HashMap<>()).keySet().stream().
 					filter(r->r.epsilonEquals(i2jNcsOrigin,0.01)).
 					findFirst();
 			matchMatrix = matchInverse.orElse(null);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalCell.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalCell.java
index 3850c0b87b..e5d1478435 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalCell.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalCell.java
@@ -488,7 +488,7 @@ public double getMaxDimension() {
 		Point3d vert7 = new Point3d(1,1,1);
 		transfToOrthonormal(vert7);
 
-		ArrayList<Double> vertDists = new ArrayList<Double>();
+		ArrayList<Double> vertDists = new ArrayList<>();
 		vertDists.add(vert0.distance(vert7));
 		vertDists.add(vert3.distance(vert4));
 		vertDists.add(vert1.distance(vert6));
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalTransform.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalTransform.java
index df3938fca6..93ecaf2766 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalTransform.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalTransform.java
@@ -72,7 +72,7 @@ public class CrystalTransform implements Serializable {
 	/**
 	 * The crystal translation (always integer)
 	 */
-	private Point3i crystalTranslation;
+	private final Point3i crystalTranslation;
 
 
 	/**
@@ -467,7 +467,7 @@ public static Vector3d getTranslScrewComponent(Matrix4d m) {
 		// For reference see:
 		// http://www.crystallography.fr/mathcryst/pdf/Gargnano/Aroyo_Gargnano_1.pdf
 
-		Vector3d transl = null;
+		Vector3d transl;
 
 		Matrix3d W =
 				new Matrix3d(m.m00,m.m01,m.m02,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
index e2e713c023..4573ddbd5b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
@@ -103,8 +103,8 @@ public SpaceGroup(int id, int multiplicity, int primitiveMultiplicity, String sh
 		this.primitiveMultiplicity = primitiveMultiplicity;
 		this.shortSymbol = shortSymbol;
 		this.altShortSymbol = altShortSymbol;
-		transformations = new ArrayList<Matrix4d>(multiplicity);
-		transfAlgebraic = new ArrayList<String>(multiplicity);
+		transformations = new ArrayList<>(multiplicity);
+		transfAlgebraic = new ArrayList<>(multiplicity);
 		cellTranslations = new Vector3d[multiplicity/primitiveMultiplicity];
 		this.bravLattice = bravLattice;
 	}
@@ -188,7 +188,7 @@ public static Matrix4d getMatrixFromAlgebraic(String transfAlgebraic) {
 	}
 
 	private static double[] convertAlgebraicStrToCoefficients(String algString) {
-		String letters = null;
+		String letters;
 		String noLetters = null;
 		Matcher m = splitPat1.matcher(algString);
 		if (m.matches()) {
@@ -215,12 +215,16 @@ private static double[] convertAlgebraicStrToCoefficients(String algString) {
 				s = -1.0;
 			}
 			String coord = m.group(2);
-			if (coord.equals("X")) {
-				coefficients[0] = s;
-			} else if (coord.equals("Y")) {
-				coefficients[1] = s;
-			} else if (coord.equals("Z")) {
-				coefficients[2] = s;
+			switch (coord) {
+				case "X":
+					coefficients[0] = s;
+					break;
+				case "Y":
+					coefficients[1] = s;
+					break;
+				case "Z":
+					coefficients[2] = s;
+					break;
 			}
 		}
 		if (noLetters!=null) {
@@ -272,7 +276,7 @@ public String getAltShortSymbol() {
 	 * @return
 	 */
 	public List<Matrix4d> getTransformations() {
-		List<Matrix4d> transfs = new ArrayList<Matrix4d>();
+		List<Matrix4d> transfs = new ArrayList<>();
 		for (int i=1;i<this.transformations.size();i++){
 			transfs.add(transformations.get(i));
 		}
@@ -541,7 +545,7 @@ public static AxisAngle4d getRotAxisAndAngle(Matrix3d m) {
 	 * @return
 	 */
 	public static int getRotAxisType(Matrix4d m) {
-		int axisType = 0;
+		int axisType;
 
 		Matrix3d rot = new Matrix3d(m.m00,m.m01,m.m02,
 				m.m10,m.m11,m.m12,
@@ -606,7 +610,7 @@ public String toString() {
 	public String toXML(){
 
 
-		JAXBContext jaxbContextStringSortedSet = null;
+		JAXBContext jaxbContextStringSortedSet;
 
 		try {
 			jaxbContextStringSortedSet= JAXBContext.newInstance(SpaceGroup.class);
@@ -645,10 +649,10 @@ public List<String> getTransfAlgebraic() {
 	public void setTransfAlgebraic(List<String> transfAlgebraic) {
 		//System.out.println("setting transfAlgebraic " + transfAlgebraic);
 		if ( transformations == null || transformations.size() == 0)
-			transformations = new ArrayList<Matrix4d>(transfAlgebraic.size());
+			transformations = new ArrayList<>(transfAlgebraic.size());
 
 		if ( this.transfAlgebraic == null || this.transfAlgebraic.size() == 0)
-			this.transfAlgebraic = new ArrayList<String>(transfAlgebraic.size());
+			this.transfAlgebraic = new ArrayList<>(transfAlgebraic.size());
 
 		for ( String transf : transfAlgebraic){
 			addTransformation(transf);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java
index 93896000b1..0781471deb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java
@@ -55,7 +55,7 @@ public class SymoplibParser {
 
 	private static final Pattern namePat = Pattern.compile(".*\\s([A-Z]+)(\\s'.+')?\\s+'(.+)'.*");
 
-	private static  TreeMap<Integer, SpaceGroup> sgs = parseSpaceGroupsXML();
+	private static final TreeMap<Integer, SpaceGroup> sgs = parseSpaceGroupsXML();
 
 
 	private static HashMap<String, SpaceGroup> name2sgs; // map for lookups based on short names
@@ -98,7 +98,7 @@ private static TreeMap<Integer, SpaceGroup> parseSpaceGroupsXML() {
 			System.exit(1);
 		}
 
-		TreeMap<Integer, SpaceGroup> map = new TreeMap<Integer, SpaceGroup>();
+		TreeMap<Integer, SpaceGroup> map = new TreeMap<>();
 
 		try {
 			map = parseSpaceGroupsXML(spaceGroupIS);
@@ -110,7 +110,7 @@ private static TreeMap<Integer, SpaceGroup> parseSpaceGroupsXML() {
 			System.exit(1);
 		}
 
-		name2sgs = new HashMap<String, SpaceGroup>();
+		name2sgs = new HashMap<>();
 
 		for (SpaceGroup sg:map.values()) {
 
@@ -147,7 +147,7 @@ private static String convertStreamToString(InputStream stream) throws IOExcepti
 		BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
 		StringBuilder sb = new StringBuilder();
 
-		String line = null;
+		String line;
 
 		while ((line = reader.readLine()) != null) {
 			sb.append(line).append(newline);
@@ -193,8 +193,8 @@ public static TreeMap<Integer,SpaceGroup> getAllSpaceGroups() {
 	 * @return
 	 */
 	public static TreeMap<Integer,SpaceGroup> parseSymopLib(InputStream symoplibIS) {
-		TreeMap<Integer, SpaceGroup> map = new TreeMap<Integer, SpaceGroup>();
-		name2sgs = new HashMap<String, SpaceGroup>();
+		TreeMap<Integer, SpaceGroup> map = new TreeMap<>();
+		name2sgs = new HashMap<>();
 		try {
 			BufferedReader br = new BufferedReader(new InputStreamReader(symoplibIS));
 			String line;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/TransformType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/TransformType.java
index a73ddb68cd..14ef3cb964 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/TransformType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/TransformType.java
@@ -52,13 +52,13 @@ public enum TransformType {
 
 
 
-	private int id;
-	private int foldType;
-	private boolean isScrew;
-	private boolean isInfinite;
-	private String shortName;
+	private final int id;
+	private final int foldType;
+	private final boolean isScrew;
+	private final boolean isInfinite;
+	private final String shortName;
 
-	private TransformType(int id, int foldType, boolean isScrew, boolean isInfinite, String shortName) {
+	TransformType(int id, int foldType, boolean isScrew, boolean isInfinite, String shortName) {
 		this.id = id;
 		this.foldType = foldType;
 		this.isScrew = isScrew;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/UnitCellBoundingBox.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/UnitCellBoundingBox.java
index fef02ce5cb..25e5ebe76a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/UnitCellBoundingBox.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/UnitCellBoundingBox.java
@@ -44,16 +44,16 @@ public class UnitCellBoundingBox {
 	 * bounding boxes of all chains of all AUs in unit cell
 	 * e.g. chainBbs[0] would be the bounding boxes for all chains in the original AU
 	 */
-	private BoundingBox[][] chainBbs;
+	private final BoundingBox[][] chainBbs;
 
 	/**
 	 * An array with dimensions numOperatorsSg to contain all bounding boxes of
 	 * all AUs in unit cell
 	 */
-	private BoundingBox[] auBbs;
+	private final BoundingBox[] auBbs;
 
-	private int numOperatorsSg; // i.e. multiplicity of space group
-	private int numPolyChainsAu;
+	private final int numOperatorsSg; // i.e. multiplicity of space group
+	private final int numPolyChainsAu;
 
 	public UnitCellBoundingBox(int numOperatorsSg, int numPolyChainsAu) {
 		this.numOperatorsSg = numOperatorsSg;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapAdapter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapAdapter.java
index 6c068f51e3..a3766ad9f6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapAdapter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapAdapter.java
@@ -31,7 +31,7 @@
 
 class SpaceGroupMapAdapter extends XmlAdapter<SpaceGroupMapElements[], Map<Integer, SpaceGroup>> {
 	@Override
-	public SpaceGroupMapElements[] marshal(Map<Integer, SpaceGroup> arg0) throws Exception {
+	public SpaceGroupMapElements[] marshal(Map<Integer, SpaceGroup> arg0) {
 		SpaceGroupMapElements[] mapElements = new SpaceGroupMapElements[arg0.size()];
 		int i = 0;
 		for (Map.Entry<Integer, SpaceGroup> entry : arg0.entrySet())
@@ -41,8 +41,8 @@ public SpaceGroupMapElements[] marshal(Map<Integer, SpaceGroup> arg0) throws Exc
 	}
 
 	@Override
-	public Map<Integer, SpaceGroup> unmarshal(SpaceGroupMapElements[] arg0) throws Exception {
-		Map<Integer, SpaceGroup> r = new TreeMap<Integer, SpaceGroup>();
+	public Map<Integer, SpaceGroup> unmarshal(SpaceGroupMapElements[] arg0) {
+		Map<Integer, SpaceGroup> r = new TreeMap<>();
 		for (SpaceGroupMapElements mapelement : arg0)
 			r.put(mapelement.key, mapelement.value);
 		return r;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.java
index e7998ee8dd..b457415f4a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.java
@@ -43,7 +43,7 @@ public class SpaceGroupMapRoot {
 	private TreeMap<Integer, SpaceGroup> mapProperty;
 
 	public SpaceGroupMapRoot() {
-		mapProperty = new TreeMap<Integer, SpaceGroup>();
+		mapProperty = new TreeMap<>();
 	}
 
 	@XmlJavaTypeAdapter(SpaceGroupMapAdapter.class)
@@ -72,7 +72,7 @@ public  String toXML() throws JAXBException {
 	}
 
 	public static SpaceGroupMapRoot fromXML(String xml) throws JAXBException{
-		SpaceGroupMapRoot job = null;
+		SpaceGroupMapRoot job;
 
 		JAXBContext jaxbContext = JAXBContext.newInstance(SpaceGroupMapRoot.class);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java
index 7e707002d8..eaef2dc30b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java
@@ -26,12 +26,13 @@
 
 import javax.xml.bind.annotation.adapters.XmlAdapter;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 public class TransfAlgebraicAdapter extends XmlAdapter<String[], List<String>>{
 
 	@Override
-	public String[] marshal(List<String> arg0) throws Exception {
+	public String[] marshal(List<String> arg0) {
 		String[] elements = new String[arg0.size()];
 		int i = 0;
 		for (String s : arg0)
@@ -40,10 +41,9 @@ public String[] marshal(List<String> arg0) throws Exception {
 	}
 
 	@Override
-	public List<String> unmarshal(String[] arg0) throws Exception {
-		List<String> l = new ArrayList<String>();
-		for (String s : arg0)
-			l.add(s);
+	public List<String> unmarshal(String[] arg0) {
+		List<String> l = new ArrayList<>();
+        l.addAll(Arrays.asList(arg0));
 		return l;
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TreeMapSpaceGroupWrapper.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TreeMapSpaceGroupWrapper.java
index 8aabe9b2f1..3a4d068cc4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TreeMapSpaceGroupWrapper.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TreeMapSpaceGroupWrapper.java
@@ -52,7 +52,7 @@ public class TreeMapSpaceGroupWrapper implements Serializable{
 
 
 	public TreeMapSpaceGroupWrapper(){
-		data = new TreeMap<Integer,SpaceGroup>();
+		data = new TreeMap<>();
 	}
 
 	public TreeMap<Integer,SpaceGroup> getData() {
@@ -85,7 +85,7 @@ public  String toXML() throws JAXBException{
 
 	public static TreeMapSpaceGroupWrapper fromXML(String xml) throws JAXBException{
 
-		TreeMapSpaceGroupWrapper job = null;
+		TreeMapSpaceGroupWrapper job;
 
 		JAXBContext jaxbContext = JAXBContext.newInstance(TreeMapSpaceGroupWrapper.class);
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/AtomPositionMapTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/AtomPositionMapTest.java
index f2b9a43437..45929ad5c1 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/AtomPositionMapTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/AtomPositionMapTest.java
@@ -29,6 +29,7 @@
 import org.junit.Test;
 
 import java.io.IOException;
+import java.util.Map;
 import java.util.NavigableMap;
 
 import static org.junit.Assert.*;
@@ -41,7 +42,7 @@
 public class AtomPositionMapTest {
 
 	@Before
-	public void setUp() throws Exception {
+	public void setUp() {
 		cache = new AtomCache(); // TODO Should mock instead of depending on real data from AtomCache
 		cache.setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior.FETCH_OBSOLETE);
 	}
@@ -62,8 +63,8 @@ public void testEasy() throws IOException, StructureException { // no insertion
 		ResidueNumber end = new ResidueNumber("A", 117, null);
 		AtomPositionMap map = new AtomPositionMap(cache.getAtoms(pdbId));
 		NavigableMap<ResidueNumber,Integer> navMap = map.getNavMap();
-		for (ResidueNumber n : navMap.keySet()) {
-			assertEquals("An element is missing", map.getPosition(n).intValue(), navMap.get(n).intValue());
+		for (Map.Entry<ResidueNumber, Integer> entry : navMap.entrySet()) {
+			assertEquals("An element is missing", map.getPosition(entry.getKey()).intValue(), entry.getValue().intValue());
 		}
 		int realLength = map.getLength(start, end);
 		assertEquals("Real atom length is wrong", length, realLength);
@@ -186,8 +187,8 @@ public void testInsertionCodes() throws IOException, StructureException {
 		AtomPositionMap map = new AtomPositionMap(cache.getAtoms(pdbId));
 		NavigableMap<ResidueNumber,Integer> navMap = map.getNavMap();
 
-		for (ResidueNumber n : navMap.keySet()) {
-			assertEquals("An element is missing", map.getPosition(n).intValue(), navMap.get(n).intValue());
+		for (Map.Entry<ResidueNumber, Integer> entry : navMap.entrySet()) {
+			assertEquals("An element is missing", map.getPosition(entry.getKey()).intValue(), entry.getValue().intValue());
 		}
 
 		int length1 = 60; // 2+37+21
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/ChemCompTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/ChemCompTest.java
index fd37644fd4..87a0da7ace 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/ChemCompTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/ChemCompTest.java
@@ -45,7 +45,7 @@ public void testALA(){
 
 		assertNotNull("residue type has not been set!", cc.getResidueType());
 
-		assertTrue (" is not amino ", cc.getResidueType().equals(ResidueType.lPeptideLinking));
+        assertEquals(" is not amino ", cc.getResidueType(), ResidueType.lPeptideLinking);
 	}
 
 	@Test
@@ -67,7 +67,7 @@ public void testMEA(){
 
 		assertNotNull(cc);
 
-		assertTrue(" is not mea" , cc.getId().equals(chemID));
+        assertEquals(" is not mea", cc.getId(), chemID);
 
 		assertEquals(" one letter code is not correct", "F", cc.getOne_letter_code());
 
@@ -79,11 +79,11 @@ public void testMEA(){
 
 		assertNotNull("residue type has not been set!", cc.getResidueType());
 
-		assertTrue (" is not amino ", cc.getResidueType().equals(ResidueType.lPeptideLinking));
+        assertEquals(" is not amino ", cc.getResidueType(), ResidueType.lPeptideLinking);
 
 		Group g = ChemCompGroupFactory.getGroupFromChemCompDictionary(chemID);
 
-		assertTrue( g.getType().equals(GroupType.AMINOACID));
+        assertEquals(g.getType(), GroupType.AMINOACID);
 
 		ChemCompGroupFactory.setChemCompProvider(oldProvider);
 	}
@@ -107,7 +107,7 @@ public void testPRR(){
 
 		assertNotNull(aa.getAminoType());
 
-		assertTrue(aa.getAminoType().equals('X'));
+        assertEquals('X', (char) aa.getAminoType());
 
 		ChemCompGroupFactory.setChemCompProvider(oldProvider);
 
@@ -127,7 +127,7 @@ public void testChangingProviders(){
 
 	assertNotNull(cc);
 
-	assertTrue(" is not mea" , cc.getId().equals(chemID));
+        assertEquals(" is not mea", cc.getId(), chemID);
 
 	assertTrue(cc.isEmpty());
 
@@ -139,7 +139,7 @@ public void testChangingProviders(){
 
 	assertNotNull(cc);
 
-	assertTrue(" is not mea" , cc.getId().equals(chemID));
+        assertEquals(" is not mea", cc.getId(), chemID);
 
 	assertEquals("MEA",cc.getThree_letter_code());
 
@@ -155,7 +155,7 @@ public void testChangingProviders(){
 
 	assertNotNull(cc);
 
-	assertTrue(" is not mea" , cc.getId().equals(chemID));
+        assertEquals(" is not mea", cc.getId(), chemID);
 
 	assertEquals("MEA",cc.getThree_letter_code());
 
@@ -166,7 +166,7 @@ public void testChangingProviders(){
 
 	assertNotNull(cc);
 
-	assertTrue(" is not mea" , cc.getId().equals(chemID));
+        assertEquals(" is not mea", cc.getId(), chemID);
 
 	//the cached description contains all information even with the ReducedProvider
 	assertNotNull(cc.getThree_letter_code());
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/ElementTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/ElementTest.java
index 81ce22d087..cef25fb307 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/ElementTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/ElementTest.java
@@ -21,7 +21,6 @@
 
 package org.biojava.nbio.structure;
 
-import junit.framework.TestCase;
 import org.junit.Assert;
 import org.junit.Test;
 
@@ -57,9 +56,9 @@ public void testIsMetal() {
 		Assert.assertTrue(la.isMetal());
 		Element ac = Element.Ac;
 		Assert.assertTrue(ac.isMetal());
-	};
+	}
 
-	@Test
+    @Test
 	public void testIsMetalloid() {
 		Element h = Element.H;
 		Assert.assertFalse(h.isMetalloid());
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/HetatomImplTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/HetatomImplTest.java
index 74556c2434..3c9b89e49b 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/HetatomImplTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/HetatomImplTest.java
@@ -33,18 +33,18 @@
  */
 public class HetatomImplTest {
 
-	private int bigTestNumber = 60000;
+	private final int bigTestNumber = 60000;
 
 	public HetatomImplTest() {
 
 	}
 
 	@BeforeClass
-	public static void setUpClass() throws Exception {
+	public static void setUpClass() {
 	}
 
 	@AfterClass
-	public static void tearDownClass() throws Exception {
+	public static void tearDownClass() {
 	}
 
 	@Before
@@ -520,7 +520,7 @@ public void testSetGetResidueNumber() {
 	@Test
 	public void testGetResidueNumberUsage() {
 //        System.out.println("testGetResidueNumberUsage");
-		List<Group> resNumgroups = new ArrayList<Group>();
+		List<Group> resNumgroups = new ArrayList<>();
 
 		for (int i = 0; i < bigTestNumber; i++) {
 			ResidueNumber resNum = new ResidueNumber("A", i, ' ');
@@ -529,7 +529,7 @@ public void testGetResidueNumberUsage() {
 			resNumgroups.add(hetAtom);
 		}
 
-		List<Integer> integers = new ArrayList<Integer>();
+		List<Integer> integers = new ArrayList<>();
 
 		for (Group group : resNumgroups) {
 			ResidueNumber resnum = group.getResidueNumber();
@@ -541,7 +541,7 @@ public void testGetResidueNumberUsage() {
 	@Test
 	public void testSetResidueNumberUsage() {
 
-		List<Group> resNumgroups = new ArrayList<Group>();
+		List<Group> resNumgroups = new ArrayList<>();
 
 		for (int i = 0; i < bigTestNumber; i++) {
 			ResidueNumber resNum = new ResidueNumber("A", i, ' ');
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java
index 8bcd2d1e98..4d4813ff10 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java
@@ -54,15 +54,15 @@ public void testGetStatus() {
 
 	@Test
 	public void testGetReplacement() {
-		Assert.assertFalse(Arrays.asList("YES").equals(Arrays.asList("NO"))); //check for deep equals
+		Assert.assertNotEquals(Arrays.asList("YES"), Arrays.asList("NO")); //check for deep equals
 
 		// 1CMW is replacedBy NONE
-		Assert.assertEquals(Arrays.asList(), PDBStatus.getReplacement("1CMW", true, false));
-		Assert.assertEquals(Arrays.asList("1CMW"), PDBStatus.getReplacement("1CMW", true, true));
+		Assert.assertEquals(Collections.emptyList(), PDBStatus.getReplacement("1CMW", true, false));
+		Assert.assertEquals(Collections.singletonList("1CMW"), PDBStatus.getReplacement("1CMW", true, true));
 
 		// 1HHB is replacedBy 2-4HHB
-		Assert.assertEquals(Arrays.asList("3HHB"), PDBStatus.getReplacement("3HHB", false, false));
-		Assert.assertEquals(Arrays.asList("3HHB"), PDBStatus.getReplacement("3HHB", false, true));
+		Assert.assertEquals(Collections.singletonList("3HHB"), PDBStatus.getReplacement("3HHB", false, false));
+		Assert.assertEquals(Collections.singletonList("3HHB"), PDBStatus.getReplacement("3HHB", false, true));
 		Assert.assertEquals(Arrays.asList("4HHB", "3HHB", "2HHB"), PDBStatus.getReplacement("1HHB", false, false));
 		Assert.assertEquals(Arrays.asList("4HHB", "3HHB", "2HHB", "1HHB"), PDBStatus.getReplacement("1HHB", false, true));
 
@@ -78,7 +78,7 @@ public void testGetReplacement() {
 	public void testGetCurrent() {
 		Assert.assertEquals("4HHB", PDBStatus.getCurrent("1HHB"));
 		Assert.assertEquals("3HHB", PDBStatus.getCurrent("3HHB"));
-		Assert.assertEquals(null, PDBStatus.getCurrent("1CMW"));
+		Assert.assertNull(PDBStatus.getCurrent("1CMW"));
 		Assert.assertEquals("3ENI", PDBStatus.getCurrent("1KSA"));
 		Assert.assertEquals("8CAT", PDBStatus.getCurrent("1CAT"));
 		Assert.assertEquals("8CAT", PDBStatus.getCurrent("3CAT"));
@@ -87,14 +87,14 @@ public void testGetCurrent() {
 
 	@Test
 	public void testGetReplaces() {
-		Assert.assertEquals(new ArrayList<String>(), Arrays.asList(new String[]{}));
+		Assert.assertEquals(new ArrayList<String>(), Collections.emptyList());
 
-		Assert.assertEquals(Arrays.asList("1HHB"), PDBStatus.getReplaces("4HHB", false));
-		Assert.assertEquals(Arrays.asList("1HHB"), PDBStatus.getReplaces("3HHB", false));
-		Assert.assertEquals(Arrays.asList(), PDBStatus.getReplaces("1HHB", false));
+		Assert.assertEquals(Collections.singletonList("1HHB"), PDBStatus.getReplaces("4HHB", false));
+		Assert.assertEquals(Collections.singletonList("1HHB"), PDBStatus.getReplaces("3HHB", false));
+		Assert.assertEquals(Collections.emptyList(), PDBStatus.getReplaces("1HHB", false));
 		Assert.assertEquals(Arrays.asList("1M50", "1KSA"), PDBStatus.getReplaces("3ENI", false));
 		Assert.assertEquals(Arrays.asList("1M50", "1KSA"), PDBStatus.getReplaces("3ENI", true));
-		Assert.assertEquals(Arrays.asList("3CAT"), PDBStatus.getReplaces("8CAT", false));
+		Assert.assertEquals(Collections.singletonList("3CAT"), PDBStatus.getReplaces("8CAT", false));
 		Assert.assertEquals(Arrays.asList("3CAT", "1CAT"), PDBStatus.getReplaces("8CAT", true));
 
 	}
@@ -113,37 +113,37 @@ public void testMergeReversed() {
 			List<String> a,b;
 
 			b = Arrays.asList("F","A");
-			a = new LinkedList<String>();
+			a = new LinkedList<>();
 			mergeReversed.invoke(null, a,b);
 			Assert.assertEquals(Arrays.asList("F", "A"), a);
 
-			a = new LinkedList<String>();
+			a = new LinkedList<>();
 			a.add("B");
 			mergeReversed.invoke(null, a,b);
 			Assert.assertEquals(Arrays.asList("F", "B", "A"), a);
 
-			a = new LinkedList<String>();
+			a = new LinkedList<>();
 			a.add("G");
 			mergeReversed.invoke(null, a,b);
 			Assert.assertEquals(Arrays.asList("G", "F", "A"), a);
 
-			a = new LinkedList<String>();
+			a = new LinkedList<>();
 			a.add("1");
 			mergeReversed.invoke(null, a,b);
 			Assert.assertEquals(Arrays.asList("F", "A", "1"), a);
 
-			a = new LinkedList<String>();
+			a = new LinkedList<>();
 			a.add("G");
 			a.add("1");
 			mergeReversed.invoke(null, a,b);
 			Assert.assertEquals(Arrays.asList("G", "F", "A", "1"), a);
 
-			b = Arrays.asList();
+			b = Collections.emptyList();
 			mergeReversed.invoke(null, a,b);
 			Assert.assertEquals(Arrays.asList("G", "F", "A", "1"), a);
 
 			b = Arrays.asList("G","D","C","A");
-			a = new LinkedList<String>();
+			a = new LinkedList<>();
 			a.add("F");
 			a.add("B");
 			a.add("1");
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/PdbFileFormat30Test.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/PdbFileFormat30Test.java
index 9daf7d7e18..a2351cfa71 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/PdbFileFormat30Test.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/PdbFileFormat30Test.java
@@ -114,7 +114,7 @@ private Structure getStructure(String fileName) throws IOException{
 		FileParsingParameters params = new FileParsingParameters();
 		params.setAlignSeqRes(false);
 		pdbpars.setFileParsingParameters(params);
-		Structure structure = null;
+		Structure structure;
 
 		structure = pdbpars.parsePDBFile(inStream) ;
 
@@ -153,7 +153,7 @@ public void testIsLegacyFormat_pdb_COMPND_handler() throws IOException{
 		// thus here we have the one specified in header plus a SO4 nonpolymer entity
 		assertEquals(2, compounds.size());
 		EntityInfo mol = compounds.get(0);
-		assertTrue(mol.getDescription().equals("6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE"));
+        assertEquals("6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE", mol.getDescription());
 		assertEquals(60, mol.getChainIds().size());
 		assertEquals(60, mol.getChains().size());
 		assertTrue(isChainNameInEntity(mol,"S"));
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueNumberTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueNumberTest.java
index c594f0dd18..5790756cb6 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueNumberTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueNumberTest.java
@@ -37,11 +37,11 @@ public ResidueNumberTest() {
 	}
 
 	@BeforeClass
-	public static void setUpClass() throws Exception {
+	public static void setUpClass() {
 	}
 
 	@AfterClass
-	public static void tearDownClass() throws Exception {
+	public static void tearDownClass() {
 	}
 
 	@Before
@@ -102,7 +102,7 @@ public void testEquals() {
 		boolean result = number2.equals(number1);
 		Assert.assertEquals(expResult, result);
 
-		Set<ResidueNumber> numberSet= new HashSet<ResidueNumber>();
+		Set<ResidueNumber> numberSet= new HashSet<>();
 		numberSet.add(number1);
 		numberSet.add(number2);
 		Assert.assertEquals(1, numberSet.size());
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueRangeTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueRangeTest.java
index 7e5d7aeaa1..721d19d41c 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueRangeTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueRangeTest.java
@@ -46,7 +46,7 @@ public class ResidueRangeTest {
 	private AtomCache cache;
 
 	@Before
-	public void setUp() throws Exception {
+	public void setUp() {
 		cache = new AtomCache(); // TODO Should mock instead of depending on
 		// real data from AtomCache
 		cache.setObsoleteBehavior(ObsoleteBehavior.FETCH_OBSOLETE);
@@ -90,7 +90,7 @@ public void testWholeChainWithMap() throws IOException, StructureException {
 	 * Tests creating ResidueRanges and calculating their lengths.
 	 */
 	@Test
-	public void testWithLengths() throws IOException, StructureException {
+	public void testWithLengths() {
 		String[] ids = new String[] { "1w0p", "3qq3", "3chc", "2ei7" }; // more:
 		// ,
 		// "2qbr"
@@ -107,7 +107,7 @@ public void testWithLengths() throws IOException, StructureException {
 				new ResidueNumber("L", 254, 't') };
 		int[] lengths = new int[] { 117 - 5, 200 - 10, 111, 55 };
 		int totalLength = 0;
-		List<ResidueRangeAndLength> ranges = new ArrayList<ResidueRangeAndLength>(
+		List<ResidueRangeAndLength> ranges = new ArrayList<>(
 				ids.length);
 		for (int i = 0; i < ids.length; i++) {
 			ResidueRangeAndLength rr = new ResidueRangeAndLength(chains[i],
@@ -261,12 +261,12 @@ public void testParseAndEqual() {
 	}
 
 	@Test(expected=IllegalArgumentException.class)
-	public void testBadSyntax() throws IOException, StructureException {
+	public void testBadSyntax() {
 		ResidueRange.parse("-");
 	}
 
 	@Test
-	public void testPartialRange() throws IOException, StructureException {
+	public void testPartialRange() {
 		String rangeStr = "C_1023-";
 		ResidueRange range = ResidueRange.parse(rangeStr);
 		assertEquals(rangeStr,1023,(int)range.getStart().getSeqNum());
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/SiteTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/SiteTest.java
index d7a64d0017..98db2c906f 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/SiteTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/SiteTest.java
@@ -63,7 +63,7 @@ public SiteTest() {
 		ser195.setResidueNumber("H", 195, ' ');
 		ser195.setPDBName("SER");
 		ser195.setChain(chain);
-		List<Group> catSiteGroups = new ArrayList<Group>();
+		List<Group> catSiteGroups = new ArrayList<>();
 		catSiteGroups.add(his57);
 		catSiteGroups.add(asp102);
 		catSiteGroups.add(ser195);
@@ -99,7 +99,7 @@ public SiteTest() {
 		hoh497.setPDBName("HOH");
 		hoh497.setChain(chain);
 
-		bindingSiteGroups = new ArrayList<Group>();
+		bindingSiteGroups = new ArrayList<>();
 
 		bindingSiteGroups.add(arg221a);
 		bindingSiteGroups.add(lys224);
@@ -118,11 +118,11 @@ public SiteTest() {
 	}
 
 	@BeforeClass
-	public static void setUpClass() throws Exception {
+	public static void setUpClass() {
 	}
 
 	@AfterClass
-	public static void tearDownClass() throws Exception {
+	public static void tearDownClass() {
 	}
 
 	@Before
@@ -155,7 +155,7 @@ public void testToPDB_0args() {
 	@Test
 	public void testToPDB_StringBuffer() {
 //        System.out.println("toPDB");
-		StringBuffer buf = new StringBuffer("");
+		StringBuffer buf = new StringBuffer();
 		String expResult =  "SITE     1 AC1  6 ARG H 221A LYS H 224  HOH H 403  HOH H 460                    " + newline +
 							"SITE     2 AC1  6 HOH H 464  HOH H 497                                          "+ newline;
 		bindingSite.toPDB(buf);
@@ -188,7 +188,7 @@ public void testRemark800ToPDB_0args() {
 	@Test
 	public void testRemark800ToPDB_StringBuffer() {
 //        System.out.println("remark800toPDB");
-		StringBuffer buf = new StringBuffer("");
+		StringBuffer buf = new StringBuffer();
 		String expResult =  "REMARK 800 SITE_IDENTIFIER: CAT                                                 " + newline +
 							"REMARK 800 EVIDENCE_CODE: UNKNOWN                                               " + newline +
 							"REMARK 800 SITE_DESCRIPTION: ACTIVE SITE                                        " + newline;
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/Test4hhb.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/Test4hhb.java
index afb5de1d59..920346c1a9 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/Test4hhb.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/Test4hhb.java
@@ -49,7 +49,7 @@ public class Test4hhb {
 	public void test4hhbPDBFile() throws IOException
 	{
 
-		Structure structure = null;
+		Structure structure;
 
 		InputStream inStream = new GZIPInputStream(this.getClass().getResourceAsStream("/4hhb.pdb.gz"));
 		assertNotNull(inStream);
@@ -70,7 +70,7 @@ public void test4hhbPDBFile() throws IOException
 		testStructure(structure);
 
 
-		Structure structure2 = null;
+		Structure structure2;
 
 		inStream = new GZIPInputStream(this.getClass().getResourceAsStream("/4hhb.cif.gz"));
 		assertNotNull(inStream);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java
index d1c6779e7c..eb2a6d1cda 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java
@@ -58,28 +58,11 @@ public void testAltLocParsing() throws StructureException, IOException{
 		List<Group> groups = a.getAtomGroups();
 		for (Group g : groups){
 			ChemComp cc = g.getChemComp();
-			if ( ResidueType.lPeptideLinking.equals(cc.getResidueType()) ||
-					PolymerType.PROTEIN_ONLY.contains(cc.getPolymerType()) ||
-					PolymerType.POLYNUCLEOTIDE_ONLY.contains(cc.getPolymerType())
-					){
-				if (! g.isWater()) {
-					//System.out.println(g);
-					groupCount ++;
-				}
-			} else {
-				// when using the Reduced Chem Comp provider
-				// there are 3 groups in 2CI1 which are non-standard: SNC, KOR, CIT
-				// they are not in the reduced set of standard definitions that will
-				// be shipped in the .jar file.
-
-				// if the download chem comp provider is used
-				// there will be CIT, which is not a peptide, but
-				// should still be counted as a valid HETATOM group...
-				if (! g.isWater()) {
-					//System.out.println(cc);
-					//System.out.println(g);
-					groupCount++;
-				}
+			//System.out.println(cc);
+			//System.out.println(g);
+			if (! g.isWater()) {
+				//System.out.println(g);
+				groupCount ++;
 			}
 		}
 
@@ -274,7 +257,7 @@ public void test3PIUpdb() throws IOException, StructureException{
 
 		//System.out.println(structure.getPdbId() + " has # CA atoms: " + ca.length);
 
-		List<Atom> caList = new ArrayList<Atom>();
+		List<Atom> caList = new ArrayList<>();
 		for ( Chain c: structure.getChains()){
 			for (Group g: c.getAtomGroups()){
 
@@ -384,9 +367,7 @@ public void testAddBondsDoesntChangeGroups() throws IOException, StructureExcept
 				// Now add support for altLocGroup
 				List<Atom> atomsList = new ArrayList<>(mainGroup.getAtoms());
 				for(Group altLocOne: mainGroup.getAltLocs()){
-					for(Atom atomAltLocOne: altLocOne.getAtoms()){
-						atomsList.add(atomAltLocOne);
-					}
+                    atomsList.addAll(altLocOne.getAtoms());
 				}
 				// Get the chem copm
 				ChemComp aminoChemComp = ChemCompGroupFactory.getChemComp(mainGroup
@@ -439,7 +420,7 @@ public void test4CUPBonds() throws IOException, StructureException{
 		Atom[] ca = StructureTools.getAtomCAArray(structure);
 
 
-		List<Atom> caList = new ArrayList<Atom>();
+		List<Atom> caList = new ArrayList<>();
 		for ( Chain c: structure.getChains()){
 			for (Group g: c.getAtomGroups()){
 
@@ -501,7 +482,7 @@ public void test3PIUmmcif() throws IOException, StructureException{
 
 		//System.out.println(structure.getPdbId() + " has # CA atoms: " + ca.length);
 
-		List<Atom> caList = new ArrayList<Atom>();
+		List<Atom> caList = new ArrayList<>();
 		for ( Chain c: structure.getChains()){
 			for (Group g: c.getAtomGroups()){
 
@@ -564,7 +545,7 @@ public void test3U7Tmmcif() throws IOException, StructureException{
 
 		//System.out.println(structure.getPdbId() + " has # CA atoms: " + ca.length);
 
-		List<Atom> caList = new ArrayList<Atom>();
+		List<Atom> caList = new ArrayList<>();
 		for ( Chain c: structure.getChains()){
 			// notice here we test the seqresgroups, because we want to check if microheterogeinity is treated correctly
 			for (Group g: c.getSeqResGroups()){
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java
index bb46670bae..25003b4122 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java
@@ -54,7 +54,7 @@ public void setUp() throws IOException {
 				"1cmw", "1hhb","4hhb"
 		};
 
-		List<LocalPDBDirectory> readers = new ArrayList<LocalPDBDirectory>();
+		List<LocalPDBDirectory> readers = new ArrayList<>();
 		readers.add(new MMCIFFileReader(cache.getPath()) );
 		readers.add(new PDBFileReader(cache.getPath()) );
 		for(LocalPDBDirectory reader : readers) {
@@ -162,7 +162,7 @@ public void testObsoleteId() throws StructureException, IOException {
 
 	// note: we expect an IOException because 1CMW is obsolete and hasn't got a replacement
 	@Test
-	public void testFetchCurrent1CMW() throws IOException, StructureException {
+	public void testFetchCurrent1CMW() throws StructureException {
 
 		cache.setFetchBehavior(FetchBehavior.FETCH_FILES);
 		cache.setObsoleteBehavior(ObsoleteBehavior.FETCH_CURRENT);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java
index ac8b728d93..0b9d7f7860 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java
@@ -149,7 +149,7 @@ public void test3piuCloning() throws StructureException, IOException {
 		compareCloned(s, c);
 	}
 
-	private void compareCloned(final Structure s, final Structure c) throws StructureException {
+	private void compareCloned(final Structure s, final Structure c) {
 
 		assertEquals(s.getChains().size(), c.getChains().size());
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDownloadChemCompProvider.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDownloadChemCompProvider.java
index bc2a8dcd41..96508dc551 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDownloadChemCompProvider.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDownloadChemCompProvider.java
@@ -21,7 +21,6 @@
 package org.biojava.nbio.structure;
 
 import org.biojava.nbio.core.util.FlatFileCache;
-import org.biojava.nbio.structure.io.LocalPDBDirectory;
 import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.junit.Test;
@@ -96,7 +95,7 @@ public void testWeDontCacheGarbage() {
 		ChemComp cc = prov.getChemComp("HEM");
 
 		// we got a 404 back from server so we shouldn't have cached a file
-		assertTrue(!file.exists());
+		assertFalse(file.exists());
 
 		file.delete();
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java
index 4f798834d3..f2459bbc85 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java
@@ -49,7 +49,7 @@ public class TestEntityHeuristics {
 	//}
 
 	@Test
-	public void test1b8gRaw() throws IOException, StructureException {
+	public void test1b8gRaw() throws IOException {
 
 		Structure s = getStructure("1b8g_raw.pdb.gz", true);
 
@@ -81,7 +81,7 @@ public void test1b8gRaw() throws IOException, StructureException {
 
 
 	@Test
-	public void test2m7yRaw() throws IOException, StructureException {
+	public void test2m7yRaw() throws IOException {
 
 		Structure s = getStructure("2m7y_raw.pdb.gz", true);
 
@@ -112,7 +112,7 @@ public void test2m7yRaw() throws IOException, StructureException {
 	}
 
 	@Test
-	public void test3c5fRaw() throws IOException, StructureException {
+	public void test3c5fRaw() throws IOException {
 
 		Structure s = getStructure("3c5f_raw.pdb.gz", true);
 
@@ -153,7 +153,7 @@ public void test3c5fRaw() throws IOException, StructureException {
 	}
 
 	@Test
-	public void test4b19Raw() throws IOException, StructureException {
+	public void test4b19Raw() throws IOException {
 
 		Structure s = getStructure("4b19_raw.pdb.gz", true);
 
@@ -184,7 +184,7 @@ public void test4b19Raw() throws IOException, StructureException {
 	}
 
 	@Test
-	public void test3ddoNoseqres() throws IOException, StructureException {
+	public void test3ddoNoseqres() throws IOException {
 
 		// 3ddo contains 6 chains in 1 entity, with residue numbering completely different in each of the chains
 
@@ -207,7 +207,7 @@ public void test3ddoNoseqres() throws IOException, StructureException {
 	}
 
 	@Test
-	public void test3ddoSeqres() throws IOException, StructureException {
+	public void test3ddoSeqres() throws IOException {
 
 		// 3ddo contains 6 chains in 1 entity, with residue numbering completely different in each of the chains
 
@@ -245,13 +245,7 @@ private Structure getStructure(String fileName, boolean setAlignSeqRes) throws I
 
 	private void checkEntitiesNumbered(List<EntityInfo> entities) {
 
-		Collections.sort(entities, new Comparator<EntityInfo>() {
-
-			@Override
-			public int compare(EntityInfo o1, EntityInfo o2) {
-				return new Integer(o1.getMolId()).compareTo(o2.getMolId());
-			}
-		});
+		entities.sort((o1, o2) -> new Integer(o1.getMolId()).compareTo(o2.getMolId()));
 
 		int id = 1;
 		for (EntityInfo compound:entities) {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestNucleotides.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestNucleotides.java
index dc865eb366..abb78dcaad 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestNucleotides.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestNucleotides.java
@@ -137,7 +137,7 @@ private Structure getStructure(String pdbId) throws IOException, StructureExcept
 	}
 
 	@Test
-	public void test1REP() throws StructureException, IOException{
+	public void test1REP() throws IOException{
 
 		PDBFileReader reader = new PDBFileReader();
 		FileParsingParameters params = new FileParsingParameters();
@@ -164,16 +164,16 @@ public void test1REP() throws StructureException, IOException{
 
 
 		assertNotNull("Could not acces Chem Comp file!" , n1.getChemComp());
-		assertTrue("ChemComp is not DC",n1.getChemComp().getId().equals("DC"));
+		assertEquals("ChemComp is not DC", "DC", n1.getChemComp().getId());
 		assertNotNull("Could not determine polymer type " , n1.getChemComp().getPolymerType());
 		//System.out.println(n1.getChemComp().getPolymerType());
-		assertTrue(n1.getChemComp().getPolymerType().equals(PolymerType.dna));
+		assertEquals(n1.getChemComp().getPolymerType(), PolymerType.dna);
 
 		assertNotNull(n1.getPDBName());
 		assertNotNull(n1.getResidueNumber());
 		assertNotNull(n2.getResidueNumber());
 		assertEquals("23", n2.getResidueNumber().toString());
-		assertTrue(n1.getResidueNumber().equals(n2.getResidueNumber()));
+		assertEquals(n1.getResidueNumber(), n2.getResidueNumber());
 
 
 	}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestParsingCalcium.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestParsingCalcium.java
index 783ca74dba..1670bc3f21 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestParsingCalcium.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestParsingCalcium.java
@@ -29,8 +29,7 @@
 
 import java.io.IOException;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
 
 
 public class TestParsingCalcium {
@@ -81,15 +80,15 @@ public void testCAreturnsCalpha() throws IOException, StructureException {
 
 		Atom[] atoms = StructureTools.getRepresentativeAtomArray(s);
 		for (Atom atom:atoms) {
-			assertTrue("atom "+atom.getPDBserial()+" of residue "+atom.getGroup().getResidueNumber()+"-"+atom.getGroup().getPDBName()+
-					" is not a Carbon alpha", atom.getElement()==Element.C);
+            assertSame("atom " + atom.getPDBserial() + " of residue " + atom.getGroup().getResidueNumber() + "-" + atom.getGroup().getPDBName() +
+                    " is not a Carbon alpha", atom.getElement(), Element.C);
 		}
 
 		for (Chain c:s.getChains()) {
 			atoms = StructureTools.getRepresentativeAtomArray(c);
 			for (Atom atom:atoms) {
-				assertTrue("atom "+atom.getPDBserial()+" of residue "+atom.getGroup().getResidueNumber()+"-"+atom.getGroup().getPDBName()+
-						" is not a Carbon alpha", atom.getElement()==Element.C);
+                assertSame("atom " + atom.getPDBserial() + " of residue " + atom.getGroup().getResidueNumber() + "-" + atom.getGroup().getPDBName() +
+                        " is not a Carbon alpha", atom.getElement(), Element.C);
 			}
 		}
 
@@ -104,7 +103,7 @@ public void testCAreturnsCalpha() throws IOException, StructureException {
 					atom.getElement()==Element.O ||
 					atom.getElement()==Element.N    );
 
-			assertTrue("backbone atoms should not contain CB atoms",!atom.getName().equals("CB"));
+            assertFalse("backbone atoms should not contain CB atoms", atom.getName().equals("CB"));
 
 			if (atom.getGroup().getPDBName().equals("GLY")) {
 				hasGlycine = true;
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java
index d2c5b2d0b8..3622561e2e 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java
@@ -139,7 +139,7 @@ public void testCrossReferencesPdbAlignSeqRes() throws IOException, StructureExc
 	}
 
 	//@Test
-	public void testCrossReferencesRawFile() throws IOException, StructureException {
+	public void testCrossReferencesRawFile() {
 		// TODO implement
 	}
 
@@ -194,7 +194,7 @@ private void doFullTest(Structure structure, boolean emptySeqRes) throws Structu
 		testStructureRefs(structure, emptySeqRes);
 	}
 
-	private void testStructureRefs(Structure s, boolean emptySeqRes) throws StructureException {
+	private void testStructureRefs(Structure s, boolean emptySeqRes) {
 
 		// structure, chain, group, atom linking
 		for (Chain c:s.getChains()) {
@@ -265,7 +265,7 @@ private void testAtomArrayRefs(Atom[] atoms, Chain c) {
 
 	}
 
-	private void testInterfaceRefs(Structure s, StructureInterface i) throws StructureException {
+	private void testInterfaceRefs(Structure s, StructureInterface i) {
 
 		for (Atom a:i.getMolecules().getFirst()) {
 			assertNotNull(a.getGroup().getChain().getEntityInfo());
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureImpl.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureImpl.java
index b38fbd95de..14ab6e6abf 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureImpl.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureImpl.java
@@ -47,7 +47,7 @@ public void testLinks() {
 
 		// Create new Structure and assign one Chain to it
 		Structure s1 = new StructureImpl();
-		s1.addModel(new ArrayList<Chain>(1));
+		s1.addModel(new ArrayList<>(1));
 
 		Chain c1 = new ChainImpl();
 		s1.addChain(c1);
@@ -73,7 +73,7 @@ public void testLinks() {
 		Atom a2 = (Atom) a1.clone();
 
 		Structure s2 = new StructureImpl();
-		s2.addModel(new ArrayList<Chain>(1));
+		s2.addModel(new ArrayList<>(1));
 		Chain c2 = new ChainImpl();
 		s2.addChain(c2);
 		Group g2 = new HetatomImpl();
@@ -88,7 +88,7 @@ public void testLinks() {
 		Group g3 = (Group) g1.clone();
 		Atom a3 = g3.getAtom(0);
 		Structure s3 = new StructureImpl();
-		s3.addModel(new ArrayList<Chain>(1));
+		s3.addModel(new ArrayList<>(1));
 		Chain c3 = new ChainImpl();
 		s3.addChain(c3);
 		c3.addGroup(g3);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureSerialization.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureSerialization.java
index f0a3e89bee..8eb7d584a8 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureSerialization.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureSerialization.java
@@ -40,7 +40,7 @@
 public class TestStructureSerialization {
 
 	@Test
-	public void testSerializeStructure() throws IOException, StructureException, ClassNotFoundException {
+	public void testSerializeStructure() throws IOException, ClassNotFoundException {
 
 		PDBFileReader reader = new PDBFileReader();
 		reader.getFileParsingParameters().setParseSecStruc(true);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestVeryLongFileName.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestVeryLongFileName.java
index 4fe347e3b8..10fdc35a38 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestVeryLongFileName.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestVeryLongFileName.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.structure;
 
-import org.junit.Assert;
 import org.junit.Test;
 
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java
index 0d76dc98ce..1069a32126 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java
@@ -81,7 +81,7 @@ public void testFilterDuplicateAFPs() throws Exception {
 		int[] expectedLen = new int[] { expected[0][0].length, expected[1][0].length };
 
 		Assert.assertTrue(Arrays.deepEquals(expected, align));
-		Assert.assertTrue(Arrays.equals(expectedLen, blkLen));
+		Assert.assertArrayEquals(expectedLen, blkLen);
 
 	}
 
@@ -129,7 +129,7 @@ public void testFilterDuplicateAFPsMinLenCTerm() throws PDBParseException, Struc
 			result = CeCPMain.filterDuplicateAFPs(afpChain, new CECalculator(null), ca1, ca2,params);
 
 			Assert.assertTrue("Wrong optAln for minCPlength=" + minCPlength, Arrays.deepEquals(filteredAln, result.getOptAln()));
-			Assert.assertTrue("Wrong optLen for minCPlength=" + minCPlength, Arrays.equals(filteredLen, result.getOptLen()));
+			Assert.assertArrayEquals("Wrong optLen for minCPlength=" + minCPlength, filteredLen, result.getOptLen());
 	}
 
 		// For minCPlength=4, filtering changes
@@ -149,7 +149,7 @@ public void testFilterDuplicateAFPsMinLenCTerm() throws PDBParseException, Struc
 		result = CeCPMain.filterDuplicateAFPs(afpChain, new CECalculator(null), ca1, ca2,params);
 
 		Assert.assertTrue("Wrong optAln for minCPlength=" + params.getMinCPLength(), Arrays.deepEquals(filteredAln, result.getOptAln()));
-		Assert.assertTrue("Wrong optLen for minCPlength=" + params.getMinCPLength(), Arrays.equals(filteredLen, result.getOptLen()));
+		Assert.assertArrayEquals("Wrong optLen for minCPlength=" + params.getMinCPLength(), filteredLen, result.getOptLen());
 
 		// For minCPlength=5, filtering changes
 		params.setMinCPLength(5);
@@ -164,13 +164,13 @@ public void testFilterDuplicateAFPsMinLenCTerm() throws PDBParseException, Struc
 		result = CeCPMain.filterDuplicateAFPs(afpChain, new CECalculator(null), ca1, ca2,params);
 
 		Assert.assertTrue("Wrong optAln for minCPlength=" + params.getMinCPLength(), Arrays.deepEquals(filteredAln, result.getOptAln()));
-		Assert.assertTrue("Wrong optLen for minCPlength=" + params.getMinCPLength(), Arrays.equals(filteredLen, result.getOptLen()));
+		Assert.assertArrayEquals("Wrong optLen for minCPlength=" + params.getMinCPLength(), filteredLen, result.getOptLen());
 
 		params.setMinCPLength(7);
 		result = CeCPMain.filterDuplicateAFPs(afpChain, new CECalculator(null), ca1, ca2,params);
 
 		Assert.assertTrue("Wrong optAln for minCPlength=" + params.getMinCPLength(), Arrays.deepEquals(filteredAln, result.getOptAln()));
-		Assert.assertTrue("Wrong optLen for minCPlength=" + params.getMinCPLength(), Arrays.equals(filteredLen, result.getOptLen()));
+		Assert.assertArrayEquals("Wrong optLen for minCPlength=" + params.getMinCPLength(), filteredLen, result.getOptLen());
 
 		// Eventually, no alignment!
 		params.setMinCPLength(8);
@@ -181,7 +181,7 @@ public void testFilterDuplicateAFPsMinLenCTerm() throws PDBParseException, Struc
 		result = CeCPMain.filterDuplicateAFPs(afpChain, new CECalculator(null), ca1, ca2,params);
 
 		Assert.assertTrue("Wrong optAln for minCPlength=" + params.getMinCPLength(), Arrays.deepEquals(filteredAln, result.getOptAln()));
-		Assert.assertTrue("Wrong optLen for minCPlength=" + params.getMinCPLength(), Arrays.equals(filteredLen, result.getOptLen()));
+		Assert.assertArrayEquals("Wrong optLen for minCPlength=" + params.getMinCPLength(), filteredLen, result.getOptLen());
 
 	}
 
@@ -228,7 +228,7 @@ public void testFilterDuplicateAFPsMinLenNTerm() throws PDBParseException, Struc
 			result = CeCPMain.filterDuplicateAFPs(afpChain, new CECalculator(null), ca1, ca2,params);
 
 			Assert.assertTrue("Wrong optAln for minCPlength=" + params.getMinCPLength(), Arrays.deepEquals(filteredAln, result.getOptAln()));
-			Assert.assertTrue("Wrong optLen for minCPlength=" + params.getMinCPLength(), Arrays.equals(filteredLen, result.getOptLen()));
+			Assert.assertArrayEquals("Wrong optLen for minCPlength=" + params.getMinCPLength(), filteredLen, result.getOptLen());
 		}
 
 		// For minCPlength=3, filtering changes
@@ -248,7 +248,7 @@ public void testFilterDuplicateAFPsMinLenNTerm() throws PDBParseException, Struc
 		result = CeCPMain.filterDuplicateAFPs(afpChain, new CECalculator(null), ca1, ca2,params);
 
 		Assert.assertTrue("Wrong optAln for minCPlength=" + params.getMinCPLength(), Arrays.deepEquals(filteredAln, result.getOptAln()));
-		Assert.assertTrue("Wrong optLen for minCPlength=" + params.getMinCPLength(), Arrays.equals(filteredLen, result.getOptLen()));
+		Assert.assertArrayEquals("Wrong optLen for minCPlength=" + params.getMinCPLength(), filteredLen, result.getOptLen());
 
 		// For minCPlength=4, filtering changes
 		params.setMinCPLength(5);
@@ -263,13 +263,13 @@ public void testFilterDuplicateAFPsMinLenNTerm() throws PDBParseException, Struc
 		result = CeCPMain.filterDuplicateAFPs(afpChain, new CECalculator(null), ca1, ca2,params);
 
 		Assert.assertTrue("Wrong optAln for minCPlength=" + params.getMinCPLength(), Arrays.deepEquals(filteredAln, result.getOptAln()));
-		Assert.assertTrue("Wrong optLen for minCPlength=" + params.getMinCPLength(), Arrays.equals(filteredLen, result.getOptLen()));
+		Assert.assertArrayEquals("Wrong optLen for minCPlength=" + params.getMinCPLength(), filteredLen, result.getOptLen());
 
 		params.setMinCPLength(8);
 		result = CeCPMain.filterDuplicateAFPs(afpChain, new CECalculator(null), ca1, ca2,params);
 
 		Assert.assertTrue("Wrong optAln for minCPlength=" + params.getMinCPLength(), Arrays.deepEquals(filteredAln, result.getOptAln()));
-		Assert.assertTrue("Wrong optLen for minCPlength=" + params.getMinCPLength(), Arrays.equals(filteredLen, result.getOptLen()));
+		Assert.assertArrayEquals("Wrong optLen for minCPlength=" + params.getMinCPLength(), filteredLen, result.getOptLen());
 
 		// Eventually, no alignment!
 		params.setMinCPLength(9);
@@ -280,7 +280,7 @@ public void testFilterDuplicateAFPsMinLenNTerm() throws PDBParseException, Struc
 		result = CeCPMain.filterDuplicateAFPs(afpChain, new CECalculator(null), ca1, ca2,params);
 
 		Assert.assertTrue("Wrong optAln for minCPlength=" + params.getMinCPLength(), Arrays.deepEquals(filteredAln, result.getOptAln()));
-		Assert.assertTrue("Wrong optLen for minCPlength=" + params.getMinCPLength(), Arrays.equals(filteredLen, result.getOptLen()));
+		Assert.assertArrayEquals("Wrong optLen for minCPlength=" + params.getMinCPLength(), filteredLen, result.getOptLen());
 
 	}
 
@@ -305,7 +305,7 @@ private AFPChain makeDummyAFPChain(int[][][] dupAlign, Atom[] ca1,Atom[] ca2) {
 
 
 	@Test
-	public void testCalculateMinCP() throws SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException, InvocationTargetException {
+	public void testCalculateMinCP() throws SecurityException, IllegalArgumentException {
 		int[] block;
 		int ca2len;
 
@@ -380,9 +380,8 @@ public void testCalculateMinCP() throws SecurityException, NoSuchMethodException
 	 *
 	 * @param len
 	 * @return
-	 * @throws PDBParseException
-	 */
-	private Atom[] makeDummyCA(int len) throws PDBParseException {
+     */
+	private Atom[] makeDummyCA(int len) {
 		Atom[] ca1;
 		Chain chain1 = new ChainImpl();
 		chain1.setId("A");
@@ -395,7 +394,7 @@ private Atom[] makeDummyCA(int len) throws PDBParseException {
 			ca1[i].setCoords(new double[] { i, 0, 0 });
 			Group aa = new AminoAcidImpl();
 			aa.setPDBName("GLY");
-			aa.setResidueNumber( ResidueNumber.fromString(i+""));
+			aa.setResidueNumber( ResidueNumber.fromString(String.valueOf(i)));
 			aa.addAtom(ca1[i]);
 			chain1.addGroup(aa);
 		}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestSmallAlignment.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestSmallAlignment.java
index 476b8bafb8..bf48dd2e6c 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestSmallAlignment.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestSmallAlignment.java
@@ -52,18 +52,18 @@ public void test1a4w() throws IOException, StructureException {
 
 		AFPChain afpChain = ce.align(ca1, ca2);
 
-		Assert.assertTrue(afpChain != null);
+        Assert.assertNotNull(afpChain);
 
 		afpChain.setName1(name1);
 		afpChain.setName2(name2);
 
-		Assert.assertTrue(afpChain.getNrEQR() == 0);
+        Assert.assertEquals(0, afpChain.getNrEQR());
 
 		String xml = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
 
 		AFPChain newChain = AFPChainXMLParser.fromXML(xml, ca1, ca2);
 
-		Assert.assertTrue(newChain != null);
+        Assert.assertNotNull(newChain);
 
 		String xml2 = AFPChainXMLConverter.toXML(newChain,ca1,ca2);
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestWebStartClient.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestWebStartClient.java
index f62b4b7beb..c8c79077cf 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestWebStartClient.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestWebStartClient.java
@@ -88,7 +88,7 @@ private void align(String name1, String name2, StructureAlignment algorithm)
 
 		Assert.assertNotNull(afpChain);
 		Assert.assertNotNull(afpChain.getAlgorithmName());
-		Assert.assertTrue(afpChain.getAlgorithmName().equals(algorithm.getAlgorithmName()));
+        Assert.assertEquals(afpChain.getAlgorithmName(), algorithm.getAlgorithmName());
 
 		String xml = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
 
@@ -97,7 +97,7 @@ private void align(String name1, String name2, StructureAlignment algorithm)
 		AFPChain afpServer = JFatCatClient.getAFPChainFromServer(serverLocation,algorithm.getAlgorithmName(), name1, name2, ca1, ca2, 5000);
 		Assert.assertNotNull(afpServer);
 
-		Assert.assertTrue("Algorithm names don't match!", afpServer.getAlgorithmName().equals(algorithm.getAlgorithmName()));
+        Assert.assertEquals("Algorithm names don't match!", afpServer.getAlgorithmName(), algorithm.getAlgorithmName());
 		Assert.assertTrue("Alignment blockNum < 1", afpServer.getBlockNum() >= 1);
 
 		String xml2 = AFPChainXMLConverter.toXML(afpServer, ca1, ca2);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/client/TestStructureName.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/client/TestStructureName.java
index 3b197d733f..3b6f403302 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/client/TestStructureName.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/client/TestStructureName.java
@@ -95,7 +95,7 @@ public void testSingleCharChainIds() throws StructureException {
 	}
 
 	@Test
-	public void testFiles() throws IOException {
+	public void testFiles() {
 		File f = new File("hopefully_this_doesnt_exist_nalkjas3");
 		assertFalse(f.exists());
 		assertNull(f.getParentFile());
@@ -114,72 +114,72 @@ public void testPrefixes() throws StructureException {
 		// Basic case
 		sn = new StructureName("PDB:4hhb");
 		assertTrue(sn.isPdbId());
-		assertTrue(sn.getSource() == PDB);
+		assertSame(sn.getSource(), PDB);
 		assertEquals("4HHB",sn.getPdbId());
 		sn = new StructureName("PDB:4hhb.A:1-50");
 		assertTrue(sn.isPdbId());
-		assertTrue(sn.getSource() == PDB);
+		assertSame(sn.getSource(), PDB);
 		assertEquals("4HHB",sn.getPdbId());
 		// Invalid strings work too, they just don't load
 		sn = new StructureName("PDB:x");
 		assertTrue(sn.isPdbId());
-		assertTrue(sn.getSource() == PDB);
+		assertSame(sn.getSource(), PDB);
 		assertEquals("x",sn.getPdbId());
 		// SCOP
 		sn = new StructureName("SCOP:d2gs2a_");
 		assertTrue(sn.isScopName());
-		assertTrue(sn.getSource() == SCOP);
+		assertSame(sn.getSource(), SCOP);
 		assertEquals("2GS2",sn.getPdbId());
 		// CATH
 		sn = new StructureName("CATH:1qvrC03");
 		assertTrue(sn.isCathID());
-		assertTrue(sn.getSource() == CATH);
+		assertSame(sn.getSource(), CATH);
 		assertEquals("1QVR",sn.getPdbId());
 		// PDP
 		sn = new StructureName("PDP:4HHBAa");
 		assertTrue(sn.isPDPDomain());
-		assertTrue(sn.getSource() == PDP);
+		assertSame(sn.getSource(), PDP);
 		assertEquals("4HHB",sn.getPdbId());
 		// URL
 		sn = new StructureName("URL:http://www.rcsb.org/pdb/files/1B8G.pdb.gz");
 		assertTrue(sn.isURL());
-		assertTrue(sn.getSource() == URL);
+		assertSame(sn.getSource(), URL);
 		assertEquals("1B8G",sn.getPdbId());
 		sn = new StructureName("URL:file:///4hhb.pdb");
 		assertTrue(sn.isURL());
-		assertTrue(sn.getSource() == URL);
+		assertSame(sn.getSource(), URL);
 		assertEquals("4HHB",sn.getPdbId());
 		// File: expand home directory (invalid URL)
 		sn = new StructureName("FILE:~/4hhb.pdb");
 		assertTrue(sn.isFile());
-		assertTrue(sn.getSource() == FILE);
+		assertSame(sn.getSource(), FILE);
 		assertEquals("4HHB",sn.getPdbId());
 		// Relative file (invalid URL)
 		sn = new StructureName("file:4hhb.pdb");
 		assertTrue(sn.isFile());
-		assertTrue(sn.getSource() == FILE);
+		assertSame(sn.getSource(), FILE);
 		assertEquals("4HHB",sn.getPdbId());
 		// Absolute paths are valid URLs
 		sn = new StructureName("file:/4hhb_other.pdb");
 		assertTrue(sn.isURL());
-		assertTrue(sn.getSource() == URL);
+		assertSame(sn.getSource(), URL);
 		assertEquals("4HHB",sn.getPdbId());
 
 		// ECOD
 		sn = new StructureName("e1lyw.1");
 		assertTrue(sn.isEcodDomain());
-		assertTrue(sn.getSource() == ECOD);
+		assertSame(sn.getSource(), ECOD);
 		assertEquals("1LYW",sn.getPdbId());
 		// BIO
 		sn = new StructureName("BIO:2ehz:1");
 		assertTrue(sn.isBioAssembly());
-		assertTrue(sn.getSource() == BIO);
+		assertSame(sn.getSource(), BIO);
 		assertEquals("2EHZ",sn.getPdbId());
 
 		// Invalid prefix
 		sn = new StructureName("XXX:2ehz");
 		assertTrue(sn.isPdbId());
-		assertTrue(sn.getSource() == PDB);
+		assertSame(sn.getSource(), PDB);
 		assertEquals("XXX:2ehz",sn.getPdbId());
 
 	}
@@ -194,40 +194,40 @@ public void testGuesses() throws StructureException {
 		// Basic case
 		sn = new StructureName("4hhb");
 		assertTrue(sn.isPdbId());
-		assertTrue(sn.getSource() == PDB);
+		assertSame(sn.getSource(), PDB);
 		assertEquals("4HHB",sn.getPdbId());
 		sn = new StructureName("4hhb.A:1-50");
 		assertTrue(sn.isPdbId());
-		assertTrue(sn.getSource() == PDB);
+		assertSame(sn.getSource(), PDB);
 		assertEquals("4HHB",sn.getPdbId());
 		// Invalid strings work too, they just don't load
 		sn = new StructureName("x");
 		assertTrue(sn.isPdbId());
-		assertTrue(sn.getSource() == PDB);
+		assertSame(sn.getSource(), PDB);
 		assertEquals("x",sn.getPdbId());
 		// SCOP
 		sn = new StructureName("d2gs2a_");
 		assertTrue(sn.isScopName());
-		assertTrue(sn.getSource() == SCOP);
+		assertSame(sn.getSource(), SCOP);
 		assertEquals("2GS2",sn.getPdbId());
 		// CATH
 		sn = new StructureName("1qvrC03");
 		assertTrue(sn.isCathID());
-		assertTrue(sn.getSource() == CATH);
+		assertSame(sn.getSource(), CATH);
 		assertEquals("1QVR",sn.getPdbId());
 		// PDP is not guessed
 		sn = new StructureName("4HHBAa");
 		assertFalse(sn.isPDPDomain());
-		assertTrue(sn.getSource() == PDB);
+		assertSame(sn.getSource(), PDB);
 		assertEquals("4HHBAa",sn.getPdbId());
 		// URL
 		sn = new StructureName("http://www.rcsb.org/pdb/files/1B8G.pdb.gz");
 		assertTrue(sn.isURL());
-		assertTrue(sn.getSource() == URL);
+		assertSame(sn.getSource(), URL);
 		assertEquals("1B8G",sn.getPdbId());
 		sn = new StructureName("file:///4hhb.pdb");
 		assertTrue(sn.isURL());
-		assertTrue(sn.getSource() == URL);
+		assertSame(sn.getSource(), URL);
 		assertEquals("4HHB",sn.getPdbId());
 
 
@@ -249,12 +249,12 @@ public void testGuesses() throws StructureException {
 		// ECOD
 		sn = new StructureName("e1lyw.1");
 		assertTrue(sn.isEcodDomain());
-		assertTrue(sn.getSource() == ECOD);
+		assertSame(sn.getSource(), ECOD);
 		assertEquals("1LYW",sn.getPdbId());
 		// BIO is not guessed
 		sn = new StructureName("2ehz:1");
 		assertFalse(sn.isBioAssembly());
-		assertTrue(sn.getSource() == PDB);
+		assertSame(sn.getSource(), PDB);
 		assertEquals("2ehz:1",sn.getPdbId());
 
 	}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestAFPChainConversion.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestAFPChainConversion.java
index bc9837f5a3..425c88b2f4 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestAFPChainConversion.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestAFPChainConversion.java
@@ -40,7 +40,7 @@
 public class TestAFPChainConversion {
 
 	@Test
-	public void testAFPconversion() throws Exception{
+	public void testAFPconversion() {
 
 		//Fill an AFPChain with the general information
 		AFPChain afp = new AFPChain("algorithm");
@@ -82,8 +82,7 @@ public void testAFPconversion() throws Exception{
 		assertEquals(afp.getName2(), ensemble.getStructureIdentifiers().get(1).getIdentifier());
 		assertEquals(afp.getAlgorithmName(), ensemble.getAlgorithmName());
 		assertEquals(afp.getVersion(),ensemble.getVersion());
-		assertTrue(ensemble.getCalculationTime().equals(
-				afp.getCalculationTime()));
+		assertEquals((long) ensemble.getCalculationTime(), afp.getCalculationTime());
 		assertEquals(afp.getBlockNum(), msa.getBlockSets().size());
 		for (int b = 0; b<afp.getBlockNum(); b++){
 			assertEquals(Calc.getTransformation(
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestSampleGenerator.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestSampleGenerator.java
index 75c05aab59..d9decd149b 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestSampleGenerator.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestSampleGenerator.java
@@ -68,14 +68,14 @@ public static MultipleAlignment testAlignment1()
 		//Obtain the structure atoms from resources
 		StructureIOFile reader = new PDBFileReader();
 		File f = new File("src/test/resources/2gox.pdb");
-		Structure structure = null;
+		Structure structure;
 		try {
 			structure = reader.getStructure(f);
 		} catch (IOException e){
 			AtomCache cache = new AtomCache();
 			structure = cache.getStructure("2gox");
 		}
-		List<Atom[]> atomArrays = new ArrayList<Atom[]>(3);
+		List<Atom[]> atomArrays = new ArrayList<>(3);
 		for (int str=0; str<3; str++){
 			Atom[] atoms = StructureTools.
 					getRepresentativeAtomArray(structure);
@@ -89,16 +89,16 @@ public static MultipleAlignment testAlignment1()
 		ensemble.setAlgorithmName("testAlignment");
 		ensemble.setVersion("1.0");
 		ensemble.setCalculationTime((long) 1000000000);
-		ensemble.setStructureIdentifiers(Arrays.<StructureIdentifier>asList(new StructureName("2gox"),new StructureName("2gox"),new StructureName("2gox")));
+		ensemble.setStructureIdentifiers(Arrays.asList(new StructureName("2gox"),new StructureName("2gox"),new StructureName("2gox")));
 
 		//Generate the MultipleAlignment - 2 blocks with 2 blocksets each
 		int[] nextResidue = new int[3];
 		for (int bs=0; bs<2; bs++){
 			BlockSet blockSet = new BlockSetImpl(msa);
 			for (int b=0; b<2; b++){
-				List<List<Integer>> alnRes = new ArrayList<List<Integer>>(3);
+				List<List<Integer>> alnRes = new ArrayList<>(3);
 				for (int str=0; str<3; str++){
-					List<Integer> chain = new ArrayList<Integer>(50);
+					List<Integer> chain = new ArrayList<>(50);
 					for (int res=0; res<10; res++){
 						//Introduce gaps and discontinuities
 						if (nextResidue[str] % (2+str) == str)chain.add(null);
@@ -138,11 +138,11 @@ public static MultipleAlignment testAlignment2()
 			throws StructureException, IOException {
 
 		//Download the globin structures
-		List<StructureIdentifier> names = Arrays.<StructureIdentifier>asList(
+		List<StructureIdentifier> names = Arrays.asList(
 				new StructureName("1mbc"), new StructureName("1hlb"),
 				new StructureName("1thb.A"), new StructureName("1ith.A"));
 		AtomCache cache = new AtomCache();
-		List<Atom[]> atomArrays = new ArrayList<Atom[]>();
+		List<Atom[]> atomArrays = new ArrayList<>();
 		for (StructureIdentifier name:names) atomArrays.add(cache.getAtoms(name));
 
 		MultipleAlignmentEnsemble ensemble =
@@ -165,9 +165,9 @@ public static MultipleAlignment testAlignment2()
 		Block block1 = new BlockImpl(blockSet1);
 		Block block2 = new BlockImpl(blockSet1);
 		Block block3 = new BlockImpl(blockSet2);
-		block1.setAlignRes(new ArrayList<List<Integer>>());
-		block2.setAlignRes(new ArrayList<List<Integer>>());
-		block3.setAlignRes(new ArrayList<List<Integer>>());
+		block1.setAlignRes(new ArrayList<>());
+		block2.setAlignRes(new ArrayList<>());
+		block3.setAlignRes(new ArrayList<>());
 
 		List<Integer> aligned11 = Arrays.asList(
 				0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java
index b080daf0b5..97a8010bee 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java
@@ -166,13 +166,13 @@ public void testMCScore() throws Exception {
 	private MultipleAlignment identityMSTA() throws StructureException {
 
 		//Generate the identical Atom arrays
-		List<Atom[]> atomArrays = new ArrayList<Atom[]>(20);
+		List<Atom[]> atomArrays = new ArrayList<>(20);
 		for (int i=0; i<3; i++) atomArrays.add(makeDummyCA(20));
 
 		//Generate the identity alignment (1-1-1,2-2-2,etc)
-		List<List<Integer>> alnRes = new ArrayList<List<Integer>>(3);
+		List<List<Integer>> alnRes = new ArrayList<>(3);
 		for (int str=0; str<3; str++){
-			List<Integer> chain = new ArrayList<Integer>(20);
+			List<Integer> chain = new ArrayList<>(20);
 			for (int res=0; res<20; res++) chain.add(res);
 			alnRes.add(chain);
 		}
@@ -196,18 +196,17 @@ private MultipleAlignment identityMSTA() throws StructureException {
 	 * Atoms but incorreclty aligned (offset of 1 position) without gaps.
 	 *
 	 * @return MultipleAlignment simple MSTA
-	 * @throws StructureException
 	 */
-	private MultipleAlignment simpleMSTA() throws StructureException{
+	private MultipleAlignment simpleMSTA() {
 
 		//Generate three identical Atom arrays
-		List<Atom[]> atomArrays = new ArrayList<Atom[]>(52);
+		List<Atom[]> atomArrays = new ArrayList<>(52);
 		for (int i=0; i<3; i++) atomArrays.add(makeDummyCA(52));
 
 		//Generate the incorrect alignment (0-1-2,1-2-3,etc)
-		List<List<Integer>> alnRes = new ArrayList<List<Integer>>(3);
+		List<List<Integer>> alnRes = new ArrayList<>(3);
 		for (int str=0; str<3; str++){
-			List<Integer> chain = new ArrayList<Integer>(50);
+			List<Integer> chain = new ArrayList<>(50);
 			for (int res=0; res<50; res++) chain.add(res+str);
 			alnRes.add(chain);
 		}
@@ -232,16 +231,15 @@ private MultipleAlignment simpleMSTA() throws StructureException{
 	 * same Atoms but incorreclty aligned with gaps.
 	 *
 	 * @return MultipleAlignment gapped MSTA
-	 * @throws StructureException
 	 */
-	private MultipleAlignment gappedMSTA() throws StructureException{
+	private MultipleAlignment gappedMSTA() {
 
 		//Generate three identical Atom arrays
-		List<Atom[]> atomArrays = new ArrayList<Atom[]>(30);
+		List<Atom[]> atomArrays = new ArrayList<>(30);
 		for (int i=0; i<3; i++) atomArrays.add(makeDummyCA(30));
 
 		//Generate alignment with nulls and some missalignments
-		List<List<Integer>> alnRes = new ArrayList<List<Integer>>(3);
+		List<List<Integer>> alnRes = new ArrayList<>(3);
 		List<Integer> chain1 = Arrays.asList(
 				1, 2, 	 3, 5, 8, 10, 12, 	 15, 17,  19, 22, null, 24, 27);
 		List<Integer> chain2 = Arrays.asList(
@@ -282,7 +280,7 @@ private Atom[] makeDummyCA(int len) {
 			ca1[i].setCoords(new double[] { i, 0, 0 });
 			Group aa = new AminoAcidImpl();
 			aa.setPDBName("GLY");
-			aa.setResidueNumber( ResidueNumber.fromString(i+""));
+			aa.setResidueNumber( ResidueNumber.fromString(String.valueOf(i)));
 			aa.addAtom(ca1[i]);
 			chain1.addGroup(aa);
 		}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentTools.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentTools.java
index 12cf116f48..a0b0b30287 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentTools.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentTools.java
@@ -48,7 +48,7 @@ public class TestMultipleAlignmentTools {
 	 */
 	public static class NamedBlock extends BlockImpl {
 		private static final long serialVersionUID = 5060618718423340848L;
-		private String name;
+		private final String name;
 		public NamedBlock(String name, BlockSet bs) {
 			super(bs);
 			this.name = name;
@@ -88,7 +88,7 @@ public void testSortBlocks() {
 				Arrays.asList( 20, 21, 22),
 				Arrays.asList( 10, 11, 12),
 				Arrays.asList( 10, null, 12),
-				Arrays.asList( (Integer)null,null,null),
+				Arrays.asList(null,null,null),
 				Arrays.asList( 10, 11, 12),
 				Arrays.asList( 10, 11, 12)
 				));
@@ -106,7 +106,7 @@ public void testSortBlocks() {
 				Arrays.asList( 40, 41, 42),
 				Arrays.asList( 30, 31, 32),
 				Arrays.asList( null, 31, 32),
-				Arrays.asList( (Integer)null,null,null),
+				Arrays.asList(null,null,null),
 				Arrays.asList( 30, 51, 52),
 				Arrays.asList( 30, 31, 32)
 				));
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentWriter.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentWriter.java
index c7f427e9c5..064643ff6d 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentWriter.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentWriter.java
@@ -47,8 +47,8 @@
  */
 public class TestMultipleAlignmentWriter {
 
-	private MultipleAlignment alignment1;
-	private MultipleAlignment alignment2;
+	private final MultipleAlignment alignment1;
+	private final MultipleAlignment alignment2;
 
 	/**
 	 * Build the alignments in common for every writer output, so that they do
@@ -70,7 +70,7 @@ public void testFASTA1() throws IOException {
 
 		FileReader file = new FileReader("src/test/resources/testMSTA1.fasta");
 		BufferedReader reader = new BufferedReader(file);
-		String line = null;
+		String line;
 		StringBuilder stringBuilder = new StringBuilder();
 
 		while ((line = reader.readLine()) != null) {
@@ -90,7 +90,7 @@ public void testFASTA2() throws IOException {
 
 		FileReader file = new FileReader("src/test/resources/testMSTA2.fasta");
 		BufferedReader reader = new BufferedReader(file);
-		String line = null;
+		String line;
 		StringBuilder stringBuilder = new StringBuilder();
 
 		while ((line = reader.readLine()) != null) {
@@ -110,7 +110,7 @@ public void testFatCat1() throws IOException {
 
 		FileReader file = new FileReader("src/test/resources/testMSTA1.fatcat");
 		BufferedReader reader = new BufferedReader(file);
-		String line = null;
+		String line;
 		StringBuilder stringBuilder = new StringBuilder();
 
 		while ((line = reader.readLine()) != null) {
@@ -130,7 +130,7 @@ public void testFatCat2() throws IOException {
 
 		FileReader file = new FileReader("src/test/resources/testMSTA2.fatcat");
 		BufferedReader reader = new BufferedReader(file);
-		String line = null;
+		String line;
 		StringBuilder stringBuilder = new StringBuilder();
 
 		while ((line = reader.readLine()) != null) {
@@ -151,7 +151,7 @@ public void testAlignedResidues1() throws IOException {
 		FileReader file = new FileReader(
 				"src/test/resources/testMSTA1_alnres.tsv");
 		BufferedReader reader = new BufferedReader(file);
-		String line = null;
+		String line;
 		StringBuilder stringBuilder = new StringBuilder();
 
 		while ((line = reader.readLine()) != null) {
@@ -172,7 +172,7 @@ public void testAlignedResidues2() throws IOException {
 		FileReader file = new FileReader(
 				"src/test/resources/testMSTA2_alnres.tsv");
 		BufferedReader reader = new BufferedReader(file);
-		String line = null;
+		String line;
 		StringBuilder stringBuilder = new StringBuilder();
 
 		while ((line = reader.readLine()) != null) {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
index 58a2623062..505c5e852b 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
@@ -75,7 +75,7 @@
  */
 public class AtomCacheTest {
 
-	private static Logger logger = LoggerFactory.getLogger(AtomCacheTest.class);
+	private static final Logger logger = LoggerFactory.getLogger(AtomCacheTest.class);
 	private AtomCache cache;
 
 	@Before
@@ -187,14 +187,14 @@ public void testGetStructureForChainlessDomains() throws IOException, StructureE
 	}
 
 	@Test
-	public void testSetPath_withTilde() throws Exception {
+	public void testSetPath_withTilde() {
 		cache.setPath("~" + File.separator);
 
 		assertEquals(System.getProperty("user.home") + File.separator, cache.getPath());
 	}
 
 	@Test
-	public void testNewInstanceWithTilder() throws Exception {
+	public void testNewInstanceWithTilder() {
 		AtomCache cache1 = new AtomCache("~" + File.separator);
 
 		assertEquals(System.getProperty("user.home") + File.separator, cache1.getPath());
@@ -399,7 +399,7 @@ public void testEmptyChemComp() throws IOException, StructureException {
 			assertNotNull(s);
 
 			Group g = s.getChain("A").getAtomGroup(0);
-			assertTrue(g.getPDBName().equals("ATP"));
+			assertEquals("ATP", g.getPDBName());
 
 			// should be unknown
 			ChemComp chem = g.getChemComp();
@@ -462,7 +462,7 @@ public void testEmptyGZChemComp() throws IOException, StructureException {
 			assertNotNull(s);
 
 			Group g = s.getChain("A").getAtomGroup(0);
-			assertTrue(g.getPDBName().equals("ATP"));
+			assertEquals("ATP", g.getPDBName());
 
 			// should be unknown
 			ChemComp chem = g.getChemComp();
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/RotationAxisTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/RotationAxisTest.java
index e610242b23..24e1513946 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/RotationAxisTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/RotationAxisTest.java
@@ -64,7 +64,7 @@
 public class RotationAxisTest {
 
 	@Test
-	public void testProjection() throws Exception{
+	public void testProjection() {
 		RotationAxis axis;
 		Atom dir,pos,projected;
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java
index 7d8cf1bfad..96c261e927 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java
@@ -88,7 +88,7 @@ public void testIntraChainContacts() throws StructureException, IOException {
 				for (int i = 0; i < cts.length; i++) {
 					logger.info((cts[i] == null ? "ALL" : cts[i][0]) + "\t" + cutoffs[i] + "\t");
 
-					AtomContactSet atomContacts = null;
+					AtomContactSet atomContacts;
 					if (cts[i] != null && cts[i][0].equals("CA")) {
 						atomContacts = StructureTools.getRepresentativeAtomsInContact(chain, cutoffs[i]);
 					} else {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPosition.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPosition.java
index eb03b4ef70..cba85c1da8 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPosition.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPosition.java
@@ -57,7 +57,7 @@ public class TestSuperPosition {
 
 	// the transformation to apply to cloud points 1 that needs to be recovered by the superposition code
 	private static final AxisAngle4d rotAxis = new AxisAngle4d(0.440, 0.302, 0.845, 1.570);
-	private static final Vector3d translation = new Vector3d(0.345, 2.453, 5.324);;
+	private static final Vector3d translation = new Vector3d(0.345, 2.453, 5.324);
 	private static Matrix4d transform;
 
 	// a translation to apply to cloud point 2 for the rmsd test only
@@ -67,13 +67,12 @@ public class TestSuperPosition {
 	 * Generate two clouds of random points of different sizes to test
 	 * correctness and performance of superposition algorithms.
 	 *
-	 * @throws StructureException
 	 */
 	@Before
-	public void setUp() throws StructureException {
+	public void setUp() {
 
-		cloud1 = new ArrayList<Point3d[]>(5);
-		cloud2 = new ArrayList<Point3d[]>(5);
+		cloud1 = new ArrayList<>(5);
+		cloud2 = new ArrayList<>(5);
 
 		Random rnd = new Random(0);
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java
index 8ae41a91cd..ad30f29e3b 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java
@@ -86,12 +86,10 @@ public static boolean compareXml(File expectedFile, File actualFile) {
 			expectedFr.close();
 			actualFr.close();
 			return isSimilar;
-		} catch (IOException e) {
-			throw new RuntimeException(e);
-		} catch (SAXException e) {
+		} catch (IOException | SAXException e) {
 			throw new RuntimeException(e);
 		}
-	}
+    }
 
 	private AtomCache cache;
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/StructureSequenceMatcherTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/StructureSequenceMatcherTest.java
index ed42a802de..d13975714e 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/StructureSequenceMatcherTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/StructureSequenceMatcherTest.java
@@ -92,7 +92,7 @@ public void setUp() throws IOException, StructureException {
 				//>2PTC:I|PDBID|CHAIN|SEQUENCE
 				"RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA";
 
-		Assert.assertTrue(seq1.length() == pdbNum1.length);
+		Assert.assertEquals(seq1.length(), pdbNum1.length);
 
 		/*// report some stats
 		System.out.println("The SEQRES and ATOM information is available via the chains:");
@@ -133,7 +133,7 @@ public void testSubstructureMatchingProteinSequence() throws CompoundNotFoundExc
 
 	@Test
 	public void testGetProteinSequenceForStructure() {
-		Map<Integer,Group> groupIndexPos = new HashMap<Integer,Group>();
+		Map<Integer,Group> groupIndexPos = new HashMap<>();
 		ProteinSequence prot = StructureSequenceMatcher.getProteinSequenceForStructure(struct1, groupIndexPos);
 
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java
index 80df942d0f..01a66ee542 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java
@@ -33,7 +33,7 @@
 public class TestDBRefParsing {
 
 	@Test
-	public void testShortLine() throws IOException, StructureException {
+	public void testShortLine() throws IOException {
 		Structure s,ref;
 		PDBFileParser pdbPars = new PDBFileParser();
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDifficultMmCIFFiles.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDifficultMmCIFFiles.java
index 5007db9b43..71ba72ed6e 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDifficultMmCIFFiles.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDifficultMmCIFFiles.java
@@ -184,7 +184,7 @@ public void testResidueNumbers() throws IOException, StructureException {
 	}
 
 	@Test
-	public void test4letterChains() throws IOException, StructureException, URISyntaxException {
+	public void test4letterChains() throws IOException, URISyntaxException {
 		String filename = "/1hh0_4char.cif.gz";
 		URL url = getClass().getResource(filename);
 		assumeNotNull("Can't find resource "+filename,url);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHardBioUnits.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHardBioUnits.java
index 6362dc2a84..047f1e7b29 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHardBioUnits.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHardBioUnits.java
@@ -136,7 +136,7 @@ public void test4A1I() throws IOException, StructureException {
 		assertEquals(2, bioAssembly.getPolyChains().size());
 
 		// here we'll store all author chain ids without the operator id part
-		Set<String> chainIdsNoOps = new HashSet<String>();
+		Set<String> chainIdsNoOps = new HashSet<>();
 
 		for (Chain poly:bioAssembly.getPolyChains()) {
 			chainIdsNoOps.add(poly.getName().split("_")[0]);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java
index 9d4c764690..fb685de8d3 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java
@@ -73,13 +73,13 @@ public void testHeaderOnly() throws StructureException, IOException {
 
 		Structure sPDB = StructureIO.getStructure(pdbID);
 
-		Assert.assertEquals(false, doSeqResHaveAtoms(sPDB));
+		Assert.assertFalse(doSeqResHaveAtoms(sPDB));
 
 		// Test 2: with mmCIF
 		cache.setUseMmCif(true);
 
 		Structure sCIF = StructureIO.getStructure(pdbID);
-		Assert.assertEquals(false, doSeqResHaveAtoms(sCIF));
+		Assert.assertFalse(doSeqResHaveAtoms(sCIF));
 
 
 	}
@@ -107,14 +107,14 @@ public void testAlignSeqres() throws StructureException, IOException {
 		StructureIO.setAtomCache(cache);
 
 		Structure sPDB = StructureIO.getStructure(pdbID);
-		Assert.assertEquals(true, doSeqResHaveAtoms(sPDB));
+		Assert.assertTrue(doSeqResHaveAtoms(sPDB));
 		check1REPChainC(sPDB); // Check particular residues to be aligned.
 
 		// Test 2: with mmCIF
 		cache.setUseMmCif(true);
 
 		Structure sCIF = StructureIO.getStructure(pdbID);
-		Assert.assertEquals(true, doSeqResHaveAtoms(sCIF));
+		Assert.assertTrue(doSeqResHaveAtoms(sCIF));
 		check1REPChainC(sCIF); // Check particular residues to be aligned.
 	}
 
@@ -148,7 +148,7 @@ public void testSpeed() {
 
 	// Test using local files.
 	@Test
-	public void testSpeed2() throws StructureException, IOException {
+	public void testSpeed2() throws IOException {
 		// Test the file parsing speed when the files are already downloaded.
 
 		InputStream cifStream = new GZIPInputStream(this.getClass().getResourceAsStream("/4hhb.cif.gz"));
@@ -222,7 +222,7 @@ public boolean hasAtoms(Group g) {
 	 *
 	 * @param s: Structure to test.
 	 */
-	public void check1REPChainC(Structure s) throws StructureException {
+	public void check1REPChainC(Structure s) {
 		String sequence = "MAETAVINHKKRKNSPRIVQSNDLTEAAYSLSRDQKRMLYLFVDQIRK" +
 				"SDGTLQEHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAGDE" +
 				"KGYESFPWFIKPAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMR" +
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java
index 71733aabaa..d8dd6100ae 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java
@@ -45,7 +45,7 @@ public class TestMMcifOrganismParsing {
 
 
 	@BeforeClass
-	public static void setUp() throws Exception {
+	public static void setUp() {
 
 		AtomCache cache = new AtomCache();
 		cache.setUseMmCif(true);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java
index f5e8e5c27e..be3b2afe6b 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java
@@ -56,7 +56,7 @@
 public class TestNonDepositedFiles {
 
 	@Test
-	public void test1B8GnoSeqresPdb() throws IOException, StructureException {
+	public void test1B8GnoSeqresPdb() throws IOException {
 
 		InputStream inStream = new GZIPInputStream(this.getClass().getResourceAsStream("/org/biojava/nbio/structure/io/1b8g_raw.pdb.gz"));
 		assertNotNull(inStream);
@@ -72,7 +72,7 @@ public void test1B8GnoSeqresPdb() throws IOException, StructureException {
 
 		assertTrue(s.isCrystallographic());
 		assertFalse(s.isNmr());
-		assertTrue(s.nrModels()==1);
+		assertEquals(1, s.nrModels());
 		assertNull(s.getPDBHeader().getExperimentalTechniques());
 
 		assertNotNull(s.getCrystallographicInfo().getCrystalCell());
@@ -126,7 +126,7 @@ public void test1B8G() throws IOException, StructureException {
 	}
 
 	@Test
-	public void test3C5F() throws IOException, StructureException {
+	public void test3C5F() throws IOException {
 		InputStream inStream = new GZIPInputStream(this.getClass().getResourceAsStream("/org/biojava/nbio/structure/io/3c5f_raw.pdb.gz"));
 		assertNotNull(inStream);
 
@@ -146,7 +146,7 @@ public void test3C5F() throws IOException, StructureException {
 	}
 
 	@Test
-	public void test4B19() throws IOException, StructureException {
+	public void test4B19() throws IOException {
 		InputStream inStream = new GZIPInputStream(this.getClass().getResourceAsStream("/org/biojava/nbio/structure/io/4b19_raw.pdb.gz"));
 		assertNotNull(inStream);
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestQuaternaryStructureProviders.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestQuaternaryStructureProviders.java
index c2d4ec71ad..9b619d2e5a 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestQuaternaryStructureProviders.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestQuaternaryStructureProviders.java
@@ -31,8 +31,7 @@
 import java.util.List;
 import java.util.Map;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
 
 public class TestQuaternaryStructureProviders {
 
@@ -66,7 +65,7 @@ public void test5LDH() throws IOException, StructureException{
 			gotException = true;
 		}
 
-		assertTrue("Bioassembly 3 for PDB id 5LDH should fail with a StructureException!", !gotException);
+        assertFalse("Bioassembly 3 for PDB id 5LDH should fail with a StructureException!", gotException);
 
 		// bioassembly 2 does exist in mmcif file, let's check that
 		gotException = false;
@@ -78,7 +77,7 @@ public void test5LDH() throws IOException, StructureException{
 		} catch (StructureException e) {
 			gotException = true;
 		}
-		assertTrue("Bioassembly 2 for PDB id 5LDH should not fail with a StructureException!", !gotException);
+        assertFalse("Bioassembly 2 for PDB id 5LDH should not fail with a StructureException!", gotException);
 
 	}
 
@@ -139,10 +138,11 @@ private void comparePdbVsMmcif(String pdbId, int bioMolecule, int mmSize) throws
 		assertEquals(mmSize, mMap.get(bioMolecule).getMacromolecularSize());
 
 
-		for ( int k : pMap.keySet()) {
-			assertTrue(mMap.containsKey(k));
+		for (Map.Entry<Integer, BioAssemblyInfo> entry : pMap.entrySet()) {
+            int k = entry.getKey();
+            assertTrue(mMap.containsKey(k));
 
-			BioAssemblyInfo pBioAssemb = pMap.get(k);
+			BioAssemblyInfo pBioAssemb = entry.getValue();
 			BioAssemblyInfo mBioAssemb = mMap.get(k);
 
 			assertEquals("Macromolecular sizes don't coincide!",pBioAssemb.getMacromolecularSize(), mBioAssemb.getMacromolecularSize());
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestChemCompProvider.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestChemCompProvider.java
index 4791f21fe7..24197868a1 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestChemCompProvider.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestChemCompProvider.java
@@ -43,7 +43,7 @@ public class TestChemCompProvider {
 	private static final Logger s_logger = LoggerFactory.getLogger(TestChemCompProvider.class);
 
 	// Short test with bad ligand name (QNA is bogus)
-	final	String DNAexample =
+	static final	String DNAexample =
 
 	"ATOM      1  H   MET A   1      11.756 -15.759  11.647  1.00  7.95\n" +
 	"ATOM      2  N   MET A   1      12.461 -16.373  11.329  1.00  7.95\n" +
@@ -186,7 +186,7 @@ public void testNormalStructure() throws StructureException, IOException {
 	}
 
 	@Test
-	public void testGetOneLetterCode() throws Exception {
+	public void testGetOneLetterCode() {
 
 		String oneLetter;
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
index d9bdb05bc0..5479cdd39d 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
@@ -139,7 +139,7 @@ private boolean checkIfAtomsSame(Structure structOne, Structure structTwo) {
 					if(!groupOne.getType().equals(groupTwo.getType())){
 						System.out.println("Error - diff group type: "+structOne.getPDBCode());
 						System.out.println(groupOne.getPDBName() + " and type: "+groupOne.getType());
-						System.out.println(groupTwo.getPDBName() + " and type: "+groupTwo.getType());;
+						System.out.println(groupTwo.getPDBName() + " and type: "+groupTwo.getType());
 					}
 					// Check the single letter amino acid is correct
 					if(groupOne.getChemComp().getOne_letter_code().length()==1 && groupTwo.getChemComp().getOne_letter_code().length()==1){
@@ -164,14 +164,10 @@ private boolean checkIfAtomsSame(Structure structOne, Structure structTwo) {
 					List<Atom> atomsTwo = new ArrayList<>(groupTwo.getAtoms());
 
 					for(Group altLocOne: groupOne.getAltLocs()){
-						for(Atom atomAltLocOne: altLocOne.getAtoms()){
-							atomsOne.add(atomAltLocOne);
-						}
+						atomsOne.addAll(altLocOne.getAtoms());
 					}
 					for(Group altLocTwo: groupTwo.getAltLocs()){
-						for(Atom atomAltLocTwo: altLocTwo.getAtoms()){
-							atomsTwo.add(atomAltLocTwo);
-						}
+						atomsTwo.addAll(altLocTwo.getAtoms());
 					}
 					if(atomsOne.size()!=atomsTwo.size()){
 						System.out.println("Error - diff number atoms: "+structOne.getPDBCode());
@@ -246,28 +242,22 @@ private void checkDiffChains(Structure structOne, Structure structTwo, int i) {
 	 * @param atomsTwo  the second list
 	 */
 	private void sortAtoms(List<Atom> atomsOne, List<Atom> atomsTwo) {
-		atomsOne.sort(new Comparator<Atom>() {
-			@Override
-			public int compare(Atom o1, Atom o2) {
-				//
-				if (o1.getPDBserial()<o2.getPDBserial()){
-					return -1;
-				}
-				else{
-					return 1;
-				}
+		atomsOne.sort((o1, o2) -> {
+			//
+			if (o1.getPDBserial()<o2.getPDBserial()){
+				return -1;
+			}
+			else{
+				return 1;
 			}
 		});
-		atomsTwo.sort(new Comparator<Atom>() {
-			@Override
-			public int compare(Atom o1, Atom o2) {
-				//
-				if (o1.getPDBserial()<o2.getPDBserial()){
-					return -1;
-				}
-				else{
-					return 1;
-				}
+		atomsTwo.sort((o1, o2) -> {
+			//
+			if (o1.getPDBserial()<o2.getPDBserial()){
+				return -1;
+			}
+			else{
+				return 1;
 			}
 		});
 	}
@@ -279,18 +269,8 @@ public int compare(Atom o1, Atom o2) {
 	 * @param chainsTwo the second list of chains
 	 */
 	private void sortChains(List<Chain> chainsOne, List<Chain> chainsTwo) {
-		Collections.sort(chainsOne, new Comparator<Chain>() {
-			@Override
-			public int compare(Chain o1, Chain o2) {
-				return o1.getId().compareTo(o2.getId());
-			}
-		});
-		Collections.sort(chainsTwo, new Comparator<Chain>() {
-			@Override
-			public int compare(Chain o1, Chain o2) {
-				return o1.getId().compareTo(o2.getId());
-			}
-		});
+		chainsOne.sort((o1, o2) -> o1.getId().compareTo(o2.getId()));
+		chainsTwo.sort((o1, o2) -> o1.getId().compareTo(o2.getId()));
 
 	}
 
@@ -324,7 +304,7 @@ private void checkSeqresGroups(Chain chainOne, Chain chainTwo) {
 	 * @param structOne the first input structure
 	 * @param structTwo the second input structure
 	 */
-	private void checkBioAssemblies1(Structure structOne, Structure structTwo) throws IOException {
+	private void checkBioAssemblies1(Structure structOne, Structure structTwo) {
 
 		Map<Integer, BioAssemblyInfo> expecteds = structOne.getPDBHeader().getBioAssemblies();
 		Map<Integer, BioAssemblyInfo> actuals = structTwo.getPDBHeader().getBioAssemblies();
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureReader.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureReader.java
index ac2d81e8d5..17e9d42d32 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureReader.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureReader.java
@@ -1,7 +1,5 @@
 package org.biojava.nbio.structure.io.mmtf;
 
-import static org.junit.Assert.assertEquals;
-
 import java.io.IOException;
 import java.nio.file.Paths;
 import java.util.List;
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureWriter.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureWriter.java
index 6f98b250d3..2ef83527c2 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureWriter.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureWriter.java
@@ -31,7 +31,6 @@
 import org.biojava.nbio.structure.Chain;
 import org.biojava.nbio.structure.ChainImpl;
 import org.biojava.nbio.structure.Element;
-import org.biojava.nbio.structure.EntityInfo;
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.PDBHeader;
 import org.biojava.nbio.structure.ResidueNumber;
@@ -87,7 +86,7 @@ public void testWrite() throws IOException {
 		structure.setPDBHeader(pdbHeader);
 
 		// Create one chain
-		structure.setEntityInfos(new ArrayList<EntityInfo>());
+		structure.setEntityInfos(new ArrayList<>());
 		Chain chain = new ChainImpl();
 		chain.setId("A");
 		chain.setName("A");
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfUtils.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfUtils.java
index ed86712893..859e24548a 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfUtils.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfUtils.java
@@ -139,14 +139,12 @@ public void microHeterogenity() throws IOException, StructureException {
 	 */
 	private List<Atom> getAllAtoms(Structure bioJavaStruct) {
 		// Get all the atoms
-		List<Atom> theseAtoms = new ArrayList<Atom>();
+		List<Atom> theseAtoms = new ArrayList<>();
 		for (int i=0; i<bioJavaStruct.nrModels(); i++){
 			List<Chain> chains = bioJavaStruct.getModel(i);
 			for (Chain c : chains) {
 				for (Group g : c.getAtomGroups()) {
-					for(Atom a: MmtfUtils.getAtomsForGroup(g)){
-						theseAtoms.add(a);
-					}
+					theseAtoms.addAll(MmtfUtils.getAtomsForGroup(g));
 				}
 			}
 		}
@@ -381,8 +379,8 @@ public void testGetSecStructTypeFromDsspIndex(){
 		assertEquals(MmtfUtils.getSecStructTypeFromDsspIndex(5).name,"Bridge");
 		assertEquals(MmtfUtils.getSecStructTypeFromDsspIndex(6).name,"Turn");
 		assertEquals(MmtfUtils.getSecStructTypeFromDsspIndex(7).name,"Coil");
-		assertEquals(MmtfUtils.getSecStructTypeFromDsspIndex(-1), null);
-		assertEquals(MmtfUtils.getSecStructTypeFromDsspIndex(10), null);
+		assertNull(MmtfUtils.getSecStructTypeFromDsspIndex(-1));
+		assertNull(MmtfUtils.getSecStructTypeFromDsspIndex(10));
 
 	}
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/rcsb/RCSBDescriptionFactoryTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/rcsb/RCSBDescriptionFactoryTest.java
index bef0e232c1..0dca56f12c 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/rcsb/RCSBDescriptionFactoryTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/rcsb/RCSBDescriptionFactoryTest.java
@@ -32,6 +32,7 @@
 import java.util.List;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
 
 /**
  * Tests {@link RCSBDescriptionFactory}.
@@ -134,17 +135,17 @@ public void testAlmostEmpty() {
 		assertEquals("notype", polymer.getType());
 		assertEquals(1, polymer.getIndex().intValue());
 		assertEquals("really close to empty", polymer.getDescription());
-		assertEquals(null, polymer.getEnzClass());
+		assertNull(polymer.getEnzClass());
 		assertEquals(10, polymer.getLength().intValue());
 		assertEquals(0, polymer.getWeight(), 0);
 
 		polymer = polymers.get(1);
-		assertEquals(null, polymer.getType()); // make sure these are null and not ""
-		assertEquals(null, polymer.getIndex());
-		assertEquals(null, polymer.getDescription());
-		assertEquals(null, polymer.getEnzClass());
-		assertEquals(null, polymer.getLength());
-		assertEquals(null, polymer.getWeight());
+		assertNull(polymer.getType()); // make sure these are null and not ""
+		assertNull(polymer.getIndex());
+		assertNull(polymer.getDescription());
+		assertNull(polymer.getEnzClass());
+		assertNull(polymer.getLength());
+		assertNull(polymer.getWeight());
 
 	}
 
@@ -163,7 +164,7 @@ public void test2() {
 		assertEquals("protein", polymer.getType());
 		assertEquals(1, polymer.getIndex().intValue());
 		assertEquals("HEMOGLOBIN (DEOXY) (ALPHA CHAIN)", polymer.getDescription());
-		assertEquals(null, polymer.getEnzClass());
+		assertNull(polymer.getEnzClass());
 		assertEquals(141, polymer.getLength().intValue());
 		assertEquals(15150.5, polymer.getWeight(), 0);
 
@@ -197,7 +198,7 @@ public void test2() {
 		assertEquals("protein", polymer.getType());
 		assertEquals(2, polymer.getIndex().intValue());
 		assertEquals("HEMOGLOBIN (DEOXY) (BETA CHAIN)", polymer.getDescription());
-		assertEquals(null, polymer.getEnzClass());
+		assertNull(polymer.getEnzClass());
 		assertEquals(146, polymer.getLength().intValue());
 		assertEquals(15890.4, polymer.getWeight(), 0);
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/redmine/Test1DARSeqAlign.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/redmine/Test1DARSeqAlign.java
index 4f351d3c74..d65bb41abe 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/redmine/Test1DARSeqAlign.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/redmine/Test1DARSeqAlign.java
@@ -72,13 +72,13 @@ public void test1DAR() throws StructureException, IOException {
 		//System.out.println(g3);
 		//System.out.println(FileConvert.toPDB(g3.getAtom(0)));
 
-		assertTrue(! a.getSeqResGroups().contains(g));
+        assertFalse(a.getSeqResGroups().contains(g));
 
 		assertTrue( g instanceof NucleotideImpl);
 
-		assertTrue(g.getType().equals(GroupType.NUCLEOTIDE));
+        assertEquals(g.getType(), GroupType.NUCLEOTIDE);
 
-		assertTrue( g3.getPDBName().equals("LYS"));
+        assertEquals("LYS", g3.getPDBName());
 		assertTrue( a.getSeqResGroups().contains(g3));
 
 		assertTrue( g3 instanceof AminoAcid);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java
index d79db697d7..b2bae0ff64 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java
@@ -22,6 +22,7 @@
 
 import java.io.IOException;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 import java.util.zip.GZIPInputStream;
 
@@ -45,7 +46,7 @@ public class TestDSSPParser {
 	public void testDSSPParser() throws IOException, StructureException {
 
 		// List of names to test the DSSP prediction
-		List<String> names = Arrays.asList("5pti");
+		List<String> names = Collections.singletonList("5pti");
 
 		for (String name : names) {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSequenceFunctionOrderDetector.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSequenceFunctionOrderDetector.java
index 6df1faf477..2dfb680fc6 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSequenceFunctionOrderDetector.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSequenceFunctionOrderDetector.java
@@ -45,7 +45,7 @@ public class TestSequenceFunctionOrderDetector {
 	@Test
 	public void testGetSymmetryOrder() throws IOException, StructureException, RefinerFailedException {
 		// List of alignments to try, along with proper symmetry
-		Map<String,Integer> orderMap = new HashMap<String,Integer>();
+		Map<String,Integer> orderMap = new HashMap<>();
 		orderMap.put("1itb.A",3); // b-trefoil, C3
 		orderMap.put("1tim.A",2); // tim-barrel, C8
 		//orderMap.put("d1p9ha_",-1); // not rotational symmetry
@@ -54,8 +54,9 @@ public void testGetSymmetryOrder() throws IOException, StructureException, Refin
 
 		AtomCache cache = new AtomCache();
 
-		for(String name : orderMap.keySet()) {
-			CESymmParameters params = new CESymmParameters();
+		for(Map.Entry<String, Integer> entry : orderMap.entrySet()) {
+            String name = entry.getKey();
+            CESymmParameters params = new CESymmParameters();
 			params.setRefineMethod(RefineMethod.NOT_REFINED);
 			Atom[] ca1 = cache.getAtoms(name);
 
@@ -64,7 +65,7 @@ public void testGetSymmetryOrder() throws IOException, StructureException, Refin
 
 			int order = new SequenceFunctionOrderDetector().calculateOrder(afpChain, ca1);
 
-			assertEquals("Wrong order for "+name,orderMap.get(name).intValue(), order);
+			assertEquals("Wrong order for "+name, entry.getValue().intValue(), order);
 		}
 	}
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSingleRefiner.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSingleRefiner.java
index 89c0140ed1..11cdc3d04f 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSingleRefiner.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSingleRefiner.java
@@ -41,7 +41,7 @@ public class TestSingleRefiner {
 	List<Map<Integer, Integer>> expecteds;
 
 	@Before
-	public void setUp() throws Exception {
+	public void setUp() {
 
 		Map<Integer,Integer> align;
 		Map<Integer,Integer> expect;
@@ -49,9 +49,9 @@ public void setUp() throws Exception {
 		// Note that all the expecteds rely on scoreAbsError being used internally
 		// by refineSymmetry
 
-		alignments = new ArrayList<Map<Integer,Integer>>();
-		orders = new ArrayList<Integer>();
-		expecteds = new ArrayList<Map<Integer,Integer>>();
+		alignments = new ArrayList<>();
+		orders = new ArrayList<>();
+		expecteds = new ArrayList<>();
 
 		/* 0. Chained alignment
 		 * 1\
@@ -60,7 +60,7 @@ public void setUp() throws Exception {
 		 * 4>8>12</
 		 * 5>9>13<--
 		 */
-		align = new HashMap<Integer,Integer>();
+		align = new HashMap<>();
 		align.put(	1,	6);
 		align.put(	2,	6);
 		align.put(	3,	7);
@@ -82,7 +82,7 @@ public void setUp() throws Exception {
 		 * 4>8>12<--
 		 * 5>9>13<--
 		 */
-		expect = new HashMap<Integer,Integer>();
+		expect = new HashMap<>();
 		expect.put(	2,	6);
 		expect.put(	3,	7);
 		expect.put(	4,	8);
@@ -102,7 +102,7 @@ public void setUp() throws Exception {
 		 * 1->5->9<--
 		 *    4->8<\
 		 */
-		align = new HashMap<Integer,Integer>();
+		align = new HashMap<>();
 		align.put(	1,	5);
 		align.put(	5,	9);
 		align.put(	9,	1);
@@ -113,7 +113,7 @@ public void setUp() throws Exception {
 		/* 1. Expect
 		 * 1->5->9<--
 		 */
-		expect = new HashMap<Integer,Integer>();
+		expect = new HashMap<>();
 		expect.put(	1,	5);
 		expect.put(	5,	9);
 		expect.put(	9,	1);
@@ -123,7 +123,7 @@ public void setUp() throws Exception {
 		 * 1->5->9<--
 		 * 2->6->10<\
 		 */
-		align = new HashMap<Integer,Integer>();
+		align = new HashMap<>();
 		align.put(	1,	5);
 		align.put(	5,	9);
 		align.put(	9,	1);
@@ -136,7 +136,7 @@ public void setUp() throws Exception {
 		 * 1->5->9<--
 		 * 2->6->10<--
 		 */
-		expect = new HashMap<Integer,Integer>();
+		expect = new HashMap<>();
 		expect.put(	1,	5);
 		expect.put(	5,	9);
 		expect.put(	9,	1);
@@ -149,7 +149,7 @@ public void setUp() throws Exception {
 		 * 1->5->9<--
 		 * 2/^6->10<--
 		 */
-		align = new HashMap<Integer,Integer>();
+		align = new HashMap<>();
 		align.put(	1,	5);
 		align.put(	5,	9);
 		align.put(	9,	1);
@@ -162,7 +162,7 @@ public void setUp() throws Exception {
 		 * 1->5->9<--
 		 * 2->6->10<--
 		 */
-		expect = new HashMap<Integer,Integer>();
+		expect = new HashMap<>();
 		expect.put(	1,	5);
 		expect.put(	5,	9);
 		expect.put(	9,	1);
@@ -174,7 +174,7 @@ public void setUp() throws Exception {
 		/* 4. Wrong order
 		 * 3->7<--
 		 */
-		align = new HashMap<Integer,Integer>();
+		align = new HashMap<>();
 		align.put(	3,	7);
 		align.put(	7,	3);
 		alignments.add(align);
@@ -182,14 +182,14 @@ public void setUp() throws Exception {
 		/*
 		 * 4. Expect empty
 		 */
-		expect = new HashMap<Integer,Integer>();
+		expect = new HashMap<>();
 		expecteds.add(expect);
 
 		/* 5. Prioritize score over chain length
 		 * 1->5->9</
 		 * 3->6->10
 		 */
-		align = new HashMap<Integer,Integer>();
+		align = new HashMap<>();
 		align.put(	1,	5);
 		align.put(	5,	9);
 		align.put(	9,	3);
@@ -200,7 +200,7 @@ public void setUp() throws Exception {
 		/* 5. Expect
 		 * 3->5->9<--
 		 */
-		expect = new HashMap<Integer,Integer>();
+		expect = new HashMap<>();
 		expect.put(	3,	5);
 		expect.put(	5,	9);
 		expect.put(	9,	3);
@@ -211,7 +211,7 @@ public void setUp() throws Exception {
 		/*
 		 * 6. Small cycles can be repaired. 3>5>7>5
 		 */
-		align = new HashMap<Integer, Integer>();
+		align = new HashMap<>();
 		align.put(3, 5);
 		align.put(5, 7);
 		align.put(7, 5);
@@ -220,7 +220,7 @@ public void setUp() throws Exception {
 		/*
 		 * 6. Expect 3>5>7<--
 		 */
-		expect = new HashMap<Integer, Integer>();
+		expect = new HashMap<>();
 		expect.put(3, 5);
 		expect.put(5, 7);
 		expect.put(7, 3);
@@ -230,7 +230,7 @@ public void setUp() throws Exception {
 		 * 7. It might be a good idea to allow cycles if their length divides the order. However, this isn't allowed
 		 * yet. 3>5<
 		 */
-		align = new HashMap<Integer, Integer>();
+		align = new HashMap<>();
 		align.put(3, 5);
 		align.put(5, 3);
 		alignments.add(align);
@@ -238,7 +238,7 @@ public void setUp() throws Exception {
 		/*
 		 * 7. Expect empty, but could argue for 3>5<--
 		 */
-		expect = new HashMap<Integer, Integer>();
+		expect = new HashMap<>();
 		expecteds.add(expect);
 	}
 
@@ -263,8 +263,9 @@ public void testExpected() throws StructureException {
 	 * @param align
 	 */
 	private void testAutomorphism(Map<Integer,Integer> align) {
-		for(Integer pre:align.keySet()) {
-			Integer post = align.get(pre);
+		for(Map.Entry<Integer, Integer> entry : align.entrySet()) {
+            Integer pre = entry.getKey();
+            Integer post = entry.getValue();
 			Assert.assertNotNull("Not automorphic: f(" + pre + ") not defined", post);
 			Assert.assertTrue("not automorphic: f(" + pre + ") = " + post + " but f(" + post + ") undefined", align.containsKey(post));
 		}
@@ -285,8 +286,9 @@ private void testSymmetric(Map<Integer,Integer> align, int k) {
 		Assert.assertEquals(align.size(), alignK.size()); // Assumption; Should be tested by AlignmentToolsTest
 
 		int refinementNum = 0;
-		for(Integer res : alignK.keySet()) {
-			Integer resK = alignK.get(res);
+		for(Map.Entry<Integer, Integer> entry : alignK.entrySet()) {
+            Integer res = entry.getKey();
+            Integer resK = entry.getValue();
 			Assert.assertEquals(String.format("Asymmetric alignment in #%d. f^%d(%d)=%d", refinementNum++, k, res, resK), res,
 					resK);
 		}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSymmetryAxes.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSymmetryAxes.java
index 89455bab86..e3c5e6b9bb 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSymmetryAxes.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSymmetryAxes.java
@@ -23,6 +23,7 @@
 import static org.junit.Assert.*;
 
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 import javax.vecmath.AxisAngle4d;
@@ -103,13 +104,13 @@ public void testClosedCase() {
 				Arrays.asList(1,3,5,7)
 				);
 		assertEquals(relation,axes.getRepeatsCyclicForm(0));
-		relation = Arrays.asList(
-				Arrays.asList(0,1)
-				);
+		relation = Collections.singletonList(
+                Arrays.asList(0, 1)
+        );
 		assertEquals(relation,axes.getRepeatsCyclicForm(1));
-		relation = Arrays.asList(
-				Arrays.asList(2,3)
-				);
+		relation = Collections.singletonList(
+                Arrays.asList(2, 3)
+        );
 		assertEquals(relation,axes.getRepeatsCyclicForm(1,2));
 		try {
 			axes.getRepeatsCyclicForm(2);
@@ -245,13 +246,13 @@ public void testOpenCase() {
 				Arrays.asList(1,3,5,7)
 				);
 		assertEquals(relation,axes.getRepeatsCyclicForm(0));
-		relation = Arrays.asList(
-				Arrays.asList(0,1)
-				);
+		relation = Collections.singletonList(
+                Arrays.asList(0, 1)
+        );
 		assertEquals(relation,axes.getRepeatsCyclicForm(1));
-		relation = Arrays.asList(
-				Arrays.asList(2,3)
-				);
+		relation = Collections.singletonList(
+                Arrays.asList(2, 3)
+        );
 		assertEquals(relation,axes.getRepeatsCyclicForm(1,2));
 		try {
 			axes.getRepeatsCyclicForm(2);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/utils/TestSymmetryTools.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/utils/TestSymmetryTools.java
index aa0c26ddcc..543d2322e5 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/utils/TestSymmetryTools.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/utils/TestSymmetryTools.java
@@ -23,6 +23,7 @@
 import static org.junit.Assert.*;
 
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 import org.junit.Test;
@@ -62,7 +63,7 @@ public void testValidFolds() {
 		assertEquals("Wrong folds for " + stoich, expected, folds);
 
 		stoich = Arrays.asList(6, 5);
-		expected = Arrays.asList(1);
+		expected = Collections.singletonList(1);
 		folds = SymmetryTools.getValidFolds(stoich);
 		assertEquals("Wrong folds for " + stoich, expected, folds);
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/test/util/GlobalsHelper.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/test/util/GlobalsHelper.java
index 9d7e5ae57d..84884f03f2 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/test/util/GlobalsHelper.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/test/util/GlobalsHelper.java
@@ -22,7 +22,6 @@
 
 import java.util.Deque;
 import java.util.LinkedList;
-import java.util.List;
 import java.util.NoSuchElementException;
 
 import org.biojava.nbio.structure.StructureIO;
@@ -65,7 +64,7 @@ public PathInfo() {
 	}
 
 	// Saves defaults as stack
-	private static Deque<PathInfo> stack = new LinkedList<>();
+	private static final Deque<PathInfo> stack = new LinkedList<>();
 	static {
 		// Save default state
 		pushState();
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/validation/TestValidationReportParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/validation/TestValidationReportParsing.java
index da1b9a9b02..010d256ec5 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/validation/TestValidationReportParsing.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/validation/TestValidationReportParsing.java
@@ -83,7 +83,7 @@ public void test() {
 
 	private void testPDB(String pdbId) {
 		try {
-			JAXBContext ctx = JAXBContext.newInstance(new Class[] {WwPDBValidationInformation.class});
+			JAXBContext ctx = JAXBContext.newInstance(WwPDBValidationInformation.class);
 
 			Unmarshaller um = ctx.createUnmarshaller();
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalCell.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalCell.java
index 37e51a7b6a..57bc703d10 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalCell.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalCell.java
@@ -34,7 +34,7 @@
 public class TestCrystalCell {
 
 	@Before
-	public void setUp() throws Exception {
+	public void setUp() {
 	}
 
 	@Test
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalInfo.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalInfo.java
index 501d6eb2af..f891b15a59 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalInfo.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalInfo.java
@@ -153,8 +153,8 @@ private void testCrystallographicInfo(Structure s1, Structure s2) {
 		CrystalCell cell1 = xtalInfo.getCrystalCell();
 		CrystalCell cell2 = xtalInfo2.getCrystalCell();
 
-		if (s1.isNmr()) assertTrue(cell1==null);
-		if (s2.isNmr()) assertTrue(cell2==null);
+		if (s1.isNmr()) assertNull(cell1);
+		if (s2.isNmr()) assertNull(cell2);
 
 		if (cell1==null && cell2==null) return;
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestInterfaceClustering.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestInterfaceClustering.java
index af80c99ae1..313d8ac334 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestInterfaceClustering.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestInterfaceClustering.java
@@ -176,7 +176,7 @@ public void test1AUY() throws IOException, StructureException {
 
 
 	@Test
-	public void test3C5FWithSeqresPdb() throws IOException, StructureException {
+	public void test3C5FWithSeqresPdb() throws IOException {
 
 		InputStream inStream = new GZIPInputStream(this.getClass().getResourceAsStream("/org/biojava/nbio/structure/io/3c5f_raw.pdb.gz"));
 		assertNotNull(inStream);
@@ -224,7 +224,7 @@ public void test3C5FWithSeqresPdb() throws IOException, StructureException {
 	// see https://github.com/eppic-team/eppic/issues/39
 	// See also TestCompoundResIndexMapping
 	//@Test
-	public void test3DDONoSeqresPdb() throws IOException, StructureException {
+	public void test3DDONoSeqresPdb() throws IOException {
 
 		// 3ddo contains 6 chains in 1 entity, with residue numbering completely different in each of the chains
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestSpaceGroup.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestSpaceGroup.java
index 79413317bf..9480bd78b0 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestSpaceGroup.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestSpaceGroup.java
@@ -40,10 +40,10 @@ public class TestSpaceGroup {
 
 	private static final double DELTA = 0.000001;
 	// use true for printing operators of all space groups (including non-enantiomorphics), or false to print only enantiomorphics
-	private static boolean PRINT_OPERATORS_FROM_ALL_SGS = false;
+	private static final boolean PRINT_OPERATORS_FROM_ALL_SGS = false;
 
 	// print information per operator
-	private static boolean VERBOSE = false;
+	private static final boolean VERBOSE = false;
 
 	@Test
 	public void testTransfConversion() {
@@ -101,9 +101,9 @@ public void testTransfConversion() {
 							Assert.assertFalse(diffz>1 && diffz<0);
 
 							// they are integer, i.e. 0 or 1
-							Assert.assertTrue(diffx == (int)diffx);
-							Assert.assertTrue(diffy == (int)diffy);
-							Assert.assertTrue(diffz == (int)diffz);
+							Assert.assertEquals(diffx, (int) diffx, 0.0);
+							Assert.assertEquals(diffy, (int) diffy, 0.0);
+							Assert.assertEquals(diffz, (int) diffz, 0.0);
 						}
 
 					}
@@ -172,11 +172,11 @@ public void testTransfConversion() {
 				if (i==0) {
 					Assert.assertTrue(ct.isIdentity());
 					Assert.assertFalse(ct.isPureCrystalTranslation());
-					Assert.assertTrue(ct.getTransformType()==TransformType.AU);
+					Assert.assertSame(ct.getTransformType(), TransformType.AU);
 				}
 
 				Assert.assertFalse(ct.isPureCrystalTranslation());
-				Assert.assertFalse(ct.getTransformType()==TransformType.XTALTRANSL);
+				Assert.assertNotSame(ct.getTransformType(), TransformType.XTALTRANSL);
 
 
 				// rotation axes and type
@@ -206,7 +206,10 @@ public void testTransfConversion() {
 				} else { // i.e. determinant -1
 					switch (foldType) {
 					case -1:
-						Assert.assertEquals(0,axisAngle.angle,DELTA);
+                        case -6:
+                        case -4:
+                        case -3:
+                            Assert.assertEquals(0,axisAngle.angle,DELTA);
 						// no glide planes
 						Assert.assertTrue(ct.getTranslScrewComponent().epsilonEquals(new Vector3d(0,0,0), DELTA));
 						break;
@@ -214,23 +217,11 @@ public void testTransfConversion() {
 						Assert.assertEquals(0,axisAngle.angle,DELTA);
 						// glide planes can happen
 						break;
-					case -3:
-						Assert.assertEquals(0,axisAngle.angle,DELTA);
-						// no glide planes
-						Assert.assertTrue(ct.getTranslScrewComponent().epsilonEquals(new Vector3d(0,0,0), DELTA));
-						break;
-					case -4:
-						Assert.assertEquals(0,axisAngle.angle,DELTA);
-						// no glide planes
-						Assert.assertTrue(ct.getTranslScrewComponent().epsilonEquals(new Vector3d(0,0,0), DELTA));
-						break;
-					case -6:
-						Assert.assertEquals(0,axisAngle.angle,DELTA);
-						// no glide planes
-						Assert.assertTrue(ct.getTranslScrewComponent().epsilonEquals(new Vector3d(0,0,0), DELTA));
-						break;
+                        // no glide planes
+                        // no glide planes
+                        // no glide planes
 
-					}
+                    }
 
 				}
 
@@ -288,14 +279,14 @@ public void testTransfConversion() {
 					}
 
 					Assert.assertTrue(ct.isFractionalTranslation());
-					Assert.assertTrue(ct.getTransformType()==TransformType.CELLTRANSL);
+					Assert.assertSame(ct.getTransformType(), TransformType.CELLTRANSL);
 				}
 				if (ct.isRotation() && !ct.isFractionalTranslation()) {
 					Assert.assertTrue(ct.getTransformType()==TransformType.TWOFOLD ||
 							ct.getTransformType()==TransformType.THREEFOLD ||
 							ct.getTransformType()==TransformType.FOURFOLD ||
 							ct.getTransformType()==TransformType.SIXFOLD);
-					Assert.assertTrue(!ct.getTransformType().isScrew());
+					Assert.assertFalse(ct.getTransformType().isScrew());
 				}
 
 				if (spaceGroup.isEnantiomorphic() || PRINT_OPERATORS_FROM_ALL_SGS) {
@@ -332,7 +323,7 @@ private static boolean eq(double d1, double d2) {
 	}
 
 	// to debug the testing code (run as java program so that we can use normal debugger)
-	public static void main(String[] args) throws Exception {
+	public static void main(String[] args) {
 		TestSpaceGroup test = new TestSpaceGroup();
 		test.testTransfConversion();
 	}
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java
index 728e6e925c..fce2e76c0a 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java
@@ -27,6 +27,7 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.LinkedHashMap;
+import java.util.Map;
 
 /**
  *
@@ -42,9 +43,9 @@ public class CoxCC {
 	static public void process(CoxInfo ci) throws Exception {
 		ArrayList<SurvivalInfo> survivalInfoList = ci.survivalInfoList;
 		//r
-		ArrayList<String> variables = new ArrayList<String>(ci.getCoefficientsList().keySet());
+		ArrayList<String> variables = new ArrayList<>(ci.getCoefficientsList().keySet());
 
-		ArrayList<Integer> strataClass = new ArrayList<Integer>(survivalInfoList.size());
+		ArrayList<Integer> strataClass = new ArrayList<>(survivalInfoList.size());
 		double[] wt = new double[survivalInfoList.size()];
 		for (int i = 0; i < survivalInfoList.size(); i++) {
 			SurvivalInfo si = survivalInfoList.get(i);
@@ -67,7 +68,7 @@ static public void process(CoxInfo ci) throws Exception {
 //            }
 //        }
 
-		double[][] rvar = null;
+		double[][] rvar;
 
 		if (ci.getNaiveVariance() != null) {
 			rvar = ci.getNaiveVariance();
@@ -75,7 +76,7 @@ static public void process(CoxInfo ci) throws Exception {
 			rvar = ci.getVariance();
 		}
 		//nj
-		LinkedHashMap<Integer, Double> nj = new LinkedHashMap<Integer, Double>();
+		LinkedHashMap<Integer, Double> nj = new LinkedHashMap<>();
 		Collections.sort(strataClass);
 		for (Integer value : strataClass) {
 			Double count = nj.get(value);
@@ -86,7 +87,7 @@ static public void process(CoxInfo ci) throws Exception {
 			nj.put(value, count);
 		}
 		//Nj
-		LinkedHashMap<Integer, Double> Nj = new LinkedHashMap<Integer, Double>();
+		LinkedHashMap<Integer, Double> Nj = new LinkedHashMap<>();
 		//N = N + Nj[key];
 		double N = 0;
 		for (int i = 0; i < survivalInfoList.size(); i++) {
@@ -106,9 +107,10 @@ static public void process(CoxInfo ci) throws Exception {
 			N = N + value;
 		}
 
-		LinkedHashMap<Integer, Double> k1j = new LinkedHashMap<Integer, Double>();
-		for (Integer key : nj.keySet()) {
-			double _nj = (nj.get(key)); //trying to copy what R is doing on precision
+		LinkedHashMap<Integer, Double> k1j = new LinkedHashMap<>();
+		for (Map.Entry<Integer, Double> entry : nj.entrySet()) {
+            Integer key = entry.getKey();
+            double _nj = (entry.getValue()); //trying to copy what R is doing on precision
 			double _Nj = (Nj.get(key));
 			//         System.out.println("nj=" + _nj + " Nj=" + _Nj);
 			k1j.put(key, _Nj * ((_Nj / _nj) - 1));
@@ -116,10 +118,11 @@ static public void process(CoxInfo ci) throws Exception {
 
 		double[][] V = new double[variables.size()][variables.size()];
 
-		for (Integer i : k1j.keySet()) {
-			//          System.out.println("Strata=" + i + " " + k1j.get(i) + " " + Nj.get(i) + " " + nj.get(i));
+		for (Map.Entry<Integer, Double> entry : k1j.entrySet()) {
+            Integer i = entry.getKey();
+            //          System.out.println("Strata=" + i + " " + k1j.get(i) + " " + Nj.get(i) + " " + nj.get(i));
 			if (nj.get(i) > 1) {
-				LinkedHashMap<String, DescriptiveStatistics> variableStatsMap = new LinkedHashMap<String, DescriptiveStatistics>();
+				LinkedHashMap<String, DescriptiveStatistics> variableStatsMap = new LinkedHashMap<>();
 
 				for (int p = 0; p < survivalInfoList.size(); p++) {
 					SurvivalInfo si = survivalInfoList.get(p);
@@ -161,7 +164,7 @@ static public void process(CoxInfo ci) throws Exception {
 		 //              System.out.println("sstrat=" + i);
 		 //              StdArrayIO.print(var_covar);
 
-					   V = Matrix.add(V, Matrix.scale(var_covar, k1j.get(i))  );
+					   V = Matrix.add(V, Matrix.scale(var_covar, entry.getValue())  );
 
 		 //       for (int m = 0; m < V.length; m++) {
 		 //           for (int n = 0; n < V.length; n++) {
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCoefficient.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCoefficient.java
index a8023284b5..6befe1e2f5 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCoefficient.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCoefficient.java
@@ -222,7 +222,7 @@ public void setStandardDeviation(double standardDeviation) {
 	 * @return
 	 */
 	public static String fmt(Double d, int precision, int pad) {
-		String value = "";
+		String value;
 		DecimalFormat dfe = new DecimalFormat("0.00E0");
 		String dpad = "0.";
 		double p = 1.0;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java
index 920fd3cc33..dfc149c54e 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java
@@ -71,7 +71,7 @@ public static CoxInfo process(String datafile, String timeColumn, String statusC
 	public static CoxInfo process(WorkSheet worksheet, String timeColumn, String statusColumn, String weightColumn, String strataColumn, String clusterColumn, ArrayList<String> variables, boolean useStrata, boolean useWeights) {
 
 		try {
-			ArrayList<SurvivalInfo> survivalInfoList = new ArrayList<SurvivalInfo>();
+			ArrayList<SurvivalInfo> survivalInfoList = new ArrayList<>();
 
 			int i = 1;
 			for (String row : worksheet.getRows()) {
@@ -152,7 +152,7 @@ public static void main(String[] args) {
 		try {
 			if (true) {
 				String datafile = "/Users/Scooter/scripps/ngs/DataSets/E2197/misc/ecoglabtransfer/500790/2013.05.10.12.28.58.313/clindasl0228.txt";
-				ArrayList<String> variables = new ArrayList<String>();
+				ArrayList<String> variables = new ArrayList<>();
 				variables.add("nndpos");
 				variables.add("meno");
 //              variables.add("er1");
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
index d60d8a316e..1eb0bcd867 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
@@ -27,6 +27,7 @@
 import java.text.DecimalFormat;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
+import java.util.Map;
 
 //import org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator;
 
@@ -59,9 +60,9 @@ public class CoxInfo {
 	int numSamples = 0;
 	int numEvents = 0;
 	private LinkedHashMap<String, String> metaDataFilter = null;
-	private LinkedHashMap<String, CoxCoefficient> coefficientsList = new LinkedHashMap<String, CoxCoefficient>();
-	LinkedHashMap<Double, Double> baselineSurvivorFunction = new LinkedHashMap<Double, Double>();
-	ArrayList<SurvivalInfo> survivalInfoList = new ArrayList<SurvivalInfo>();
+	private final LinkedHashMap<String, CoxCoefficient> coefficientsList = new LinkedHashMap<>();
+	LinkedHashMap<Double, Double> baselineSurvivorFunction = new LinkedHashMap<>();
+	ArrayList<SurvivalInfo> survivalInfoList = new ArrayList<>();
 	/**
 	 *
 	 */
@@ -82,18 +83,15 @@ public ArrayList<SurvivalInfo> getSurvivalInfoList() {
 	/**
 	 *
 	 * @param var
-	 * @throws Exception
 	 */
-	public void setVariance(double[][] var) throws Exception {
+	public void setVariance(double[][] var) {
 
 		//   if (Math.abs(var[0][1] - var[1][0]) > .0000000000001) { //in the CoxCC correction looks like a precision error keeps these from being equal 10-19
 		//       throw new Exception("Expecting diagonal to be equal");
 		//   }
 		imat = new double[var.length][var[0].length];
 		for (int i = 0; i < var.length; i++) {
-			for (int j = 0; j < var[0].length; j++) {
-				imat[i][j] = var[i][j];
-			}
+            System.arraycopy(var[i], 0, imat[i], 0, var[0].length);
 		}
 		calcSummaryValues();
 	}
@@ -105,9 +103,7 @@ public void setVariance(double[][] var) throws Exception {
 	public double[][] getVariance() {
 		double[][] var = new double[imat.length][imat[0].length];
 		for (int i = 0; i < var.length; i++) {
-			for (int j = 0; j < var[0].length; j++) {
-				var[i][j] = imat[i][j];
-			}
+            System.arraycopy(imat[i], 0, var[i], 0, var[0].length);
 		}
 
 		return var;
@@ -116,9 +112,8 @@ public double[][] getVariance() {
 	/**
 	 *
 	 * @param var
-	 * @throws Exception
 	 */
-	public void setNaiveVariance(double[][] var) throws Exception {
+	public void setNaiveVariance(double[][] var) {
 //        if (var[0][1] != var[1][0]) {
 //            throw new Exception("Expecting diagonal to be equal");
 //        }
@@ -126,9 +121,7 @@ public void setNaiveVariance(double[][] var) throws Exception {
 
 		naive_imat = new double[var.length][var[0].length];
 		for (int i = 0; i < var.length; i++) {
-			for (int j = 0; j < var[0].length; j++) {
-				naive_imat[i][j] = var[i][j];
-			}
+            System.arraycopy(var[i], 0, naive_imat[i], 0, var[0].length);
 		}
 
 		calcSummaryValues();
@@ -141,9 +134,7 @@ public void setNaiveVariance(double[][] var) throws Exception {
 	public double[][] getNaiveVariance() {
 		double[][] var = new double[imat.length][imat[0].length];
 		for (int i = 0; i < var.length; i++) {
-			for (int j = 0; j < var[0].length; j++) {
-				var[i][j] = naive_imat[i][j];
-			}
+            System.arraycopy(naive_imat[i], 0, var[i], 0, var[0].length);
 		}
 
 		return var;
@@ -184,7 +175,7 @@ public double[] getWeighted() {
 	 * @return
 	 */
 	public double[][] getVariableResiduals() {
-		ArrayList<String> variables = new ArrayList<String>(coefficientsList.keySet());
+		ArrayList<String> variables = new ArrayList<>(coefficientsList.keySet());
 		double[][] rr = new double[survivalInfoList.size()][variables.size()];
 		int p = 0;
 		for (SurvivalInfo si : this.survivalInfoList) {
@@ -204,7 +195,7 @@ public double[][] getVariableResiduals() {
 	 * @param rr
 	 */
 	public void setVariableResiduals(double[][] rr) {
-		ArrayList<String> variables = new ArrayList<String>(coefficientsList.keySet());
+		ArrayList<String> variables = new ArrayList<>(coefficientsList.keySet());
 
 		int p = 0;
 		for (SurvivalInfo si : this.survivalInfoList) {
@@ -265,7 +256,7 @@ public String getCoefficientText(boolean header, String beginLine, String beginC
 
 		for (CoxCoefficient coe : coefficientsList.values()) {
 			String robust = "";
-			String stderror = "";
+			String stderror;
 			if (naive_imat != null) {
 				stderror = beginCell + fmt(coe.getRobustStdError(), 5, 9) + endCell;
 				robust = beginCell + fmt(coe.getStdError(), 5, 9) + endCell;
@@ -289,7 +280,7 @@ public static String fmt(Double d, int precision, int pad) {
 			return "";
 		if(Double.isNaN(d))
 			return "";
-		String value = "";
+		String value;
 		DecimalFormat dfe = new DecimalFormat("0.00E0");
 		String dpad = "0.";
 		double p = 1.0;
@@ -320,7 +311,7 @@ private void calcSummaryValues() {
 
 		//beta
 
-		ArrayList<String> variables = new ArrayList<String>(coefficientsList.keySet());
+		ArrayList<String> variables = new ArrayList<>(coefficientsList.keySet());
 		for (int i = 0; i < variables.size(); i++) {
 			String variable = variables.get(i);
 			CoxCoefficient coe = coefficientsList.get(variable);
@@ -507,9 +498,9 @@ public String toString(String beginLine, String del, String endLine) {
 
 		if (baselineSurvivorFunction.size() > 0) {
 			o = o + beginLine + "Baseline Survivor Function (at predictor means)" + endLine;
-			for (Double time : baselineSurvivorFunction.keySet()) {
-				Double mean = baselineSurvivorFunction.get(time);
-				o = o + beginLine + fmt(time, 4, 10) + fmt(mean, 4, 10) + endLine;
+			for (Map.Entry<Double, Double> entry : baselineSurvivorFunction.entrySet()) {
+				Double mean = entry.getValue();
+				o = o + beginLine + fmt(entry.getKey(), 4, 10) + fmt(mean, 4, 10) + endLine;
 			}
 		}
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMart.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMart.java
index d49545efa6..0dd7064b69 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMart.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMart.java
@@ -59,7 +59,7 @@ static public double[] process(CoxMethod method, ArrayList<SurvivalInfo> surviva
 		int i, j;
 		int lastone;
 		int n = survivalInfoList.size();
-		double deaths, denom = 0, e_denom = 0;
+		double deaths, denom = 0, e_denom;
 		double hazard;
 		double temp, wtsum;
 		double downwt;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java
index 6a3002f492..9a7437c3f2 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java
@@ -155,7 +155,7 @@ public CoxInfo process(ArrayList<String> variables, ArrayList<SurvivalInfo> data
 		SurvivalInfoHelper.categorizeData(data);
 		//create variables if testing for interaction
 		for (String variable : variables) {
-			if (variable.indexOf(":") != -1) {
+			if (variable.contains(":")) {
 				String[] d = variable.split(":");
 				SurvivalInfoHelper.addInteraction(d[0], d[1], data);
 			}
@@ -203,7 +203,7 @@ public CoxInfo process(ArrayList<String> variables, ArrayList<SurvivalInfo> data
 
 
 		double sctest;
-		int flag = 0;
+		int flag;
 		int iter = 0;
 		//SEXP rlist, rlistnames;
 		//  int nprotect;  /* number of protect calls I have issued */
@@ -273,7 +273,7 @@ public CoxInfo process(ArrayList<String> variables, ArrayList<SurvivalInfo> data
 		ArrayList<String> clusterList = null;
 
 		if(cluster){
-			clusterList = new ArrayList<String>();
+			clusterList = new ArrayList<>();
 		}
 		//copy data over to local arrays to minimuze changing code
 		for (person = 0; person < nused; person++) {
@@ -303,7 +303,7 @@ public CoxInfo process(ArrayList<String> variables, ArrayList<SurvivalInfo> data
 			}
 		}
 
-		double tempsd = 0;
+		double tempsd;
 		i = 0;
 		for (i = 0; i < nvar; i++) {
 
@@ -797,13 +797,14 @@ public void coxphfitSCleanup(CoxInfo ci, boolean useWeighted,boolean robust, Arr
 		double[] infs = Matrix.abs(Matrix.multiply(ci.u, ci.getVariance()));
 //        StdArrayIO.print(infs);
 
-		ArrayList<CoxCoefficient> coxCoefficients = new ArrayList<CoxCoefficient>(ci.getCoefficientsList().values());
+		ArrayList<CoxCoefficient> coxCoefficients = new ArrayList<>(ci.getCoefficientsList().values());
 
 		for (int i = 0; i < infs.length; i++) {
 			double inf = infs[i];
 			double coe = coxCoefficients.get(i).getCoeff();
 			if (inf > ci.eps && inf > (ci.toler * Math.abs(coe))) {
 				ci.message = "Loglik converged before variable ";
+				break;
 			}
 		}
 
@@ -958,7 +959,7 @@ public static void main(String[] args) {
 
 
 				WorkSheet worksheet = WorkSheet.readCSV(is, '\t');
-				ArrayList<SurvivalInfo> survivalInfoList = new ArrayList<SurvivalInfo>();
+				ArrayList<SurvivalInfo> survivalInfoList = new ArrayList<>();
 				int i = 0;
 				for (String row : worksheet.getRows()) {
 					double time = worksheet.getCellDouble(row, "TIME");
@@ -977,7 +978,7 @@ public static void main(String[] args) {
 				}
 
 				CoxR cox = new CoxR();
-				ArrayList<String> variables = new ArrayList<String>();
+				ArrayList<String> variables = new ArrayList<>();
 				//               variables.add("AGE");
 
 				variables.add("AGE");
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java
index dd8e73822e..cc51ec4d3f 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java
@@ -41,7 +41,7 @@ public static double[][] process(CoxMethod method, ArrayList<SurvivalInfo> survi
 		double temp;
 		int n = survivalInfoList.size();
 
-		ArrayList<String> variables = new ArrayList<String>(coxInfo.getCoefficientsList().keySet());
+		ArrayList<String> variables = new ArrayList<>(coxInfo.getCoefficientsList().keySet());
 		int nvar = variables.size();
 
 		double deaths;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java
index bfcaa5bd97..c4bfc4c7de 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java
@@ -30,9 +30,9 @@
 public class CoxVariables {
 
 	//   public GeneSetResults gsr;
-	private String cohortName = "";
-	private String geneSet = "";
-	private String genes = "";
+	private String cohortName;
+	private String geneSet;
+	private String genes;
 
 	/**
 	 *
@@ -55,7 +55,7 @@ public int getUniqueID() {
 		String link = geneSet + "_" + cohortName;
 		return link.hashCode();
 	}
-	private LinkedHashMap<String, CoxInfo> coxInfoHashMap = new LinkedHashMap<String, CoxInfo>();
+	private final LinkedHashMap<String, CoxInfo> coxInfoHashMap = new LinkedHashMap<>();
 
 	/**
 	 *
@@ -98,7 +98,7 @@ public String encodeFileURL(String file) {
 	 * @return
 	 */
 	public static String fmt(Double d, int precision, int pad) {
-		String value = "";
+		String value;
 		DecimalFormat dfe = new DecimalFormat("0.00E0");
 		String dpad = "0.";
 		double p = 1.0;
@@ -128,10 +128,9 @@ public String toString() {
 		//    co = co + genes + "\r\n";
 		coxOutput = coxOutput + cohortName + "," + genes.replace(',', ' ') + "\r\n";
 		coxOutput = coxOutput + ",Coe,StdErr,p-value,HR,HR Lo 95%,HR Hi 95%\r\n";
-		for (String variables : coxInfoHashMap.keySet()) {
-			CoxInfo ci = coxInfoHashMap.get(variables);
+		for (CoxInfo ci : coxInfoHashMap.values()) {
 
-			coxOutput = coxOutput + "Overall Model Fit p-value=" + fmt(ci.getOverallModelFitPvalue(), 5, 0) + "\r\n";
+            coxOutput = coxOutput + "Overall Model Fit p-value=" + fmt(ci.getOverallModelFitPvalue(), 5, 0) + "\r\n";
 			coxOutput = coxOutput + ci.getCoefficientText(false, "", ",", "", "");
 			coxOutput = coxOutput + "\r\n";
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java
index 819ad24e0b..b155e45916 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java
@@ -49,7 +49,7 @@ public enum Type {
 		/**
 		 *
 		 */
-		score;
+		score
 	}
 
 	/**
@@ -86,7 +86,7 @@ public static double[][] process(CoxInfo ci, Type type, boolean useWeighted, Arr
 //        }
 
 
-		double[][] vv = null;
+		double[][] vv;
 		if (ci.getNaiveVariance() != null) {
 			vv = ci.getNaiveVariance();
 		} else {
@@ -124,7 +124,7 @@ public static double[][] process(CoxInfo ci, Type type, boolean useWeighted, Arr
 	 * @return
 	 */
 	private static double[][] rowsum(double[][] rr, ArrayList<String> sets) throws Exception {
-		LinkedHashMap<String, Double> sumMap = new LinkedHashMap<String, Double>();
+		LinkedHashMap<String, Double> sumMap = new LinkedHashMap<>();
 		if (rr.length != sets.size()) {
 			throw new Exception("Cluster value for each sample are not of equal length n=" + rr.length + " cluster length=" + sets.size());
 		}
@@ -144,7 +144,7 @@ private static double[][] rowsum(double[][] rr, ArrayList<String> sets) throws E
 				sum = new double[sumMap.size()][rr[0].length];
 			}
 
-			ArrayList<String> index = new ArrayList<String>(sumMap.keySet());
+			ArrayList<String> index = new ArrayList<>(sumMap.keySet());
 			//sorting does seem to make a difference in test cases at the .0000000001
 	   //     ArrayList<Integer> in = new ArrayList<Integer>();
 	   //     for (String s : index) {
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java
index 11b01cf41c..57d7b016f3 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java
@@ -31,19 +31,19 @@
  */
 public class StrataInfo {
 
-	private ArrayList<Double> time = new ArrayList<Double>();
-	private ArrayList<Integer> status = new ArrayList<Integer>();
-	private ArrayList<Double> nevent = new ArrayList<Double>();
-	private ArrayList<Double> ncens = new ArrayList<Double>();
-	private ArrayList<Double> nrisk = new ArrayList<Double>();
-	private ArrayList<Double> weight = new ArrayList<Double>();
-	private ArrayList<Double> surv = new ArrayList<Double>();
-	private ArrayList<Double> varhaz = new ArrayList<Double>();
-	private ArrayList<Double> stderr = new ArrayList<Double>();
-	private ArrayList<Double> stdlow = new ArrayList<Double>();
-	private ArrayList<Double> upper = new ArrayList<Double>();
-	private ArrayList<Double> lower = new ArrayList<Double>();
-	private LinkedHashMap<Double, Integer> ndead = new LinkedHashMap<Double, Integer>();
+	private final ArrayList<Double> time = new ArrayList<>();
+	private final ArrayList<Integer> status = new ArrayList<>();
+	private final ArrayList<Double> nevent = new ArrayList<>();
+	private final ArrayList<Double> ncens = new ArrayList<>();
+	private final ArrayList<Double> nrisk = new ArrayList<>();
+	private final ArrayList<Double> weight = new ArrayList<>();
+	private final ArrayList<Double> surv = new ArrayList<>();
+	private final ArrayList<Double> varhaz = new ArrayList<>();
+	private final ArrayList<Double> stderr = new ArrayList<>();
+	private ArrayList<Double> stdlow = new ArrayList<>();
+	private final ArrayList<Double> upper = new ArrayList<>();
+	private final ArrayList<Double> lower = new ArrayList<>();
+	private final LinkedHashMap<Double, Integer> ndead = new LinkedHashMap<>();
 	DecimalFormat df = new DecimalFormat("#.######");
 	DecimalFormat dfe = new DecimalFormat("0.000000E0");
 
@@ -67,7 +67,7 @@ public Double getNearestTime(double timePercentage) {
 				maxTime = t;
 			}
 		}
-		Double timeRange = maxTime - minTime;
+		double timeRange = maxTime - minTime;
 		Double targetTime = minTime + timePercentage * timeRange;
 		Double previousTime = null;
 		for (Double t : time) {
@@ -89,7 +89,7 @@ public Double getNearestTime(double timePercentage) {
 	 * @return
 	 */
 	public Double getNearestAtRisk(double t) {
-		Integer index = 0;
+		int index = 0;
 /*       String timeValue = t + "";
 		String format = "#";
 		int numDecimals = 0;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java
index 0d2567a78b..abe1be095e 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java
@@ -21,6 +21,7 @@
 package org.biojava.nbio.survival.cox;
 
 import java.util.LinkedHashMap;
+import java.util.Map;
 
 /**
  * Contains info for graphing km figures
@@ -29,8 +30,8 @@
  */
 public class SurvFitInfo {
 
-	private LinkedHashMap<String, StrataInfo> strataInfoHashMap = new LinkedHashMap<String, StrataInfo>();
-	private LinkedHashMap<String, StrataInfo> unweightedStrataInfoHashMap = new LinkedHashMap<String, StrataInfo>();
+	private LinkedHashMap<String, StrataInfo> strataInfoHashMap = new LinkedHashMap<>();
+	private LinkedHashMap<String, StrataInfo> unweightedStrataInfoHashMap = new LinkedHashMap<>();
 	private boolean weighted = false;
 
 
@@ -70,9 +71,9 @@ public void setStrataInfoHashMap(LinkedHashMap<String, StrataInfo> strataInfoHas
 	 * @param label
 	 */
 	public void addStrataInfoHashMap(LinkedHashMap<String, StrataInfo> siHashMap, String label) {
-		for (String key : siHashMap.keySet()) {
-			StrataInfo si = siHashMap.get(key);
-			strataInfoHashMap.put(label + " " + key, si);
+		for (Map.Entry<String, StrataInfo> entry : siHashMap.entrySet()) {
+			StrataInfo si = entry.getValue();
+			strataInfoHashMap.put(label + " " + entry.getKey(), si);
 		}
 	}
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java
index 6d4455193e..67a46b9802 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java
@@ -22,6 +22,7 @@
 
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
+import java.util.Map;
 
 /**
  * Data class to represent a single sample where time and event/censor status is required
@@ -45,12 +46,12 @@ public class SurvivalInfo implements Comparable<SurvivalInfo> {
 	private double residual = 0.0;
 	private String clusterValue = "";
 
-	LinkedHashMap<String,Double> residualVariableMap = new LinkedHashMap<String,Double>();
+	LinkedHashMap<String,Double> residualVariableMap = new LinkedHashMap<>();
 
-	LinkedHashMap<String, Double> data = new LinkedHashMap<String, Double>();
+	LinkedHashMap<String, Double> data = new LinkedHashMap<>();
 	//    LinkedHashMap<String, Double> discreteData = new LinkedHashMap<String, Double>();
-	LinkedHashMap<String, String> unknownDataType = new LinkedHashMap<String, String>();
-	LinkedHashMap<String, String> originalMetaData = new LinkedHashMap<String,String>();
+	LinkedHashMap<String, String> unknownDataType = new LinkedHashMap<>();
+	LinkedHashMap<String, String> originalMetaData = new LinkedHashMap<>();
 
 	/**
 	 *
@@ -74,9 +75,9 @@ public SurvivalInfo(double t, int e, LinkedHashMap<String, Double> d) {
 		status = e;
 
 		data = d;
-		for(String key : d.keySet()){
-			Double value = d.get(key);
-			originalMetaData.put(key, value + "");
+		for(Map.Entry<String, Double> entry : d.entrySet()){
+			Double value = entry.getValue();
+			originalMetaData.put(entry.getKey(), String.valueOf(value));
 		}
 	}
 
@@ -158,7 +159,7 @@ public void updateContinousVariable(String variable, Double value){
 	 * @param value
 	 */
 	public void addContinuousVariable(String variable, Double value) {
-		originalMetaData.put(variable, value + "");
+		originalMetaData.put(variable, String.valueOf(value));
 		data.put(variable, value);
 	}
 
@@ -177,7 +178,7 @@ public Double getContinuousVariable(String variable) {
 	 * @return
 	 */
 	public ArrayList<String> getGroupCategories(String groupName) {
-		ArrayList<String> groupNameList = new ArrayList<String>();
+		ArrayList<String> groupNameList = new ArrayList<>();
 		for (String key : data.keySet()) {
 			if (key.startsWith(groupName + "_")) {
 				groupNameList.add(key);
@@ -199,7 +200,7 @@ public ArrayList<String> getGroupCategories(String groupName) {
 	 * @return
 	 */
 	public ArrayList<String> getDataVariables(){
-		ArrayList<String> v = new ArrayList<String>();
+		ArrayList<String> v = new ArrayList<>();
 		v.addAll(data.keySet());
 		v.addAll(unknownDataType.keySet());
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java
index 4e5c0981c0..dec820aa25 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java
@@ -24,6 +24,7 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.LinkedHashMap;
+import java.util.Map;
 
 /**
  * Used to work with SurvivalInfo
@@ -86,23 +87,18 @@ private static boolean isCategorical(LinkedHashMap<String, Double> values) {
 	public static void categorizeData(ArrayList<SurvivalInfo> DataT) {
 
 		//Go through and get all variable value pairs
-		LinkedHashMap<String, LinkedHashMap<String, Double>> valueMap = new LinkedHashMap<String, LinkedHashMap<String, Double>>();
+		LinkedHashMap<String, LinkedHashMap<String, Double>> valueMap = new LinkedHashMap<>();
 		for (SurvivalInfo si : DataT) {
 
-			for (String key : si.unknownDataType.keySet()) {
-				LinkedHashMap<String, Double> map = valueMap.get(key);
-				if (map == null) {
-					map = new LinkedHashMap<String, Double>();
-					valueMap.put(key, map);
-				}
-				map.put(si.unknownDataType.get(key), null);
+			for (Map.Entry<String, String> entry : si.unknownDataType.entrySet()) {
+				LinkedHashMap<String, Double> map = valueMap.computeIfAbsent(entry.getKey(), k -> new LinkedHashMap<>());
+				map.put(entry.getValue(), null);
 			}
 		}
 
-		for (String variable : valueMap.keySet()) {
-			LinkedHashMap<String, Double> values = valueMap.get(variable);
-			if (isCategorical(values)) {
-				ArrayList<String> categories = new ArrayList<String>(values.keySet());
+		for (LinkedHashMap<String, Double> values : valueMap.values()) {
+            if (isCategorical(values)) {
+				ArrayList<String> categories = new ArrayList<>(values.keySet());
 				Collections.sort(categories); //go ahead and put in alphabetical order
 				if (categories.size() == 2) {
 					for (String value : values.keySet()) {
@@ -125,9 +121,10 @@ public static void categorizeData(ArrayList<SurvivalInfo> DataT) {
 		}
 
 		for (SurvivalInfo si : DataT) {
-			for (String key : si.unknownDataType.keySet()) {
-				LinkedHashMap<String, Double> map = valueMap.get(key);
-				String value = si.unknownDataType.get(key);
+			for (Map.Entry<String, String> entry : si.unknownDataType.entrySet()) {
+                String key = entry.getKey();
+                LinkedHashMap<String, Double> map = valueMap.get(key);
+				String value = entry.getValue();
 				Double d = map.get(value);
 				si.data.put(key, d);
 			}
@@ -147,7 +144,7 @@ public static void categorizeData(ArrayList<SurvivalInfo> DataT) {
 	 * @return
 	 */
 	public static ArrayList<String> addInteraction(String variable1, String variable2, ArrayList<SurvivalInfo> survivalInfoList) {
-		ArrayList<String> variables = new ArrayList<String>();
+		ArrayList<String> variables = new ArrayList<>();
 		variables.add(variable1);
 		variables.add(variable2);
 		variables.add(variable1 + ":" + variable2);
@@ -170,9 +167,9 @@ public static ArrayList<String> addInteraction(String variable1, String variable
 	 * @throws Exception
 	 */
 	public static void groupByRange(double[] range, String variable, String groupName, ArrayList<SurvivalInfo> survivalInfoList) throws Exception {
-		ArrayList<String> labels = new ArrayList<String>();
+		ArrayList<String> labels = new ArrayList<>();
 		for (int i = 0; i < range.length; i++) {
-			String label = "";
+			String label;
 			if (i == 0) {
 				label = "[<=" + range[i] + "]";
 			} else if (i == range.length - 1) {
@@ -184,7 +181,7 @@ public static void groupByRange(double[] range, String variable, String groupNam
 			}
 			labels.add(label);
 		}
-		ArrayList<String> validLabels = new ArrayList<String>();
+		ArrayList<String> validLabels = new ArrayList<>();
 
 		//need to find the categories so we can set 1 and 0 and not include ranges with no values
 		for (SurvivalInfo si : survivalInfoList) {
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoIndex.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoIndex.java
index 51c443b0b7..3894425fc8 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoIndex.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoIndex.java
@@ -26,9 +26,9 @@
  */
 public class SurvivalInfoIndex implements Comparable<SurvivalInfoIndex> {
 
-	private double time;
-	private int event;
-	private int index;
+	private final double time;
+	private final int event;
+	private final int index;
 	private double[] data;
 
 	/**
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTest.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTest.java
index fb011e3cf4..b6d9d811b1 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTest.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTest.java
@@ -41,9 +41,7 @@ public class WaldTest {
 	public static WaldTestInfo process(double[][] var, double[] b, double toler_chol) {
 		double[][] b_ = new double[1][b.length];
 
-		for(int i = 0; i < b.length; i++){
-			b_[0][i] = b[i];
-		}
+        System.arraycopy(b, 0, b_[0], 0, b.length);
 
 		return process(var,b_,toler_chol);
 
@@ -59,7 +57,7 @@ public static WaldTestInfo process(double[][] var, double[] b, double toler_chol
 	public static WaldTestInfo process(double[][] var, double[][] b, double toler_chol) {
 
 
-		int i = 0;
+		int i;
 
 	//      if(ci.coefficientsList.size() == 1){
 	//          double b_ = b[0][i];
@@ -71,7 +69,7 @@ public static WaldTestInfo process(double[][] var, double[][] b, double toler_ch
 		//  double toler_chol = ci.toler;
 		int ntest = 1;
 		int nvar = b[0].length;
-		double sum = 0;
+		double sum;
 		double[][] solve = new double[ntest][nvar];
 		double[] bsum = new double[ntest];
 
@@ -85,9 +83,7 @@ public static WaldTestInfo process(double[][] var, double[][] b, double toler_ch
 		}
 
 		for (i = 0; i < ntest; i++) {
-			for (int j = 0; j < nvar; j++) {
-				solve[i][j] = b[i][j];
-			}
+            System.arraycopy(b[i], 0, solve[i], 0, nvar);
 			Chsolve2.process(var, nvar, solve, i);   /*solve now has b* var-inverse */
 
 			sum = 0;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.java
index 703936e751..0bd486a0de 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.java
@@ -30,8 +30,8 @@
  * @author Scooter Willis <willishf at gmail dot com>
  */
 public interface CoxComparatorInterface extends Comparator<CoxVariables> {
-	public String getDescription();
-	public void setDescription(String description);
-	public String getModelVariables();
-	public String getSortVariable();
+	String getDescription();
+	void setDescription(String description);
+	String getModelVariables();
+	String getSortVariable();
 }
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java
index 964b1e254f..cccbae421b 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java
@@ -33,7 +33,7 @@
 public class CoxVariablesOverallModelFitComparator implements Comparator<CoxVariables>, Serializable {
 	private static final long serialVersionUID = 1;
 
-	String variables = "";
+	String variables;
 
 	/**
 	 * Variables are stored as a string representation of an ArrayList
@@ -49,13 +49,7 @@ public int compare(CoxVariables coxVariables1, CoxVariables coxVariables2) {
 		CoxInfo ci1 = coxVariables1.getCoxInfo(variables);
 		CoxInfo ci2 = coxVariables2.getCoxInfo(variables);
 
-		if (ci1.getWaldTestInfo().getPvalue() < ci2.getWaldTestInfo().getPvalue()) {
-			return -1;
-		} else if (ci1.getWaldTestInfo().getPvalue() > ci2.getWaldTestInfo().getPvalue()) {
-			return 1;
-		} else {
-			return 0;
-		}
+        return Double.compare(ci1.getWaldTestInfo().getPvalue(), ci2.getWaldTestInfo().getPvalue());
 		//ascending order
 		// return coxVariables1.compareTo(coxVariables2);
 	}
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java
index 1c48b2dcf0..aab32d5721 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java
@@ -29,8 +29,8 @@
  */
 public class CoxVariablesVariableComparator implements CoxComparatorInterface {
 
-	String variables = "";
-	String variable = "";
+	String variables;
+	String variable;
 
 	/**
 	 *
@@ -55,13 +55,7 @@ public int compare(CoxVariables coxVariables1, CoxVariables coxVariables2) {
 			return 1;
 		if(ci2 == null && ci1 != null)
 			return -1;
-		if (ci1.getCoefficientsList().get(variable).getPvalue() < ci2.getCoefficientsList().get(variable).getPvalue()) {
-			return -1;
-		} else if (ci1.getCoefficientsList().get(variable).getPvalue() > ci2.getCoefficientsList().get(variable).getPvalue()) {
-			return 1;
-		} else {
-			return 0;
-		}
+        return Double.compare(ci1.getCoefficientsList().get(variable).getPvalue(), ci2.getCoefficientsList().get(variable).getPvalue());
 		//ascending order
 		// return coxVariables1.compareTo(coxVariables2);
 	}
@@ -70,7 +64,7 @@ public int compare(CoxVariables coxVariables1, CoxVariables coxVariables2) {
 	public String getDescription() {
 	   return description;
 	}
-	String description = "Signatures ranked by p-value ";
+	String description;
 
 	@Override
 	public void setDescription(String description) {
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java
index 5f61766a25..65aef84fb6 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java
@@ -33,7 +33,7 @@
 public class MeanModelComparator implements Comparator<CoxVariables>, Serializable {
 	private static final long serialVersionUID = 1;
 
-	String variable = "";
+	String variable;
 
 	/**
 	 *
@@ -64,13 +64,7 @@ public int compare(CoxVariables coxVariables1, CoxVariables coxVariables2) {
 
 	   double c2ratio = Math.min(c2LTpvalue, c2GTpvalue) / Math.max(c2LTpvalue, c2GTpvalue);
 
-		if (c1ratio > c2ratio) {
-			return 1;
-		} else if (c1ratio < c2ratio) {
-			return -1;
-		} else {
-			return 0;
-		}
+        return Double.compare(c1ratio, c2ratio);
 		//ascending order
 		// return coxVariables1.compareTo(coxVariables2);
 	}
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java
index 81098c46cf..583283e88f 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java
@@ -32,7 +32,7 @@
 public class SurvivalInfoValueComparator implements Comparator<SurvivalInfo>, Serializable {
 	private static final long serialVersionUID = 1;
 
-	String variable = "";
+	String variable;
 
 	/**
 	 *
@@ -46,12 +46,7 @@ public SurvivalInfoValueComparator(String variable){
 	public int compare(SurvivalInfo t, SurvivalInfo t1) {
 		double v = t.getContinuousVariable(variable);
 		double v1 = t1.getContinuousVariable(variable);
-		if(v < v1)
-			return -1;
-		else if(v > v1)
-			return 1;
-		else
-			return 0;
+        return Double.compare(v, v1);
 	}
 
 }
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java
index ba85c9084b..5cd339bc29 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java
@@ -45,7 +45,7 @@ public static double[][] process(CoxMethod method, ArrayList<SurvivalInfo> survi
 		//double temp;
 		int n = survivalInfoList.size();
 
-		ArrayList<String> variables = new ArrayList<String>(coxInfo.getCoefficientsList().keySet());
+		ArrayList<String> variables = new ArrayList<>(coxInfo.getCoefficientsList().keySet());
 		int nvar = variables.size();
 
 
@@ -66,11 +66,11 @@ public static double[][] process(CoxMethod method, ArrayList<SurvivalInfo> survi
 		double[] mh2 = new double[nvar];
 		double[] mh3 = new double[nvar];
 
-		double denom = 0;
-		double time = 0;
-		double e_denom = 0;
-		double meanwt = 0;
-		double deaths = 0;
+		double denom;
+		double time;
+		double e_denom;
+		double meanwt;
+		double deaths;
 		double risk;
 		double[][] covar = new double[nvar][n];
 		double[][] resid = new double[nvar][n];
@@ -78,7 +78,7 @@ public static double[][] process(CoxMethod method, ArrayList<SurvivalInfo> survi
 		double downwt, temp1, temp2, d2;
 
 
-		int person = 0;
+		int person;
 
 		//  n = *nx;
 		//  nvar  = *nvarx;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/ChangeValue.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/ChangeValue.java
index b5841d9f63..eb5d7b8a56 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/ChangeValue.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/ChangeValue.java
@@ -32,5 +32,5 @@ public interface ChangeValue {
 	 * @param originalValue
 	 * @return
 	 */
-	public String change(String originalValue);
+    String change(String originalValue);
 }
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
index 57f0e983ce..2d31639865 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
@@ -31,10 +31,10 @@
  */
 public class WorkSheet {
 
-	private LinkedHashMap<String, HeaderInfo> columnLookup = new LinkedHashMap<String, HeaderInfo>();
-	private LinkedHashMap<String, HeaderInfo> rowLookup = new LinkedHashMap<String, HeaderInfo>();
+	private final LinkedHashMap<String, HeaderInfo> columnLookup = new LinkedHashMap<>();
+	private final LinkedHashMap<String, HeaderInfo> rowLookup = new LinkedHashMap<>();
 	private CompactCharSequence[][] data = new CompactCharSequence[1][1];
-	HashMap<String, String> dataGrid = new HashMap<String, String>();
+	HashMap<String, String> dataGrid = new HashMap<>();
 	private String indexColumnName = "";
 
 	/**
@@ -233,14 +233,14 @@ public WorkSheet(CompactCharSequence[][] values) {
 
 		data = values;
 	}
-	private LinkedHashMap<String, String> metaDataColumnsHashMap = new LinkedHashMap<String, String>();
+	private final LinkedHashMap<String, String> metaDataColumnsHashMap = new LinkedHashMap<>();
 
 	/**
 	 *
 	 * @return
 	 */
 	public ArrayList<String> getMetaDataColumns() {
-		ArrayList<String> metaColumns = new ArrayList<String>();
+		ArrayList<String> metaColumns = new ArrayList<>();
 		for (String key : metaDataColumnsHashMap.keySet()) {
 			HeaderInfo hi = columnLookup.get(key);
 			if (!hi.isHide()) {
@@ -255,7 +255,7 @@ public ArrayList<String> getMetaDataColumns() {
 	 * @return
 	 */
 	public ArrayList<String> getMetaDataRows() {
-		ArrayList<String> metaRows = new ArrayList<String>();
+		ArrayList<String> metaRows = new ArrayList<>();
 		for (String key : metaDataRowsHashMap.keySet()) {
 			HeaderInfo hi = rowLookup.get(key);
 			if (!hi.isHide()) {
@@ -270,7 +270,7 @@ public ArrayList<String> getMetaDataRows() {
 	 * @return
 	 */
 	public ArrayList<String> getDataColumns() {
-		ArrayList<String> dataColumns = new ArrayList<String>();
+		ArrayList<String> dataColumns = new ArrayList<>();
 		ArrayList<String> columns = this.getColumns();
 		for (String column : columns) {
 			if (!metaDataColumnsHashMap.containsKey(column)) {
@@ -292,7 +292,7 @@ public void shuffleColumnsAndThenRows(ArrayList<String> columns, ArrayList<Strin
 		doubleValues.clear();
 
 		for (String column : columns) { //shuffle all values in the column
-			ArrayList<Integer> rowIndex = new ArrayList<Integer>();
+			ArrayList<Integer> rowIndex = new ArrayList<>();
 			for (int i = 0; i < rows.size(); i++) {
 				rowIndex.add(i);
 			}
@@ -311,7 +311,7 @@ public void shuffleColumnsAndThenRows(ArrayList<String> columns, ArrayList<Strin
 		}
 
 		for (String row : rows) {
-			ArrayList<Integer> columnIndex = new ArrayList<Integer>();
+			ArrayList<Integer> columnIndex = new ArrayList<>();
 			for (int i = 0; i < columns.size(); i++) {
 				columnIndex.add(i);
 			}
@@ -344,7 +344,7 @@ public void shuffleColumnValues(ArrayList<String> columns) throws Exception {
 		doubleValues.clear();
 		ArrayList<String> rows = this.getDataRows();
 		for (String column : columns) { //shuffle all values in the column
-			ArrayList<Integer> rowIndex = new ArrayList<Integer>();
+			ArrayList<Integer> rowIndex = new ArrayList<>();
 			for (int i = 0; i < rows.size(); i++) {
 				rowIndex.add(i);
 			}
@@ -375,7 +375,7 @@ public void shuffleRowValues(ArrayList<String> rows) throws Exception {
 		doubleValues.clear();
 		ArrayList<String> columns = this.getColumns();
 		for (String row : rows) {
-			ArrayList<Integer> columnIndex = new ArrayList<Integer>();
+			ArrayList<Integer> columnIndex = new ArrayList<>();
 			for (int i = 0; i < columns.size(); i++) {
 				columnIndex.add(i);
 			}
@@ -521,7 +521,7 @@ public boolean isMetaDataRow(String row) {
 			return true;
 		}
 	}
-	private LinkedHashMap<String, String> metaDataRowsHashMap = new LinkedHashMap<String, String>();
+	private final LinkedHashMap<String, String> metaDataRowsHashMap = new LinkedHashMap<>();
 
 	/**
 	 *
@@ -646,7 +646,7 @@ public void applyColumnFilter(String column, ChangeValue changeValue) throws Exc
 	 * @param defaultValue
 	 */
 	public void addColumn(String column, String defaultValue) {
-		ArrayList<String> columns = new ArrayList<String>();
+		ArrayList<String> columns = new ArrayList<>();
 		columns.add(column);
 		addColumns(columns, defaultValue);
 	}
@@ -694,7 +694,7 @@ public void addColumns(ArrayList<String> columns, String defaultValue) {
 	 * @param defaultValue
 	 */
 	public void addRow(String row, String defaultValue) {
-		ArrayList<String> rows = new ArrayList<String>();
+		ArrayList<String> rows = new ArrayList<>();
 		rows.add(row);
 		addRows(rows, defaultValue);
 	}
@@ -808,7 +808,7 @@ public boolean isValidColumn(String col) {
 		}
 	}
 	//When we do gene signatures we ask for the same data value often. This method took up 50% of the time.
-	HashMap<String, Double> doubleValues = new HashMap<String, Double>();
+	HashMap<String, Double> doubleValues = new HashMap<>();
 	boolean cacheDoubleValues = false;
 
 	/**
@@ -871,9 +871,9 @@ public String getCell(String row, String col) throws Exception {
 
 		if (rowIndex == null) {
 			//allow for case insentive search
-			for (String rowtable : rowLookup.keySet()) {
-				if (row.equalsIgnoreCase(rowtable)) {
-					rowIndex = rowLookup.get(rowtable);
+			for (Map.Entry<String, HeaderInfo> entry : rowLookup.entrySet()) {
+				if (row.equalsIgnoreCase(entry.getKey())) {
+					rowIndex = entry.getValue();
 					break;
 				}
 			}
@@ -883,9 +883,9 @@ public String getCell(String row, String col) throws Exception {
 		}
 		if (colIndex == null) {
 			//allow for case insentive search
-			for (String coltable : columnLookup.keySet()) {
-				if (col.equalsIgnoreCase(coltable)) {
-					colIndex = columnLookup.get(coltable);
+			for (Map.Entry<String, HeaderInfo> entry : columnLookup.entrySet()) {
+				if (col.equalsIgnoreCase(entry.getKey())) {
+					colIndex = entry.getValue();
 					break;
 				}
 			}
@@ -909,7 +909,7 @@ public String getCell(String row, String col) throws Exception {
 	 * @param changeValue
 	 */
 	public void changeRowHeader(ChangeValue changeValue) {
-		ArrayList<String> rows = new ArrayList<String>(rowLookup.keySet());
+		ArrayList<String> rows = new ArrayList<>(rowLookup.keySet());
 		for (String row : rows) {
 			String newRow = changeValue.change(row);
 			HeaderInfo value = rowLookup.get(row);
@@ -923,7 +923,7 @@ public void changeRowHeader(ChangeValue changeValue) {
 	 * @param changeValue
 	 */
 	public void changeColumnHeader(ChangeValue changeValue) {
-		ArrayList<String> columns = new ArrayList<String>(columnLookup.keySet());
+		ArrayList<String> columns = new ArrayList<>(columnLookup.keySet());
 		for (String col : columns) {
 			String newCol = changeValue.change(col);
 			HeaderInfo value = columnLookup.get(col);
@@ -958,9 +958,9 @@ public void changeRowHeader(String row, String newRow) throws Exception {
 	 * @throws Exception
 	 */
 	public void changeColumnsHeaders(LinkedHashMap<String, String> newColumnValues) throws Exception {
-		for (String oldColumn : newColumnValues.keySet()) {
-			String newColumn = newColumnValues.get(oldColumn);
-			changeColumnHeader(oldColumn, newColumn);
+		for (Map.Entry<String, String> entry : newColumnValues.entrySet()) {
+			String newColumn = entry.getValue();
+			changeColumnHeader(entry.getKey(), newColumn);
 		}
 
 	}
@@ -1030,8 +1030,8 @@ public ArrayList<String> getRandomDataColumns(int number) {
 	 * @return
 	 */
 	public ArrayList<String> getRandomDataColumns(int number, ArrayList<String> columns) {
-		ArrayList<String> randomColumns = new ArrayList<String>();
-		HashMap<String, String> picked = new HashMap<String, String>();
+		ArrayList<String> randomColumns = new ArrayList<>();
+		HashMap<String, String> picked = new HashMap<>();
 		while (picked.size() < number) {
 			double v = Math.random();
 			int index = (int) (v * columns.size());
@@ -1051,10 +1051,8 @@ public ArrayList<String> getRandomDataColumns(int number, ArrayList<String> colu
 	 * @return
 	 */
 	public ArrayList<String> getAllColumns() {
-		ArrayList<String> columns = new ArrayList<String>();
-		for (String col : columnLookup.keySet()) {
-			columns.add(col);
-		}
+		ArrayList<String> columns = new ArrayList<>();
+		columns.addAll(columnLookup.keySet());
 		return columns;
 	}
 
@@ -1064,11 +1062,11 @@ public ArrayList<String> getAllColumns() {
 	 * @return
 	 */
 	public ArrayList<String> getColumns() {
-		ArrayList<String> columns = new ArrayList<String>();
-		for (String col : columnLookup.keySet()) {
-			HeaderInfo hi = columnLookup.get(col);
+		ArrayList<String> columns = new ArrayList<>();
+		for (Map.Entry<String, HeaderInfo> entry : columnLookup.entrySet()) {
+			HeaderInfo hi = entry.getValue();
 			if (!hi.isHide()) {
-				columns.add(col);
+				columns.add(entry.getKey());
 			}
 		}
 		return columns;
@@ -1082,8 +1080,8 @@ public ArrayList<String> getColumns() {
 	 * @throws Exception
 	 */
 	public ArrayList<String> getDiscreteColumnValues(String column) throws Exception {
-		HashMap<String, String> hashMapValues = new HashMap<String, String>();
-		ArrayList<String> values = new ArrayList<String>();
+		HashMap<String, String> hashMapValues = new HashMap<>();
+		ArrayList<String> values = new ArrayList<>();
 		ArrayList<String> rows = getDataRows();
 		for (String row : rows) {
 			String value = getCell(row, column);
@@ -1103,8 +1101,8 @@ public ArrayList<String> getDiscreteColumnValues(String column) throws Exception
 	 * @throws Exception
 	 */
 	public ArrayList<String> getDiscreteRowValues(String row) throws Exception {
-		HashMap<String, String> hashMapValues = new HashMap<String, String>();
-		ArrayList<String> values = new ArrayList<String>();
+		HashMap<String, String> hashMapValues = new HashMap<>();
+		ArrayList<String> values = new ArrayList<>();
 		for (String column : getColumns()) {
 			String value = getCell(row, column);
 			if (!hashMapValues.containsKey(value)) {
@@ -1121,10 +1119,8 @@ public ArrayList<String> getDiscreteRowValues(String row) throws Exception {
 	 * @return
 	 */
 	public ArrayList<String> getAllRows() {
-		ArrayList<String> rows = new ArrayList<String>();
-		for (String row : rowLookup.keySet()) {
-			rows.add(row);
-		}
+		ArrayList<String> rows = new ArrayList<>();
+		rows.addAll(rowLookup.keySet());
 		return rows;
 
 	}
@@ -1135,11 +1131,11 @@ public ArrayList<String> getAllRows() {
 	 * @return
 	 */
 	public ArrayList<String> getRows() {
-		ArrayList<String> rows = new ArrayList<String>();
-		for (String row : rowLookup.keySet()) {
-			HeaderInfo hi = rowLookup.get(row);
+		ArrayList<String> rows = new ArrayList<>();
+		for (Map.Entry<String, HeaderInfo> entry : rowLookup.entrySet()) {
+			HeaderInfo hi = entry.getValue();
 			if (!hi.isHide()) {
-				rows.add(row);
+				rows.add(entry.getKey());
 			}
 		}
 		return rows;
@@ -1151,12 +1147,13 @@ public ArrayList<String> getRows() {
 	 * @return
 	 */
 	public ArrayList<String> getDataRows() {
-		ArrayList<String> rows = new ArrayList<String>();
-		for (String row : rowLookup.keySet()) {
+		ArrayList<String> rows = new ArrayList<>();
+		for (Map.Entry<String, HeaderInfo> entry : rowLookup.entrySet()) {
+			String row = entry.getKey();
 			if (this.isMetaDataRow(row)) {
 				continue;
 			}
-			HeaderInfo hi = rowLookup.get(row);
+			HeaderInfo hi = entry.getValue();
 			if (!hi.isHide()) {
 				rows.add(row);
 			}
@@ -1198,13 +1195,13 @@ public WorkSheet getLogScale(double base, double zeroValue) throws Exception {
 				} else {
 					String value = getCell(row, col);
 					try {
-						Double d = Double.parseDouble(value);
+						double d = Double.parseDouble(value);
 						if (d == 0.0) {
 							d = zeroValue;
 						} else {
 							d = Math.log(d) / Math.log(base);
 						}
-						workSheet.addCell(row, col, d + "");
+						workSheet.addCell(row, col, String.valueOf(d));
 					} catch (Exception e) {
 						workSheet.addCell(row, col, value);
 					}
@@ -1262,7 +1259,7 @@ static CompactCharSequence[][] getAllValuesCompactCharSequence(InputStream is, c
 		BufferedReader br = new BufferedReader(new InputStreamReader(is));
 
 
-		ArrayList<CompactCharSequence[]> rows = new ArrayList<CompactCharSequence[]>();
+		ArrayList<CompactCharSequence[]> rows = new ArrayList<>();
 
 		String line = br.readLine();
 		int numcolumns = -1;
@@ -1309,7 +1306,7 @@ static CompactCharSequence[][] getAllValuesCompactCharSequence(InputStream is, c
 	static String[][] getAllValues(String fileName, char delimiter) throws Exception {
 		FileReader reader = new FileReader(fileName);
 		BufferedReader br = new BufferedReader(reader);
-		ArrayList<String[]> rows = new ArrayList<String[]>();
+		ArrayList<String[]> rows = new ArrayList<>();
 
 		String line = br.readLine();
 		int numcolumns = -1;
@@ -1388,7 +1385,7 @@ static public WorkSheet unionWorkSheetsRowJoin(WorkSheet w1, WorkSheet w2, boole
 			}
 		}
 
-		ArrayList<String> joinedColumns = new ArrayList<String>();
+		ArrayList<String> joinedColumns = new ArrayList<>();
 		joinedColumns.addAll(w1DataColumns);
 		joinedColumns.addAll(w2DataColumns);
 		if (!joinedColumns.contains("META_DATA") && (w1MetaDataColumns.size() > 0 || w2MetaDataColumns.size() > 0)) {
@@ -1406,9 +1403,9 @@ static public WorkSheet unionWorkSheetsRowJoin(WorkSheet w1, WorkSheet w2, boole
 		}
 		ArrayList<String> w1Rows = w1.getRows();
 		ArrayList<String> w2Rows = w2.getRows();
-		ArrayList<String> rows = new ArrayList<String>();
+		ArrayList<String> rows = new ArrayList<>();
 
-		HashSet<String> w1Key = new HashSet<String>(w1Rows);
+		HashSet<String> w1Key = new HashSet<>(w1Rows);
 		for (String key : w2Rows) {
 			if (w1Key.contains(key)) {
 				rows.add(key);
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/CensorStatusSelect.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/CensorStatusSelect.java
index 067a8814c9..073a163f5b 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/CensorStatusSelect.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/CensorStatusSelect.java
@@ -34,7 +34,6 @@ public interface CensorStatusSelect {
 	 * @param worksheet
 	 * @param row
 	 * @return
-	 * @throws Exception
 	 */
-	public CensorStatus select(WorkSheet worksheet,String row) throws Exception;
+    CensorStatus select(WorkSheet worksheet, String row);
 }
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
index a6fda3f095..6755586ca7 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
@@ -41,7 +41,7 @@ public class ExpressionFigure extends JPanel {
 
 	private static final long serialVersionUID = 1L;
 
-	ArrayList<String> title = new ArrayList<String>();
+	ArrayList<String> title = new ArrayList<>();
 	/**
 	 *
 	 */
@@ -70,8 +70,8 @@ public class ExpressionFigure extends JPanel {
 	FontMetrics fm;
 	KMFigureInfo kmfi = new KMFigureInfo();
 //    LinkedHashMap<String, ArrayList<CensorStatus>> survivalData = new LinkedHashMap<String, ArrayList<CensorStatus>>();
-	ArrayList<String> lineInfoList = new ArrayList<String>();
-	ArrayList<SurvivalInfo> siList = new ArrayList<SurvivalInfo>();
+	ArrayList<String> lineInfoList = new ArrayList<>();
+	ArrayList<SurvivalInfo> siList = new ArrayList<>();
 	String variable = "";
 	private String fileName = "";
 
@@ -120,7 +120,7 @@ public void setFigureLineInfo(ArrayList<String> lineInfoList) {
 	 * @param variable
 	 */
 	public void setSurvivalInfo(ArrayList<String> title, ArrayList<SurvivalInfo> _siList, String variable) {
-		this.siList = new ArrayList<SurvivalInfo>();
+		this.siList = new ArrayList<>();
 		this.title = title;
 		this.variable = variable;
 
@@ -132,7 +132,7 @@ public void setSurvivalInfo(ArrayList<String> title, ArrayList<SurvivalInfo> _si
 		for (SurvivalInfo si : _siList) {
 			this.siList.add(si);
 			String v = si.getOriginalMetaData(variable);
-			Double value = Double.parseDouble(v);
+			double value = Double.parseDouble(v);
 			ds.addValue(value);
 			if (maxTime == null || maxTime < si.getTime()) {
 				maxTime = si.getTime();
@@ -140,12 +140,12 @@ public void setSurvivalInfo(ArrayList<String> title, ArrayList<SurvivalInfo> _si
 
 		}
 		SurvivalInfoValueComparator sivc = new SurvivalInfoValueComparator(variable);
-		Collections.sort(this.siList, sivc);
+		this.siList.sort(sivc);
 		mean = ds.getMean();
 		minY = ds.getMin();
 		maxY = ds.getMax();
-		minY = (double) Math.floor(minY);
-		maxY = (double) Math.ceil(maxY);
+		minY = Math.floor(minY);
+		maxY = Math.ceil(maxY);
 
 
 		this.repaint();
@@ -278,7 +278,7 @@ private void drawLegend(Graphics g) {
 		//  increment = increment * 10.0;
 		double d = minY + increment;
 		//double graphHeight = top - bottom;
-		String label = "";
+		String label;
 		while (d < maxY) {
 			int yvalue = getY(maxY - d);
 			label = df.format(d);
@@ -372,13 +372,13 @@ public static void main(String[] args) {
 			application.setSize(500, 400);         // window is 500 pixels wide, 400 high
 			application.setVisible(true);
 
-			ArrayList<String> titles = new ArrayList<String>();
+			ArrayList<String> titles = new ArrayList<>();
 			titles.add("Line 1");
 			titles.add("line 2");
 
-			ArrayList<String> figureInfo = new ArrayList<String>();
+			ArrayList<String> figureInfo = new ArrayList<>();
 
-			ArrayList<SurvivalInfo> survivalInfoList = new ArrayList<SurvivalInfo>();
+			ArrayList<SurvivalInfo> survivalInfoList = new ArrayList<>();
 
 			for (int i = 0; i < 600; i++) {
 				double r = Math.random();
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java
index 24f053d592..cae28fe6e2 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java
@@ -87,7 +87,7 @@ public class KMFigureInfo {
 	 *
 	 */
 	public Color[] legendColor = {Color.RED, Color.BLUE, Color.GREEN, Color.CYAN, Color.ORANGE, Color.YELLOW, Color.MAGENTA, Color.PINK};
-	public ArrayList<Double> xAxisLabels = new ArrayList<Double>();//new ArrayList<Double>(Arrays.asList(0.0, 5.0, 10.0, 15.0, 20.0));
+	public ArrayList<Double> xAxisLabels = new ArrayList<>();//new ArrayList<Double>(Arrays.asList(0.0, 5.0, 10.0, 15.0, 20.0));
 	public String xAxisLegend = "";
 	public String yAxisLegend = "";
 	public Color getColor(int index) {
@@ -114,7 +114,7 @@ public void init(String propertyFileName) throws Exception {
 		if (properties.containsKey("xAxisLabels")) {
 			String values = properties.getProperty("xAxisLabels").trim();
 			if (values.startsWith("[") || values.startsWith("(") || values.startsWith("{")) {
-				values = values.substring(1, values.length()).trim();
+				values = values.substring(1).trim();
 			}
 			if (values.endsWith("]") || values.endsWith(")") || values.endsWith("}")) {
 				values = values.substring(0, values.length() - 1).trim();
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java
index c5d358cbeb..f48116d832 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java
@@ -42,7 +42,7 @@ public class KaplanMeierFigure extends JPanel {
 
 	private static final long serialVersionUID = 1L;
 
-	ArrayList<String> title = new ArrayList<String>();
+	ArrayList<String> title = new ArrayList<>();
 	/**
 	 *
 	 */
@@ -55,7 +55,7 @@ public class KaplanMeierFigure extends JPanel {
 	 *
 	 */
 	private int left;
-	private int yaxisLabel = 20;
+	private final int yaxisLabel = 20;
 	/**
 	 *
 	 */
@@ -69,12 +69,12 @@ public class KaplanMeierFigure extends JPanel {
 	double maxPercentage = 1.0;
 	FontMetrics fm;
 	KMFigureInfo kmfi = new KMFigureInfo();
-	LinkedHashMap<String, ArrayList<CensorStatus>> survivalData = new LinkedHashMap<String, ArrayList<CensorStatus>>();
-	ArrayList<String> lineInfoList = new ArrayList<String>();
+	LinkedHashMap<String, ArrayList<CensorStatus>> survivalData = new LinkedHashMap<>();
+	ArrayList<String> lineInfoList = new ArrayList<>();
 	SurvFitInfo sfi = new SurvFitInfo();
 	private String fileName = "";
-	private ArrayList<Double> xAxisTimeValues = new ArrayList<Double>();
-	private ArrayList<Integer> xAxisTimeCoordinates = new ArrayList<Integer>();
+	private final ArrayList<Double> xAxisTimeValues = new ArrayList<>();
+	private final ArrayList<Integer> xAxisTimeCoordinates = new ArrayList<>();
 
 	/**
 	 *
@@ -91,7 +91,7 @@ public KaplanMeierFigure() {
 	 * @return
 	 */
 	public ArrayList<String> getGroups() {
-		return new ArrayList<String>(survivalData.keySet());
+		return new ArrayList<>(survivalData.keySet());
 	}
 
 	/**
@@ -160,7 +160,7 @@ public void setFigureLineInfo(ArrayList<String> lineInfoList) {
 	 * @throws Exception
 	 */
 	public void setCoxInfo(ArrayList<String> title, CoxInfo ci, String strataVariable, LinkedHashMap<String, String> legendMap, Boolean useWeighted) throws Exception {
-		LinkedHashMap<String, ArrayList<CensorStatus>> survivalData = new LinkedHashMap<String, ArrayList<CensorStatus>>();
+		LinkedHashMap<String, ArrayList<CensorStatus>> survivalData = new LinkedHashMap<>();
 		ArrayList<SurvivalInfo> siList = ci.getSurvivalInfoList();
 		int n = 0;
 		int event = 0;
@@ -171,12 +171,8 @@ public void setCoxInfo(ArrayList<String> title, CoxInfo ci, String strataVariabl
 
 				legend = strata;
 			}
-			ArrayList<CensorStatus> censorStatusList = survivalData.get(legend);
-			if (censorStatusList == null) {
-				censorStatusList = new ArrayList<CensorStatus>();
-				survivalData.put(legend, censorStatusList);
-			}
-			CensorStatus cs = new CensorStatus(strata, si.getTime(), si.getStatus() + "");
+			ArrayList<CensorStatus> censorStatusList = survivalData.computeIfAbsent(legend, k -> new ArrayList<>());
+			CensorStatus cs = new CensorStatus(strata, si.getTime(), String.valueOf(si.getStatus()));
 			cs.weight = si.getWeight();
 			censorStatusList.add(cs);
 			n++;
@@ -195,7 +191,7 @@ public void setCoxInfo(ArrayList<String> title, CoxInfo ci, String strataVariabl
 //        System.out.println("setCoxInfo=" + cc.pvalue + " " + title);
 
 
-		ArrayList<String> lines = new ArrayList<String>();
+		ArrayList<String> lines = new ArrayList<>();
 		lines.add(line1);
 		lines.add(line2);
 		lines.add(line3);
@@ -210,7 +206,7 @@ public void setCoxInfo(ArrayList<String> title, CoxInfo ci, String strataVariabl
 	 * @return
 	 */
 	public static String fmt(Double d, int precision, int pad) {
-		String value = "";
+		String value;
 		DecimalFormat dfe = new DecimalFormat("0.00E0");
 		String dpad = "0.";
 		double p = 1.0;
@@ -303,7 +299,7 @@ public void setSurvivalData(ArrayList<String> title, LinkedHashMap<String, Array
 		this.title = title;
 		this.survivalData = survivalData;
 		Double mTime = null;
-		ArrayList<String> labels = new ArrayList<String>(survivalData.keySet());
+		ArrayList<String> labels = new ArrayList<>(survivalData.keySet());
 		Collections.sort(labels);
 		for (String legend : labels) {
 			ArrayList<CensorStatus> censorStatusList = survivalData.get(legend);
@@ -341,8 +337,7 @@ public void saveSurvivalData(String fileName) throws Exception {
 		FileWriter fw = new FileWriter(fileName);
 		fw.write("index\tTIME\tSTATUS\tGROUP\r\n");
 		int index = 0;
-		for (String group : survivalData.keySet()) {
-			ArrayList<CensorStatus> sd = survivalData.get(group);
+		for (ArrayList<CensorStatus> sd : survivalData.values()) {
 			for (CensorStatus cs : sd) {
 				String line = index + "\t" + cs.time + "\t" + cs.censored + "\t" + cs.group + "\r\n";
 				index++;
@@ -394,7 +389,7 @@ private void drawSurvivalCurves(Graphics g) {
 
 
 		int colorIndex = 0;
-		ArrayList<String> labels = new ArrayList<String>(sfi.getStrataInfoHashMap().keySet());
+		ArrayList<String> labels = new ArrayList<>(sfi.getStrataInfoHashMap().keySet());
 		Collections.sort(labels);
 
 		LinkedHashMap<String, StrataInfo> strataInfoHashMap = sfi.getStrataInfoHashMap();
@@ -521,7 +516,7 @@ public ArrayList<Integer> getxAxisTimeCoordinates() {
 		return xAxisTimeCoordinates;
 	}
 
-	class PlotInfo {
+	static class PlotInfo {
 
 		double time;
 		double atRisk;
@@ -763,7 +758,7 @@ public static void main(String[] args) {
 		try {
 
 			KaplanMeierFigure kaplanMeierFigure = new KaplanMeierFigure();
-			LinkedHashMap<String, ArrayList<CensorStatus>> survivalDataHashMap = new LinkedHashMap<String, ArrayList<CensorStatus>>();
+			LinkedHashMap<String, ArrayList<CensorStatus>> survivalDataHashMap = new LinkedHashMap<>();
 
 //            if (false) { //http://sph.bu.edu/otlt/MPH-Modules/BS/BS704_Survival/
 //                ArrayList<CensorStatus> graph1 = new ArrayList<CensorStatus>();
@@ -801,7 +796,7 @@ public static void main(String[] args) {
 
 
 
-				ArrayList<CensorStatus> graph1 = new ArrayList<CensorStatus>();
+				ArrayList<CensorStatus> graph1 = new ArrayList<>();
 				graph1.add(new CensorStatus("A", 1.0, "1"));
 				graph1.add(new CensorStatus("A", 1.0, "1"));
 				graph1.add(new CensorStatus("A", 1.0, "1"));
@@ -841,7 +836,7 @@ public static void main(String[] args) {
 
 				survivalDataHashMap.put("Label 1", graph1);
 
-				ArrayList<CensorStatus> graph2 = new ArrayList<CensorStatus>();
+				ArrayList<CensorStatus> graph2 = new ArrayList<>();
 				graph2.add(new CensorStatus("A", 1.0, "1"));
 				graph2.add(new CensorStatus("A", 1.0, "1"));
 				graph2.add(new CensorStatus("A", 1.0, "0"));
@@ -882,7 +877,7 @@ public static void main(String[] args) {
 				survivalDataHashMap.put("Label 2", graph2);
 			}
 
-			ArrayList<String> figureInfo = new ArrayList<String>();
+			ArrayList<String> figureInfo = new ArrayList<>();
 			//DecimalFormat dfe = new DecimalFormat("0.00E0");
 			//DecimalFormat df = new DecimalFormat("0.00");
 
@@ -896,7 +891,7 @@ public static void main(String[] args) {
 			application.setSize(500, 400);         // window is 500 pixels wide, 400 high
 			application.setVisible(true);
 
-			ArrayList<String> titles = new ArrayList<String>();
+			ArrayList<String> titles = new ArrayList<>();
 			titles.add("Line 1");
 			titles.add("Line 2");
 			kaplanMeierFigure.setSurvivalData(titles, survivalDataHashMap, true);
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
index 9bc6d0572a..2433e0f976 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
@@ -69,7 +69,7 @@ private void paintTable(Graphics g) {
 		g2.setStroke(kmfi.kmStroke);
 		SurvFitInfo sfi = kmf.getSurvivalFitInfo();
 
-		LinkedHashMap<String, StrataInfo> sfiHashMap = new LinkedHashMap<String, StrataInfo>();
+		LinkedHashMap<String, StrataInfo> sfiHashMap;
 		if(sfi.isWeighted()){
 			sfiHashMap = sfi.getUnweightedStrataInfoHashMap();
 		}else{
@@ -94,7 +94,7 @@ private void paintTable(Graphics g) {
 		ArrayList<Double> xaxisTimeValues = kmf.getxAxisTimeValues();
 		ArrayList<Integer> xAxisTimeCoordinates = kmf.getxAxisTimeCoordinates();
 
-		ArrayList<String> labels = new ArrayList<String>(sfiHashMap.keySet());
+		ArrayList<String> labels = new ArrayList<>(sfiHashMap.keySet());
 		Collections.sort(labels);
 
 		for (String group : labels) {
@@ -113,7 +113,7 @@ private void paintTable(Graphics g) {
 				Double time = xaxisTimeValues.get(i);
 				int xvalue = xAxisTimeCoordinates.get(i);
 				Double value = si.getNearestAtRisk(time);
-				String nrisk = "";
+				String nrisk;
 				if(value == null){
 					nrisk = "";
 				}else{
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java
index f315eaaf0a..91e11e3b29 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java
@@ -29,6 +29,7 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.LinkedHashMap;
+import java.util.Map;
 
 /**
  * Ported from survfitKM.S When combining multiple entries with same time not
@@ -54,7 +55,7 @@ public enum Method {
 		/**
 		 *
 		 */
-		fh2;
+		fh2
 	}
 
 	/**
@@ -69,7 +70,7 @@ public enum Error {
 		/**
 		 *
 		 */
-		tsiatis;
+		tsiatis
 	}
 
 	/**
@@ -92,7 +93,7 @@ public enum ConfType {
 		/**
 		 *
 		 */
-		none;
+		none
 	}
 
 	/**
@@ -111,7 +112,7 @@ public enum ConfLower {
 		/**
 		 *
 		 */
-		modified;
+		modified
 	}
 
 	/**
@@ -122,17 +123,17 @@ public enum ConfLower {
 	 * @throws Exception
 	 */
 	public SurvFitInfo process(LinkedHashMap<String, ArrayList<CensorStatus>> survivalData, boolean useWeights) throws Exception {
-		ArrayList<SurvivalInfo> survivalInfoList = new ArrayList<SurvivalInfo>();
+		ArrayList<SurvivalInfo> survivalInfoList = new ArrayList<>();
 		int i = 0;
-		for (String strata : survivalData.keySet()) {
-			ArrayList<CensorStatus> csList = survivalData.get(strata);
+		for (Map.Entry<String, ArrayList<CensorStatus>> entry : survivalData.entrySet()) {
+			ArrayList<CensorStatus> csList = entry.getValue();
 			for (CensorStatus cs : csList) {
 				SurvivalInfo si = new SurvivalInfo(cs.time, Integer.parseInt(cs.censored));
 				si.setOrder(i);
 				i++;
 				si.setWeight(cs.weight);
-				si.addUnknownDataTypeVariable("STRATA", strata);
-				si.addUnknownDataTypeVariable("VALUE", cs.value + "");
+				si.addUnknownDataTypeVariable("STRATA", entry.getKey());
+				si.addUnknownDataTypeVariable("VALUE", String.valueOf(cs.value));
 				survivalInfoList.add(si);
 			}
 		}
@@ -154,7 +155,7 @@ public SurvFitInfo process(LinkedHashMap<String, ArrayList<CensorStatus>> surviv
 	 */
 	public SurvFitInfo process(String datafile, String timeColumn, String statusColumn, String weightColumn, String variableColumn, boolean useWeights) throws Exception {
 		WorkSheet worksheet = WorkSheet.readCSV(datafile, '\t');
-		ArrayList<SurvivalInfo> survivalInfoList = new ArrayList<SurvivalInfo>();
+		ArrayList<SurvivalInfo> survivalInfoList = new ArrayList<>();
 
 		int i = 1;
 		for (String row : worksheet.getRows()) {
@@ -223,8 +224,8 @@ public LinkedHashMap<String, StrataInfo>  processStrataInfo(String variable, Arr
 		int n = dataT.size();
 
 
-		LinkedHashMap<String, Integer> levels = new LinkedHashMap<String, Integer>();
-		LinkedHashMap<String, ArrayList<SurvivalInfo>> strataHashMap = new LinkedHashMap<String, ArrayList<SurvivalInfo>>();
+		LinkedHashMap<String, Integer> levels = new LinkedHashMap<>();
+		LinkedHashMap<String, ArrayList<SurvivalInfo>> strataHashMap = new LinkedHashMap<>();
 
 		for (int i = 0; i < n; i++) {
 			SurvivalInfo si = dataT.get(i);
@@ -235,24 +236,20 @@ public LinkedHashMap<String, StrataInfo>  processStrataInfo(String variable, Arr
 			}
 			count++;
 			levels.put(value, count);
-			ArrayList<SurvivalInfo> strataList = strataHashMap.get(value);
-			if (strataList == null) {
-				strataList = new ArrayList<SurvivalInfo>();
-				strataHashMap.put(value, strataList);
-			}
+			ArrayList<SurvivalInfo> strataList = strataHashMap.computeIfAbsent(value, k -> new ArrayList<>());
 			strataList.add(si);
 
 		}
 
 		//int nstrat = levels.size();
 
-		LinkedHashMap<String, StrataInfo> strataInfoHashMap = new LinkedHashMap<String, StrataInfo>();
+		LinkedHashMap<String, StrataInfo> strataInfoHashMap = new LinkedHashMap<>();
 
-		for (String strata : strataHashMap.keySet()) {
+		for (Map.Entry<String, ArrayList<SurvivalInfo>> entry : strataHashMap.entrySet()) {
 
-			ArrayList<SurvivalInfo> strataList = strataHashMap.get(strata);
+			ArrayList<SurvivalInfo> strataList = entry.getValue();
 			StrataInfo strataInfo = new StrataInfo();
-			strataInfoHashMap.put(strata, strataInfo);
+			strataInfoHashMap.put(entry.getKey(), strataInfo);
 
 
 			Double previousTime = null;
@@ -379,8 +376,8 @@ public LinkedHashMap<String, StrataInfo>  processStrataInfo(String variable, Arr
 
 		}
 
-		ArrayList<Boolean> events = new ArrayList<Boolean>();
-		ArrayList<Double> nrisk = new ArrayList<Double>();
+		ArrayList<Boolean> events = new ArrayList<>();
+		ArrayList<Double> nrisk = new ArrayList<>();
 		for (StrataInfo strataInfo : strataInfoHashMap.values()) {
 			boolean firsttime = true;
 			for (int j = 0; j < strataInfo.getNevent().size(); j++) {
@@ -395,19 +392,19 @@ public LinkedHashMap<String, StrataInfo>  processStrataInfo(String variable, Arr
 			}
 
 		}
-		ArrayList<Integer> zz = new ArrayList<Integer>();
+		ArrayList<Integer> zz = new ArrayList<>();
 		for (int i = 0; i < events.size(); i++) {
 			if (events.get(i)) {
 				zz.add(i + 1);
 			}
 		}
 		zz.add(events.size() + 1);
-		ArrayList<Integer> diffzz = new ArrayList<Integer>();
+		ArrayList<Integer> diffzz = new ArrayList<>();
 		for (int i = 0; i < zz.size() - 1; i++) {
 			diffzz.add(zz.get(i + 1) - zz.get(i));
 		}
 		//System.out.println(diffzz);
-		ArrayList<Double> nlag = new ArrayList<Double>();
+		ArrayList<Double> nlag = new ArrayList<>();
 		for (int j = 0; j < nrisk.size(); j++) {
 			int count = diffzz.get(j);
 			for (int c = 0; c < count; c++) {
@@ -542,12 +539,12 @@ public static void main(String[] args) {
 				application.setSize(500, 400);         // window is 500 pixels wide, 400 high
 				application.setVisible(true);
 
-				ArrayList<String> titles = new ArrayList<String>();
+				ArrayList<String> titles = new ArrayList<>();
 				titles.add("Line 1");
 				titles.add("line 2");
 				kaplanMeierFigure.setSurvivalData(titles, si, null);
 
-				ArrayList<String> figureInfo = new ArrayList<String>();
+				ArrayList<String> figureInfo = new ArrayList<>();
 				//   figureInfo.add("HR=2.1 95% CI(1.8-2.5)");
 				//   figureInfo.add("p-value=.001");
 				kaplanMeierFigure.setFigureLineInfo(figureInfo);
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java
index b75cc2d3ad..3b1ca8fe15 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java
@@ -66,7 +66,7 @@ static public void process(WorkSheet worksheet, String sensorMapColumn, LinkedHa
 	public static void main(String[] args) {
 
 		try {
-			LinkedHashMap<String, String> censorMap = new LinkedHashMap<String, String>();
+			LinkedHashMap<String, String> censorMap = new LinkedHashMap<>();
 			censorMap.put("a", "0");
 			censorMap.put("d", "1");
 			censorMap.put("d-d.s.", "1");
@@ -74,7 +74,7 @@ public static void main(String[] args) {
 			String timeColumn = "TIME";
 			String sensorMapColumn = "last_follow_up_status"; // "survstat3";
 			double timeScale = 1.0;
-			ArrayList<MetaDataInfo> metaDataInfoList = new ArrayList<MetaDataInfo>();
+			ArrayList<MetaDataInfo> metaDataInfoList = new ArrayList<>();
 			metaDataInfoList.add(new MetaDataInfo("age_at_diagnosis", true, new MeanQuantizer()));
 			metaDataInfoList.add(new MetaDataInfo("size", true, new MeanQuantizer()));
 			metaDataInfoList.add(new MetaDataInfo("lymph_nodes_positive", true, new MeanQuantizer()));
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.java
index 5c80054a72..b902150400 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.java
@@ -33,6 +33,6 @@ public interface DiscreteQuantizerInterface {
 	 * @param worksheet
 	 * @param column
 	 */
-	public void process(WorkSheet worksheet, String column);
+    void process(WorkSheet worksheet, String column);
 
 }
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java
index 964a365cdc..228d7d3579 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java
@@ -44,10 +44,10 @@ public void process(WorkSheet worksheet, String column) {
 			} catch (Exception e) {
 			}
 		}
-		Double mean = ds.getMean();
+		double mean = ds.getMean();
 		for (String row : worksheet.getRows()) {
 			try {
-				Double d = Double.parseDouble(worksheet.getCell(row, column));
+				double d = Double.parseDouble(worksheet.getCell(row, column));
 				if (d < mean) {
 					worksheet.addCell(row, column, "L");
 				} else {
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java
index 26bcef3081..d3edd72143 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java
@@ -33,7 +33,7 @@ public class MetaDataInfo {
 	/**
 	 *
 	 */
-	public String column = "";
+	public String column;
 	/**
 	 *
 	 */
@@ -42,7 +42,7 @@ public class MetaDataInfo {
 	 *
 	 */
 	public DiscreteQuantizerInterface discreteQuantizer = null;
-	ArrayList<String> discreteValues = new ArrayList<String>();
+	ArrayList<String> discreteValues = new ArrayList<>();
 
 	/**
 	 *
diff --git a/biojava-ws/src/main/java/demo/HmmerDemo.java b/biojava-ws/src/main/java/demo/HmmerDemo.java
index 689d62ec92..9511463c59 100644
--- a/biojava-ws/src/main/java/demo/HmmerDemo.java
+++ b/biojava-ws/src/main/java/demo/HmmerDemo.java
@@ -86,7 +86,7 @@ public static void main(String[] args) throws Exception {
 	private static ProteinSequence getUniprot(String uniProtID) throws Exception {
 
 		AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
-		UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<AminoAcidCompound>(uniProtID,set);
+		UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<>(uniProtID, set);
 
 		ProteinSequence seq = new ProteinSequence(uniprotSequence);
 
diff --git a/biojava-ws/src/main/java/demo/NCBIQBlastServiceDemo.java b/biojava-ws/src/main/java/demo/NCBIQBlastServiceDemo.java
index 1b3c5a1c9a..32b1ef13e4 100644
--- a/biojava-ws/src/main/java/demo/NCBIQBlastServiceDemo.java
+++ b/biojava-ws/src/main/java/demo/NCBIQBlastServiceDemo.java
@@ -41,7 +41,7 @@ public class NCBIQBlastServiceDemo {
 	private static final String SEQUENCE = "MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKS";
 
 	public static void main(String[] args) {
-		NCBIQBlastService service = null;
+		NCBIQBlastService service;
 		if (args.length == 1) {
 			service = new NCBIQBlastService(args[0]);
 		} else {
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentOutputProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentOutputProperties.java
index d8ca2d2b4b..9e465782c6 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentOutputProperties.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentOutputProperties.java
@@ -37,16 +37,15 @@ public interface RemotePairwiseAlignmentOutputProperties extends Serializable{
 	/**
 	 *
 	 */
-	public static final long serialVersionUID = 1L;
+    long serialVersionUID = 1L;
 
 	/**
 	 * Method that returns the value associated with the key given in parameter.
 	 *
 	 * @param key :a String with the required key for this map.
 	 * @return a String with the value associated with this key
-	 * @throws Exception if key is not in the map of output options.
 	 */
-	public String getOutputOption(String key) throws Exception;
+    String getOutputOption(String key);
 
 
 	/**
@@ -55,12 +54,12 @@ public interface RemotePairwiseAlignmentOutputProperties extends Serializable{
 	 * @param key :the key use to designate the value to be stored
 	 * @param val :the actual value matched to key
 	 */
-	public void setOutputOption(String key,String val);
+    void setOutputOption(String key, String val);
 
 	/**
 	 * Method to get all keys to the information stored in this object.
 	 *
 	 * @return a <code>Set</code> with all keys held in this instance of the object
 	 */
-	public Set<String> getOutputOptions();
+    Set<String> getOutputOptions();
 }
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentProperties.java
index 83ac02a612..a8f489fde8 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentProperties.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentProperties.java
@@ -39,16 +39,15 @@
  */
 public interface RemotePairwiseAlignmentProperties extends Serializable{
 
-	public static final long serialVersionUID = 1L;
+	long serialVersionUID = 1L;
 
 	/**
 	 * Method that returns the value associated with the key given in parameter.
 	 *
 	 * @param key :a String with the required key for this map.
 	 * @return a String with the value associated with this key
-	 * @throws Exception if key is not in the map of output options.
 	 */
-	public String getAlignmentOption(String key) throws Exception;
+    String getAlignmentOption(String key);
 
 	/**
 	 * Method to set the value for a specific alignment parameter using a key to store in a map.
@@ -56,12 +55,12 @@ public interface RemotePairwiseAlignmentProperties extends Serializable{
 	 * @param key :the key use to designate the value to be stored
 	 * @param val :the actual value matched to key
 	 */
-	public void setAlignementOption(String key,String val);
+    void setAlignementOption(String key, String val);
 
 	/**
 	 * Method to get all keys to the information stored in this object.
 	 *
 	 * @return a <code>Set</code> with all keys held in this instance of the object
 	 */
-	public Set<String> getAlignmentOptions();
+    Set<String> getAlignmentOptions();
 }
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentService.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentService.java
index 3df4f39f01..d39f85422f 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentService.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentService.java
@@ -41,7 +41,7 @@ public interface RemotePairwiseAlignmentService {
 	 *
 	 * @throws Exception
 	 */
-	public String sendAlignmentRequest(Sequence<Compound> seq, RemotePairwiseAlignmentProperties rpa) throws Exception;
+    String sendAlignmentRequest(Sequence<Compound> seq, RemotePairwiseAlignmentProperties rpa) throws Exception;
 
 	/**
 	 * Doing the actual analysis on the instantiated service using specified parameters on the string representation
@@ -49,7 +49,7 @@ public interface RemotePairwiseAlignmentService {
 	 *
 	 * @throws Exception
 	 */
-	public String sendAlignmentRequest(String str, RemotePairwiseAlignmentProperties rpa) throws Exception;
+    String sendAlignmentRequest(String str, RemotePairwiseAlignmentProperties rpa) throws Exception;
 
 	/**
 	 * Simple method to check if the specified request has been completed by the service used.
@@ -59,7 +59,7 @@ public interface RemotePairwiseAlignmentService {
 	 * @return a boolean value telling if this requestID has been completed or not.
 	 * @throws Exception if the ID does not exist.
 	 */
-	public boolean isReady(String id,long present) throws Exception;
+    boolean isReady(String id, long present) throws Exception;
 
 	/**
 	 * Getting the actual alignment results from this instantiated service for a given ID with specific
@@ -70,5 +70,5 @@ public interface RemotePairwiseAlignmentService {
 	 * @return : an <code>InputStream</code> with the actual alignment results
 	 * @throws Exception
 	 */
-	public InputStream getAlignmentResults(String rid,RemotePairwiseAlignmentOutputProperties out) throws Exception;
+    InputStream getAlignmentResults(String rid, RemotePairwiseAlignmentOutputProperties out) throws Exception;
 }
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java
index 3fc154d009..bf59d06944 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java
@@ -83,12 +83,13 @@ public MapToStringTransformer(String mappingSequence, String separatorSequence,
 	 */
 	public String transform(Map<?, ?> map) {
 		StringBuilder sb = new StringBuilder();
-		for (Object key : map.keySet()) {
-			sb.append(getSeparatorSequence());
+		for (Map.Entry<?, ?> entry : map.entrySet()) {
+            Object key = entry.getKey();
+            sb.append(getSeparatorSequence());
 			String keyString = key != null ? key.toString() : getNullValue();
 			sb.append(keyString);
 			sb.append(getMappingSequence());
-			String valueString = map.get(key) != null ? map.get(key).toString() : getNullValue();
+			String valueString = entry.getValue() != null ? entry.getValue().toString() : getNullValue();
 			sb.append(valueString);
 		}
 		return sb.substring(1);
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
index 3d9ad05377..1811f6fb15 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
@@ -45,7 +45,7 @@
 public class NCBIQBlastAlignmentProperties implements RemotePairwiseAlignmentProperties {
 	private static final long serialVersionUID = 7158270364392309841L;
 
-	private Map<BlastAlignmentParameterEnum, String> param = new HashMap<BlastAlignmentParameterEnum, String>();
+	private final Map<BlastAlignmentParameterEnum, String> param = new HashMap<>();
 
 	/**
 	 * This method forwards to {@link #getAlignmentOption(BlastAlignmentParameterEnum)}. Consider using it instead.
@@ -69,7 +69,7 @@ public void setAlignementOption(String key, String val) {
 	 */
 	@Override
 	public Set<String> getAlignmentOptions() {
-		Set<String> result = new HashSet<String>();
+		Set<String> result = new HashSet<>();
 		for (BlastAlignmentParameterEnum parameter : param.keySet()) {
 			result.add(parameter.name());
 		}
@@ -302,7 +302,9 @@ public void setBlastMatrix(BlastMatrixEnum matrix) {
 				setBlastGapCosts(9, 1);
 				break;
 			case PAM70:
-				setBlastGapCosts(10, 1);
+                case BLOSUM80:
+                case BLOSUM90:
+                    setBlastGapCosts(10, 1);
 				break;
 			case PAM250:
 				setBlastGapCosts(14, 2);
@@ -313,11 +315,7 @@ public void setBlastMatrix(BlastMatrixEnum matrix) {
 			case BLOSUM50:
 				setBlastGapCosts(13, 2);
 				break;
-			case BLOSUM80:
-			case BLOSUM90:
-				setBlastGapCosts(10, 1);
-				break;
-			case BLOSUM62:
+                case BLOSUM62:
 				break;
 			default:
 				break;
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java
index 8efc91908b..70fefd5899 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java
@@ -41,7 +41,7 @@
 public class NCBIQBlastOutputProperties implements RemotePairwiseAlignmentOutputProperties {
 	private static final long serialVersionUID = -9202060390925345163L;
 
-	private Map<BlastOutputParameterEnum, String> param = new HashMap<BlastOutputParameterEnum, String>();
+	private final Map<BlastOutputParameterEnum, String> param = new HashMap<>();
 
 	/**
 	 * This constructor builds the parameters for the output of the GET command sent to the QBlast service with default
@@ -96,7 +96,7 @@ public void setOutputOption(BlastOutputParameterEnum key, String value) {
 	 */
 	@Override
 	public Set<String> getOutputOptions() {
-		Set<String> result = new HashSet<String>();
+		Set<String> result = new HashSet<>();
 		for (BlastOutputParameterEnum parameter : param.keySet()) {
 			result.add(parameter.name());
 		}
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
index c63a4b7eb9..10f4c3bf5c 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
@@ -72,7 +72,7 @@ public class NCBIQBlastService implements RemotePairwiseAlignmentService {
 	private String email = DEFAULT_EMAIL;
 	private String tool = DEFAULT_TOOL;
 
-	private Map<String, BlastJob> jobs = new HashMap<String, BlastJob>();
+	private final Map<String, BlastJob> jobs = new HashMap<>();
 
 	/** Constructs a service object that targets the public NCBI BLAST network
 	 * service.
@@ -164,7 +164,7 @@ public String sendAlignmentRequest(int gid, RemotePairwiseAlignmentProperties rp
 	 */
 	@Override
 	public String sendAlignmentRequest(String query, RemotePairwiseAlignmentProperties alignmentProperties) throws Exception {
-		Map<String, String> params = new HashMap<String, String>();
+		Map<String, String> params = new HashMap<>();
 		for (String key : alignmentProperties.getAlignmentOptions()) {
 			params.put(key, alignmentProperties.getAlignmentOption(key));
 		}
@@ -318,7 +318,7 @@ public boolean isReady(String id, long present) throws Exception {
 	 */
 	@Override
 	public InputStream getAlignmentResults(String id, RemotePairwiseAlignmentOutputProperties outputProperties) throws Exception {
-		Map<String, String> params = new HashMap<String, String>();
+		Map<String, String> params = new HashMap<>();
 		for (String key : outputProperties.getOutputOptions()) {
 			params.put(key, outputProperties.getOutputOption(key));
 		}
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerDomain.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerDomain.java
index d9b8e3de89..6935568168 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerDomain.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerDomain.java
@@ -129,10 +129,7 @@ public int compareTo(HmmerDomain o) {
 		return (this.getSqFrom().compareTo(o.getSqFrom()));
 	}
 	private boolean emptyDomain(HmmerDomain o) {
-
-		if  ( o.getSqFrom() == null)
-			return true;
-		return false;
+		return o.getSqFrom() == null;
 	}
 
 	/*
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
index 3304e78d4f..6fd2918780 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
@@ -140,9 +140,8 @@ public int compareTo(HmmerResult o) {
 		return(me.getSqFrom().compareTo(other.getSqFrom()));
 	}
 	private boolean emptyDomains(HmmerResult o) {
-		if ( o.getDomains() == null || o.getDomains().size() == 0)
-			return true;
-		return false;
+		SortedSet<HmmerDomain> d = o.getDomains();
+		return d == null || d.size() == 0;
 	}
 
 
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerScan.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerScan.java
index 854995d39e..60e96253c8 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerScan.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerScan.java
@@ -32,6 +32,6 @@
  */
 public interface HmmerScan {
 
-	public  SortedSet<HmmerResult> scan(ProteinSequence sequence) throws IOException;
+	SortedSet<HmmerResult> scan(ProteinSequence sequence) throws IOException;
 
 }
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
index 2083db63aa..bac977b6d5 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
@@ -69,7 +69,7 @@ public  SortedSet<HmmerResult> scan(ProteinSequence sequence) throws IOException
 	 */
 	public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation) throws IOException{
 
-		StringBuffer postContent = new StringBuffer();
+		StringBuilder postContent = new StringBuilder();
 
 		postContent.append("hmmdb=pfam");
 
@@ -94,8 +94,7 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 
 		connection.setRequestProperty("Accept","application/json");
 
-		connection.setRequestProperty("Content-Length", "" +
-				Integer.toString(postContent.toString().getBytes().length));
+		connection.setRequestProperty("Content-Length", String.valueOf(postContent.toString().getBytes().length));
 
 		//Send request
 		DataOutputStream wr = new DataOutputStream (
@@ -125,7 +124,7 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 
 		String inputLine;
 
-		StringBuffer result = new StringBuffer();
+		StringBuilder result = new StringBuilder();
 		while ((inputLine = in.readLine()) != null) {
 			result.append(inputLine);
 		}
@@ -134,7 +133,7 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 
 		// process the response and build up a container for the data.
 
-		SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
+		SortedSet<HmmerResult> results = new TreeSet<>();
 		try {
 			JSONObject json =  JSONObject.fromObject(result.toString());
 
@@ -149,7 +148,7 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 				HmmerResult hmmResult = new HmmerResult();
 
 				Object dclO = hit.get("dcl");
-				Integer dcl = -1;
+				int dcl = -1;
 				if ( dclO instanceof Long){
 					Long dclL = (Long) dclO;
 					dcl = dclL.intValue();
@@ -170,7 +169,7 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 
 				JSONArray hmmdomains = hit.getJSONArray("domains");
 
-				SortedSet<HmmerDomain> domains = new TreeSet<HmmerDomain>();
+				SortedSet<HmmerDomain> domains = new TreeSet<>();
 				for ( int j= 0 ; j < hmmdomains.size() ; j++){
 					JSONObject d = hmmdomains.getJSONObject(j);
 					Integer is_included = getInteger(d.get("is_included"));
diff --git a/pom.xml b/pom.xml
index 13cecbdb8a..b680b89f62 100644
--- a/pom.xml
+++ b/pom.xml
@@ -549,7 +549,7 @@
 			</plugin>
 			<plugin>
 				<artifactId>maven-project-info-reports-plugin</artifactId>
-				<version>2.9</version>
+				<version>3.0.0</version>
 				<reportSets>
 					<reportSet>
 						<reports>
@@ -573,12 +573,12 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-checkstyle-plugin</artifactId>
-				<version>2.17</version>
+				<version>3.0.0</version>
 			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-jxr-plugin</artifactId>
-				<version>2.5</version>
+				<version>3.0.0</version>
 			</plugin>
 		</plugins>
 	</reporting>
@@ -600,7 +600,7 @@
 
 						<groupId>org.apache.maven.plugins</groupId>
 						<artifactId>maven-jarsigner-plugin</artifactId>
-						<version>1.4</version>
+						<version>3.0.0</version>
 						<executions>
 							<execution>
 								<id>sign</id>

From 031f84bddbf04dfd3b8e544d291d7586d0c3af95 Mon Sep 17 00:00:00 2001
From: me <seh@internet.earth>
Date: Sat, 7 Mar 2020 16:39:03 -0500
Subject: [PATCH 06/18] cleanup continued; core and structure unit tests still
 pass, other modules untested

---
 .../sequence/io/BufferedReaderBytesRead.java  |   2 +-
 .../core/sequence/location/FuzzyPoint.java    |  15 +-
 .../core/sequence/location/SimplePoint.java   |   8 +-
 .../sequence/location/template/Point.java     |   2 +-
 .../template/AbstractCompoundSet.java         |   2 +-
 .../AbstractNucleotideCompoundSet.java        |   5 +-
 .../sequence/template/AbstractSequence.java   |  27 +-
 .../alignment/SimpleAlignedSequenceTest.java  |  12 +-
 .../nbio/structure/test/StructureTest.java    |  11 +-
 .../align/gui/jmol/MultipleAlignmentJmol.java |   2 +-
 .../gui/jmol/StructureAlignmentJmol.java      |   8 +-
 .../symmetry/gui/SymmetryListener.java        |  10 +-
 .../structure/SubstructureIdentifier.java     |   8 +-
 .../structure/align/client/StructureName.java |   4 +-
 .../MultipleAlignmentEnsembleImpl.java        |   3 +-
 .../util/MultipleAlignmentWriter.java         |   2 +-
 .../nbio/structure/domain/PDPDomain.java      |   4 +-
 .../structure/domain/RemotePDPProvider.java   |   6 +-
 .../domain/pdp/GetDistanceMatrix.java         | 276 ++++++++----------
 .../nbio/structure/io/LocalPDBDirectory.java  |   3 +-
 .../nbio/structure/io/PDBFileParser.java      |  40 +--
 .../symmetry/internal/CeSymmResult.java       |   3 +-
 .../biojava/nbio/structure/TestAtomCache.java |   2 +-
 .../nbio/structure/TestURLIdentifier.java     |   4 +-
 24 files changed, 218 insertions(+), 241 deletions(-)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java
index 3dc587fc22..fc5a9b0bad 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java
@@ -417,7 +417,7 @@ private String readLine(boolean ignoreLF) throws IOException {
 	public String readLine() throws IOException {
 		String line = readLine(false);
 		if (line != null) {
-			bytesRead = bytesRead + line.length();
+			bytesRead += line.length();
 		}
 		return line;
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java
index 8dc999a66d..426ea18302 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java
@@ -70,11 +70,14 @@ public FuzzyPoint(int minPoint, int maxPoint, Resolver<FuzzyPoint> resolver, boo
 	}
 
 	@Override
-	public Integer getPosition() {
-		if(super.getPosition() == -1) {
-			super.setPosition(getResolver().resolve(this));
-		}
-		return super.getPosition();
+	public int getPosition() {
+		int prevPos = super.getPosition();
+		if(prevPos == -1) {
+			int nextPos = getResolver().resolve(this);
+			super.setPosition(nextPos);
+			return nextPos;
+		} else
+			return prevPos;
 	}
 
 	protected Integer getMax() {
@@ -106,6 +109,7 @@ public Point offset(int distance) {
 
 	@Override
 	public boolean equals(Object obj) {
+		if (this == obj) return true;
 		boolean equals = false;
 		if (Equals.classEqual(this, obj)) {
 			FuzzyPoint p = (FuzzyPoint) obj;
@@ -130,6 +134,7 @@ public int hashCode() {
 
 	@Override
 	public int compareTo(Point point) {
+		if (this == point) return 0;
 		//If we can assign this to a FuzzyPoint then work with a bit more info
 		if(FuzzyPoint.class.isAssignableFrom(point.getClass())) {
 			FuzzyPoint fuzzy = (FuzzyPoint)point;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java
index 69c3aea801..d8e2b60acd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java
@@ -56,7 +56,7 @@ public SimplePoint(int position, boolean unknown, boolean uncertain) {
 	}
 
 	@Override
-	public Integer getPosition() {
+	public int getPosition() {
 		return position;
 	}
 
@@ -100,6 +100,7 @@ protected int reverse(int position, int length) {
 
 	@Override
 	public boolean equals(Object obj) {
+		if (this == obj) return true;
 		boolean equals = false;
 		if (Equals.classEqual(this, obj)) {
 			SimplePoint p = (SimplePoint) obj;
@@ -125,8 +126,9 @@ public String toString() {
 	}
 
 	@Override
-	public int compareTo(Point o) {
-		return getPosition().compareTo(o.getPosition());
+	public int compareTo(Point point) {
+		if (this == point) return 0;
+		return Integer.compare(getPosition(), point.getPosition());
 	}
 
 	@Override
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Point.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Point.java
index 04cdd07398..2319570917 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Point.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Point.java
@@ -36,7 +36,7 @@ interface Resolver<T extends Point> {
 	/**
 	 * Returns the position held by this object
 	 */
-	Integer getPosition();
+	int getPosition();
 
 	/**
 	 * Returns true if the current position is unknown but is
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
index 08415bb48b..d32f1e51ac 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
@@ -166,7 +166,7 @@ public boolean isValidSequence(Sequence<C> sequence) {
 
 
 	@Override
-public List<C> getAllCompounds() {
+	public List<C> getAllCompounds() {
 		return new ArrayList<>(charSeqToCompound.values());
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java
index a279a67437..26a0a983a4 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java
@@ -45,7 +45,7 @@ protected void addNucleotideCompound(String base, String complement, String... e
 		C upper = newNucleotideCompound(base.toUpperCase(), complement.toUpperCase(), upperEquivalents);
 		C lower = newNucleotideCompound(base.toLowerCase(), complement.toLowerCase(), lowerEquivalents);
 
-		List<C> equivalentCompounds = new ArrayList<>();
+		List<C> equivalentCompounds = new ArrayList<>(equivalents.length*2);
 
 		for(int i=0; i<equivalents.length; i++) {
 			equivalentCompounds.add(getCompoundForString(upperEquivalents[i]));
@@ -68,9 +68,8 @@ protected void calculateIndirectAmbiguities() {
 
 		List<NucleotideCompound> ambiguousCompounds = new ArrayList<>();
 		for(NucleotideCompound compound: getAllCompounds()) {
-			if (!compound.isAmbiguous()) {
+			if (!compound.isAmbiguous())
 				continue;
-			}
 			ambiguousCompounds.add(compound);
 		}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
index 5c3c614e09..a2e3b145ca 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
@@ -35,6 +35,7 @@
 import org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader;
 import org.biojava.nbio.core.sequence.location.SequenceLocation;
 import org.biojava.nbio.core.sequence.location.SimpleLocation;
+import org.biojava.nbio.core.sequence.location.template.AbstractLocation;
 import org.biojava.nbio.core.sequence.location.template.Location;
 import org.biojava.nbio.core.sequence.reference.AbstractReference;
 import org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader;
@@ -126,7 +127,7 @@ public void setProxySequenceReader(SequenceReader<C> proxyLoader) {
 
 		if (proxyLoader instanceof FeatureRetriever) {
 			this.setFeatureRetriever((FeatureRetriever) sequenceStorage);
-			HashMap<String, ArrayList<AbstractFeature>> ff = getFeatureRetriever().getFeatures();
+			Map<String, ArrayList<AbstractFeature>> ff = getFeatureRetriever().getFeatures();
 			for (ArrayList<AbstractFeature> abstractFeatures : ff.values()){
 				for (AbstractFeature f: abstractFeatures){
 					this.addFeature(f);
@@ -153,11 +154,7 @@ public SequenceReader<C> getProxySequenceReader() {
 	 * @return the bioBegin
 	 */
 	public Integer getBioBegin() {
-		if (bioBegin == null) {
-			return 1;
-		} else {
-			return bioBegin;
-		}
+		return bioBegin == null ? 1 : bioBegin;
 	}
 
 	/**
@@ -171,11 +168,7 @@ public void setBioBegin(Integer bioBegin) {
 	 * @return the bioEnd
 	 */
 	public Integer getBioEnd() {
-		if (bioEnd == null) {
-			return this.getLength();
-		} else {
-			return bioEnd;
-		}
+		return bioEnd == null ? this.getLength() : bioEnd;
 	}
 
 	/**
@@ -265,13 +258,10 @@ public void setParentSequence(AbstractSequence<?> parentSequence) {
 	 * @return the source
 	 */
 	public String getSource() {
-		if (source != null) {
+		if (source != null)
 			return source;
-		}
-		if (parentSequence != null) {
-			return parentSequence.getSource();
-		}
-		return null;
+		else
+			return parentSequence != null ? parentSequence.getSource() : null;
 	}
 
 	/**
@@ -353,7 +343,8 @@ public List<FeatureInterface<AbstractSequence<C>, C>> getFeatures(String feature
 		List<FeatureInterface<AbstractSequence<C>, C>> features = getFeaturesByType(featureType);
 		if (features != null) {
 			for (FeatureInterface<AbstractSequence<C>, C> feature : features) {
-				if (bioSequencePosition >= feature.getLocations().getStart().getPosition() && bioSequencePosition <= feature.getLocations().getEnd().getPosition()) {
+				AbstractLocation locs = feature.getLocations();
+				if (bioSequencePosition >= locs.getStart().getPosition() && bioSequencePosition <= locs.getEnd().getPosition()) {
 					featureHits.add(feature);
 				}
 			}
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java
index 43a87c4c3e..72b9300b23 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java
@@ -117,9 +117,9 @@ public void testGetAlignmentIndexAtOutOfBounds4() {
 
 	@Test
 	public void testGetEnd() {
-		assertEquals(global.getEnd().getPosition(), Integer.valueOf(6));
-		assertEquals(local.getEnd().getPosition(), Integer.valueOf(8));
-		assertEquals(local2.getEnd().getPosition(), Integer.valueOf(3));
+		assertEquals(6, global.getEnd().getPosition());
+		assertEquals(8, local.getEnd().getPosition());
+		assertEquals(3, local2.getEnd().getPosition());
 	}
 
 	@Test
@@ -211,9 +211,9 @@ public void testGetSequenceIndexAtOutOfBounds4() {
 
 	@Test
 	public void testGetStart() {
-		assertEquals(global.getStart().getPosition(), Integer.valueOf(2));
-		assertEquals(local.getStart().getPosition(), Integer.valueOf(1));
-		assertEquals(local2.getStart().getPosition(), Integer.valueOf(1));
+		assertEquals(2, global.getStart().getPosition());
+		assertEquals(1, local.getStart().getPosition());
+		assertEquals(1, local2.getStart().getPosition());
 	}
 
 	@Test
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java
index cfb11a465e..a7826fced2 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java
@@ -222,12 +222,11 @@ public void testCreateVirtualCBAtom(){
 
 		if ( g1.getPDBName().equals("GLY")){
 			if ( g1 instanceof AminoAcid){
-				try {
-					Atom cb = Calc.createVirtualCBAtom((AminoAcid)g1);
-					g1.addAtom(cb);
-				} catch (StructureException e){
-					fail ("createVirtualCBAtom failed with " + e.getMessage());
-				}
+//				try {
+				g1.addAtom(Calc.createVirtualCBAtom((AminoAcid)g1));
+//				} catch (StructureException e){
+//					fail ("createVirtualCBAtom failed with " + e.getMessage());
+//				}
 			}
 		} else {
 			fail("the group at position 11 is not a GLY!");
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
index 3b0a119ae1..da57ea4863 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
@@ -76,7 +76,7 @@ public class MultipleAlignmentJmol extends AbstractAlignmentJmol {
 
 	private MultipleAlignment multAln;
 	private List<Atom[]> transformedAtoms;
-	private final JCheckBox colorByBlocks;
+	private JCheckBox colorByBlocks;
 	private final List<JCheckBox> selectedStructures;
 
 	private static final String LIGAND_DISPLAY_SCRIPT = "select ligand; wireframe 40; spacefill 120; color CPK;";
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java
index aa9eedf736..044e2ece20 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java
@@ -325,7 +325,7 @@ public void windowClosing(WindowEvent e) {
 
 	@Override
 	protected void initCoords() {
-		try {
+//		try {
 			if (ca1 == null || ca2 == null) {
 				if (structure != null)
 					setStructure(structure);
@@ -342,9 +342,9 @@ protected void initCoords() {
 			header.setTitle(title);
 			artificial.setPDBHeader(header);
 			setStructure(artificial);
-		} catch (StructureException e) {
-			e.printStackTrace();
-		}
+//		} catch (StructureException e) {
+//			e.printStackTrace();
+//		}
 	}
 
 	@Override
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java
index d6f617225d..1edb84d550 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java
@@ -82,7 +82,7 @@ public void actionPerformed(ActionEvent ae) {
 
 					break;
 				}
-				case "Optimal Self Alignment":
+				case "Optimal Self Alignment": {
 					Atom[] cloned = StructureTools.cloneAtomArray(symm.getAtoms());
 					AbstractAlignmentJmol jmol = StructureAlignmentDisplay.display(
 							symm.getSelfAlignment(), symm.getAtoms(), cloned);
@@ -91,14 +91,12 @@ public void actionPerformed(ActionEvent ae) {
 					jmol.setTitle(SymmetryDisplay.getSymmTitle(symm));
 
 					break;
+				}
 				case "Show Symmetry Group":
-					String script = SymmetryDisplay.printSymmetryGroup(symm);
-					jmol.evalString(script);
-
+					jmol.evalString(SymmetryDisplay.printSymmetryGroup(symm));
 					break;
 				case "Show Symmetry Axes": {
-					String s = SymmetryDisplay.printSymmetryAxes(symm);
-					jmol.evalString(s);
+					jmol.evalString(SymmetryDisplay.printSymmetryAxes(symm));
 					break;
 				}
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
index 924bc9d66c..a6681c69b5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
@@ -75,7 +75,7 @@ public class SubstructureIdentifier implements StructureIdentifier {
 	private static final Logger logger = LoggerFactory.getLogger(SubstructureIdentifier.class);
 
 
-	private final String pdbId;
+	public final String pdbId;
 	private final List<ResidueRange> ranges;
 
 	/**
@@ -290,10 +290,8 @@ public Structure reduce(Structure s) throws StructureException {
 	 */
 	@Override
 	public Structure loadStructure(AtomCache cache) throws IOException, StructureException {
-		String pdb = getPdbId();
-		if(pdb == null)
-			return null;
-		return cache.getStructureForPdbId(pdb);
+		String pdb = pdbId;
+		return pdb == null ? null : cache.getStructureForPdbId(pdb);
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
index ceb8dfb0b0..ce8e34b3e6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
@@ -308,7 +308,7 @@ private boolean initFromPDB(String suffix) {
 		SubstructureIdentifier si = new SubstructureIdentifier(suffix);
 		base = si; // Safe to realize immediately
 
-		pdbId = si.getPdbId();
+        pdbId = si.pdbId;
 		// Set chainName if unique
 		Set<String> chains = getChainNames(si);
 		if(chains.size() == 1) {
@@ -361,7 +361,7 @@ private static Set<String> getChainNames(SubstructureIdentifier si) {
 	 */
 	public String getPdbId() throws StructureException {
 		if( pdbId == null) {
-			pdbId = toCanonical().getPdbId();
+            pdbId = toCanonical().pdbId;
 		}
 		return pdbId;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
index 4445821ab1..210e27487e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
@@ -173,7 +173,8 @@ public MultipleAlignmentEnsembleImpl(AFPChain afp, Atom[] ca1, Atom[] ca2,
 		calculationTime = afp.getCalculationTime();
 
 		MultipleAlignment msa = new MultipleAlignmentImpl(this);
-		setMultipleAlignments(Collections.singletonList(msa));
+		ArrayList<MultipleAlignment> ms1 = new ArrayList<>(1); ms1.add(msa);
+		setMultipleAlignments(ms1);
 
 		// Convert the rotation and translation to a Matrix4D and set it
 		Matrix4d ident = new Matrix4d();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
index 15c83accff..a34d6e7b90 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
@@ -326,7 +326,7 @@ public static String to3DFormat(MultipleAlignment alignment,
 		StructureIdentifier tName = alignment.getEnsemble().getStructureIdentifiers()
 				.get(templateIndex);
 		SubstructureIdentifier canon = tName.toCanonical();
-		String tPdbId = canon.getPdbId();
+        String tPdbId = canon.pdbId;
 		String tChain = null;
 		for(ResidueRange range : canon.getResidueRanges()) {
 			tChain = range.getChainName();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java
index 2b108bf41e..947557eef6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java
@@ -56,8 +56,8 @@ public String getIdentifier() {
 	}
 
 	public String getPdbId() {
-		return canonical.getPdbId();
-	}
+        return canonical.pdbId;
+    }
 
 	@Override
 	public SubstructureIdentifier toCanonical() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
index 30882691f9..c40fda1509 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
@@ -196,9 +196,9 @@ public PDPDomain getPDPDomain(String pdpDomainName) throws IOException{
 		List<ResidueRange> ranges = new ArrayList<>();
 		for(String domainRange : domainRanges) {
 			SubstructureIdentifier strucId = new SubstructureIdentifier(domainRange);
-			if(pdbId == null) {
-				pdbId = strucId.getPdbId();
-			} else if(!pdbId.equals(strucId.getPdbId())) {
+            if(pdbId == null) {
+                pdbId = strucId.pdbId;
+			} else if(!pdbId.equals(strucId.pdbId)) {
 				// should never happen with correct server implementation
 				throw new RuntimeException("Don't know how to take the union of domains from multiple PDB IDs.");
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java
index 1bdad14a7c..f2038754b8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java
@@ -25,164 +25,144 @@
 
 public class GetDistanceMatrix {
 
-
-	/** A set of Calpha atoms that are representing the protein
-	 *
-	 * @param protein
-	 */
-	public  PDPDistanceMatrix getDistanceMatrix(Atom[] protein) {
-		int[][] dist = new int[protein.length+3][protein.length+3];
-		int i,j;
-		double d,dt1,dt2,dt3,dt4;
-		int nclose=0;
-		int[] iclose = new int[protein.length*protein.length];
-		int[] jclose= new int[protein.length*protein.length];
-
-		if(protein.length >= PDPParameters.MAXLEN) {
-			System.err.println(String.format("%d protein.len > MAXLEN %d\n",protein.length,PDPParameters.MAXLEN));
-			return null;
-		}
-		for(i=0;i<protein.length;i++) {
-			for(j=i;j<protein.length;j++) {
-				dist[i][j]=0;
-				dist[j][i]=0;
-
-				d=0;
-
-				Atom ca1 = protein[i];
-				Atom ca2 = protein[j];
-				Group g1 = ca1.getGroup();
-				Group g2 = ca2.getGroup();
-
-				Atom cb1 = getCBeta(g1);
-				Atom cb2 = getCBeta(g2);
-				boolean hasCbeta1 = cb1 != null;
-				boolean hasCbeta2 = cb2 != null;
-
-				dt1=81;
-				dt2=64;
-				dt3=49;
-				dt4=36;
-
-				if(hasCbeta1 && hasCbeta2) {
-					double distance = Calc.getDistance(cb1,cb2);
-					d+= distance*distance;
-				}
-				else if(hasCbeta1 && ! hasCbeta2) {
-					double distance;
-
+    private static final double dt1 = 81;
+    private static final double dt2 = 64;
+    private static final double dt3 = 49;
+    private static final double dt4 = 36;
+
+    /**
+     * A set of Calpha atoms that are representing the protein
+     *
+     * @param protein
+     */
+    public PDPDistanceMatrix getDistanceMatrix(final Atom[] protein) {
+        int n = protein.length;
+        int[][] dist = new int[n + 3][n + 3];
+        int i, j;
+        int nclose = 0;
+        int[] iclose = new int[n * n];
+        int[] jclose = new int[n * n];
+
+        if (n >= PDPParameters.MAXLEN) {
+            System.err.println(String.format("%d protein.len > MAXLEN %d\n", n, PDPParameters.MAXLEN));
+            return null;
+        }
+        for (i = 0; i < n; i++) {
+            for (j = i; j < n; j++) {
+                dist[i][j] = 0;
+                dist[j][i] = 0;
+
+
+                Atom ca1 = protein[i];
+                Atom ca2 = protein[j];
+                Group g1 = ca1.getGroup();
+                Group g2 = ca2.getGroup();
+
+                Atom cb1 = getCBeta(g1);
+                Atom cb2 = getCBeta(g2);
+                boolean hasCbeta1 = cb1 != null;
+                boolean hasCbeta2 = cb2 != null;
+
+				double d = 0;
+
+                double distance;
+                if (hasCbeta1 && hasCbeta2) {
+                    distance = Calc.getDistance(cb1, cb2);
+                } else if (hasCbeta1 && !hasCbeta2) {
 					distance = Calc.getDistance(cb1, ca2);
-					d += distance * distance;
-				}
-				else if(!hasCbeta1&&hasCbeta2) {
-					double distance = Calc.getDistance(ca1, cb2);
-					d += distance * distance;
-				}
-				else if( ! hasCbeta1&&!hasCbeta2) {
-					double distance = Calc.getDistance(ca1, ca2);
-					d += distance * distance;
-				}
-
-				if(d<dt1) {
-					dist[i][j]=1;
-					dist[j][i]=1;
-					if(d<dt2) {
-						dist[i][j]=2;
-						dist[j][i]=2;
-						if(j-i>35) {
-							iclose[nclose]=i;
-							jclose[nclose]=j;
-							nclose++;
-						}
-						if(d<dt3) {
-							dist[i][j]=4;
-							dist[j][i]=4;
-							if(d<dt4) {
-								dist[i][j]=6;
-								dist[j][i]=6;
-							}
-						}
-					}
-				}
-			}
-		}
-		/* secondary structure interaction */
-		for(i=1;i<protein.length;i++) {
-			for(j=i;j<protein.length-1;j++) {
-				/* beta-sheet */
-				if(dist[i][j]>=2&&j-i>5) {
-					if(dist[i-1][j-1]>=2&&dist[i+1][j+1]>=2||dist[i-1][j+1]>=2&&dist[i+1][j-1]>=2) {
-						dist[i][j]+=4;
-						dist[j][i]+=4;
+                } else if (!hasCbeta1 && hasCbeta2) {
+                    distance = Calc.getDistance(ca1, cb2);
+                } else /*if (!hasCbeta1 && !hasCbeta2)*/ {
+                    distance = Calc.getDistance(ca1, ca2);
+                }
+				d += distance * distance;
+
+                if (d < dt1) {
+                    dist[i][j] = dist[j][i] = 1;
+                    if (d < dt2) {
+                        dist[i][j] = dist[j][i] = 2;
+                        if (j - i > 35) {
+                            iclose[nclose] = i;
+                            jclose[nclose] = j;
+                            nclose++;
+                        }
+                        if (d < dt3) {
+                            dist[i][j] = dist[j][i] = 4;
+                            if (d < dt4) {
+                                dist[i][j] = dist[j][i] = 6;
+                            }
+                        }
+                    }
+                }
+            }
+        }
+        /* secondary structure interaction */
+        for (i = 1; i < n; i++) {
+            for (j = i; j < n - 1; j++) {
+                /* beta-sheet */
+                if (dist[i][j] >= 2 && j - i > 5) {
+                    if (dist[i - 1][j - 1] >= 2 && dist[i + 1][j + 1] >= 2 || dist[i - 1][j + 1] >= 2 && dist[i + 1][j - 1] >= 2) {
+                        dist[i][j] += 4;
+                        dist[j][i] += 4;
 						/*
 					printf("1: %d %d %d\n",i,j,dist[i][j]);
 						 */
-					}
-					/* alpha-helices */
-					else if(i>2&&j<protein.length-2) {
-						if(dist[i-3][j-3]>=1&&dist[i+3][j+3]>=1||dist[i-3][j+3]>=1&&dist[i+3][j-3]>=1) {
-							dist[i][j]+=4;
-							dist[j][i]+=4;
+                    }
+                    /* alpha-helices */
+                    else if (i > 2 && j < n - 2) {
+                        if (dist[i - 3][j - 3] >= 1 && dist[i + 3][j + 3] >= 1 || dist[i - 3][j + 3] >= 1 && dist[i + 3][j - 3] >= 1) {
+                            dist[i][j] += 4;
+                            dist[j][i] += 4;
 							/*
 						printf("3: %d %d %d\n",i,j,dist[i][j]);
 							 */
-						}
-						else if(i>3&&j<protein.length-3) {
-							if((dist[i-3][j-3]>=1||dist[i-3][j-4]>=1||dist[i-4][j-3]>=1||dist[i-4][j-4]>=1)&&
-									(dist[i+4][j+4]>=1||dist[i+4][j+3]>=1||dist[i+3][j+3]>=1||dist[i+3][j+4]>=1)
-									||(dist[i-4][j+4]>=1||dist[i-4][j+3]>=1||dist[i-3][j+4]>=1||dist[i-3][j+3]>=1)&&
-									(dist[i+4][j-4]>=1||dist[i+4][j-3]>=1||dist[i+3][j-4]>=1||dist[i+3][j-3]>=1)) {
-								dist[i][j]+=4;
-								dist[j][i]+=4;
+                        } else if (i > 3 && j < n - 3) {
+                            if ((dist[i - 3][j - 3] >= 1 || dist[i - 3][j - 4] >= 1 || dist[i - 4][j - 3] >= 1 || dist[i - 4][j - 4] >= 1) &&
+                                    (dist[i + 4][j + 4] >= 1 || dist[i + 4][j + 3] >= 1 || dist[i + 3][j + 3] >= 1 || dist[i + 3][j + 4] >= 1)
+                                    || (dist[i - 4][j + 4] >= 1 || dist[i - 4][j + 3] >= 1 || dist[i - 3][j + 4] >= 1 || dist[i - 3][j + 3] >= 1) &&
+                                    (dist[i + 4][j - 4] >= 1 || dist[i + 4][j - 3] >= 1 || dist[i + 3][j - 4] >= 1 || dist[i + 3][j - 3] >= 1)) {
+                                dist[i][j] += 4;
+                                dist[j][i] += 4;
 								/*
 							printf("4: %d %d %d\n",i,j,dist[i][j]);
 								 */
-							}
-						}
-					}
-				}
-			}
-		}
-
-		PDPDistanceMatrix matrix = new PDPDistanceMatrix();
-
-		matrix.setNclose(nclose);
-		matrix.setIclose(iclose);
-		matrix.setJclose(jclose);
-		matrix.setDist(dist);
-		return matrix;
-
-	}
-
-
-
-	private Atom getCBeta(Group g1) {
-		Atom cb;
-
-
-		cb = g1.getAtom("CB");
-		if ( cb == null)
-			{
-			if ( g1 instanceof AminoAcid) {
-				AminoAcid aa = (AminoAcid) g1;
-
-				try {
-					cb = Calc.createVirtualCBAtom(aa);
-				} catch (StructureException e1) {
-					// TODO Auto-generated catch block
-					e1.printStackTrace();
-				}
-			}
-		}
-		return cb;
-	}
-
-
-
-
-
-
-
+                            }
+                        }
+                    }
+                }
+            }
+        }
+
+        PDPDistanceMatrix matrix = new PDPDistanceMatrix();
+
+        matrix.setNclose(nclose);
+        matrix.setIclose(iclose);
+        matrix.setJclose(jclose);
+        matrix.setDist(dist);
+        return matrix;
+
+    }
+
+
+    private Atom getCBeta(Group g1) {
+        Atom cb;
+
+
+        cb = g1.getAtom("CB");
+        if (cb == null) {
+            if (g1 instanceof AminoAcid) {
+                AminoAcid aa = (AminoAcid) g1;
+
+//				try {
+                cb = Calc.createVirtualCBAtom(aa);
+//				} catch (StructureException e1) {
+//					// TODO Auto-generated catch block
+//					e1.printStackTrace();
+//				}
+            }
+        }
+        return cb;
+    }
 
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
index 6ec299ef90..f22a2bcdfe 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
@@ -324,9 +324,8 @@ public Structure getStructure(File filename) throws IOException {
 
 	@Override
 	public Structure getStructureById(String pdbId) throws IOException {
-		InputStream inStream = getInputStream(pdbId);
 
-		return getStructure(inStream);
+		return getStructure(getInputStream(pdbId));
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
index 91fbe32045..80b8d31c79 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -1361,6 +1361,10 @@ private void sourceValueSetter(String field, String value) {
 
 	}
 
+	static final Pattern resolutionRangePattern = Pattern.compile("^REMARK   3   RESOLUTION RANGE HIGH \\(ANGSTROMS\\) :\\s+(\\d+\\.\\d+).*");
+	static final Pattern remarkFreeRValue = Pattern.compile("^REMARK   3   FREE R VALUE\\s+:\\s+(\\d?\\.\\d+).*");
+	static final Pattern remark3FreeRValueNoCutOff = Pattern.compile("^REMARK   3   FREE R VALUE\\s+(?:\\(NO CUTOFF\\))?\\s+:\\s+(\\d?\\.\\d+).*");
+
 	/**
 	 * Handler for REMARK lines
 	 */
@@ -1394,8 +1398,8 @@ private void pdb_REMARK_Handler(String line) {
 			// a) take the '(NO CUTOFF)' value if the only one available (shelx software, e.g. 1x7q)
 			// b) don't take it if also a line without '(NO CUTOFF)' is present (CNX software, e.g. 3lak)
 
-			Pattern pR = Pattern.compile("^REMARK   3 {3}FREE R VALUE\\s+(?:\\(NO CUTOFF\\))?\\s+:\\s+(\\d?\\.\\d+).**");
-			Matcher mR = pR.matcher(line);
+
+			Matcher mR = remark3FreeRValueNoCutOff.matcher(line);
 			if (mR.matches()) {
 				try {
 					rfreeNoCutoffLine = Float.parseFloat(mR.group(1));
@@ -1403,8 +1407,8 @@ private void pdb_REMARK_Handler(String line) {
 					logger.info("Rfree value "+mR.group(1)+" does not look like a number, will ignore it");
 				}
 			}
-			pR = Pattern.compile("^REMARK   3 {3}FREE R VALUE\\s+:\\s+(\\d?\\.\\d+).**");
-			mR = pR.matcher(line);
+
+			mR = remarkFreeRValue.matcher(line);
 			if (mR.matches()) {
 				try {
 					rfreeStandardLine = Float.parseFloat(mR.group(1));
@@ -1417,8 +1421,7 @@ private void pdb_REMARK_Handler(String line) {
 		// note: if more than 1 value present (occurring in hybrid experimental technique entries, e.g. 3ins, 4n9m)
 		// then last one encountered will be taken
 		} else if (line.startsWith("REMARK   3   RESOLUTION RANGE HIGH")){
-			Pattern pR = Pattern.compile("^REMARK   3 {3}RESOLUTION RANGE HIGH \\(ANGSTROMS\\) :\\s+(\\d+\\.\\d+).**");
-			Matcher mR = pR.matcher(line);
+			Matcher mR = resolutionRangePattern.matcher(line);
 			if (mR.matches()) {
 				try {
 					float res = Float.parseFloat(mR.group(1));
@@ -2671,6 +2674,7 @@ public  Structure parsePDBFile(BufferedReader buf)
 				recordName = line.substring (0, 6).trim ();
 
 			try {
+				//TODO switch(recordName)
 				if (recordName.equals("ATOM"))
 					pdb_ATOM_Handler(line);
 				else if (recordName.equals("SEQRES"))
@@ -2713,17 +2717,19 @@ else if (recordName.equals("SSBOND"))
 					pdb_SSBOND_Handler(line);
 				else if (recordName.equals("LINK"))
 					pdb_LINK_Handler(line);
-				else if ( params.isParseSecStruc()) {
-					switch (recordName) {
-						case "HELIX":
-							pdb_HELIX_Handler(line);
-							break;
-						case "SHEET":
-							pdb_SHEET_Handler(line);
-							break;
-						case "TURN":
-							pdb_TURN_Handler(line);
-							break;
+				else {
+					if ( params.isParseSecStruc()) {
+						switch (recordName) {
+							case "HELIX":
+								pdb_HELIX_Handler(line);
+								break;
+							case "SHEET":
+								pdb_SHEET_Handler(line);
+								break;
+							case "TURN":
+								pdb_TURN_Handler(line);
+								break;
+						}
 					}
 				}
 			} catch (StringIndexOutOfBoundsException | NullPointerException ex) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java
index 8376220e57..fac56358f5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java
@@ -21,7 +21,6 @@
 package org.biojava.nbio.structure.symmetry.internal;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 
@@ -109,7 +108,7 @@ public List<StructureIdentifier> getRepeatsID() throws StructureException {
 		List<StructureIdentifier> repeats = new ArrayList<>(
 				numRepeats);
 
-		String pdbId = structureId.toCanonical().getPdbId();
+        String pdbId = structureId.toCanonical().pdbId;
 		Block align = multipleAlignment.getBlocks().get(0);
 
 		for (int su = 0; su < numRepeats; su++) {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java
index 25003b4122..0c04a68383 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java
@@ -42,7 +42,7 @@
 // TODO dmyersturnbull: we should merge TestAtomCache and AtomCacheTest
 public class TestAtomCache {
 
-	public static final String lineSplit = System.getProperty("file.separator");
+//	public static final String lineSplit = System.getProperty("file.separator");
 	private AtomCache cache;
 
 	@Before
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java
index cfa32a1cc2..41f4ff5def 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java
@@ -79,7 +79,7 @@ public void testURLParameters() throws StructureException, IOException {
 
 		full = id.loadStructure(cache);
 		assertNotNull(full);
-		assertEquals("2POS",id.toCanonical().getPdbId());
+        assertEquals("2POS", id.toCanonical().pdbId);
 //		assertEquals("2POS",full.getName()); // What should this get set to with identifiers?
 
 		url = new URL("file://" + base + "?residues=A:1-5");
@@ -106,7 +106,7 @@ public void testURLParameters() throws StructureException, IOException {
 
 			full = id.loadStructure(cache);
 			assertNotNull(full);
-			assertEquals("1B8G",id.toCanonical().getPdbId());
+            assertEquals("1B8G", id.toCanonical().pdbId);
 		} catch(UnknownHostException e) {
 			logger.error("Unable to connect to rcsb.org");
 			// still pass

From 348eb30b872914e2ddcc0bc64037b3ec7d2f1bdb Mon Sep 17 00:00:00 2001
From: me <seh@internet.earth>
Date: Sat, 7 Mar 2020 16:57:28 -0500
Subject: [PATCH 07/18] updates

---
 .../GeneChromosomePositionParser.java         |  9 ++--
 .../genome/util/ChromosomeMappingTools.java   | 49 ++++++++++---------
 .../genome/TestChromosomeMappingTools.java    | 12 ++---
 .../nbio/genome/TestGenomeMapping.java        |  9 ++--
 .../structure/align/gui/jmol/JmolPanel.java   |  7 ++-
 .../structure/align/gui/jmol/JmolTools.java   |  2 +-
 .../structure/align/util/AlignmentTools.java  |  5 +-
 7 files changed, 50 insertions(+), 43 deletions(-)

diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
index 368d3e6d84..0bf7035ea0 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
@@ -94,8 +94,7 @@ public static List<GeneChromosomePosition> getChromosomeMappings(InputStream inS
 	}
 
 	private static GeneChromosomePosition getGeneChromosomePosition(String line) {
-		if ( line == null)
-			return null;
+
 		String[] spl = line.split("\t");
 
 		if ( spl.length != 11) {
@@ -114,10 +113,8 @@ private static GeneChromosomePosition getGeneChromosomePosition(String line) {
 		g.setCdsStart(Integer.parseInt(spl[6]));
 		g.setCdsEnd(Integer.parseInt(spl[7]));
 		g.setExonCount(Integer.parseInt(spl[8]));
-		String exonStarts = spl[9];
-		String exonEnds = spl[10];
-		g.setExonStarts(getIntegerList(exonStarts));
-		g.setExonEnds(getIntegerList(exonEnds));
+		g.setExonStarts(getIntegerList(spl[9]));
+		g.setExonEnds(getIntegerList(spl[10]));
 
 		//System.out.println(line);
 		//System.out.println(Arrays.asList(spl) + " " + spl.length);
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
index aa91bf2ad5..a241f2220c 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
@@ -49,10 +49,10 @@ public class ChromosomeMappingTools {
 	public static final String CHROMOSOME = "CHROMOSOME";
 	public static final String CDS = "CDS";
 
-	private static int base = 1;
-	public static void setCoordinateSystem(int baseInt) {
-		base = baseInt;
-	}
+//	private static final int base = 1;
+//	public static void setCoordinateSystem(int baseInt) {
+//		base = baseInt;
+//	}
 
 	/**
 	 * Pretty print the details of a GeneChromosomePosition to a String
@@ -207,7 +207,7 @@ private static String formatExonStructureReverse(GeneChromosomePosition chromPos
 	 * @param chromPos
 	 * @return length of the CDS in nucleotides.
 	 */
-	public static int getCDSLength(GeneChromosomePosition chromPos) {
+	public static int getCDSLength(GeneChromosomePosition chromPos, int base) {
 
 		List<Integer> exonStarts = chromPos.getExonStarts();
 		List<Integer> exonEnds = chromPos.getExonEnds();
@@ -217,9 +217,9 @@ public static int getCDSLength(GeneChromosomePosition chromPos) {
 
 		int codingLength;
 		if (chromPos.getOrientation().equals('+'))
-			codingLength = ChromosomeMappingTools.getCDSLengthForward(exonStarts, exonEnds, cdsStart, cdsEnd);
+			codingLength = ChromosomeMappingTools.getCDSLengthForward(exonStarts, exonEnds, cdsStart, cdsEnd, base);
 		else
-			codingLength = ChromosomeMappingTools.getCDSLengthReverse(exonStarts, exonEnds, cdsStart, cdsEnd);
+			codingLength = ChromosomeMappingTools.getCDSLengthReverse(exonStarts, exonEnds, cdsStart, cdsEnd, base);
 		return codingLength;
 	}
 
@@ -498,7 +498,7 @@ public static ChromPos getChromPosForward(int cdsPos, List<Integer> exonStarts,
 	 * @param cdsEnd
 	 * @return
 	 */
-	public static int getCDSLengthReverse(List<Integer> exonStarts, List<Integer> exonEnds, int cdsStart, int cdsEnd) {
+	public static int getCDSLengthReverse(List<Integer> exonStarts, List<Integer> exonEnds, int cdsStart, int cdsEnd, int base) {
 
 		int codingLength = 0;
 
@@ -545,7 +545,7 @@ public static int getCDSLengthReverse(List<Integer> exonStarts, List<Integer> ex
 	 * @param cdsEnd
 	 * @return
 	 */
-	public static int getCDSLengthForward(List<Integer> exonStarts, List<Integer> exonEnds, int cdsStart, int cdsEnd) {
+	public static int getCDSLengthForward(List<Integer> exonStarts, List<Integer> exonEnds, int cdsStart, int cdsEnd, int base) {
 
 		int codingLength = 0;
 
@@ -773,23 +773,24 @@ private static List<Range<Integer>> getCDSExonRangesForward(GeneChromosomePositi
 	 * I have a genomic coordinate, where is it on the mRNA
 	 *
 	 * @param coordinate
-	 * @param chromosomePosition
+	 * @param p
 	 * @return
 	 */
-	public static int getCDSPosForChromosomeCoordinate(int coordinate, GeneChromosomePosition chromosomePosition) {
+	public static int getCDSPosForChromosomeCoordinate(int coordinate, GeneChromosomePosition p, int base) {
 
-		if ( chromosomePosition.getOrientation() == '+')
+		if ( p.getOrientation() == '+')
 			return getCDSPosForward(coordinate,
-					chromosomePosition.getExonStarts(),
-					chromosomePosition.getExonEnds(),
-					chromosomePosition.getCdsStart(),
-					chromosomePosition.getCdsEnd());
-
-		return getCDSPosReverse(coordinate,
-				chromosomePosition.getExonStarts(),
-				chromosomePosition.getExonEnds(),
-				chromosomePosition.getCdsStart(),
-				chromosomePosition.getCdsEnd());
+					p.getExonStarts(),
+					p.getExonEnds(),
+					p.getCdsStart(),
+					p.getCdsEnd(), base);
+
+		else
+			return getCDSPosReverse(coordinate,
+				p.getExonStarts(),
+				p.getExonEnds(),
+				p.getCdsStart(),
+				p.getCdsEnd(), base);
 	}
 
 	/**
@@ -807,7 +808,7 @@ public static int getCDSPosForChromosomeCoordinate(int coordinate, GeneChromosom
 	 * @author Yana Valasatava
 	 */
 	public static int getCDSPosForward(int chromPos, List<Integer> exonStarts, List<Integer> exonEnds,
-			int cdsStart, int cdsEnd) {
+									   int cdsStart, int cdsEnd, int base) {
 
 		// the genetic coordinate is not in a coding region
 		if ( (chromPos < (cdsStart+base) ) || ( chromPos > (cdsEnd+base) ) ) {
@@ -854,7 +855,7 @@ public static int getCDSPosForward(int chromPos, List<Integer> exonStarts, List<
 	 * @author Yana Valasatava
 	 */
 	public static int getCDSPosReverse(int chromPos, List<Integer> exonStarts, List<Integer> exonEnds,
-			int cdsStart, int cdsEnd) {
+			int cdsStart, int cdsEnd, int base) {
 
 		// the genetic coordinate is not in a coding region
 		if ( (chromPos < (cdsStart+base)) || ( chromPos > (cdsEnd+base) ) ) {
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestChromosomeMappingTools.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestChromosomeMappingTools.java
index 9ddd43357a..59facf95e7 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestChromosomeMappingTools.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestChromosomeMappingTools.java
@@ -43,8 +43,8 @@ public void testGetCDSLengthForward() {
 		int cdsEnd = 75;
 
 		int cdsDesired = 23 - 3;
-		ChromosomeMappingTools.setCoordinateSystem(0);
-		int cdsTest = ChromosomeMappingTools.getCDSLengthForward(exonStarts, exonEnds, cdsStart, cdsEnd);
+
+		int cdsTest = ChromosomeMappingTools.getCDSLengthForward(exonStarts, exonEnds, cdsStart, cdsEnd, 0);
 
 		assertEquals(cdsDesired, cdsTest);
 	}
@@ -58,8 +58,8 @@ public void testGetCDSLengthReverseAsc() {
 		int cdsEnd = 75;
 
 		int cdsDesired = 12 - 3;
-		ChromosomeMappingTools.setCoordinateSystem(0);
-		int cdsTest = ChromosomeMappingTools.getCDSLengthReverse(exonStarts, exonEnds, cdsStart, cdsEnd);
+
+		int cdsTest = ChromosomeMappingTools.getCDSLengthReverse(exonStarts, exonEnds, cdsStart, cdsEnd, 0);
 
 		assertEquals(cdsDesired, cdsTest);
 	}
@@ -73,8 +73,8 @@ public void testGetCDSLengthReverseDesc() {
 		int cdsEnd = 50;
 
 		int cdsDesired = 17 - 3;
-		ChromosomeMappingTools.setCoordinateSystem(0);
-		int cdsTest = ChromosomeMappingTools.getCDSLengthReverse(exonStarts, exonEnds, cdsStart, cdsEnd);
+
+		int cdsTest = ChromosomeMappingTools.getCDSLengthReverse(exonStarts, exonEnds, cdsStart, cdsEnd, 0);
 
 		assertEquals(cdsDesired, cdsTest);
 	}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
index a7b47ae0a3..ba68ae3917 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
@@ -88,7 +88,7 @@ public void testAK1() {
 				validateExon(5,516,585, cdsranges  );
 
 
-				int cdslength = ChromosomeMappingTools.getCDSLength(pos);
+				int cdslength = ChromosomeMappingTools.getCDSLength(pos, 1);
 
 				Assert.assertEquals("CDS length should be 582, but is " + cdslength, cdslength, (uniProtLength * 3));
 
@@ -173,16 +173,19 @@ private void validateExon(int exonNr, int start, int stop, List<Range<Integer>>
 	 *
 	 * @author Yana Valasatava
 	 */
-	private int getPositionInmRNA(String geneName, String genebankId, int posChrom) {
+	private int getPositionInmRNA(String geneName, String genebankId, int posChrom, int base) {
 		for (GeneChromosomePosition gcp : gcps) {
 			if ( gcp.getGeneName().equals(geneName) ) {
 				if ( gcp.getGenebankId().equals(genebankId) ) {
-					return ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posChrom, gcp);
+					return ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posChrom, gcp, base);
 				}
 			}
 		}
 		return -1;
 	}
+	private int getPositionInmRNA(String geneName, String genebankId, int posChrom) {
+		return getPositionInmRNA(geneName, genebankId, posChrom, 1);
+	}
 
 	/** Make sure the mapping tool correctly retrieves the mRNA position for a gene
 	 * living on the forward DNA strand for different chromosome positions.
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java
index 57925259de..54df47a0ed 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java
@@ -63,6 +63,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import static org.jmol.util.Logger.LEVEL_FATAL;
+
 
 public class JmolPanel
 extends JPrintPanel
@@ -91,6 +93,7 @@ public JmolPanel() {
 				adapter,
 				null,null,null,null,
 				statusListener);
+		setIgnoreRepaint(true);
 
 	}
 
@@ -410,7 +413,9 @@ public int getLogLevel() {
 				return org.jmol.util.Logger.LEVEL_WARN;
 			if( slf.isErrorEnabled() )
 				return org.jmol.util.Logger.LEVEL_ERROR;
-			throw new IllegalStateException("Unknown SLF4J error level");
+
+			return LEVEL_FATAL;
+			//throw new IllegalStateException("Unknown SLF4J error level");
 		}
 		@Override
 		public void debug(String txt) {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolTools.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolTools.java
index 1630276b46..d0cf56e5d7 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolTools.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolTools.java
@@ -112,7 +112,7 @@ public static final String getPdbInfo(Atom a, boolean printResName){
 
 
 
-		if ( ! chain1.equals("")){
+		if (chain1!=null && ! chain1.equals("")){
 			buf.append(":");
 			buf.append(chain1);
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
index 0a7ea5ea13..6e32db9656 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -1194,7 +1194,7 @@ public static void alignmentToSIF(Writer out,AFPChain afpChain,
 	 * @return a list of Chains that is built up from the Atoms in the ca array
 	 * @throws StructureException
 	 */
-	public static final List<Chain> getAlignedModel(Atom[] ca){
+	public static List<Chain> getAlignedModel(Atom[] ca){
 
 		List<Chain> model = new ArrayList<>();
 		for ( Atom a: ca){
@@ -1204,7 +1204,8 @@ public static final List<Chain> getAlignedModel(Atom[] ca){
 
 			Chain newChain = null;
 			for ( Chain c :  model) {
-				if ( c.getId().equals(parentC.getId())){
+				String cid = c.getId();
+				if ( cid!=null && cid.equals(parentC.getId())){
 					newChain = c;
 					break;
 				}

From 7cf26c57c7f9550eb715d9172726a6d110d7f8ed Mon Sep 17 00:00:00 2001
From: me <seh@internet.earth>
Date: Sat, 7 Mar 2020 18:42:13 -0500
Subject: [PATCH 08/18] updates

---
 .../aaproperties/AminoAcidProperties.java     |   8 +-
 .../nbio/aaproperties/CommandPrompt.java      |   3 +-
 .../nbio/aaproperties/PeptideProperties.java  |  46 +--
 .../org/biojava/nbio/aaproperties/Utils.java  |  14 +-
 .../profeat/ProfeatPropertiesImpl.java        |   1 -
 .../xml/CaseFreeAminoAcidCompoundSet.java     |  16 +-
 .../PeptidePropertiesImplTest.java            |   2 +-
 .../xml/GenerateJavaCodesFromTextTest.java    |   4 +-
 .../src/main/java/demo/DemoDistanceTree.java  |   5 +-
 .../biojava/nbio/alignment/Alignments.java    |   2 +-
 .../nbio/alignment/io/StockholmStructure.java |   9 +-
 .../org/biojava/nbio/phylo/Comparison.java    |   6 +-
 .../biojava/nbio/phylo/ForesterWrapper.java   |   1 -
 .../nbio/alignment/CookbookMSAProfiler.java   |   3 +-
 .../SimpleSubstitutionMatrixTest.java         |   8 +-
 .../nbio/alignment/TestDNAAlignment.java      |   6 +-
 .../alignment/aaindex/TestAAINDEXLoading.java |   4 +-
 .../nbio/phylo/TestForesterWrapper.java       |  10 +-
 .../main/java/demo/ParseFastaFileDemo.java    |   4 +-
 .../nbio/core/alignment/SimpleProfile.java    |   2 +-
 .../alignment/matrices/AAIndexFileParser.java |   2 +-
 .../matrices/DefaultAAIndexProvider.java      |   2 +-
 .../matrices/ScaledSubstitutionMatrix.java    |   2 +-
 .../matrices/SimpleSubstitutionMatrix.java    |   2 +-
 .../matrices/SubstitutionMatrixHelper.java    |   4 +-
 .../org/biojava/nbio/core/search/io/Hsp.java  |   6 +-
 .../biojava/nbio/core/search/io/SearchIO.java |   2 +-
 .../search/io/blast/BlastTabularParser.java   |  39 ++-
 .../core/search/io/blast/BlastXMLParser.java  |  32 +-
 .../nbio/core/sequence/AccessionID.java       |   2 +-
 .../nbio/core/sequence/GeneSequence.java      |   1 -
 .../nbio/core/sequence/ProteinSequence.java   |   6 +-
 .../nbio/core/sequence/TaxonomyID.java        |   2 +-
 .../core/sequence/TranscriptSequence.java     |   3 +-
 .../sequence/compound/AminoAcidCompound.java  | 102 +++----
 .../compound/AminoAcidCompoundSet.java        |  38 +--
 .../core/sequence/compound/CodonCompound.java | 277 +++++++++---------
 .../sequence/compound/NucleotideCompound.java |  58 ++--
 .../nbio/core/sequence/edits/Edit.java        |   2 +-
 .../sequence/features/AbstractFeature.java    |  17 +-
 .../CasePreservingProteinSequenceCreator.java |   2 +-
 .../nbio/core/sequence/io/FastaReader.java    |   9 +-
 .../core/sequence/io/FastaReaderHelper.java   |   4 +-
 .../nbio/core/sequence/io/FastaWriter.java    |   2 +-
 .../core/sequence/io/GenbankReaderHelper.java |   8 +-
 .../sequence/io/GenbankSequenceParser.java    |  12 +-
 .../core/sequence/io/GenbankWriterHelper.java |  17 +-
 .../io/GenericGenbankHeaderFormat.java        |   2 +-
 .../sequence/io/GenericInsdcHeaderFormat.java |   4 +-
 .../nbio/core/sequence/io/util/IOUtils.java   |   5 +-
 .../loader/GenbankProxySequenceReader.java    |  23 +-
 .../loader/UniprotProxySequenceReader.java    |   4 +-
 .../core/sequence/location/FuzzyPoint.java    |   4 +-
 .../core/sequence/location/InsdcParser.java   |   5 +-
 .../sequence/storage/BitSequenceReader.java   |   1 -
 .../storage/JoiningSequenceReader.java        |   1 -
 .../storage/SingleCompoundSequenceReader.java |   1 -
 .../sequence/template/AbstractCompound.java   | 182 ++++++------
 .../nbio/core/sequence/template/Compound.java |   4 +-
 .../CaseInsensitiveCompound.java              | 230 +++++++--------
 .../core/sequence/transcription/Table.java    |  10 +-
 .../transcription/TranscriptionEngine.java    |   4 +-
 .../core/sequence/views/RnaSequenceView.java  |   1 -
 .../nbio/core/util/FileDownloadUtils.java     |   4 +-
 .../nbio/core/util/PrettyXMLWriter.java       |  16 +-
 .../core/util/SingleLinkageClusterer.java     |   2 +-
 .../org/biojava/nbio/core/util/XMLWriter.java |   2 +-
 .../alignment/SimpleAlignedSequenceTest.java  |   2 +-
 .../core/alignment/SimpleProfileTest.java     |  10 +-
 .../nbio/core/fasta/TestFASTAReader.java      |  12 +-
 .../MultipleSequenceAlignmentTest.java        |   2 +-
 .../nbio/core/sequence/TranslationTest.java   |   4 +-
 ...ePreservingProteinSequenceCreatorTest.java |   2 +-
 .../core/sequence/io/FastaReaderTest.java     |  12 +-
 .../core/sequence/io/GenbankCookbookTest.java |   8 +-
 .../core/sequence/io/GenbankReaderTest.java   |  12 +-
 .../core/sequence/io/GenbankWriterTest.java   |   3 +-
 .../GenbankProxySequenceReaderTest.java       |   4 +-
 .../SimpleGenbankProxySequenceReaderTest.java |   4 +-
 .../location/TargetedLocationParserTest.java  |   6 +-
 .../homology/GFF3FromUniprotBlastHits.java    |   2 +-
 .../genome/io/fastq/AbstractFastqReader.java  |   1 -
 .../biojava/nbio/genome/io/fastq/Fastq.java   |   2 +-
 .../nbio/genome/io/fastq/FastqParser.java     |  36 +--
 .../nbio/genome/parsers/gff/Feature.java      |   2 +-
 .../nbio/genome/parsers/gff/FeatureList.java  |   2 +-
 .../nbio/genome/parsers/gff/GFF3Writer.java   |   1 -
 .../genome/parsers/gff/GeneIDGFF2Reader.java  |   5 +-
 .../genome/parsers/gff/GeneMarkGTFReader.java |   4 +-
 .../nbio/genome/parsers/gff/Location.java     |   2 +-
 .../genome/parsers/twobit/TwoBitFacade.java   |   4 +-
 .../genome/util/ChromosomeMappingTools.java   |  24 +-
 .../biojava/nbio/genome/util/SplitFasta.java  |   2 +-
 .../fatcat/TestFlexibleRotationMatrices.java  |   2 +-
 .../test/align/fatcat/TestOutputStrings.java  |  12 +-
 .../structure/test/ecod/EcodParseTest.java    |   2 +
 .../test/io/TestLongPdbVsMmCifParsing.java    |   5 +-
 .../org/biojava/nbio/phosphosite/Dataset.java |   4 +-
 .../org/biojava/nbio/phosphosite/Site.java    |  21 +-
 .../io/ModifiedCompoundXMLConverter.java      |   1 -
 .../protmod/phosphosite/TestAcetylation.java  |   2 +-
 .../src/main/java/demo/ParseGO.java           |   1 -
 .../org/biojava/nbio/ontology/OntoTools.java  |   2 +-
 .../biojava/nbio/ontology/io/GOParser.java    |   2 +-
 .../biojava/nbio/ontology/io/OboParser.java   |   4 -
 .../nbio/ontology/io/TabDelimParser.java      |  14 +-
 .../nbio/ontology/obo/OboFileParser.java      |   8 +-
 .../nbio/ontology/TestOboFileParsing.java     |   2 +-
 .../biojava/nbio/ontology/TestParseOBO.java   |   2 +-
 .../src/main/java/demo/PredictDisorder.java   |   4 +-
 .../biojava/nbio/ronn/NullOutputStream.java   |   1 -
 .../org/biojava/nbio/ronn/ORonnModel.java     |   2 +-
 .../ronn/NonstandardProteinCompoundTest.java  |   4 +-
 .../src/main/java/demo/AFPFromFasta.java      |   3 -
 .../java/demo/DemoAlignmentFromFasta.java     |   5 +-
 .../src/main/java/demo/DemoMultipleMC.java    |   1 -
 .../java/demo/DemoStructureFromFasta.java     |   3 +-
 .../nbio/structure/align/gui/AboutDialog.java |   3 -
 .../structure/align/gui/AlignmentGui.java     |   4 +-
 .../nbio/structure/align/gui/DBSearchGUI.java |   2 -
 .../nbio/structure/align/gui/DisplayAFP.java  |  12 +-
 .../nbio/structure/align/gui/HelpDialog.java  |   3 -
 .../nbio/structure/align/gui/JPrintPanel.java |   1 -
 .../align/gui/MultipleAlignmentGUI.java       |  10 +-
 .../structure/align/gui/ParameterGUI.java     |   2 -
 .../nbio/structure/align/gui/SystemInfo.java  |   3 -
 .../align/gui/aligpanel/AligPanel.java        |   2 +-
 .../gui/aligpanel/MultipleAligPanel.java      |   3 +-
 .../align/gui/autosuggest/JAutoSuggest.java   |   6 +-
 .../structure/align/gui/jmol/AtomInfo.java    |   8 +-
 .../structure/align/gui/jmol/JmolTools.java   |  12 +-
 .../align/gui/jmol/MultipleAlignmentJmol.java |  26 +-
 .../align/gui/jmol/RasmolCommandListener.java |   2 +-
 .../gui/jmol/StructureAlignmentJmol.java      |   4 +-
 .../align/webstart/WebStartMain.java          |   4 +-
 .../nbio/structure/gui/util/MenuCreator.java  |   2 -
 .../structure/gui/util/PDBUploadPanel.java    |   2 +-
 .../structure/gui/util/ScopSelectPanel.java   |   8 +-
 .../gui/util/SelectMultiplePanel.java         |   2 +-
 .../JmolSymmetryScriptGeneratorH.java         |   4 +-
 ...JmolSymmetryScriptGeneratorPointGroup.java |   2 +-
 .../java/demo/DemoCommandLineStartup.java     |   2 +-
 .../src/main/java/demo/DemoMmtfReader.java    |   1 -
 .../src/main/java/demo/DemoMultipleMC.java    |   1 -
 .../org/biojava/nbio/structure/Author.java    |   2 +-
 .../java/org/biojava/nbio/structure/Calc.java |  89 +++---
 .../biojava/nbio/structure/EntityInfo.java    |   1 -
 .../nbio/structure/JournalArticle.java        |   8 +-
 .../org/biojava/nbio/structure/Mutator.java   |   6 +-
 .../org/biojava/nbio/structure/PDBHeader.java |   2 +-
 .../nbio/structure/PassthroughIdentifier.java |   1 -
 .../nbio/structure/SeqMisMatchImpl.java       |  12 +-
 .../biojava/nbio/structure/StructureImpl.java |   3 +-
 .../nbio/structure/StructureTools.java        |  40 +--
 .../biojava/nbio/structure/URLIdentifier.java |   5 +-
 .../nbio/structure/align/AFPTwister.java      |   5 +-
 .../biojava/nbio/structure/align/FarmJob.java |   2 +-
 .../structure/align/StructurePairAligner.java |  25 +-
 .../ce/AbstractUserArgumentProcessor.java     |  18 +-
 .../nbio/structure/align/ce/CECalculator.java |  13 +-
 .../nbio/structure/align/ce/CeCPMain.java     |   1 -
 .../align/ce/CeCalculatorEnhanced.java        |  13 +-
 .../structure/align/ce/CeSideChainMain.java   |   1 -
 .../align/ce/UserArgumentProcessor.java       |   2 -
 .../align/client/FarmJobRunnable.java         |   2 +-
 .../structure/align/client/JFatCatClient.java |  29 +-
 .../structure/align/client/StructureName.java |   2 +-
 .../nbio/structure/align/fatcat/FatCat.java   |   1 -
 .../align/fatcat/calc/AFPCalculator.java      |  18 +-
 .../align/fatcat/calc/AFPChainer.java         |   5 +-
 .../calc/StructureAlignmentOptimizer.java     |   6 +-
 .../align/helper/JointFragments.java          |   2 -
 .../MultipleAlignmentEnsembleImpl.java        |   1 -
 .../align/multiple/mc/MultipleMcMain.java     |   5 +-
 .../multiple/mc/MultipleMcOptimizer.java      |   9 +-
 .../align/multiple/util/CoreSuperimposer.java |   1 -
 .../util/MultipleAlignmentScorer.java         |   6 +-
 .../multiple/util/MultipleAlignmentTools.java |   6 +-
 .../util/MultipleAlignmentWriter.java         |  15 +-
 .../multiple/util/MultipleSuperimposer.java   |   1 -
 .../multiple/util/ReferenceSuperimposer.java  |   1 -
 .../align/pairwise/AlternativeAlignment.java  |  17 +-
 .../align/pairwise/FragmentJoiner.java        |   2 +-
 .../align/seq/SmithWaterman3Daligner.java     |   5 +-
 .../structure/align/util/AlignmentTools.java  |  14 +-
 .../nbio/structure/align/util/AtomCache.java  |   3 +-
 .../nbio/structure/align/util/CliTools.java   |   3 +-
 .../structure/align/xml/AFPChainFlipper.java  |   1 -
 .../align/xml/AFPChainXMLParser.java          |   2 +-
 .../align/xml/MultipleAlignmentXMLParser.java |   6 +-
 .../align/xml/RepresentativeXMLConverter.java |   4 +-
 .../basepairs/BasePairParameters.java         |   8 +-
 .../nbio/structure/cath/CathCategory.java     |   2 +-
 .../nbio/structure/cath/CathInstallation.java |   8 +-
 .../structure/contact/StructureInterface.java |   2 +-
 .../domain/LocalProteinDomainParser.java      |   5 +-
 .../structure/domain/PDBDomainProvider.java   |   1 -
 .../domain/RemoteDomainProvider.java          |   3 +-
 .../structure/domain/RemotePDPProvider.java   |   3 +-
 .../structure/domain/pdp/ClusterDomains.java  |  12 +-
 .../nbio/structure/domain/pdp/CutDomain.java  |   2 +-
 .../nbio/structure/io/EntityFinder.java       |   3 +-
 .../structure/io/FastaAFPChainConverter.java  |   6 +-
 .../nbio/structure/io/FileConvert.java        |   8 +-
 .../biojava/nbio/structure/io/GroupToSDF.java |   6 +-
 .../structure/io/PDBBioAssemblyParser.java    |   2 +-
 .../nbio/structure/io/PDBFileParser.java      |  46 +--
 .../nbio/structure/io/SeqRes2AtomAligner.java |   3 +-
 .../io/StructureSequenceMatcher.java          |   8 +-
 .../structure/io/cif/CifFileConsumerImpl.java |   2 +-
 .../structure/io/mmcif/MMCIFFileTools.java    |   8 +-
 .../io/mmcif/SimpleMMcifConsumer.java         |   8 +-
 .../structure/io/mmcif/SimpleMMcifParser.java |  12 +-
 .../io/mmcif/ZipChemCompProvider.java         |   3 +-
 .../io/mmcif/chem/ChemCompTools.java          |   2 +-
 .../io/mmcif/model/AbstractBean.java          |   2 +-
 .../io/mmtf/MmtfStructureWriter.java          |   4 +-
 .../quaternary/BioAssemblyTools.java          |   4 +-
 .../quaternary/CartesianProduct.java          |   5 +-
 .../structure/rcsb/RCSBLigandsFactory.java    |   4 +-
 .../nbio/structure/scop/ScopFactory.java      |   6 +-
 .../nbio/structure/secstruc/DSSPParser.java   |  14 +-
 .../nbio/structure/secstruc/SecStrucCalc.java |  19 +-
 .../symmetry/axis/HelixAxisAligner.java       |   4 +-
 .../symmetry/axis/RotationAxisAligner.java    |   4 +-
 .../symmetry/core/HelicalRepeatUnit.java      |   2 +-
 .../nbio/structure/symmetry/core/Helix.java   |  11 +-
 .../symmetry/core/HelixExtender.java          |   4 +-
 .../structure/symmetry/core/HelixSolver.java  |   6 +-
 .../symmetry/core/PermutationGroup.java       |   2 +-
 .../symmetry/core/QuatSymmetrySubunits.java   |   2 +-
 .../symmetry/core/RotationGroup.java          |   4 +-
 .../symmetry/core/RotationSolver.java         |   4 +-
 .../symmetry/core/SystematicSolver.java       |   4 +-
 .../symmetry/geometry/Octahedron.java         |   1 -
 .../structure/symmetry/geometry/Prism.java    |   2 +-
 .../symmetry/geometry/RectangularPrism.java   |   6 +-
 .../symmetry/internal/SymmOptimizer.java      |  32 +-
 .../symmetry/misc/ChainSignature.java         |   6 +-
 .../misc/ProteinComplexSignature.java         |   6 +-
 .../symmetry/utils/BlastClustReader.java      |   2 +-
 .../nbio/structure/xtal/CrystalBuilder.java   |   6 +-
 .../xtal/io/TransfAlgebraicAdapter.java       |   3 +-
 .../biojava/nbio/structure/TestAltLocs.java   |   2 -
 .../nbio/structure/TestEntityHeuristics.java  |   4 +-
 .../nbio/structure/TestParsingCalcium.java    |   2 +-
 .../TestStructureCrossReferences.java         |   2 +-
 .../nbio/structure/align/ce/CeCPMainTest.java |   5 +-
 .../align/client/TestStructureName.java       |   1 -
 .../util/TestMultipleAlignmentScorer.java     |   5 +-
 .../structure/geometry/TestSuperPosition.java |   1 -
 .../nbio/structure/io/TestDBRefParsing.java   |   1 -
 .../structure/io/mmtf/TestMmtfRoundTrip.java  |   5 +-
 .../structure/secstruc/TestDSSPParser.java    |   1 -
 .../symmetry/internal/TestSingleRefiner.java  |   6 +-
 .../nbio/survival/cox/CoxVariables.java       |   6 +-
 .../biojava/nbio/survival/data/WorkSheet.java |   6 +-
 .../kaplanmeier/figure/ExpressionFigure.java  |   1 -
 .../kaplanmeier/metadata/MeanQuantizer.java   |   2 +-
 biojava-ws/src/main/java/demo/HmmerDemo.java  |   2 +-
 .../nbio/ws/hmmer/TestRemoteHmmerScan.java    |   1 +
 261 files changed, 1144 insertions(+), 1375 deletions(-)

diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/AminoAcidProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/AminoAcidProperties.java
index 896e0cb37a..fb52a2d410 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/AminoAcidProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/AminoAcidProperties.java
@@ -43,7 +43,7 @@ public class AminoAcidProperties {
 	 * @param aa The one-letter amino acid code
 	 * @return true if amino acid is charged
 	 */
-	public static final boolean isCharged(char aa) {
+	public static boolean isCharged(char aa) {
 		if (negChargedAAs.contains(String.valueOf(aa))) {
 			return true;
 		}
@@ -60,7 +60,7 @@ else if (posChargedAAs.contains(String.valueOf(aa))) {
 	 * @param aa The one-letter amino acid code
 	 * @return the charge of amino acid (1 if positively charged, -1 if negatively charged, 0 if not charged)
 	 */
-	public static final int getChargeOfAminoAcid(char aa) {
+	public static int getChargeOfAminoAcid(char aa) {
 		if (negChargedAAs.contains(String.valueOf(aa))) {
 			return -1;
 		}
@@ -76,7 +76,7 @@ else if (posChargedAAs.contains(String.valueOf(aa))) {
 	 * @param aa The one-letter amino acid code
 	 * @return true if amino acid is polar
 	 */
-	public static final boolean isPolar(char aa) {
+	public static boolean isPolar(char aa) {
 		if (polarAAs.contains(String.valueOf(aa))) {
 			return true;
 		}
@@ -89,7 +89,7 @@ public static final boolean isPolar(char aa) {
 	 * @param aa The one-letter amino acid code
 	 * @return the polarity of amino acid (1 if polar, 0 if not polar)
 	 */
-	public static final int getPolarityOfAminoAcid(char aa) {
+	public static int getPolarityOfAminoAcid(char aa) {
 		if (polarAAs.contains(String.valueOf(aa))) {
 			return 1;
 		}
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java
index ae7375ad82..53206e13c3 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java
@@ -31,7 +31,6 @@
 
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.IOException;
 import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
@@ -272,7 +271,7 @@ private static void compute(PrintStream output, String header, String sequence,
 		}else{
 			sequence = Utils.checkSequence(sequence);
 			pSequence = new ProteinSequence(sequence);
-			aaSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+            aaSet = AminoAcidCompoundSet.aminoAcidCompoundSet;
 		}
 		IPeptideProperties pp = new PeptidePropertiesImpl();
 
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
index 9ee64f5a65..f1f7ef390a 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
@@ -78,7 +78,7 @@ public enum SingleLetterAACode { W, C, M, H, Y, F, Q, N, I, R, D, P, T, K, E, V,
 	 * 	a protein sequence consisting of non-ambiguous characters only
 	 * @return the total molecular weight of sequence + weight of water molecule
 	 */
-	public static final double getMolecularWeight(String sequence){
+	public static double getMolecularWeight(String sequence){
 		sequence = Utils.checkSequence(sequence);
 		ProteinSequence pSequence = null;
 		try {
@@ -109,7 +109,7 @@ public static final double getMolecularWeight(String sequence){
 	 * @throws JAXBException
 	 * 	thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
 	 */
-	public static final double getMolecularWeight(String sequence, File elementMassFile, File aminoAcidCompositionFile)
+	public static double getMolecularWeight(String sequence, File elementMassFile, File aminoAcidCompositionFile)
 	throws FileNotFoundException, JAXBException{
 		sequence = Utils.checkSequence(sequence);
 		ProteinSequence pSequence = null;
@@ -140,7 +140,7 @@ public static final double getMolecularWeight(String sequence, File elementMassF
 	 * @throws FileNotFoundException
 	 * 	thrown if either elementMassFile or aminoAcidCompositionFile are not found
 	 */
-	public static final double getMolecularWeight(String sequence, File aminoAcidCompositionFile) throws FileNotFoundException, JAXBException{
+	public static double getMolecularWeight(String sequence, File aminoAcidCompositionFile) throws FileNotFoundException, JAXBException{
 		sequence = Utils.checkSequence(sequence);
 		ProteinSequence pSequence = null;
 		try {
@@ -166,7 +166,7 @@ public static final double getMolecularWeight(String sequence, File aminoAcidCom
 	 * @throws FileNotFoundException
 	 * 	thrown if either elementMassFile or aminoAcidCompositionFile are not found
 	 */
-	public static final AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile)
+	public static AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile)
 	throws JAXBException, FileNotFoundException{
 		IPeptideProperties pp = new PeptidePropertiesImpl();
 		return pp.obtainAminoAcidCompositionTable(aminoAcidCompositionFile);
@@ -186,7 +186,7 @@ public static final AminoAcidCompositionTable obtainAminoAcidCompositionTable(Fi
 	 * @throws FileNotFoundException
 	 * 	thrown if either elementMassFile or aminoAcidCompositionFile are not found
 	 */
-	public static final AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMassFile, File aminoAcidCompositionFile)
+	public static AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMassFile, File aminoAcidCompositionFile)
 	throws JAXBException, FileNotFoundException{
 		IPeptideProperties pp = new PeptidePropertiesImpl();
 		return pp.obtainAminoAcidCompositionTable(elementMassFile, aminoAcidCompositionFile);
@@ -230,7 +230,7 @@ public static double getMolecularWeightBasedOnXML(String sequence, AminoAcidComp
 	 * 	true if Cys are assumed to be reduced and false if Cys are assumed to form cystines
 	 * @return the absorbance (optical density) of sequence
 	 */
-	public static final double getAbsorbance(String sequence, boolean assumeCysReduced){
+	public static double getAbsorbance(String sequence, boolean assumeCysReduced){
 		sequence = Utils.checkSequence(sequence);
 		ProteinSequence pSequence = null;
 		try {
@@ -259,7 +259,7 @@ public static final double getAbsorbance(String sequence, boolean assumeCysReduc
 	 *            assumed to form cystines
 	 * @return the extinction coefficient of sequence
 	 */
-	public static final double getExtinctionCoefficient(String sequence, boolean assumeCysReduced) {
+	public static double getExtinctionCoefficient(String sequence, boolean assumeCysReduced) {
 		sequence = Utils.checkSequence(sequence);
 		ProteinSequence pSequence = null;
 		try {
@@ -283,7 +283,7 @@ public static final double getExtinctionCoefficient(String sequence, boolean ass
 	 * 		a protein sequence consisting of non-ambiguous characters only
 	 * @return the instability index of sequence
 	 */
-	public static final double getInstabilityIndex(String sequence) {
+	public static double getInstabilityIndex(String sequence) {
 		sequence = Utils.checkSequence(sequence);
 		ProteinSequence pSequence = null;
 		try {
@@ -310,7 +310,7 @@ public static final double getInstabilityIndex(String sequence) {
 	 * 		a protein sequence consisting of non-ambiguous characters only
 	 * @return the aliphatic index of sequence
 	 */
-	public static final double getApliphaticIndex(String sequence) {
+	public static double getApliphaticIndex(String sequence) {
 		sequence = Utils.checkSequence(sequence);
 		ProteinSequence pSequence = null;
 		try {
@@ -337,7 +337,7 @@ public static final double getApliphaticIndex(String sequence) {
 	 * 		a protein sequence consisting of non-ambiguous characters only
 	 * @return the average hydropathy value of sequence
 	 */
-	public static final double getAvgHydropathy(String sequence) {
+	public static double getAvgHydropathy(String sequence) {
 		sequence = Utils.checkSequence(sequence);
 		ProteinSequence pSequence = null;
 		try {
@@ -369,7 +369,7 @@ public static final double getAvgHydropathy(String sequence) {
 	 * 		whether to use Expasy values (Default) or Innovagen values
 	 * @return the isoelectric point of sequence
 	 */
-	public static final double getIsoelectricPoint(String sequence, boolean useExpasyValues) {
+	public static double getIsoelectricPoint(String sequence, boolean useExpasyValues) {
 		sequence = Utils.checkSequence(sequence);
 		ProteinSequence pSequence = null;
 		try {
@@ -382,7 +382,7 @@ public static final double getIsoelectricPoint(String sequence, boolean useExpas
 		return pp.getIsoelectricPoint(pSequence, useExpasyValues);
 	}
 
-	public static final double getIsoelectricPoint(String sequence){
+	public static double getIsoelectricPoint(String sequence){
 		return getIsoelectricPoint(sequence, true);
 	}
 
@@ -405,7 +405,7 @@ public static final double getIsoelectricPoint(String sequence){
 	 * 		the pH value to use for computation of the net charge. Default at 7.
 	 * @return the net charge of sequence at given pHPoint
 	 */
-	public static final double getNetCharge(String sequence, boolean useExpasyValues, double pHPoint){
+	public static double getNetCharge(String sequence, boolean useExpasyValues, double pHPoint){
 		sequence = Utils.checkSequence(sequence);
 		ProteinSequence pSequence = null;
 		try {
@@ -418,11 +418,11 @@ public static final double getNetCharge(String sequence, boolean useExpasyValues
 		return pp.getNetCharge(pSequence, useExpasyValues, pHPoint);
 	}
 
-	public static final double getNetCharge(String sequence, boolean useExpasyValues) {
+	public static double getNetCharge(String sequence, boolean useExpasyValues) {
 		return getNetCharge(sequence, useExpasyValues, 7.0);
 	}
 
-	public static final double getNetCharge(String sequence){
+	public static double getNetCharge(String sequence){
 		return getNetCharge(sequence, true);
 	}
 
@@ -441,7 +441,7 @@ public static final double getNetCharge(String sequence){
 	 * @return the composition of specified amino acid in the sequence
 	 * @see SingleLetterAACode
 	 */
-	public static final double getEnrichment(String sequence, SingleLetterAACode aminoAcidCode) {
+	public static double getEnrichment(String sequence, SingleLetterAACode aminoAcidCode) {
 		return getEnrichment(sequence, aminoAcidCode.toString());
 	}
 
@@ -459,7 +459,7 @@ public static final double getEnrichment(String sequence, SingleLetterAACode ami
 	 * 		the code of the amino acid to compute
 	 * @return the composition of specified amino acid in the sequence
 	 */
-	public static final double getEnrichment(String sequence, char aminoAcidCode){
+	public static double getEnrichment(String sequence, char aminoAcidCode){
 		return getEnrichment(sequence, aminoAcidCode);
 	}
 
@@ -477,7 +477,7 @@ public static final double getEnrichment(String sequence, char aminoAcidCode){
 	 *            the code of the amino acid to compute
 	 * @return the composition of specified amino acid in the sequence
 	 */
-	public static final double getEnrichment(String sequence, String aminoAcidCode){
+	public static double getEnrichment(String sequence, String aminoAcidCode){
 		sequence = Utils.checkSequence(sequence);
 		ProteinSequence pSequence = null;
 		try {
@@ -503,7 +503,7 @@ public static final double getEnrichment(String sequence, String aminoAcidCode){
 	 * @return the composition of the 20 standard amino acid in the sequence
 	 * @see AminoAcidCompound
 	 */
-	public static final Map<AminoAcidCompound, Double> getAAComposition(String sequence) {
+	public static Map<AminoAcidCompound, Double> getAAComposition(String sequence) {
 		sequence = Utils.checkSequence(sequence);
 		ProteinSequence pSequence = null;
 		try {
@@ -527,7 +527,7 @@ public static final Map<AminoAcidCompound, Double> getAAComposition(String seque
 	 * 		a protein sequence consisting of non-ambiguous characters only
 	 * @return the composition of the 20 standard amino acid in the sequence
 	 */
-	public static final Map<String, Double> getAACompositionString(String sequence){
+	public static Map<String, Double> getAACompositionString(String sequence){
 		Map<AminoAcidCompound, Double> aa2Composition = getAAComposition(sequence);
 		Map<String, Double> aaString2Composition = new HashMap<>();
 		for(Map.Entry<AminoAcidCompound, Double> entry : aa2Composition.entrySet()){
@@ -547,7 +547,7 @@ public static final Map<String, Double> getAACompositionString(String sequence){
 	 * 		a protein sequence consisting of non-ambiguous characters only
 	 * @return the composition of the 20 standard amino acid in the sequence
 	 */
-	public static final Map<Character, Double> getAACompositionChar(String sequence){
+	public static Map<Character, Double> getAACompositionChar(String sequence){
 		Map<AminoAcidCompound, Double> aa2Composition = getAAComposition(sequence);
 		Map<Character, Double> aaChar2Composition = new HashMap<>();
 		for(Map.Entry<AminoAcidCompound, Double> entry : aa2Composition.entrySet()){
@@ -564,7 +564,7 @@ public static final Map<Character, Double> getAACompositionChar(String sequence)
 	 * 		a protein sequence consisting of non-ambiguous characters only
 	 * @return the array of charges of amino acids in the protein (1 if amino acid is positively charged, -1 if negatively charged, 0 if not charged)
 	 */
-	public static final int[] getChargesOfAminoAcids(String sequence) {
+	public static int[] getChargesOfAminoAcids(String sequence) {
 		int[] charges = new int[sequence.length()];
 		for ( int i=0; i < sequence.length(); i++ ) {
 			char aa = sequence.toCharArray()[i];
@@ -580,7 +580,7 @@ public static final int[] getChargesOfAminoAcids(String sequence) {
 	 * 		a protein sequence consisting of non-ambiguous characters only
 	 * @return the array of polarity of amino acids in the protein (1 if amino acid is polar, 0 if not)
 	 */
-	public static final int[] getPolarityOfAminoAcids(String sequence) {
+	public static int[] getPolarityOfAminoAcids(String sequence) {
 		int[] polarity = new int[sequence.length()];
 		for ( int i=0; i < sequence.length(); i++ ) {
 			char aa = sequence.toCharArray()[i];
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java
index 381158d730..bea1ab69db 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java
@@ -48,7 +48,7 @@ public class Utils {
 	 * @return
 	 * 		a value with the given number of decimal places.
 	 */
-	public final static double roundToDecimals(double d, int c) {
+	public static double roundToDecimals(double d, int c) {
 		if(c < 0) return d;
 		double p = Math.pow(10,c);
 		d = d * p;
@@ -67,7 +67,7 @@ public final static double roundToDecimals(double d, int c) {
 	 * @return
 	 * 		true if invalid characters are found, else return false.
 	 */
-	public final static boolean doesSequenceContainInvalidChar(String sequence, Set<Character> cSet){
+	public static boolean doesSequenceContainInvalidChar(String sequence, Set<Character> cSet){
 		for(char c:sequence.toCharArray()){
 			if(!cSet.contains(c)) return true;
 		}
@@ -86,7 +86,7 @@ public final static boolean doesSequenceContainInvalidChar(String sequence, Set<
 	 * @return
 	 * 		the number of invalid characters in sequence.
 	 */
-	public final static int getNumberOfInvalidChar(String sequence, Set<Character> cSet, boolean ignoreCase){
+	public static int getNumberOfInvalidChar(String sequence, Set<Character> cSet, boolean ignoreCase){
 		int total = 0;
 		char[] cArray;
 		if(ignoreCase) cArray = sequence.toUpperCase().toCharArray();
@@ -109,7 +109,7 @@ public final static int getNumberOfInvalidChar(String sequence, Set<Character> c
 	 * @return
 	 * 		a new sequence with all invalid characters being replaced by '-'.
 	 */
-	public final static String cleanSequence(String sequence, Set<Character> cSet){
+	public static String cleanSequence(String sequence, Set<Character> cSet){
 		Set<Character> invalidCharSet = new HashSet<>();
 		StringBuilder cleanSeq = new StringBuilder();
 		if(cSet == null) cSet = PeptideProperties.standardAASet;
@@ -125,7 +125,7 @@ public final static String cleanSequence(String sequence, Set<Character> cSet){
 		// TODO: Should be StringJoiner once JDK8 used
 		StringBuilder stringBuilder = new StringBuilder();
 		for(char c: invalidCharSet){
-			stringBuilder.append("\'" + c + "\'");
+			stringBuilder.append("\'").append(c).append("\'");
 		}
 		stringBuilder.deleteCharAt(stringBuilder.length()-1);
 		stringBuilder.append(" are being replaced with '-'");
@@ -145,7 +145,7 @@ public final static String cleanSequence(String sequence, Set<Character> cSet){
 	 * @return
 	 * 		a sequence with no invalid characters.
 	 */
-	public static final String checkSequence(String sequence){
+	public static String checkSequence(String sequence){
 		return checkSequence(sequence, null);
 	}
 
@@ -162,7 +162,7 @@ public static final String checkSequence(String sequence){
 	 * @return
 	 * 		a sequence with no invalid characters.
 	 */
-	public static final String checkSequence(String sequence, Set<Character> cSet){
+	public static String checkSequence(String sequence, Set<Character> cSet){
 		boolean containInvalid;
 		if(cSet != null){
 			containInvalid = sequence != null && doesSequenceContainInvalidChar(sequence, cSet);
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java
index 1d663923d7..cad2700a22 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java
@@ -24,7 +24,6 @@
 import org.biojava.nbio.core.sequence.ProteinSequence;
 
 import java.util.EnumMap;
-import java.util.HashMap;
 import java.util.Map;
 
 public class ProfeatPropertiesImpl implements IProfeatProperties{
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
index 3b5079bcc7..d9082a1ca4 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
@@ -64,14 +64,14 @@ public CaseFreeAminoAcidCompoundSet() {
 		aminoAcidCompoundCache.put("W", new AminoAcidCompound(null, "W", "Trp", "Tryptophan", 186.2132f));
 		aminoAcidCompoundCache.put("Y", new AminoAcidCompound(null, "Y", "Tyr", "Tyrosine", 163.1760f));
 		aminoAcidCompoundCache.put("V", new AminoAcidCompound(null, "V", "Val", "Valine", 99.1326f));
-		aminoAcidCompoundCache.put("B", new AminoAcidCompound(null, "B", "Asx", "Asparagine or Aspartic acid", null));
-		aminoAcidCompoundCache.put("Z", new AminoAcidCompound(null, "Z", "Glx", "Glutamine or Glutamic acid", null));
-		aminoAcidCompoundCache.put("J", new AminoAcidCompound(null, "J", "Xle", "Leucine or Isoleucine", null));
-		aminoAcidCompoundCache.put("X", new AminoAcidCompound(null, "X", "Xaa", "Unspecified", null));
-		aminoAcidCompoundCache.put("-", new AminoAcidCompound(null, "-", "---", "Unspecified", null));
-		aminoAcidCompoundCache.put(".", new AminoAcidCompound(null, ".", "...", "Unspecified", null));
-		aminoAcidCompoundCache.put("_", new AminoAcidCompound(null, "_", "___", "Unspecified", null));
-		aminoAcidCompoundCache.put("*", new AminoAcidCompound(null, "*", "***", "Stop", null));
+		aminoAcidCompoundCache.put("B", new AminoAcidCompound(null, "B", "Asx", "Asparagine or Aspartic acid", Float.NaN));
+		aminoAcidCompoundCache.put("Z", new AminoAcidCompound(null, "Z", "Glx", "Glutamine or Glutamic acid", Float.NaN));
+		aminoAcidCompoundCache.put("J", new AminoAcidCompound(null, "J", "Xle", "Leucine or Isoleucine", Float.NaN));
+		aminoAcidCompoundCache.put("X", new AminoAcidCompound(null, "X", "Xaa", "Unspecified", Float.NaN));
+		aminoAcidCompoundCache.put("-", new AminoAcidCompound(null, "-", "---", "Unspecified", Float.NaN));
+		aminoAcidCompoundCache.put(".", new AminoAcidCompound(null, ".", "...", "Unspecified", Float.NaN));
+		aminoAcidCompoundCache.put("_", new AminoAcidCompound(null, "_", "___", "Unspecified", Float.NaN));
+		aminoAcidCompoundCache.put("*", new AminoAcidCompound(null, "*", "***", "Stop", Float.NaN));
 
 		//Selenocysteine - this is encoded by UGA with the presence
 		//of a SECIS element (SElenoCysteine Insertion Sequence) in the mRNA
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java
index 915bc06b5c..a23d6adc3c 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java
@@ -345,7 +345,7 @@ public void testNetCharge(){
 			logger.debug(p);
 			logger.debug("pH\tInnovagen\tExpasy\tdiff");
 			for ( int i = 1; i < 15; i++) {
-				double phPoint = new Double(i);
+				double phPoint = (double) i;
 				double chrgInnovagen = PeptideProperties.getNetCharge(p,false,phPoint);
 				double chrgExpasy = PeptideProperties.getNetCharge(p,true,phPoint);
 				logger.debug(String.format("%2.1f\t%2.2f\t%2.2f\t%2.2f", phPoint, chrgInnovagen,
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/GenerateJavaCodesFromTextTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/GenerateJavaCodesFromTextTest.java
index a23c24f5e2..ab2df5fec7 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/GenerateJavaCodesFromTextTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/GenerateJavaCodesFromTextTest.java
@@ -55,7 +55,7 @@ public void generateCodes() throws IOException{
 		List<String> elementNameList = new ArrayList<>();
 		String elementName = null;
 		String elementNameLower = null;
-		Double elementMass;
+		double elementMass;
 		while((line = input.readLine()) != null){
 			String[] sA = line.split("\t");
 			if(sA[0].length() > 0){
@@ -90,7 +90,7 @@ public void generateCodes() throws IOException{
 	}
 
 	private double cleanNumber(String s){
-		int index = s.indexOf("(");
+		int index = s.indexOf('(');
 		if(index != -1) s = s.substring(0, index);
 		return Double.parseDouble(s.replace(" ", "").replace("[", "").replace("]", ""));
 	}
diff --git a/biojava-alignment/src/main/java/demo/DemoDistanceTree.java b/biojava-alignment/src/main/java/demo/DemoDistanceTree.java
index 4cf86d7cc3..ae0fe1661e 100644
--- a/biojava-alignment/src/main/java/demo/DemoDistanceTree.java
+++ b/biojava-alignment/src/main/java/demo/DemoDistanceTree.java
@@ -57,12 +57,11 @@ public static void main(String[] args) throws Exception {
 		InputStream inStream = TreeConstructor.class
 				.getResourceAsStream("/PF00104_small.fasta");
 
-		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader =
+        FastaReader<ProteinSequence, AminoAcidCompound> fastaReader =
 				new FastaReader<>(
 						inStream,
 						new GenericFastaHeaderParser<>(),
-						new ProteinSequenceCreator(AminoAcidCompoundSet
-								.getAminoAcidCompoundSet()));
+						new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet));
 
 		LinkedHashMap<String, ProteinSequence> proteinSequences =
 				fastaReader.process();
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
index 6584a22c0a..9193b4299b 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
@@ -150,7 +150,7 @@ public static <S extends Sequence<C>, C extends Compound> Profile<S, C> getMulti
 		PairwiseSequenceScorerType ps = PairwiseSequenceScorerType.GLOBAL_IDENTITIES;
 		GapPenalty gapPenalty = new SimpleGapPenalty();
 		SubstitutionMatrix<C> subMatrix = null;
-		if (cs == AminoAcidCompoundSet.getAminoAcidCompoundSet()) {
+        if (cs == AminoAcidCompoundSet.aminoAcidCompoundSet) {
 			@SuppressWarnings("unchecked") // compound types must be equal since compound sets are equal
 			SubstitutionMatrix<C> temp = (SubstitutionMatrix<C>) SubstitutionMatrixHelper.getBlosum62();
 			subMatrix = temp;
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
index ce403bf4aa..692f26d8bc 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
@@ -257,9 +257,8 @@ else if (forcedSequenceType.equals(PFAM))
 			}
 			String[] seqDetails = splitSeqName(sequencename);
 			seq.setDescription(seqDetails[0]);
-			seq.setBioBegin((seqDetails[1] == null || seqDetails[1].trim().equals("") ? null : new Integer(
-					seqDetails[1])));
-			seq.setBioEnd((seqDetails[2] == null || seqDetails[2].trim().equals("") ? null : new Integer(seqDetails[2])));
+			seq.setBioBegin((seqDetails[1] == null || seqDetails[1].trim().isEmpty() ? null : Integer.valueOf(seqDetails[1])));
+			seq.setBioEnd((seqDetails[2] == null || seqDetails[2].trim().isEmpty() ? null : Integer.valueOf(seqDetails[2])));
 
 			seqs.add(seq);
 		}
@@ -322,9 +321,9 @@ public String toString() {
 			} else {
 				result.append(sequenceAsString);
 			}
-			result.append(" " + sequence.getDescription() + "\n");
+			result.append(" ").append(sequence.getDescription()).append("\n");
 		}
-		result.append("Alignment with " + bioSeqs.size() + " rows and " + sequenceLength + " columns");
+		result.append("Alignment with ").append(bioSeqs.size()).append(" rows and ").append(sequenceLength).append(" columns");
 
 		return result.toString();
 	}
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java
index 9071b4e857..f5081a04f6 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java
@@ -44,12 +44,12 @@ public class Comparison {
 	 *            SequenceI
 	 * @return float
 	 */
-	public final static float PID(String seq1, String seq2) {
+	public static float PID(String seq1, String seq2) {
 		return PID(seq1, seq2, 0, seq1.length());
 	}
 
 	// Another pid with region specification
-	public final static float PID(String seq1, String seq2, int start, int end) {
+	public static float PID(String seq1, String seq2, int start, int end) {
 
 		int s1len = seq1.length();
 		int s2len = seq2.length();
@@ -100,7 +100,7 @@ public final static float PID(String seq1, String seq2, int start, int end) {
 	 *
 	 * @return true if it is a gap, false otherwise
 	 */
-	public static final boolean isGap(char c) {
+	public static boolean isGap(char c) {
 		return c == '-' || c == '.' || c == ' ';
 	}
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java
index 047f8efbdb..7df77176c1 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java
@@ -25,7 +25,6 @@
 import java.io.OutputStream;
 import org.biojava.nbio.core.sequence.MultipleSequenceAlignment;
 import org.biojava.nbio.core.sequence.io.FastaWriter;
-import org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSAProfiler.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSAProfiler.java
index 46964a2b67..00e42e7e03 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSAProfiler.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSAProfiler.java
@@ -81,8 +81,7 @@ public static void main(String[] args) throws Exception {
 		Profiler profiler = new Profiler();
 
 		System.out.printf("Loading sequences from %s... ", args[0]);
-		List<ProteinSequence> list = new ArrayList<>();
-		list.addAll(FastaReaderHelper.readFastaProteinSequence(new File(args[0])).values());
+        List<ProteinSequence> list = new ArrayList<>(FastaReaderHelper.readFastaProteinSequence(new File(args[0])).values());
 		if (args.length > 1 && Integer.parseInt(args[1]) < list.size()) {
 			System.out.printf("%s/%d", args[1], list.size());
 			list = list.subList(0, Integer.parseInt(args[1]));
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleSubstitutionMatrixTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleSubstitutionMatrixTest.java
index 702bc4960f..30150e5483 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleSubstitutionMatrixTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleSubstitutionMatrixTest.java
@@ -42,7 +42,7 @@ public class SimpleSubstitutionMatrixTest {
 
 	@Test(expected=FileNotFoundException.class)
 	public void testSimpleSubstitutionMatrixNotFound() throws FileNotFoundException {
-		new SimpleSubstitutionMatrix<>(AminoAcidCompoundSet.getAminoAcidCompoundSet(),
+        new SimpleSubstitutionMatrix<>(AminoAcidCompoundSet.aminoAcidCompoundSet,
 				new File("blosum63.txt"));
 	}
 
@@ -61,7 +61,7 @@ public void test() throws CompoundNotFoundException {
 	@Test()
 	public void testSimpleSubstitutionMatrix() {
 		SubstitutionMatrix<AminoAcidCompound> matrix = SimpleSubstitutionMatrix.getBlosum62();
-		assertEquals(matrix.getCompoundSet(), AminoAcidCompoundSet.getAminoAcidCompoundSet());
+        assertEquals(matrix.getCompoundSet(), AminoAcidCompoundSet.aminoAcidCompoundSet);
 		assertEquals(matrix.getName(), "blosum62");
 		assertEquals(matrix.getMaxValue(), 11);
 		assertEquals(matrix.getMinValue(), -4);
@@ -83,8 +83,8 @@ public void testSimpleSubstitutionMatrixCompoundSetOfCStringString() {
 
 	@Test
 	public void testSimpleSubstitutionMatrixCompoundSetOfCShortShort() {
-		SubstitutionMatrix<AminoAcidCompound> matrix = new SimpleSubstitutionMatrix<>(
-				AminoAcidCompoundSet.getAminoAcidCompoundSet(), (short) 5, (short) 1);
+        SubstitutionMatrix<AminoAcidCompound> matrix = new SimpleSubstitutionMatrix<>(
+                AminoAcidCompoundSet.aminoAcidCompoundSet, (short) 5, (short) 1);
 		assertEquals(matrix.getName(), "IDENTITY_5_1");
 	}
 
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java
index cb21de52b4..df6cbf9cf2 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java
@@ -74,14 +74,12 @@ public void testDNAAlignment() {
 
 	private static List<DNASequence> getDNAFASTAFile() throws Exception {
 
-		InputStream inStream = TestDNAAlignment.class.getResourceAsStream(String.format("/dna-fasta.txt"));
+		InputStream inStream = TestDNAAlignment.class.getResourceAsStream("/dna-fasta.txt");
 		LinkedHashMap<String, DNASequence> fastas = FastaReaderHelper.readFastaDNASequence(inStream);
 
 		List<DNASequence> sequences = new ArrayList<>();
 
-		for (DNASequence seq : fastas.values()) {
-            sequences.add(seq);
-		}
+        sequences.addAll(fastas.values());
 
 		return sequences;
 	}
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/aaindex/TestAAINDEXLoading.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/aaindex/TestAAINDEXLoading.java
index ba380cce44..91c16b1aa3 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/aaindex/TestAAINDEXLoading.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/aaindex/TestAAINDEXLoading.java
@@ -71,7 +71,7 @@ public void testSDMmatrix(){
 		}
 
 
-		AminoAcidCompoundSet aas = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet aas = AminoAcidCompoundSet.aminoAcidCompoundSet;
 
 		AminoAcidCompound v = aas.getCompoundForString("V");
 		AminoAcidCompound w = aas.getCompoundForString("W");
@@ -149,7 +149,7 @@ public void testOVEJ920104(){
 			Assert.assertEquals(1000, scale);
 		}
 
-		AminoAcidCompoundSet aas = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet aas = AminoAcidCompoundSet.aminoAcidCompoundSet;
 
 		AminoAcidCompound minus = aas.getCompoundForString("-");
 
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestForesterWrapper.java b/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestForesterWrapper.java
index 8d4e2c563f..adf224c213 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestForesterWrapper.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestForesterWrapper.java
@@ -33,7 +33,6 @@
 import org.biojava.nbio.core.sequence.io.FastaWriter;
 import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
 import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
-import org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface;
 import org.forester.msa.Msa;
 import org.junit.Test;
 
@@ -54,12 +53,11 @@ public void testMSAconversion() throws Exception {
 		InputStream inStream = TestForesterWrapper.class
 				.getResourceAsStream("/1u6d_symm.fasta");
 
-		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader =
+        FastaReader<ProteinSequence, AminoAcidCompound> fastaReader =
 				new FastaReader<>(
 						inStream,
 						new GenericFastaHeaderParser<>(),
-						new ProteinSequenceCreator(AminoAcidCompoundSet
-								.getAminoAcidCompoundSet()));
+						new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet));
 
 		LinkedHashMap<String, ProteinSequence> proteinSequences = fastaReader
 				.process();
@@ -90,8 +88,8 @@ public void testMSAconversion() throws Exception {
 
 		StringBuilder sb = new StringBuilder();
 		for (int i = 0; i < fMsa.getNumberOfSequences(); i++) {
-			sb.append(">" + fMsa.getIdentifier(i) + System.lineSeparator());
-			sb.append(fMsa.getSequenceAsString(i) + System.lineSeparator());
+			sb.append(">").append(fMsa.getIdentifier(i)).append(System.lineSeparator());
+			sb.append(fMsa.getSequenceAsString(i)).append(System.lineSeparator());
 		}
 		String forester = sb.toString();
 
diff --git a/biojava-core/src/main/java/demo/ParseFastaFileDemo.java b/biojava-core/src/main/java/demo/ParseFastaFileDemo.java
index f201adc24f..a2e734cf9a 100644
--- a/biojava-core/src/main/java/demo/ParseFastaFileDemo.java
+++ b/biojava-core/src/main/java/demo/ParseFastaFileDemo.java
@@ -96,10 +96,10 @@ public static void main(String[] args) throws Exception {
 		InputStream inStream = isp.getInputStream(f);
 
 
-		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
+        FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
 				inStream,
 				new GenericFastaHeaderParser<>(),
-				new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+				new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet));
 
 		LinkedHashMap<String, ProteinSequence> b;
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
index 81f1c09ac1..3614777b36 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
@@ -566,7 +566,7 @@ private void printConservation(StringBuilder s, String idFormat, int seqIndexPad
 	protected static final SubstitutionMatrix<AminoAcidCompound> matrix = SubstitutionMatrixHelper.getBlosum65();
 
 	private boolean isSimilar(char c1, char c2) {
-		AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet set = AminoAcidCompoundSet.aminoAcidCompoundSet;
 
 		AminoAcidCompound aa1 = set.getCompoundForString(String.valueOf(c1));
 		AminoAcidCompound aa2 = set.getCompoundForString(String.valueOf(c2));
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java
index a9f400f054..55441e5b7c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java
@@ -182,7 +182,7 @@ private void initMatrix(String line) {
 
 
 		//System.out.println(">" + currentRows+"<");
-		AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.aminoAcidCompoundSet;
 		for ( int i = 0 ; i < currentRows.length() ; i ++){
 			char c = currentRows.charAt(i);
 			AminoAcidCompound aa = compoundSet.getCompoundForString(String.valueOf(c));
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.java
index d9119ed7e8..2bd95ea29d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.java
@@ -65,7 +65,7 @@ public SubstitutionMatrix<AminoAcidCompound> getMatrix(String matrixName) {
 	}
 
 	public InputStream getInputStreamToAAindexFile(){
-		 return SubstitutionMatrixHelper.class.getResourceAsStream(String.format("/matrices/AAINDEX.txt"));
+		 return SubstitutionMatrixHelper.class.getResourceAsStream("/matrices/AAINDEX.txt");
 	}
 
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java
index 86042a9d38..c1cf9e51f8 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java
@@ -59,7 +59,7 @@ public class ScaledSubstitutionMatrix implements
 	private int scale;
 
 	public ScaledSubstitutionMatrix(){
-		compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        compoundSet = AminoAcidCompoundSet.aminoAcidCompoundSet;
 	}
 
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java
index 8f9e8dbf52..99d9fd33ab 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java
@@ -58,7 +58,7 @@ public class SimpleSubstitutionMatrix<C extends Compound> implements Substitutio
 	private final List<C> cols;
 
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum62() {
-		return new SimpleSubstitutionMatrix<>(AminoAcidCompoundSet.getAminoAcidCompoundSet(), new InputStreamReader(
+        return new SimpleSubstitutionMatrix<>(AminoAcidCompoundSet.aminoAcidCompoundSet, new InputStreamReader(
 				SimpleSubstitutionMatrix.class.getResourceAsStream("/matrices/blosum62.txt")), "blosum62");
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java
index 067ecee1b1..ad37e92e37 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java
@@ -251,8 +251,8 @@ public static SubstitutionMatrix<AminoAcidCompound> getAminoAcidSubstitutionMatr
 	// reads in an amino acid substitution matrix, if necessary
 	private static SubstitutionMatrix<AminoAcidCompound> getAminoAcidMatrix(String file) {
 		if (!aminoAcidMatrices.containsKey(file)) {
-			aminoAcidMatrices.put(file, new SimpleSubstitutionMatrix<>(
-					AminoAcidCompoundSet.getAminoAcidCompoundSet(), getReader(file), file));
+            aminoAcidMatrices.put(file, new SimpleSubstitutionMatrix<>(
+                    AminoAcidCompoundSet.aminoAcidCompoundSet, getReader(file), file));
 		}
 		return aminoAcidMatrices.get(file);
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
index 1a648eebbd..892f09c5e3 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
@@ -70,8 +70,8 @@ public abstract class Hsp <S extends Sequence<C>, C extends Compound> {
 	private final String hspQseq;
 	private final String hspHseq;
 	private final String hspIdentityString;
-	private Double percentageIdentity;
-	private Integer mismatchCount;
+	private final Double percentageIdentity;
+	private final Integer mismatchCount;
 	private SimpleSequencePair<S, C> returnAln;
 
 	@Override
@@ -137,7 +137,7 @@ private static Sequence getSequence(String gappedSequenceString){
 			else if (sequenceString.matches("^[ACUG]+$"))
 				returnSeq = new RNASequence(sequenceString, DNACompoundSet.getDNACompoundSet());
 			else
-				returnSeq = new ProteinSequence(sequenceString, AminoAcidCompoundSet.getAminoAcidCompoundSet());
+                returnSeq = new ProteinSequence(sequenceString, AminoAcidCompoundSet.aminoAcidCompoundSet);
 		} catch (CompoundNotFoundException ex) {
 			logger.error("Unexpected error, could not find compound when creating Sequence object from Hsp", ex);
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
index 9e34739361..0ef0b92bf5 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
@@ -149,7 +149,7 @@ private ResultFactory guessFactory(File f){
 		}
 
 		String filename = f.getAbsolutePath();
-		int extensionPos = filename.lastIndexOf(".");
+		int extensionPos = filename.lastIndexOf('.');
 		String extension = filename.substring(extensionPos + 1);
 		if (extensionFactoryAssociation.get(extension) == null)
 			throw new UnsupportedOperationException(NOT_SUPPORTED_FILE_EXCEPTION
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java
index cd32503354..bba300d344 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java
@@ -26,10 +26,8 @@
 import java.io.IOException;
 import java.io.LineNumberReader;
 import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Scanner;
+import java.util.*;
+
 import org.biojava.nbio.core.search.io.Hit;
 import org.biojava.nbio.core.search.io.Hsp;
 import org.biojava.nbio.core.search.io.Result;
@@ -71,7 +69,7 @@ private enum PARSING_CONSISTENCY {
 
 	// data imported private:
 	int queryIdNumber = 0;
-	HashMap<String,String> queryIdMapping = new HashMap<>();
+	Map<String,String> queryIdMapping = new HashMap<>();
 	String programName=null, queryName = null, databaseFile = null;
 	private String queryId      ;
 	private String subjectId    ;
@@ -136,23 +134,23 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
 
 					String currentSubjectId=subjectId;
 					while (currentSubjectId.equals(subjectId) && lineNumber < fileLinesCount){
-						if (new Double(evalue) > maxEScore) {
+						if (Double.parseDouble(evalue) > maxEScore) {
 							line = fetchData(scanner);
 							lineNumber++;
 							continue;
 						}
 						BlastHspBuilder hspBuilder = new BlastHspBuilder();
 						hspBuilder
-							.setHspAlignLen(new Integer(alnLength))
-							.setHspGaps(new Integer(gapOpenCount))
-							.setHspQueryFrom(new Integer(queryStart))
-							.setHspQueryTo(new Integer(queryEnd))
-							.setHspHitFrom(new Integer(subjectStart))
-							.setHspHitTo(new Integer(subjectEnd))
-							.setHspEvalue(new Double(evalue))
-							.setHspBitScore(new Double(bitScore))
-							.setPercentageIdentity(new Double(percIdentity)/100)
-							.setMismatchCount(new Integer(mismatchCount));
+							.setHspAlignLen(Integer.parseInt(alnLength))
+							.setHspGaps(Integer.parseInt(gapOpenCount))
+							.setHspQueryFrom(Integer.parseInt(queryStart))
+							.setHspQueryTo(Integer.parseInt(queryEnd))
+							.setHspHitFrom(Integer.parseInt(subjectStart))
+							.setHspHitTo(Integer.parseInt(subjectEnd))
+							.setHspEvalue(Double.parseDouble(evalue))
+							.setHspBitScore(Double.parseDouble(bitScore))
+							.setPercentageIdentity(Double.parseDouble(percIdentity)/100)
+							.setMismatchCount(Integer.parseInt(mismatchCount));
 						hsps.add(hspBuilder.createBlastHsp());
 						if (scanner.hasNext()) line = fetchData(scanner);
 						lineNumber++;
@@ -172,7 +170,7 @@ private String fetchData(Scanner scanner){
 		String[] split;
 
 		line = scanner.nextLine();
-		while (line.startsWith("#")){
+		while (line.charAt(0) == '#'){
 			// blast tabular with header options contains some more informations
 			if (line.matches("#\\s.?BLAST.+")) programName = line.replace("#\\s","");
 			if (line.startsWith("# Query:")) queryName = line.replace("# Query: ","");
@@ -203,13 +201,10 @@ private String fetchData(Scanner scanner){
 		// blast tabular reports only the first word of the query name.
 		// If it was specified in the header it is better to use that definition
 		if (parsingConsistency == PARSING_CONSISTENCY.IMPROVED && headerFound) {
-			if (queryIdMapping.get(queryId)==null) {
-				queryIdNumber ++;
-				queryIdMapping.put(queryId,"Query_" + queryIdNumber);
-			}
+
 			// If a complete definition of the query name was readed, than we can use
 			// a queryID schema that is consistent with blast xml report
-			queryId = queryIdMapping.get(queryId);
+			queryId = queryIdMapping.computeIfAbsent(queryId, x-> "Query_" + (++queryIdNumber));
 		}
 		if (!headerFound) queryName = queryId;
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
index bdb2396fe1..e8b354a7d4 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
@@ -117,10 +117,10 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
 
 				// Iteration* section keys:
 				resultBuilder
-					.setIterationNumber(new Integer(XMLHelper.selectSingleElement(element,"Iteration_iter-num").getTextContent()))
+					.setIterationNumber(Integer.valueOf(XMLHelper.selectSingleElement(element, "Iteration_iter-num").getTextContent()))
 					.setQueryID(XMLHelper.selectSingleElement(element,"Iteration_query-ID").getTextContent())
 					.setQueryDef(XMLHelper.selectSingleElement(element, "Iteration_query-def").getTextContent())
-					.setQueryLength(new Integer(XMLHelper.selectSingleElement(element,"Iteration_query-len").getTextContent()));
+					.setQueryLength(Integer.valueOf(XMLHelper.selectSingleElement(element, "Iteration_query-len").getTextContent()));
 
 				if (queryReferences != null) resultBuilder.setQuerySequence(queryReferencesMap.get(
 						XMLHelper.selectSingleElement(element,"Iteration_query-ID").getTextContent()
@@ -135,11 +135,11 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
 				for (Element hitElement : hitList) {
 					BlastHitBuilder blastHitBuilder = new BlastHitBuilder();
 					blastHitBuilder
-						.setHitNum(new Integer(XMLHelper.selectSingleElement(hitElement, "Hit_num").getTextContent()))
+						.setHitNum(Integer.valueOf(XMLHelper.selectSingleElement(hitElement, "Hit_num").getTextContent()))
 						.setHitId(XMLHelper.selectSingleElement(hitElement, "Hit_id").getTextContent())
 						.setHitDef(XMLHelper.selectSingleElement(hitElement, "Hit_def").getTextContent())
 						.setHitAccession(XMLHelper.selectSingleElement(hitElement, "Hit_accession").getTextContent())
-						.setHitLen(new Integer(XMLHelper.selectSingleElement(hitElement, "Hit_len").getTextContent()));
+						.setHitLen(Integer.valueOf(XMLHelper.selectSingleElement(hitElement, "Hit_len").getTextContent()));
 
 					if (databaseReferences != null) blastHitBuilder.setHitSequence(databaseReferencesMap.get(
 						XMLHelper.selectSingleElement(hitElement, "Hit_id").getTextContent()
@@ -156,20 +156,20 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
 						if (evalue <= maxEScore) {
 							BlastHspBuilder blastHspBuilder = new BlastHspBuilder();
 							blastHspBuilder
-								.setHspNum(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_num").getTextContent()))
+								.setHspNum(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_num").getTextContent()))
 								.setHspBitScore(new Double(XMLHelper.selectSingleElement(hspElement, "Hsp_bit-score").getTextContent()))
-								.setHspScore(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_score").getTextContent()))
+								.setHspScore(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_score").getTextContent()))
 								.setHspEvalue(evalue)
-								.setHspQueryFrom(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_query-from").getTextContent()))
-								.setHspQueryTo(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_query-to").getTextContent()))
-								.setHspHitFrom(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-from").getTextContent()))
-								.setHspHitTo(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-to").getTextContent()))
-								.setHspQueryFrame(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_query-frame").getTextContent()))
-								.setHspHitFrame(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-frame").getTextContent()))
-								.setHspIdentity(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_identity").getTextContent()))
-								.setHspPositive(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_positive").getTextContent()))
-								.setHspGaps(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_gaps").getTextContent()))
-								.setHspAlignLen(new Integer(XMLHelper.selectSingleElement(hspElement, "Hsp_align-len").getTextContent()))
+								.setHspQueryFrom(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_query-from").getTextContent()))
+								.setHspQueryTo(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_query-to").getTextContent()))
+								.setHspHitFrom(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-from").getTextContent()))
+								.setHspHitTo(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-to").getTextContent()))
+								.setHspQueryFrame(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_query-frame").getTextContent()))
+								.setHspHitFrame(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-frame").getTextContent()))
+								.setHspIdentity(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_identity").getTextContent()))
+								.setHspPositive(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_positive").getTextContent()))
+								.setHspGaps(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_gaps").getTextContent()))
+								.setHspAlignLen(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_align-len").getTextContent()))
 								.setHspQseq(XMLHelper.selectSingleElement(hspElement, "Hsp_qseq").getTextContent())
 								.setHspHseq(XMLHelper.selectSingleElement(hspElement, "Hsp_hseq").getTextContent())
 								.setHspIdentityString(XMLHelper.selectSingleElement(hspElement, "Hsp_midline").getTextContent());
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java
index 397f1f1d5a..ebbca86a2a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java
@@ -36,7 +36,7 @@
  */
 public class AccessionID {
 
-	private String id;
+	private final String id;
 	private DataSource source = DataSource.LOCAL;
 	private Integer version;
 	private String identifier = null;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java
index 04511fe7f1..05a040344a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java
@@ -30,7 +30,6 @@
 import org.slf4j.LoggerFactory;
 
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.LinkedHashMap;
 
 /**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
index acdbfa9396..eb50b453b7 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
@@ -67,7 +67,7 @@ public class ProteinSequence extends AbstractSequence<AminoAcidCompound> {
 	 * @throws CompoundNotFoundException
 	 */
 	public ProteinSequence(String seqString) throws CompoundNotFoundException {
-		this(seqString, AminoAcidCompoundSet.getAminoAcidCompoundSet());
+        this(seqString, AminoAcidCompoundSet.aminoAcidCompoundSet);
 	}
 
 	/**
@@ -89,7 +89,7 @@ public ProteinSequence(String seqString, CompoundSet<AminoAcidCompound> compound
 	 * @param proxyLoader
 	 */
 	public ProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader) {
-		this(proxyLoader, AminoAcidCompoundSet.getAminoAcidCompoundSet());
+        this(proxyLoader, AminoAcidCompoundSet.aminoAcidCompoundSet);
 	}
 
 	/**
@@ -203,7 +203,7 @@ public static void main(String[] args) throws Exception {
 		ProteinSequence proteinSequence = new ProteinSequence("ARNDCEQGHILKMFPSTWYVBZJX");
 		logger.info("Protein Sequence: {}", proteinSequence.toString());
 
-		StringProxySequenceReader<AminoAcidCompound> sequenceStringProxyLoader = new StringProxySequenceReader<>("XRNDCEQGHILKMFPSTWYVBZJA", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+        StringProxySequenceReader<AminoAcidCompound> sequenceStringProxyLoader = new StringProxySequenceReader<>("XRNDCEQGHILKMFPSTWYVBZJA", AminoAcidCompoundSet.aminoAcidCompoundSet);
 		ProteinSequence proteinSequenceFromProxy = new ProteinSequence(sequenceStringProxyLoader);
 		logger.info("Protein Sequence from Proxy: {}", proteinSequenceFromProxy.toString());
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TaxonomyID.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TaxonomyID.java
index 402df2ca0a..cc53c46cd0 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TaxonomyID.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TaxonomyID.java
@@ -30,7 +30,7 @@
 public class TaxonomyID {
 
 
-	private String id;
+	private final String id;
 	DataSource dataSource;
 
 	public TaxonomyID(String id, DataSource dataSource) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java
index f7aeb796cf..cf26496582 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java
@@ -29,7 +29,6 @@
 import org.slf4j.LoggerFactory;
 
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.LinkedHashMap;
 
 /**
@@ -45,7 +44,7 @@ public class TranscriptSequence extends DNASequence {
 	private final LinkedHashMap<String, CDSSequence> cdsSequenceHashMap = new LinkedHashMap<>();
 	private StartCodonSequence startCodonSequence = null;
 	private StopCodonSequence stopCodonSequence = null;
-	private GeneSequence parentGeneSequence;
+	private final GeneSequence parentGeneSequence;
 
 	/**
 	 *
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompound.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompound.java
index b1906b81a3..dbab8aa4b7 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompound.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompound.java
@@ -31,67 +31,69 @@
 
 /**
  * Used to describe an Amino Acid.
+ *
  * @author Richard Holland
  * @author Scooter Willis
  * @author Andy Yates
  */
 public class AminoAcidCompound extends AbstractCompound implements Serializable {
 
-	/**
-	 *
-	 */
-private static final long serialVersionUID = -1955116496725902319L;
-private final AminoAcidCompoundSet compoundSet;
+    /**
+     *
+     */
+    private static final long serialVersionUID = -1955116496725902319L;
+    private final AminoAcidCompoundSet compoundSet;
 
 
-	public AminoAcidCompound(AminoAcidCompoundSet compoundSet, String shortName,
-			String longName, String description, Float molecularWeight) {
-		super(shortName);
-		setShortName(shortName);
-		setLongName(longName);
-		setDescription(description);
-		setMolecularWeight(molecularWeight);
-		this.compoundSet = compoundSet;
-	}
+    public AminoAcidCompound(AminoAcidCompoundSet compoundSet, String shortName,
+                             String longName, String description, float molecularWeight) {
+        super(shortName);
+        setShortName(shortName);
+        setLongName(longName);
+        setDescription(description);
+        this.molecularWeight = molecularWeight;
+        this.compoundSet = compoundSet;
+    }
 
-	// TODO need to allow for modified name; that's not equality though is it?
-	@Override
-public boolean equals(Object obj) {
-		if (obj == null) {
-			return false;
-		}
-		if (!(obj instanceof AminoAcidCompound)) {
-			return false;
-		}
-		AminoAcidCompound them = (AminoAcidCompound) obj;
-		if (toString().equals(them.toString())) {
-			return true;
-		}
-		return getLongName().equals(them.getLongName());
+//    // TODO need to allow for modified name; that's not equality though is it?
+//    @Override
+//    public boolean equals(Object obj) {
+//        if (obj == null) {
+//            return false;
+//        }
+//        if (!(obj instanceof AminoAcidCompound)) {
+//            return false;
+//        }
+//        AminoAcidCompound them = (AminoAcidCompound) obj;
+//        if (toString().equals(them.toString())) {
+//            return true;
+//        }
+//        return getLongName().equals(them.getLongName());
+//
+//    }
 
-	}
 
-	@Override
-public int hashCode() {
-		return toString().hashCode();
-	}
+//    @Override
+//    public int hashCode() {
+//        return toString().hashCode();
+//    }
 
-	@Override
-public boolean equalsIgnoreCase(Compound compound) {
-		if (compound == null) {
-			return false;
-		}
-		if (!(compound instanceof AminoAcidCompound)) {
-			return false;
-		}
-		AminoAcidCompound them = (AminoAcidCompound) compound;
-		if (toString().equalsIgnoreCase(them.toString())) {
-			return true;
-		}
-		return getLongName().equalsIgnoreCase(them.getLongName());
-	}
+//    @Override
+//    public boolean equalsIgnoreCase(Compound compound) {
+//        if (compound == null) {
+//            return false;
+//        }
+//        if (!(compound instanceof AminoAcidCompound)) {
+//            return false;
+//        }
+//        AminoAcidCompound them = (AminoAcidCompound) compound;
+//        if (toString().equalsIgnoreCase(them.toString())) {
+//            return true;
+//        }
+//        return getLongName().equalsIgnoreCase(them.getLongName());
+//    }
 
-	public CompoundSet<AminoAcidCompound> getCompoundSet() {
-		return compoundSet;
-	}
+    public CompoundSet<AminoAcidCompound> getCompoundSet() {
+        return compoundSet;
+    }
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java
index 125fb362e8..22c766c39a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java
@@ -71,14 +71,14 @@ public AminoAcidCompoundSet() {
 		aminoAcidCompoundCache.put("W", new AminoAcidCompound(this, "W", "Trp", "Tryptophan", 186.2132f));
 		aminoAcidCompoundCache.put("Y", new AminoAcidCompound(this, "Y", "Tyr", "Tyrosine", 163.1760f));
 		aminoAcidCompoundCache.put("V", new AminoAcidCompound(this, "V", "Val", "Valine", 99.1326f));
-		aminoAcidCompoundCache.put("B", new AminoAcidCompound(this, "B", "Asx", "Asparagine or Aspartic acid", null));
-		aminoAcidCompoundCache.put("Z", new AminoAcidCompound(this, "Z", "Glx", "Glutamine or Glutamic acid", null));
-		aminoAcidCompoundCache.put("J", new AminoAcidCompound(this, "J", "Xle", "Leucine or Isoleucine", null));
-		aminoAcidCompoundCache.put("X", new AminoAcidCompound(this, "X", "Xaa", "Unspecified", null));
-		aminoAcidCompoundCache.put("-", new AminoAcidCompound(this, "-", "---", "Unspecified", null));
-		aminoAcidCompoundCache.put(".", new AminoAcidCompound(this, ".", "...", "Unspecified", null));
-		aminoAcidCompoundCache.put("_", new AminoAcidCompound(this, "_", "___", "Unspecified", null));
-		aminoAcidCompoundCache.put("*", new AminoAcidCompound(this, "*", "***", "Stop", null));
+		aminoAcidCompoundCache.put("B", new AminoAcidCompound(this, "B", "Asx", "Asparagine or Aspartic acid", Float.NaN));
+		aminoAcidCompoundCache.put("Z", new AminoAcidCompound(this, "Z", "Glx", "Glutamine or Glutamic acid", Float.NaN));
+		aminoAcidCompoundCache.put("J", new AminoAcidCompound(this, "J", "Xle", "Leucine or Isoleucine", Float.NaN));
+		aminoAcidCompoundCache.put("X", new AminoAcidCompound(this, "X", "Xaa", "Unspecified", Float.NaN));
+		aminoAcidCompoundCache.put("-", new AminoAcidCompound(this, "-", "---", "Unspecified", Float.NaN));
+		aminoAcidCompoundCache.put(".", new AminoAcidCompound(this, ".", "...", "Unspecified", Float.NaN));
+		aminoAcidCompoundCache.put("_", new AminoAcidCompound(this, "_", "___", "Unspecified", Float.NaN));
+		aminoAcidCompoundCache.put("*", new AminoAcidCompound(this, "*", "***", "Stop", Float.NaN));
 
 		//Selenocysteine - this is encoded by UGA with the presence
 		//of a SECIS element (SElenoCysteine Insertion Sequence) in the mRNA
@@ -90,10 +90,8 @@ public AminoAcidCompoundSet() {
 		//which then does the actual conversion to Pyl.
 		aminoAcidCompoundCache.put("O", new AminoAcidCompound(this, "O", "Pyl", "Pyrrolysine", 255.3172f));
 
-		for(AminoAcidCompound aa : aminoAcidCompoundCache.values()) {
-            String threeLtr = aa.getLongName().toUpperCase();
-			aminoAcidCompoundCache3Letter.put(threeLtr, aa);
-		}
+		for(AminoAcidCompound aa : aminoAcidCompoundCache.values())
+			aminoAcidCompoundCache3Letter.put(aa.getLongName().toUpperCase(), aa);
 	}
 
 	@Override
@@ -103,15 +101,13 @@ public String getStringForCompound(AminoAcidCompound compound) {
 
 	@Override
 	public AminoAcidCompound getCompoundForString(String string) {
-		if (string.length() == 0) {
+		int sl = string.length();
+		if (sl == 0)
 			return null;
-		}
-		if (string.length() == 3) {
+		if (sl == 3)
 			return this.aminoAcidCompoundCache3Letter.get(string.toUpperCase());
-		}
-		if (string.length() > this.getMaxSingleCompoundStringLength()) {
+		if (sl > this.getMaxSingleCompoundStringLength())
 			throw new IllegalArgumentException("String supplied ("+string+") is too long. Max is "+getMaxSingleCompoundStringLength());
-		}
 		return this.aminoAcidCompoundCache.get(string.toUpperCase());
 	}
 
@@ -126,11 +122,7 @@ public boolean isCompoundStringLengthEqual() {
 		return true;
 	}
 
-	private final static AminoAcidCompoundSet aminoAcidCompoundSet = new AminoAcidCompoundSet();
-
-	public static AminoAcidCompoundSet getAminoAcidCompoundSet() {
-		return aminoAcidCompoundSet;
-	}
+	public final static AminoAcidCompoundSet aminoAcidCompoundSet = new AminoAcidCompoundSet();
 
 	@Override
 	public boolean compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/CodonCompound.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/CodonCompound.java
index d78b307b42..35180fa4ef 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/CodonCompound.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/CodonCompound.java
@@ -1,139 +1,138 @@
-/*
- *                    BioJava development code
- *
- * This code may be freely distributed and modified under the
- * terms of the GNU Lesser General Public Licence.  This should
- * be distributed with the code.  If you do not have a copy,
- * see:
- *
- *      http://www.gnu.org/copyleft/lesser.html
- *
- * Copyright for this code is held jointly by the individual
- * authors.  These should be listed in @author doc comments.
- *
- * For more information on the BioJava project and its aims,
- * or to join the biojava-l mailing list, visit the home page
- * at:
- *
- *      http://www.biojava.org/
- *
- * Created on 01-21-2010
- */
-package org.biojava.nbio.core.sequence.compound;
-
-import org.biojava.nbio.core.sequence.template.AbstractCompound;
-import org.biojava.nbio.core.sequence.template.Compound;
-/**
- * Define a codon
- * @author Andy Yates
- */
-public class CodonCompound extends AbstractCompound {
-
-	private final NucleotideCompound one;
-	private final NucleotideCompound two;
-	private final NucleotideCompound three;
-	private final boolean start;
-
-	public CodonCompound(NucleotideCompound one, NucleotideCompound two,
-			NucleotideCompound three, boolean start) {
-		super(one.toString()+two.toString()+three.toString());
-		this.one = one;
-		this.two = two;
-		this.three = three;
-		this.start = start;
-	}
-
-	@Override
-public boolean equalsIgnoreCase(Compound compound) {
-		if (compound == null) {
-			return false;
-		}
-		if (!(compound instanceof CodonCompound)) {
-			return false;
-		}
-		CodonCompound them = (CodonCompound) compound;
-		return toString().equalsIgnoreCase(them.toString());
-	}
-
-	@Override
-public boolean equals(Object obj) {
-		if (obj == null) {
-			return false;
-		}
-		if (!(obj instanceof CodonCompound)) {
-			return false;
-		}
-		CodonCompound them = (CodonCompound)obj;
-		return toString().equals(them.toString());
-	}
-
-	@Override
-public int hashCode() {
-		return toString().hashCode();
-	}
-
-	public NucleotideCompound getOne() {
-		return one;
-	}
-
-	public NucleotideCompound getTwo() {
-		return two;
-	}
-
-	public NucleotideCompound getThree() {
-		return three;
-	}
-
-	public boolean isStart() {
-		return start;
-	}
-
-	@Override
-public String getDescription() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-public String getLongName() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-public Float getMolecularWeight() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-public String getShortName() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-public void setDescription(String description) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-public void setLongName(String longName) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-public void setMolecularWeight(Float molecularWeight) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-public void setShortName(String shortName) {
-		// TODO Auto-generated method stub
-
-	}
-
-}
+///*
+// *                    BioJava development code
+// *
+// * This code may be freely distributed and modified under the
+// * terms of the GNU Lesser General Public Licence.  This should
+// * be distributed with the code.  If you do not have a copy,
+// * see:
+// *
+// *      http://www.gnu.org/copyleft/lesser.html
+// *
+// * Copyright for this code is held jointly by the individual
+// * authors.  These should be listed in @author doc comments.
+// *
+// * For more information on the BioJava project and its aims,
+// * or to join the biojava-l mailing list, visit the home page
+// * at:
+// *
+// *      http://www.biojava.org/
+// *
+// * Created on 01-21-2010
+// */
+//package org.biojava.nbio.core.sequence.compound;
+//
+//import org.biojava.nbio.core.sequence.template.AbstractCompound;
+//import org.biojava.nbio.core.sequence.template.Compound;
+///**
+// * Define a codon
+// * @author Andy Yates
+// */
+//public class CodonCompound extends AbstractCompound {
+//
+//	private final NucleotideCompound one;
+//	private final NucleotideCompound two;
+//	private final NucleotideCompound three;
+//	private final boolean start;
+//
+//	public CodonCompound(NucleotideCompound one, NucleotideCompound two,
+//			NucleotideCompound three, boolean start) {
+//		super(one.toString()+two.toString()+three.toString());
+//		this.one = one;
+//		this.two = two;
+//		this.three = three;
+//		this.start = start;
+//	}
+//
+//	@Override
+//public boolean equalsIgnoreCase(Compound compound) {
+//		if (compound == null) {
+//			return false;
+//		}
+//		if (!(compound instanceof CodonCompound)) {
+//			return false;
+//		}
+//		CodonCompound them = (CodonCompound) compound;
+//		return toString().equalsIgnoreCase(them.toString());
+//	}
+//
+//	@Override
+//public boolean equals(Object obj) {
+//		if (obj == null) {
+//			return false;
+//		}
+//		if (!(obj instanceof CodonCompound)) {
+//			return false;
+//		}
+//		CodonCompound them = (CodonCompound)obj;
+//		return toString().equals(them.toString());
+//	}
+//
+//	@Override
+//public int hashCode() {
+//		return toString().hashCode();
+//	}
+//
+//	public NucleotideCompound getOne() {
+//		return one;
+//	}
+//
+//	public NucleotideCompound getTwo() {
+//		return two;
+//	}
+//
+//	public NucleotideCompound getThree() {
+//		return three;
+//	}
+//
+//	public boolean isStart() {
+//		return start;
+//	}
+//
+//	@Override
+//public String getDescription() {
+//		// TODO Auto-generated method stub
+//		return null;
+//	}
+//
+//	@Override
+//public String getLongName() {
+//		// TODO Auto-generated method stub
+//		return null;
+//	}
+//
+//	@Override
+//public Float getMolecularWeight() {
+//		// TODO Auto-generated method stub
+//		return null;
+//	}
+//
+//	@Override
+//public String getShortName() {
+//		// TODO Auto-generated method stub
+//		return null;
+//	}
+//
+//	@Override
+//public void setDescription(String description) {
+//		// TODO Auto-generated method stub
+//
+//	}
+//
+//	@Override
+//public void setLongName(String longName) {
+//		// TODO Auto-generated method stub
+//
+//	}
+//
+//	public void setMolecularWeight(Float molecularWeight) {
+//		// TODO Auto-generated method stub
+//
+//	}
+//
+//	@Override
+//public void setShortName(String shortName) {
+//		// TODO Auto-generated method stub
+//
+//	}
+//
+//}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/NucleotideCompound.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/NucleotideCompound.java
index 6ed0cbb270..3ed4a4d1be 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/NucleotideCompound.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/NucleotideCompound.java
@@ -71,35 +71,35 @@ public String getShortName() {
 	public ComplementCompound getComplement() {
 		return compoundSet.getCompoundForString(complementStr);
 	}
-
-	@Override
-	public boolean equals(Object obj) {
-		if (obj == null) {
-			return false;
-		}
-		if (!(obj instanceof NucleotideCompound)) {
-			return false;
-		}
-		NucleotideCompound them = (NucleotideCompound) obj;
-		return toString().equals(them.toString());
-	}
-
-	@Override
-	public int hashCode() {
-		return toString().hashCode();
-	}
-
-	@Override
-	public boolean equalsIgnoreCase(Compound compound) {
-		if (compound == null) {
-			return false;
-		}
-		if (!(compound instanceof NucleotideCompound)) {
-			return false;
-		}
-		NucleotideCompound them = (NucleotideCompound) compound;
-		return toString().equalsIgnoreCase(them.toString());
-	}
+//
+//	@Override
+//	public boolean equals(Object obj) {
+//		if (obj == null) {
+//			return false;
+//		}
+//		if (!(obj instanceof NucleotideCompound)) {
+//			return false;
+//		}
+//		NucleotideCompound them = (NucleotideCompound) obj;
+//		return toString().equals(them.toString());
+//	}
+//
+//	@Override
+//	public int hashCode() {
+//		return toString().hashCode();
+//	}
+//
+//	@Override
+//	public boolean equalsIgnoreCase(Compound compound) {
+//		if (compound == null) {
+//			return false;
+//		}
+//		if (!(compound instanceof NucleotideCompound)) {
+//			return false;
+//		}
+//		NucleotideCompound them = (NucleotideCompound) compound;
+//		return toString().equalsIgnoreCase(them.toString());
+//	}
 
 	public Set<NucleotideCompound> getConstituents() {
 	  return constituents;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java
index bbce920b82..2279df647e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java
@@ -86,7 +86,7 @@ public Sequence<C> edit(Sequence<C> editingSequence) {
 
 			return new JoiningSequenceReader<>(sequences);
 		}
-		private int start;
+		private final int start;
 		private int end = -1;
 		private String stringSequence;
 		private Sequence<C> sequence;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
index f32148dbc1..edf60c675b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
@@ -206,12 +206,7 @@ public void setShortDescription(String shortDescription) {
 		} else {
 			double end1 = e1.getLocations().getEnd().getPosition();
 			double end2 = e2.getLocations().getEnd().getPosition();
-			if(end1 > end2)
-				return -1;
-			else if(end1 < end2)
-				return 1;
-			else
-			return 0;
+            return Double.compare(end2, end1);
 		}
 
 	};
@@ -224,20 +219,14 @@ else if(end1 < end2)
 	static public final Comparator<FeatureInterface<?, ?>> LENGTH = (e1, e2) -> {
 		double v1 = Math.abs(e1.getLocations().getEnd().getPosition()- e1.getLocations().getStart().getPosition());
 		double v2 = Math.abs(e2.getLocations().getEnd().getPosition() -  e2.getLocations().getStart().getPosition());
-		if (v1 < v2) {
-			return -1;
-		} else if (v1 > v2) {
-			return 1;
-		} else {
-			return 0;
-		}
+         return Double.compare(v1, v2);
 
 	};
 
 	/**
 	 * Sort features by type
 	 */
-	public static final Comparator<FeatureInterface<?, ?>> TYPE = (o1, o2) -> o1.getType().compareTo(o2.getType());
+	public static final Comparator<FeatureInterface<?, ?>> TYPE = Comparator.comparing(FeatureInterface::getType);
 
 	/**
 	 * @return the userObject
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java
index c3ebb861ae..13a8ce7f1a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java
@@ -117,7 +117,7 @@ private static List<Object> getStringCase(String str) {
 	}
 
 	public static void main(String[] args) throws Exception {
-		CasePreservingProteinSequenceCreator creator = new CasePreservingProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet());
+        CasePreservingProteinSequenceCreator creator = new CasePreservingProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet);
 		AbstractSequence<AminoAcidCompound> seq = creator.getSequence("aaAA",0);
 		logger.info("Sequence: {}", seq.getSequenceAsString()); //"AAAA"
 		logger.info("User Collection: {}", seq.getUserCollection()); //"[false, false, true, true]"
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
index 39b061688a..4cf22e9d63 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
@@ -190,11 +190,12 @@ public LinkedHashMap<String,S> process(int max) throws IOException {
 
 			if (line == null) {
 				//i.e. EOF
-				if ( sb.length() == 0 && header.length() != 0 ) {
+				int sbl = sb.length();
+				if ( sbl == 0 && header.length() != 0 ) {
 					logger.warn("Can't parse sequence {}. Got sequence of length 0!", sequenceIndex);
 					logger.warn("header: {}", header);
 					header = null;
-				} else if ( sb.length() > 0 ) {
+				} else if ( sbl > 0 ) {
 					//logger.info("Sequence index=" + sequenceIndex + " " + fileIndex );
 					try {
 						@SuppressWarnings("unchecked")
@@ -239,7 +240,7 @@ public static void main(String[] args) {
 
 			if ( is == null)
 				System.err.println("Could not get input file " + inputFile);
-			FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(is, new GenericFastaHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+			FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(is, new GenericFastaHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet));
 			LinkedHashMap<String,ProteinSequence> proteinSequences = fastaReader.process();
 			is.close();
 
@@ -253,7 +254,7 @@ public static void main(String[] args) {
 							new GenericFastaHeaderParser<>(),
 							new FileProxyProteinSequenceCreator(
 									file,
-									AminoAcidCompoundSet.getAminoAcidCompoundSet(),
+									AminoAcidCompoundSet.aminoAcidCompoundSet,
 									new FastaSequenceParser()
 							)
 					);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
index 825b2ba545..6eff327754 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
@@ -124,10 +124,10 @@ public static LinkedHashMap<String, ProteinSequence> readFastaProteinSequence(
 	 */
 	public static LinkedHashMap<String, ProteinSequence> readFastaProteinSequence(
 			InputStream inStream) throws IOException {
-		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
+        FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
 				inStream,
 				new GenericFastaHeaderParser<>(),
-				new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+				new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet));
 		return fastaReader.process();
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
index 5be5b1973f..d46a84ca33 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
@@ -133,7 +133,7 @@ public static void main(String[] args) {
 			FileInputStream is = new FileInputStream("/Users/Scooter/scripps/dyadic/c1-454Scaffolds.faa");
 
 
-			FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(is, new GenericFastaHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+            FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(is, new GenericFastaHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet));
 			LinkedHashMap<String, ProteinSequence> proteinSequences = fastaReader.process();
 			is.close();
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
index 3e8e4e8241..dea62c706e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
@@ -88,13 +88,13 @@ public static LinkedHashMap<String, ProteinSequence> readGenbankProteinSequence(
 			return readGenbankProteinSequence(file);
 		}
 
-		GenbankReader<ProteinSequence, AminoAcidCompound> GenbankProxyReader =
+        GenbankReader<ProteinSequence, AminoAcidCompound> GenbankProxyReader =
 				new GenbankReader<>(
 						file,
 						new GenericGenbankHeaderParser<>(),
 						new FileProxyProteinSequenceCreator(
 								file,
-								AminoAcidCompoundSet.getAminoAcidCompoundSet(),
+                                AminoAcidCompoundSet.aminoAcidCompoundSet,
 								new GenbankSequenceParser<AbstractSequence<AminoAcidCompound>, AminoAcidCompound>()
 						)
 				);
@@ -156,10 +156,10 @@ public static LinkedHashMap<String, ProteinSequence> readGenbankProteinSequence(
 	 */
 	public static LinkedHashMap<String, ProteinSequence> readGenbankProteinSequence(
 			InputStream inStream) throws Exception {
-		GenbankReader<ProteinSequence, AminoAcidCompound> GenbankReader = new GenbankReader<>(
+        GenbankReader<ProteinSequence, AminoAcidCompound> GenbankReader = new GenbankReader<>(
 				inStream,
 				new GenericGenbankHeaderParser<>(),
-				new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+				new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet));
 		return GenbankReader.process();
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
index 700b50a087..e016068652 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
@@ -166,7 +166,7 @@ private String parse(BufferedReader bufferedReader) {
 						String type = m.group(5);
 
 						if (lengthUnits.equalsIgnoreCase("aa")) {
-							compoundType = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+							compoundType = AminoAcidCompoundSet.aminoAcidCompoundSet;
 						} else if (lengthUnits.equalsIgnoreCase("bp")) {
 							if (type != null) {
 								if (type.contains("RNA")) {
@@ -268,11 +268,11 @@ private String parse(BufferedReader bufferedReader) {
 								if (m.matches()) {
 									String dbname = m.group(1);
 									String raccession = m.group(2);
-									Qualifier xref = new DBReferenceInfo(dbname, raccession);
+									DBReferenceInfo xref = new DBReferenceInfo(dbname, raccession);
 									gbFeature.addQualifier(key, xref);
 
 									ArrayList<DBReferenceInfo> listDBEntry = new ArrayList<>();
-									listDBEntry.add((DBReferenceInfo) xref);
+									listDBEntry.add(xref);
 									mapDB.put(key, listDBEntry);
 								} else {
 									throw new ParserException("Bad dbxref");
@@ -321,12 +321,8 @@ private String parse(BufferedReader bufferedReader) {
 					seqData = seq.toString().replaceAll("\\s+", "").replaceAll("[\\.|~]", "-").toUpperCase();
 					break;
 				case DBSOURCE:
-					//TODO
-					break;
-				case PRIMARY:
-					//TODO
-					break;
 				case DBLINK:
+				case PRIMARY:
 					//TODO
 					break;
 				default:
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java
index 4894daf38a..4480cab662 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java
@@ -70,11 +70,10 @@ public static void writeProteinSequence(File file,
 	 *
 	 * @param outputStream
 	 * @param proteinSequences
-	 * @throws Exception
-	 */
+     */
 
 	public static void writeProteinSequence(OutputStream outputStream,
-			Collection<ProteinSequence> proteinSequences) throws Exception {
+			Collection<ProteinSequence> proteinSequences) {
 
 		GenbankWriter<ProteinSequence, AminoAcidCompound> genbankWriter = new GenbankWriter<>(
 				outputStream,
@@ -120,12 +119,10 @@ public static void writeNucleotideSequence(OutputStream outputStream,
 	 * @param outputStream
 	 * @param dnaSequences
 	 * @param seqType
-	 * @throws Exception
-	 */
+     */
 
 	public static void writeNucleotideSequence(OutputStream outputStream,
-			Collection<DNASequence> dnaSequences, String seqType)
-			throws Exception {
+			Collection<DNASequence> dnaSequences, String seqType) {
 		GenericGenbankHeaderFormat<DNASequence, NucleotideCompound> genericGenbankHeaderFormat = new GenericGenbankHeaderFormat<>(
 				seqType);
 		// genericGenbankHeaderFormat.setLineSeparator(lineSep);
@@ -185,11 +182,9 @@ private static Collection<Sequence<?>> singleSeqToCollection(
 	 *            Stream to write to; can be System.out
 	 * @param sequences
 	 *            The sequences to write out
-	 * @throws Exception
-	 *             Thrown normally thanks to IO problems
-	 */
+     */
 	public static void writeSequences(OutputStream outputStream,
-			Collection<Sequence<?>> sequences) throws Exception {
+			Collection<Sequence<?>> sequences) {
 
 		GenbankHeaderFormatInterface<Sequence<?>, Compound> fhfi = sequence -> sequence.getAccession().toString();
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.java
index bef63c559f..902c50bfa6 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.java
@@ -36,7 +36,7 @@ public class GenericGenbankHeaderFormat<S extends AbstractSequence<C>, C extends
 		GenbankHeaderFormatInterface<S, C> {
 	private static final int HEADER_WIDTH = 12;
 	private static final String lineSep = "%n";
-	private String seqType;
+	private final String seqType;
 
 	public GenericGenbankHeaderFormat() {
 		seqType = null;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java
index 98a5952858..8d1ecedeff 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java
@@ -70,7 +70,7 @@ private String _write_feature_qualifier(String key, String value, boolean quote)
 			return line + lineSep;
 		}
 		String goodlines = "";
-		while(!"".equals(line.replaceAll("^\\s+", ""))) {
+		while(!line.replaceAll("^\\s+", "").isEmpty()) {
 			if(line.length() <= MAX_WIDTH) {
 				goodlines += line + lineSep;
 				break;
@@ -101,7 +101,7 @@ private String _wrap_location(String location) {
 		if(location.length() <= length) {
 			return location;
 		}
-		int index = location.substring(length).lastIndexOf(",");
+		int index = location.substring(length).lastIndexOf(',');
 		if(-1 == index) {
 			//No good place to split (!)
 			return location;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java
index dbd2a29245..19547a7ba8 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java
@@ -111,7 +111,7 @@ public static void processReader(BufferedReader br, ReaderProcessor processor) t
 	 */
 	public static List<String> getList(BufferedReader br) throws ParserException {
 		final List<String> list = new ArrayList<>();
-		processReader(br, line -> list.add(line));
+		processReader(br, list::add);
 		return list;
 	}
 
@@ -328,8 +328,7 @@ public static void print(String string, File file) throws IOException {
 		try (PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(file)))) {
 			out.print(string);
 			out.flush();
-			out.close();
-		}
+        }
 	}
 
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
index 93233c3e91..1e681bab09 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
@@ -148,18 +148,17 @@ private InputStream getEutilsInputStream(String accessionID, String db) throws I
 		String genbankURL = eutilBaseURL + "efetch.fcgi?db=" + db + "&id=" + accessionID + "&rettype=gb&retmode=text";
 		logger.trace("Loading: {}", genbankURL);
 		URL genbank = new URL(genbankURL);
-		URLConnection genbankConnection = genbank.openConnection();
-		return genbankConnection.getInputStream();
+		return genbank.openConnection().getInputStream();
 	}
 
-	/**
-	 * Local directory cache of Genbank that can be downloaded
-	 *
-	 * @return the uniprotDirectoryCache
-	 */
-	public String getGenbankDirectoryCache() {
-		return genbankDirectoryCache;
-	}
+//	/**
+//	 * Local directory cache of Genbank that can be downloaded
+//	 *
+//	 * @return the uniprotDirectoryCache
+//	 */
+//	public String getGenbankDirectoryCache() {
+//		return genbankDirectoryCache;
+//	}
 
 	/**
 	 * @param genbankDirectoryCache
@@ -198,8 +197,8 @@ public ArrayList<String> getKeyWords() {
 
 	public static void main(String[] args) throws Throwable {
 
-		GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
-				= new GenbankProxySequenceReader<>("/tmp", "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+        GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
+				= new GenbankProxySequenceReader<>("/tmp", "NP_000257", AminoAcidCompoundSet.aminoAcidCompoundSet);
 		ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
 		genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
 		logger.info("Sequence ({},{})={}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
index f0ca633ab5..0982c35ff8 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
@@ -512,7 +512,7 @@ public final int countCompounds(C... compounds) {
 	 * @return
 	 * @throws IOException
 	 */
-	private Document getUniprotXML(String accession) throws IOException, CompoundNotFoundException {
+	private Document getUniprotXML(String accession) throws IOException {
 		StringBuilder sb = new StringBuilder();
 		// try in cache
 		if (uniprotDirectoryCache != null && uniprotDirectoryCache.length() > 0) {
@@ -721,7 +721,7 @@ public static void setUniprotDirectoryCache(String aUniprotDirectoryCache) {
 	public static void main(String[] args) {
 
 		try {
-			UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<>("YA745_GIBZE", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+            UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<>("YA745_GIBZE", AminoAcidCompoundSet.aminoAcidCompoundSet);
 			ProteinSequence proteinSequence = new ProteinSequence(uniprotSequence);
 			logger.info("Accession: {}", proteinSequence.getAccession().getID());
 			logger.info("Sequence: {}", proteinSequence.getSequenceAsString());
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java
index 426ea18302..b6a8963685 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java
@@ -36,12 +36,12 @@ public class FuzzyPoint extends SimplePoint {
 	/**
 	 * Always uses the min point to resolve a location
 	 */
-	public static final Resolver<FuzzyPoint> MIN_RESOLVER = point -> point.getMin();
+	public static final Resolver<FuzzyPoint> MIN_RESOLVER = FuzzyPoint::getMin;
 
 	/**
 	 * Always uses the max point to resolve a location
 	 */
-	public static final Resolver<FuzzyPoint> MAX_RESOLVER = point -> point.getMax();
+	public static final Resolver<FuzzyPoint> MAX_RESOLVER = FuzzyPoint::getMax;
 
 	/**
 	 * Combines min and max and then gets the mean of it
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
index b2178c5ac9..0befcc1110 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
@@ -32,7 +32,6 @@
 import org.biojava.nbio.core.sequence.template.AbstractSequence;
 import org.biojava.nbio.core.sequence.template.Compound;
 
-import java.io.IOException;
 import java.io.Reader;
 import java.util.ArrayList;
 import java.util.List;
@@ -228,7 +227,7 @@ private List<Location> parseLocationString(String string, int versus) throws Par
 				String accession = m.group(1);
 				Strand s = versus == 1 ? Strand.POSITIVE : Strand.NEGATIVE;
 				int start = Integer.parseInt(m.group(3));
-				int end = m.group(6) == null ? start : new Integer(m.group(6));
+				int end = m.group(6) == null ? start : Integer.valueOf(m.group(6));
 
 				if (featureGlobalStart > start) {
 					featureGlobalStart = start;
@@ -252,7 +251,7 @@ private List<Location> parseLocationString(String string, int versus) throws Par
 					l.setPartialOn3prime(true);
 				}
 
-				if (!(accession == null || "".equals(accession))) l.setAccession(new AccessionID(accession));
+				if (!(accession == null || accession.isEmpty())) l.setAccession(new AccessionID(accession));
 
 				boundedLocationsCollection.add(l);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
index d3922f8d3d..6ee1e2177e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.core.sequence.storage;
 
-import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.AccessionID;
 import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
 import org.biojava.nbio.core.sequence.template.*;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
index 4de2e003bf..ecd8ac3faf 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.core.sequence.storage;
 
-import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.AccessionID;
 import org.biojava.nbio.core.sequence.template.*;
 import org.biojava.nbio.core.util.Equals;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
index 23db800fd5..09e695914f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.core.sequence.storage;
 
-import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.AccessionID;
 import org.biojava.nbio.core.sequence.template.*;
 import org.biojava.nbio.core.util.Equals;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompound.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompound.java
index b548f1b5ce..6a9ea1843b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompound.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompound.java
@@ -24,108 +24,90 @@
 
 /**
  * The details of a Compound
+ *
  * @author Andy Yates
  */
 public abstract class AbstractCompound implements Compound {
 
-	private final String base;
-	private final String upperedBase;
-	private String shortName = null;
-	private String longName = null;
-	private String description = null;
-	private Float molecularWeight = null;
-
-
-	// Added an empty constructor for Serialization
-	public AbstractCompound(){
-		this.base = null;
-		this.upperedBase = null;
-	}
-
-	public AbstractCompound(String base) {
-		this.base = base;
-		this.upperedBase = base.toUpperCase();
-	}
-
-	public String getBase() {
-		return base;
-	}
-
-	public String getUpperedBase() {
-		return upperedBase;
-	}
-
-	@Override
-public String getDescription() {
-		return description;
-	}
-
-	@Override
-public void setDescription(String description) {
-		this.description = description;
-	}
-
-	@Override
-public String getShortName() {
-		return shortName;
-	}
-
-	@Override
-public void setShortName(String shortName) {
-		this.shortName = shortName;
-	}
-
-	@Override
-public String getLongName() {
-		return longName;
-	}
-
-	@Override
-public void setLongName(String longName) {
-		this.longName = longName;
-	}
-
-	@Override
-public Float getMolecularWeight() {
-		return molecularWeight;
-	}
-
-	@Override
-public void setMolecularWeight(Float molecularWeight) {
-		this.molecularWeight = molecularWeight;
-	}
-
-	@Override
-	public String toString() {
-		return base;
-	}
-
-	@Override
-	public boolean equals(Object obj) {
-		if (obj == null) {
-			return false;
-		}
-		if (!(obj instanceof AbstractCompound)) {
-			return false;
-		}
-		AbstractCompound them = (AbstractCompound) obj;
-		return this.base.equals(them.base);
-	}
-
-	@Override
-	public int hashCode() {
-		return this.base.hashCode();
-	}
-
-	@Override
-	public boolean equalsIgnoreCase(Compound compound) {
-		if (compound == null) {
-			return false;
-		}
-		if (!(compound instanceof AbstractCompound)) {
-			return false;
-		}
-		AbstractCompound them = (AbstractCompound) compound;
-		return this.base.equalsIgnoreCase(them.base);
-	}
+    private final String base;
+    private final String upperedBase;
+    private String shortName = null;
+    private String longName = null;
+    private String description = null;
+    protected float molecularWeight = Float.NaN;
+    final int hash;
+
+    protected AbstractCompound(String base) {
+        this.base = base;
+        this.upperedBase = base.toUpperCase();
+        this.hash = base.hashCode();
+    }
+
+    public String getBase() {
+        return base;
+    }
+
+    public String getUpperedBase() {
+        return upperedBase;
+    }
+
+    @Override
+    public String getDescription() {
+        return description;
+    }
+
+    @Override
+    public void setDescription(String description) {
+        this.description = description;
+    }
+
+    @Override
+    public String getShortName() {
+        return shortName;
+    }
+
+    @Override
+    public void setShortName(String shortName) {
+        this.shortName = shortName;
+    }
+
+    @Override
+    public String getLongName() {
+        return longName;
+    }
+
+    @Override
+    public void setLongName(String longName) {
+        this.longName = longName;
+    }
+
+    @Override
+    public final float getMolecularWeight() {
+        return molecularWeight;
+    }
+
+    @Override
+    public final String toString() {
+        return base;
+    }
+
+    @Override
+    public final boolean equals(Object obj) {
+        return obj == this || (obj instanceof AbstractCompound && this.base.equals(((AbstractCompound) obj).base));
+    }
+
+    @Override
+    public final int hashCode() {
+        return hash;
+    }
+
+    @Override
+    public final boolean equalsIgnoreCase(Compound compound) {
+        if (this == compound) return true;
+        if (!(compound instanceof AbstractCompound)) {
+            return false;
+        }
+        AbstractCompound them = (AbstractCompound) compound;
+        return this.base.equalsIgnoreCase(them.base);
+    }
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java
index eb2db9da93..113fc05736 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java
@@ -42,7 +42,7 @@ public interface Compound {
 
 	void setLongName(String longName);
 
-	Float getMolecularWeight();
+	float getMolecularWeight();
 
-	void setMolecularWeight(Float molecularWeight);
+//	void setMolecularWeight(Float molecularWeight);
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/CaseInsensitiveCompound.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/CaseInsensitiveCompound.java
index 5c00b511d6..af2adba614 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/CaseInsensitiveCompound.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/CaseInsensitiveCompound.java
@@ -1,115 +1,115 @@
-/*
- *                    BioJava development code
- *
- * This code may be freely distributed and modified under the
- * terms of the GNU Lesser General Public Licence.  This should
- * be distributed with the code.  If you do not have a copy,
- * see:
- *
- *      http://www.gnu.org/copyleft/lesser.html
- *
- * Copyright for this code is held jointly by the individual
- * authors.  These should be listed in @author doc comments.
- *
- * For more information on the BioJava project and its aims,
- * or to join the biojava-l mailing list, visit the home page
- * at:
- *
- *      http://www.biojava.org/
- *
- * Created on 01-21-2010
- */
-package org.biojava.nbio.core.sequence.transcription;
-
-import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
-import org.biojava.nbio.core.sequence.template.Compound;
-
-/**
- * Attempts to wrap compounds so it is possible to view them
- * in a case insensitive manner
- */
-public class CaseInsensitiveCompound implements Compound {
-
-	private final NucleotideCompound compound;
-
-	public CaseInsensitiveCompound(NucleotideCompound compound) {
-		this.compound = compound;
-	}
-
-	@Override
-public boolean equalsIgnoreCase(Compound compound) {
-		if (compound == null) {
-			return false;
-		}
-		if (!(compound instanceof CaseInsensitiveCompound)) {
-			return false;
-		}
-		CaseInsensitiveCompound them = (CaseInsensitiveCompound) compound;
-		return toString().equalsIgnoreCase(them.toString());
-	}
-
-	@Override
-public boolean equals(Object obj) {
-		if (obj == null) {
-			return false;
-		}
-		if (!(obj instanceof CaseInsensitiveCompound)) {
-			return false;
-		}
-		return equalsIgnoreCase((Compound)obj);
-	}
-
-	@Override
-public int hashCode() {
-		return toString().toUpperCase().hashCode();
-	}
-
-	public NucleotideCompound getUnderlyingCompound() {
-		return this.compound;
-	}
-
-	@Override
-public String getDescription() {
-		return getUnderlyingCompound().getDescription();
-	}
-
-	@Override
-public String getLongName() {
-		return getUnderlyingCompound().getLongName();
-	}
-
-	@Override
-public Float getMolecularWeight() {
-		return getUnderlyingCompound().getMolecularWeight();
-	}
-
-	@Override
-public String getShortName() {
-		return getUnderlyingCompound().getShortName();
-	}
-
-	@Override
-public String toString() {
-		return getUnderlyingCompound().toString();
-	}
-
-	@Override
-public void setDescription(String description) {
-		//Nothing
-	}
-
-	@Override
-public void setLongName(String longName) {
-		//Nothing
-	}
-
-	@Override
-public void setMolecularWeight(Float molecularWeight) {
-		//Nothing
-	}
-
-	@Override
-public void setShortName(String shortName) {
-		//Nothing
-	}
-}
+///*
+// *                    BioJava development code
+// *
+// * This code may be freely distributed and modified under the
+// * terms of the GNU Lesser General Public Licence.  This should
+// * be distributed with the code.  If you do not have a copy,
+// * see:
+// *
+// *      http://www.gnu.org/copyleft/lesser.html
+// *
+// * Copyright for this code is held jointly by the individual
+// * authors.  These should be listed in @author doc comments.
+// *
+// * For more information on the BioJava project and its aims,
+// * or to join the biojava-l mailing list, visit the home page
+// * at:
+// *
+// *      http://www.biojava.org/
+// *
+// * Created on 01-21-2010
+// */
+//package org.biojava.nbio.core.sequence.transcription;
+//
+//import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
+//import org.biojava.nbio.core.sequence.template.Compound;
+//
+///**
+// * Attempts to wrap compounds so it is possible to view them
+// * in a case insensitive manner
+// */
+//public class CaseInsensitiveCompound implements Compound {
+//
+//	private final NucleotideCompound compound;
+//
+//	public CaseInsensitiveCompound(NucleotideCompound compound) {
+//		this.compound = compound;
+//	}
+//
+//	@Override
+//public boolean equalsIgnoreCase(Compound compound) {
+//		if (compound == null) {
+//			return false;
+//		}
+//		if (!(compound instanceof CaseInsensitiveCompound)) {
+//			return false;
+//		}
+//		CaseInsensitiveCompound them = (CaseInsensitiveCompound) compound;
+//		return toString().equalsIgnoreCase(them.toString());
+//	}
+//
+//	@Override
+//public boolean equals(Object obj) {
+//		if (obj == null) {
+//			return false;
+//		}
+//		if (!(obj instanceof CaseInsensitiveCompound)) {
+//			return false;
+//		}
+//		return equalsIgnoreCase((Compound)obj);
+//	}
+//
+//	@Override
+//public int hashCode() {
+//		return toString().toUpperCase().hashCode();
+//	}
+//
+//	public NucleotideCompound getUnderlyingCompound() {
+//		return this.compound;
+//	}
+//
+//	@Override
+//public String getDescription() {
+//		return getUnderlyingCompound().getDescription();
+//	}
+//
+//	@Override
+//public String getLongName() {
+//		return getUnderlyingCompound().getLongName();
+//	}
+//
+//	@Override
+//public Float getMolecularWeight() {
+//		return getUnderlyingCompound().getMolecularWeight();
+//	}
+//
+//	@Override
+//public String getShortName() {
+//		return getUnderlyingCompound().getShortName();
+//	}
+//
+//	@Override
+//public String toString() {
+//		return getUnderlyingCompound().toString();
+//	}
+//
+//	@Override
+//public void setDescription(String description) {
+//		//Nothing
+//	}
+//
+//	@Override
+//public void setLongName(String longName) {
+//		//Nothing
+//	}
+//
+//	@Override
+//public void setMolecularWeight(Float molecularWeight) {
+//		//Nothing
+//	}
+//
+//	@Override
+//public void setShortName(String shortName) {
+//		//Nothing
+//	}
+//}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
index 7ebdc1a2ff..6bfd4215b2 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
@@ -157,7 +157,7 @@ public String getLongName() {
 		}
 
 		@Override
-		public Float getMolecularWeight() {
+		public float getMolecularWeight() {
 			throw new UnsupportedOperationException("Not supported");
 		}
 
@@ -176,10 +176,10 @@ public void setLongName(String longName) {
 			throw new UnsupportedOperationException("Not supported");
 		}
 
-		@Override
-		public void setMolecularWeight(Float molecularWeight) {
-			throw new UnsupportedOperationException("Not supported");
-		}
+//		@Override
+//		public void setMolecularWeight(Float molecularWeight) {
+//			throw new UnsupportedOperationException("Not supported");
+//		}
 
 		@Override
 		public void setShortName(String shortName) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java
index 162d760f05..0ee18cdb66 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java
@@ -327,8 +327,8 @@ private CompoundSet<AminoAcidCompound> getAminoAcidCompounds() {
 			if (aminoAcidCompounds != null) {
 				return aminoAcidCompounds;
 			}
-			return AminoAcidCompoundSet.getAminoAcidCompoundSet();
-		}
+            return AminoAcidCompoundSet.aminoAcidCompoundSet;
+        }
 
 		private DNAToRNATranslator getDnaRnaTranslator() {
 			if (dnaRnaTranslator != null) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/RnaSequenceView.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/RnaSequenceView.java
index 48fea9da1e..05eb1a86d8 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/RnaSequenceView.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/RnaSequenceView.java
@@ -23,7 +23,6 @@
  */
 package org.biojava.nbio.core.sequence.views;
 
-import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
 import org.biojava.nbio.core.sequence.compound.RNACompoundSet;
 import org.biojava.nbio.core.sequence.template.*;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
index beb86f865c..3aed298810 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
@@ -72,7 +72,7 @@ public static void copy(File src, File dst) throws IOException {
 	public static String getFileExtension(File f) {
 		String fileName = f.getName();
 		String ext;
-		int mid = fileName.lastIndexOf(".");
+		int mid = fileName.lastIndexOf('.');
 		ext = fileName.substring(mid + 1);
 		return ext;
 	}
@@ -81,7 +81,7 @@ public static String getFilePrefix(File f) {
 		String fileName = f.getName();
 		String fname;
 
-		int mid = fileName.indexOf(".");
+		int mid = fileName.indexOf('.');
 		fname = fileName.substring(0, mid);
 
 		return fname;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java
index 4a55867c1a..dc06da9683 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java
@@ -84,9 +84,7 @@ protected void writeIndent() {
 		}
 	}
 
-	private void _openTag()
-		throws IOException
-	{
+	private void _openTag() {
 		if (isOpeningTag) {
 			writer.println('>');
 			afterNewline = true;
@@ -223,9 +221,7 @@ public void closeTag(String nsURI, String localName)
 	}
 
 	@Override
-	public void closeTag(String qName)
-		throws IOException
-	{
+	public void closeTag(String qName) {
 		indent--;
 
 		if (isOpeningTag) {
@@ -271,9 +267,7 @@ public void printRaw(String data) {
 	writer.println(data);
 	}
 
-	protected void printChars(String data)
-		throws IOException
-	{
+	protected void printChars(String data) {
 	if (data == null) {
 		printChars("null");
 		return;
@@ -289,9 +283,7 @@ protected void printChars(String data)
 	}
 	}
 
-	protected void printAttributeValue(String data)
-		throws IOException
-	{
+	protected void printAttributeValue(String data) {
 	if (data == null) {
 		printAttributeValue("null");
 		return;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java
index 20aa61164a..b946a43f1f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java
@@ -199,7 +199,7 @@ private void updateIndicesToCheck(int m) {
 
 		if (m==0) return;
 
-		indicesToCheck.remove(new Integer(dendrogram[m-1].getFirst()));
+		indicesToCheck.remove(Integer.valueOf(dendrogram[m - 1].getFirst()));
 	}
 
 	private LinkedPair getClosestPair() {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
index d5875aa2e4..d17193cc0e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
@@ -106,7 +106,7 @@ public interface XMLWriter {
 	 * @param name The tag name
 	 */
 
-    void closeTag(String name) throws IOException;
+    void closeTag(String name);
 
 	/**
 	 * Hints that a namespace is going to be used in a sub-tree.  Use this method
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java
index 72b9300b23..aba01a2820 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java
@@ -53,7 +53,7 @@ public void setup() throws CompoundNotFoundException {
 		local = new SimpleAlignedSequence<>(lo, Arrays.asList(Step.COMPOUND, Step.COMPOUND, Step.GAP, Step.GAP, Step.COMPOUND, Step.GAP, Step.COMPOUND,
                 Step.COMPOUND), 1, 3);
 		local2 = new SimpleAlignedSequence<>(go, Arrays.asList(Step.COMPOUND, Step.COMPOUND, Step.COMPOUND), 1, 0);
-		cs = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        cs = AminoAcidCompoundSet.aminoAcidCompoundSet;
 	}
 
 	@Test(expected=IllegalArgumentException.class)
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleProfileTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleProfileTest.java
index 65a619e10a..60e58cd002 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleProfileTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleProfileTest.java
@@ -261,9 +261,9 @@ public void testGetCompoundAtSIntOutOfBounds5() {
 
 	@Test
 	public void testGetCompoundSet() {
-		assertEquals(global.getCompoundSet(), AminoAcidCompoundSet.getAminoAcidCompoundSet());
-		assertEquals(local.getCompoundSet(), AminoAcidCompoundSet.getAminoAcidCompoundSet());
-		assertEquals(single.getCompoundSet(), AminoAcidCompoundSet.getAminoAcidCompoundSet());
+        assertEquals(global.getCompoundSet(), AminoAcidCompoundSet.aminoAcidCompoundSet);
+        assertEquals(local.getCompoundSet(), AminoAcidCompoundSet.aminoAcidCompoundSet);
+        assertEquals(single.getCompoundSet(), AminoAcidCompoundSet.aminoAcidCompoundSet);
 	}
 
 	@Test
@@ -313,7 +313,7 @@ public void testGetCompoundsAtOutOfBounds6() {
 
 	@Test
 	public void testGetIndexOf() {
-		AminoAcidCompoundSet cs = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet cs = AminoAcidCompoundSet.aminoAcidCompoundSet;
 		assertEquals(global.getIndexOf(cs.getCompoundForString("A")), 1);
 		assertEquals(global.getIndexOf(cs.getCompoundForString("R")), 2);
 		assertEquals(global.getIndexOf(cs.getCompoundForString("N")), 3);
@@ -381,7 +381,7 @@ public void testGetIndicesAtOutOfBounds6() {
 
 	@Test
 	public void testGetLastIndexOf() {
-		AminoAcidCompoundSet cs = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet cs = AminoAcidCompoundSet.aminoAcidCompoundSet;
 		assertEquals(global.getLastIndexOf(cs.getCompoundForString("A")), 1);
 		assertEquals(global.getLastIndexOf(cs.getCompoundForString("R")), 2);
 		assertEquals(global.getLastIndexOf(cs.getCompoundForString("N")), 3);
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java b/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
index c09956fb40..7f4760af96 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
@@ -42,10 +42,10 @@ private void testProcessAll(String path) throws Exception {
 		ClasspathResource r = new ClasspathResource(path);
 		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
 		try( InputStream inStream = r.getInputStream() ) {
-			fastaReader = new FastaReader<>(
+            fastaReader = new FastaReader<>(
 					inStream,
 					new GenericFastaHeaderParser<>(),
-					new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+					new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet));
 			LinkedHashMap<String, ProteinSequence> sequences = fastaReader.process();
 			assertThat(sequences,is(notNullValue()));
 			assertThat(sequences.size(),is(1));
@@ -82,10 +82,10 @@ private void testProcess1(String path) throws Exception {
 		ClasspathResource r = new ClasspathResource(path);
 		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
 		try( InputStream inStream = r.getInputStream() ) {
-			fastaReader = new FastaReader<>(
+            fastaReader = new FastaReader<>(
 					inStream,
 					new GenericFastaHeaderParser<>(),
-					new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+					new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet));
 			LinkedHashMap<String,ProteinSequence> out1 = fastaReader.process(1);
 			assertThat(out1,is(notNullValue()));
 			assertThat(out1.size(),is(1));
@@ -124,10 +124,10 @@ private void testProcess2(String path) throws Exception {
 		ClasspathResource r = new ClasspathResource(path);
 		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
 		try( InputStream inStream = r.getInputStream() ) {
-			fastaReader = new FastaReader<>(
+            fastaReader = new FastaReader<>(
 					inStream,
 					new GenericFastaHeaderParser<>(),
-					new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+					new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet));
 			LinkedHashMap<String,ProteinSequence> out1 = fastaReader.process(1);
 			assertThat(out1,is(notNullValue()));
 			assertThat(out1.size(),is(1));
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignmentTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignmentTest.java
index ea922decf6..145e226ff4 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignmentTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignmentTest.java
@@ -55,7 +55,7 @@ public void setup() throws CompoundNotFoundException {
 
 	@Test
 	public void testGetCompoundsAt() {
-		AminoAcidCompound aminoAcid = AminoAcidCompoundSet.getAminoAcidCompoundSet().getCompoundForString("N");
+        AminoAcidCompound aminoAcid = AminoAcidCompoundSet.aminoAcidCompoundSet.getCompoundForString("N");
 		List<AminoAcidCompound> colProteins = new ArrayList<>();
 		for (int i = 0; i < 8; i++) {
 			colProteins.add(aminoAcid);
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TranslationTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TranslationTest.java
index b0113bfdfa..a4abf15e7f 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TranslationTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TranslationTest.java
@@ -52,8 +52,8 @@ public class TranslationTest {
 	private final static Logger logger = LoggerFactory.getLogger(TranslationTest.class);
 
 	private static final DNACompoundSet dnaCs = DNACompoundSet.getDNACompoundSet();
-	private static final AminoAcidCompoundSet aaCs = AminoAcidCompoundSet.getAminoAcidCompoundSet();
-	private static DNASequence brca2Dna;
+	private static final AminoAcidCompoundSet aaCs = AminoAcidCompoundSet.aminoAcidCompoundSet;
+    private static DNASequence brca2Dna;
 	private static Sequence<AminoAcidCompound> brca2Pep;
 	private static Sequence<NucleotideCompound> volvoxDna;
 	private static Sequence<AminoAcidCompound> volvoxPep;
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreatorTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreatorTest.java
index 42a11ff7cb..88be79397f 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreatorTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreatorTest.java
@@ -33,7 +33,7 @@ public class CasePreservingProteinSequenceCreatorTest {
 
 	@Test
 	public void testConstructor() throws CompoundNotFoundException {
-		CasePreservingProteinSequenceCreator creator = new CasePreservingProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet());
+        CasePreservingProteinSequenceCreator creator = new CasePreservingProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet);
 
 		String seq = "aCDEfgHI-Jkl";
 		ProteinSequence prot = (ProteinSequence) creator.getSequence(seq, 0);
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java
index 1be322de07..6df7f1c31b 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java
@@ -68,7 +68,7 @@ public void testProcess() throws Exception {
 		Assert.assertNotNull(inStream);
 
 
-		FastaReader<ProteinSequence,AminoAcidCompound> fastaReader = new FastaReader<>(inStream, new GenericFastaHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+        FastaReader<ProteinSequence,AminoAcidCompound> fastaReader = new FastaReader<>(inStream, new GenericFastaHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet));
 		LinkedHashMap<String,ProteinSequence> proteinSequences = fastaReader.process();
 		inStream.close();
 
@@ -104,7 +104,7 @@ public void processIntTest() throws Exception {
 		logger.info("process(int)");
 		InputStream inStream = this.getClass().getResourceAsStream("/PF00104_small.fasta");
 		Assert.assertNotNull(inStream);
-		FastaReader<ProteinSequence,AminoAcidCompound> fastaReader = new FastaReader<>(inStream, new GenericFastaHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+        FastaReader<ProteinSequence,AminoAcidCompound> fastaReader = new FastaReader<>(inStream, new GenericFastaHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet));
 		LinkedHashMap<String,ProteinSequence> proteinSequences = fastaReader.process(200);
 
 		//Should have 200 sequences
@@ -160,10 +160,10 @@ public void testSmallFasta() throws IOException {
 
 		InputStream inStream = this.getClass().getResourceAsStream("/test.fasta");
 
-		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
+        FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
 				inStream,
 				new GenericFastaHeaderParser<>(),
-				new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+				new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet));
 
 		LinkedHashMap<String, ProteinSequence> b;
 
@@ -188,10 +188,10 @@ public void testSmallFasta2() throws IOException {
 
 		InputStream inStream = this.getClass().getResourceAsStream("/test.fasta");
 
-		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
+        FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
 				inStream,
 				new GenericFastaHeaderParser<>(),
-				new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+				new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet));
 
 
 		int nrSeq = 0;
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
index b04357f6ee..1ce4df936d 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
@@ -70,8 +70,8 @@ public void testProcess() throws Throwable {
 		 * Method 1: With the GenbankProxySequenceReader
 		 */
 		//Try with the GenbankProxySequenceReader
-		GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
-				= new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"), "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+        GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
+				= new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"), "NP_000257", AminoAcidCompoundSet.aminoAcidCompoundSet);
 		ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
 		genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
 		//logger.info("Sequence({},{}) = {}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
@@ -114,10 +114,10 @@ public void testProcess() throws Throwable {
 		logger.debug("DNA Sequence: {}", dnaSequences);
 
 
-		GenbankReader<ProteinSequence, AminoAcidCompound> protReader = new GenbankReader<>(
+        GenbankReader<ProteinSequence, AminoAcidCompound> protReader = new GenbankReader<>(
 				protResource.getInputStream(),
 				new GenericGenbankHeaderParser<>(),
-				new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())
+				new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet)
 		);
 		protSequences = protReader.process();
 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
index e94d8bc0f7..7795370994 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
@@ -97,11 +97,11 @@ public void testProcess() throws Exception {
 		InputStream inStream = this.getClass().getResourceAsStream("/BondFeature.gb");
 		assertNotNull(inStream);
 
-		GenbankReader<ProteinSequence, AminoAcidCompound> genbankProtein
+        GenbankReader<ProteinSequence, AminoAcidCompound> genbankProtein
 				= new GenbankReader<>(
 						inStream,
 						new GenericGenbankHeaderParser<>(),
-						new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())
+						new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet)
 				);
 
 		LinkedHashMap<String, ProteinSequence> proteinSequences = genbankProtein.process();
@@ -207,11 +207,11 @@ public void CDStest() throws Exception {
 		CheckableInputStream inStream = new CheckableInputStream(this.getClass().getResourceAsStream("/BondFeature.gb"));
 		assertNotNull(inStream);
 
-		GenbankReader<ProteinSequence, AminoAcidCompound> GenbankProtein
+        GenbankReader<ProteinSequence, AminoAcidCompound> GenbankProtein
 				= new GenbankReader<>(
 						inStream,
 						new GenericGenbankHeaderParser<>(),
-						new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())
+						new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet)
 				);
 		LinkedHashMap<String, ProteinSequence> proteinSequences = GenbankProtein.process();
 		assertTrue(inStream.isclosed());
@@ -260,11 +260,11 @@ private RNASequence readGenbankRNAResource(final String resource) throws IOExcep
 	
 	private ProteinSequence readGenbankProteinResource(final String resource) throws IOException, CompoundNotFoundException {
 		InputStream inputStream = getClass().getResourceAsStream(resource);
-		GenbankReader<ProteinSequence, AminoAcidCompound> genbankProtein
+        GenbankReader<ProteinSequence, AminoAcidCompound> genbankProtein
 		= new GenbankReader<>(
 				inputStream,
 				new GenericGenbankHeaderParser<>(),
-				new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())
+				new ProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet)
 				);
 		LinkedHashMap<String, ProteinSequence> proteinSequences = genbankProtein.process();
 		return proteinSequences.values().iterator().next();	
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankWriterTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankWriterTest.java
index 9ac1f1b830..33bfaced9c 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankWriterTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankWriterTest.java
@@ -49,8 +49,7 @@ public void testProcess() throws Exception {
 		//File dnaFile = new File("src/test/resources/NM_000266.gb");
 		LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence( inStream );
 		ByteArrayOutputStream fragwriter = new ByteArrayOutputStream();
-		ArrayList<DNASequence> seqs = new ArrayList<>();
-        seqs.addAll(dnaSequences.values());
+        ArrayList<DNASequence> seqs = new ArrayList<>(dnaSequences.values());
 		GenbankWriterHelper.writeNucleotideSequence(fragwriter, seqs,
 				GenbankWriterHelper.LINEAR_DNA);
 		//System.out.println(fragwriter.toString());
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
index edcba6c41b..a56cc6ecdd 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
@@ -127,7 +127,7 @@ public void testFeatures() throws IOException, InterruptedException, CompoundNot
 		GenbankProxySequenceReader<AminoAcidCompound> genbankReader
 				= new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"),
 						this.gi,
-						AminoAcidCompoundSet.getAminoAcidCompoundSet());
+				AminoAcidCompoundSet.aminoAcidCompoundSet);
 
 		// why only tests on protein sequences?
 		ProteinSequence seq = new ProteinSequence(genbankReader);
@@ -182,7 +182,7 @@ public void testProteinSequenceFactoring() throws Exception {
 		GenbankProxySequenceReader<AminoAcidCompound> genbankReader
 				= new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"),
 						this.gi,
-						AminoAcidCompoundSet.getAminoAcidCompoundSet());
+				AminoAcidCompoundSet.aminoAcidCompoundSet);
 
 		ProteinSequence seq = new ProteinSequence(genbankReader);
 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
index e7967abe81..438af45111 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
@@ -47,10 +47,10 @@ public void testWrongSequence() throws Exception {
 
 		String wrongGi = "34567";
 
-		GenbankProxySequenceReader<AminoAcidCompound> genbankReader
+        GenbankProxySequenceReader<AminoAcidCompound> genbankReader
 				= new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"),
 				wrongGi,
-				AminoAcidCompoundSet.getAminoAcidCompoundSet());
+                AminoAcidCompoundSet.aminoAcidCompoundSet);
 
 		ProteinSequence seq = new ProteinSequence(genbankReader);
 	}
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/TargetedLocationParserTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/TargetedLocationParserTest.java
index 0f0267c8de..1681619b3e 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/TargetedLocationParserTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/TargetedLocationParserTest.java
@@ -61,11 +61,11 @@ public Data(String gi, CompoundSet<?> originType, String Insdc, CompoundSet<?> c
 	public static Collection<Data[]> getLocations() {
 
 
-		Data[][] out = new Data[][]{
-			{new Data("7525057", AminoAcidCompoundSet.getAminoAcidCompoundSet(),
+        Data[][] out = new Data[][]{
+			{new Data("7525057", AminoAcidCompoundSet.aminoAcidCompoundSet,
 					"join(complement(NC_000932.1:69611..69724),NC_000932.1:139856..140087,NC_000932.1:140625..140650)", DNACompoundSet.getDNACompoundSet())},
 
-			{new Data("7525059", AminoAcidCompoundSet.getAminoAcidCompoundSet(),
+			{new Data("7525059", AminoAcidCompoundSet.aminoAcidCompoundSet,
 					"NC_000932.1:72371..73897", DNACompoundSet.getDNACompoundSet())},
 
 			{new Data("7525073", DNACompoundSet.getDNACompoundSet() ,
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
index 7efaf5de2f..4e5c14c44d 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
@@ -79,7 +79,7 @@ public void process(LinkedHashMap<String, ArrayList<String>> hits, LinkedHashMap
 				}
 				ArrayList<String> uniprotProteinHits = stringArrayListEntry.getValue();
 				String uniprotBestHit = uniprotProteinHits.get(0);
-				UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<>(uniprotBestHit, AminoAcidCompoundSet.getAminoAcidCompoundSet());
+                UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<>(uniprotBestHit, AminoAcidCompoundSet.aminoAcidCompoundSet);
 
 				ProteinSequence proteinSequence = new ProteinSequence(uniprotSequence);
 				String hitSequence = proteinSequence.getSequenceAsString();
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReader.java
index e6326dc29e..3fe2767711 100755
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReader.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqReader.java
@@ -26,7 +26,6 @@
 
 import java.io.*;
 import java.net.URL;
-import java.nio.charset.Charset;
 import java.nio.charset.StandardCharsets;
 import java.util.List;
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/Fastq.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/Fastq.java
index 2de9e05713..75fb3d4054 100755
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/Fastq.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/Fastq.java
@@ -141,7 +141,7 @@ public Fastq convertTo(final FastqVariant variant)
 	 *
 	 * @return a new FastqBuilder
 	 */
-	public static final FastqBuilder builder()
+	public static FastqBuilder builder()
 	{
 		return new FastqBuilder();
 	}
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqParser.java
index b636415775..1ba652c669 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqParser.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqParser.java
@@ -63,7 +63,7 @@ static void parse(final Readable readable, final ParseListener listener)
 	/**
 	 * FASTQ formatted sequence parser line processor.
 	 */
-	private static final class FastqParserLineProcessor implements LineProcessor<Object>
+	private static final class FastqParserLineProcessor implements LineProcessor<Void>
 	{
 		/** Parser state. */
 		private State state = State.DESCRIPTION;
@@ -114,22 +114,22 @@ private void setState(final State state)
 		}
 
 		@Override
-		public Object getResult()
+		public Void getResult()
 		{
 			return null;
 		}
 
 		@Override
-		public boolean processLine(final String line) throws IOException
+		public boolean processLine(String line) throws IOException
 		{
-			String sequence;
-			String quality;
+			line = line.trim();
+
 			switch (state)
 			{
 			case DESCRIPTION:
 				if (line.startsWith("@"))
 				{
-					listener.description(line.substring(1).trim());
+					listener.description(line.substring(1));
 					state = State.SEQUENCE;
 				}
 				else
@@ -138,28 +138,25 @@ public boolean processLine(final String line) throws IOException
 				}
 				break;
 			case SEQUENCE:
-				sequence = line.trim();
-				listener.sequence(sequence);
-				sequenceLength = sequence.length();
+				listener.sequence(line);
+				sequenceLength = line.length();
 				state = State.REPEAT_DESCRIPTION;
 				break;
 			case REPEAT_DESCRIPTION:
 				if (line.startsWith("+"))
 				{
-					listener.repeatDescription(line.substring(1).trim());
+					listener.repeatDescription(line.substring(1));
 					state = State.QUALITY;
 				}
 				else
 				{
-					sequence = line.trim();
-					listener.appendSequence(sequence);
-					sequenceLength += sequence.length();
+					listener.appendSequence(line);
+					sequenceLength += line.length();
 				}
 				break;
 			case QUALITY:
-				quality = line.trim();
-				listener.quality(quality);
-				qualityLength = quality.length();
+				listener.quality(line);
+				qualityLength = line.length();
 				state = State.COMPLETE;
 				break;
 			case COMPLETE:
@@ -169,7 +166,7 @@ public boolean processLine(final String line) throws IOException
 
 					if (line.startsWith("@"))
 					{
-						listener.description(line.substring(1).trim());
+						listener.description(line.substring(1));
 						state = State.SEQUENCE;
 					}
 					else
@@ -179,9 +176,8 @@ public boolean processLine(final String line) throws IOException
 				}
 				else
 				{
-					quality = line.trim();
-					listener.appendQuality(quality);
-					qualityLength += quality.length();
+					listener.appendQuality(line);
+					qualityLength += line.length();
 				}
 				break;
 			default:
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java
index b498fb0e86..84d3ea7279 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java
@@ -193,7 +193,7 @@ private void initAttributeHashMap(){
 	   String[] values = mAttributes.split(";");
 	   for(String attribute : values){
 		   attribute = attribute.trim();
-		   int equalindex = attribute.indexOf("=");
+		   int equalindex = attribute.indexOf('=');
 		   String splitData = "=";
 		   if(equalindex == -1) //gtf uses space and gff3 uses =
 			   splitData = " ";
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java
index 1910b0eee7..0d91c7259d 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java
@@ -455,7 +455,7 @@ public boolean hasAttribute(String key, String value) {
 	public String toString() {
 		StringBuilder  s = new StringBuilder("FeatureList: >>\n");
 		for (FeatureI f : this) {
-			s.append( f.seqname() + ":" + f.toString() + "\n");
+			s.append(f.seqname()).append(":").append(f.toString()).append("\n");
 		}
 
 		s.append("\n<<\n");
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
index 4e38a1a166..1f5a3f30c9 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
@@ -27,7 +27,6 @@
 import java.io.FileOutputStream;
 import java.io.OutputStream;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.LinkedHashMap;
 import java.util.Map;
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.java
index 2cd712b0a5..2b8851c311 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.java
@@ -24,7 +24,6 @@
 import org.slf4j.LoggerFactory;
 
 import java.io.*;
-import java.util.ListIterator;
 
 /**
  * http://www.bioperl.org/wiki/GTF
@@ -147,9 +146,9 @@ private static Feature parseLine(String s) {
 		end = s.indexOf('#', start);
 		String attributes;
 		if (end < 0) {
-			attributes = new String(s.substring(start));
+			attributes = s.substring(start);
 		} else {
-			attributes = new String(s.substring(start, end));
+			attributes = s.substring(start, end);
 		}
 		//need to add in attribute assignment for geneid where it just provides a gene name and will make it gtf like
 		attributes = "gene_id " + '"' + attributes + '"' + ";";
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.java
index 2808383979..c0c191d07a 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.java
@@ -147,9 +147,9 @@ private static Feature parseLine(String s) {
 		end = s.indexOf('#', start);
 		String attributes;
 		if (end < 0) {
-			attributes = new String(s.substring(start));
+			attributes = s.substring(start);
 		} else {
-			attributes = new String(s.substring(start, end));
+			attributes = s.substring(start, end);
 		}
 
 		return new Feature(seqname, source, type, location, score, frame, attributes);
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
index 483295572e..96b0ed6b18 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
@@ -835,7 +835,7 @@ public boolean isSameStrand( Location other )
 	@Override
 	public String toString()
 	{
-		return new String( "[L=" + (mEnd - mStart) + "; S=" + mStart + "; E=" + mEnd +"]" );
+		return "[L=" + (mEnd - mStart) + "; S=" + mStart + "; E=" + mEnd + "]";
 	}
 
 	/* (non-Javadoc)
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitFacade.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitFacade.java
index 6dbf1f0ba3..f90b33d4f2 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitFacade.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitFacade.java
@@ -28,7 +28,7 @@
  */
 public class TwoBitFacade {
 
-	private TwoBitParser twoBitParser;
+	private final TwoBitParser twoBitParser;
 
 
 	/**
@@ -43,7 +43,7 @@ public TwoBitFacade(File file) throws Exception {
 	/**
 	 *  Closes .2bit file twoBitParser.
 	 */
-	public void close() throws Exception {
+	public void close() {
 		if (twoBitParser != null)
 			twoBitParser.close();
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
index a241f2220c..0805920bae 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
@@ -100,7 +100,7 @@ private static String formatExonStructureForward(GeneChromosomePosition chromPos
 
 				s.append(" <-  Exon        : ").append(format(start + 1)).append(" - ").append(format(cdsEnd)).append(" | ").append(Integer.toString(cdsEnd - start)).append(" | ").append(Integer.toString(codingLength)).append(" | ").append(Integer.toString(codingLength % 3));
 				s.append(newline);
-				s.append("     UTR         : " + (cdsEnd +1) + " - " + format(end));
+				s.append("     UTR         : ").append(String.valueOf(cdsEnd + 1)).append(" - ").append(format(end));
 				s.append(newline);
 
 			} else if (inCoding) {
@@ -159,7 +159,7 @@ private static String formatExonStructureReverse(GeneChromosomePosition chromPos
 				}
 				codingLength += (cdsEnd - tmpstart);
 
-				s.append("     UTR         :" + format(cdsEnd + 1) + " | " + format(end));
+				s.append("     UTR         :").append(format(cdsEnd + 1)).append(" | ").append(format(end));
 				s.append(newline);
 				if (tmpstart == start)
 					s.append(" ->  ");
@@ -169,16 +169,16 @@ private static String formatExonStructureReverse(GeneChromosomePosition chromPos
 				s.append(newline);
 				// single exon with UTR on both ends
 				if (tmpstart != start)
-					s.append("     UTR         :" + format(cdsStart ) + " - " + format(start + 1));
+					s.append("     UTR         :").append(format(cdsStart)).append(" - ").append(format(start + 1));
 				s.append(newline);
 
 			} else if (start <= cdsStart && end >= cdsStart) {
 				inCoding = false;
 				codingLength += (end - cdsStart);
 
-				s.append(" <-  Exon        : " + format(cdsStart+1) + " - " + format(end) + " | " + (end - cdsStart) + " | " + codingLength + " | " + (codingLength % 3));
+				s.append(" <-  Exon        : ").append(format(cdsStart + 1)).append(" - ").append(format(end)).append(" | ").append(String.valueOf(end - cdsStart)).append(" | ").append(String.valueOf(codingLength)).append(" | ").append(String.valueOf(codingLength % 3));
 				s.append(newline);
-				s.append("     UTR         : " + format(start+1) + " - " + format(cdsStart ));
+				s.append("     UTR         : ").append(format(start + 1)).append(" - ").append(format(cdsStart));
 				s.append(newline);
 
 
@@ -186,7 +186,7 @@ private static String formatExonStructureReverse(GeneChromosomePosition chromPos
 				// full exon is coding
 				codingLength += (end - start);
 
-				s.append("     Exon        : " + format(start+1) + " - " + format(end) + " | " + (end - start) + " | " + codingLength + " | " + (codingLength % 3));
+				s.append("     Exon        : ").append(format(start + 1)).append(" - ").append(format(end)).append(" | ").append(String.valueOf(end - start)).append(" | ").append(String.valueOf(codingLength)).append(" | ").append(String.valueOf(codingLength % 3));
 				s.append(newline);
 			} else {
 				// e.g. see UBQLN3
@@ -335,16 +335,16 @@ public static ChromPos getChromPosReverse(int cdsPos, List<Integer> exonStarts,
 
 					StringBuilder b = new StringBuilder();
 
-					b.append("     UTR         :" + format(cdsEnd + 1) + " - " + format(end) + newline);
+					b.append("     UTR         :").append(format(cdsEnd + 1)).append(" - ").append(format(end)).append(newline);
 					if (tmpstart == start)
 						b.append(" ->  ");
 					else
 						b.append(" <-> ");
-					b.append("Exon        :" + format(tmpstart + 1) + " - " + (cdsEnd) + " | " + format(cdsEnd - tmpstart + 1) + " - " + codingLength + " | " + (codingLength % 3) + newline);
+					b.append("Exon        :").append(format(tmpstart + 1)).append(" - ").append(cdsEnd).append(" | ").append(format(cdsEnd - tmpstart + 1)).append(" - ").append(codingLength).append(" | ").append(codingLength % 3).append(newline);
 
 					// single exon with UTR on both ends
 					if (tmpstart != start)
-						b.append("     UTR         :" + format(cdsStart) + " - " + format(start + 1) + newline);
+						b.append("     UTR         :").append(format(cdsStart)).append(" - ").append(format(start + 1)).append(newline);
 
 					logger.debug(b.toString());
 				}
@@ -678,7 +678,7 @@ private static List<Range<Integer>> getCDSExonRangesReverse(GeneChromosomePositi
 
 				codingLength += (end - cdsStart);
 				if  (debug) {
-					s.append(" <-  Exon        : " + format(cdsStart + 1) + " - " + format(end) + " | " + (end - cdsStart) + " | " + codingLength + " | " + (codingLength % 3));
+					s.append(" <-  Exon        : ").append(format(cdsStart + 1)).append(" - ").append(format(end)).append(" | ").append(end - cdsStart).append(" | ").append(codingLength).append(" | ").append(codingLength % 3);
 					s.append(newline);
 					s.append("     UTR         : ").append(format(start + 1)).append(" - ").append(format(cdsStart));
 					s.append(newline);
@@ -694,13 +694,13 @@ private static List<Range<Integer>> getCDSExonRangesReverse(GeneChromosomePositi
 
 				codingLength += (end - start);
 				if  (debug) {
-					s.append("     Exon        : " + format(start + 1) + " - " + format(end) + " | " + (end - start) + " | " + codingLength + " | " + (codingLength % 3));
+					s.append("     Exon        : ").append(format(start + 1)).append(" - ").append(format(end)).append(" | ").append(end - start).append(" | ").append(codingLength).append(" | ").append(codingLength % 3);
 					s.append(newline);
 				}
 			} else {
 				// e.g. see UBQLN3
 				if ( debug ) {
-					s.append(" no translation! UTR: " + format(start) + " - " + format(end));
+					s.append(" no translation! UTR: ").append(format(start)).append(" - ").append(format(end));
 					s.append(newline);
 				}
 			}
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java
index ff733d1d06..fa7a4f6dfb 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java
@@ -61,7 +61,7 @@ public static void processNucleotides(File fastaFileName, String uniqueid, File
 
 		public static void main( String[] args ){
 		try{
-			SplitFasta splitFasta = new SplitFasta();
+//			SplitFasta splitFasta = new SplitFasta();
 			SplitFasta.processNucleotides(new File("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/454Scaffolds.fna"), "", new File("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/individual"));
 		}catch(Exception e){
 			logger.error("Exception: ", e);
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java
index 3016dc7737..170030616b 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java
@@ -140,7 +140,7 @@ private boolean compareRmsd(double rmsdOrig, double rmsdNew) {
 	}
 
 	private void compareBlock(int blockNr, AFPChain afpChain, AFPChain newChain,
-			Atom[] ca1, Atom[] ca2) throws StructureException {
+			Atom[] ca1, Atom[] ca2) {
 
 
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestOutputStrings.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestOutputStrings.java
index e50d0c3135..0b9c1a7c4a 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestOutputStrings.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestOutputStrings.java
@@ -207,10 +207,10 @@ public void test1buz1aliFlexible(){
 		String pdb2 = "1ali";
 		String chain2 ="A";
 
-		String originalOutput = "Align 1buzA.pdb 116 with 1aliA.pdb 446" + newline + "Twists 1 ini-len 64 ini-rmsd 3.12 opt-equ 88 opt-rmsd 3.34 chain-rmsd 5.32 Score 103.72 align-len 199 gaps 111 (55.78%)" + newline + "P-value 3.26e-01 Afp-num 15578 Identity 6.25% Similarity 25.89%" + newline + "Block  0 afp  1 score 23.14 rmsd  0.76 gap 0 (0.00%)" + newline + "Block  1 afp  7 score 100.08 rmsd  3.32 gap 17 (0.23%)" + newline + "" + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:    5 DMNVKESVLCIRLTGELDH---------------------------------HTAETLKQKVTQSLEKDD" + newline + "              1 11111111111111                                    222222222222222222" + newline + "Chain 2:  246 VTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEK" + newline + "" + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:   42 IRHIVLNLEDLS------------FMDSSGLGVILGRYKQIK-QIGGEMVVCAISPAVKRLFDMSGLFKI" + newline + "              222222222222            222222222222222222 2222222222222              " + newline + "Chain 2:  316 GFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPG" + newline + "" + newline + "                  .    :    .    :    .    :    .    :    .    :    ." + newline + "Chain 1:   99 I---------------------------------RFEQSE--------QQALLTLGVAS" + newline + "                                                22            222222 2222" + newline + "Chain 2:  386 LTQALNTKDGAVMVMSYGNSEEDSQENTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKA" + newline + newline + "Note: positions are from PDB; the numbers between alignments are block index" + newline;
+		String originalOutput = "Align 1buzA.pdb 116 with 1aliA.pdb 446" + newline + "Twists 1 ini-len 64 ini-rmsd 3.12 opt-equ 88 opt-rmsd 3.34 chain-rmsd 5.32 Score 103.72 align-len 199 gaps 111 (55.78%)" + newline + "P-value 3.26e-01 Afp-num 15578 Identity 6.25% Similarity 25.89%" + newline + "Block  0 afp  1 score 23.14 rmsd  0.76 gap 0 (0.00%)" + newline + "Block  1 afp  7 score 100.08 rmsd  3.32 gap 17 (0.23%)" + newline + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:    5 DMNVKESVLCIRLTGELDH---------------------------------HTAETLKQKVTQSLEKDD" + newline + "              1 11111111111111                                    222222222222222222" + newline + "Chain 2:  246 VTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEK" + newline + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:   42 IRHIVLNLEDLS------------FMDSSGLGVILGRYKQIK-QIGGEMVVCAISPAVKRLFDMSGLFKI" + newline + "              222222222222            222222222222222222 2222222222222              " + newline + "Chain 2:  316 GFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPG" + newline + newline + "                  .    :    .    :    .    :    .    :    .    :    ." + newline + "Chain 1:   99 I---------------------------------RFEQSE--------QQALLTLGVAS" + newline + "                                                22            222222 2222" + newline + "Chain 2:  386 LTQALNTKDGAVMVMSYGNSEEDSQENTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKA" + newline + newline + "Note: positions are from PDB; the numbers between alignments are block index" + newline;
 
 		String result = MyTestHelper.compareAlignment(pdb1, chain1, pdb2, chain2, originalOutput,false);
-		if (! result.equals("")){
+		if (!result.isEmpty()){
 			String msg = "the created alignment images are not identical! ";
 			printMismatch(originalOutput,result);
 			printFirstMismatch(result, originalOutput);
@@ -306,9 +306,9 @@ public void test1a641hngFlexible(){
 		String pdb2 = "1hng";
 		String chain2 ="B";
 
-		String originalOutput= "Align 1a64A.pdb 94 with 1hngB.pdb 175" + newline + "Twists 1 ini-len 88 ini-rmsd 1.84 opt-equ 94 opt-rmsd 0.64 chain-rmsd 20.77 Score 235.94 align-len 96 gaps 2 (2.08%)" + newline + "P-value 4.23e-13 Afp-num 6497 Identity 98.94% Similarity 100.00%" + newline + "Block  0 afp  5 score 118.80 rmsd  0.75 gap 0 (0.00%)" + newline + "Block  1 afp  6 score 143.14 rmsd  0.46 gap 0 (0.00%)" + newline + "" + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:    4 GTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKR--KPFLKSGAFEILANGDLKIKNLTRDDS" + newline + "              11111111111111111111111111111111111111111  222222222222222222222222222" + newline + "Chain 2:    4 GTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKMKPFLKSGAFEILANGDLKIKNLTRDDS" + newline + "" + newline + "                  .    :    .    :    ." + newline + "Chain 1:   74 GTYNVTVYSTNGTRILDKALDLRILE" + newline + "              22222222222222222222222222" + newline + "Chain 2:   74 GTYNVTVYSTNGTRILNKALDLRILE" + newline + newline + "Note: positions are from PDB; the numbers between alignments are block index" + newline;
+		String originalOutput= "Align 1a64A.pdb 94 with 1hngB.pdb 175" + newline + "Twists 1 ini-len 88 ini-rmsd 1.84 opt-equ 94 opt-rmsd 0.64 chain-rmsd 20.77 Score 235.94 align-len 96 gaps 2 (2.08%)" + newline + "P-value 4.23e-13 Afp-num 6497 Identity 98.94% Similarity 100.00%" + newline + "Block  0 afp  5 score 118.80 rmsd  0.75 gap 0 (0.00%)" + newline + "Block  1 afp  6 score 143.14 rmsd  0.46 gap 0 (0.00%)" + newline + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:    4 GTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKR--KPFLKSGAFEILANGDLKIKNLTRDDS" + newline + "              11111111111111111111111111111111111111111  222222222222222222222222222" + newline + "Chain 2:    4 GTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKMKPFLKSGAFEILANGDLKIKNLTRDDS" + newline + newline + "                  .    :    .    :    ." + newline + "Chain 1:   74 GTYNVTVYSTNGTRILDKALDLRILE" + newline + "              22222222222222222222222222" + newline + "Chain 2:   74 GTYNVTVYSTNGTRILNKALDLRILE" + newline + newline + "Note: positions are from PDB; the numbers between alignments are block index" + newline;
 		String result = MyTestHelper.compareAlignment(pdb1, chain1, pdb2, chain2, originalOutput,false);
-		if (! result.equals("")){
+		if (!result.isEmpty()){
 			String msg = "the created alignment images are not identical! ";
 			printMismatch(originalOutput,result);
 			printFirstMismatch(result, originalOutput);
@@ -472,10 +472,10 @@ public void test1a211hwgFlexible(){
 		String pdb2 = "1hwg";
 		String chain2 ="C";
 
-		String originalOutput= "Align 1a21A.pdb 194 with 1hwgC.pdb 191" + newline + "Twists 1 ini-len 120 ini-rmsd 3.04 opt-equ 150 opt-rmsd 2.96 chain-rmsd 4.21 Score 233.34 align-len 210 gaps 60 (28.57%)" + newline + "P-value 1.15e-05 Afp-num 12696 Identity 11.98% Similarity 23.95%" + newline + "Block  0 afp  4 score 66.42 rmsd  2.03 gap 6 (0.16%)" + newline + "Block  1 afp 11 score 184.29 rmsd  3.24 gap 69 (0.44%)" + newline + "" + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:    6 RAYNLTWKSTN-FKTILEWEPKSIDHVYTVQISTRLENWKSKCFLTAE---TECDLTDEVVKDVGQTYMA" + newline + "              11111111111 111111111     111111111111111111       222222222   222222 " + newline + "Chain 2:   32 EPKFTKCRSPERETFSCHWTD-----PIQLFYTRRNQEWKECPDYVSAGENSCYFNSSFT---SIWIPYC" + newline + "" + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:   72 RVLSYPARNTTGFPEEPPFRNSPEFTPYLDTNLGQPTIQSFEQVG-------TKLNVTVQDARTLVTFLS" + newline + "                                    22222222222222222222222       222222222222   222" + newline + "Chain 2:  109 IKLTSNGGTVDE----------KCFSVDEIVQPDPPIALNWTLLNVSLTGIHADIQVRWEAPRN---ADI" + newline + "" + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:  141 LRAVFGKDLNYTLYYWR-----KKTAT-TNTNEFLIDVDKGE-NYCFSVQAVIPSRKRKQRSPESLTECT" + newline + "              222222  222222222     22222 22222222222222 2222222222222  222222222222" + newline + "Chain 2:  166 QKGWMV--LEYELQYKEVNETKWKMMDPILTTSVPVYSLKVDKEYEVRVRSKQRNS--GNYGEFSEVLYV" + newline + newline + "Note: positions are from PDB; the numbers between alignments are block index" + newline;
+		String originalOutput= "Align 1a21A.pdb 194 with 1hwgC.pdb 191" + newline + "Twists 1 ini-len 120 ini-rmsd 3.04 opt-equ 150 opt-rmsd 2.96 chain-rmsd 4.21 Score 233.34 align-len 210 gaps 60 (28.57%)" + newline + "P-value 1.15e-05 Afp-num 12696 Identity 11.98% Similarity 23.95%" + newline + "Block  0 afp  4 score 66.42 rmsd  2.03 gap 6 (0.16%)" + newline + "Block  1 afp 11 score 184.29 rmsd  3.24 gap 69 (0.44%)" + newline + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:    6 RAYNLTWKSTN-FKTILEWEPKSIDHVYTVQISTRLENWKSKCFLTAE---TECDLTDEVVKDVGQTYMA" + newline + "              11111111111 111111111     111111111111111111       222222222   222222 " + newline + "Chain 2:   32 EPKFTKCRSPERETFSCHWTD-----PIQLFYTRRNQEWKECPDYVSAGENSCYFNSSFT---SIWIPYC" + newline + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:   72 RVLSYPARNTTGFPEEPPFRNSPEFTPYLDTNLGQPTIQSFEQVG-------TKLNVTVQDARTLVTFLS" + newline + "                                    22222222222222222222222       222222222222   222" + newline + "Chain 2:  109 IKLTSNGGTVDE----------KCFSVDEIVQPDPPIALNWTLLNVSLTGIHADIQVRWEAPRN---ADI" + newline + newline + "                  .    :    .    :    .    :    .    :    .    :    .    :    .    :" + newline + "Chain 1:  141 LRAVFGKDLNYTLYYWR-----KKTAT-TNTNEFLIDVDKGE-NYCFSVQAVIPSRKRKQRSPESLTECT" + newline + "              222222  222222222     22222 22222222222222 2222222222222  222222222222" + newline + "Chain 2:  166 QKGWMV--LEYELQYKEVNETKWKMMDPILTTSVPVYSLKVDKEYEVRVRSKQRNS--GNYGEFSEVLYV" + newline + newline + "Note: positions are from PDB; the numbers between alignments are block index" + newline;
 
 		String result = MyTestHelper.compareAlignment(pdb1, chain1, pdb2, chain2, originalOutput,false);
-		if (! result.equals("")){
+		if (!result.isEmpty()){
 			String msg = "the created alignment images are not identical! ";
 			printMismatch(originalOutput,result);
 			printFirstMismatch(result, originalOutput);
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java
index d8ae01bc2a..cbd5dda443 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java
@@ -107,6 +107,7 @@ private static int testVersion(String ecodVersion) throws IOException {
 			for(ResidueRange r : ranges) {
 				if( r == null ) {
 					clean = false;
+					break;
 				}
 			}
 			if( ! clean ) {
@@ -166,6 +167,7 @@ private static int testVersion(String ecodVersion) throws IOException {
 			for(ResidueRange r : ranges) {
 				if( r == null ) {
 					clean = false;
+					break;
 				}
 			}
 			if( ! clean ) {
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java
index 6450f9ed44..4346adcf2d 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java
@@ -229,7 +229,10 @@ private void testStructureMethods(Structure sPdb, Structure sCif) {
 		// sugar polymers are not in pdb at all: we avoid them
 		boolean canCompareEntityCounts = true;
 		for (EntityInfo e:sCif.getEntityInfos()) {
-			if (e.getDescription().contains("SUGAR")) canCompareEntityCounts = false;
+			if (e.getDescription().contains("SUGAR")) {
+				canCompareEntityCounts = false;
+				break;
+			}
 		}
 		if (canCompareEntityCounts) {
 			int entCountCif = 0;
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java b/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java
index 7452b9b737..a993a42ace 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java
@@ -86,7 +86,7 @@ public File[] getLocalFiles(){
 		for ( String f : rfiles) {
 
 
-			int slashIndex = f.lastIndexOf("/");
+			int slashIndex = f.lastIndexOf('/');
 
 			String fileName = f.substring(slashIndex);
 
@@ -135,7 +135,7 @@ public void download(){
 			try {
 
 
-				int slashIndex = f.lastIndexOf("/");
+				int slashIndex = f.lastIndexOf('/');
 
 				String fileName = f.substring(slashIndex);
 
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Site.java b/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Site.java
index d22cce8ff2..bb3c1f52e4 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Site.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Site.java
@@ -132,8 +132,7 @@ public static List<Site> parseSites(File f) throws IOException {
 	private static List<String> parseHeaderFields(String line) {
 		String[] spl = line.split("\t");
 
-		List<String> h = new ArrayList<>();
-        h.addAll(Arrays.asList(spl));
+        List<String> h = new ArrayList<>(Arrays.asList(spl));
 
 		return h;
 	}
@@ -215,24 +214,22 @@ public void setOrganism(String organism) {
 	public String toString() {
 		StringBuilder s = new StringBuilder();
 
-		s.append("Site{" +
-				"protein='" + protein + '\'');
+		s.append("Site{" + "protein='").append(protein).append('\'');
 		if ( uniprot != null)
-				s.append(", uniprot='" + uniprot + '\'' );
+				s.append(", uniprot='").append(uniprot).append('\'');
 		if ( geneSymb != null)
-			s.append(
-				", geneSymb='" + geneSymb + '\'' );
+			s.append(", geneSymb='").append(geneSymb).append('\'');
 		if (chrLoc != null)
-				s.append(", chrLoc='" + chrLoc + '\'' );
+				s.append(", chrLoc='").append(chrLoc).append('\'');
 		if (modType != null)
-			s.append(", modType='" + modType + '\'' );
+			s.append(", modType='").append(modType).append('\'');
 
 		if (residue != null)
-			s.append(        ", residue='" + residue + '\'' );
+			s.append(", residue='").append(residue).append('\'');
 		if ( group != null)
-				s.append(", group='" + group + '\'' );
+				s.append(", group='").append(group).append('\'');
 		if (organism != null)
-			s.append(", organism='" + organism + '\'' );
+			s.append(", organism='").append(organism).append('\'');
 
 		  s.append(      '}');
 
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java
index cb795276a9..df0d78e6d2 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java
@@ -31,7 +31,6 @@
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
 import org.xml.sax.SAXParseException;
 
 import javax.xml.parsers.DocumentBuilder;
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java
index 2f2fc65983..357d112c02 100644
--- a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java
+++ b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java
@@ -79,7 +79,7 @@ private File getLocalFileName(String phosphoSiteFileLocation){
 				fail("Could not create directory " + localDir.getAbsolutePath());
 		}
 
-		int slashIndex = phosphoSiteFileLocation.lastIndexOf("/");
+		int slashIndex = phosphoSiteFileLocation.lastIndexOf('/');
 
 		String fileName = phosphoSiteFileLocation.substring(slashIndex);
 
diff --git a/biojava-ontology/src/main/java/demo/ParseGO.java b/biojava-ontology/src/main/java/demo/ParseGO.java
index b3397bccb3..827a7e699e 100644
--- a/biojava-ontology/src/main/java/demo/ParseGO.java
+++ b/biojava-ontology/src/main/java/demo/ParseGO.java
@@ -34,7 +34,6 @@
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.net.URL;
-import java.util.Iterator;
 import java.util.Set;
 
 public class ParseGO {
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntoTools.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntoTools.java
index cd83cc2372..c7b548e215 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntoTools.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/OntoTools.java
@@ -73,7 +73,7 @@ public final class OntoTools {
 	public static final Term PARTIAL_ORDER;
 
 	static {
-		DEFAULT_FACTORY = (name, desc) -> new Ontology.Impl(name, desc);
+		DEFAULT_FACTORY = Ontology.Impl::new;
 
 		try {
 			BufferedReader reader = new BufferedReader(
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java
index 0f861ed00d..55471c7926 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java
@@ -42,7 +42,7 @@ public Ontology parseGO(BufferedReader goFile,
 							String ontoName,
 							String ontoDescription,
 							OntologyFactory factory)
-		throws ParseException, IOException
+		throws IOException
 	{
 		try {
 			Ontology onto = factory.createOntology(ontoName, ontoDescription);
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/OboParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/OboParser.java
index 940a25bd3e..093f292d66 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/OboParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/OboParser.java
@@ -24,15 +24,11 @@
 package org.biojava.nbio.ontology.io;
 
 import org.biojava.nbio.ontology.*;
-import org.biojava.nbio.ontology.obo.OboFileEventListener;
 import org.biojava.nbio.ontology.obo.OboFileHandler;
 import org.biojava.nbio.ontology.obo.OboFileParser;
 
 import java.io.BufferedReader;
 import java.io.IOException;
-import java.text.ParseException;
-
-
 
 
 /** Parses an OBO file.
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java
index 22ab4749ef..f035375236 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java
@@ -86,11 +86,9 @@ public class TabDelimParser {
 	 * @param of  an OntologyFactory used to create the Ontology instance
 	 * @return  a new Ontology
 	 * @throws IOException if there is some problem with the buffered reader
-	 * @throws OntologyException if it was not possible to instantiate a new
-	 *         ontology
-	 */
+     */
 	public Ontology parse(BufferedReader in, OntologyFactory of)
-	throws IOException, OntologyException {
+	throws IOException {
 		String name = "";
 		String description = "";
 		Ontology onto = null;
@@ -139,8 +137,8 @@ public Ontology parse(BufferedReader in, OntologyFactory of)
 						Term objT = resolveTerm(object, onto);
 						Term relT = resolveTerm(predicate, onto);
 
-						Triple trip = resolveTriple(subT, objT, relT, onto);
-						trip = trip; // prevent unused field error
+						/*Triple trip =*/ resolveTriple(subT, objT, relT, onto);
+						//trip = trip; // prevent unused field error
 					} catch (StringIndexOutOfBoundsException e) {
 						throw new IOException("Could not parse line: " + line);
 					}
@@ -159,8 +157,8 @@ private Term resolveTerm(String termName, Ontology onto) {
 		} else {
 			try {
 				if(isTrippleTerm) {
-					int c1 = termName.indexOf(",");
-					int c2 = termName.indexOf(",", c1 + 1);
+					int c1 = termName.indexOf(',');
+					int c2 = termName.indexOf(',', c1 + 1);
 
 					String source = termName.substring(1, c1);
 					String target = termName.substring(c2 + 1, termName.length() - 1);
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
index 90d6f466c8..06d79205fd 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
@@ -82,9 +82,9 @@ public class OboFileParser {
 		escapeChars.put('[', '[');
 		escapeChars.put(']', ']');
 		escapeChars.put('!', '!');
-		for (Character key : escapeChars.keySet()) {
-			Character value = escapeChars.get(key);
-			unescapeChars.put(value, key);
+		for (Map.Entry<Character, Character> entry : escapeChars.entrySet()) {
+			Character value = entry.getValue();
+			unescapeChars.put(value, entry.getKey());
 		}
 	}
 
@@ -276,8 +276,6 @@ private Synonym parseSynonym(String key, String value) throws IOException{
 			if (i == 0) {
 				switch (token) {
 					case "RELATED":
-						scope = Synonym.RELATED_SYNONYM;
-						break;
 					case "UNSPECIFIED":
 						scope = Synonym.RELATED_SYNONYM;
 						break;
diff --git a/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestOboFileParsing.java b/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestOboFileParsing.java
index 6fc38eb944..e7f1e7ab91 100644
--- a/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestOboFileParsing.java
+++ b/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestOboFileParsing.java
@@ -34,7 +34,7 @@
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.util.Set;
-import java.util.Iterator;
+
 import org.biojava.nbio.ontology.utils.Annotation;
 
 public class TestOboFileParsing {
diff --git a/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java b/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java
index b9fe2df034..cb12e10109 100644
--- a/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java
+++ b/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java
@@ -35,7 +35,7 @@
 public class TestParseOBO {
 
 	@Test
-	public void testNamespace() throws IOException, ParseException {
+	public void testNamespace() throws IOException {
 
 		String testTermEntry = "\n[Term]\n" +
 		"id: SO:0000691\n" +
diff --git a/biojava-protein-disorder/src/main/java/demo/PredictDisorder.java b/biojava-protein-disorder/src/main/java/demo/PredictDisorder.java
index 1678ebd418..7fad8197d8 100644
--- a/biojava-protein-disorder/src/main/java/demo/PredictDisorder.java
+++ b/biojava-protein-disorder/src/main/java/demo/PredictDisorder.java
@@ -36,7 +36,7 @@ public static void main(String[] args) throws Exception{
 
 		ProteinSequence seq = getUniprot(uniprotID);
 		System.out.println("Protein Sequence: "+ seq.toString());
-		AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.aminoAcidCompoundSet;
 
 		if (!compoundSet.isValidSequence(seq) ) {
 			System.err.println("Invalid sequence, exiting");
@@ -58,7 +58,7 @@ public static void main(String[] args) throws Exception{
 	 */
 	private static ProteinSequence getUniprot(String uniProtID) throws Exception {
 
-		AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet set = AminoAcidCompoundSet.aminoAcidCompoundSet;
 		UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<>(uniProtID, set);
 
 		ProteinSequence seq = new ProteinSequence(uniprotSequence);
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/NullOutputStream.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/NullOutputStream.java
index 3b9395fdd6..cfcae3d36e 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/NullOutputStream.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/NullOutputStream.java
@@ -27,7 +27,6 @@
 
 package org.biojava.nbio.ronn;
 
-import java.io.IOException;
 import java.io.OutputStream;
 
 /**
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java
index e5ef18de4c..fe4dcaef12 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java
@@ -139,7 +139,7 @@ public void getScores(final File outfile) throws FileNotFoundException {
 	}
 
 	// sResidue query sequence index and dIndex database sequence index
-	private final float[] align(final int sResidue, final int dIndex) {
+	private float[] align(final int sResidue, final int dIndex) {
 	int dResidue, r;
 	float maxScore = -1000000;
 	float rho1;
diff --git a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
index 6c8dca3379..e71e4351b5 100644
--- a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
+++ b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
@@ -69,7 +69,7 @@ private void testUniprot(String uniprotID) throws CompoundNotFoundException, IOE
 
 		ProteinSequence seq = getUniprot(uniprotID);
 
-		AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.aminoAcidCompoundSet;
 
 /*		for (AminoAcidCompound compound : seq) {
 			System.out.println(compound.getShortName() + " " + compound.getLongName() + " " + compound.getDescription() + " | " + compoundSet.getEquivalentCompounds(compound) + " " + compound.getMolecularWeight() + " " + compound.getBase());
@@ -94,7 +94,7 @@ private void testUniprot(String uniprotID) throws CompoundNotFoundException, IOE
 	 */
 	private static ProteinSequence getUniprot(String uniProtID) throws CompoundNotFoundException, IOException {
 
-		AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet set = AminoAcidCompoundSet.aminoAcidCompoundSet;
 		UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence =
 				new UniprotProxySequenceReader<>(uniProtID, set);
 
diff --git a/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java b/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java
index 97f32828be..8eec576679 100644
--- a/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java
+++ b/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java
@@ -26,7 +26,6 @@
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.StructureAlignment;
 import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay;
@@ -37,8 +36,6 @@
 import org.biojava.nbio.structure.io.FastaAFPChainConverter;
 import org.biojava.nbio.structure.io.FastaStructureParser;
 
-import java.io.IOException;
-
 /**
  * Demo displaying a structural alignment from a FASTA file using {@link FastaAFPChainConverter}.
  *
diff --git a/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java b/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
index c63afe6cf0..8535e7c0a9 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
@@ -23,7 +23,6 @@
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.UnsupportedEncodingException;
 import java.nio.charset.StandardCharsets;
 
 import org.biojava.nbio.core.sequence.ProteinSequence;
@@ -54,7 +53,7 @@
  */
 public class DemoAlignmentFromFasta {
 
-	public static void getAlignmentFromFasta() throws StructureException {
+	public static void getAlignmentFromFasta() {
 
 		// Load a test sequence
 		// Normally this would come from a file, eg
@@ -83,7 +82,7 @@ public static void getAlignmentFromFasta() throws StructureException {
 		AtomCache cache = new AtomCache();
 
 		// Create SequenceCreator. This converts a String to a ProteinSequence
-		AminoAcidCompoundSet aaSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet aaSet = AminoAcidCompoundSet.aminoAcidCompoundSet;
 		SequenceCreatorInterface<AminoAcidCompound> creator;
 		creator = new CasePreservingProteinSequenceCreator(aaSet);
 
diff --git a/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java b/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java
index 6deb62bf8c..8fa4594ee2 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java
@@ -24,7 +24,6 @@
 import java.util.Arrays;
 import java.util.List;
 import java.util.ArrayList;
-import java.util.concurrent.ExecutionException;
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
diff --git a/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java b/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java
index 8f31e5ce66..238c85b9f4 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java
@@ -37,7 +37,6 @@
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.UnsupportedEncodingException;
 import java.nio.charset.StandardCharsets;
 
 /**
@@ -75,7 +74,7 @@ public static void getStructureFromFasta() {
 		AtomCache cache = new AtomCache();
 
 		// Create SequenceCreator. This converts a String to a ProteinSequence
-		AminoAcidCompoundSet aaSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet aaSet = AminoAcidCompoundSet.aminoAcidCompoundSet;
 		SequenceCreatorInterface<AminoAcidCompound> creator;
 		creator = new ProteinSequenceCreator(aaSet);
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AboutDialog.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AboutDialog.java
index d364e00343..afa66cb16d 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AboutDialog.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AboutDialog.java
@@ -26,10 +26,7 @@
 
 import javax.swing.*;
 import javax.swing.event.HyperlinkEvent;
-import javax.swing.event.HyperlinkListener;
 import java.awt.*;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 
 public class AboutDialog
 {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java
index f40ecfe9a2..e57d3ce862 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java
@@ -447,14 +447,14 @@ private void calcDBSearch() {
 		}
 
 		String name1 = s.getName();
-		if ( name1 == null || name1.equals(""))
+		if ( name1 == null || name1.isEmpty())
 			name1 = s.getPDBCode();
 
 
 
 		System.out.println("name1 in alig gui:" + name1);
 		String file = dbsearch.getOutFileLocation();
-		if ( file == null || file.equals("") ){
+		if ( file == null || file.isEmpty()){
 			JOptionPane.showMessageDialog(null,"Please select a directory to contain the DB search results.");
 			return;
 		}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBSearchGUI.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBSearchGUI.java
index a17bb5cab4..b1dbd9dfcb 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBSearchGUI.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBSearchGUI.java
@@ -31,8 +31,6 @@
 import org.biojava.nbio.structure.gui.util.ScopSelectPanel;
 
 import javax.swing.*;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 import java.io.File;
 
 public class DBSearchGUI extends JPanel {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
index ddab5d5a5f..43acfb5108 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
@@ -54,7 +54,7 @@ public class DisplayAFP {
 	private static final Logger logger = LoggerFactory.getLogger(DisplayAFP.class);
 
 	//TODO: same as getEqrPos??? !!!
-	public static final List<Integer> getEQRAlignmentPos(AFPChain afpChain){
+	public static List<Integer> getEQRAlignmentPos(AFPChain afpChain){
 		List<Integer> lst = new ArrayList<>();
 
 		char[] s1 = afpChain.getAlnseq1();
@@ -105,7 +105,7 @@ private static boolean isAlignedPosition(int i, char c1, char c2, boolean isFatC
 	 * @param afpChain
 	 * @param ca
 	 */
-	public static final List<String> getPDBresnum(int aligPos, AFPChain afpChain, Atom[] ca){
+	public static List<String> getPDBresnum(int aligPos, AFPChain afpChain, Atom[] ca){
 		List<String> lst = new ArrayList<>();
 		if ( aligPos > 1) {
 			System.err.println("multiple alignments not supported yet!");
@@ -144,7 +144,7 @@ public static final List<String> getPDBresnum(int aligPos, AFPChain afpChain, At
 	 * @param getPrevious gives the previous position if false, gives the next posible atom
 	 * @return a CA atom that is at a particular position of the alignment
 	 */
-	public static final Atom getAtomForAligPos(AFPChain afpChain,int chainNr, int aligPos, Atom[] ca , boolean getPrevious ) throws StructureException{
+	public static Atom getAtomForAligPos(AFPChain afpChain, int chainNr, int aligPos, Atom[] ca , boolean getPrevious ) throws StructureException{
 		int[] optLen = afpChain.getOptLen();
 		// int[][][] optAln = afpChain.getOptAln();
 
@@ -311,7 +311,7 @@ private static int getNextFatCatPos(AFPChain afpChain, int chainNr,
 
 	}
 
-	private static final int getUngappedFatCatPos(AFPChain afpChain, int chainNr, int aligPos){
+	private static int getUngappedFatCatPos(AFPChain afpChain, int chainNr, int aligPos){
 		char[] aseq;
 		if ( chainNr == 0 )
 			aseq = afpChain.getAlnseq1();
@@ -404,7 +404,7 @@ private static final int getUngappedFatCatPos(AFPChain afpChain, int chainNr, in
 	 * @param hetatms
 	 * @return
 	 */
-	public static final Atom[] getAtomArray(Atom[] ca,List<Group> hetatms ) {
+	public static Atom[] getAtomArray(Atom[] ca, List<Group> hetatms ) {
 		List<Atom> atoms = new ArrayList<>();
 		Collections.addAll(atoms, ca);
 
@@ -432,7 +432,7 @@ public static final Atom[] getAtomArray(Atom[] ca,List<Group> hetatms ) {
 	/** Note: ca2, hetatoms2 and nucleotides2 should not be rotated. This will be done here...
 	 * */
 
-	public static final StructureAlignmentJmol display(AFPChain afpChain,Group[] twistedGroups, Atom[] ca1, Atom[] ca2,List<Group> hetatms1, List<Group> hetatms2 ) throws StructureException {
+	public static StructureAlignmentJmol display(AFPChain afpChain, Group[] twistedGroups, Atom[] ca1, Atom[] ca2, List<Group> hetatms1, List<Group> hetatms2 ) {
 
 		List<Atom> twistedAs = new ArrayList<>();
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/HelpDialog.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/HelpDialog.java
index 26f1bd540f..81113bc20c 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/HelpDialog.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/HelpDialog.java
@@ -29,10 +29,7 @@
 
 import javax.swing.*;
 import javax.swing.event.HyperlinkEvent;
-import javax.swing.event.HyperlinkListener;
 import java.awt.*;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 
 public class HelpDialog {
 	Box vBox;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/JPrintPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/JPrintPanel.java
index 4ce35415b1..8f9e8322c4 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/JPrintPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/JPrintPanel.java
@@ -30,7 +30,6 @@
 import java.awt.event.ActionListener;
 import java.awt.print.PageFormat;
 import java.awt.print.Printable;
-import java.awt.print.PrinterException;
 import java.awt.print.PrinterJob;
 
 public class JPrintPanel extends JPanel implements Printable,ActionListener{
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.java
index f523e9c574..9b4a848b89 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.java
@@ -284,7 +284,7 @@ public void cleanUp() {
 
 	private void calcAlignment() {
 
-		try {
+//		try {
 			List<Structure> structures = tab.getStructures();
 
 			if ( structures.size() < 2) {
@@ -309,10 +309,10 @@ private void calcAlignment() {
 			ProgressThreadDrawer drawer = new ProgressThreadDrawer(progress);
 			drawer.start();
 
-		} catch (StructureException e){
-			JOptionPane.showMessageDialog(null,"Could not align structures. "
-					+ "Exception: " + e.getMessage());
-		}
+//		} catch (StructureException e){
+//			JOptionPane.showMessageDialog(null,"Could not align structures. "
+//					+ "Exception: " + e.getMessage());
+//		}
 
 	}
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ParameterGUI.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ParameterGUI.java
index e0bd5cbdf5..afa9f5500d 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ParameterGUI.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ParameterGUI.java
@@ -24,8 +24,6 @@
 
 import javax.swing.*;
 import java.awt.*;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 import java.lang.reflect.Method;
 import java.util.ArrayList;
 import java.util.List;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SystemInfo.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SystemInfo.java
index dba6865fe1..7e6d26fa1d 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SystemInfo.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SystemInfo.java
@@ -29,10 +29,7 @@
 import javax.swing.*;
 import javax.swing.border.EtchedBorder;
 import javax.swing.event.HyperlinkEvent;
-import javax.swing.event.HyperlinkListener;
 import java.awt.*;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 import java.util.Enumeration;
 import java.util.Properties;
 import java.util.StringTokenizer;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.java
index bc98ffe2b8..312186cfc2 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.java
@@ -450,7 +450,7 @@ private void updateJmolDisplay() {
 						select2 = JmolTools.getPdbInfo(a2);
 
 					// nothing to display
-					if ( select1.equals("") && select2.equals(""))
+					if (select1.isEmpty() && select2.isEmpty())
 						continue;
 
 					if ( nrSelected > 0)
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
index 289ec9774c..78a6dc2b8f 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
@@ -35,7 +35,6 @@
 import java.util.List;
 
 import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.gui.JPrintPanel;
 import org.biojava.nbio.structure.align.gui.MenuCreator;
 import org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay;
@@ -359,7 +358,7 @@ private void updateJmolDisplay() {
 							multAln, mapSeqToStruct,str,i);
 					if (a != null) {
 						cmd.append(JmolTools.getPdbInfo(a));
-						cmd.append("/"+(str+1)+", ");
+						cmd.append("/").append(str + 1).append(", ");
 					}
 				}
 				nrSelected++;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java
index 1cbaebf6c1..fae350ef65 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java
@@ -135,11 +135,11 @@ public void focusLost(FocusEvent e) {
 				System.out.println("Lost Focus");
 				dialog.setVisible(false);
 
-				if (getText().trim().equals("") && e.getOppositeComponent() != null && e.getOppositeComponent().getName() != null) {
+				if (getText().trim().isEmpty() && e.getOppositeComponent() != null && e.getOppositeComponent().getName() != null) {
 					if (!e.getOppositeComponent().getName().equals("suggestFieldDropdownButton")) {
 						setText(defaultText);
 					}
-				} else if (getText().trim().equals("")) {
+				} else if (getText().trim().isEmpty()) {
 					setText(defaultText);
 				}
 			}
@@ -352,7 +352,7 @@ public String doInBackground() {
 			try {
 				setFont(busy);
 				String userInput = getText().trim();
-				if ( userInput == null || userInput.equals(""))
+				if ( userInput == null || userInput.isEmpty())
 					return "";
 
 				if ( previousWord != null){
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfo.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfo.java
index b4c27afb9b..83b93ac1bc 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfo.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfo.java
@@ -118,13 +118,13 @@ public String toString() {
 
 		StringBuilder buf = new StringBuilder();
 		if ( printResName) {
-			if ( !aa3.equals("")){
+			if (!aa3.isEmpty()){
 				buf.append("[");
 				buf.append(aa3);
 				buf.append("]");
 			}
 		}
-		if ( ! res1.equals("")) {
+		if (!res1.isEmpty()) {
 
 			// let's check if there is an insertion code...
 			Matcher matcher = inscodePatter.matcher(res1);
@@ -137,7 +137,7 @@ public String toString() {
 				String residueNumber = matcher.group(1);
 				String insCode = matcher.group(2);
 				buf.append(residueNumber);
-				if ( insCode != null && ! ( insCode.equals(""))) {
+				if ( insCode != null && ! (insCode.isEmpty())) {
 					buf.append("^");
 					buf.append(insCode);
 				}
@@ -145,7 +145,7 @@ public String toString() {
 
 		}
 
-		if ( ! chain1.equals("")){
+		if (!chain1.isEmpty()){
 			buf.append(":");
 			buf.append(chain1);
 		}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolTools.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolTools.java
index d0cf56e5d7..9d9044015d 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolTools.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolTools.java
@@ -34,7 +34,7 @@ public class JmolTools {
 	 *
 	 * @return a String representation in Jmol style of the PDB information of this atom
 	 */
-	public static final String getPdbInfo(Atom a){
+	public static String getPdbInfo(Atom a){
 		return getPdbInfo(a,true);
 	}
 
@@ -63,7 +63,7 @@ public static void main(String[] args){
 
 	// TODO: move this to AtomInfo class
 
-	public static final String getPdbInfo(Atom a, boolean printResName){
+	public static String getPdbInfo(Atom a, boolean printResName){
 		String aa3 = "";
 
 		String chain1 ="";
@@ -82,13 +82,13 @@ public static final String getPdbInfo(Atom a, boolean printResName){
 
 		StringBuilder buf = new StringBuilder();
 		if ( printResName) {
-			if ( !aa3.equals("")){
+			if (!aa3.isEmpty()){
 				buf.append("[");
 				buf.append(aa3);
 				buf.append("]");
 			}
 		}
-		if ( ! res1.equals("")) {
+		if (!res1.isEmpty()) {
 
 			// let's check if there is an insertion code...
 			Matcher matcher = inscodePatter.matcher(res1);
@@ -101,7 +101,7 @@ public static final String getPdbInfo(Atom a, boolean printResName){
 				String residueNumber = matcher.group(1);
 				String insCode = matcher.group(2);
 				buf.append(residueNumber);
-				if ( insCode != null && ! ( insCode.equals(""))) {
+				if ( insCode != null && ! (insCode.isEmpty())) {
 					buf.append("^");
 					buf.append(insCode);
 				}
@@ -112,7 +112,7 @@ public static final String getPdbInfo(Atom a, boolean printResName){
 
 
 
-		if (chain1!=null && ! chain1.equals("")){
+		if (chain1!=null && !chain1.isEmpty()){
 			buf.append(":");
 			buf.append(chain1);
 		}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
index da57ea4863..1962a7657b 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
@@ -25,9 +25,7 @@
 import java.awt.Container;
 import java.awt.Dimension;
 import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.io.StringWriter;
@@ -323,7 +321,7 @@ public void windowClosing(WindowEvent e) {
 
 	@Override
 	protected void initCoords() {
-		try {
+//		try {
 			if (multAln == null) {
 				if (structure != null)
 					setStructure(structure);
@@ -334,10 +332,11 @@ protected void initCoords() {
 			}
 			Structure artificial = MultipleAlignmentTools.toMultimodelStructure(multAln, transformedAtoms);
 			setStructure(artificial);
-			logger.info(artificial.getPDBHeader().getTitle());
-		} catch (StructureException e) {
-			e.printStackTrace();
-		}
+			if (logger.isInfoEnabled())
+				logger.info(artificial.getPDBHeader().getTitle());
+//		} catch (StructureException e) {
+//			e.printStackTrace();
+//		}
 	}
 
 	@Override
@@ -437,12 +436,11 @@ public static String getJmolString(MultipleAlignment multAln,
 				pos++;
 
 				sel.append(res);
-				sel.append("/" + (i + 1));
+				sel.append("/").append(i + 1);
 			}
 			if (pos == 0)
 				sel.append("none");
-			sel.append("; backbone 0.3 ; color [" + colors[i].getRed() + ","
-					+ colors[i].getGreen() + "," + colors[i].getBlue() + "]; ");
+			sel.append("; backbone 0.3 ; color [").append(colors[i].getRed()).append(",").append(colors[i].getGreen()).append(",").append(colors[i].getBlue()).append("]; ");
 		}
 
 		j.append(sel);
@@ -470,8 +468,7 @@ public static String getMultiBlockJmolString(MultipleAlignment multAln,
 
 		// For every structure color all the blocks with the printBlock method
 		for (int str = 0; str < transformedAtoms.size(); str++) {
-			jmol.append("select */" + (str + 1) + "; color lightgrey; model "
-					+ (str + 1) + "; ");
+			jmol.append("select */").append(String.valueOf(str + 1)).append("; color lightgrey; model ").append(String.valueOf(str + 1)).append("; ");
 
 			int index = 0;
 			for (BlockSet bs : multAln.getBlockSets()) {
@@ -513,12 +510,11 @@ private static void printJmolScript4Block(Atom[] atoms,
 			if (count > 0)
 				buf.append(",");
 			buf.append(res);
-			buf.append("/" + (str + 1));
+			buf.append("/").append(str + 1);
 			count++;
 		}
 
-		buf.append("; backbone 0.3 ; color [" + blockColor.getRed() + ","
-				+ blockColor.getGreen() + "," + blockColor.getBlue() + "]; ");
+		buf.append("; backbone 0.3 ; color [").append(blockColor.getRed()).append(",").append(blockColor.getGreen()).append(",").append(blockColor.getBlue()).append("]; ");
 
 		jmol.append(buf);
 	}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java
index c762df85f6..ef230064c3 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java
@@ -69,7 +69,7 @@ public void actionPerformed(ActionEvent event) {
 		// now comes history part:
 
 		// no need for history:
-		if ( cmd.equals("")) return;
+		if (cmd.isEmpty()) return;
 
 		// check last command in history
 		// if equivalent, don't add,
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java
index 044e2ece20..8e04e2cee3 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java
@@ -576,7 +576,7 @@ private static void printJmolScript4Block(Atom[] ca1, Atom[] ca2, int blockNum,
 			count++;
 		}
 
-		buf.append("; backbone 0.6 ; color [" + c1.getRed() + "," + c1.getGreen() + "," + c1.getBlue() + "]; select ");
+		buf.append("; backbone 0.6 ; color [").append(c1.getRed()).append(",").append(c1.getGreen()).append(",").append(c1.getBlue()).append("]; select ");
 
 		count = 0;
 		for (String res : pdb2) {
@@ -589,7 +589,7 @@ private static void printJmolScript4Block(Atom[] ca1, Atom[] ca2, int blockNum,
 		}
 		// buf.append("; set display selected;");
 
-		buf.append("; backbone 0.6 ; color [" + c2.getRed() + "," + c2.getGreen() + "," + c2.getBlue() + "];");
+		buf.append("; backbone 0.6 ; color [").append(c2.getRed()).append(",").append(c2.getGreen()).append(",").append(c2.getBlue()).append("];");
 
 		// now color this block:
 		jmol.append(buf);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java
index c9fedcfbd8..9a778d7664 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java
@@ -73,7 +73,7 @@ public static void main(String[] args){
 
 			// we did not get enough arguments, show the general user interface...
 
-			javax.swing.SwingUtilities.invokeLater(() -> AlignmentGui.getInstance());
+			javax.swing.SwingUtilities.invokeLater(AlignmentGui::getInstance);
 
 			return;
 
@@ -82,7 +82,7 @@ public static void main(String[] args){
 		else if ( args.length < 3){
 			//String arg0 = args[0];
 
-			javax.swing.SwingUtilities.invokeLater(() -> AlignmentGui.getInstance());
+			javax.swing.SwingUtilities.invokeLater(AlignmentGui::getInstance);
 
 			return;
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/MenuCreator.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/MenuCreator.java
index f149dd2152..668dbc7503 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/MenuCreator.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/MenuCreator.java
@@ -28,8 +28,6 @@
 
 import javax.swing.*;
 import java.awt.*;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 import java.awt.event.KeyEvent;
 import java.io.File;
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java
index 95dcc1a8f6..05795bc91a 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java
@@ -157,7 +157,7 @@ private Structure getStructure(JTextField filePath,JTextField chainId) throws St
 
 			URL u ;
 
-			if ( chainId.getText() == null || chainId.getText().equals("")){
+			if ( chainId.getText() == null || chainId.getText().isEmpty()){
 
 				u = f.toURI().toURL();
 			} else {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopSelectPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopSelectPanel.java
index 5ab2bff7c9..4c9c7d6d0f 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopSelectPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopSelectPanel.java
@@ -113,22 +113,20 @@ private Box getDomainPanel(int pos ,JTextField f){
 	}
 
 	@Override
-	public Structure getStructure1() throws StructureException
-	{
+	public Structure getStructure1() {
 		String scop1 = dom1.getText();
 		return getStructure(scop1);
 	}
 
 	@Override
-	public Structure getStructure2() throws StructureException
-	{
+	public Structure getStructure2() {
 		return getStructure(dom2.getText());
 	}
 
 	private Structure getStructure(String domainID) {
 		//PDBFileReader reader = new PDBFileReader();
 
-		if ( domainID == null || domainID.equals(""))
+		if ( domainID == null || domainID.isEmpty())
 			return null;
 
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java
index 502e6264ea..b9e0d528ac 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java
@@ -88,7 +88,7 @@ private Box getDomainPanel(JTextField f){
 		return hBox;
 	}
 
-	public List<Structure> getStructures() throws StructureException {
+	public List<Structure> getStructures() {
 
 		List<Structure> structures = new ArrayList<>();
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java
index 608c8b69ff..7873a454e3 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java
@@ -41,8 +41,8 @@
 public class JmolSymmetryScriptGeneratorH extends JmolSymmetryScriptGenerator {
 	private static final double AXIS_SCALE_FACTOR = 1.2;
 	private static final double SIDE_CHAIN_EXTENSION = 6.0;
-	private HelixAxisAligner helixAxisAligner;
-	private String name;
+	private final HelixAxisAligner helixAxisAligner;
+	private final String name;
 	private String defaultColoring = "";
 	private boolean onTheFly = false;
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
index 8c968eb7c0..902b6cc867 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
@@ -49,7 +49,7 @@ public abstract class JmolSymmetryScriptGeneratorPointGroup extends JmolSymmetry
 	private RotationAxisAligner rotationAxisAligner;
 	private RotationGroup rotationGroup;
 	private Polyhedron polyhedron = null;
-	private String name;
+	private final String name;
 	private String defaultColoring = "";
 	private boolean onTheFly = true;
 
diff --git a/biojava-structure/src/main/java/demo/DemoCommandLineStartup.java b/biojava-structure/src/main/java/demo/DemoCommandLineStartup.java
index 7d9b24e123..a84ad81444 100644
--- a/biojava-structure/src/main/java/demo/DemoCommandLineStartup.java
+++ b/biojava-structure/src/main/java/demo/DemoCommandLineStartup.java
@@ -29,7 +29,7 @@
 public class DemoCommandLineStartup
 {
 
-	public static void main(String[] arg) throws Exception {
+	public static void main(String[] arg) {
 
 		// demo how to use with command line parameters
 		String commandLine = "-file1 /tmp/cd/pdb1cdg.ent.gz -file2 file:///tmp/ti/pdb1tim.ent.gz -printCE";
diff --git a/biojava-structure/src/main/java/demo/DemoMmtfReader.java b/biojava-structure/src/main/java/demo/DemoMmtfReader.java
index a5dacae622..e7cdce5283 100644
--- a/biojava-structure/src/main/java/demo/DemoMmtfReader.java
+++ b/biojava-structure/src/main/java/demo/DemoMmtfReader.java
@@ -23,7 +23,6 @@
 import java.io.IOException;
 
 import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.io.mmtf.MmtfActions;
 
 /**
diff --git a/biojava-structure/src/main/java/demo/DemoMultipleMC.java b/biojava-structure/src/main/java/demo/DemoMultipleMC.java
index 37979e28ea..9f91a913fa 100644
--- a/biojava-structure/src/main/java/demo/DemoMultipleMC.java
+++ b/biojava-structure/src/main/java/demo/DemoMultipleMC.java
@@ -24,7 +24,6 @@
 import java.util.Arrays;
 import java.util.List;
 import java.util.ArrayList;
-import java.util.concurrent.ExecutionException;
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
index df2eefaf47..1ab5a9a0b0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
@@ -63,7 +63,7 @@ public boolean equals(Object obj) {
 		if (!Objects.equals(this.surname, other.surname)) {
 			return false;
 		}
-		return !(!Objects.equals(this.initials, other.initials));
+		return Objects.equals(this.initials, other.initials);
 	}
 
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
index 6bd5c47faa..f4cfd1bba3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -65,7 +65,7 @@ public class Calc {
 	 *            an Atom object
 	 * @return a double
 	 */
-	public static final double getDistance(Atom a, Atom b) {
+	public static double getDistance(Atom a, Atom b) {
 		double x = a.getX() - b.getX();
 		double y = a.getY() - b.getY();
 		double z = a.getZ() - b.getZ();
@@ -95,7 +95,7 @@ public static double getDistanceFast(Atom a, Atom b) {
 		return x * x  + y * y + z * z;
 	}
 
-	public static final Atom invert(Atom a) {
+	public static Atom invert(Atom a) {
 		double[] coords = new double[]{0.0,0.0,0.0} ;
 		Atom zero = new AtomImpl();
 		zero.setCoords(coords);
@@ -111,7 +111,7 @@ public static final Atom invert(Atom a) {
 	 *            an Atom object
 	 * @return an Atom object
 	 */
-	public static final Atom add(Atom a, Atom b){
+	public static Atom add(Atom a, Atom b){
 
 		Atom c = new AtomImpl();
 		c.setX( a.getX() + b.getX() );
@@ -130,7 +130,7 @@ public static final Atom add(Atom a, Atom b){
 	 *            an Atom object
 	 * @return n new Atom object representing the difference
 	 */
-	public static final Atom subtract(Atom a, Atom b) {
+	public static Atom subtract(Atom a, Atom b) {
 		Atom c = new AtomImpl();
 		c.setX( a.getX() - b.getX() );
 		c.setY( a.getY() - b.getY() );
@@ -148,7 +148,7 @@ public static final Atom subtract(Atom a, Atom b) {
 	 *            an Atom object
 	 * @return an Atom object
 	 */
-	public static final Atom vectorProduct(Atom a , Atom b){
+	public static Atom vectorProduct(Atom a , Atom b){
 
 		Atom c = new AtomImpl();
 		c.setX( a.getY() * b.getZ() - a.getZ() * b.getY() ) ;
@@ -167,7 +167,7 @@ public static final Atom vectorProduct(Atom a , Atom b){
 	 *            an Atom object
 	 * @return a double
 	 */
-	public static final double scalarProduct(Atom a, Atom b) {
+	public static double scalarProduct(Atom a, Atom b) {
 		return a.getX() * b.getX() + a.getY() * b.getY() + a.getZ() * b.getZ();
 	}
 
@@ -178,7 +178,7 @@ public static final double scalarProduct(Atom a, Atom b) {
 	 *            an Atom object
 	 * @return Square root of the sum of the squared elements
 	 */
-	public static final double amount(Atom a){
+	public static double amount(Atom a){
 		return Math.sqrt(scalarProduct(a,a));
 	}
 
@@ -192,7 +192,7 @@ public static final double amount(Atom a){
 	 * @return Angle between a and b in degrees, in range [0,180]. If either
 	 *         vector has length 0 then angle is not defined and NaN is returned
 	 */
-	public static final double angle(Atom a, Atom b){
+	public static double angle(Atom a, Atom b){
 
 		Vector3d va = new Vector3d(a.getCoordsAsPoint3d());
 		Vector3d vb = new Vector3d(b.getCoordsAsPoint3d());
@@ -208,7 +208,7 @@ public static final double angle(Atom a, Atom b){
 	 *            an Atom object
 	 * @return an Atom object
 	 */
-	public static final Atom unitVector(Atom a) {
+	public static Atom unitVector(Atom a) {
 		double amount = amount(a) ;
 
 		double[] coords = new double[3];
@@ -239,7 +239,7 @@ public static final Atom unitVector(Atom a) {
 	 *         3 or last 3 atoms are colinear then torsion angle is not defined
 	 *         and NaN is returned
 	 */
-	public static final double torsionAngle(Atom a, Atom b, Atom c, Atom d) {
+	public static double torsionAngle(Atom a, Atom b, Atom c, Atom d) {
 
 		Atom ab = subtract(a,b);
 		Atom cb = subtract(c,b);
@@ -272,7 +272,7 @@ public static final double torsionAngle(Atom a, Atom b, Atom c, Atom d) {
 	 *             if aminoacids not connected or if any of the 4 needed atoms
 	 *             missing
 	 */
-	public static final double getPhi(AminoAcid a, AminoAcid b)
+	public static double getPhi(AminoAcid a, AminoAcid b)
 			throws StructureException {
 
 		if ( ! isConnected(a,b)){
@@ -305,7 +305,7 @@ public static final double getPhi(AminoAcid a, AminoAcid b)
 	 *             if aminoacids not connected or if any of the 4 needed atoms
 	 *             missing
 	 */
-	public static final double getPsi(AminoAcid a, AminoAcid b)
+	public static double getPsi(AminoAcid a, AminoAcid b)
 			throws StructureException {
 		if ( ! isConnected(a,b)) {
 			throw new StructureException(
@@ -338,7 +338,7 @@ public static final double getPsi(AminoAcid a, AminoAcid b)
 	 *            an AminoAcid object
 	 * @return true if ...
 	 */
-	public static final boolean isConnected(AminoAcid a, AminoAcid b) {
+	public static boolean isConnected(AminoAcid a, AminoAcid b) {
 		Atom C;
 		Atom N;
 
@@ -365,7 +365,7 @@ public static final boolean isConnected(AminoAcid a, AminoAcid b) {
 	 * @param m
 	 *            a rotation matrix represented as a double[3][3] array
 	 */
-	public static final void rotate(Atom atom, double[][] m){
+	public static void rotate(Atom atom, double[][] m){
 
 		double x = atom.getX();
 		double y = atom.getY() ;
@@ -391,8 +391,8 @@ public static final void rotate(Atom atom, double[][] m){
 	 * @throws StructureException
 	 *             ...
 	 */
-	public static final void rotate(Structure structure,
-			double[][] rotationmatrix) throws StructureException {
+	public static void rotate(Structure structure,
+                              double[][] rotationmatrix) throws StructureException {
 
 		if ( rotationmatrix.length != 3 ) {
 			throw new StructureException ("matrix does not have size 3x3 !");
@@ -414,7 +414,7 @@ public static final void rotate(Structure structure,
 	 * @throws StructureException
 	 *             ...
 	 */
-	public static final void rotate(Group group, double[][] rotationmatrix)
+	public static void rotate(Group group, double[][] rotationmatrix)
 			throws StructureException {
 
 		if ( rotationmatrix.length != 3 ) {
@@ -439,7 +439,7 @@ public static final void rotate(Group group, double[][] rotationmatrix)
 	 * @param m
 	 *            rotation matrix to be applied to the atom
 	 */
-	public static final void rotate(Atom atom, Matrix m){
+	public static void rotate(Atom atom, Matrix m){
 
 		double x = atom.getX();
 		double y = atom.getY();
@@ -464,7 +464,7 @@ public static final void rotate(Atom atom, Matrix m){
 	 * @param m
 	 *            a Matrix object representing the rotation matrix
 	 */
-	public static final void rotate(Group group, Matrix m){
+	public static void rotate(Group group, Matrix m){
 
 		AtomIterator iter = new AtomIterator(group) ;
 
@@ -485,7 +485,7 @@ public static final void rotate(Group group, Matrix m){
 	 * @param m
 	 *            rotation matrix to be applied
 	 */
-	public static final void rotate(Structure structure, Matrix m){
+	public static void rotate(Structure structure, Matrix m){
 
 		AtomIterator iter = new AtomIterator(structure) ;
 
@@ -519,7 +519,7 @@ public static void transform(Atom[] ca, Matrix4d t) {
 	 * @param atom
 	 * @param m
 	 */
-	public static final void transform (Atom atom, Matrix4d m) {
+	public static void transform (Atom atom, Matrix4d m) {
 
 		Point3d p = new Point3d(atom.getX(),atom.getY(),atom.getZ());
 		m.transform(p);
@@ -537,7 +537,7 @@ public static final void transform (Atom atom, Matrix4d m) {
 	 * @param group
 	 * @param m
 	 */
-	public static final void transform(Group group, Matrix4d m) {
+	public static void transform(Group group, Matrix4d m) {
 		for (Atom atom : group.getAtoms()) {
 			transform(atom, m);
 		}
@@ -554,7 +554,7 @@ public static final void transform(Group group, Matrix4d m) {
 	 * @param structure
 	 * @param m
 	 */
-	public static final void transform(Structure structure, Matrix4d m) {
+	public static void transform(Structure structure, Matrix4d m) {
 		for (int n=0; n<structure.nrModels();n++) {
 			for (Chain c : structure.getChains(n)) {
 				transform(c, m);
@@ -570,7 +570,7 @@ public static final void transform(Structure structure, Matrix4d m) {
 	 * @param chain
 	 * @param m
 	 */
-	public static final void transform (Chain chain, Matrix4d m) {
+	public static void transform (Chain chain, Matrix4d m) {
 
 		for (Group g : chain.getAtomGroups()) {
 			transform(g, m);
@@ -584,7 +584,7 @@ public static final void transform (Chain chain, Matrix4d m) {
 	 * @param atom
 	 * @param v
 	 */
-	public static final void translate (Atom atom, Vector3d v) {
+	public static void translate (Atom atom, Vector3d v) {
 
 		atom.setX(atom.getX()+v.x);
 		atom.setY(atom.getY()+v.y);
@@ -598,7 +598,7 @@ public static final void translate (Atom atom, Vector3d v) {
 	 * @param group
 	 * @param v
 	 */
-	public static final void translate (Group group, Vector3d v) {
+	public static void translate (Group group, Vector3d v) {
 
 		for (Atom atom : group.getAtoms()) {
 			translate(atom,v);
@@ -615,7 +615,7 @@ public static final void translate (Group group, Vector3d v) {
 	 * @param chain
 	 * @param v
 	 */
-	public static final void translate (Chain chain, Vector3d v) {
+	public static void translate (Chain chain, Vector3d v) {
 
 		for (Group g:chain.getAtomGroups()) {
 			translate(g, v);
@@ -629,7 +629,7 @@ public static final void translate (Chain chain, Vector3d v) {
 	 * @param structure
 	 * @param v
 	 */
-	public static final void translate (Structure structure, Vector3d v) {
+	public static void translate (Structure structure, Vector3d v) {
 
 		for (int n=0; n<structure.nrModels();n++) {
 			for (Chain c : structure.getChains(n)) {
@@ -646,7 +646,7 @@ public static final void translate (Structure structure, Vector3d v) {
 	 * @param matrix
 	 *            a Matrix object
 	 */
-	public static final void plus(Structure s, Matrix matrix){
+	public static void plus(Structure s, Matrix matrix){
 		AtomIterator iter = new AtomIterator(s) ;
 		Atom oldAtom = null;
 		Atom rotOldAtom = null;
@@ -696,7 +696,7 @@ public static final void plus(Structure s, Matrix matrix){
 	 * @param a
 	 *            an Atom object representing a shift vector
 	 */
-	public static final void shift(Structure structure, Atom a ){
+	public static void shift(Structure structure, Atom a ){
 
 		AtomIterator iter = new AtomIterator(structure) ;
 		while (iter.hasNext() ) {
@@ -723,7 +723,7 @@ public static final void shift(Structure structure, Atom a ){
 	 * @param b
 	 *            vector b
 	 */
-	public static final void shift(Atom a, Atom b){
+	public static void shift(Atom a, Atom b){
 
 		Atom natom = add(a,b);
 		double x = natom.getX();
@@ -742,7 +742,7 @@ public static final void shift(Atom a, Atom b){
 	 * @param a
 	 *            an Atom object representing a shift vector
 	 */
-	public static final void shift(Group group , Atom a ){
+	public static void shift(Group group , Atom a ){
 
 		AtomIterator iter = new AtomIterator(group) ;
 		while (iter.hasNext() ) {
@@ -768,7 +768,7 @@ public static final void shift(Group group , Atom a ){
 	 *            a set of Atoms
 	 * @return an Atom representing the Centroid of the set of atoms
 	 */
-	public static final Atom getCentroid(Atom[] atomSet){
+	public static Atom getCentroid(Atom[] atomSet){
 
 		// if we don't catch this case, the centroid returned is (NaN,NaN,NaN), which can cause lots of problems down the line
 		if (atomSet.length==0)
@@ -898,7 +898,7 @@ public static Atom scaleAdd(double s, Atom x, Atom b){
 	 * @return the vector needed to shift the set of atoms to its geometric
 	 *         center
 	 */
-	public static final Atom getCenterVector(Atom[] atomSet){
+	public static Atom getCenterVector(Atom[] atomSet){
 		Atom centroid = getCentroid(atomSet);
 
 		return getCenterVector(atomSet,centroid);
@@ -914,7 +914,7 @@ public static final Atom getCenterVector(Atom[] atomSet){
 	 * @return the vector needed to shift the set of atoms to its geometric
 	 *         center
 	 */
-	public static final Atom getCenterVector(Atom[] atomSet, Atom centroid){
+	public static Atom getCenterVector(Atom[] atomSet, Atom centroid){
 
 		double[] coords = new double[3];
 		coords[0] = 0 - centroid.getX();
@@ -932,11 +932,8 @@ public static final Atom getCenterVector(Atom[] atomSet, Atom centroid){
 	 *
 	 * @param atomSet
 	 *            a set of Atoms
-	 * @return an Atom representing the Centroid of the set of atoms
-	 * @throws StructureException
-	 * */
-	public static final Atom[] centerAtoms(Atom[] atomSet)
-			throws StructureException {
+	 * @return an Atom representing the Centroid of the set of atoms */
+	public static Atom[] centerAtoms(Atom[] atomSet) {
 
 		Atom centroid = getCentroid(atomSet);
 		return centerAtoms(atomSet, centroid);
@@ -948,7 +945,7 @@ public static final Atom[] centerAtoms(Atom[] atomSet)
 	 * @param atomSet
 	 *            a set of Atoms
 	 * @return an Atom representing the Centroid of the set of atoms */
-	public static final Atom[] centerAtoms(Atom[] atomSet, Atom centroid) {
+	public static Atom[] centerAtoms(Atom[] atomSet, Atom centroid) {
 
 		Atom shiftVector = getCenterVector(atomSet, centroid);
 
@@ -972,7 +969,7 @@ public static final Atom[] centerAtoms(Atom[] atomSet, Atom centroid) {
 	 *            calculated
 	 * @return a "virtual" CB atom
      */
-	public static final Atom createVirtualCBAtom(AminoAcid amino) {
+	public static Atom createVirtualCBAtom(AminoAcid amino) {
 
 		AminoAcid  ala = StandardAminoAcid.getAminoAcid("ALA");
 		Atom aN  = ala.getN();
@@ -1014,7 +1011,7 @@ public static final Atom createVirtualCBAtom(AminoAcid amino) {
 	 *            the rotation matrix
 	 * @return the euler values for a rotation around Z, Y, Z in degrees...
 	 */
-	public static final double[] getZYZEuler(Matrix m) {
+	public static double[] getZYZEuler(Matrix m) {
 		double m22 = m.get(2,2);
 		double rY = Math.toDegrees(Math.acos(m22));
 		double rZ1, rZ2;
@@ -1040,7 +1037,7 @@ public static final double[] getZYZEuler(Matrix m) {
 	 * @return a array of three doubles containing the three euler angles in
 	 *         radians
 	 */
-	public static final double[] getXYZEuler(Matrix m){
+	public static double[] getXYZEuler(Matrix m){
 		double heading, attitude, bank;
 
 		// Assuming the angles are in radians.
@@ -1078,8 +1075,8 @@ public static final double[] getXYZEuler(Matrix m){
 	 *            in radians
 	 * @return the rotation matrix
 	 */
-	public static final Matrix matrixFromEuler(double heading, double attitude,
-			double bank) {
+	public static Matrix matrixFromEuler(double heading, double attitude,
+                                         double bank) {
 		// Assuming the angles are in radians.
 		double ch = Math.cos(heading);
 		double sh = Math.sin(heading);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java
index cf6dd2ec74..cca63ffc8f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java
@@ -29,7 +29,6 @@
 
 import java.io.Serializable;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.LinkedHashMap;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/JournalArticle.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/JournalArticle.java
index 3723136daa..4b17317d79 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/JournalArticle.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/JournalArticle.java
@@ -258,19 +258,19 @@ public String toString() {
 		}
 		refString.append(ref);
 		jrnlString.append(refString).append(eol);
-		if (!publisher.equals("")) {
+		if (!publisher.isEmpty()) {
 			publString.append(publisher);
 			jrnlString.append(publString).append(eol);
 		}
-		if (!refn.equals("")) {
+		if (!refn.isEmpty()) {
 			refnString.append(refn);
 			jrnlString.append(refnString).append(eol);
 		}
-		if (!pmid.equals("")) {
+		if (!pmid.isEmpty()) {
 			pmidString.append(pmid);
 			jrnlString.append(pmidString).append(eol);
 		}
-		if (!doi.equals("")) {
+		if (!doi.isEmpty()) {
 			doiString.append(doi);
 			jrnlString.append(doiString).append(eol);
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java
index 0a82563f07..16dfe6a0fa 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java
@@ -78,10 +78,8 @@ public Mutator(){
 	 * @param pdbResnum the PDB residue number of the residue
 	 * @param newType the new residue type (3 characters)
 	 * @return a structure object where one residue has been modified
-	 * @throws PDBParseException
-	 */
-	public Structure  mutate(Structure struc, String chainId, String pdbResnum, String newType)
-	throws PDBParseException{
+     */
+	public Structure  mutate(Structure struc, String chainId, String pdbResnum, String newType) {
 
 
 		// create a  container for the new structure
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
index 04223ae778..2e5d5724e4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
@@ -214,7 +214,7 @@ private void printAuthors(StringBuffer buf){
 		String authors = getAuthors();
 		if ( authors == null)
 			return;
-		if ( authors.equals("")){
+		if (authors.isEmpty()){
 			return;
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PassthroughIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PassthroughIdentifier.java
index 2a7c654919..f5acaa639f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/PassthroughIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/PassthroughIdentifier.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.structure;
 
-import java.io.IOException;
 import java.util.ArrayList;
 
 import org.biojava.nbio.structure.align.util.AtomCache;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/SeqMisMatchImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/SeqMisMatchImpl.java
index 21b2033adc..73e48950aa 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/SeqMisMatchImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/SeqMisMatchImpl.java
@@ -115,20 +115,20 @@ public String toString() {
 		s.append("seqNum=" );
 		s.append(seqNum );
 		s.append(", origGroup='" );
-		s.append(origGroup + '\'' );
+		s.append(origGroup).append('\'');
 		s.append(", pdbGroup='" );
-		s.append(pdbGroup + '\'' );
+		s.append(pdbGroup).append('\'');
 		s.append(", details='" );
-		s.append(details + '\'' );
+		s.append(details).append('\'');
 		s.append(", uniProtId='" );
-		s.append(uniProtId + '\'' );
+		s.append(uniProtId).append('\'');
 		s.append(", pdbResNum='" );
-		s.append(pdbResNum + '\'' );
+		s.append(pdbResNum).append('\'');
 
 		if ( insCode == null)
 			s.append(", insCode=null ") ;
 		else
-			s.append(", insCode='" + insCode + '\'') ;
+			s.append(", insCode='").append(insCode).append('\'');
 
 		s.append('}');
 		return s.toString();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
index 336f350dad..4acb36c41c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
@@ -203,9 +203,8 @@ public Group findGroup(String chainName, String pdbResnum, int modelnr)
 		// first we need to gather all groups with the author id chainName: polymers, non-polymers and waters
 		Chain polyChain = getPolyChainByPDB(chainName, modelnr);
 		if(polyChain != null) {
-			List<Group> groups = new ArrayList<>();
 
-			groups.addAll(polyChain.getAtomGroups());
+            List<Group> groups = new ArrayList<>(polyChain.getAtomGroups());
 
 
 			// there can be more than one non-poly chain for a given author id
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
index 7043e264fe..892fbe113a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -256,7 +256,7 @@ public class StructureTools {
 	 *            the structure object
 	 * @return the number of Atoms in this Structure
 	 */
-	public static final int getNrAtoms(Structure s) {
+	public static int getNrAtoms(Structure s) {
 
 		int nrAtoms = 0;
 
@@ -277,7 +277,7 @@ public static final int getNrAtoms(Structure s) {
 	 *            the structure object
 	 * @return the number of groups in the structure
 	 */
-	public static final int getNrGroups(Structure s) {
+	public static int getNrGroups(Structure s) {
 		int nrGroups = 0;
 
 		List<Chain> chains = s.getChains(0);
@@ -302,7 +302,7 @@ public static final int getNrGroups(Structure s) {
 	 *            contains the atom names to be used.
 	 * @return an Atom[] array
 	 */
-	public static final Atom[] getAtomArray(Structure s, String[] atomNames) {
+	public static Atom[] getAtomArray(Structure s, String[] atomNames) {
 		List<Chain> chains = s.getModel(0);
 
 		List<Atom> atoms = new ArrayList<>();
@@ -328,8 +328,8 @@ public static final Atom[] getAtomArray(Structure s, String[] atomNames) {
 	 *            contains the atom names to be used.
 	 * @return an Atom[] array
 	 */
-	public static final Atom[] getAtomArrayAllModels(Structure s,
-			String[] atomNames) {
+	public static Atom[] getAtomArrayAllModels(Structure s,
+											   String[] atomNames) {
 
 		List<Atom> atoms = new ArrayList<>();
 
@@ -348,7 +348,7 @@ public static final Atom[] getAtomArrayAllModels(Structure s,
 	 *            input structure
 	 * @return all atom array
 	 */
-	public static final Atom[] getAllAtomArray(Structure s) {
+	public static Atom[] getAllAtomArray(Structure s) {
 		List<Atom> atoms = new ArrayList<>();
 
 		AtomIterator iter = new AtomIterator(s);
@@ -365,7 +365,7 @@ public static final Atom[] getAllAtomArray(Structure s) {
 	 *            input structure
 	 * @return all atom array
 	 */
-	public static final Atom[] getAllAtomArray(Structure s, int model) {
+	public static Atom[] getAllAtomArray(Structure s, int model) {
 		List<Atom> atoms = new ArrayList<>();
 
 		AtomIterator iter = new AtomIterator(s,model);
@@ -385,7 +385,7 @@ public static final Atom[] getAllAtomArray(Structure s, int model) {
 	 *            input chain
 	 * @return all atom array
 	 */
-	public static final Atom[] getAllAtomArray(Chain c) {
+	public static Atom[] getAllAtomArray(Chain c) {
 		List<Atom> atoms = new ArrayList<>();
 
 		for (Group g : c.getAtomGroups()) {
@@ -658,7 +658,7 @@ public static Set<Group> getAllGroupsFromSubset(Atom[] atoms,GroupType types) {
 	 *            if true HET atoms are included in array, if false they are not
 	 * @return
 	 */
-	public static final Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms) {
+	public static Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms) {
 		AtomIterator iter = new AtomIterator(s);
 		return getAllNonHAtomArray(s, hetAtoms, iter);
 	}
@@ -672,11 +672,11 @@ public static final Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms) {
 	 * @param modelNr Model number to draw atoms from
 	 * @return
 	 */
-	public static final Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, int modelNr) {
+	public static Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, int modelNr) {
 		AtomIterator iter = new AtomIterator(s,modelNr);
 		return getAllNonHAtomArray(s, hetAtoms, iter);
 	}
-	private static final Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, AtomIterator iter) {
+	private static Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, AtomIterator iter) {
 		List<Atom> atoms = new ArrayList<>();
 
 		while (iter.hasNext()) {
@@ -706,7 +706,7 @@ private static final Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, A
 	 *            if true HET atoms are included in array, if false they are not
 	 * @return
 	 */
-	public static final Atom[] getAllNonHAtomArray(Chain c, boolean hetAtoms) {
+	public static Atom[] getAllNonHAtomArray(Chain c, boolean hetAtoms) {
 		List<Atom> atoms = new ArrayList<>();
 
 		for (Group g : c.getAtomGroups()) {
@@ -735,7 +735,7 @@ public static final Atom[] getAllNonHAtomArray(Chain c, boolean hetAtoms) {
 	 *            if true HET atoms are included in array, if false they are not
 	 * @return
 	 */
-	public static final Point3d[] getAllNonHCoordsArray(Chain c, boolean hetAtoms) {
+	public static Point3d[] getAllNonHCoordsArray(Chain c, boolean hetAtoms) {
 		List<Point3d> atoms = new ArrayList<>();
 
 		for (Group g : c.getAtomGroups()) {
@@ -807,7 +807,7 @@ private static void extractAtoms(String[] atomNames, List<Chain> chains,
 	 *            contains the atom names to be used.
 	 * @return an Atom[] array
 	 */
-	public static final Atom[] getAtomArray(Chain c, String[] atomNames) {
+	public static Atom[] getAtomArray(Chain c, String[] atomNames) {
 
 		List<Atom> atoms = new ArrayList<>();
 
@@ -850,7 +850,7 @@ public static final Atom[] getAtomArray(Chain c, String[] atomNames) {
 	 * @return an Atom[] array
 	 * @see #getRepresentativeAtomArray(Chain)
 	 */
-	public static final Atom[] getAtomCAArray(Chain c) {
+	public static Atom[] getAtomCAArray(Chain c) {
 		List<Atom> atoms = new ArrayList<>();
 
 		for (Group g : c.getAtomGroups()) {
@@ -877,7 +877,7 @@ public static final Atom[] getAtomCAArray(Chain c) {
 	 * @return representative Atoms of the chain backbone
 	 * @since Biojava 4.1.0
 	 */
-	public static final Atom[] getRepresentativeAtomArray(Chain c) {
+	public static Atom[] getRepresentativeAtomArray(Chain c) {
 		List<Atom> atoms = new ArrayList<>();
 
 		for (Group g : c.getAtomGroups()) {
@@ -913,7 +913,7 @@ public static final Atom[] getRepresentativeAtomArray(Chain c) {
 	 * @return Atom array
 	 * @since Biojava 4.1.0
 	 */
-	public static final Atom[] cloneAtomArray(Atom[] ca) {
+	public static Atom[] cloneAtomArray(Atom[] ca) {
 		Atom[] newCA = new Atom[ca.length];
 
 		List<Chain> model = new ArrayList<>();
@@ -1191,7 +1191,7 @@ public static Atom[] getBackboneAtomArray(Structure s) {
 	 *            a three character amino acid representation String
 	 * @see {@link #get1LetterCode(String)}
 	 */
-	public static final Character get1LetterCodeAmino(String groupCode3) {
+	public static Character get1LetterCodeAmino(String groupCode3) {
 		return aminoAcids.get(groupCode3);
 	}
 
@@ -1206,7 +1206,7 @@ public static final Character get1LetterCodeAmino(String groupCode3) {
 	 *            three letter representation
 	 * @return The 1-letter abbreviation
 	 */
-	public static final Character get1LetterCode(String groupCode3) {
+	public static Character get1LetterCode(String groupCode3) {
 
 		Character code1;
 
@@ -1284,7 +1284,7 @@ public static Structure getReducedStructure(Structure s,
 		if (chainId != null)
 			chainId = chainId.trim();
 
-		if (chainId == null || chainId.equals("")) {
+		if (chainId == null || chainId.isEmpty()) {
 			// only get model 0
 			List<Chain> model0 = s.getModel(0);
 			for (Chain c : model0) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
index f48927ec32..ee1bb75f42 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
@@ -28,7 +28,6 @@
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLDecoder;
-import java.util.Arrays;
 import java.util.Collections;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -123,7 +122,7 @@ public SubstructureIdentifier toCanonical() {
 		}
 		if(pdbId == null) {
 			String path = url.getPath();
-			pdbId = guessPDBID(path.substring(path.lastIndexOf("/")+1));
+			pdbId = guessPDBID(path.substring(path.lastIndexOf('/')+1));
 		}
 		return new SubstructureIdentifier(pdbId, ranges);
 	}
@@ -225,7 +224,7 @@ private static Map<String,String> parseQuery(URL url) throws UnsupportedEncoding
 		}
 		String[] pairs = url.getQuery().split("&");
 		for(String pair: pairs) {
-			int i = pair.indexOf("=");
+			int i = pair.indexOf('=');
 			String key = pair;
 			if(i > 0) {
 				key = URLDecoder.decode(pair.substring(0, i), "UTF-8");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
index ab6fade89e..cae663df67 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
@@ -165,10 +165,9 @@ public static Group[] twistPDB(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
 	 * @param ca1
 	 * @param ca2
 	 * @return Group array twisted.
-	 * @throws StructureException
-	 */
+     */
 	public static Group[] twistOptimized(AFPChain afpChain, Atom[] ca1,
-			Atom[] ca2) throws StructureException {
+			Atom[] ca2) {
 
 		Atom[] optTwistPdb = new Atom[ca2.length];
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/FarmJob.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/FarmJob.java
index 71f9ea8736..9452fad207 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/FarmJob.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/FarmJob.java
@@ -165,7 +165,7 @@ public void run(){
 		System.setProperty(UserConfiguration.PDB_DIR,path);
 
 		String cachePath = params.getCacheFilePath();
-		if ( cachePath != null && ! cachePath.equals(""))
+		if ( cachePath != null && !cachePath.isEmpty())
 			System.setProperty(UserConfiguration.PDB_CACHE_DIR,cachePath);
 		else {
 			// if not provided, we use pdbFilePath as the default CACHE path
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
index a196c8e022..d8a2d4b506 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
@@ -135,8 +135,7 @@
  */
 public class StructurePairAligner {
 
-	private final static Logger logger = LoggerFactory
-			.getLogger(StructurePairAligner.class);
+	private final static Logger logger = LoggerFactory.getLogger(StructurePairAligner.class);
 
 	AlternativeAlignment[] alts;
 	Matrix distanceMatrix;
@@ -544,18 +543,14 @@ public void align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)
 			a.setAltAligNumber(i + 1);
 			a.setDistanceMatrix(distanceMatrix);
 
-			try {
-				if (params.getMaxIter() > 0) {
-
+//			try {
+				if (params.getMaxIter() > 0)
 					a.refine(params, ca1, ca2);
-				} else {
-
+				else
 					a.finish(params, ca1, ca2);
-
-				}
-			} catch (StructureException e) {
-				logger.error("Refinement of fragment {} failed", i, e);
-			}
+//			} catch (StructureException e) {
+//				logger.error("Refinement of fragment {} failed", i, e);
+//			}
 			a.calcScores(ca1, ca2);
 			aas.add(a);
 		}
@@ -568,10 +563,8 @@ public void align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)
 		alts = aas.toArray(new AlternativeAlignment[0]);
 		// do final numbering of alternative solutions
 		int aanbr = 0;
-		for (AlternativeAlignment a : alts) {
-			aanbr++;
-			a.setAltAligNumber(aanbr);
-		}
+		for (AlternativeAlignment a : alts)
+			a.setAltAligNumber(++aanbr);
 
 		logger.debug("total calculation time: {} ms.",
 				(System.currentTimeMillis() - timeStart));
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
index 8c196cb65f..f3469c1f1e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
@@ -242,7 +242,7 @@ private void runDBSearch() throws ConfigurationException{
 
 		String pdbFilePath = params.getPdbFilePath();
 
-		if ( pdbFilePath == null || pdbFilePath.equals("")){
+		if ( pdbFilePath == null || pdbFilePath.isEmpty()){
 
 			UserConfiguration c = new UserConfiguration();
 			pdbFilePath = c.getPdbFilePath();
@@ -251,7 +251,7 @@ private void runDBSearch() throws ConfigurationException{
 
 		String cacheFilePath = params.getCacheFilePath();
 
-		if ( cacheFilePath == null || cacheFilePath.equals("")){
+		if ( cacheFilePath == null || cacheFilePath.isEmpty()){
 			cacheFilePath = pdbFilePath;
 
 		}
@@ -263,21 +263,21 @@ private void runDBSearch() throws ConfigurationException{
 
 		String searchFile = params.getSearchFile();
 
-		if ( alignPairs == null || alignPairs.equals("")) {
-			if ( searchFile == null || searchFile.equals("")){
+		if ( alignPairs == null || alignPairs.isEmpty()) {
+			if ( searchFile == null || searchFile.isEmpty()){
 				throw new ConfigurationException("Please specify -alignPairs or -searchFile !");
 			}
 		}
 
 		String outputFile = params.getOutFile();
 
-		if ( outputFile == null || outputFile.equals("")){
+		if ( outputFile == null || outputFile.isEmpty()){
 			throw new ConfigurationException("Please specify the mandatory argument -outFile!");
 		}
 
 		System.out.println("running DB search with parameters: " + params);
 
-		if ( alignPairs != null && ! alignPairs.equals("")) {
+		if ( alignPairs != null && !alignPairs.isEmpty()) {
 			runAlignPairs(cache, alignPairs, outputFile);
 		}  else {
 			// must be a searchFile request...
@@ -701,12 +701,12 @@ private Structure getStructure(AtomCache cache, String name1, String file)
 	 */
 	private Structure fixStructureName(Structure s, String file) {
 
-		if ( s.getName() != null && (! s.getName().equals("")))
+		if ( s.getName() != null && (!s.getName().isEmpty()))
 			return s;
 
 		s.setName(s.getPDBCode());
 
-		if ( s.getName() == null || s.getName().equals("")){
+		if ( s.getName() == null || s.getName().isEmpty()){
 			File f = new File(file);
 			s.setName(f.getName());
 		}
@@ -723,7 +723,7 @@ public String printHelp() {
 		StructureAlignment alg = getAlgorithm();
 
 		buf.append("-------------------").append(newline);
-		buf.append(alg.getAlgorithmName() + " v." + alg.getVersion() + " help: " + newline);
+		buf.append(alg.getAlgorithmName()).append(" v.").append(alg.getVersion()).append(" help: ").append(newline);
 		buf.append("-------------------").append(newline);
 		buf.append(newline);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
index cf730bbdaa..c3b5dd959a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
@@ -359,10 +359,8 @@ else if ( params.getScoringStrategy() == CeParameters.ScoringStrategy.CA_AND_SID
 	 * @param ca
 	 * @param nse
 	 * @return
-	 * @throws StructureException
-	 */
-	private double[][] initIntraDistmatrix(Atom[] ca, int nse) throws StructureException
-	{
+     */
+	private double[][] initIntraDistmatrix(Atom[] ca, int nse) {
 
 
 		double[][] intraDist = new double[nse][nse];
@@ -1535,7 +1533,7 @@ public static double[][] updateMatrixWithSequenceConservation(double[][] max, At
 		}
 
 
-		AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet set = AminoAcidCompoundSet.aminoAcidCompoundSet;
 
 		for (int i = 0 ; i < origM.getRowDimension() ; i++){
 			for ( int j =0; j < origM.getColumnDimension() ; j ++ ) {
@@ -1887,10 +1885,9 @@ private void rot_mol(Atom[] caA, Atom[] caB, int nse2, Matrix m , Atom shift) {
 	 * @param strLen Number of atoms from pro1 and pro2 to use
 	 * @param storeTransform Store rotation and shift matrices locally
 	 * @return RMSD
-	 * @throws StructureException
-	 */
+     */
 	public double calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen,
-			boolean storeTransform) throws StructureException {
+			boolean storeTransform) {
 
 		Atom[] cod1 = getAtoms(pro1,  strLen,false);
 		Atom[] cod2 = getAtoms(pro2,  strLen,true);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
index d040ddc229..e0b6893991 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
@@ -28,7 +28,6 @@
 import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AFPAlignmentDisplay;
-import org.biojava.nbio.structure.align.util.ConfigurationException;
 import org.biojava.nbio.structure.geometry.Matrices;
 import org.biojava.nbio.structure.geometry.SuperPositions;
 import org.biojava.nbio.structure.jama.Matrix;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
index 5a4c8b69ec..198813783d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
@@ -358,10 +358,8 @@ else if ( params.getScoringStrategy() == CeParameters.ScoringStrategy.CA_AND_SID
 	 * @param ca
 	 * @param nse
 	 * @return
-	 * @throws StructureException
-	 */
-	private double[][] initIntraDistmatrix(Atom[] ca, int nse) throws StructureException
-	{
+     */
+	private double[][] initIntraDistmatrix(Atom[] ca, int nse) {
 
 
 		double[][] intraDist = new double[nse][nse];
@@ -1541,7 +1539,7 @@ public static double[][] updateMatrixWithSequenceConservation(double[][] max, At
 		}
 
 
-		AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet set = AminoAcidCompoundSet.aminoAcidCompoundSet;
 
 		for (int i = 0 ; i < origM.getRowDimension() ; i++){
 			for ( int j =0; j < origM.getColumnDimension() ; j ++ ) {
@@ -1960,9 +1958,8 @@ private void rot_mol(Atom[] caA, Atom[] caB, int nse2, Matrix m , Atom shift) {
 	 * @param storeTransform
 	 * @param show
 	 * @return RMSD
-	 * @throws StructureException
-	 */
-	public double calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform, boolean show) throws StructureException {
+     */
+	public double calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform, boolean show) {
 
 		Atom[] cod1 = getAtoms(pro1,  strLen,false);
 		Atom[] cod2 = getAtoms(pro2,  strLen,true);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeSideChainMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeSideChainMain.java
index 6d3a366dee..034ea5b581 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeSideChainMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeSideChainMain.java
@@ -21,7 +21,6 @@
 package org.biojava.nbio.structure.align.ce;
 
 import org.biojava.nbio.structure.align.StructureAlignment;
-import org.biojava.nbio.structure.align.util.ConfigurationException;
 
 
 public class CeSideChainMain  extends CeMain implements StructureAlignment {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/UserArgumentProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/UserArgumentProcessor.java
index f1ded24d04..e286356b8c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/UserArgumentProcessor.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/UserArgumentProcessor.java
@@ -20,8 +20,6 @@
  */
 package org.biojava.nbio.structure.align.ce;
 
-import org.biojava.nbio.structure.align.util.ConfigurationException;
-
 public interface UserArgumentProcessor {
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java
index cd7a2332f0..c19b840c08 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java
@@ -111,7 +111,7 @@ public FarmJobRunnable(FarmJobParameters params){
 		cache = new AtomCache( params.getPdbFilePath(), params.getCacheFilePath());
 
 
-		if ( params.getServer()!= null && (!params.getServer().equals("") ) ) {
+		if ( params.getServer()!= null && (!params.getServer().isEmpty()) ) {
 
 			RemotePDPProvider pdpprovider = new RemotePDPProvider();
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
index afb83ad348..6759265628 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
@@ -31,10 +31,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
+import java.io.*;
+import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLEncoder;
 import java.util.Random;
@@ -184,21 +182,18 @@ public static AFPChain getAFPChainFromServer(String serverLocation , String meth
 			// 5 sec
 			InputStream stream = URLConnectionTools.getInputStream(url,timeout);
 
-			String xml = null;
 
-			if ( stream != null) {
 
-				xml = convertStreamToString(stream);
+			if ( stream != null) {
+				String xml = convertStreamToString(stream);
+				return AFPChainXMLParser.fromXML(xml, name1, name2, ca1, ca2);
 			}
-			if (xml != null) {
 
-				return AFPChainXMLParser.fromXML (xml, name1, name2, ca1, ca2);
 
-			} else {
-				return null;
-			}
+			return null;
+
 			// TODO dmyersturnbull: method should throw; we shouldn't catch here
-		} catch (IOException | StructureException e){
+		} catch (IOException e){
 			logger.error("error in JFatCatClient: getAFPChainFromServer",e);
 		}
 		return null;
@@ -293,7 +288,7 @@ public static int getRandomSleepTime() {
 	}
 
 
-	public static final void sendAFPChainToServer(String serverLocation, AFPChain afpChain,Atom[] ca1, Atom[] ca2) throws JobKillException
+	public static void sendAFPChainToServer(String serverLocation, AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws JobKillException
 	{
 
 		String sendURL = serverLocation + sendAPPEND;
@@ -327,7 +322,7 @@ public static final void sendAFPChainToServer(String serverLocation, AFPChain af
 
 	}
 
-	public static final int getTimeout(){
+	public static int getTimeout(){
 		String timeoutS = resourceManager.getString("connection.timeout");
 		int timeout = 60000;
 
@@ -340,7 +335,7 @@ public static final int getTimeout(){
 	}
 
 
-	public static final PdbPairsMessage getPdbPairs(String url,int nrPair, String username) throws IOException, JobKillException {
+	public static PdbPairsMessage getPdbPairs(String url, int nrPair, String username) throws IOException, JobKillException {
 
 
 		String urlS= url + "getPairs?" + "nrPairs=" + nrPair + "&username=" + URLEncoder.encode(username, "UTF-8");
@@ -371,7 +366,7 @@ public static final PdbPairsMessage getPdbPairs(String url,int nrPair, String us
 	}
 
 
-	public static final SortedSet<String> getRepresentatives(String serverLocation, int cutoff){
+	public static SortedSet<String> getRepresentatives(String serverLocation, int cutoff){
 		SortedSet<String> representatives = new TreeSet<>();
 
 		String representURL = serverLocation + representAPPEND;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
index ce8e34b3e6..d6b8962da1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
@@ -662,7 +662,7 @@ public static ScopDomain guessScopDomain(String name, ScopDatabase scopDB) {
 			ScopDomain bestMatch = match.next();
 			if(logger.isWarnEnabled()) {
 				StringBuilder warnMsg = new StringBuilder();
-				warnMsg.append("Trying domain " + bestMatch.getScopId() + ".");
+				warnMsg.append("Trying domain ").append(bestMatch.getScopId()).append(".");
 				if (match.hasNext()) {
 					warnMsg.append(" Other possibilities: ");
 					while (match.hasNext()) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java
index ae3acd965e..00572209e8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java
@@ -32,7 +32,6 @@
 import org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner;
 import org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters;
 import org.biojava.nbio.structure.align.model.AFPChain;
-import org.biojava.nbio.structure.align.util.ConfigurationException;
 
 
 public class FatCat
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
index 92dd9a08e4..eba0840f89 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
@@ -45,7 +45,7 @@ public class AFPCalculator
 	public static final boolean debug = FatCatAligner.debug;
 
 
-	public static final  void extractAFPChains(FatCatParameters params, AFPChain afpChain,Atom[] ca1,Atom[] ca2) throws StructureException {
+	public static void extractAFPChains(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2) {
 
 
 
@@ -144,7 +144,7 @@ public static final  void extractAFPChains(FatCatParameters params, AFPChain afp
 	 * @param p2e
 	 * @return
 	 */
-	private static final double getEnd2EndDistance(Atom[] ca1, Atom[] ca2, int p1b, int p1e, int p2b, int p2e)
+	private static double getEnd2EndDistance(Atom[] ca1, Atom[] ca2, int p1b, int p1e, int p2b, int p2e)
 	{
 
 		double min;
@@ -164,7 +164,7 @@ private static final double getEnd2EndDistance(Atom[] ca1, Atom[] ca2, int p1b,
 	 * @return
 	 */
 
-	private static final  boolean filterTerminal(Atom[] ca1, Atom[] ca2, int p1b, int p1e, int p2b, int p2e, int fragLen, int minLen)
+	private static boolean filterTerminal(Atom[] ca1, Atom[] ca2, int p1b, int p1e, int p2b, int p2e, int fragLen, int minLen)
 	{
 		int     d1 = Math.min(p1b, p2b);
 		int     d2 = Math.min((ca1.length - p1e), (ca2.length - p2e));
@@ -178,8 +178,8 @@ private static final  boolean filterTerminal(Atom[] ca1, Atom[] ca2, int p1b, in
 
 	}
 
-	private static final double getRmsd(Atom[] ca1, Atom[] ca2, int fragLen,
-			int p1, int p2, Matrix m, Atom t) {
+	private static double getRmsd(Atom[] ca1, Atom[] ca2, int fragLen,
+                                  int p1, int p2, Matrix m, Atom t) {
 
 
 		double rmsd = 99.9;
@@ -208,8 +208,8 @@ private static final double getRmsd(Atom[] ca1, Atom[] ca2, int fragLen,
 	 * @param clone: returns a copy of the atom (in case the coordinate get manipulated...)
 	 * @return an Atom[] array
 	 */
-	private static final Atom[] getFragment(Atom[] caall, int pos, int fragmentLength ,
-			boolean clone){
+	private static Atom[] getFragment(Atom[] caall, int pos, int fragmentLength ,
+                                      boolean clone){
 
 		if ( pos+fragmentLength > caall.length)
 			return null;
@@ -232,7 +232,7 @@ private static final Atom[] getFragment(Atom[] caall, int pos, int fragmentLengt
 	 * Assign score to each AFP
 	 */
 
-	private static final double scoreAfp(AFP afp, double badRmsd, double fragScore)
+	private static double scoreAfp(AFP afp, double badRmsd, double fragScore)
 	{
 		//longer AFP with low rmsd is better
 		double  s, w;
@@ -246,7 +246,7 @@ private static final double scoreAfp(AFP afp, double badRmsd, double fragScore)
 	//------------------------------------------------------------------
 	//Sort the AFPs in increase of their diagonals(i,j)
 	//------------------------------------------------------------------
-	public static final  void sortAfps(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
+	public static void sortAfps(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
 	{
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
index db9a385b0c..a2775962e7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
@@ -28,7 +28,6 @@
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.AFPTwister;
 import org.biojava.nbio.structure.align.model.AFP;
 import org.biojava.nbio.structure.align.model.AFPChain;
@@ -309,8 +308,8 @@ public static boolean afpPairConn(int afp1, int afp2,  FatCatParameters params,
 
 	{
 
-		Double conn;
-		Double dvar;
+		double conn;
+		double dvar;
 
 		double misScore = params.getMisScore();
 		double maxPenalty = params.getMaxPenalty();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
index 96aa0217af..203c004b91 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
@@ -119,7 +119,7 @@ public StructureAlignmentOptimizer(int b1, int end1, Atom[] c1, int b2, int end2
 			equSet[0][i] = iniSet[0][i];
 			equSet[1][i] = iniSet[1][i];
 			if(iniSet[0][i] > len1 || iniSet[1][i] > len2)  {
-				throw new RuntimeException(String.format("StructureAlignmentOptimizer: focus exceeds the protein 1 or 2 length!"));
+				throw new RuntimeException("StructureAlignmentOptimizer: focus exceeds the protein 1 or 2 length!");
 			}
 		}
 
@@ -353,9 +353,7 @@ private void calMatrix() {
 	 * the equivalent residues: residues where Dij &lt;= Dc and i,j is an aligned pair
 	 * use the previous superimposing
 	 */
-	private boolean defineEquPos(int alnLen, int[][] alnList)
-	throws StructureException
-	{
+	private boolean defineEquPos(int alnLen, int[][] alnList) {
 		int     i, r1, r2;
 		int     equLenOld = equLen;
 		int[][]    equSetOld = new int[2][equLenOld];
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java
index 659ebd1780..965bd590a8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java
@@ -23,8 +23,6 @@
 package org.biojava.nbio.structure.align.helper;
 
 import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Iterator;
 import java.util.List;
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
index 210e27487e..484df94c85 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
@@ -24,7 +24,6 @@
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collections;
 import java.util.List;
 
 import javax.vecmath.Matrix4d;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
index ce50208f14..3a87e917d1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
@@ -115,11 +115,10 @@ public MultipleMcMain(StructureAlignment pairwiseAlgo){
 	 * @return MultipleAlignment seed alignment
 	 * @throws ExecutionException
 	 * @throws InterruptedException
-	 * @throws StructureException
-	 */
+     */
 	private MultipleAlignment generateSeed(List<Atom[]> atomArrays)
 			throws InterruptedException,
-			ExecutionException, StructureException {
+			ExecutionException {
 
 		int size = atomArrays.size();
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
index b1f6ced268..5b331f7ae5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -251,8 +251,7 @@ public MultipleAlignment optimize() throws StructureException {
 			MultipleAlignment lastMSA = msa.clone();
 			List<SortedSet<Integer>> lastFreePool = new ArrayList<>();
 			for (int k = 0; k < size; k++) {
-				SortedSet<Integer> p = new TreeSet<>();
-				p.addAll(freePool.get(k));
+                SortedSet<Integer> p = new TreeSet<>(freePool.get(k));
 				lastFreePool.add(p);
 			}
 			double lastScore = mcScore;
@@ -843,9 +842,9 @@ private void saveHistory(String filePath) throws IOException {
 
 		for (int i = 0; i < lengthHistory.size(); i++) {
 			writer.append(String.valueOf(i * 100));
-			writer.append("," + lengthHistory.get(i));
-			writer.append("," + rmsdHistory.get(i));
-			writer.append("," + scoreHistory.get(i) + "\n");
+			writer.append(",").append(String.valueOf(lengthHistory.get(i)));
+			writer.append(",").append(String.valueOf(rmsdHistory.get(i)));
+			writer.append(",").append(String.valueOf(scoreHistory.get(i))).append("\n");
 		}
 		writer.flush();
 		writer.close();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java
index 19cb367441..de74dc2549 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java
@@ -27,7 +27,6 @@
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.multiple.Block;
 import org.biojava.nbio.structure.align.multiple.BlockSet;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
index 82ff77eff3..d3f91cf501 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
@@ -395,11 +395,9 @@ public static double getRefTMScore(List<Atom[]> transformed,
 	 * @param dCutoff
 	 *            the distance cutoff
 	 * @return the value of the score
-	 * @throws StructureException
-	 */
+     */
 	public static double getMCScore(MultipleAlignment alignment,
-			double gapOpen, double gapExtension, double dCutoff)
-			throws StructureException {
+			double gapOpen, double gapExtension, double dCutoff) {
 
 		List<Atom[]> trans = MultipleAlignmentTools.transformAtoms(alignment);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
index 68b07632b0..bb67cbc64a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
@@ -23,8 +23,6 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -818,7 +816,7 @@ public static MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> toPr
 		return msa;
 	}
 
-	public static Structure toMultimodelStructure(MultipleAlignment multAln, List<Atom[]> transformedAtoms) throws StructureException {
+	public static Structure toMultimodelStructure(MultipleAlignment multAln, List<Atom[]> transformedAtoms) {
 		PDBHeader header = new PDBHeader();
 		String title = multAln.getEnsemble().getAlgorithmName() + " V."
 				+ multAln.getEnsemble().getVersion() + " : ";
@@ -843,7 +841,7 @@ public static Structure toMultimodelStructure(MultipleAlignment multAln, List<At
 	 * @return a structure object containing a set of models,
 	 * 			one for each input array of Atoms.
 	 */
-	public static final Structure getAlignedStructure(List<Atom[]> atomArrays) {
+	public static Structure getAlignedStructure(List<Atom[]> atomArrays) {
 
 		Structure s = new StructureImpl();
 		for (int i=0; i<atomArrays.size(); i++){
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
index a34d6e7b90..ffd7408a04 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
@@ -90,7 +90,7 @@ public static String toFatCat(MultipleAlignment alignment) {
 
 		// Initialize the String and put the summary information
 		StringWriter fatcat = new StringWriter();
-		fatcat.append(alignment.toString() + "\n\n");
+		fatcat.append(alignment.toString()).append("\n\n");
 
 		// Get the alignment sequences and the mapping
 		List<Integer> mapSeqToStruct = new ArrayList<>();
@@ -111,14 +111,12 @@ public static String toFatCat(MultipleAlignment alignment) {
 		// Write the Sequence Alignment
 		for (int str = 0; str < alignment.size(); str++) {
 			if (str < 9) {
-				fatcat.append("Chain 0" + (str + 1) + ": "
-						+ alnSequences.get(str) + "\n");
+				fatcat.append("Chain 0").append(String.valueOf(str + 1)).append(": ").append(alnSequences.get(str)).append("\n");
 			} else {
-				fatcat.append("Chain " + (str + 1) + ": "
-						+ alnSequences.get(str) + "\n");
+				fatcat.append("Chain ").append(String.valueOf(str + 1)).append(": ").append(alnSequences.get(str)).append("\n");
 			}
 			if (str != alignment.size() - 1) {
-				fatcat.append("          " + blockNumbers + "\n");
+				fatcat.append("          ").append(blockNumbers).append("\n");
 			}
 		}
 		return fatcat.toString();
@@ -145,15 +143,14 @@ public static String toAlignedResidues(MultipleAlignment multAln) {
 
 		// Write structure names & PDB codes
 		for (int str = 0; str < multAln.size(); str++) {
-			residueGroup.append("#Struct" + (str + 1) + ":\t");
+			residueGroup.append("#Struct").append(String.valueOf(str + 1)).append(":\t");
 			residueGroup.append(multAln.getEnsemble().getStructureIdentifiers()
 					.get(str).getIdentifier());
 			residueGroup.append("\n");
 		}
 		// Whrite header for columns
 		for (int str = 0; str < multAln.size(); str++)
-			residueGroup.append("#Num" + (str + 1) + "\tChain" + (str + 1)
-					+ "\tAA" + (str + 1) + "\t");
+			residueGroup.append("#Num").append(String.valueOf(str + 1)).append("\tChain").append(String.valueOf(str + 1)).append("\tAA").append(String.valueOf(str + 1)).append("\t");
 		residueGroup.append("\n");
 
 		// Write optimally aligned pairs
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.java
index c6068e1365..9a0a32ea37 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.java
@@ -22,7 +22,6 @@
 
 import java.util.List;
 
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.multiple.BlockSet;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java
index a11fcdef4b..c7b0c57192 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java
@@ -27,7 +27,6 @@
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.multiple.Block;
 import org.biojava.nbio.structure.align.multiple.BlockSet;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
index c9dab3c084..e8fe142693 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
@@ -134,13 +134,7 @@ public String toString(){
 		d2.setMinimumFractionDigits(2);
 		d2.setMaximumFractionDigits(2);
 		StringBuilder s = new StringBuilder();
-		s.append("#" + getAltAligNumber() +
-				" cluster:" + cluster +
-				" eqr:" + getEqr() +
-				" rmsd:" + d2.format(getRmsd()) +
-				" %id:" + getPercId() +
-				" gaps:" + getGaps() +
-				" score:" + d2.format(score)	);
+		s.append("#").append(getAltAligNumber()).append(" cluster:").append(cluster).append(" eqr:").append(getEqr()).append(" rmsd:").append(d2.format(getRmsd())).append(" %id:").append(getPercId()).append(" gaps:").append(getGaps()).append(" score:").append(d2.format(score));
 
 		return s.toString();
 	}
@@ -305,7 +299,7 @@ private void rotateShiftAtoms(Atom[] ca){
 		//System.out.println("after " + ca[0]);
 	}
 
-	public void finish(StrucAligParameters params,Atom[]ca1,Atom[]ca2) throws StructureException{
+	public void finish(StrucAligParameters params,Atom[]ca1,Atom[]ca2) {
 
 		Atom[] ca3 = new Atom[ca2.length];
 		for ( int i = 0 ; i < ca2.length;i++){
@@ -450,10 +444,9 @@ private static Alignable getInitalStrCompAlignment(
 	 * @param params the parameters
 	 * @param ca1 atoms of structure 1
 	 * @param ca2 atoms of structure 2
-	 * @throws StructureException
-	 */
+     */
 
-	public void refine(StrucAligParameters params,Atom[]ca1,Atom[]ca2) throws StructureException{
+	public void refine(StrucAligParameters params,Atom[]ca1,Atom[]ca2) {
 		// System.out.println("refine Alternative Alignment #"+ getAltAligNumber()+" l1:" + ca1.length + " l2:" + ca2.length);
 		//		for ( int i= 0 ; i < idx1.length;i++){
 		//		System.out.println(idx1[i] + " " + idx2[i]);
@@ -738,7 +731,7 @@ private int count_gaps(int[] i1, int[] i2){
 
 
 
-	public void calculateSuperpositionByIdx(Atom[] ca1, Atom[] ca2)throws StructureException {
+	public void calculateSuperpositionByIdx(Atom[] ca1, Atom[] ca2) {
 
 		super_pos_alig(ca1,ca2,idx1,idx2,false);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
index 4dc944ee9c..4ceecdf37a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
@@ -215,7 +215,7 @@ public JointFragments[] approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] frag
 
 	private boolean densityCheckOk(Atom[] aa1, Atom[] aa2, List<int[]> idxlist,
 											 int p2i, int p2j, int l2,
-											 double densityCutoff) throws StructureException {
+											 double densityCutoff) {
 		JointFragments ftmp = new JointFragments();
 		ftmp.setIdxlist(idxlist);
 		ftmp.add(p2i,p2j,0,l2);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java
index bba233c390..ed127b7529 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java
@@ -41,7 +41,6 @@
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AFPAlignmentDisplay;
 import org.biojava.nbio.structure.align.util.AlignmentTools;
-import org.biojava.nbio.structure.align.util.ConfigurationException;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
@@ -77,7 +76,7 @@ public class SmithWaterman3Daligner extends AbstractStructureAlignment implement
 	private static final String version = "1.1";
 	private SmithWaterman3DParameters params;
 
-	public static void main(String[] args) throws ConfigurationException {
+	public static void main(String[] args) {
 		//args = new String[]{"-pdb1","1cdg.A","-pdb2","1tim.A","-pdbFilePath","/tmp/","-show3d","-printFatCat"};
 		UserArgumentProcessor processor = new SmithWatermanUserArgumentProcessor();
 		processor.process(args);
@@ -184,7 +183,7 @@ private AFPChain convert(Atom[] ca1, Atom[] ca2,  SequencePair<ProteinSequence,
 		char[] alnseq2 = new char[ca1Length+ca2Length+1] ;
 		char[] alnsymb = new char[ca1Length+ca2Length+1];
 
-		Compound gapSymbol =  AminoAcidCompoundSet.getAminoAcidCompoundSet().getCompoundForString("-");
+        Compound gapSymbol =  AminoAcidCompoundSet.aminoAcidCompoundSet.getCompoundForString("-");
 
 		int pos = 0 ; // aligned positions
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
index 6e32db9656..aa52b671c2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -1092,19 +1092,15 @@ public static int[] calculateBlockGap(int[][][] optAln){
 			//Loop for every position in the block
 			for (int j=0; j<optAln[i][0].length; j++){
 				//If the first position is evaluated initialize the last positions
-				if (j==0){
-					last1 = optAln[i][0][j];
-					last2 = optAln[i][1][j];
-				}
-				else{
+				if (j != 0) {
 					//If one of the positions or both are not contiguous increment the number of gaps
-					if (optAln[i][0][j] > last1+1 || optAln[i][1][j] > last2+1){
+					if (optAln[i][0][j] > last1 + 1 || optAln[i][1][j] > last2 + 1) {
 						gaps++;
 					}
 					//Otherwise just set the last position to the current one
-					last1 = optAln[i][0][j];
-					last2 = optAln[i][1][j];
 				}
+				last1 = optAln[i][0][j];
+				last2 = optAln[i][1][j];
 			}
 			blockGap[i] = gaps;
 		}
@@ -1233,7 +1229,7 @@ public static List<Chain> getAlignedModel(Atom[] ca){
 	 * @param ca2
 	 * @return a structure object containing two models, one for each set of Atoms.
 	 */
-	public static final Structure getAlignedStructure(Atom[] ca1, Atom[] ca2) {
+	public static Structure getAlignedStructure(Atom[] ca1, Atom[] ca2) {
 
 		/* Previous implementation commented
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index 728c211add..8584c901b1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -510,8 +510,7 @@ public Structure getStructure(String name) throws IOException, StructureExceptio
 	 * @throws StructureException
 	 */
 	public Structure getStructure(StructureIdentifier strucId) throws IOException, StructureException {
-		Structure s = strucId.loadStructure(this);
-		Structure r = strucId.reduce(s);
+		Structure r = strucId.reduce(strucId.loadStructure(this));
 		r.setStructureIdentifier(strucId);
 		return r;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java
index c4697356e3..cb828bb7d4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java
@@ -39,7 +39,6 @@
 import java.beans.PropertyDescriptor;
 import java.io.*;
 import java.lang.reflect.Array;
-import java.lang.reflect.InvocationTargetException;
 import java.util.*;
 
 /**
@@ -153,7 +152,7 @@ public static String[] configureBean(Object bean, String[] args)
 
 					if (propType == Integer.TYPE) {
 						try {
-							propVal = new Integer(args[++i]);
+							propVal = Integer.valueOf(args[++i]);
 						} catch (Exception ex) {
 							throw new ConfigurationException("Option " + arg + " requires an integer parameter");
 						}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainFlipper.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainFlipper.java
index c1640aecf2..231c82581f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainFlipper.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainFlipper.java
@@ -26,7 +26,6 @@
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.jama.Matrix;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java
index aa98063e4d..eb77f56bd1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java
@@ -61,7 +61,7 @@ public class AFPChainXMLParser
 	 * @param ca2
 	 * @return
 	 */
-	 public static AFPChain fromXML(String xml, String name1, String name2, Atom[] ca1, Atom[] ca2) throws IOException, StructureException{
+	 public static AFPChain fromXML(String xml, String name1, String name2, Atom[] ca1, Atom[] ca2) throws IOException {
 			AFPChain[] afps = parseMultiXML( xml);
 			if ( afps.length > 0 ) {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java
index 1e174584b3..a8526fd6cd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java
@@ -206,7 +206,7 @@ public static Block parseBlock(Node root, BlockSet blockSet) {
 					if (residue.equals("null")){
 						alignRes.get(str-1).add(null);
 					} else {
-						alignRes.get(str-1).add(new Integer(residue));
+						alignRes.get(str-1).add(Integer.valueOf(residue));
 					}
 
 					str++;
@@ -268,12 +268,12 @@ public static void parseHeader(Node node,
 
 		String ioTime = atts.getNamedItem("IOTime").getTextContent();
 		if (!ioTime.equals("null")){
-			ensemble.setIoTime(new Long(ioTime));
+			ensemble.setIoTime(Long.valueOf(ioTime));
 		}
 
 		String time = atts.getNamedItem("CalculationTime").getTextContent();
 		if (!time.equals("null")){
-			ensemble.setCalculationTime(new Long(time));
+			ensemble.setCalculationTime(Long.valueOf(time));
 		}
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/RepresentativeXMLConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/RepresentativeXMLConverter.java
index db0ce1331b..ff713b592a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/RepresentativeXMLConverter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/RepresentativeXMLConverter.java
@@ -39,7 +39,7 @@
 public class RepresentativeXMLConverter {
 
 
-	public static final String toXML(SortedSet<String> representatives){
+	public static String toXML(SortedSet<String> representatives){
 		StringWriter sw = new StringWriter();
 		PrintWriter writer = new PrintWriter(sw);
 
@@ -59,7 +59,7 @@ public static final String toXML(SortedSet<String> representatives){
 		return sw.toString();
 	}
 
-	public static final SortedSet<String> fromXML(String xml){
+	public static SortedSet<String> fromXML(String xml){
 		SortedSet<String> representatives = new TreeSet<>();
 		try {
 			DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java
index 386003b903..031b635628 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java
@@ -630,14 +630,14 @@ public Matrix4d basePairReferenceFrame(Pair<Group> pair) {
 	public String toString() {
 		if (getPairingParameters() == null) return "No data";
 		StringBuilder result = new StringBuilder(10000);
-		result.append(pairingParameters.length + " base pairs\n");
+		result.append(pairingParameters.length).append(" base pairs\n");
 		result.append("bp: buckle propeller opening shear stretch stagger tilt roll twist shift slide rise\n");
 		for (int i = 0; i < pairingParameters.length; i++) {
-			result.append(pairingNames.get(i)+": ");
+			result.append(pairingNames.get(i)).append(": ");
 			for (int j = 0; j < 6; j++)
-				result.append(String.format("%5.4f", pairingParameters[i][j]) + " ");
+				result.append(String.format("%5.4f", pairingParameters[i][j])).append(" ");
 			for (int j = 0; j < 6; j++)
-				result.append(String.format("%5.4f", stepParameters[i][j]) + " ");
+				result.append(String.format("%5.4f", stepParameters[i][j])).append(" ");
 			result.append("\n");
 		}
 		return result.toString();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathCategory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathCategory.java
index dfdd74d65f..14f30e7cda 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathCategory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathCategory.java
@@ -98,7 +98,7 @@ public String toString() {
 	public static CathCategory fromCathCode(String code) {
 		int count = 0;
 		int idx = 0;
-		while ((idx = code.indexOf(".",idx)) != -1) {
+		while ((idx = code.indexOf('.',idx)) != -1) {
 			count++;
 			idx++;
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
index ea2f7cbb00..ba6017cffb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
@@ -450,9 +450,9 @@ private void parseCathDomainDescriptionFile(BufferedReader bufferedReader) throw
 				sseqh = new StringBuilder();
 				sseqs = new StringBuilder();
 			} else if ( line.startsWith("SRANGE") ) {
-				int startStart = line.indexOf("=",10) + 1;
-				int startStop = line.indexOf(" ",10);
-				int stopStart = line.indexOf("=",startStop) + 1;
+				int startStart = line.indexOf('=',10) + 1;
+				int startStop = line.indexOf(' ',10);
+				int stopStart = line.indexOf('=',startStop) + 1;
 //                Integer start = Integer.parseInt( line.substring(startStart,startStop) );
 //                Integer stop = Integer.parseInt( line.substring(stopStart, line.length()) );
 				segment.setStart( line.substring(startStart,startStop) );
@@ -524,7 +524,7 @@ private CathNode parseCathNamesFileLine(String line) {
 		CathNode cathNode = new CathNode();
 		String[] token = line.split("\\s+",3);
 		cathNode.setNodeId( token[0] );
-		int idx = token[0].lastIndexOf(".");
+		int idx = token[0].lastIndexOf('.');
 		if ( idx == -1 ) idx = token[0].length();
 		cathNode.setParentId( token[0].substring( 0, idx ) );
 		cathNode.setRepresentative( token[1] );
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
index e2d3183db7..cd29c164e0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
@@ -300,7 +300,7 @@ protected Atom[] getAtomsForAsa(int cofactorSizeToUse) {
 	 * non-Hydrogen atoms are not included
 	 * @return
 	 */
-	private static final Atom[] getAllNonHAtomArray(Atom[] m, int minSizeHetAtomToInclude) {
+	private static Atom[] getAllNonHAtomArray(Atom[] m, int minSizeHetAtomToInclude) {
 		List<Atom> atoms = new ArrayList<>();
 
 		for (Atom a:m){
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java
index 3b621d9be6..28ff97bd7c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java
@@ -74,9 +74,8 @@ public static List<Domain> suggestDomains(Structure s) throws StructureException
 	 *
 	 * @param ca an array of Calpha atoms
 	 * @return a list of possible domains
-	 * @throws StructureException
-	 */
-	public static List<Domain> suggestDomains(Atom[] ca) throws StructureException{
+     */
+	public static List<Domain> suggestDomains(Atom[] ca) {
 
 		GetDistanceMatrix distMaxCalculator = new GetDistanceMatrix();
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java
index a333ff6fe9..d20ca5c2e6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java
@@ -30,7 +30,6 @@
 import javax.xml.parsers.SAXParser;
 import javax.xml.parsers.SAXParserFactory;
 import java.io.*;
-import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.SortedSet;
 import java.util.TreeSet;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java
index 9e8eda55e7..541ae282f2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java
@@ -108,9 +108,8 @@ private void loadRepresentativeDomainAssignments() throws IOException {
 				// work around list in results;
 
 				String[] spl = range.split(",");
-				SortedSet<String> value = new TreeSet<>();
 
-                value.addAll(Arrays.asList(spl));
+                SortedSet<String> value = new TreeSet<>(Arrays.asList(spl));
 				serializedCache.put(entry.getKey(), value);
 			}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
index c40fda1509..0e92516846 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
@@ -123,9 +123,8 @@ private void loadRepresentativeDomains() throws IOException {
 				// work around list in results;
 
 				String[] spl = range.split(",");
-				SortedSet<String> value = new TreeSet<>();
 
-                value.addAll(Arrays.asList(spl));
+                SortedSet<String> value = new TreeSet<>(Arrays.asList(spl));
 				serializedCache.put(entry.getKey(), value);
 			}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java
index 345e849c74..6ffb9d594b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java
@@ -144,7 +144,7 @@ public static List<Domain> cluster(List<Domain> domains, PDPDistanceMatrix pdpDi
 			domains.get(Si).avd=domcont(domains.get(Si));
 			domains.get(Sj).avd=domcont(domains.get(Sj));
 				 */
-				if(verbose) System.out.println(String.format(" Listing the domains after combining..."));
+				if(verbose) System.out.println(" Listing the domains after combining...");
 				if(verbose) listdomains (domains);
 			}
 			else if (maximum_valuem > PDPParameters.CUT_OFF_VALUE1M) {
@@ -162,7 +162,7 @@ else if (maximum_valuem > PDPParameters.CUT_OFF_VALUE1M) {
 			domains[Sim].avd=domcont(domains[Sim]);
 			domains[Sjm].avd=domcont(domains[Sjm]);
 				 */
-				if(verbose) System.out.println(String.format(" Listing the domains after combining..."));
+				if(verbose) System.out.println(" Listing the domains after combining...");
 				if(verbose) listdomains (domains);
 			}
 			else if (maximum_values > PDPParameters.CUT_OFF_VALUE1S) {
@@ -180,11 +180,11 @@ else if (maximum_values > PDPParameters.CUT_OFF_VALUE1S) {
 			domains[Sis].avd=domcont(domains[Sis]);
 			domains[Sjs].avd=domcont(domains[Sjs]);
 				 */
-				if(verbose) System.out.println(String.format(" Listing the domains after combining..."));
+				if(verbose) System.out.println(" Listing the domains after combining...");
 				if(verbose) listdomains(domains);
 			}
 			else {
-				if(verbose) System.out.println(String.format(" Maximum value is less than cut off value. (max:" + maximum_value+")" ));
+				if(verbose) System.out.println(" Maximum value is less than cut off value. (max:" + maximum_value+")");
 				maximum_value = -1.0;
 				maximum_values = -1.0;
 				maximum_valuem = -1.0;
@@ -192,7 +192,7 @@ else if (maximum_values > PDPParameters.CUT_OFF_VALUE1S) {
 			}
 		} while ( maximum_value > 0.0||maximum_values>0.0||maximum_valuem>0.0);
 
-		if(verbose) System.out.println(String.format(" The domains are:"));
+		if(verbose) System.out.println(" The domains are:");
 		if(verbose) listdomains(domains);
 		return domains;
 	}
@@ -268,7 +268,7 @@ private static long calc_S (int a1,int b1,int a2,int b2, PDPDistanceMatrix pdpDi
 		return contacts;
 	}
 
-	private static final void listdomains(List<Domain> domains){
+	private static void listdomains(List<Domain> domains){
 
 		int i = -1;
 		for ( Domain dom : domains){
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/CutDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/CutDomain.java
index d16bfe6c30..870882fe75 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/CutDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/CutDomain.java
@@ -67,7 +67,7 @@ public  void cutDomain(Domain dom, CutSites cut_sites, PDPDistanceMatrix pdpMatr
 		val.first_cut = true;
 
 
-		Cut cut = new Cut();
+//		Cut cut = new Cut();
 
 		site = Cut.cut(ca,dom,val, dist, pdpMatrix);
 		if ( verbose )
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java
index d6fed972c8..c91a573b5c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java
@@ -40,7 +40,6 @@
 
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.Comparator;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -131,7 +130,7 @@ public static void createPurelyNonPolyEntities(List<List<Chain>> nonPolyModels,
 		// let's find first the max entity id to assign entity ids to the newly found entities
 		int maxMolId = 0;
 		if (!entities.isEmpty()) {
-			maxMolId = Collections.max(entities, (o1, o2) -> new Integer(o1.getMolId()).compareTo(o2.getMolId())).getMolId();
+			maxMolId = Collections.max(entities, (o1, o2) -> Integer.compare(o1.getMolId(), o2.getMolId())).getMolId();
 		}
 		// we go one over the max
 		int molId = maxMolId + 1;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
index e2e28a77db..f69c3d7580 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
@@ -84,7 +84,7 @@ public static AFPChain cpFastaToAfpChain(String first, String second, Structure
 	 */
 	public static AFPChain cpFastaToAfpChain(File fastaFile, Structure structure, int cpSite) throws IOException, StructureException {
 		InputStream inStream = new FileInputStream(fastaFile);
-		SequenceCreatorInterface<AminoAcidCompound> creator = new CasePreservingProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet());
+        SequenceCreatorInterface<AminoAcidCompound> creator = new CasePreservingProteinSequenceCreator(AminoAcidCompoundSet.aminoAcidCompoundSet);
 		SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound> headerParser = new GenericFastaHeaderParser<>();
 		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(inStream, headerParser, creator);
 		LinkedHashMap<String, ProteinSequence> sequences = fastaReader.process();
@@ -194,8 +194,8 @@ public static AFPChain cpFastaToAfpChain(ProteinSequence first, ProteinSequence
 	public static AFPChain fastaFileToAfpChain(File fastaFile, Structure structure1, Structure structure2)
 			throws IOException, StructureException {
 		InputStream inStream = new FileInputStream(fastaFile);
-		SequenceCreatorInterface<AminoAcidCompound> creator = new CasePreservingProteinSequenceCreator(
-				AminoAcidCompoundSet.getAminoAcidCompoundSet());
+        SequenceCreatorInterface<AminoAcidCompound> creator = new CasePreservingProteinSequenceCreator(
+                AminoAcidCompoundSet.aminoAcidCompoundSet);
 		SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound> headerParser = new GenericFastaHeaderParser<>();
 		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
 				inStream, headerParser, creator);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java
index 1f5f9da245..df6c66de50 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java
@@ -187,13 +187,13 @@ public String toPDB() {
 		// do for all models
 		int nrModels = structure.nrModels() ;
 		if ( structure.isNmr()) {
-			str.append("EXPDTA    NMR, "+ nrModels+" STRUCTURES"+newline) ;
+			str.append("EXPDTA    NMR, ").append(nrModels).append(" STRUCTURES").append(newline);
 		}
 		for (int m = 0 ; m < nrModels ; m++) {
 
 
 			if ( nrModels>1 ) {
-				str.append("MODEL      " + (m+1)+ newline);
+				str.append("MODEL      ").append(m + 1).append(newline);
 			}
 
 			List<Chain> polyChains = structure.getPolyChains(m);
@@ -598,7 +598,7 @@ public String toMMCIF() {
 
 		StringBuilder str = new StringBuilder();
 
-		str.append(SimpleMMcifParser.MMCIF_TOP_HEADER+"BioJava_mmCIF_file"+newline);
+		str.append(SimpleMMcifParser.MMCIF_TOP_HEADER + "BioJava_mmCIF_file").append(newline);
 
 		if (structure.getPDBHeader()!=null && structure.getPDBHeader().getCrystallographicInfo()!=null &&
 				structure.getPDBHeader().getCrystallographicInfo().getSpaceGroup()!=null &&
@@ -637,7 +637,7 @@ public static String toMMCIF(Chain chain, String authId, String asymId, boolean
 
 	public static String toMMCIF(Chain chain, boolean writeHeader) {
 		StringBuilder sb = new StringBuilder();
-		sb.append(SimpleMMcifParser.MMCIF_TOP_HEADER+"BioJava_mmCIF_file"+newline);
+		sb.append(SimpleMMcifParser.MMCIF_TOP_HEADER + "BioJava_mmCIF_file").append(newline);
 		sb.append(toMMCIF(chain, chain.getName(), chain.getId(),writeHeader));
 		return sb.toString();
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java
index 6350a3551f..1ab5e3d3fc 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java
@@ -53,7 +53,7 @@ private String getCtab(Group thisGroup){
 			String spaceY = getSpace(10, df.format(a.getY()));
 			String spaceZ = getSpace(10, df.format(a.getZ()));
 			String spaceEle = getSpace(4, a.getElement().toString());
-			atomList.append(spaceX+df.format(a.getX())+spaceY+df.format(a.getY())+spaceZ+df.format(a.getZ())+" "+a.getElement().toString()+spaceEle+"0  0  0  0  0  0  0  0  0  0  0  0\n");
+			atomList.append(spaceX).append(df.format(a.getX())).append(spaceY).append(df.format(a.getY())).append(spaceZ).append(df.format(a.getZ())).append(" ").append(a.getElement().toString()).append(spaceEle).append("0  0  0  0  0  0  0  0  0  0  0  0\n");
 			for(Bond b: a.getBonds()){
 				Atom otherAtom = b.getOther(a);
 				if(atoms.indexOf(otherAtom)>=atoms.indexOf(a)){
@@ -106,8 +106,8 @@ private Object getCharges(Group thisGroup) {
 				if(chargeCount==0){
 					outS.append("M  CHG   N");
 				}
-				outS.append(getSpace(4, Integer.toString(i))+(i+1));
-				outS.append(getSpace(4, Short.toString(charge))+charge);
+				outS.append(getSpace(4, Integer.toString(i))).append(i + 1);
+				outS.append(getSpace(4, Short.toString(charge))).append(charge);
 				chargeCount++;
 			}
 			//
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java
index 678b011370..fd2439b37b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java
@@ -151,7 +151,7 @@ private void saveMatrix() {
 	 * Parses list of chain ids (A, B, C, etc.)
 	 */
 	private void addToCurrentChainList(String line) {
-		int index = line.indexOf(":");
+		int index = line.indexOf(':');
 		String chainList = line.substring(index+1).trim();
 		// split by spaces or commas
 		String[] chainIds = chainList.split("[ ,]+");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
index 80b8d31c79..ae8474b990 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -850,7 +850,7 @@ private void pdb_TITLE_Handler(String line) {
 			title = line.substring(10).trim();
 
 		String t = pdbHeader.getTitle();
-		if ( (t != null) && (! t.equals("")) ){
+		if ( (t != null) && (!t.isEmpty()) ){
 			if (t.endsWith("-"))
 				t += ""; // if last line ends with a hyphen then we don't add space
 			else
@@ -932,7 +932,7 @@ private void pdb_COMPND_Handler(String line) {
 		if ((fl >0 ) && compndFieldValues.contains(fieldList[0])) {
 
 			continuationField = fieldList[0];
-			if (previousContinuationField.equals("")) {
+			if (previousContinuationField.isEmpty()) {
 				previousContinuationField = continuationField;
 			}
 
@@ -958,7 +958,7 @@ private void pdb_COMPND_Handler(String line) {
 		while (compndTokens.hasMoreTokens()) {
 			String token = compndTokens.nextToken();
 
-			if (previousContinuationField.equals("")) {
+			if (previousContinuationField.isEmpty()) {
 				previousContinuationField = continuationField;
 			}
 
@@ -976,7 +976,7 @@ private void pdb_COMPND_Handler(String line) {
 			}
 			if (!continuationField.equals(previousContinuationField)) {
 
-				if (continuationString.equals("")) {
+				if (continuationString.isEmpty()) {
 					continuationString = token;
 
 				} else {
@@ -1157,28 +1157,28 @@ private void pdb_SOURCE_Handler(String line) {
 
 		String[] fieldList = line.split("\\s+");
 
-		if (!fieldList[0].equals("")
+		if (!fieldList[0].isEmpty()
 				&& sourceFieldValues.contains(fieldList[0])) {
 			//			System.out.println("[PDBFileParser.pdb_COMPND_Handler] Setting continuationField to '" + fieldList[0] + "'");
 			continuationField = fieldList[0];
-			if (previousContinuationField.equals("")) {
+			if (previousContinuationField.isEmpty()) {
 				previousContinuationField = continuationField;
 			}
 
 		} else if ((fieldList.length > 1) && ( sourceFieldValues.contains(fieldList[1]))) {
 			//			System.out.println("[PDBFileParser.pdb_COMPND_Handler] Setting continuationField to '" + fieldList[1] + "'");
 			continuationField = fieldList[1];
-			if (previousContinuationField.equals("")) {
+			if (previousContinuationField.isEmpty()) {
 				previousContinuationField = continuationField;
 			}
 
 		} else {
-			if (continuationNr.equals("")) {
+			if (continuationNr.isEmpty()) {
 
 				logger.debug("looks like an old PDB file");
 
 				continuationField = "MOLECULE:";
-				if (previousContinuationField.equals("")) {
+				if (previousContinuationField.isEmpty()) {
 					previousContinuationField = continuationField;
 				}
 			}
@@ -1194,7 +1194,7 @@ private void pdb_SOURCE_Handler(String line) {
 		while (compndTokens.hasMoreTokens()) {
 			String token = compndTokens.nextToken();
 
-			if (previousContinuationField.equals("")) {
+			if (previousContinuationField.isEmpty()) {
 				//				System.out.println("previousContinuationField is empty. Setting to : " + continuationField);
 				previousContinuationField = continuationField;
 			}
@@ -1211,7 +1211,7 @@ private void pdb_SOURCE_Handler(String line) {
 			}
 			if (!continuationField.equals(previousContinuationField)) {
 
-				if (continuationString.equals("")) {
+				if (continuationString.isEmpty()) {
 					continuationString = token;
 
 				} else {
@@ -2042,7 +2042,7 @@ private Integer conect_helper (String line,int start,int end) {
 		int bond;
 		Integer b = null ;
 
-		if ( ! sbond.equals("")) {
+		if (!sbond.isEmpty()) {
 			bond = Integer.parseInt(sbond);
 			b = bond;
 		}
@@ -2266,7 +2266,7 @@ private void pdb_SSBOND_Handler(String line){
 			String symop2 = line.substring(66, 72).trim();
 
 			// until we implement proper treatment of symmetry in biojava #220, we can't deal with sym-related parteners properly, skipping them
-			if (!symop1.equals("") && !symop2.equals("") && // in case the field is missing
+			if (!symop1.isEmpty() && !symop2.isEmpty() && // in case the field is missing
 					(!symop1.equals("1555") || !symop2.equals("1555")) ) {
 				logger.info("Skipping ss bond between groups {} and {} belonging to different symmetry partners, because it is not supported yet", seqNum1+icode1, seqNum2+icode2);
 				return;
@@ -2651,7 +2651,7 @@ public  Structure parsePDBFile(BufferedReader buf)
 		while ((line = buf.readLine()) != null) {
 
 			// ignore empty lines
-			if ( line.equals("") ||
+			if (line.isEmpty() ||
 					(line.equals(NEWLINE))){
 				continue;
 			}
@@ -3386,7 +3386,7 @@ private void buildjournalArticle() {
 			if (subField.equals("AUTH")) {
 				auth.append(line.substring(19).trim());
 
-				logger.debug("AUTH '" + auth.toString() + "'");
+				logger.debug("AUTH '" + auth + "'");
 
 			}
 			if (subField.equals("TITL")) {
@@ -3394,26 +3394,26 @@ private void buildjournalArticle() {
 				//words on the join won't be concatenated
 				titl.append(line.substring(19).trim()).append(" ");
 
-				logger.debug("TITL '" + titl.toString() + "'");
+				logger.debug("TITL '" + titl + "'");
 
 			}
 			if (subField.equals("EDIT")) {
 				edit.append(line.substring(19).trim());
 
-				logger.debug("EDIT '" + edit.toString() + "'");
+				logger.debug("EDIT '" + edit + "'");
 
 			}
 			//        JRNL        REF    NAT.IMMUNOL.                  V.   8   430 2007
 			if (subField.equals("REF ")) {
 				ref.append(line.substring(19).trim()).append(" ");
 
-				logger.debug("REF '" + ref.toString() + "'");
+				logger.debug("REF '" + ref + "'");
 
 			}
 			if (subField.equals("PUBL")) {
 				publ.append(line.substring(19).trim()).append(" ");
 
-				logger.debug("PUBL '" + publ.toString() + "'");
+				logger.debug("PUBL '" + publ + "'");
 
 			}
 			//        JRNL        REFN                   ISSN 1529-2908
@@ -3424,21 +3424,21 @@ private void buildjournalArticle() {
 				}
 				refn.append(line.substring(35).trim());
 
-				logger.debug("REFN '" + refn.toString() + "'");
+				logger.debug("REFN '" + refn + "'");
 
 			}
 			//        JRNL        PMID   17351618
 			if (subField.equals("PMID")) {
 				pmid.append(line.substring(19).trim());
 
-				logger.debug("PMID '" + pmid.toString() + "'");
+				logger.debug("PMID '" + pmid + "'");
 
 			}
 			//        JRNL        DOI    10.1038/NI1450
 			if (subField.equals("DOI ")) {
 				doi.append(line.substring(19).trim());
 
-				logger.debug("DOI '" + doi.toString() + "'");
+				logger.debug("DOI '" + doi + "'");
 
 			}
 		}
@@ -3593,7 +3593,7 @@ private String getVolume() {
 	private List<Author> authorBuilder(String authorString) {
 		ArrayList<Author> authorList = new ArrayList<>();
 
-		if (authorString.equals("")) {
+		if (authorString.isEmpty()) {
 			return authorList;
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java
index fc2ca86a54..68e9b14000 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java
@@ -26,7 +26,6 @@
 
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
@@ -639,7 +638,7 @@ private boolean mapChains(List<Group> seqResGroups, List<Group> atomRes,
 		// make sure we actually find an alignment
 		boolean noMatchFound = true;
 
-		Compound gapSymbol =  AminoAcidCompoundSet.getAminoAcidCompoundSet().getCompoundForString("-");
+        Compound gapSymbol =  AminoAcidCompoundSet.aminoAcidCompoundSet.getCompoundForString("-");
 
 		mainLoop:
 			for (int i = 1; i <= aligLength ; i++) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
index 585f790e00..7f02f20e33 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
@@ -171,12 +171,12 @@ public static ResidueNumber[] matchSequenceToStructure(ProteinSequence seq, Stru
 		//2. Run Smith-Waterman to get the alignment
 		// Identity substitution matrix with +1 for match, -1 for mismatch
 		// TODO
-		SubstitutionMatrix<AminoAcidCompound> matrix =
+        SubstitutionMatrix<AminoAcidCompound> matrix =
 				new SimpleSubstitutionMatrix<>(
-						AminoAcidCompoundSet.getAminoAcidCompoundSet(),
+                        AminoAcidCompoundSet.aminoAcidCompoundSet,
 						(short) 1, (short) -1);
-		matrix = new SimpleSubstitutionMatrix<>(
-				AminoAcidCompoundSet.getAminoAcidCompoundSet(),
+        matrix = new SimpleSubstitutionMatrix<>(
+                AminoAcidCompoundSet.aminoAcidCompoundSet,
 				new InputStreamReader(
 						SimpleSubstitutionMatrix.class.getResourceAsStream("/matrices/blosum100.txt")),
 				"blosum100");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java
index 90f987056b..b5d6fa8143 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java
@@ -517,7 +517,7 @@ public void consumeAuditAuthor(AuditAuthor auditAuthor) {
             if (auth == null) {
                 pdbHeader.setAuthors(newaa.toString());
             } else {
-                auth += "," + newaa.toString();
+                auth += "," + newaa;
                 pdbHeader.setAuthors(auth);
             }
         }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
index 182250f427..39a6dd1050 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
@@ -87,12 +87,12 @@ public class MMCIFFileTools {
 	public static String toLoopMmCifHeaderString(String categoryName, String className) throws ClassNotFoundException {
 		StringBuilder str = new StringBuilder();
 
-		str.append(SimpleMMcifParser.LOOP_START+newline);
+		str.append(SimpleMMcifParser.LOOP_START).append(newline);
 
 		Class<?> c = Class.forName(className);
 
 		for (Field f : getFields(c)) {
-			str.append(categoryName+"."+f.getName()+newline);
+			str.append(categoryName).append(".").append(f.getName()).append(newline);
 		}
 
 		return str.toString();
@@ -148,7 +148,7 @@ public static String toMMCIF(String categoryName, Object o) {
 
 		}
 
-		sb.append(SimpleMMcifParser.COMMENT_CHAR+newline);
+		sb.append(SimpleMMcifParser.COMMENT_CHAR).append(newline);
 
 		return sb.toString();
 	}
@@ -220,7 +220,7 @@ public static <T> String toMMCIF(List<T> list, Class<T> klass) {
 			sb.append(toSingleLoopLineMmCifString(o, fields, sizes));
 		}
 
-		sb.append(SimpleMMcifParser.COMMENT_CHAR+newline);
+		sb.append(SimpleMMcifParser.COMMENT_CHAR).append(newline);
 
 		return sb.toString();
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
index 5279083e25..860ba62a52 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
@@ -1101,13 +1101,13 @@ private void alignSeqRes() {
 	private int getInternalNr(Group atomG) {
 		if ( atomG.getType().equals(GroupType.AMINOACID)) {
 			AminoAcidImpl aa = (AminoAcidImpl) atomG;
-			return new Long(aa.getId()).intValue();
+			return Long.valueOf(aa.getId()).intValue();
 		} else if ( atomG.getType().equals(GroupType.NUCLEOTIDE)) {
 			NucleotideImpl nu = (NucleotideImpl) atomG;
-			return new Long(nu.getId()).intValue();
+			return Long.valueOf(nu.getId()).intValue();
 		} else {
 			HetatomImpl he = (HetatomImpl) atomG;
-			return new Long(he.getId()).intValue();
+			return Long.valueOf(he.getId()).intValue();
 		}
 	}
 
@@ -1596,7 +1596,7 @@ public void newAuditAuthor(AuditAuthor aa){
 		if (auth == null) {
 			header.setAuthors(newaa.toString());
 		}else {
-			auth += "," + newaa.toString();
+			auth += "," + newaa;
 			header.setAuthors(auth);
 
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
index 6430db5e9c..5c9267ccfc 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
@@ -272,7 +272,7 @@ public void parse(BufferedReader buf)
 							continue;
 						}
 						String key = data.get(0);
-						int pos = key.indexOf(".");
+						int pos = key.indexOf('.');
 						if ( pos < 0 ) {
 							// looks like a chem_comp file
 							// line should start with data, otherwise something is wrong!
@@ -358,7 +358,7 @@ public void parse(BufferedReader buf)
 						continue;
 					}
 					String key = data.get(0);
-					int pos = key.indexOf(".");
+					int pos = key.indexOf('.');
 					if ( pos < 0 ) {
 						// looks like a chem_comp file
 						// line should start with data, otherwise something is wrong!
@@ -443,7 +443,7 @@ private List<String> processSingleLine(String line){
 			if  (c == ' ') {
 
 				if ( ! inString){
-					if ( ! word.equals(""))
+					if (!word.isEmpty())
 						data.add(word.trim());
 					word = "";
 				} else {
@@ -467,7 +467,7 @@ private List<String> processSingleLine(String line){
 					if ( wordEnd ) {
 
 						// at end of string
-						if ( ! word.equals(""))
+						if (!word.isEmpty())
 							data.add(word.trim());
 						word     = "";
 						inString = false;
@@ -497,7 +497,7 @@ private List<String> processSingleLine(String line){
 					if ( wordEnd ) {
 
 						// at end of string
-						if ( ! word.equals(""))
+						if (!word.isEmpty())
 							data.add(word.trim());
 						word     = "";
 						inString = false;
@@ -517,7 +517,7 @@ private List<String> processSingleLine(String line){
 			}
 
 		}
-		if ( ! word.trim().equals(""))
+		if (!word.trim().isEmpty())
 			data.add(word);
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
index 57e4f7f622..5ffa87abf1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
@@ -23,7 +23,6 @@
 import java.io.BufferedOutputStream;
 import java.io.File;
 import java.io.FileOutputStream;
-import java.io.FilenameFilter;
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.file.FileSystem;
@@ -82,7 +81,7 @@ public ZipChemCompProvider(String chemicalComponentDictionaryFile, String tempDi
 		this.m_zipFile = Paths.get(chemicalComponentDictionaryFile);
 
 		// Use a default temporary directory if not passed a value.
-		if (tempDir == null || tempDir.equals("")) {
+		if (tempDir == null || tempDir.isEmpty()) {
 			this.m_tempDir = Paths.get(System.getProperty("java.io.tmpdir"));
 		} else {
 			this.m_tempDir = Paths.get(tempDir);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java
index 5f66ade976..44da26cd85 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java
@@ -157,7 +157,7 @@ public static String getDNATwoLetter(Character c){
 		return DNA_LOOKUP_1TO2.get(c);
 	}
 
-	public static final boolean isStandardChemComp(ChemComp cc){
+	public static boolean isStandardChemComp(ChemComp cc){
 
 		String pid = cc.getMon_nstd_parent_comp_id();
 		String one = cc.getOne_letter_code();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/AbstractBean.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/AbstractBean.java
index 07b83b782b..f39d31d812 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/AbstractBean.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/AbstractBean.java
@@ -65,7 +65,7 @@ public String toString(){
 
 					Object o  = m.invoke(this);
 					if ( o instanceof String){
-						buf.append(name.substring(3)+": "+ o + " ");
+						buf.append(name.substring(3)).append(": ").append(o).append(" ");
 					}
 					else if ( o instanceof List){
 						buf.append(name.substring(3)).append(": ");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java
index 568fe15c8d..05a56340f4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java
@@ -139,8 +139,8 @@ private void addBonds(Atom atom, List<Atom> atomsInGroup, List<Atom> allAtoms) {
 			Atom other = bond.getOther(atom);
 			// If both atoms are in the group
 			if (atomsInGroup.contains(other)){
-				Integer firstBondIndex = atomsInGroup.indexOf(atom);
-				Integer secondBondIndex = atomsInGroup.indexOf(other);
+				int firstBondIndex = atomsInGroup.indexOf(atom);
+				int secondBondIndex = atomsInGroup.indexOf(other);
 				// Don't add the same bond twice
 				if(firstBondIndex>secondBondIndex){
 					int bondOrder = bond.getBondOrder();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
index bff90ac251..8c457e15dd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
@@ -50,8 +50,8 @@ public class BioAssemblyTools {
 	 * @return true if expression is a unary operator expression
 	 */
 	public static boolean isUnaryExpression(String expression) {
-		int first = expression.indexOf("(");
-		int last = expression.lastIndexOf("(");
+		int first = expression.indexOf('(');
+		int last = expression.lastIndexOf('(');
 		if (first < 0 || last < 0) {
 			return true;
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/CartesianProduct.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/CartesianProduct.java
index 5011f8cca2..76dceed781 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/CartesianProduct.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/CartesianProduct.java
@@ -21,7 +21,6 @@
 package org.biojava.nbio.structure.quaternary;
 
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.List;
 
 
@@ -43,8 +42,8 @@
  */
 public class CartesianProduct<T> {
 
-	private List<T> list1;
-	private List<T> list2;
+	private final List<T> list1;
+	private final List<T> list2;
 
 	/**
 	 * Class constructor specifying the two lists of a cartesian product.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBLigandsFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBLigandsFactory.java
index 49e5a93ac0..e2f145a277 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBLigandsFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBLigandsFactory.java
@@ -150,7 +150,7 @@ public static List<RCSBLigand> getFromHeteroAtomIds(String... heteroAtomIds) {
 		}
 		InputStream is;
 		try {
-			URL url = new URL(HET_URL_STUB + sb.toString());
+			URL url = new URL(HET_URL_STUB + sb);
 			is = url.openConnection().getInputStream();
 		} catch (IOException e) {
 			logger.warn("Couldn't open connection", e);
@@ -329,7 +329,7 @@ public static List<RCSBLigands> getFromPdbIds(String... pdbIds) {
 			sb.append(pdbIds[i]);
 		}
 		try {
-			URL url = new URL(PDB_URL_STUB + sb.toString());
+			URL url = new URL(PDB_URL_STUB + sb);
 			is = url.openConnection().getInputStream();
 		} catch (IOException e) {
 			logger.warn("Couldn't open connection", e);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java
index bf591b65be..e2a6eb1f35 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java
@@ -25,7 +25,7 @@
 
 import java.util.HashMap;
 import java.util.Map;
-
+import java.util.concurrent.ConcurrentHashMap;
 
 
 /**
@@ -83,7 +83,7 @@ public class ScopFactory {
 	public static final String LATEST_VERSION = VERSION_2_0_7;
 
 	// Hold one instance for each version
-	private static final Map<String,ScopDatabase> versionedScopDBs = new HashMap<>();
+	private static final Map<String,ScopDatabase> versionedScopDBs = new ConcurrentHashMap<>();
 	private static String defaultVersion = LATEST_VERSION;
 
 	/**
@@ -140,7 +140,7 @@ public static ScopDatabase getSCOP(String version, boolean forceLocalData){
 		ScopDatabase scop = versionedScopDBs.get(version);
 		if ( forceLocalData) {
 			// Use a local installation
-			if( scop == null || !(scop instanceof LocalScopDatabase) ) {
+			if(!(scop instanceof LocalScopDatabase)) {
 				logger.info("Creating new {}, version {}", BerkeleyScopInstallation.class.getSimpleName(), version);
 				BerkeleyScopInstallation berkeley = new BerkeleyScopInstallation();
 				berkeley.setScopVersion(version);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java
index fb5db72895..aa06a9b641 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java
@@ -165,7 +165,7 @@ private static List<SecStrucState> generalParse(BufferedReader reader,
 			String resNumStr = line.substring(5,10).trim();
 
 			//Only happens if dssp inserts a line indicating a chain break
-			if(!resNumStr.equals("")) {
+			if(!resNumStr.isEmpty()) {
 
 				int index = Integer.parseInt(indexStr);
 				//Get the group of the structure corresponding to the residue
@@ -183,14 +183,14 @@ private static List<SecStrucState> generalParse(BufferedReader reader,
 
 				//Parse the Bridge partners - TODO parallel or antiparallel?
 				String bp = line.substring(25,29).trim();
-				if (bp != "") {
+				if (!bp.isEmpty()) {
 					BetaBridge bb = new BetaBridge(
 							index, Integer.parseInt(bp), BridgeType.parallel);
 					ss.addBridge(bb);
 				} else logger.warn("Unable to parse beta Bridge for resn "+index);
 
 				bp = line.substring(29,33).trim();
-				if (bp != "") {
+				if (!bp.isEmpty()) {
 					BetaBridge bb = new BetaBridge(
 							index, Integer.parseInt(bp), BridgeType.parallel);
 					ss.addBridge(bb);
@@ -203,7 +203,7 @@ private static List<SecStrucState> generalParse(BufferedReader reader,
 					int b = a + 8;
 
 					String val = line.substring(a,b).trim();
-					if (val == "") {
+					if (val.isEmpty()) {
 						logger.warn("Unable to parse energy for resn "+index);
 						continue;
 					}
@@ -236,15 +236,15 @@ private static List<SecStrucState> generalParse(BufferedReader reader,
 
 				//Angle properties
 				String val = line.substring(91,97).trim();
-				if (val != "") ss.setKappa(Float.parseFloat(val));
+				if (!val.isEmpty()) ss.setKappa(Float.parseFloat(val));
 				else logger.warn("Unable to parse kappa for resn "+index);
 
 				val = line.substring(103,109).trim();
-				if (val != "") ss.setPhi(Float.parseFloat(val));
+				if (!val.isEmpty()) ss.setPhi(Float.parseFloat(val));
 				else logger.warn("Unable to parse phi for resn "+index);
 
 				val = line.substring(109,116).trim();
-				if (val != "") ss.setPsi(Float.parseFloat(val));
+				if (!val.isEmpty()) ss.setPsi(Float.parseFloat(val));
 				else logger.warn("Unable to parse psi for resn "+index);
 
 				if (assign) parent.setProperty(Group.SEC_STRUC, ss);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java
index 0034bbd293..cc66c9a4a2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java
@@ -30,8 +30,6 @@
 
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
@@ -470,13 +468,7 @@ private void findBridges() {
 			} else if (o1.getFirst() > o2.getFirst()) {
 				return +1;
 			} else {
-				if (o1.getSecond() < o2.getSecond()) {
-					return -1;
-				} else if (o1.getSecond() > o2.getSecond()) {
-					return 1;
-				} else {
-					return 0;
-				}
+				return o1.getSecond().compareTo(o2.getSecond());
 			}
 		});
 
@@ -598,8 +590,7 @@ public String printDSSP() {
 		String nl = System.getProperty("line.separator");
 
 		//Header Line
-		buf.append("==== Secondary Structure Definition by BioJava"
-				+ " DSSP implementation, Version October 2015 ===="+nl);
+		buf.append("==== Secondary Structure Definition by BioJava" + " DSSP implementation, Version October 2015 ====").append(nl);
 
 		//First line with column definition
 		buf.append("  #  RESIDUE AA STRUCTURE BP1 BP2  ACC     "
@@ -650,8 +641,8 @@ public String printHelixSummary() {
 			aa.append(StructureTools.get1LetterCode(groups[k].getPDBName()));
 		}
 
-		return g.toString()+nl+h.toString()+nl+
-				i.toString()+nl+ss.toString()+nl+aa.toString();
+		return g +nl+ h +nl+
+				i +nl+ ss +nl+ aa;
 	}
 
 	/**
@@ -663,7 +654,7 @@ public String printFASTA() {
 
 		StringBuilder buf = new StringBuilder();
 		String nl = System.getProperty("line.separator");
-		buf.append(">"+groups[0].getChain().getStructure().getIdentifier()+nl);
+		buf.append(">").append(groups[0].getChain().getStructure().getIdentifier()).append(nl);
 
 		for (int g = 0; g < groups.length; g++){
 			buf.append(getSecStrucState(g).getType());
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java
index 7a34d2e47b..1c8159dde7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java
@@ -42,8 +42,8 @@ public class HelixAxisAligner extends AxisAligner {
 	private static final Vector3d Y_AXIS = new Vector3d(0,1,0);
 	private static final Vector3d Z_AXIS = new Vector3d(0,0,1);
 
-	private QuatSymmetrySubunits subunits;
-	private HelixLayers helixLayers;
+	private final QuatSymmetrySubunits subunits;
+	private final HelixLayers helixLayers;
 
 	private Matrix4d transformationMatrix = new Matrix4d();
 	private final Matrix4d reverseTransformationMatrix = new Matrix4d();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java
index 4f86920492..950429401e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java
@@ -42,8 +42,8 @@ public class RotationAxisAligner extends AxisAligner{
 	private static final Vector3d Y_AXIS = new Vector3d(0,1,0);
 	private static final Vector3d Z_AXIS = new Vector3d(0,0,1);
 
-	private QuatSymmetrySubunits subunits;
-	private RotationGroup rotationGroup;
+	private final QuatSymmetrySubunits subunits;
+	private final RotationGroup rotationGroup;
 
 	private Matrix4d transformationMatrix = new Matrix4d();
 	private final Matrix4d reverseTransformationMatrix = new Matrix4d();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
index 1b306f2753..9d6850f5e5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
@@ -27,7 +27,7 @@
 import java.util.Map.Entry;
 
 public class HelicalRepeatUnit {
-	private QuatSymmetrySubunits subunits;
+	private final QuatSymmetrySubunits subunits;
 	private List<Point3d> repeatUnitCenters = new ArrayList<>();
 	private List<Point3d[]> repeatUnits = new ArrayList<>();
 	private final List<List<Integer>> repeatUnitIndices = new ArrayList<>();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java
index 824e2e7300..d2e9161dc2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java
@@ -24,7 +24,6 @@
 import javax.vecmath.AxisAngle4d;
 import javax.vecmath.Matrix4d;
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
 
 /**
@@ -152,11 +151,11 @@ public void setContacts(int contacts) {
 	@Override
 	public String toString() {
 		StringBuilder sb = new StringBuilder();
-		sb.append("Permutation   : " + getPermutation() + "\n");
-		sb.append("Repeat units  : " + getRepeatUnits() + "\n");
-		sb.append("Rise          : " + getRise() + "\n");
-		sb.append("Angle         : " + Math.toDegrees(getAngle()) +"\n");
-		sb.append("Fold          : " + getFold() + "\n");
+		sb.append("Permutation   : ").append(getPermutation()).append("\n");
+		sb.append("Repeat units  : ").append(getRepeatUnits()).append("\n");
+		sb.append("Rise          : ").append(getRise()).append("\n");
+		sb.append("Angle         : ").append(Math.toDegrees(getAngle())).append("\n");
+		sb.append("Fold          : ").append(getFold()).append("\n");
 		return sb.toString();
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java
index c17ab9f64d..7a5af85d39 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java
@@ -29,8 +29,8 @@
 import java.util.List;
 
 public class HelixExtender {
-	private QuatSymmetrySubunits subunits;
-	private Helix helix;
+	private final QuatSymmetrySubunits subunits;
+	private final Helix helix;
 
 	public HelixExtender(QuatSymmetrySubunits subunits, Helix helix) {
 		this.subunits = subunits;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
index ccb70c2a1f..39ca6dcd94 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
@@ -44,10 +44,10 @@ public class HelixSolver {
 	private static final Logger logger = LoggerFactory
 			.getLogger(HelixSolver.class);
 
-	private QuatSymmetrySubunits subunits;
-	private int fold;
+	private final QuatSymmetrySubunits subunits;
+	private final int fold;
 	private final HelixLayers helixLayers = new HelixLayers();
-	private QuatSymmetryParameters parameters;
+	private final QuatSymmetryParameters parameters;
 	boolean modified = true;
 
 	public HelixSolver(QuatSymmetrySubunits subunits, int fold,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
index e1f4792410..ed0ab1636d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
@@ -85,7 +85,7 @@ public void completeGroup() {
 	@Override
 	public String toString() {
 		StringBuilder sb = new StringBuilder();
-		sb.append("Permutation Group: " + permutations.size() + " permutation");
+		sb.append("Permutation Group: ").append(permutations.size()).append(" permutation");
 		for (List<Integer> permutation : permutations) {
 			sb.append(permutation.toString());
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
index 827a3f12fe..63452a9f76 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
@@ -51,7 +51,7 @@ public class QuatSymmetrySubunits {
 	private final List<Point3d> centers = new ArrayList<>();
 	private final List<Vector3d> unitVectors = new ArrayList<>();
 
-	private List<Integer> folds;
+	private final List<Integer> folds;
 	private final List<Integer> clusterIds = new ArrayList<>();
 	private final List<SubunitCluster> clusters;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
index fd662fac3b..dbc1759c16 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
@@ -25,8 +25,6 @@
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Vector3d;
 import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
 import java.util.Iterator;
 import java.util.List;
 
@@ -192,7 +190,7 @@ public boolean isComplete() {
 	@Override
 	public String toString() {
 		StringBuilder sb = new StringBuilder();
-		sb.append("Rotations: " + rotations.size() + "\n");
+		sb.append("Rotations: ").append(rotations.size()).append("\n");
 		for (Rotation s: rotations) {
 			sb.append(s.toString()).append("\n");
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
index 8a29271e0f..6f451d0097 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
@@ -46,8 +46,8 @@
  * @author Peter
  */
 public class RotationSolver implements QuatSymmetrySolver {
-	private QuatSymmetrySubunits subunits;
-	private QuatSymmetryParameters parameters;
+	private final QuatSymmetrySubunits subunits;
+	private final QuatSymmetryParameters parameters;
 
 	private double distanceThreshold = 0.0f;
 	private DistanceBox<Integer> box = null;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
index dd5f7e1473..4ae3d06a54 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
@@ -42,8 +42,8 @@
  * @author Peter
  */
 public class SystematicSolver implements QuatSymmetrySolver {
-	private QuatSymmetrySubunits subunits;
-	private QuatSymmetryParameters parameters;
+	private final QuatSymmetrySubunits subunits;
+	private final QuatSymmetryParameters parameters;
 
 	private Point3d[] originalCoords = null;
 	private Point3d[] transformedCoords = null;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java
index b6e1b4f4c7..9256188b8a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java
@@ -22,7 +22,6 @@
 
 import javax.vecmath.Matrix3d;
 import javax.vecmath.Point3d;
-import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java
index dd33c96bea..94a1338497 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java
@@ -34,7 +34,7 @@
  *
  */
 public class Prism implements Polyhedron {
-	private int n;
+	private final int n;
 	private double circumscribedRadius = 1.0;
 	private double height = 1.0;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java
index e3794eed65..b6c3f1099b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java
@@ -31,9 +31,9 @@ public class RectangularPrism implements Polyhedron {
 	private static final int[] lineLoop2 = {1,5};
 	private static final int[] lineLoop3 = {2,6};
 	private static final int[] lineLoop4 = {3,7};
-	private double length;
-	private double width;
-	private double height;
+	private final double length;
+	private final double width;
+	private final double height;
 	private static final String[] viewNames = {"Front", "Left", "Back", "Right", "Top", "Bottom"};
 
 	public RectangularPrism(double length, double width, double height) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
index 67e1878675..fded24ae09 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
@@ -67,7 +67,7 @@ public class SymmOptimizer {
 	private final Random rnd;
 
 	// Optimization parameters
-	private int Rmin; // min aligned repeats per column
+	private final int Rmin; // min aligned repeats per column
 	private final int Lmin; // min repeat length
 	private int maxIter; // max iterations
 	private double C = 20; // probability of accept bad moves constant
@@ -197,11 +197,9 @@ public MultipleAlignment optimize() throws StructureException,
 
 		// Save the optimal alignment
 		List<List<Integer>> optBlock = new ArrayList<>();
-		List<Integer> optFreePool = new ArrayList<>();
-		optFreePool.addAll(freePool);
+        List<Integer> optFreePool = new ArrayList<>(freePool);
 		for (int k = 0; k < order; k++) {
-			List<Integer> b = new ArrayList<>();
-			b.addAll(block.get(k));
+            List<Integer> b = new ArrayList<>(block.get(k));
 			optBlock.add(b);
 		}
 		double optScore = mcScore;
@@ -215,11 +213,9 @@ public MultipleAlignment optimize() throws StructureException,
 
 			// Save the state of the system
 			List<List<Integer>> lastBlock = new ArrayList<>();
-			List<Integer> lastFreePool = new ArrayList<>();
-			lastFreePool.addAll(freePool);
+            List<Integer> lastFreePool = new ArrayList<>(freePool);
 			for (int k = 0; k < order; k++) {
-				List<Integer> b = new ArrayList<>();
-				b.addAll(block.get(k));
+                List<Integer> b = new ArrayList<>(block.get(k));
 				lastBlock.add(b);
 			}
 			double lastScore = mcScore;
@@ -282,11 +278,9 @@ public MultipleAlignment optimize() throws StructureException,
 			// Store as the optimal alignment if better
 			if (mcScore > optScore) {
 				optBlock = new ArrayList<>();
-				optFreePool = new ArrayList<>();
-				optFreePool.addAll(freePool);
+                optFreePool = new ArrayList<>(freePool);
 				for (int k = 0; k < order; k++) {
-					List<Integer> b = new ArrayList<>();
-					b.addAll(block.get(k));
+                    List<Integer> b = new ArrayList<>(block.get(k));
 					optBlock.add(b);
 				}
 				optScore = mcScore;
@@ -842,12 +836,12 @@ private void saveHistory(String folder) throws IOException {
 		writer.append("Step,Time,RepeatLength,RMSD,TMscore,MCscore\n");
 
 		for (int i = 0; i < lengthHistory.size(); i++) {
-			writer.append(i * saveStep + ",");
-			writer.append(timeHistory.get(i) + ",");
-			writer.append(lengthHistory.get(i) + ",");
-			writer.append(rmsdHistory.get(i) + ",");
-			writer.append(tmScoreHistory.get(i) + ",");
-			writer.append(mcScoreHistory.get(i) + "\n");
+			writer.append(String.valueOf(i * saveStep)).append(",");
+			writer.append(String.valueOf(timeHistory.get(i))).append(",");
+			writer.append(String.valueOf(lengthHistory.get(i))).append(",");
+			writer.append(String.valueOf(rmsdHistory.get(i))).append(",");
+			writer.append(String.valueOf(tmScoreHistory.get(i))).append(",");
+			writer.append(String.valueOf(mcScoreHistory.get(i))).append("\n");
 		}
 
 		writer.flush();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ChainSignature.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ChainSignature.java
index cf9c295a0a..96f717a1c1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ChainSignature.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ChainSignature.java
@@ -23,10 +23,10 @@
 import java.util.List;
 
 public class ChainSignature implements Comparable<ChainSignature> {
-	private int chainCount;
-	private String representative;
+	private final int chainCount;
+	private final String representative;
 	private String compositionId = "";
-	private List<String> chainIds;
+	private final List<String> chainIds;
 
 	public ChainSignature(String representative, int chainCount, List<String> chainIds) {
 		this.representative = representative;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.java
index 5b3da7b27d..9f6ac18721 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.java
@@ -26,9 +26,9 @@
 import java.util.Map.Entry;
 
 public class ProteinComplexSignature {
-	private BlastClustReader blastClust;
-	private String pdbId;
-	private List<String> chainIds;
+	private final BlastClustReader blastClust;
+	private final String pdbId;
+	private final List<String> chainIds;
 	private final List<ChainSignature> chainSignatures = new ArrayList<>();
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java
index d3ef8c2932..d827a03f48 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java
@@ -38,7 +38,7 @@ public class BlastClustReader implements Serializable {
 
 	private static final Logger logger = LoggerFactory.getLogger(BlastClustReader.class);
 
-	private int sequenceIdentity;
+	private final int sequenceIdentity;
 	private final List<List<String>> clusters = new ArrayList<>();
 	// https://cdn.rcsb.org/resources/sequence/clusters/bc-95.out
 	private static final String coreUrl = "https://cdn.rcsb.org/resources/sequence/clusters/";
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalBuilder.java
index 6e4fc5394c..07836e405d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalBuilder.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalBuilder.java
@@ -390,11 +390,11 @@ private void calcInterfacesCrystal(StructureInterfaceList set, double cutoff) {
 
 						if( verbose ) {
 							if (a==0 && b==0 && c==0 && n==0)
-								builder.append(" "+contactsFound+"("+(numPolyChainsAu*(numPolyChainsAu-1))/2+")");
+								builder.append(" ").append(contactsFound).append("(").append((numPolyChainsAu * (numPolyChainsAu - 1)) / 2).append(")");
 							else if (selfEquivalent)
-								builder.append(" "+contactsFound+"("+(numPolyChainsAu*(numPolyChainsAu+1))/2+")");
+								builder.append(" ").append(contactsFound).append("(").append((numPolyChainsAu * (numPolyChainsAu + 1)) / 2).append(")");
 							else
-								builder.append(" "+contactsFound+"("+numPolyChainsAu*numPolyChainsAu+")");
+								builder.append(" ").append(contactsFound).append("(").append(numPolyChainsAu * numPolyChainsAu).append(")");
 
 							logger.debug(builder.toString());
 						}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java
index eaef2dc30b..93a57ab686 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java
@@ -42,8 +42,7 @@ public String[] marshal(List<String> arg0) {
 
 	@Override
 	public List<String> unmarshal(String[] arg0) {
-		List<String> l = new ArrayList<>();
-        l.addAll(Arrays.asList(arg0));
+        List<String> l = new ArrayList<>(Arrays.asList(arg0));
 		return l;
 	}
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java
index eb2a6d1cda..ef2d0967c0 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java
@@ -26,8 +26,6 @@
 import org.biojava.nbio.structure.io.mmcif.MMCIFFileTools;
 import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
 import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
-import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
-import org.biojava.nbio.structure.io.mmcif.chem.ResidueType;
 import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.biojava.nbio.structure.io.mmcif.model.ChemCompBond;
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java
index f2459bbc85..c457bc3db4 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java
@@ -26,8 +26,6 @@
 
 import java.io.IOException;
 import java.io.InputStream;
-import java.util.Collections;
-import java.util.Comparator;
 import java.util.List;
 import java.util.zip.GZIPInputStream;
 
@@ -245,7 +243,7 @@ private Structure getStructure(String fileName, boolean setAlignSeqRes) throws I
 
 	private void checkEntitiesNumbered(List<EntityInfo> entities) {
 
-		entities.sort((o1, o2) -> new Integer(o1.getMolId()).compareTo(o2.getMolId()));
+		entities.sort((o1, o2) -> Integer.compare(o1.getMolId(), o2.getMolId()));
 
 		int id = 1;
 		for (EntityInfo compound:entities) {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestParsingCalcium.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestParsingCalcium.java
index 1670bc3f21..88faee44f8 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestParsingCalcium.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestParsingCalcium.java
@@ -103,7 +103,7 @@ public void testCAreturnsCalpha() throws IOException, StructureException {
 					atom.getElement()==Element.O ||
 					atom.getElement()==Element.N    );
 
-            assertFalse("backbone atoms should not contain CB atoms", atom.getName().equals("CB"));
+            assertNotEquals("backbone atoms should not contain CB atoms", "CB", atom.getName());
 
 			if (atom.getGroup().getPDBName().equals("GLY")) {
 				hasGlycine = true;
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java
index 3622561e2e..a448d327b8 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java
@@ -143,7 +143,7 @@ public void testCrossReferencesRawFile() {
 		// TODO implement
 	}
 
-	private void doFullTest(Structure structure, boolean emptySeqRes) throws StructureException {
+	private void doFullTest(Structure structure, boolean emptySeqRes) {
 
 		//System.out.println("Testing references in original structure");
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java
index 1069a32126..5118756f3a 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java
@@ -33,7 +33,6 @@
 import org.junit.Test;
 
 import java.io.IOException;
-import java.lang.reflect.InvocationTargetException;
 import java.util.Arrays;
 
 
@@ -86,7 +85,7 @@ public void testFilterDuplicateAFPs() throws Exception {
 	}
 
 	@Test
-	public void testFilterDuplicateAFPsMinLenCTerm() throws PDBParseException, StructureException {
+	public void testFilterDuplicateAFPsMinLenCTerm() throws StructureException {
 		int[][][] startAln, filteredAln;
 		int[] filteredLen;
 		int ca2len;
@@ -186,7 +185,7 @@ public void testFilterDuplicateAFPsMinLenCTerm() throws PDBParseException, Struc
 	}
 
 	@Test
-	public void testFilterDuplicateAFPsMinLenNTerm() throws PDBParseException, StructureException {
+	public void testFilterDuplicateAFPsMinLenNTerm() throws StructureException {
 		int[][][] startAln, filteredAln;
 		int ca2len;
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/client/TestStructureName.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/client/TestStructureName.java
index 3b6f403302..c40bfa84f2 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/client/TestStructureName.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/client/TestStructureName.java
@@ -24,7 +24,6 @@
 import static org.junit.Assert.*;
 
 import java.io.File;
-import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java
index 97a8010bee..86b3874888 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java
@@ -161,9 +161,8 @@ public void testMCScore() throws Exception {
 	 * the same Atoms and perfectly aligned, so that TM-score = 1
 	 * and RMSD = 0.
 	 * @return MultipleAlignment identity
-	 * @throws StructureException
-	 */
-	private MultipleAlignment identityMSTA() throws StructureException {
+     */
+	private MultipleAlignment identityMSTA() {
 
 		//Generate the identical Atom arrays
 		List<Atom[]> atomArrays = new ArrayList<>(20);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPosition.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPosition.java
index cba85c1da8..d963d5872f 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPosition.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPosition.java
@@ -32,7 +32,6 @@
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
 
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.geometry.SuperPositionQuat;
 import org.biojava.nbio.structure.geometry.SuperPositionQCP;
 import org.junit.Before;
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java
index 01a66ee542..1368649f61 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java
@@ -27,7 +27,6 @@
 import java.io.InputStream;
 
 import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
 import org.junit.Test;
 
 public class TestDBRefParsing {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
index 5479cdd39d..a4acb727ee 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
@@ -27,7 +27,6 @@
 
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.Comparator;
 import java.util.List;
 import java.util.Map;
@@ -269,8 +268,8 @@ private void sortAtoms(List<Atom> atomsOne, List<Atom> atomsTwo) {
 	 * @param chainsTwo the second list of chains
 	 */
 	private void sortChains(List<Chain> chainsOne, List<Chain> chainsTwo) {
-		chainsOne.sort((o1, o2) -> o1.getId().compareTo(o2.getId()));
-		chainsTwo.sort((o1, o2) -> o1.getId().compareTo(o2.getId()));
+		chainsOne.sort(Comparator.comparing(Chain::getId));
+		chainsTwo.sort(Comparator.comparing(Chain::getId));
 
 	}
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java
index b2bae0ff64..6eb2c43a01 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java
@@ -21,7 +21,6 @@
 package org.biojava.nbio.structure.secstruc;
 
 import java.io.IOException;
-import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 import java.util.zip.GZIPInputStream;
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSingleRefiner.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSingleRefiner.java
index 11cdc3d04f..fa160be574 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSingleRefiner.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSingleRefiner.java
@@ -243,7 +243,7 @@ public void setUp() {
 	}
 
 	@Test
-	public void testExpected() throws StructureException {
+	public void testExpected() {
 
 		for(int i=0;i<alignments.size(); i++) {
 			Map<Integer,Integer> align = alignments.get(i);
@@ -272,7 +272,7 @@ private void testAutomorphism(Map<Integer,Integer> align) {
 	}
 
 	@Test
-	public void testAutomorphism() throws StructureException {
+	public void testAutomorphism() {
 		for(int i=0;i<alignments.size(); i++) {
 			Map<Integer,Integer> align = alignments.get(i);
 
@@ -295,7 +295,7 @@ private void testSymmetric(Map<Integer,Integer> align, int k) {
 	}
 
 	@Test
-	public void testSymmetric() throws StructureException {
+	public void testSymmetric() {
 		for(int i=0;i<alignments.size(); i++) {
 			Map<Integer,Integer> align = alignments.get(i);
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java
index c4bfc4c7de..e40724bbe7 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java
@@ -30,9 +30,9 @@
 public class CoxVariables {
 
 	//   public GeneSetResults gsr;
-	private String cohortName;
-	private String geneSet;
-	private String genes;
+	private final String cohortName;
+	private final String geneSet;
+	private final String genes;
 
 	/**
 	 *
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
index 2d31639865..c31c93ae5a 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
@@ -1051,8 +1051,7 @@ public ArrayList<String> getRandomDataColumns(int number, ArrayList<String> colu
 	 * @return
 	 */
 	public ArrayList<String> getAllColumns() {
-		ArrayList<String> columns = new ArrayList<>();
-		columns.addAll(columnLookup.keySet());
+        ArrayList<String> columns = new ArrayList<>(columnLookup.keySet());
 		return columns;
 	}
 
@@ -1119,8 +1118,7 @@ public ArrayList<String> getDiscreteRowValues(String row) throws Exception {
 	 * @return
 	 */
 	public ArrayList<String> getAllRows() {
-		ArrayList<String> rows = new ArrayList<>();
-		rows.addAll(rowLookup.keySet());
+        ArrayList<String> rows = new ArrayList<>(rowLookup.keySet());
 		return rows;
 
 	}
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
index 6755586ca7..11f3ae57d9 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
@@ -31,7 +31,6 @@
 import java.io.File;
 import java.text.DecimalFormat;
 import java.util.ArrayList;
-import java.util.Collections;
 
 /**
  *
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java
index 228d7d3579..7a0a55aff4 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java
@@ -39,7 +39,7 @@ public void process(WorkSheet worksheet, String column) {
 		DescriptiveStatistics ds = new DescriptiveStatistics();
 		for (String row : worksheet.getRows()) {
 			try {
-				Double d = Double.parseDouble(worksheet.getCell(row, column));
+				double d = Double.parseDouble(worksheet.getCell(row, column));
 				ds.addValue(d);
 			} catch (Exception e) {
 			}
diff --git a/biojava-ws/src/main/java/demo/HmmerDemo.java b/biojava-ws/src/main/java/demo/HmmerDemo.java
index 9511463c59..d3a7374928 100644
--- a/biojava-ws/src/main/java/demo/HmmerDemo.java
+++ b/biojava-ws/src/main/java/demo/HmmerDemo.java
@@ -85,7 +85,7 @@ public static void main(String[] args) throws Exception {
 	 */
 	private static ProteinSequence getUniprot(String uniProtID) throws Exception {
 
-		AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+        AminoAcidCompoundSet set = AminoAcidCompoundSet.aminoAcidCompoundSet;
 		UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<>(uniProtID, set);
 
 		ProteinSequence seq = new ProteinSequence(uniprotSequence);
diff --git a/biojava-ws/src/test/java/org/biojava/nbio/ws/hmmer/TestRemoteHmmerScan.java b/biojava-ws/src/test/java/org/biojava/nbio/ws/hmmer/TestRemoteHmmerScan.java
index a5b493809b..59686a2de0 100644
--- a/biojava-ws/src/test/java/org/biojava/nbio/ws/hmmer/TestRemoteHmmerScan.java
+++ b/biojava-ws/src/test/java/org/biojava/nbio/ws/hmmer/TestRemoteHmmerScan.java
@@ -57,6 +57,7 @@ public void testHmmerWs() throws Exception {
 		for (HmmerResult hmmerResult : results) {
 			if (hmmerResult.getName().equals("HTH_5")) {
 				gotSh2Domain = true;
+				break;
 			}
 		}
 

From 7d107b3e575d75e9c555fbcc933bfbb042e60e62 Mon Sep 17 00:00:00 2001
From: me <seh@internet.earth>
Date: Sat, 7 Mar 2020 19:36:16 -0500
Subject: [PATCH 09/18] updates

---
 .../nbio/aaproperties/Constraints.java        |  54 +++----
 .../nbio/aaproperties/PeptideProperties.java  |   2 +-
 .../nbio/aaproperties/CommandPromptTest.java  |   1 -
 .../nbio/aaproperties/CookBookTest.java       |   1 -
 .../GenbankCommandPromptTest.java             |   1 -
 .../PeptidePropertiesImplTest.java            |   4 +-
 .../aaproperties/profeat/CookBookTest.java    |   4 +-
 .../nbio/aaproperties/xml/ElementTest.java    |   4 -
 .../src/main/java/demo/DemoAlignProteins.java |   2 +-
 .../src/main/java/demo/DemoDistanceTree.java  |  12 +-
 .../java/demo/TestDNANeedlemanWunsch.java     |   2 +-
 .../biojava/nbio/alignment/Alignments.java    |   6 +-
 .../FractionalIdentityInProfileScorer.java    |   2 +-
 .../alignment/FractionalIdentityScorer.java   |   4 +-
 .../FractionalSimilarityInProfileScorer.java  |   2 +-
 .../alignment/FractionalSimilarityScorer.java |   4 +-
 .../org/biojava/nbio/alignment/GuideTree.java |   3 +-
 .../nbio/alignment/NeedlemanWunsch.java       |   2 +-
 .../nbio/alignment/SimpleGapPenalty.java      |   4 +-
 .../SimpleProfileProfileAligner.java          |  10 +-
 .../biojava/nbio/alignment/SmithWaterman.java |   4 +-
 .../alignment/StandardRescoreRefiner.java     |   2 +-
 .../AnchoredPairwiseSequenceAligner.java      |   4 +-
 .../alignment/routines/GuanUberbacher.java    |   2 +-
 .../template/AbstractMatrixAligner.java       |   4 +-
 .../AbstractProfileProfileAligner.java        |   4 +-
 .../alignment/template/GuideTreeNode.java     |   2 +-
 .../nbio/phylo/DistanceMatrixCalculator.java  |   5 +-
 .../biojava/nbio/phylo/ForesterWrapper.java   |   7 +-
 .../alignment/CookbookAlignAllGlobal.java     |   2 +-
 .../nbio/alignment/CookbookAlignAllLocal.java |   2 +-
 .../alignment/CookbookAlignPairGlobal.java    |   2 +-
 .../alignment/CookbookAlignPairLocal.java     |   2 +-
 .../nbio/alignment/CookbookMSAProfiler.java   |   2 +-
 .../FractionalIdentityScorerTest.java         |   2 +-
 .../FractionalSimilarityScorerTest.java       |   2 +-
 .../biojava/nbio/alignment/GuideTreeTest.java |   2 +-
 .../nbio/alignment/LocalAlignmentTest.java    |   2 +-
 .../nbio/alignment/NeedlemanWunschTest.java   |   8 +-
 .../nbio/alignment/SimpleProfilePairTest.java |   6 +-
 .../nbio/alignment/SmithWatermanTest.java     |   2 +-
 .../nbio/alignment/TestDNAAlignment.java      |   6 +-
 .../nbio/alignment/TestSubOptimalMSA.java     |   4 +-
 .../routines/GuanUberbacherTest.java          |   2 +-
 .../nbio/phylo/TestDistanceTreeEvaluator.java |   2 +-
 .../nbio/phylo/TestForesterWrapper.java       |  12 +-
 .../main/java/demo/ParseFastaFileDemo.java    |  10 +-
 .../alignment/matrices/AAIndexFileParser.java |   2 +-
 .../matrices/DefaultAAIndexProvider.java      |   2 +-
 .../template/MutableAlignedSequence.java      |   1 -
 .../alignment/template/MutableProfile.java    |   2 -
 .../template/MutableProfilePair.java          |   2 -
 .../template/MutableSequencePair.java         |   2 -
 .../org/biojava/nbio/core/search/io/Hit.java  |   4 +-
 .../org/biojava/nbio/core/search/io/Hsp.java  |   8 +-
 .../biojava/nbio/core/search/io/Result.java   |   4 +-
 .../nbio/core/search/io/ResultFactory.java    |   3 +-
 .../biojava/nbio/core/search/io/SearchIO.java |   6 +-
 .../core/search/io/blast/BlastHitBuilder.java |   3 +-
 .../core/search/io/blast/BlastResult.java     |   3 +-
 .../search/io/blast/BlastResultBuilder.java   |   3 +-
 .../search/io/blast/BlastTabularParser.java   |  16 +--
 .../core/search/io/blast/BlastXMLParser.java  |  64 ++++-----
 .../nbio/core/sequence/CDSSequence.java       |   4 +-
 .../nbio/core/sequence/ProteinSequence.java   |   2 +-
 .../core/sequence/StartCodonSequence.java     |   2 +-
 .../nbio/core/sequence/StopCodonSequence.java |   2 +-
 .../nbio/core/sequence/TaxonomyID.java        |   2 +-
 .../sequence/compound/AminoAcidCompound.java  |   5 +-
 .../sequence/compound/NucleotideCompound.java |   1 -
 .../sequence/features/AbstractFeature.java    |   6 +-
 .../sequence/features/FeatureInterface.java   |   6 +-
 .../features/FeaturesKeyWordInterface.java    |   4 +-
 .../nbio/core/sequence/io/ABITrace.java       |  20 +--
 .../core/sequence/io/FastaGeneWriter.java     |   8 +-
 .../nbio/core/sequence/io/FastaReader.java    |   2 +-
 .../core/sequence/io/FastaReaderHelper.java   |   6 +-
 .../nbio/core/sequence/io/FastaWriter.java    |  12 +-
 .../io/FileProxyDNASequenceCreator.java       |   6 +-
 .../io/FileProxyProteinSequenceCreator.java   |   6 +-
 .../io/FileProxyRNASequenceCreator.java       |   6 +-
 .../nbio/core/sequence/io/GenbankReader.java  |   8 +-
 .../core/sequence/io/GenbankReaderHelper.java |   6 +-
 .../nbio/core/sequence/io/GenbankWriter.java  |   8 +-
 .../io/GenericGenbankHeaderParser.java        |   3 +-
 .../sequence/io/GenericInsdcHeaderFormat.java |   6 +-
 .../core/sequence/io/embl/EmblReader.java     |   5 +-
 .../loader/GenbankProxySequenceReader.java    |  24 +---
 .../loader/SequenceFileProxyLoader.java       |   8 +-
 .../loader/UniprotProxySequenceReader.java    | 110 +++++++--------
 .../core/sequence/location/InsdcParser.java   |   2 +-
 .../core/sequence/location/SimplePoint.java   |   4 +-
 .../location/template/AbstractLocation.java   |   3 +
 .../template/AbstractCompoundSet.java         |   2 +-
 .../nbio/core/util/FileDownloadUtils.java     |  16 +--
 .../org/biojava/nbio/core/util/XMLHelper.java |  37 ++---
 .../nbio/core/fasta/TestFASTAReader.java      |  12 +-
 .../biojava/nbio/core/search/io/HspTest.java  |  13 +-
 .../nbio/core/search/io/SearchIOTest.java     |  12 +-
 .../io/blast/BlastTabularParserTest.java      |  16 +--
 .../search/io/blast/BlastXMLParserTest.java   |  15 +-
 .../core/sequence/TestSequenceEquals.java     |   3 +-
 .../nbio/core/sequence/io/ABITracerTest.java  |   3 +-
 .../core/sequence/io/GenbankReaderTest.java   |  27 +---
 .../SimpleGenbankProxySequenceReaderTest.java |   3 +-
 .../sequence/location/InsdcParserTest.java    |   5 +-
 .../core/util/TestUncompressInputStream.java  |   7 +-
 .../nbio/genome/GeneFeatureHelper.java        |   2 +-
 .../homology/GFF3FromUniprotBlastHits.java    |  35 ++---
 .../genome/io/fastq/AbstractFastqWriter.java  |   9 +-
 .../parsers/geneid/GeneIDXMLReader.java       |   8 +-
 .../GeneChromosomePositionParser.java         |   2 +-
 .../nbio/genome/parsers/gff/Feature.java      |   2 +-
 .../nbio/genome/parsers/gff/FeatureList.java  |   2 +-
 .../nbio/genome/parsers/gff/GFF3Writer.java   |   2 +-
 .../genome/parsers/twobit/TwoBitParser.java   |   2 +-
 .../nbio/genome/query/BlastXMLQuery.java      |   7 +-
 .../nbio/genome/GeneFeatureHelperTest.java    |   6 +-
 .../org/biojava/nbio/genome/TestIssue355.java |   5 +-
 .../org/biojava/nbio/genome/TestLocation.java |   4 +-
 .../nbio/genome/io/fastq/ConvertTest.java     |  10 +-
 .../nbio/genome/io/fastq/FastqToolsTest.java  |   1 -
 .../genome/io/fastq/FastqVariantTest.java     |   4 +-
 .../io/fastq/IlluminaFastqReaderTest.java     |   3 +-
 .../nbio/structure/test/MMcifTest.java        |   3 +-
 .../structure/test/PDBFileParserTest.java     |  20 +--
 .../nbio/structure/test/StructureTest.java    |   9 +-
 .../structure/test/StructureToolsTest.java    |   3 +-
 .../biojava/nbio/structure/test/Test1o2f.java |   1 -
 .../nbio/structure/test/TestSECalignment.java |   2 +-
 .../test/align/ce/OptimalCECPMainTest.java    |   5 +-
 .../fatcat/AFPChainSerialisationTest.java     |   3 +-
 .../test/align/fatcat/FlipAFPChainTest.java   |   5 +-
 .../fatcat/TestFlexibleRotationMatrices.java  |   8 +-
 .../align/qsalign/TestQsAlignExamples.java    |   9 +-
 .../align/seq/TestSmithWaterman3Daligner.java |   9 +-
 .../cluster/TestSubunitClustererExamples.java |  15 +-
 .../test/ecod/EcodInstallationTest.java       |  27 ++--
 .../structure/test/ecod/EcodParseTest.java    |  15 +-
 .../geometry/TestProteinSuperposition.java    |  18 +--
 .../structure/test/io/StructureIOTest.java    |   8 +-
 .../nbio/structure/test/io/Test4v5a.java      |   5 +-
 .../structure/test/io/TestBioassemblies.java  |  10 +-
 .../test/io/TestCrystallographicMetadata.java |   6 +-
 .../test/io/TestLongPdbVsMmCifParsing.java    |   6 +-
 .../structure/test/io/TestNcsOpsParsing.java  |  11 +-
 .../structure/test/io/TestSeqResParsing.java  |  11 +-
 .../io/TestStructWithMultiparentChemComp.java |   7 +-
 .../cif/CifFileConsumerIntegrationTest.java   |  14 +-
 .../cif/CifFileSupplierIntegrationTest.java   |  13 +-
 .../structure/test/scop/ScopDatabaseTest.java |   4 +-
 .../nbio/structure/test/scop/ScopTest.java    |  11 +-
 .../TestQuatSymmetryDetectorExamples.java     |  13 +-
 .../test/xtal/TestCrystalBuilder.java         |   2 +-
 .../protmod/io/ComponentXMLConverter.java     |   2 +-
 .../io/ModifiedCompoundXMLConverter.java      |   2 +-
 .../protmod/io/StructureAtomXMLConverter.java |   2 +-
 .../io/StructureGroupXMLConverter.java        |   2 +-
 .../ProteinModificationParserTest.java        |   4 +-
 .../nbio/protmod/structure/TmpAtomCache.java  |   4 +-
 .../biojava/nbio/ontology/io/GOParser.java    |   1 -
 .../biojava/nbio/ontology/io/OboParser.java   |   4 +-
 .../nbio/ontology/obo/OboFileHandler.java     |   2 +-
 .../nbio/ontology/obo/OboFileParser.java      |  12 +-
 .../nbio/ontology/TestOboFileParsing.java     |   3 +-
 .../biojava/nbio/ontology/TestParseOBO.java   |   1 -
 .../org/biojava/nbio/ronn/ModelLoader.java    |   4 +-
 .../java/demo/DemoAlignmentFromFasta.java     |  16 +--
 .../src/main/java/demo/DemoCeSymm.java        |   3 +-
 .../src/main/java/demo/DemoMultipleMC.java    |  10 +-
 .../main/java/demo/DemoShowBiolAssembly.java  |   2 +-
 .../main/java/demo/DemoShowCATHDomain.java    |   2 +-
 .../main/java/demo/DemoShowLargeAssembly.java |   2 +-
 .../java/demo/DemoShowValidationResults.java  |   2 +-
 .../java/demo/DemoStructureFromFasta.java     |  12 +-
 .../main/java/demo/ShowStructureInJmol.java   |   2 +-
 .../structure/align/gui/AlignmentCalc.java    |   4 +-
 .../structure/align/gui/AlignmentCalcDB.java  |   8 +-
 .../structure/align/gui/AlignmentGui.java     |  35 ++---
 .../align/gui/AlignmentTextPanel.java         |   2 +-
 .../structure/align/gui/ChooseDirAction.java  |   2 +-
 .../align/gui/ConfigPDBInstallPanel.java      |   4 +-
 .../nbio/structure/align/gui/DBSearchGUI.java |   8 +-
 .../nbio/structure/align/gui/DisplayAFP.java  |  22 +--
 .../gui/GUIAlignmentProgressListener.java     |   2 +-
 .../align/gui/GUIFarmJobRunnable.java         |   2 +-
 .../structure/align/gui/MemoryMonitor.java    |   8 +-
 .../nbio/structure/align/gui/MenuCreator.java |   1 -
 .../align/gui/MultipleAlignmentCalc.java      |  12 +-
 .../align/gui/MultipleAlignmentGUI.java       |  21 +--
 .../gui/MultipleAlignmentJmolDisplay.java     |  14 +-
 .../align/gui/MyAlignmentLoadListener.java    |   3 +-
 .../align/gui/MyDistMaxListener.java          |   3 +-
 .../structure/align/gui/MyExportListener.java |   4 +-
 .../align/gui/MySaveFileListener.java         |   1 -
 .../structure/align/gui/MyTableRowSorter.java |   2 +-
 .../structure/align/gui/SelectPDBPanel.java   |  32 ++---
 .../align/gui/StructureAlignmentDisplay.java  |   4 +-
 .../align/gui/StructureLoaderThread.java      |   6 +-
 .../nbio/structure/align/gui/SystemInfo.java  |   2 +-
 .../AligPanelMouseMotionListener.java         |   2 +-
 .../gui/aligpanel/MultipleAligPanel.java      |  22 ++-
 .../gui/aligpanel/MultipleStatusDisplay.java  |  12 +-
 .../autosuggest/SCOPAutoSuggestProvider.java  |   4 +-
 .../align/gui/jmol/AbstractAlignmentJmol.java |  22 +--
 .../align/gui/jmol/AtomInfoParser.java        |   2 +-
 .../structure/align/gui/jmol/JmolPanel.java   |  32 ++---
 .../align/gui/jmol/MultipleAlignmentJmol.java |  33 ++---
 .../align/gui/jmol/MyJmolStatusListener.java  |   7 +-
 .../align/gui/jmol/RasmolCommandListener.java |   6 +-
 .../gui/jmol/StructureAlignmentJmol.java      |  10 +-
 .../align/webstart/ConfigXMLHandler.java      |   2 +-
 .../align/webstart/WebStartMain.java          |   1 -
 .../nbio/structure/gui/BiojavaJmol.java       |   8 +-
 .../nbio/structure/gui/JMatrixPanel.java      |   2 +-
 .../nbio/structure/gui/JmolViewerImpl.java    |   2 +-
 .../structure/gui/ScaleableMatrixPanel.java   |  14 +-
 .../nbio/structure/gui/SequenceDisplay.java   |  18 +--
 .../nbio/structure/gui/WrapLayout.java        |   3 +-
 .../events/JmolAlignedPositionListener.java   |   4 +-
 .../gui/util/AlternativeAlignmentFrame.java   |  14 +-
 .../gui/util/JTableDataButtonModel.java       |   4 +-
 .../nbio/structure/gui/util/PDBDirPanel.java  |  14 +-
 .../structure/gui/util/PDBServerPanel.java    |  10 +-
 .../structure/gui/util/PDBUploadPanel.java    |  10 +-
 .../gui/util/ScopInstallationInstance.java    |   4 +-
 .../structure/gui/util/ScopSelectPanel.java   |   5 +-
 .../gui/util/SelectMultiplePanel.java         |  18 +--
 .../gui/util/SequenceMouseListener.java       |   8 +-
 .../gui/util/StructurePairSelector.java       |   4 +-
 .../structure/gui/util/color/ColorUtils.java  |   6 +-
 .../color/ContinuousColorMapperTransform.java |   2 +-
 .../symmetry/gui/SymmetryDisplay.java         |  15 +-
 .../structure/symmetry/gui/SymmetryGui.java   |  23 +--
 .../symmetry/gui/SymmetryListener.java        |   6 +-
 .../JmolSymmetryScriptGenerator.java          |   1 -
 .../JmolSymmetryScriptGeneratorH.java         |   3 +-
 ...JmolSymmetryScriptGeneratorPointGroup.java |   5 +-
 .../src/main/java/demo/DemoAtomCache.java     |   2 +-
 .../src/main/java/demo/DemoBioAssemblies.java |   4 +-
 .../src/main/java/demo/DemoCeSymm.java        |   4 +-
 .../main/java/demo/DemoCrystalInterfaces.java |   2 +-
 .../src/main/java/demo/DemoLoadSecStruc.java  |   6 +-
 .../src/main/java/demo/DemoLoadStructure.java |   2 +-
 .../java/demo/DemoMmcifToPdbConverter.java    |   7 +-
 .../src/main/java/demo/DemoMmtfReader.java    |   4 +-
 .../src/main/java/demo/DemoMmtfWriter.java    |   6 +-
 .../src/main/java/demo/DemoMultipleMC.java    |  10 +-
 .../src/main/java/demo/DemoQsAlign.java       |   4 +-
 .../src/main/java/demo/DemoSecStrucCalc.java  |   8 +-
 .../src/main/java/demo/DemoSymmetry.java      |   4 +-
 .../java/org/biojava/nbio/structure/Atom.java |   3 +-
 .../org/biojava/nbio/structure/AtomImpl.java  |   3 +-
 .../nbio/structure/AtomPositionMap.java       |  12 +-
 .../nbio/structure/BioAssemblyIdentifier.java |   4 +-
 .../java/org/biojava/nbio/structure/Calc.java |  17 ++-
 .../org/biojava/nbio/structure/ChainImpl.java |  13 +-
 .../biojava/nbio/structure/EntityInfo.java    |   9 +-
 .../org/biojava/nbio/structure/GroupType.java |   4 +-
 .../org/biojava/nbio/structure/Model.java     |   6 +-
 .../org/biojava/nbio/structure/Mutator.java   |   4 +-
 .../nbio/structure/PassthroughIdentifier.java |   4 +-
 .../nbio/structure/ResidueRangeAndLength.java |   6 +-
 .../nbio/structure/StructureFiletype.java     |  27 ++++
 .../biojava/nbio/structure/StructureIO.java   | 101 ++++----------
 .../nbio/structure/StructureIdentifier.java   |   4 +-
 .../biojava/nbio/structure/StructureImpl.java |   8 +-
 .../nbio/structure/StructureTools.java        |  17 ++-
 .../structure/SubstructureIdentifier.java     |  10 +-
 .../biojava/nbio/structure/URLIdentifier.java |  25 ++--
 .../nbio/structure/align/AFPTwister.java      |   3 +-
 .../biojava/nbio/structure/align/FarmJob.java |   2 +-
 .../align/MultiThreadedDBSearch.java          |   8 +-
 .../align/MultipleStructureAligner.java       |   4 +-
 .../structure/align/StructurePairAligner.java |   5 +-
 .../ce/AbstractUserArgumentProcessor.java     |   4 +-
 .../nbio/structure/align/ce/CECalculator.java |  19 +--
 .../nbio/structure/align/ce/CeCPMain.java     |  15 +-
 .../align/ce/CeCalculatorEnhanced.java        |  13 +-
 .../nbio/structure/align/ce/CeParameters.java |   4 +-
 .../align/client/FarmJobRunnable.java         |  12 +-
 .../structure/align/client/JFatCatClient.java |   9 +-
 .../structure/align/client/StructureName.java |  34 ++---
 .../fatcat/FatCatUserArgumentProcessor.java   |   2 +-
 .../align/fatcat/calc/AFPCalculator.java      |   4 +-
 .../align/fatcat/calc/AFPChainer.java         |   3 +-
 .../calc/StructureAlignmentOptimizer.java     |  21 +--
 .../align/helper/JointFragments.java          |   2 +-
 .../structure/align/multiple/BlockImpl.java   |   4 +-
 .../structure/align/multiple/BlockSet.java    |   3 +-
 .../align/multiple/BlockSetImpl.java          |   3 +-
 .../align/multiple/MultipleAlignment.java     |   4 +-
 .../multiple/MultipleAlignmentEnsemble.java   |   4 +-
 .../MultipleAlignmentEnsembleImpl.java        |  15 +-
 .../align/multiple/MultipleAlignmentImpl.java |   8 +-
 .../structure/align/multiple/ScoresCache.java |   4 +-
 .../align/multiple/mc/MultipleMcMain.java     |  23 +--
 .../multiple/mc/MultipleMcOptimizer.java      |  15 +-
 .../multiple/mc/MultipleMcParameters.java     |   4 +-
 .../align/multiple/util/CoreSuperimposer.java |   9 +-
 .../util/MultipleAlignmentDisplay.java        |   1 -
 .../util/MultipleAlignmentScorer.java         |   8 +-
 .../multiple/util/MultipleAlignmentTools.java |  27 +---
 .../util/MultipleAlignmentWriter.java         |  21 ++-
 .../multiple/util/MultipleSuperimposer.java   |   4 +-
 .../multiple/util/ReferenceSuperimposer.java  |   9 +-
 .../align/pairwise/AlternativeAlignment.java  |   4 +-
 .../nbio/structure/align/pairwise/Gotoh.java  |   4 +-
 .../structure/align/quaternary/QsAlign.java   |  33 +----
 .../align/quaternary/QsAlignResult.java       |  15 +-
 .../align/seq/SmithWaterman3Daligner.java     |  12 +-
 .../align/util/AFPAlignmentDisplay.java       |   3 +-
 .../structure/align/util/AFPChainScorer.java  |   4 +-
 .../structure/align/util/AlignmentTools.java  |   5 +-
 .../nbio/structure/align/util/AtomCache.java  | 132 +++++++++---------
 .../structure/align/util/RotationAxis.java    |  13 +-
 .../align/util/SynchronizedOutFile.java       |   2 +-
 .../align/util/UserConfiguration.java         |   4 +-
 .../align/xml/AFPChainXMLConverter.java       |   2 +-
 .../xml/MultipleAlignmentXMLConverter.java    |  15 +-
 .../align/xml/MultipleAlignmentXMLParser.java |  29 ++--
 .../align/xml/PdbPairXMLConverter.java        |   2 +-
 .../basepairs/BasePairParameters.java         |  25 ++--
 .../nbio/structure/cath/CathDomain.java       |  16 +--
 .../nbio/structure/cath/CathInstallation.java |   4 +-
 .../structure/cluster/SubunitCluster.java     |  20 +--
 .../structure/cluster/SubunitClusterer.java   |   6 +-
 .../structure/cluster/SubunitExtractor.java   |   5 +-
 .../nbio/structure/contact/AtomContact.java   |   4 +-
 .../nbio/structure/contact/BoundingBox.java   |   4 +-
 .../biojava/nbio/structure/contact/Grid.java  |   9 +-
 .../nbio/structure/contact/GridCell.java      |   3 +-
 .../structure/contact/ResidueIdentifier.java  |   4 +-
 .../structure/contact/StructureInterface.java |  21 +--
 .../contact/StructureInterfaceList.java       |  13 +-
 .../nbio/structure/domain/DomainProvider.java |   4 +-
 .../nbio/structure/domain/PDPDomain.java      |  10 +-
 .../nbio/structure/domain/PDPProvider.java    |   6 +-
 .../domain/RemoteDomainProvider.java          |  14 +-
 .../structure/domain/RemotePDPProvider.java   |  12 +-
 .../structure/domain/SerializableCache.java   |   2 +-
 .../nbio/structure/domain/pdp/Cut.java        |   2 +-
 .../nbio/structure/domain/pdp/CutDomain.java  |   8 +-
 .../domain/pdp/GetDistanceMatrix.java         |   5 +-
 .../nbio/structure/ecod/EcodFactory.java      |  12 +-
 .../nbio/structure/ecod/EcodInstallation.java |  27 +---
 .../nbio/structure/geometry/CalcPoint.java    |   4 +-
 .../nbio/structure/geometry/Matrices.java     |   4 +-
 .../structure/geometry/MomentsOfInertia.java  |   1 -
 .../structure/geometry/SuperPositionQCP.java  |   6 +-
 .../structure/geometry/SuperPositionQuat.java |   5 +-
 .../structure/geometry/SuperPositionSVD.java  |   6 +-
 .../structure/geometry/UnitQuaternions.java   |   6 +-
 .../biojava/nbio/structure/io/BondMaker.java  |   7 +-
 .../nbio/structure/io/ChargeAdder.java        |   4 +-
 .../nbio/structure/io/EntityFinder.java       |  13 +-
 .../structure/io/FastaAFPChainConverter.java  |   8 +-
 .../structure/io/FastaStructureParser.java    |   8 +-
 .../nbio/structure/io/FileConvert.java        |  29 ++--
 .../structure/io/FileParsingParameters.java   |   4 +-
 .../biojava/nbio/structure/io/GroupToSDF.java |   7 +-
 .../nbio/structure/io/LocalPDBDirectory.java  |   4 +-
 .../nbio/structure/io/MMTFFileReader.java     |   6 +-
 .../structure/io/PDBBioAssemblyParser.java    |   5 +-
 .../nbio/structure/io/PDBFileParser.java      |  61 ++------
 .../nbio/structure/io/PDBFileReader.java      |   1 +
 .../biojava/nbio/structure/io/SSBondImpl.java |   6 +-
 .../io/SandboxStyleStructureProvider.java     |   2 +-
 .../nbio/structure/io/SeqRes2AtomAligner.java |  28 +---
 .../io/StructureSequenceMatcher.java          |   2 +-
 .../structure/io/cif/CifFileConsumer.java     |  46 +-----
 .../structure/io/cif/CifFileConsumerImpl.java |  77 +---------
 .../structure/io/cif/CifFileSupplierImpl.java |  15 +-
 .../io/mmcif/AllChemCompProvider.java         |   6 +-
 .../structure/io/mmcif/ChemCompConsumer.java  |   2 +-
 .../io/mmcif/ChemCompGroupFactory.java        |   6 +-
 .../io/mmcif/DownloadChemCompProvider.java    |  28 ++--
 .../structure/io/mmcif/MMCIFFileTools.java    |  21 +--
 .../structure/io/mmcif/MetalBondConsumer.java |   2 +-
 .../structure/io/mmcif/MetalBondParser.java   |   6 +-
 .../io/mmcif/ReducedChemCompProvider.java     |   8 +-
 .../io/mmcif/SimpleMMcifConsumer.java         |  89 ++----------
 .../structure/io/mmcif/SimpleMMcifParser.java |  63 ++-------
 .../io/mmcif/ZipChemCompProvider.java         |  24 ++--
 .../structure/io/mmcif/chem/PolymerType.java  |   2 +-
 .../structure/io/mmcif/chem/ResidueType.java  |   2 +-
 .../io/mmcif/model/ChemCompBond.java          |   4 +-
 .../nbio/structure/io/mmtf/MmtfActions.java   |  12 +-
 .../io/mmtf/MmtfStructureReader.java          |  37 +----
 .../io/mmtf/MmtfStructureWriter.java          |  18 +--
 .../io/mmtf/MmtfSummaryDataBean.java          |   6 +-
 .../nbio/structure/io/mmtf/MmtfUtils.java     |  33 +----
 .../io/sifts/SiftsChainToUniprotMapping.java  |   2 +-
 .../io/sifts/SiftsMappingProvider.java        |   2 +-
 .../structure/io/sifts/SiftsXMLParser.java    |   3 +-
 .../quaternary/BioAssemblyTools.java          |   3 +-
 .../quaternary/BiologicalAssemblyBuilder.java |   5 +-
 .../BiologicalAssemblyTransformation.java     |   2 +-
 .../nbio/structure/rcsb/PdbIdLists.java       |   3 +-
 .../scop/BerkeleyScopInstallation.java        |   4 +-
 .../scop/CachedRemoteScopInstallation.java    |   4 +-
 .../nbio/structure/scop/ScopDomain.java       |  17 +--
 .../nbio/structure/scop/ScopFactory.java      |   1 -
 .../nbio/structure/scop/ScopInstallation.java |   9 +-
 .../scop/server/ListStringWrapper.java        |   2 +-
 .../scop/server/ScopDescriptions.java         |   2 +-
 .../structure/scop/server/ScopDomains.java    |   2 +-
 .../nbio/structure/scop/server/ScopNodes.java |   2 +-
 .../scop/server/TreeSetStringWrapper.java     |   2 +-
 .../nbio/structure/scop/server/XMLUtil.java   |  12 +-
 .../nbio/structure/secstruc/BetaBridge.java   |   6 +-
 .../nbio/structure/secstruc/DSSPParser.java   |  19 +--
 .../nbio/structure/secstruc/SecStrucCalc.java |   7 +-
 .../structure/secstruc/SecStrucElement.java   |   4 +-
 .../nbio/structure/secstruc/SecStrucInfo.java |   8 +-
 .../structure/secstruc/SecStrucTools.java     |   7 +-
 .../structure/symmetry/axis/AxisAligner.java  |   7 +-
 .../symmetry/axis/HelixAxisAligner.java       |   1 -
 .../symmetry/axis/RotationAxisAligner.java    |   3 +-
 .../symmetry/core/C2RotationSolver.java       |   7 +-
 .../symmetry/core/HelicalRepeatUnit.java      |   2 +-
 .../symmetry/core/HelixExtender.java          |   2 +-
 .../structure/symmetry/core/HelixSolver.java  |   1 -
 .../symmetry/core/PermutationGroup.java       |   8 +-
 .../core/QuatSuperpositionScorer.java         |   1 -
 .../symmetry/core/QuatSymmetryDetector.java   |  14 +-
 .../symmetry/core/QuatSymmetrySubunits.java   |   4 +-
 .../symmetry/core/RotationSolver.java         |  16 +--
 .../symmetry/core/Stoichiometry.java          |  13 +-
 .../symmetry/core/SystematicSolver.java       |   7 +-
 .../symmetry/geometry/Tetrahedron.java        |   4 +-
 .../internal/AngleOrderDetectorPlus.java      |   7 +-
 .../symmetry/internal/CESymmParameters.java   |   4 +-
 .../structure/symmetry/internal/CeSymm.java   |  15 +-
 .../symmetry/internal/CeSymmIterative.java    |  18 +--
 .../symmetry/internal/CeSymmResult.java       |  15 +-
 .../internal/GraphComponentOrderDetector.java |  10 +-
 .../internal/GraphComponentRefiner.java       |  15 +-
 .../SequenceFunctionOrderDetector.java        |   4 +-
 .../internal/SequenceFunctionRefiner.java     |  11 +-
 .../symmetry/internal/SymmOptimizer.java      |  14 +-
 .../symmetry/internal/SymmetryAxes.java       |  11 +-
 .../symmetry/utils/BlastClustReader.java      |   9 +-
 .../structure/symmetry/utils/PowerSet.java    |   4 +-
 .../symmetry/utils/SymmetryTools.java         |  34 +----
 .../WwPDBValidationInformation.java           |   1 -
 .../nbio/structure/xtal/SpaceGroup.java       |   1 -
 .../structure/xtal/UnitCellBoundingBox.java   |   3 +-
 .../nbio/structure/AtomPositionMapTest.java   |   2 +-
 .../nbio/structure/PdbFileFormat30Test.java   |   3 +-
 .../org/biojava/nbio/structure/Test2JA5.java  |   8 +-
 .../nbio/structure/TestAtomIterator.java      |  11 +-
 .../structure/TestBioAssemblyIdentifier.java  |   7 +-
 .../org/biojava/nbio/structure/TestBond.java  |  11 +-
 .../org/biojava/nbio/structure/TestCalc.java  |   9 +-
 .../nbio/structure/TestChargeAdder.java       |   6 +-
 .../biojava/nbio/structure/TestCloning.java   |   8 +-
 .../nbio/structure/TestDNAAlignment.java      |   9 +-
 .../TestDownloadChemCompProvider.java         |   3 +-
 .../nbio/structure/TestEntityHeuristics.java  |   6 +-
 .../structure/TestEntityResIndexMapping.java  |  12 +-
 .../TestStructureCrossReferences.java         |  14 +-
 .../nbio/structure/TestStructureImpl.java     |   4 +-
 .../structure/TestStructureSerialization.java |   8 +-
 .../nbio/structure/TestURLIdentifier.java     |  10 +-
 .../align/TestAlignmentConsistency.java       |   3 +-
 .../nbio/structure/align/ce/CeCPMainTest.java |   1 -
 .../align/ce/TestWebStartClient.java          |   2 +-
 .../align/client/TestStructureName.java       |  10 +-
 .../multiple/TestAFPChainConversion.java      |   2 +-
 .../align/multiple/TestSampleGenerator.java   |  18 +--
 .../util/TestMultipleAlignmentScorer.java     |  27 +---
 .../util/TestMultipleAlignmentTools.java      |  13 +-
 .../util/TestMultipleAlignmentWriter.java     |  11 +-
 .../util/TestMultipleAlignmentXMLParser.java  |  22 ++-
 .../structure/align/util/AtomCacheTest.java   |  47 +++----
 .../align/util/RotationAxisTest.java          |   6 +-
 .../nbio/structure/asa/TestAsaCalc.java       |  13 +-
 .../basepairs/TestBasePairParameters.java     |   3 +-
 .../structure/cluster/TestSubunitCluster.java |  20 +--
 .../cluster/TestSubunitExtractor.java         |  12 +-
 .../structure/contact/TestContactCalc.java    |   1 -
 .../structure/geometry/TestSuperPosition.java |  22 ++-
 .../geometry/TestSuperPositionQCP.java        |  14 +-
 .../geometry/TestUnitQuaternions.java         |  21 +--
 .../io/FastaAFPChainConverterTest.java        |   4 +-
 .../io/StructureSequenceMatcherTest.java      |   4 +-
 .../nbio/structure/io/TestDBRefParsing.java   |   6 +-
 .../structure/io/TestDifficultMmCIFFiles.java |  34 ++---
 .../nbio/structure/io/TestHardBioUnits.java   |  14 +-
 .../nbio/structure/io/TestHeaderOnly.java     |  20 ++-
 .../nbio/structure/io/TestMMCIFWriting.java   |  30 +---
 .../io/TestMMcifOrganismParsing.java          |  10 +-
 .../structure/io/TestMmCIFSpecialCases.java   |   6 +-
 .../structure/io/TestNonDepositedFiles.java   |  23 +--
 .../structure/io/TestParseMmCIFFeatures.java  |  14 +-
 .../structure/io/TestParseMmCIFLigands.java   |  15 +-
 .../nbio/structure/io/TestParseOnAsymId.java  |  10 +-
 .../nbio/structure/io/TestShortLines.java     |  14 +-
 .../structure/io/TestURLBasedFileParsing.java |   7 +-
 .../io/TestWriteLargeCoordinatePDB.java       |  12 +-
 .../io/mmcif/TestChemCompProvider.java        |  16 +--
 .../io/mmcif/TestEntityNameAndType.java       |  14 +-
 .../io/mmcif/TestMmcifV5Changes.java          |  12 +-
 .../io/mmcif/TestParseInternalChainId.java    |   8 +-
 .../io/mmcif/TestParseMmcifHeader.java        |  14 +-
 .../structure/io/mmtf/TestBondFinding.java    |  20 +--
 .../io/mmtf/TestMmtfPerformance.java          |   5 +-
 .../structure/io/mmtf/TestMmtfRoundTrip.java  |  27 ++--
 .../io/mmtf/TestMmtfStructureReader.java      |  12 +-
 .../io/mmtf/TestMmtfStructureWriter.java      |  23 +--
 .../nbio/structure/io/mmtf/TestMmtfUtils.java |  42 ++----
 .../sifts/SiftsChainToUniprotMappingTest.java |   6 +-
 .../structure/redmine/Test1DARSeqAlign.java   |   3 +-
 .../structure/secstruc/TestDSSPParser.java    |  13 +-
 .../structure/secstruc/TestSecStrucCalc.java  |  12 +-
 .../symmetry/internal/TestCeSymm.java         |  10 +-
 .../TestSequenceFunctionOrderDetector.java    |  15 +-
 .../symmetry/internal/TestSingleRefiner.java  |  11 +-
 .../symmetry/internal/TestSymmetryAxes.java   |  15 +-
 .../symmetry/utils/TestSymmetryTools.java     |   4 +-
 .../structure/test/util/GlobalsHelper.java    |  10 +-
 .../nbio/structure/xtal/TestCrystalCell.java  |   9 +-
 .../xtal/TestInterfaceClustering.java         |  19 ++-
 .../biojava/nbio/survival/cox/CoxInfo.java    |   2 +-
 .../biojava/nbio/survival/cox/StrataInfo.java |   2 +-
 .../nbio/survival/cox/SurvivalInfo.java       |   6 +-
 ...CoxVariablesOverallModelFitComparator.java |   2 +-
 .../CoxVariablesVariableComparator.java       |   4 +-
 .../cox/comparators/MeanModelComparator.java  |   2 +-
 .../SurvivalInfoValueComparator.java          |   2 +-
 .../biojava/nbio/survival/data/WorkSheet.java |   4 +-
 .../kaplanmeier/figure/ExpressionFigure.java  |   2 +-
 .../kaplanmeier/figure/KMFigureInfo.java      |  26 ++--
 .../kaplanmeier/figure/KaplanMeierFigure.java |   6 +-
 .../kaplanmeier/metadata/MetaDataInfo.java    |   2 +-
 .../qblast/NCBIQBlastAlignmentProperties.java |   3 +-
 .../nbio/ws/hmmer/RemoteHmmerScan.java        |   5 +-
 .../nbio/ws/hmmer/TestRemoteHmmerScan.java    |   5 +-
 pom.xml                                       |  14 +-
 540 files changed, 2007 insertions(+), 3177 deletions(-)
 create mode 100644 biojava-structure/src/main/java/org/biojava/nbio/structure/StructureFiletype.java

diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
index a35ecfafa9..e300da2e7f 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
@@ -43,35 +43,35 @@
 public class Constraints {
 	private static final AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
 	//A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y, V
-	public static AminoAcidCompound A = aaSet.getCompoundForString("A");
-	public static AminoAcidCompound R = aaSet.getCompoundForString("R");
-	public static AminoAcidCompound N = aaSet.getCompoundForString("N");
-	public static AminoAcidCompound D = aaSet.getCompoundForString("D");
-	public static AminoAcidCompound C = aaSet.getCompoundForString("C");
-	public static AminoAcidCompound E = aaSet.getCompoundForString("E");
-	public static AminoAcidCompound Q = aaSet.getCompoundForString("Q");
-	public static AminoAcidCompound G = aaSet.getCompoundForString("G");
-	public static AminoAcidCompound H = aaSet.getCompoundForString("H");
-	public static AminoAcidCompound I = aaSet.getCompoundForString("I");
-	public static AminoAcidCompound L = aaSet.getCompoundForString("L");
-	public static AminoAcidCompound K = aaSet.getCompoundForString("K");
-	public static AminoAcidCompound M = aaSet.getCompoundForString("M");
-	public static AminoAcidCompound F = aaSet.getCompoundForString("F");
-	public static AminoAcidCompound P = aaSet.getCompoundForString("P");
-	public static AminoAcidCompound S = aaSet.getCompoundForString("S");
-	public static AminoAcidCompound T = aaSet.getCompoundForString("T");
-	public static AminoAcidCompound W = aaSet.getCompoundForString("W");
-	public static AminoAcidCompound Y = aaSet.getCompoundForString("Y");
-	public static AminoAcidCompound V = aaSet.getCompoundForString("V");
+	public static final AminoAcidCompound A = aaSet.getCompoundForString("A");
+	public static final AminoAcidCompound R = aaSet.getCompoundForString("R");
+	public static final AminoAcidCompound N = aaSet.getCompoundForString("N");
+	public static final AminoAcidCompound D = aaSet.getCompoundForString("D");
+	public static final AminoAcidCompound C = aaSet.getCompoundForString("C");
+	public static final AminoAcidCompound E = aaSet.getCompoundForString("E");
+	public static final AminoAcidCompound Q = aaSet.getCompoundForString("Q");
+	public static final AminoAcidCompound G = aaSet.getCompoundForString("G");
+	public static final AminoAcidCompound H = aaSet.getCompoundForString("H");
+	public static final AminoAcidCompound I = aaSet.getCompoundForString("I");
+	public static final AminoAcidCompound L = aaSet.getCompoundForString("L");
+	public static final AminoAcidCompound K = aaSet.getCompoundForString("K");
+	public static final AminoAcidCompound M = aaSet.getCompoundForString("M");
+	public static final AminoAcidCompound F = aaSet.getCompoundForString("F");
+	public static final AminoAcidCompound P = aaSet.getCompoundForString("P");
+	public static final AminoAcidCompound S = aaSet.getCompoundForString("S");
+	public static final AminoAcidCompound T = aaSet.getCompoundForString("T");
+	public static final AminoAcidCompound W = aaSet.getCompoundForString("W");
+	public static final AminoAcidCompound Y = aaSet.getCompoundForString("Y");
+	public static final AminoAcidCompound V = aaSet.getCompoundForString("V");
 
-	public static Map<AminoAcidCompound, Double> aa2ExtinctionCoefficient = new HashMap<>();
-	public static Map<AminoAcidCompound, Double> aa2MolecularWeight = new HashMap<>();
-	public static Map<AminoAcidCompound, Double> aa2Hydrophathicity = new HashMap<>();
-	public static Map<AminoAcidCompound, Double> aa2PKa = new HashMap<>();
-	public static Map<String, Double> diAA2Instability = new HashMap<>();
+	public static final Map<AminoAcidCompound, Double> aa2ExtinctionCoefficient = new HashMap<>();
+	public static final Map<AminoAcidCompound, Double> aa2MolecularWeight = new HashMap<>();
+	public static final Map<AminoAcidCompound, Double> aa2Hydrophathicity = new HashMap<>();
+	public static final Map<AminoAcidCompound, Double> aa2PKa = new HashMap<>();
+	public static final Map<String, Double> diAA2Instability = new HashMap<>();
 
-	public static Map<AminoAcidCompound, Double> aa2NTerminalPka = new HashMap<>();
-	public static Map<AminoAcidCompound, Double> aa2CTerminalPka = new HashMap<>();
+	public static final Map<AminoAcidCompound, Double> aa2NTerminalPka = new HashMap<>();
+	public static final Map<AminoAcidCompound, Double> aa2CTerminalPka = new HashMap<>();
 
 	static{
 		initMolecularWeight();
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
index f1f7ef390a..473022a0a7 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
@@ -58,7 +58,7 @@ public enum SingleLetterAACode { W, C, M, H, Y, F, Q, N, I, R, D, P, T, K, E, V,
 	/**
 	 * Contains the 20 standard AA code in a set
 	 */
-	public static Set<Character> standardAASet;
+	public static final Set<Character> standardAASet;
 
 	/**
 	 * To initialize the standardAASet
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CommandPromptTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CommandPromptTest.java
index 58ed18dc16..bf37136610 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CommandPromptTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CommandPromptTest.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.aaproperties;
 
-import org.biojava.nbio.aaproperties.CommandPrompt;
 import org.junit.Test;
 
 import java.io.File;
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java
index 78e916a377..aa51ac3876 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.aaproperties;
 
-import org.biojava.nbio.aaproperties.PeptideProperties;
 import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
 import org.junit.Test;
 import org.slf4j.Logger;
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/GenbankCommandPromptTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/GenbankCommandPromptTest.java
index 846e7092f4..15261ae05c 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/GenbankCommandPromptTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/GenbankCommandPromptTest.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.aaproperties;
 
-import org.biojava.nbio.aaproperties.CommandPrompt;
 import org.junit.Test;
 
 import java.io.File;
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java
index a23d6adc3c..ae82803012 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java
@@ -20,8 +20,6 @@
  */
 package org.biojava.nbio.aaproperties;
 
-import org.biojava.nbio.aaproperties.PeptideProperties;
-import org.biojava.nbio.aaproperties.Utils;
 import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
 import org.junit.Test;
 import org.slf4j.Logger;
@@ -345,7 +343,7 @@ public void testNetCharge(){
 			logger.debug(p);
 			logger.debug("pH\tInnovagen\tExpasy\tdiff");
 			for ( int i = 1; i < 15; i++) {
-				double phPoint = (double) i;
+				double phPoint = i;
 				double chrgInnovagen = PeptideProperties.getNetCharge(p,false,phPoint);
 				double chrgExpasy = PeptideProperties.getNetCharge(p,true,phPoint);
 				logger.debug(String.format("%2.1f\t%2.2f\t%2.2f\t%2.2f", phPoint, chrgInnovagen,
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/profeat/CookBookTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/profeat/CookBookTest.java
index aa98c006f7..51f9735488 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/profeat/CookBookTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/profeat/CookBookTest.java
@@ -24,13 +24,13 @@
 import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION;
 import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING;
 import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION;
-import org.biojava.nbio.aaproperties.profeat.ProfeatProperties;
-//import org.junit.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.util.Map;
 
+//import org.junit.Test;
+
 public class CookBookTest {
 
 	private final static Logger logger = LoggerFactory.getLogger(CookBookTest.class);
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java
index 07d2a76cf7..801f4f28d7 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java
@@ -20,10 +20,6 @@
  */
 package org.biojava.nbio.aaproperties.xml;
 
-import org.biojava.nbio.aaproperties.xml.Element;
-import org.biojava.nbio.aaproperties.xml.ElementTable;
-import org.biojava.nbio.aaproperties.xml.Isotope;
-import org.biojava.nbio.aaproperties.xml.SchemaGenerator;
 import org.junit.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
diff --git a/biojava-alignment/src/main/java/demo/DemoAlignProteins.java b/biojava-alignment/src/main/java/demo/DemoAlignProteins.java
index 079dab8409..9aef5ed5fa 100644
--- a/biojava-alignment/src/main/java/demo/DemoAlignProteins.java
+++ b/biojava-alignment/src/main/java/demo/DemoAlignProteins.java
@@ -23,9 +23,9 @@
 import org.biojava.nbio.alignment.Alignments;
 import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
 import org.biojava.nbio.alignment.SimpleGapPenalty;
-import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.alignment.template.GapPenalty;
 import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
+import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.SequencePair;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.ProteinSequence;
diff --git a/biojava-alignment/src/main/java/demo/DemoDistanceTree.java b/biojava-alignment/src/main/java/demo/DemoDistanceTree.java
index ae0fe1661e..cddbe85b01 100644
--- a/biojava-alignment/src/main/java/demo/DemoDistanceTree.java
+++ b/biojava-alignment/src/main/java/demo/DemoDistanceTree.java
@@ -20,9 +20,6 @@
  */
 package demo;
 
-import java.io.InputStream;
-import java.util.LinkedHashMap;
-
 import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.MultipleSequenceAlignment;
@@ -32,15 +29,14 @@
 import org.biojava.nbio.core.sequence.io.FastaReader;
 import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
 import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
-import org.biojava.nbio.phylo.DistanceMatrixCalculator;
-import org.biojava.nbio.phylo.DistanceTreeEvaluator;
-import org.biojava.nbio.phylo.ForesterWrapper;
-import org.biojava.nbio.phylo.TreeConstructor;
-import org.biojava.nbio.phylo.TreeConstructorType;
+import org.biojava.nbio.phylo.*;
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.phylogeny.Phylogeny;
 
+import java.io.InputStream;
+import java.util.LinkedHashMap;
+
 /**
  * This demo contains the CookBook example to create a phylogenetic tree from a
  * multiple sequence alignment (MSA).
diff --git a/biojava-alignment/src/main/java/demo/TestDNANeedlemanWunsch.java b/biojava-alignment/src/main/java/demo/TestDNANeedlemanWunsch.java
index c94e22d934..07ad2cda69 100644
--- a/biojava-alignment/src/main/java/demo/TestDNANeedlemanWunsch.java
+++ b/biojava-alignment/src/main/java/demo/TestDNANeedlemanWunsch.java
@@ -23,9 +23,9 @@
 import org.biojava.nbio.alignment.Alignments;
 import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
 import org.biojava.nbio.alignment.SimpleGapPenalty;
-import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.alignment.template.GapPenalty;
 import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
+import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.SequencePair;
 import org.biojava.nbio.core.sequence.DNASequence;
 import org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet;
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
index 9193b4299b..33967f0221 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
@@ -23,12 +23,12 @@
 
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.template.ProfilePair;
-import org.biojava.nbio.core.alignment.template.SequencePair;
+import org.biojava.nbio.alignment.template.*;
 import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.Profile;
+import org.biojava.nbio.core.alignment.template.ProfilePair;
+import org.biojava.nbio.core.alignment.template.SequencePair;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
-import org.biojava.nbio.alignment.template.*;
 import org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
 import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityInProfileScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityInProfileScorer.java
index 179a4cf1ce..5d0006ba0d 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityInProfileScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityInProfileScorer.java
@@ -23,9 +23,9 @@
 
 package org.biojava.nbio.alignment;
 
+import org.biojava.nbio.alignment.template.PairInProfileScorer;
 import org.biojava.nbio.core.alignment.SimpleSequencePair;
 import org.biojava.nbio.core.alignment.template.AlignedSequence;
-import org.biojava.nbio.alignment.template.PairInProfileScorer;
 import org.biojava.nbio.core.alignment.template.Profile;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java
index 9217cfbe4d..538f7a97ec 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java
@@ -23,8 +23,10 @@
 
 package org.biojava.nbio.alignment;
 
+import org.biojava.nbio.alignment.template.AbstractScorer;
+import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
+import org.biojava.nbio.alignment.template.PairwiseSequenceScorer;
 import org.biojava.nbio.core.alignment.template.SequencePair;
-import org.biojava.nbio.alignment.template.*;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityInProfileScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityInProfileScorer.java
index 52292e27e3..de826a6d4c 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityInProfileScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityInProfileScorer.java
@@ -23,9 +23,9 @@
 
 package org.biojava.nbio.alignment;
 
+import org.biojava.nbio.alignment.template.PairInProfileScorer;
 import org.biojava.nbio.core.alignment.SimpleSequencePair;
 import org.biojava.nbio.core.alignment.template.AlignedSequence;
-import org.biojava.nbio.alignment.template.PairInProfileScorer;
 import org.biojava.nbio.core.alignment.template.Profile;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java
index cecfb87932..df59360b1b 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java
@@ -23,8 +23,10 @@
 
 package org.biojava.nbio.alignment;
 
+import org.biojava.nbio.alignment.template.AbstractScorer;
+import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
+import org.biojava.nbio.alignment.template.PairwiseSequenceScorer;
 import org.biojava.nbio.core.alignment.template.SequencePair;
-import org.biojava.nbio.alignment.template.*;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java
index 5b4fd7d099..a1fdddc364 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java
@@ -23,9 +23,9 @@
 
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.SimpleProfile;
 import org.biojava.nbio.alignment.template.GuideTreeNode;
 import org.biojava.nbio.alignment.template.PairwiseSequenceScorer;
+import org.biojava.nbio.core.alignment.SimpleProfile;
 import org.biojava.nbio.core.alignment.template.Profile;
 import org.biojava.nbio.core.alignment.template.ProfilePair;
 import org.biojava.nbio.core.sequence.AccessionID;
@@ -39,7 +39,6 @@
 import org.forester.phylogeny.PhylogenyNode;
 
 import javax.swing.tree.TreeNode;
-
 import java.util.*;
 import java.util.concurrent.Future;
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/NeedlemanWunsch.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/NeedlemanWunsch.java
index 81fc49d803..1f9aeefa21 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/NeedlemanWunsch.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/NeedlemanWunsch.java
@@ -24,8 +24,8 @@
 package org.biojava.nbio.alignment;
 
 import org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner;
-import org.biojava.nbio.core.alignment.template.AlignedSequence;
 import org.biojava.nbio.alignment.template.GapPenalty;
+import org.biojava.nbio.core.alignment.template.AlignedSequence;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleGapPenalty.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleGapPenalty.java
index d45c2a1bc8..54e0e0f967 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleGapPenalty.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleGapPenalty.java
@@ -23,10 +23,10 @@
 
 package org.biojava.nbio.alignment;
 
-import java.io.Serializable;
-
 import org.biojava.nbio.alignment.template.GapPenalty;
 
+import java.io.Serializable;
+
 /**
  * Implements a data structure for the gap penalties used during a sequence alignment routine.
  *
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java
index 47fb7976e0..fb4c3011e0 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java
@@ -23,12 +23,14 @@
 
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.template.ProfilePair;
-import org.biojava.nbio.core.alignment.template.Profile;
-import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
+import org.biojava.nbio.alignment.template.AbstractProfileProfileAligner;
+import org.biojava.nbio.alignment.template.Aligner;
+import org.biojava.nbio.alignment.template.GapPenalty;
 import org.biojava.nbio.core.alignment.SimpleProfilePair;
-import org.biojava.nbio.alignment.template.*;
 import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
+import org.biojava.nbio.core.alignment.template.Profile;
+import org.biojava.nbio.core.alignment.template.ProfilePair;
+import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SmithWaterman.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SmithWaterman.java
index 819d8f5187..6317a6341a 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SmithWaterman.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SmithWaterman.java
@@ -23,11 +23,11 @@
 
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.SimpleSequencePair;
 import org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner;
+import org.biojava.nbio.alignment.template.GapPenalty;
+import org.biojava.nbio.core.alignment.SimpleSequencePair;
 import org.biojava.nbio.core.alignment.template.AlignedSequence;
 import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
-import org.biojava.nbio.alignment.template.GapPenalty;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/StandardRescoreRefiner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/StandardRescoreRefiner.java
index f61670ebae..e0e7d553fb 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/StandardRescoreRefiner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/StandardRescoreRefiner.java
@@ -26,8 +26,8 @@
 import org.biojava.nbio.alignment.Alignments.PairInProfileScorerType;
 import org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType;
 import org.biojava.nbio.alignment.template.AbstractScorer;
-import org.biojava.nbio.core.alignment.template.Profile;
 import org.biojava.nbio.alignment.template.RescoreRefiner;
+import org.biojava.nbio.core.alignment.template.Profile;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java
index 73a7650ae2..64b32ff317 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java
@@ -23,12 +23,12 @@
 
 package org.biojava.nbio.alignment.routines;
 
-import org.biojava.nbio.core.alignment.SimpleSequencePair;
 import org.biojava.nbio.alignment.routines.AlignerHelper.Anchor;
 import org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner;
+import org.biojava.nbio.alignment.template.GapPenalty;
+import org.biojava.nbio.core.alignment.SimpleSequencePair;
 import org.biojava.nbio.core.alignment.template.AlignedSequence;
 import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
-import org.biojava.nbio.alignment.template.GapPenalty;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java
index 363d543d34..e1471ffab4 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java
@@ -23,8 +23,8 @@
 
 package org.biojava.nbio.alignment.routines;
 
-import org.biojava.nbio.core.alignment.template.AlignedSequence;
 import org.biojava.nbio.alignment.template.GapPenalty;
+import org.biojava.nbio.core.alignment.template.AlignedSequence;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
index 5179c87729..c1831c24c1 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
@@ -23,12 +23,12 @@
 
 package org.biojava.nbio.alignment.template;
 
-import org.biojava.nbio.core.alignment.template.Profile;
-import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.alignment.routines.AlignerHelper.Anchor;
 import org.biojava.nbio.alignment.routines.AlignerHelper.Last;
 import org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem;
 import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
+import org.biojava.nbio.core.alignment.template.Profile;
+import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.CompoundSet;
 import org.biojava.nbio.core.sequence.template.Sequence;
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
index aa3e47b824..0f2662d571 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
@@ -23,10 +23,10 @@
 
 package org.biojava.nbio.alignment.template;
 
-import org.biojava.nbio.core.alignment.template.ProfilePair;
+import org.biojava.nbio.alignment.template.GapPenalty.Type;
 import org.biojava.nbio.core.alignment.template.Profile;
+import org.biojava.nbio.core.alignment.template.ProfilePair;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
-import org.biojava.nbio.alignment.template.GapPenalty.Type;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.CompoundSet;
 import org.biojava.nbio.core.sequence.template.Sequence;
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/GuideTreeNode.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/GuideTreeNode.java
index 76b16261e6..a212fac464 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/GuideTreeNode.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/GuideTreeNode.java
@@ -23,8 +23,8 @@
 
 package org.biojava.nbio.alignment.template;
 
-import org.biojava.nbio.core.alignment.template.ProfilePair;
 import org.biojava.nbio.core.alignment.template.Profile;
+import org.biojava.nbio.core.alignment.template.ProfilePair;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java
index d0464bae8b..f8fd3bb1fc 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java
@@ -20,8 +20,6 @@
  */
 package org.biojava.nbio.phylo;
 
-import java.io.IOException;
-import java.util.List;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.MultipleSequenceAlignment;
 import org.biojava.nbio.core.sequence.template.Compound;
@@ -33,6 +31,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.IOException;
+import java.util.List;
+
 /**
  * The DistanceMatrixCalculator methods generate a {@link DistanceMatrix} from a
  * {@link MultipleSequenceAlignment} or other indirect distance infomation (RMSD).
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java
index 7df77176c1..34acacc00b 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java
@@ -20,9 +20,6 @@
  */
 package org.biojava.nbio.phylo;
 
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
 import org.biojava.nbio.core.sequence.MultipleSequenceAlignment;
 import org.biojava.nbio.core.sequence.io.FastaWriter;
 import org.biojava.nbio.core.sequence.template.Compound;
@@ -33,6 +30,10 @@
 import org.forester.msa.Msa;
 import org.forester.phylogeny.Phylogeny;
 
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+
 /**
  * This class contains wrapper methods for communication between BioJava and
  * forester (e.g, Data Structure conversion).
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllGlobal.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllGlobal.java
index 1671027958..8d5d3f2543 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllGlobal.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllGlobal.java
@@ -20,8 +20,8 @@
  */
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
 import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
+import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
 import org.biojava.nbio.core.alignment.template.SequencePair;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.ProteinSequence;
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllLocal.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllLocal.java
index 117a2be947..888a1e6cc5 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllLocal.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllLocal.java
@@ -20,8 +20,8 @@
  */
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
 import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
+import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
 import org.biojava.nbio.core.alignment.template.SequencePair;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.ProteinSequence;
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairGlobal.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairGlobal.java
index e93dc28b07..a56961a395 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairGlobal.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairGlobal.java
@@ -20,8 +20,8 @@
  */
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
 import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
+import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
 import org.biojava.nbio.core.alignment.template.SequencePair;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.ProteinSequence;
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairLocal.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairLocal.java
index 40ff627d29..c5a8a0ff1c 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairLocal.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairLocal.java
@@ -20,8 +20,8 @@
  */
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
 import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
+import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
 import org.biojava.nbio.core.alignment.template.SequencePair;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.ProteinSequence;
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSAProfiler.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSAProfiler.java
index 00e42e7e03..a290ff09b1 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSAProfiler.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSAProfiler.java
@@ -20,11 +20,11 @@
  */
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
 import org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType;
 import org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType;
 import org.biojava.nbio.alignment.template.GapPenalty;
 import org.biojava.nbio.alignment.template.PairwiseSequenceScorer;
+import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
 import org.biojava.nbio.core.alignment.template.Profile;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.ProteinSequence;
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalIdentityScorerTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalIdentityScorerTest.java
index b36a0ffd82..5528155d8e 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalIdentityScorerTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalIdentityScorerTest.java
@@ -23,9 +23,9 @@
 
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.alignment.template.GapPenalty;
 import org.biojava.nbio.alignment.template.PairwiseSequenceScorer;
+import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.ProteinSequence;
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalSimilarityScorerTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalSimilarityScorerTest.java
index 752d17e13f..5f03604f26 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalSimilarityScorerTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/FractionalSimilarityScorerTest.java
@@ -24,9 +24,9 @@
 
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.alignment.template.GapPenalty;
 import org.biojava.nbio.alignment.template.PairwiseSequenceScorer;
+import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.ProteinSequence;
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/GuideTreeTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/GuideTreeTest.java
index 1c5bf3df99..a9ba7f6c78 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/GuideTreeTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/GuideTreeTest.java
@@ -23,11 +23,11 @@
 
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType;
 import org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType;
 import org.biojava.nbio.alignment.template.GapPenalty;
 import org.biojava.nbio.alignment.template.GuideTreeNode;
+import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.ProteinSequence;
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/LocalAlignmentTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/LocalAlignmentTest.java
index c4d88ebddb..c99d59b945 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/LocalAlignmentTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/LocalAlignmentTest.java
@@ -22,9 +22,9 @@
  */
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
 import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
+import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.DNASequence;
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/NeedlemanWunschTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/NeedlemanWunschTest.java
index 5382edabb3..2cc98c4315 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/NeedlemanWunschTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/NeedlemanWunschTest.java
@@ -23,10 +23,10 @@
 
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
-import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.alignment.template.GapPenalty;
 import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
+import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
+import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.DNASequence;
@@ -38,9 +38,7 @@
 import org.junit.Before;
 import org.junit.Test;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
 
 public class NeedlemanWunschTest {
 
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleProfilePairTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleProfilePairTest.java
index 3a75f71f68..3e3c887ede 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleProfilePairTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleProfilePairTest.java
@@ -23,9 +23,10 @@
 
 package org.biojava.nbio.alignment;
 
+import org.biojava.nbio.alignment.template.GapPenalty;
 import org.biojava.nbio.core.alignment.SimpleProfilePair;
+import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
-import org.biojava.nbio.alignment.template.GapPenalty;
 import org.biojava.nbio.core.alignment.template.Profile;
 import org.biojava.nbio.core.alignment.template.ProfilePair;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
@@ -36,9 +37,6 @@
 import org.junit.Test;
 
 import java.util.Arrays;
-import org.biojava.nbio.alignment.NeedlemanWunsch;
-import org.biojava.nbio.alignment.SimpleGapPenalty;
-import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 
 import static org.junit.Assert.assertEquals;
 
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SmithWatermanTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SmithWatermanTest.java
index c51d294525..cb3e94a349 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SmithWatermanTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SmithWatermanTest.java
@@ -23,8 +23,8 @@
 
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.alignment.template.GapPenalty;
+import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.ProteinSequence;
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java
index df6cbf9cf2..6d7312dd33 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java
@@ -23,9 +23,9 @@
  */
 package org.biojava.nbio.alignment;
 
-import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
 import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
+import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.Profile;
 import org.biojava.nbio.core.alignment.template.SequencePair;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
@@ -77,9 +77,7 @@ private static List<DNASequence> getDNAFASTAFile() throws Exception {
 		InputStream inStream = TestDNAAlignment.class.getResourceAsStream("/dna-fasta.txt");
 		LinkedHashMap<String, DNASequence> fastas = FastaReaderHelper.readFastaDNASequence(inStream);
 
-		List<DNASequence> sequences = new ArrayList<>();
-
-        sequences.addAll(fastas.values());
+		List<DNASequence> sequences = new ArrayList<>(fastas.values());
 
 		return sequences;
 	}
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestSubOptimalMSA.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestSubOptimalMSA.java
index 1785d45e53..11c68570dc 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestSubOptimalMSA.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestSubOptimalMSA.java
@@ -20,8 +20,6 @@
  */
 package org.biojava.nbio.alignment;
 
-import static org.junit.Assert.*;
-
 import org.biojava.nbio.core.alignment.template.Profile;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.DNASequence;
@@ -34,6 +32,8 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import static org.junit.Assert.assertEquals;
+
 public class TestSubOptimalMSA {
 
 	private final List<DNASequence> sequences = new ArrayList<>();
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/routines/GuanUberbacherTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/routines/GuanUberbacherTest.java
index f97e84d16e..03447629be 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/routines/GuanUberbacherTest.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/routines/GuanUberbacherTest.java
@@ -24,8 +24,8 @@
 package org.biojava.nbio.alignment.routines;
 
 import org.biojava.nbio.alignment.SimpleGapPenalty;
-import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.alignment.template.GapPenalty;
+import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.DNASequence;
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestDistanceTreeEvaluator.java b/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestDistanceTreeEvaluator.java
index 1b006690fc..ddb841d7d5 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestDistanceTreeEvaluator.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestDistanceTreeEvaluator.java
@@ -24,7 +24,7 @@
 import org.forester.phylogeny.Phylogeny;
 import org.junit.Test;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
 
 /**
  * Test for the evaluation of distance trees.
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestForesterWrapper.java b/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestForesterWrapper.java
index adf224c213..3fa5e7c20d 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestForesterWrapper.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestForesterWrapper.java
@@ -20,11 +20,6 @@
  */
 package org.biojava.nbio.phylo;
 
-import java.io.ByteArrayOutputStream;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.util.LinkedHashMap;
-
 import org.biojava.nbio.core.sequence.MultipleSequenceAlignment;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
@@ -36,7 +31,12 @@
 import org.forester.msa.Msa;
 import org.junit.Test;
 
-import static org.junit.Assert.*;
+import java.io.ByteArrayOutputStream;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.util.LinkedHashMap;
+
+import static org.junit.Assert.assertEquals;
 
 /**
  * Test the BioJava-forester wrapper methods.
diff --git a/biojava-core/src/main/java/demo/ParseFastaFileDemo.java b/biojava-core/src/main/java/demo/ParseFastaFileDemo.java
index a2e734cf9a..ec1ad49772 100644
--- a/biojava-core/src/main/java/demo/ParseFastaFileDemo.java
+++ b/biojava-core/src/main/java/demo/ParseFastaFileDemo.java
@@ -21,11 +21,6 @@
 package demo;
 
 
-import java.io.File;
-import java.io.InputStream;
-import java.util.LinkedHashMap;
-import java.util.Map;
-
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
@@ -34,6 +29,11 @@
 import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
 import org.biojava.nbio.core.util.InputStreamProvider;
 
+import java.io.File;
+import java.io.InputStream;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
 
 /**
  * Created by andreas on 6/17/15.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java
index 55441e5b7c..7b60bb3bc2 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java
@@ -38,7 +38,7 @@
 public class AAIndexFileParser {
 	int scale = -1;
 
-	Map<String,SubstitutionMatrix<AminoAcidCompound>> matrices;
+	final Map<String,SubstitutionMatrix<AminoAcidCompound>> matrices;
 
 	ScaledSubstitutionMatrix currentMatrix;
 	String currentRows;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.java
index 2bd95ea29d..f105cc4ba1 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.java
@@ -38,7 +38,7 @@ public class DefaultAAIndexProvider implements AAIndexProvider {
 
 	private final static Logger logger = LoggerFactory.getLogger(DefaultAAIndexProvider.class);
 
-	Map<String,SubstitutionMatrix<AminoAcidCompound>> matrices;
+	final Map<String,SubstitutionMatrix<AminoAcidCompound>> matrices;
 
 	public DefaultAAIndexProvider(){
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.java
index cfe85f7d33..1291eda8ad 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.java
@@ -23,7 +23,6 @@
 
 package org.biojava.nbio.core.alignment.template;
 
-import org.biojava.nbio.core.alignment.template.AlignedSequence;
 import org.biojava.nbio.core.sequence.location.template.Location;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableProfile.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableProfile.java
index eed30626de..522896c774 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableProfile.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableProfile.java
@@ -23,8 +23,6 @@
 
 package org.biojava.nbio.core.alignment.template;
 
-import org.biojava.nbio.core.alignment.template.Profile;
-import org.biojava.nbio.core.alignment.template.AlignedSequence;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableProfilePair.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableProfilePair.java
index 70bd1d6410..3d63b0fd39 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableProfilePair.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableProfilePair.java
@@ -23,8 +23,6 @@
 
 package org.biojava.nbio.core.alignment.template;
 
-import org.biojava.nbio.core.alignment.template.ProfilePair;
-import org.biojava.nbio.core.alignment.template.Profile;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableSequencePair.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableSequencePair.java
index 86304b7448..78480912c4 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableSequencePair.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableSequencePair.java
@@ -23,8 +23,6 @@
 
 package org.biojava.nbio.core.alignment.template;
 
-import org.biojava.nbio.core.alignment.template.SequencePair;
-import org.biojava.nbio.core.alignment.template.AlignedSequence;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hit.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hit.java
index 6505ba50c9..0a3ba9cae4 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hit.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hit.java
@@ -20,13 +20,13 @@
  */
 package org.biojava.nbio.core.search.io;
 
+import org.biojava.nbio.core.sequence.template.Sequence;
+
 import java.util.Iterator;
 import java.util.List;
 import java.util.NoSuchElementException;
 import java.util.Objects;
 
-import org.biojava.nbio.core.sequence.template.Sequence;
-
 /**
  * This class models a search Hit.
  * You will retrieve a list of this using iterator of a Result
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
index 892f09c5e3..a94f8c29fc 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
@@ -20,10 +20,6 @@
  */
 package org.biojava.nbio.core.search.io;
 
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Objects;
-
 import org.biojava.nbio.core.alignment.SimpleAlignedSequence;
 import org.biojava.nbio.core.alignment.SimpleSequencePair;
 import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
@@ -39,6 +35,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Objects;
+
 /**
  * This class models a search Hsp.
  * You will retrieve a list of this using iterator of a Hit
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java
index 37e604dab6..d547e002da 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java
@@ -20,10 +20,10 @@
  */
 package org.biojava.nbio.core.search.io;
 
-import java.util.*;
-
 import org.biojava.nbio.core.sequence.template.Sequence;
 
+import java.util.*;
+
 /**
  * This class models a search result.
  * You will find one of this for every query sequence specified in the run.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java
index d769fe7358..5e2693b997 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java
@@ -20,11 +20,12 @@
  */
 package org.biojava.nbio.core.search.io;
 
+import org.biojava.nbio.core.sequence.template.Sequence;
+
 import java.io.File;
 import java.io.IOException;
 import java.text.ParseException;
 import java.util.List;
-import org.biojava.nbio.core.sequence.template.Sequence;
 
 /**
  * Designed by Paolo Pavan.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
index 0ef0b92bf5..ce41e1c248 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
@@ -23,11 +23,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.text.ParseException;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.ServiceLoader;
-import java.util.NoSuchElementException;
+import java.util.*;
 
 /**
  * Designed by Paolo Pavan.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastHitBuilder.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastHitBuilder.java
index f227e9a68b..ba2e8b5232 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastHitBuilder.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastHitBuilder.java
@@ -22,9 +22,10 @@
 
 
 import org.biojava.nbio.core.search.io.Hsp;
-import java.util.List;
 import org.biojava.nbio.core.sequence.template.Sequence;
 
+import java.util.List;
+
 /**
  * Designed by Paolo Pavan.
  * You may want to find my contacts on Github and LinkedIn for code info
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResult.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResult.java
index bcacdde20d..00a2340455 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResult.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResult.java
@@ -22,9 +22,10 @@
 
 import org.biojava.nbio.core.search.io.Hit;
 import org.biojava.nbio.core.search.io.Result;
+import org.biojava.nbio.core.sequence.template.Sequence;
+
 import java.util.HashMap;
 import java.util.List;
-import org.biojava.nbio.core.sequence.template.Sequence;
 
 /**
  * This class models a Blast/Blast plus result.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResultBuilder.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResultBuilder.java
index 8d7e06a89e..95a5891cb7 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResultBuilder.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResultBuilder.java
@@ -21,9 +21,10 @@
 package org.biojava.nbio.core.search.io.blast;
 
 import org.biojava.nbio.core.search.io.Hit;
+import org.biojava.nbio.core.sequence.template.Sequence;
+
 import java.util.HashMap;
 import java.util.List;
-import org.biojava.nbio.core.sequence.template.Sequence;
 
 /**
  * Designed by Paolo Pavan.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java
index bba300d344..0f408c0ef0 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java
@@ -20,14 +20,6 @@
  */
 package org.biojava.nbio.core.search.io.blast;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.LineNumberReader;
-import java.text.ParseException;
-import java.util.*;
-
 import org.biojava.nbio.core.search.io.Hit;
 import org.biojava.nbio.core.search.io.Hsp;
 import org.biojava.nbio.core.search.io.Result;
@@ -36,6 +28,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.*;
+import java.text.ParseException;
+import java.util.*;
+
 /**
  * Designed by Paolo Pavan.
  * You may want to find my contacts on Github and LinkedIn for code info
@@ -69,7 +65,7 @@ private enum PARSING_CONSISTENCY {
 
 	// data imported private:
 	int queryIdNumber = 0;
-	Map<String,String> queryIdMapping = new HashMap<>();
+	final Map<String,String> queryIdMapping = new HashMap<>();
 	String programName=null, queryName = null, databaseFile = null;
 	private String queryId      ;
 	private String subjectId    ;
@@ -204,7 +200,7 @@ private String fetchData(Scanner scanner){
 
 			// If a complete definition of the query name was readed, than we can use
 			// a queryID schema that is consistent with blast xml report
-			queryId = queryIdMapping.computeIfAbsent(queryId, x-> "Query_" + (++queryIdNumber));
+			queryId = queryIdMapping.computeIfAbsent(queryId, x -> "Query_" + (++queryIdNumber));
 		}
 		if (!headerFound) queryName = queryId;
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
index e8b354a7d4..25efda84cd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
@@ -25,6 +25,15 @@
 import org.biojava.nbio.core.search.io.Hsp;
 import org.biojava.nbio.core.search.io.Result;
 import org.biojava.nbio.core.search.io.ResultFactory;
+import org.biojava.nbio.core.sequence.template.Sequence;
+import org.biojava.nbio.core.util.XMLHelper;
+import org.slf4j.LoggerFactory;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.xml.sax.SAXException;
+
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.xpath.XPathException;
 import java.io.File;
 import java.io.IOException;
 import java.text.ParseException;
@@ -32,14 +41,6 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.xpath.XPathException;
-import org.biojava.nbio.core.sequence.template.Sequence;
-import org.biojava.nbio.core.util.XMLHelper;
-import org.slf4j.LoggerFactory;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.xml.sax.SAXException;
 
 /**
  * Re-designed by Paolo Pavan on the footprint of:
@@ -102,7 +103,7 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
 			String dbFile = XMLHelper.selectSingleElement(blastDoc.getDocumentElement(),"BlastOutput_db").getTextContent();
 
 			logger.info("Query for hits in "+ targetFile);
-			ArrayList<Element> IterationsList = XMLHelper.selectElements(blastDoc.getDocumentElement(), "BlastOutput_iterations/Iteration[Iteration_hits]");
+			List<Element> IterationsList = XMLHelper.selectElements(blastDoc.getDocumentElement(), "BlastOutput_iterations/Iteration[Iteration_hits]");
 			logger.info(IterationsList.size() + " results");
 
 			resultsCollection = new ArrayList<>();
@@ -117,10 +118,10 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
 
 				// Iteration* section keys:
 				resultBuilder
-					.setIterationNumber(Integer.valueOf(XMLHelper.selectSingleElement(element, "Iteration_iter-num").getTextContent()))
+					.setIterationNumber(Integer.parseInt(XMLHelper.selectSingleElement(element, "Iteration_iter-num").getTextContent()))
 					.setQueryID(XMLHelper.selectSingleElement(element,"Iteration_query-ID").getTextContent())
 					.setQueryDef(XMLHelper.selectSingleElement(element, "Iteration_query-def").getTextContent())
-					.setQueryLength(Integer.valueOf(XMLHelper.selectSingleElement(element, "Iteration_query-len").getTextContent()));
+					.setQueryLength(Integer.parseInt(XMLHelper.selectSingleElement(element, "Iteration_query-len").getTextContent()));
 
 				if (queryReferences != null) resultBuilder.setQuerySequence(queryReferencesMap.get(
 						XMLHelper.selectSingleElement(element,"Iteration_query-ID").getTextContent()
@@ -128,25 +129,26 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
 
 
 
+				hitsCollection = new ArrayList<>();
+
 				Element iterationHitsElement = XMLHelper.selectSingleElement(element, "Iteration_hits");
-				ArrayList<Element> hitList = XMLHelper.selectElements(iterationHitsElement, "Hit");
+				List<Element> hitList = XMLHelper.selectElements(iterationHitsElement, "Hit");
 
-				hitsCollection = new ArrayList<>();
 				for (Element hitElement : hitList) {
 					BlastHitBuilder blastHitBuilder = new BlastHitBuilder();
 					blastHitBuilder
-						.setHitNum(Integer.valueOf(XMLHelper.selectSingleElement(hitElement, "Hit_num").getTextContent()))
+						.setHitNum(Integer.parseInt(XMLHelper.selectSingleElement(hitElement, "Hit_num").getTextContent()))
 						.setHitId(XMLHelper.selectSingleElement(hitElement, "Hit_id").getTextContent())
 						.setHitDef(XMLHelper.selectSingleElement(hitElement, "Hit_def").getTextContent())
 						.setHitAccession(XMLHelper.selectSingleElement(hitElement, "Hit_accession").getTextContent())
-						.setHitLen(Integer.valueOf(XMLHelper.selectSingleElement(hitElement, "Hit_len").getTextContent()));
+						.setHitLen(Integer.parseInt(XMLHelper.selectSingleElement(hitElement, "Hit_len").getTextContent()));
 
 					if (databaseReferences != null) blastHitBuilder.setHitSequence(databaseReferencesMap.get(
 						XMLHelper.selectSingleElement(hitElement, "Hit_id").getTextContent()
 					));
 
 					Element hithspsElement = XMLHelper.selectSingleElement(hitElement, "Hit_hsps");
-					ArrayList<Element> hspList = XMLHelper.selectElements(hithspsElement, "Hsp");
+					List<Element> hspList = XMLHelper.selectElements(hithspsElement, "Hsp");
 
 					hspsCollection = new ArrayList<>();
 					for (Element hspElement : hspList) {
@@ -156,20 +158,20 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
 						if (evalue <= maxEScore) {
 							BlastHspBuilder blastHspBuilder = new BlastHspBuilder();
 							blastHspBuilder
-								.setHspNum(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_num").getTextContent()))
+								.setHspNum(Integer.parseInt(XMLHelper.selectSingleElement(hspElement, "Hsp_num").getTextContent()))
 								.setHspBitScore(new Double(XMLHelper.selectSingleElement(hspElement, "Hsp_bit-score").getTextContent()))
-								.setHspScore(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_score").getTextContent()))
+								.setHspScore(Integer.parseInt(XMLHelper.selectSingleElement(hspElement, "Hsp_score").getTextContent()))
 								.setHspEvalue(evalue)
-								.setHspQueryFrom(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_query-from").getTextContent()))
-								.setHspQueryTo(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_query-to").getTextContent()))
-								.setHspHitFrom(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-from").getTextContent()))
-								.setHspHitTo(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-to").getTextContent()))
-								.setHspQueryFrame(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_query-frame").getTextContent()))
-								.setHspHitFrame(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-frame").getTextContent()))
-								.setHspIdentity(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_identity").getTextContent()))
-								.setHspPositive(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_positive").getTextContent()))
-								.setHspGaps(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_gaps").getTextContent()))
-								.setHspAlignLen(Integer.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_align-len").getTextContent()))
+								.setHspQueryFrom(Integer.parseInt(XMLHelper.selectSingleElement(hspElement, "Hsp_query-from").getTextContent()))
+								.setHspQueryTo(Integer.parseInt(XMLHelper.selectSingleElement(hspElement, "Hsp_query-to").getTextContent()))
+								.setHspHitFrom(Integer.parseInt(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-from").getTextContent()))
+								.setHspHitTo(Integer.parseInt(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-to").getTextContent()))
+								.setHspQueryFrame(Integer.parseInt(XMLHelper.selectSingleElement(hspElement, "Hsp_query-frame").getTextContent()))
+								.setHspHitFrame(Integer.parseInt(XMLHelper.selectSingleElement(hspElement, "Hsp_hit-frame").getTextContent()))
+								.setHspIdentity(Integer.parseInt(XMLHelper.selectSingleElement(hspElement, "Hsp_identity").getTextContent()))
+								.setHspPositive(Integer.parseInt(XMLHelper.selectSingleElement(hspElement, "Hsp_positive").getTextContent()))
+								.setHspGaps(Integer.parseInt(XMLHelper.selectSingleElement(hspElement, "Hsp_gaps").getTextContent()))
+								.setHspAlignLen(Integer.parseInt(XMLHelper.selectSingleElement(hspElement, "Hsp_align-len").getTextContent()))
 								.setHspQseq(XMLHelper.selectSingleElement(hspElement, "Hsp_qseq").getTextContent())
 								.setHspHseq(XMLHelper.selectSingleElement(hspElement, "Hsp_hseq").getTextContent())
 								.setHspIdentityString(XMLHelper.selectSingleElement(hspElement, "Hsp_midline").getTextContent());
@@ -217,8 +219,7 @@ private void mapIds() {
 		if (queryReferences != null) {
 			queryReferencesMap = new HashMap<>(queryReferences.size());
 			for (int counter=0; counter < queryReferences.size() ; counter ++){
-				String id = "Query_"+(counter+1);
-				queryReferencesMap.put(id, queryReferences.get(counter));
+				queryReferencesMap.put("Query_"+(counter+1), queryReferences.get(counter));
 			}
 		}
 
@@ -226,8 +227,7 @@ private void mapIds() {
 			databaseReferencesMap = new HashMap<>(databaseReferences.size());
 			for (int counter=0; counter < databaseReferences.size() ; counter ++){
 				// this is strange: while Query_id are 1 based, Hit (database) id are 0 based
-				String id = "gnl|BL_ORD_ID|"+(counter);
-				databaseReferencesMap.put(id, databaseReferences.get(counter));
+				databaseReferencesMap.put("gnl|BL_ORD_ID|"+(counter), databaseReferences.get(counter));
 			}
 		}
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java
index 9aeb3ae08c..e240327ffa 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java
@@ -37,8 +37,8 @@
 public class CDSSequence extends DNASequence {
 
 	//private static final Logger log = Logger.getLogger(CDSSequence.class.getName());
-	Integer phase; // 0, 1, 2
-	TranscriptSequence parentTranscriptSequence;
+    final Integer phase; // 0, 1, 2
+	final TranscriptSequence parentTranscriptSequence;
 
 	/**
 	 *
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
index eb50b453b7..94016b7a81 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
@@ -25,6 +25,7 @@
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.compound.*;
 import org.biojava.nbio.core.sequence.features.FeatureInterface;
+import org.biojava.nbio.core.sequence.features.Qualifier;
 import org.biojava.nbio.core.sequence.io.DNASequenceCreator;
 import org.biojava.nbio.core.sequence.io.FastaReader;
 import org.biojava.nbio.core.sequence.io.PlainFastaHeaderParser;
@@ -42,7 +43,6 @@
 import java.net.URL;
 import java.util.LinkedHashMap;
 import java.util.List;
-import org.biojava.nbio.core.sequence.features.Qualifier;
 
 /**
  * The representation of a ProteinSequence
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StartCodonSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StartCodonSequence.java
index 279970a3a8..f900ea3d2d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StartCodonSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StartCodonSequence.java
@@ -29,7 +29,7 @@
  * @author Scooter Willis
  */
 public class StartCodonSequence extends DNASequence {
-public DNASequence parentGeneSequence;
+public final DNASequence parentGeneSequence;
 
 
 	public StartCodonSequence(TranscriptSequence parentGeneSequence, int begin, int end){
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StopCodonSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StopCodonSequence.java
index b2c71b790e..990a1d09ab 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StopCodonSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/StopCodonSequence.java
@@ -30,7 +30,7 @@
  */
 public class StopCodonSequence extends DNASequence {
 
-public DNASequence parentGeneSequence;
+public final DNASequence parentGeneSequence;
 
 
 	public StopCodonSequence(TranscriptSequence parentGeneSequence, int begin, int end){
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TaxonomyID.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TaxonomyID.java
index cc53c46cd0..b83755bc98 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TaxonomyID.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TaxonomyID.java
@@ -31,7 +31,7 @@ public class TaxonomyID {
 
 
 	private final String id;
-	DataSource dataSource;
+	final DataSource dataSource;
 
 	public TaxonomyID(String id, DataSource dataSource) {
 		this.id = id;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompound.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompound.java
index dbab8aa4b7..6be60ed5aa 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompound.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompound.java
@@ -23,12 +23,11 @@
 
 package org.biojava.nbio.core.sequence.compound;
 
-import java.io.Serializable;
-
 import org.biojava.nbio.core.sequence.template.AbstractCompound;
-import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.CompoundSet;
 
+import java.io.Serializable;
+
 /**
  * Used to describe an Amino Acid.
  *
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/NucleotideCompound.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/NucleotideCompound.java
index 3ed4a4d1be..48d6e31a59 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/NucleotideCompound.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/NucleotideCompound.java
@@ -27,7 +27,6 @@
 
 import org.biojava.nbio.core.sequence.template.AbstractCompound;
 import org.biojava.nbio.core.sequence.template.ComplementCompound;
-import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.CompoundSet;
 
 import java.util.Collections;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
index edf60c675b..41f94eb72f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
@@ -26,11 +26,7 @@
 import org.biojava.nbio.core.sequence.template.AbstractSequence;
 import org.biojava.nbio.core.sequence.template.Compound;
 
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 /**
  * A feature is currently any descriptive item that can be associated with a sequence position(s)
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
index da05c79668..0c1d26e478 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
@@ -21,13 +21,13 @@
 
 package org.biojava.nbio.core.sequence.features;
 
-import java.util.List;
-import java.util.Map;
-
 import org.biojava.nbio.core.sequence.location.template.AbstractLocation;
 import org.biojava.nbio.core.sequence.template.AbstractSequence;
 import org.biojava.nbio.core.sequence.template.Compound;
 
+import java.util.List;
+import java.util.Map;
+
 /**
  * Interface class to handle describing arbitrary features. A feature can be found at multiple locations in a sequence such as
  * the surface of a protein where different sequence positions make up that feature. Ligand binding pocket is another example.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java
index 54e8afeac6..e8b62432b1 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java
@@ -22,7 +22,7 @@
 
 package org.biojava.nbio.core.sequence.features;
 
-import java.util.ArrayList;
+import java.util.List;
 
 /**
  * Models the keywords that are annotated for a protein sequence at Uniprot. If a ProxySequenceReader
@@ -36,5 +36,5 @@ public interface FeaturesKeyWordInterface {
 	 *
 	 * @return
 	 */
-    ArrayList<String> getKeyWords() ;
+    List<String> getKeyWords() ;
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java
index 08d49ee686..8b7fdc65a8 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java
@@ -22,23 +22,15 @@
 
 package org.biojava.nbio.core.sequence.io;
 
-import java.io.IOException;
-import java.io.File;
-import java.io.BufferedInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.FileInputStream;
-import java.io.DataInputStream;
-import java.io.ByteArrayInputStream;
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.image.BufferedImage;
-import java.net.URL;
-import java.io.InputStream;
-
+import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.compound.ABITracerCompoundSet;
 import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
 import org.biojava.nbio.core.sequence.template.AbstractSequence;
-import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
+
+import java.awt.*;
+import java.awt.image.BufferedImage;
+import java.io.*;
+import java.net.URL;
 
 /**
  * Title: ABITrace<p><p>
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java
index bfd8dd4305..c7351a526e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java
@@ -42,10 +42,10 @@ public class FastaGeneWriter {
 
 	private final static Logger logger = LoggerFactory.getLogger(FastaGeneWriter.class);
 
-	boolean showExonUppercase;
-	OutputStream os;
-	Collection<GeneSequence> sequences;
-	FastaHeaderFormatInterface<GeneSequence, NucleotideCompound> headerFormat;
+	final boolean showExonUppercase;
+	final OutputStream os;
+	final Collection<GeneSequence> sequences;
+	final FastaHeaderFormatInterface<GeneSequence, NucleotideCompound> headerFormat;
 	private int lineLength;
 /**
  *
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
index 4cf22e9d63..fa1d1bf323 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
@@ -47,7 +47,7 @@ public class FastaReader<S extends Sequence<?>, C extends Compound> {
 	private final static Logger logger = LoggerFactory.getLogger(FastaReader.class);
 
 	SequenceCreatorInterface<C> sequenceCreator;
-	SequenceHeaderParserInterface<S,C> headerParser;
+	final SequenceHeaderParserInterface<S,C> headerParser;
 	BufferedReaderBytesRead br;
 	InputStreamReader isr;
 	FileInputStream fi = null;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
index 6eff327754..ab882378cb 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
@@ -24,11 +24,7 @@
 import org.biojava.nbio.core.sequence.DNASequence;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.RNASequence;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
-import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
-import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
-import org.biojava.nbio.core.sequence.compound.RNACompoundSet;
+import org.biojava.nbio.core.sequence.compound.*;
 
 import java.io.File;
 import java.io.FileInputStream;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
index d46a84ca33..248e21ad52 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
@@ -30,11 +30,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.BufferedOutputStream;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
+import java.io.*;
 import java.util.Collection;
 import java.util.LinkedHashMap;
 
@@ -50,9 +46,9 @@ public class FastaWriter<S extends Sequence<?>, C extends Compound> {
 
 	private final static Logger logger = LoggerFactory.getLogger(FastaWriter.class);
 
-	OutputStream os;
-	Collection<S> sequences;
-	FastaHeaderFormatInterface<S, C> headerFormat;
+	final OutputStream os;
+	final Collection<S> sequences;
+	final FastaHeaderFormatInterface<S, C> headerFormat;
 	private int lineLength = 60;
 	byte[] lineSep = System.getProperty("line.separator").getBytes();
 /**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
index d077eaa007..a23ddce00b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
@@ -50,9 +50,9 @@
 public class FileProxyDNASequenceCreator implements
 		SequenceCreatorInterface<NucleotideCompound> {
 
-	CompoundSet<NucleotideCompound> compoundSet;
-	File file;
-	SequenceParserInterface sequenceParser;
+	final CompoundSet<NucleotideCompound> compoundSet;
+	final File file;
+	final SequenceParserInterface sequenceParser;
 
 	/**
 	 * Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java
index 5048850579..f9749302b8 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java
@@ -49,9 +49,9 @@
  */
 public class FileProxyProteinSequenceCreator implements SequenceCreatorInterface<AminoAcidCompound> {
 
-	CompoundSet<AminoAcidCompound> compoundSet;
-	File file;
-	SequenceParserInterface sequenceParser;
+	final CompoundSet<AminoAcidCompound> compoundSet;
+	final File file;
+	final SequenceParserInterface sequenceParser;
 
 	/**
 	 * Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
index 7d117ffaa4..bc6c4f7941 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
@@ -50,9 +50,9 @@
 public class FileProxyRNASequenceCreator implements
 		SequenceCreatorInterface<NucleotideCompound> {
 
-	CompoundSet<NucleotideCompound> compoundSet;
-	File file;
-	SequenceParserInterface sequenceParser;
+	final CompoundSet<NucleotideCompound> compoundSet;
+	final File file;
+	final SequenceParserInterface sequenceParser;
 
 	/**
 	 * Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
index d8c88bd1b2..b8c69f9311 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
@@ -36,13 +36,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
+import java.io.*;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
index dea62c706e..38d4eb408d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
@@ -24,11 +24,7 @@
 import org.biojava.nbio.core.sequence.DNASequence;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.RNASequence;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
-import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
-import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
-import org.biojava.nbio.core.sequence.compound.RNACompoundSet;
+import org.biojava.nbio.core.sequence.compound.*;
 import org.biojava.nbio.core.sequence.template.AbstractSequence;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java
index b3ad294c47..819e785df0 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java
@@ -38,11 +38,11 @@
  *
  */
 public class GenbankWriter<S extends Sequence<?>, C extends Compound> {
-	int SEQUENCE_INDENT = 9;
+	final int SEQUENCE_INDENT = 9;
 
-	OutputStream os;
-	Collection<S> sequences;
-	GenbankHeaderFormatInterface<S, C> headerFormat;
+	final OutputStream os;
+	final Collection<S> sequences;
+	final GenbankHeaderFormatInterface<S, C> headerFormat;
 	private int lineLength = 60;
 
 	// byte[] lineSep = System.getProperty("line.separator").getBytes();
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java
index 443443e62e..279c0cdbfc 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java
@@ -25,6 +25,7 @@
 
 import org.biojava.nbio.core.exceptions.ParserException;
 import org.biojava.nbio.core.sequence.AccessionID;
+import org.biojava.nbio.core.sequence.DataSource;
 import org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface;
 import org.biojava.nbio.core.sequence.reference.AbstractReference;
 import org.biojava.nbio.core.sequence.template.AbstractSequence;
@@ -33,8 +34,6 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import org.biojava.nbio.core.sequence.DataSource;
-
 public class GenericGenbankHeaderParser<S extends AbstractSequence<C>, C extends Compound> implements SequenceHeaderParserInterface<S,C> {
 
 	private String accession = null;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java
index 8d1ecedeff..870e526c43 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java
@@ -32,11 +32,7 @@
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.util.StringManipulationHelper;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Formatter;
-import java.util.List;
-import java.util.Locale;
+import java.util.*;
 
 /**
  * @author mckeee1
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblReader.java
index f0f73caf21..18f2db965e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblReader.java
@@ -21,7 +21,10 @@
 package org.biojava.nbio.core.sequence.io.embl;
 
 
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
 import java.util.Arrays;
 import java.util.LinkedList;
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
index 1e681bab09..b1b6ebfe4c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
@@ -32,11 +32,7 @@
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
 import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
 import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
-import org.biojava.nbio.core.sequence.features.AbstractFeature;
-import org.biojava.nbio.core.sequence.features.DBReferenceInfo;
-import org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface;
-import org.biojava.nbio.core.sequence.features.FeatureRetriever;
-import org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface;
+import org.biojava.nbio.core.sequence.features.*;
 import org.biojava.nbio.core.sequence.io.GenbankSequenceParser;
 import org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser;
 import org.biojava.nbio.core.sequence.template.AbstractSequence;
@@ -45,16 +41,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.BufferedInputStream;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
+import java.io.*;
 import java.net.URL;
-import java.net.URLConnection;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
@@ -211,9 +199,11 @@ public static void main(String[] args) throws Throwable {
 		DNASequence dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		dnaSequence.setAccession(new AccessionID("NM_001126"));
-		logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
-		logger.info("Keywords: {}", genbankDNAReader.getKeyWords());
-		logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
+		if (logger.isInfoEnabled()) {
+			logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
+			logger.info("Keywords: {}", genbankDNAReader.getKeyWords());
+			logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
+		}
 
 		genbankDNAReader
 				= new GenbankProxySequenceReader<>("/tmp", "NM_000266", DNACompoundSet.getDNACompoundSet());
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
index c7fe81733f..2585d1ae5e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
@@ -55,12 +55,12 @@
  */
 public class SequenceFileProxyLoader<C extends Compound> implements ProxySequenceReader<C> {
 
-	SequenceParserInterface sequenceParser;
+	final SequenceParserInterface sequenceParser;
 	private CompoundSet<C> compoundSet;
 	private final List<C> parsedCompounds = new ArrayList<>();
-	File file;
-	long sequenceStartIndex;
-	int sequenceLength;
+	final File file;
+	final long sequenceStartIndex;
+	final int sequenceLength;
 	//private boolean initialized = false;
 
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
index 0982c35ff8..05ab1c8c5f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
@@ -50,10 +50,7 @@
 import java.net.HttpURLConnection;
 import java.net.URL;
 import java.rmi.RemoteException;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
+import java.util.*;
 import java.util.regex.Pattern;
 
 /**
@@ -350,8 +347,7 @@ public ArrayList<AccessionID> getAccessions() throws XPathExpressionException {
 		}
 		Element uniprotElement = uniprotDoc.getDocumentElement();
 		Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
-		ArrayList<Element> keyWordElementList = XMLHelper.selectElements(entryElement, "accession");
-		for (Element element : keyWordElementList) {
+		for (Element element : XMLHelper.selectElements(entryElement, "accession")) {
 			AccessionID accessionID = new AccessionID(element.getTextContent(), DataSource.UNIPROT);
 			accessionList.add(accessionID);
 		}
@@ -366,75 +362,71 @@ public ArrayList<AccessionID> getAccessions() throws XPathExpressionException {
 	 * @return
 	 * @throws XPathExpressionException
 	 */
-	public ArrayList<String> getAliases() throws XPathExpressionException {
+	public List<String> getAliases() throws XPathExpressionException {
 
 		return getProteinAliases();
 	}
+
 	/**
 	 * Pull uniprot protein aliases associated with this sequence
 	 * @return
 	 * @throws XPathExpressionException
 	 */
-	public ArrayList<String> getProteinAliases() throws XPathExpressionException {
-		ArrayList<String> aliasList = new ArrayList<>();
-		if (uniprotDoc == null) {
-			return aliasList;
-		}
+	public List<String> getProteinAliases() throws XPathExpressionException {
+		if (uniprotDoc == null)
+			return Collections.EMPTY_LIST;
+
+		ArrayList<String> a = new ArrayList<>();
+
 		Element uniprotElement = uniprotDoc.getDocumentElement();
 		Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
 		Element proteinElement = XMLHelper.selectSingleElement(entryElement, "protein");
 		
-		ArrayList<Element> keyWordElementList;
-		getProteinAliasesFromNameGroup(aliasList, proteinElement);
+
+		getProteinAliasesFromNameGroup(a, proteinElement);
 		
-		keyWordElementList = XMLHelper.selectElements(proteinElement, "component");
-		for (Element element : keyWordElementList) {
-			getProteinAliasesFromNameGroup(aliasList, element);
+
+		for (Element element : XMLHelper.selectElements(proteinElement, "component")) {
+			getProteinAliasesFromNameGroup(a, element);
 		}
 
-		keyWordElementList = XMLHelper.selectElements(proteinElement, "domain");
-		for (Element element : keyWordElementList) {
-			getProteinAliasesFromNameGroup(aliasList, element);
+		for (Element element : XMLHelper.selectElements(proteinElement, "domain")) {
+			getProteinAliasesFromNameGroup(a, element);
 		}
 
-		keyWordElementList = XMLHelper.selectElements(proteinElement, "submittedName");
-		for (Element element : keyWordElementList) {
-			getProteinAliasesFromNameGroup(aliasList, element);
+		for (Element element : XMLHelper.selectElements(proteinElement, "submittedName")) {
+			getProteinAliasesFromNameGroup(a, element);
 		}
 
-		keyWordElementList = XMLHelper.selectElements(proteinElement, "cdAntigenName");
-		for (Element element : keyWordElementList) {
+		for (Element element : XMLHelper.selectElements(proteinElement, "cdAntigenName")) {
 			String cdAntigenName = element.getTextContent();
 			if(null != cdAntigenName && !cdAntigenName.trim().isEmpty()) {
-				aliasList.add(cdAntigenName);
+				a.add(cdAntigenName);
 			}
 		}
-			
-		keyWordElementList = XMLHelper.selectElements(proteinElement, "innName");
-		for (Element element : keyWordElementList) {
+
+		for (Element element : XMLHelper.selectElements(proteinElement, "innName")) {
 			String cdAntigenName = element.getTextContent();
 			if(null != cdAntigenName && !cdAntigenName.trim().isEmpty()) {
-				aliasList.add(cdAntigenName);
+				a.add(cdAntigenName);
 			}
 		}
 
-		keyWordElementList = XMLHelper.selectElements(proteinElement, "biotechName");
-		for (Element element : keyWordElementList) {
+		for (Element element : XMLHelper.selectElements(proteinElement, "biotechName")) {
 			String cdAntigenName = element.getTextContent();
 			if(null != cdAntigenName && !cdAntigenName.trim().isEmpty()) {
-				aliasList.add(cdAntigenName);
+				a.add(cdAntigenName);
 			}
 		}
 
-		keyWordElementList = XMLHelper.selectElements(proteinElement, "allergenName");
-		for (Element element : keyWordElementList) {
+		for (Element element : XMLHelper.selectElements(proteinElement, "allergenName")) {
 			String cdAntigenName = element.getTextContent();
 			if(null != cdAntigenName && !cdAntigenName.trim().isEmpty()) {
-				aliasList.add(cdAntigenName);
+				a.add(cdAntigenName);
 			}
 		}
 
-		return aliasList;
+		return a;
 	}
 
 	/**
@@ -444,15 +436,11 @@ public ArrayList<String> getProteinAliases() throws XPathExpressionException {
 	 */
 	private void getProteinAliasesFromNameGroup(ArrayList<String> aliasList, Element proteinElement)
 			throws XPathExpressionException {
-		ArrayList<Element> keyWordElementList = XMLHelper.selectElements(proteinElement, "alternativeName");
-		for (Element element : keyWordElementList) {
-			getProteinAliasesFromElement(aliasList, element);
-		}
-		
-		keyWordElementList = XMLHelper.selectElements(proteinElement, "recommendedName");
-		for (Element element : keyWordElementList) {
-			getProteinAliasesFromElement(aliasList, element);
-		}
+		for (Element e : XMLHelper.selectElements(proteinElement, "alternativeName"))
+			getProteinAliasesFromElement(aliasList, e);
+
+		for (Element e : XMLHelper.selectElements(proteinElement, "recommendedName"))
+			getProteinAliasesFromElement(aliasList, e);
 	}
 
 	/**
@@ -485,9 +473,9 @@ public ArrayList<String> getGeneAliases() throws XPathExpressionException {
 		}
 		Element uniprotElement = uniprotDoc.getDocumentElement();
 		Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
-		ArrayList<Element> proteinElements = XMLHelper.selectElements(entryElement, "gene");
+		List<Element> proteinElements = XMLHelper.selectElements(entryElement, "gene");
 		for(Element proteinElement : proteinElements) {
-			ArrayList<Element> keyWordElementList = XMLHelper.selectElements(proteinElement, "name");
+			List<Element> keyWordElementList = XMLHelper.selectElements(proteinElement, "name");
 			for (Element element : keyWordElementList) {
 				aliasList.add(element.getTextContent());
 			}
@@ -789,19 +777,18 @@ public String getOrganismName() {
 	 * @return
 	 */
 	@Override
-	public ArrayList<String> getKeyWords() {
+	public List<String> getKeyWords() {
+		if (uniprotDoc == null)
+			return Collections.EMPTY_LIST;
+
 		ArrayList<String> keyWordsList = new ArrayList<>();
-		if (uniprotDoc == null) {
-			return keyWordsList;
-		}
 		try {
 			Element uniprotElement = uniprotDoc.getDocumentElement();
 
 			Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
-			ArrayList<Element> keyWordElementList = XMLHelper.selectElements(entryElement, "keyword");
-			for (Element element : keyWordElementList) {
+			for (Element element : XMLHelper.selectElements(entryElement, "keyword"))
 				keyWordsList.add(element.getTextContent());
-			}
+
 		} catch (XPathExpressionException e) {
 			logger.error("Problems while parsing keywords in UniProt XML: {}. No keywords will be available.",e.getMessage());
 			return new ArrayList<>();
@@ -824,18 +811,15 @@ public LinkedHashMap<String, ArrayList<DBReferenceInfo>> getDatabaseReferences()
 		try {
 			Element uniprotElement = uniprotDoc.getDocumentElement();
 			Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
-			ArrayList<Element> dbreferenceElementList = XMLHelper.selectElements(entryElement, "dbReference");
-			for (Element element : dbreferenceElementList) {
+			for (Element element : XMLHelper.selectElements(entryElement, "dbReference")) {
 				String type = element.getAttribute("type");
 				String id = element.getAttribute("id");
 				ArrayList<DBReferenceInfo> idlist = databaseReferencesHashMap.computeIfAbsent(type, k -> new ArrayList<>());
 				DBReferenceInfo dbreferenceInfo = new DBReferenceInfo(type, id);
-				ArrayList<Element> propertyElementList = XMLHelper.selectElements(element, "property");
-				for (Element propertyElement : propertyElementList) {
-					String propertyType = propertyElement.getAttribute("type");
-					String propertyValue = propertyElement.getAttribute("value");
-					dbreferenceInfo.addProperty(propertyType, propertyValue);
-				}
+				List<Element> propertyElementList = XMLHelper.selectElements(element, "property");
+
+				for (Element pe : propertyElementList)
+					dbreferenceInfo.addProperty(pe.getAttribute("type"), pe.getAttribute("value"));
 
 				idlist.add(dbreferenceInfo);
 			}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
index 0befcc1110..53028b338b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
@@ -227,7 +227,7 @@ private List<Location> parseLocationString(String string, int versus) throws Par
 				String accession = m.group(1);
 				Strand s = versus == 1 ? Strand.POSITIVE : Strand.NEGATIVE;
 				int start = Integer.parseInt(m.group(3));
-				int end = m.group(6) == null ? start : Integer.valueOf(m.group(6));
+				int end = m.group(6) == null ? start : Integer.parseInt(m.group(6));
 
 				if (featureGlobalStart > start) {
 					featureGlobalStart = start;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java
index d8e2b60acd..517c1414fd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java
@@ -21,12 +21,12 @@
  */
 package org.biojava.nbio.core.sequence.location;
 
-import java.io.Serializable;
-
 import org.biojava.nbio.core.sequence.location.template.Point;
 import org.biojava.nbio.core.util.Equals;
 import org.biojava.nbio.core.util.Hashcoder;
 
+import java.io.Serializable;
+
 /**
  * Basic implementation of the Point interface.
  *
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
index 11a16ccb9b..9e5d842cfe 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
@@ -260,6 +260,9 @@ private List<Location> getAllSubLocations(Location location) {
 
 	@Override
 	public boolean equals(Object obj) {
+		if (this == obj)
+			return true;
+
 		boolean equals = false;
 		if (classEqual(this, obj)) {
 			AbstractLocation l = (AbstractLocation) obj;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
index d32f1e51ac..c8790da2f8 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
@@ -43,7 +43,7 @@ public abstract class AbstractCompoundSet<C extends Compound> implements Compoun
 	private int maxCompoundCharSequenceLength = -1;
 	private Boolean compoundStringLengthEqual = null;
 
-	Map<C,Set<C>> equivalentsMap = new HashMap<>();
+	final Map<C,Set<C>> equivalentsMap = new HashMap<>();
 
 	protected void addCompound(C compound, C lowerCasedCompound, Iterable<C> equivalents) {
 		addCompound(compound);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
index 3aed298810..a0caca5964 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
@@ -21,11 +21,13 @@
  */
 package org.biojava.nbio.core.util;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
-import java.io.InputStream;
 import java.net.HttpURLConnection;
 import java.net.SocketTimeoutException;
 import java.net.URL;
@@ -33,16 +35,9 @@
 import java.nio.channels.Channels;
 import java.nio.channels.FileChannel;
 import java.nio.channels.ReadableByteChannel;
-import java.nio.file.FileVisitResult;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.nio.file.SimpleFileVisitor;
+import java.nio.file.*;
 import java.nio.file.attribute.BasicFileAttributes;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 public class FileDownloadUtils {
 
 	private static final Logger logger = LoggerFactory.getLogger(FileDownloadUtils.class);
@@ -113,9 +108,8 @@ public static void downloadFile(URL url, File destination) throws IOException {
 			try {
 				URLConnection connection = prepareURLConnection(url.toString(), timeout);
 				connection.connect();
-				InputStream inputStream = connection.getInputStream();
 
-				rbc = Channels.newChannel(inputStream);
+				rbc = Channels.newChannel(connection.getInputStream());
 				fos = new FileOutputStream(tempFile);
 				fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
 				break;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java
index 525c5b09da..0a58829228 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java
@@ -40,6 +40,8 @@
 import javax.xml.xpath.XPathFactory;
 import java.io.*;
 import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
 
 import static org.biojava.nbio.core.sequence.io.util.IOUtils.close;
 import static org.biojava.nbio.core.sequence.io.util.IOUtils.openFile;
@@ -76,9 +78,12 @@ static public Document loadXML(String fileName) throws SAXException, IOException
 
 	static public Document inputStreamToDocument(InputStream inputStream) throws SAXException, IOException, ParserConfigurationException  {
 		DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+		dbf.setIgnoringComments(true);
+		dbf.setIgnoringElementContentWhitespace(true);
 
 		DocumentBuilder db = dbf.newDocumentBuilder();
 
+
 		Document doc = db.parse(inputStream);
 		doc.getDocumentElement().normalize();
 
@@ -125,11 +130,11 @@ static public Element selectParentElement(Element element, String parentName) {
 	static public Element selectSingleElement(Element element, String xpathExpression) throws XPathExpressionException {
 		if (!xpathExpression.contains("/")) {
 			NodeList nodeList = element.getChildNodes();
-			for (int i = 0; i < nodeList.getLength(); i++) {
+			int nn = nodeList.getLength();
+			for (int i = 0; i < nn; i++) {
 				Node node = nodeList.item(i);
-				if (node.getNodeType() == Node.ELEMENT_NODE && node.getNodeName().equals(xpathExpression)) {
+				if (node.getNodeType() == Node.ELEMENT_NODE && node.getNodeName().equals(xpathExpression))
 					return (Element) node;
-				}
 			}
 			//  NodeList nodes = element.getElementsByTagName(xpathExpression);
 			//  if (nodes.getLength() > 0) {
@@ -139,34 +144,34 @@ static public Element selectSingleElement(Element element, String xpathExpressio
 			//  }
 		} else {
 			XPath xpath = XPathFactory.newInstance().newXPath();
-			Element node = (Element) xpath.evaluate(xpathExpression, element, XPathConstants.NODE);
-			return node;
+			return (Element) xpath.evaluate(xpathExpression, element, XPathConstants.NODE);
 		}
 	}
 
-	static public ArrayList<Element> selectElements(Element element, String xpathExpression) throws XPathExpressionException {
-		ArrayList<Element> resultVector = new ArrayList<>();
+	static public List<Element> selectElements(Element element, String xpathExpression) throws XPathExpressionException {
 		if (element == null) {
-			return resultVector;
+			return Collections.EMPTY_LIST;
 		}
+		ArrayList<Element> r = new ArrayList<>();
 		if (!xpathExpression.contains("/")) {
 			NodeList nodeList = element.getChildNodes();
-			for (int i = 0; i < nodeList.getLength(); i++) {
+			int nn = nodeList.getLength();
+			for (int i = 0; i < nn; i++) {
 				Node node = nodeList.item(i);
 				if (node.getNodeType() == Node.ELEMENT_NODE && node.getNodeName().equals(xpathExpression)) {
-					resultVector.add((Element) node);
+					r.add((Element) node);
 				}
 			}
 		} else {
 			XPath xpath = XPathFactory.newInstance().newXPath();
 			NodeList nodes = (NodeList) xpath.evaluate(xpathExpression, element, XPathConstants.NODESET);
 
-
-			for (int i = 0; i < nodes.getLength(); i++) {
-				Node node = nodes.item(i);
-				resultVector.add((Element) node);
-			}
+			int nn = nodes.getLength();
+			for (int i = 0; i < nn; i++)
+				r.add((Element) nodes.item(i));
 		}
-		return resultVector;
+		return r.isEmpty() ?
+				Collections.EMPTY_LIST :
+				r;
 	}
 }
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java b/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
index 7f4760af96..6f8263fd91 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
@@ -20,12 +20,6 @@
  */
 package org.biojava.nbio.core.fasta;
 
-import java.io.InputStream;
-import java.util.LinkedHashMap;
-
-import static org.junit.Assert.* ;
-import static org.hamcrest.CoreMatchers.* ;
-
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
@@ -35,6 +29,12 @@
 import org.biojava.nbio.core.sequence.io.util.ClasspathResource;
 import org.junit.Test;
 
+import java.io.InputStream;
+import java.util.LinkedHashMap;
+
+import static org.hamcrest.CoreMatchers.*;
+import static org.junit.Assert.assertThat;
+
 
 public class TestFASTAReader {
 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java
index 0dcaae2c33..0da89818a2 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java
@@ -24,12 +24,9 @@
 import org.biojava.nbio.core.search.io.blast.BlastHspBuilder;
 import org.biojava.nbio.core.sequence.DNASequence;
 import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import static org.junit.Assert.*;
+import org.junit.*;
+
+import static org.junit.Assert.assertEquals;
 
 /**
  * @author Paolo Pavan
@@ -37,7 +34,7 @@
 
 public class HspTest {
 
-	Hsp hspImpl = new BlastHspBuilder()
+	final Hsp hspImpl = new BlastHspBuilder()
 				.setHspNum(1)
 				.setHspBitScore(377.211)
 				.setHspEvalue(8.04143e-093)
@@ -55,7 +52,7 @@ public class HspTest {
 				.setHspIdentityString("||||||||| |||||||||||||||||| ||||||||| |||||||||||||||||||||||| |||||||| |||||||||||||||||||||||  |||||||  |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| ||||||||| ||||||| |||||||||||||||||||||||| |||||")
 				.createBlastHsp();
 
-	Hsp uncompleteHsp = new BlastHspBuilder()
+	final Hsp uncompleteHsp = new BlastHspBuilder()
 				.setPercentageIdentity(100.00/100)
 				.setHspAlignLen(48)
 				.setMismatchCount(0)
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java
index a49dae544a..3f5a344c43 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java
@@ -20,15 +20,13 @@
  */
 package org.biojava.nbio.core.search.io;
 
+import org.biojava.nbio.core.search.io.blast.BlastXMLParser;
+import org.junit.*;
+
 import java.io.File;
 import java.net.URL;
-import org.biojava.nbio.core.search.io.blast.BlastXMLParser;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import static org.junit.Assert.*;
+
+import static org.junit.Assert.fail;
 
 /**
  * Designed by Paolo Pavan.
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastTabularParserTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastTabularParserTest.java
index a5ac5c311f..6c4f94926f 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastTabularParserTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastTabularParserTest.java
@@ -20,19 +20,17 @@
  */
 package org.biojava.nbio.core.search.io.blast;
 
+import org.biojava.nbio.core.search.io.Hit;
+import org.biojava.nbio.core.search.io.Hsp;
+import org.biojava.nbio.core.search.io.Result;
+import org.junit.*;
+
 import java.io.File;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
-import org.biojava.nbio.core.search.io.Hit;
-import org.biojava.nbio.core.search.io.Hsp;
-import org.biojava.nbio.core.search.io.Result;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import static org.junit.Assert.*;
+
+import static org.junit.Assert.assertEquals;
 
 /**
  *
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java
index 89c73b4d7e..ba107fe34e 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java
@@ -20,20 +20,17 @@
  */
 package org.biojava.nbio.core.search.io.blast;
 
+import org.biojava.nbio.core.search.io.Hit;
+import org.biojava.nbio.core.search.io.Hsp;
+import org.biojava.nbio.core.search.io.Result;
+import org.junit.*;
+
 import java.io.File;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
-import org.biojava.nbio.core.search.io.Hit;
-import org.biojava.nbio.core.search.io.Hsp;
-import org.biojava.nbio.core.search.io.Result;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
+
 import static org.junit.Assert.*;
-import org.junit.Ignore;
 
 /**
  *
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TestSequenceEquals.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TestSequenceEquals.java
index 3f0fcc53a5..d3bac9e212 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TestSequenceEquals.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TestSequenceEquals.java
@@ -22,7 +22,8 @@
 
 import org.junit.Test;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
 
 /**
  * Created by yana on 3/27/17.
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/ABITracerTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/ABITracerTest.java
index 66cef29fac..b27907b79b 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/ABITracerTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/ABITracerTest.java
@@ -21,10 +21,11 @@
 
 package org.biojava.nbio.core.sequence.io;
 
+import org.junit.*;
+
 import java.awt.image.BufferedImage;
 import java.io.File;
 import java.net.URL;
-import org.junit.*;
 
 /**
  * Test file 3730.ab1 is from https://github.com/biopython/biopython/blob/master/Tests/Abi/3730.ab1
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
index 7795370994..7544a84247 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
@@ -22,41 +22,24 @@
 
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.DNASequence;
-import org.biojava.nbio.core.sequence.RNASequence;
 import org.biojava.nbio.core.sequence.ProteinSequence;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
-import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
-import org.biojava.nbio.core.sequence.compound.RNACompoundSet;
-import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
+import org.biojava.nbio.core.sequence.RNASequence;
+import org.biojava.nbio.core.sequence.compound.*;
 import org.biojava.nbio.core.sequence.features.FeatureInterface;
 import org.biojava.nbio.core.sequence.features.Qualifier;
 import org.biojava.nbio.core.sequence.template.AbstractSequence;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Assert;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.junit.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.BufferedInputStream;
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
+import java.io.*;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 
 import static org.hamcrest.CoreMatchers.is;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
 
 /**
  *
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
index 438af45111..6bcd55360d 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.core.sequence.loader;
 
-import java.io.IOException;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
@@ -28,6 +27,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.IOException;
+
 
 /**
  * Testing example for issue #834
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/InsdcParserTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/InsdcParserTest.java
index 99b6b96793..144aba0058 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/InsdcParserTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/InsdcParserTest.java
@@ -20,8 +20,6 @@
  */
 package org.biojava.nbio.core.sequence.location;
 
-import java.util.Arrays;
-import java.util.Collection;
 import org.biojava.nbio.core.sequence.DataSource;
 import org.biojava.nbio.core.sequence.location.template.Location;
 import org.junit.Assert;
@@ -31,6 +29,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.Arrays;
+import java.util.Collection;
+
 /**
  *
  * @author Jacek Grzebyta
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/util/TestUncompressInputStream.java b/biojava-core/src/test/java/org/biojava/nbio/core/util/TestUncompressInputStream.java
index be889f6ba3..008d57e600 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/util/TestUncompressInputStream.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/util/TestUncompressInputStream.java
@@ -20,13 +20,14 @@
  */
 package org.biojava.nbio.core.util;
 
-import java.io.BufferedInputStream;
+import org.junit.Assert;
 import org.junit.Test;
-import static org.junit.Assert.*;
 
+import java.io.BufferedInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.InputStream;
-import org.junit.Assert;
+
+import static org.junit.Assert.assertEquals;
 
 public class TestUncompressInputStream {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java
index e6a7459918..b8828a99cd 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java
@@ -20,9 +20,9 @@
  */
 package org.biojava.nbio.genome;
 
-import org.biojava.nbio.genome.parsers.gff.*;
 import org.biojava.nbio.core.sequence.*;
 import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
+import org.biojava.nbio.genome.parsers.gff.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
index 4e5c14c44d..2ceae673c4 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.genome.homology;
 
-import org.biojava.nbio.genome.GeneFeatureHelper;
 import org.biojava.nbio.alignment.Alignments;
 import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
 import org.biojava.nbio.alignment.SimpleGapPenalty;
@@ -33,6 +32,7 @@
 import org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface;
 import org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface;
 import org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader;
+import org.biojava.nbio.genome.GeneFeatureHelper;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -41,6 +41,7 @@
 import java.io.OutputStream;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
+import java.util.List;
 import java.util.Map;
 
 /**
@@ -96,11 +97,13 @@ public void process(LinkedHashMap<String, ArrayList<String>> hits, LinkedHashMap
 					}
 					if (!testSequence.equals(predictedProteinSequence) && (!predictedProteinSequence.equals(testSequence.substring(0, testSequence.length() - 1)))) {
 						DNASequence codingSequence = transcriptSequence.getDNACodingSequence();
-						logger.info("Coding Sequence: {}", codingSequence.getSequenceAsString());
-						logger.info("Sequence agreement error");
-						logger.info("CDS seq={}", testSequence);
-						logger.info("PRE seq={}", predictedProteinSequence);
-						logger.info("UNI seq={}", hitSequence);
+						if (logger.isInfoEnabled()) {
+							logger.info("Coding Sequence: {}", codingSequence.getSequenceAsString());
+							logger.info("Sequence agreement error");
+							logger.info("CDS seq={}", testSequence);
+							logger.info("PRE seq={}", predictedProteinSequence);
+							logger.info("UNI seq={}", hitSequence);
+						}
 						//  throw new Exception("Protein Sequence compare error " + id);
 					}
 
@@ -117,22 +120,20 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
 					for (int i = 0; i < cdsProteinList.size(); i++) {
 						ProteinSequence peptideSequence = cdsProteinList.get(i);
 						String seq = peptideSequence.getSequenceAsString();
-						Integer startIndex = null;
+						int startIndex = -1;
 						int offsetStartIndex = 0;
 						for (int s = 0; s < seq.length(); s++) {
 							startIndex = alignment.getIndexInTargetForQueryAt(proteinIndex + s);
-							if (startIndex != null) {
-								startIndex = startIndex + 1;
-								offsetStartIndex = s;
-								break;
-							}
+							startIndex = startIndex + 1;
+							offsetStartIndex = s;
+							break;
 						}
-						Integer endIndex = null;
+						int endIndex = -1;
 
 						int offsetEndIndex = 0;
 						for (int e = 0; e < seq.length(); e++) {
 							endIndex = alignment.getIndexInTargetForQueryAt(proteinIndex + seq.length() - 1 - e);
-							if (endIndex != null) {
+							{
 								endIndex = endIndex + 1;
 								offsetEndIndex = e;
 								break;
@@ -140,7 +141,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
 						}
 
 						proteinIndex = proteinIndex + seq.length();
-						if (startIndex != null && endIndex != null && startIndex != endIndex) {
+						if (startIndex != endIndex) {
 							CDSSequence cdsSequence = cdsSequenceList.get(i);
 							String hitLabel;
 							if (transcriptSequence.getStrand() == Strand.POSITIVE) {
@@ -162,7 +163,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
 								FeaturesKeyWordInterface featureKeyWords = proteinSequence.getFeaturesKeyWord();
 								String notes = "";
 								if (featureKeyWords != null) {
-									ArrayList<String> keyWords = featureKeyWords.getKeyWords();
+									List<String> keyWords = featureKeyWords.getKeyWords();
 									if (keyWords.size() > 0) {
 										notes = ";Note=";
 										for (String note : keyWords) {
@@ -182,7 +183,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
 
 								DatabaseReferenceInterface databaseReferences = proteinSequence.getDatabaseReferences();
 								if (databaseReferences != null) {
-									LinkedHashMap<String, ArrayList<DBReferenceInfo>> databaseReferenceHashMap = databaseReferences.getDatabaseReferences();
+									Map<String, ArrayList<DBReferenceInfo>> databaseReferenceHashMap = databaseReferences.getDatabaseReferences();
 									ArrayList<DBReferenceInfo> pfamList = databaseReferenceHashMap.get("Pfam");
 									ArrayList<DBReferenceInfo> cazyList = databaseReferenceHashMap.get("CAZy");
 									ArrayList<DBReferenceInfo> goList = databaseReferenceHashMap.get("GO");
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriter.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriter.java
index f438cfec63..305977f633 100755
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriter.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/AbstractFastqWriter.java
@@ -20,14 +20,7 @@
  */
 package org.biojava.nbio.genome.io.fastq;
 
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.io.Writer;
-
+import java.io.*;
 import java.util.Arrays;
 
 /**
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java
index c6ba1a0d4c..d2559768bf 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java
@@ -31,8 +31,8 @@
 import org.w3c.dom.Element;
 
 import java.io.File;
-import java.util.ArrayList;
 import java.util.LinkedHashMap;
+import java.util.List;
 
 /**
  *
@@ -52,7 +52,7 @@ public GeneIDXMLReader(String geneidXMLFile) throws Exception {
 
 	public LinkedHashMap<String, ProteinSequence> getProteinSequences() throws Exception {
 		LinkedHashMap<String, ProteinSequence> proteinSequenceList = new LinkedHashMap<>();
-		ArrayList<Element> elementList = XMLHelper.selectElements(geneidDoc.getDocumentElement(), "prediction/gene/protein");
+		List<Element> elementList = XMLHelper.selectElements(geneidDoc.getDocumentElement(), "prediction/gene/protein");
 		logger.info("{} hits", elementList.size());
 
 		for (Element proteinElement : elementList) {
@@ -69,10 +69,8 @@ public LinkedHashMap<String, ProteinSequence> getProteinSequences() throws Excep
 
 	public LinkedHashMap<String, DNASequence> getDNACodingSequences() throws Exception {
 		LinkedHashMap<String, DNASequence> dnaSequenceList = new LinkedHashMap<>();
-		ArrayList<Element> elementList = XMLHelper.selectElements(geneidDoc.getDocumentElement(), "prediction/gene/cDNA");
-		logger.info("{} hits", elementList.size());
 
-		for (Element dnaElement : elementList) {
+		for (Element dnaElement : XMLHelper.selectElements(geneidDoc.getDocumentElement(), "prediction/gene/cDNA")) {
 			Element geneElement = (Element) dnaElement.getParentNode();
 			String sequence = dnaElement.getTextContent().replaceAll("\\W","");
 			DNASequence dnaSequence = new DNASequence(sequence);
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
index 0bf7035ea0..d79caf1ac0 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
@@ -23,8 +23,8 @@
 
 package org.biojava.nbio.genome.parsers.genename;
 
-import org.biojava.nbio.genome.App;
 import org.biojava.nbio.core.util.InputStreamProvider;
+import org.biojava.nbio.genome.App;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java
index 84d3ea7279..7457f7048d 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java
@@ -187,7 +187,7 @@ public HashMap<String, String> userData() {
 		return mUserMap;
 	}
 
-	 HashMap<String,String> attributeHashMap = new HashMap<>();
+	 final HashMap<String,String> attributeHashMap = new HashMap<>();
 
 	private void initAttributeHashMap(){
 	   String[] values = mAttributes.split(";");
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java
index 0d91c7259d..45aac4219c 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java
@@ -40,7 +40,7 @@
 @SuppressWarnings("serial")
 public class FeatureList extends ArrayList<FeatureI> {
 
-	 Map<String, Map<String,List<FeatureI>>> featindex = new HashMap<>();
+	 final Map<String, Map<String,List<FeatureI>>> featindex = new HashMap<>();
 	Location mLocation;			//genomic location (union of feature locations)
 
 	/**
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
index 1f5a3f30c9..9f1df17ea1 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
@@ -20,8 +20,8 @@
  */
 package org.biojava.nbio.genome.parsers.gff;
 
-import org.biojava.nbio.genome.GeneFeatureHelper;
 import org.biojava.nbio.core.sequence.*;
+import org.biojava.nbio.genome.GeneFeatureHelper;
 
 import java.io.File;
 import java.io.FileOutputStream;
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java
index b66dd3b014..9e74f1dda8 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java
@@ -46,7 +46,7 @@ public class TwoBitParser extends InputStream {
 
 	private static final Logger logger = LoggerFactory.getLogger(TwoBitParser.class);
 
-	public int DEFAULT_BUFFER_SIZE = 10000;
+	public final int DEFAULT_BUFFER_SIZE = 10000;
 	//
 	private final RandomAccessFile raf;
 	private final File f;
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java
index 61d5475037..241eb19df7 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java
@@ -29,6 +29,7 @@
 
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
+import java.util.List;
 
 /**
  *
@@ -49,19 +50,19 @@ public BlastXMLQuery(String blastFile) throws Exception {
 	public LinkedHashMap<String, ArrayList<String>> getHitsQueryDef(double maxEScore) throws Exception {
 		LinkedHashMap<String, ArrayList<String>> hitsHashMap = new LinkedHashMap<>();
 		logger.info("Query for hits");
-		ArrayList<Element> elementList = XMLHelper.selectElements(blastDoc.getDocumentElement(), "BlastOutput_iterations/Iteration[Iteration_hits]");
+		List<Element> elementList = XMLHelper.selectElements(blastDoc.getDocumentElement(), "BlastOutput_iterations/Iteration[Iteration_hits]");
 		logger.info("{} hits", elementList.size());
 
 		for (Element element : elementList) {
 			Element iterationquerydefElement = XMLHelper.selectSingleElement(element, "Iteration_query-def");
 			String querydef = iterationquerydefElement.getTextContent();
 			Element iterationHitsElement = XMLHelper.selectSingleElement(element, "Iteration_hits");
-			ArrayList<Element> hitList = XMLHelper.selectElements(iterationHitsElement, "Hit");
+			List<Element> hitList = XMLHelper.selectElements(iterationHitsElement, "Hit");
 			for (Element hitElement : hitList) {
 				Element hitaccessionElement = XMLHelper.selectSingleElement(hitElement, "Hit_accession");
 				String hitaccession = hitaccessionElement.getTextContent();
 				Element hithspsElement = XMLHelper.selectSingleElement(hitElement, "Hit_hsps");
-				ArrayList<Element> hspList = XMLHelper.selectElements(hithspsElement, "Hsp");
+				List<Element> hspList = XMLHelper.selectElements(hithspsElement, "Hsp");
 				for (Element hspElement : hspList) {
 					Element evalueElement = XMLHelper.selectSingleElement(hspElement, "Hsp_evalue");
 					String value = evalueElement.getTextContent();
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
index 1bb9d1ed4b..bf710a01f0 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
@@ -21,13 +21,13 @@
 package org.biojava.nbio.genome;
 
 import junitx.framework.FileAssert;
-import org.biojava.nbio.genome.parsers.gff.FeatureList;
-import org.biojava.nbio.genome.parsers.gff.GFF3Reader;
-import org.biojava.nbio.genome.parsers.gff.GFF3Writer;
 import org.biojava.nbio.core.sequence.ChromosomeSequence;
 import org.biojava.nbio.core.sequence.GeneSequence;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.io.FastaWriterHelper;
+import org.biojava.nbio.genome.parsers.gff.FeatureList;
+import org.biojava.nbio.genome.parsers.gff.GFF3Reader;
+import org.biojava.nbio.genome.parsers.gff.GFF3Writer;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestIssue355.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestIssue355.java
index 5543682f17..3691555999 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestIssue355.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestIssue355.java
@@ -20,11 +20,12 @@
  */
 package org.biojava.nbio.genome;
 
-import static org.junit.Assert.*;
-
 import org.biojava.nbio.genome.parsers.gff.Location;
 import org.junit.Test;
 
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
 public class TestIssue355 {
 
 	@Test
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestLocation.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestLocation.java
index f1ff2b1636..2153db9843 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestLocation.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestLocation.java
@@ -20,11 +20,11 @@
  */
 package org.biojava.nbio.genome;
 
-import static org.junit.Assert.*;
-
 import org.biojava.nbio.genome.parsers.gff.Location;
 import org.junit.Test;
 
+import static org.junit.Assert.*;
+
 public class TestLocation {
 
 	@Test
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/ConvertTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/ConvertTest.java
index fb634ac088..aa32f8b7de 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/ConvertTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/ConvertTest.java
@@ -20,16 +20,16 @@
  */
 package org.biojava.nbio.genome.io.fastq;
 
+import com.google.common.collect.Lists;
+import com.google.common.collect.Maps;
+import org.junit.Test;
+
 import java.io.File;
 import java.io.FileWriter;
 import java.util.List;
 import java.util.Map;
 
-import org.junit.Test;
-import static org.junit.Assert.*;
-
-import com.google.common.collect.Lists;
-import com.google.common.collect.Maps;
+import static org.junit.Assert.assertEquals;
 
 /**
  * Round trip conversion functional tests.
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqToolsTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqToolsTest.java
index 2e4150e60d..6aca0fda15 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqToolsTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqToolsTest.java
@@ -30,7 +30,6 @@
 import org.junit.Assert;
 import org.junit.Test;
 
-
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqVariantTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqVariantTest.java
index a1705057d6..af7a33f79f 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqVariantTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/FastqVariantTest.java
@@ -20,11 +20,11 @@
  */
 package org.biojava.nbio.genome.io.fastq;
 
-import static org.biojava.nbio.genome.io.fastq.FastqVariant.*;
-
 import org.junit.Assert;
 import org.junit.Test;
 
+import static org.biojava.nbio.genome.io.fastq.FastqVariant.*;
+
 /**
  * Unit test for FastqVariant.
  */
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqReaderTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqReaderTest.java
index 1a67f2a9d7..54fd055615 100755
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqReaderTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/io/fastq/IlluminaFastqReaderTest.java
@@ -21,12 +21,13 @@
 package org.biojava.nbio.genome.io.fastq;
 
 import org.junit.Test;
-import static org.junit.Assert.*;
 
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URL;
 
+import static org.junit.Assert.*;
+
 
 /**
  * Unit test for IlluminaFastqReader.
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/MMcifTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/MMcifTest.java
index a83bfe1fd0..284533d954 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/MMcifTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/MMcifTest.java
@@ -28,7 +28,6 @@
 import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
 import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
 import org.junit.Test;
-import static org.junit.Assert.*;
 
 import java.io.BufferedReader;
 import java.io.IOException;
@@ -36,6 +35,8 @@
 import java.io.InputStreamReader;
 import java.util.List;
 
+import static org.junit.Assert.*;
+
 public class MMcifTest {
 
 	private static boolean headerOnly;
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/PDBFileParserTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/PDBFileParserTest.java
index f94b5faaaf..9256483e15 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/PDBFileParserTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/PDBFileParserTest.java
@@ -24,20 +24,7 @@
  */
 package org.biojava.nbio.structure.test;
 
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringReader;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.JournalArticle;
-import org.biojava.nbio.structure.PDBHeader;
-import org.biojava.nbio.structure.Site;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.io.PDBFileParser;
@@ -45,6 +32,11 @@
 import org.junit.Before;
 import org.junit.Test;
 
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringReader;
+
 import static org.junit.Assert.*;
 
 /**
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java
index a7826fced2..d13c3c2bf5 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java
@@ -25,16 +25,15 @@
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.io.PDBFileParser;
 import org.biojava.nbio.structure.io.SSBondImpl;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import javax.vecmath.Matrix4d;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.List;
 import java.util.Set;
 
-import javax.vecmath.Matrix4d;
-
-import org.junit.BeforeClass;
-import org.junit.Test;
-
 import static org.junit.Assert.*;
 
 /**
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java
index b2ae39611c..337c8900cb 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java
@@ -35,8 +35,9 @@
 import java.io.IOException;
 import java.io.InputStream;
 
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
 import static org.junit.Assume.assumeNoException;
-import static org.junit.Assert.*;
 
 public class StructureToolsTest {
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1o2f.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1o2f.java
index 7acde4166e..d99b9a4153 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1o2f.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1o2f.java
@@ -25,7 +25,6 @@
 import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
-
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/TestSECalignment.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/TestSECalignment.java
index 6a9516251b..9716ce5d63 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/TestSECalignment.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/TestSECalignment.java
@@ -23,6 +23,7 @@
 package org.biojava.nbio.structure.test;
 
 import junit.framework.TestCase;
+import org.biojava.nbio.core.util.StringManipulationHelper;
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.align.StructureAlignment;
 import org.biojava.nbio.structure.align.StructureAlignmentFactory;
@@ -33,7 +34,6 @@
 import org.biojava.nbio.structure.align.xml.AFPChainXMLParser;
 import org.biojava.nbio.structure.test.align.fatcat.FlipAFPChainTest;
 import org.biojava.nbio.structure.test.util.StringManipulationTestsHelper;
-import org.biojava.nbio.core.util.StringManipulationHelper;
 
 import java.io.InputStream;
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/ce/OptimalCECPMainTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/ce/OptimalCECPMainTest.java
index 76f9005b47..4b055b27eb 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/ce/OptimalCECPMainTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/ce/OptimalCECPMainTest.java
@@ -25,8 +25,11 @@
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.StructureAlignmentFactory;
-import org.biojava.nbio.structure.align.ce.*;
+import org.biojava.nbio.structure.align.ce.CECPParameters;
 import org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint;
+import org.biojava.nbio.structure.align.ce.CeCPMain;
+import org.biojava.nbio.structure.align.ce.CeMain;
+import org.biojava.nbio.structure.align.ce.OptimalCECPMain;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.junit.Assert;
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/AFPChainSerialisationTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/AFPChainSerialisationTest.java
index dadba4d471..391e98506e 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/AFPChainSerialisationTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/AFPChainSerialisationTest.java
@@ -29,7 +29,8 @@
 
 import java.io.IOException;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
 
 public class AFPChainSerialisationTest
 {
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/FlipAFPChainTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/FlipAFPChainTest.java
index cf58a0c3c1..85fa4750ca 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/FlipAFPChainTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/FlipAFPChainTest.java
@@ -24,7 +24,10 @@
 
 package org.biojava.nbio.structure.test.align.fatcat;
 
-import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Calc;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.StructureAlignment;
 import org.biojava.nbio.structure.align.StructureAlignmentFactory;
 import org.biojava.nbio.structure.align.ce.CeMain;
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java
index 170030616b..9b2b380e00 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java
@@ -24,7 +24,10 @@
 
 package org.biojava.nbio.structure.test.align.fatcat;
 
-import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Calc;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.StructureAlignment;
 import org.biojava.nbio.structure.align.fatcat.FatCatFlexible;
 import org.biojava.nbio.structure.align.fatcat.FatCatRigid;
@@ -38,12 +41,11 @@
 import org.biojava.nbio.structure.jama.Matrix;
 import org.junit.Test;
 
+import javax.vecmath.Matrix4d;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.vecmath.Matrix4d;
-
 import static org.junit.Assert.*;
 
 public class TestFlexibleRotationMatrices {
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/qsalign/TestQsAlignExamples.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/qsalign/TestQsAlignExamples.java
index b9ad316c4b..f30670097b 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/qsalign/TestQsAlignExamples.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/qsalign/TestQsAlignExamples.java
@@ -20,10 +20,6 @@
  */
 package org.biojava.nbio.structure.test.align.qsalign;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
@@ -34,6 +30,11 @@
 import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
 import org.junit.Test;
 
+import java.io.IOException;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
 /**
  * Test the correctness of the {@link QsAlign} algorithm with some examples of
  * different levels of quaternary structure similarity.
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/seq/TestSmithWaterman3Daligner.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/seq/TestSmithWaterman3Daligner.java
index ce6ade5543..129717d1b2 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/seq/TestSmithWaterman3Daligner.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/seq/TestSmithWaterman3Daligner.java
@@ -20,10 +20,6 @@
  */
 package org.biojava.nbio.structure.test.align.seq;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
@@ -33,6 +29,11 @@
 import org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner;
 import org.junit.Test;
 
+import java.io.IOException;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
 /**
  * Test the superposition based on a sequence alignment on different cases.
  *
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/cluster/TestSubunitClustererExamples.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/cluster/TestSubunitClustererExamples.java
index 161a4c8b96..6f5b8ffdba 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/cluster/TestSubunitClustererExamples.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/cluster/TestSubunitClustererExamples.java
@@ -20,13 +20,6 @@
  */
 package org.biojava.nbio.structure.test.cluster;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-import java.util.List;
-import java.util.function.Function;
-import java.util.stream.Collectors;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
@@ -37,6 +30,14 @@
 import org.biojava.nbio.structure.symmetry.core.Stoichiometry;
 import org.junit.Test;
 
+import java.io.IOException;
+import java.util.List;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
 /**
  * Test the {@link SubunitClusterer} clustering correctness on different real
  * structures with different types of chain clustering difficulties.
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java
index 439f86cbf8..63dc49048e 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java
@@ -20,24 +20,6 @@
 
 package org.biojava.nbio.structure.test.ecod;
 
-import static org.junit.Assert.*;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-import java.util.concurrent.Callable;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.Future;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
 import org.biojava.nbio.core.util.ConcurrencyTools;
 import org.biojava.nbio.structure.ResidueNumber;
 import org.biojava.nbio.structure.ResidueRange;
@@ -54,6 +36,15 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.*;
+import java.util.concurrent.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import static org.junit.Assert.*;
+
 /**
  * @author Spencer Bliven
  *
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java
index cbd5dda443..1d741033a7 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java
@@ -20,17 +20,7 @@
  */
 package org.biojava.nbio.structure.test.ecod;
 
-import java.io.IOException;
-import java.util.List;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.AtomPositionMap;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.ResidueRange;
-import org.biojava.nbio.structure.ResidueRangeAndLength;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.ecod.EcodDatabase;
 import org.biojava.nbio.structure.ecod.EcodDomain;
@@ -39,6 +29,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.IOException;
+import java.util.List;
+
 /**
  * This is not a unit test.
  *
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/geometry/TestProteinSuperposition.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/geometry/TestProteinSuperposition.java
index 8d30a82f4d..4464b7d1dd 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/geometry/TestProteinSuperposition.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/geometry/TestProteinSuperposition.java
@@ -20,18 +20,7 @@
  */
 package org.biojava.nbio.structure.test.geometry;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-
-import javax.vecmath.Point3d;
-
-import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.geometry.SuperPosition;
 import org.biojava.nbio.structure.geometry.SuperPositionQCP;
 import org.biojava.nbio.structure.geometry.SuperPositionQuat;
@@ -39,6 +28,11 @@
 import org.junit.BeforeClass;
 import org.junit.Test;
 
+import javax.vecmath.Point3d;
+import java.io.IOException;
+
+import static org.junit.Assert.assertEquals;
+
 public class TestProteinSuperposition {
 
 	private static Point3d[] chain1;
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/StructureIOTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/StructureIOTest.java
index c6a3cdab86..7082c455f5 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/StructureIOTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/StructureIOTest.java
@@ -20,14 +20,14 @@
  */
 package org.biojava.nbio.structure.test.io;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
 import org.junit.Test;
 
+import java.io.IOException;
+
+import static org.junit.Assert.assertEquals;
+
 /**
  * Test StructureIO methods.
  *
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/Test4v5a.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/Test4v5a.java
index 006396e8cb..c9b65aa83e 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/Test4v5a.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/Test4v5a.java
@@ -22,9 +22,6 @@
 
 //import static org.junit.Assert.*;
 
-import java.io.IOException;
-
-
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.align.util.AtomCache;
@@ -32,6 +29,8 @@
 import org.junit.Ignore;
 import org.junit.Test;
 
+import java.io.IOException;
+
 /**
  * Test for a difficult large mmCIF file (a ribosome) with many 2-letter chain ids.
  * Both tests are set to Ignore because the parsing of the file takes too long.
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java
index 6f394a34b8..b8370dbd02 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java
@@ -20,11 +20,6 @@
  */
 package org.biojava.nbio.structure.test.io;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-import java.util.List;
-
 import org.biojava.nbio.structure.Chain;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
@@ -32,6 +27,11 @@
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.junit.Test;
 
+import java.io.IOException;
+import java.util.List;
+
+import static org.junit.Assert.*;
+
 public class TestBioassemblies {
 
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestCrystallographicMetadata.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestCrystallographicMetadata.java
index 26f83b7a28..f52a6d2524 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestCrystallographicMetadata.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestCrystallographicMetadata.java
@@ -20,12 +20,12 @@
  */
 package org.biojava.nbio.structure.test.io;
 
-import org.junit.Test;
-import static org.junit.Assert.*;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.align.util.AtomCache;
+import org.junit.Test;
+
+import static org.junit.Assert.*;
 
 /**
  * A test for the parsing of some crystallographic metadata: non standard space group and non standard coordinate frame convention.
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java
index 4346adcf2d..efcc5686f8 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java
@@ -26,11 +26,7 @@
 import org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior;
 import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
 import org.biojava.nbio.structure.xtal.CrystalCell;
-import org.junit.After;
-import org.junit.BeforeClass;
-import org.junit.ComparisonFailure;
-import org.junit.Ignore;
-import org.junit.Test;
+import org.junit.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestNcsOpsParsing.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestNcsOpsParsing.java
index 390d68eab7..6ccb5e9fb8 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestNcsOpsParsing.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestNcsOpsParsing.java
@@ -20,18 +20,17 @@
  */
 package org.biojava.nbio.structure.test.io;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-
-import javax.vecmath.Matrix4d;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.junit.Test;
 
+import javax.vecmath.Matrix4d;
+import java.io.IOException;
+
+import static org.junit.Assert.*;
+
 public class TestNcsOpsParsing {
 
 	/**
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java
index de6c072719..3e45656211 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java
@@ -24,16 +24,11 @@
 package org.biojava.nbio.structure.test.io;
 
 
-import java.io.IOException;
-
-import org.biojava.nbio.structure.AminoAcid;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.junit.Test;
-import org.biojava.nbio.structure.StructureIO;
+
+import java.io.IOException;
 
 import static org.junit.Assert.*;
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestStructWithMultiparentChemComp.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestStructWithMultiparentChemComp.java
index cbedb5b108..7eefa0e010 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestStructWithMultiparentChemComp.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestStructWithMultiparentChemComp.java
@@ -20,14 +20,13 @@
  */
 package org.biojava.nbio.structure.test.io;
 
-import org.junit.Test;
-import static org.junit.Assert.*;
-
-
 import org.biojava.nbio.structure.Chain;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.align.util.AtomCache;
+import org.junit.Test;
+
+import static org.junit.Assert.*;
 
 public class TestStructWithMultiparentChemComp {
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileConsumerIntegrationTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileConsumerIntegrationTest.java
index 9101ee5524..fc03ec003b 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileConsumerIntegrationTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileConsumerIntegrationTest.java
@@ -1,17 +1,7 @@
 package org.biojava.nbio.structure.test.io.cif;
 
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.DBRef;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.GroupType;
-import org.biojava.nbio.structure.PDBHeader;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.io.BcifFileReader;
-import org.biojava.nbio.structure.io.CifFileReader;
-import org.biojava.nbio.structure.io.FileParsingParameters;
-import org.biojava.nbio.structure.io.LocalPDBDirectory;
-import org.biojava.nbio.structure.io.PDBFileParser;
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.io.*;
 import org.junit.Test;
 
 import java.io.IOException;
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileSupplierIntegrationTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileSupplierIntegrationTest.java
index 03e2f6f060..16076c1fea 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileSupplierIntegrationTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileSupplierIntegrationTest.java
@@ -1,17 +1,6 @@
 package org.biojava.nbio.structure.test.io.cif;
 
-import org.biojava.nbio.structure.AminoAcidImpl;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.AtomImpl;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.Element;
-import org.biojava.nbio.structure.EntityInfo;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureImpl;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.io.cif.CifFileConverter;
 import org.junit.Test;
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDatabaseTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDatabaseTest.java
index 30a5c6e738..3813498846 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDatabaseTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDatabaseTest.java
@@ -46,8 +46,8 @@
  */
 @RunWith(Parameterized.class)
 public abstract class ScopDatabaseTest {
-	protected ScopDatabase scop;
-	String tag;
+	protected final ScopDatabase scop;
+	final String tag;
 
 	/**
 	 *
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopTest.java
index 8405c83837..305916aea5 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopTest.java
@@ -20,11 +20,7 @@
  */
 package org.biojava.nbio.structure.test.scop;
 
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.GroupIterator;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.scop.ScopDatabase;
 import org.biojava.nbio.structure.scop.ScopDomain;
@@ -35,7 +31,8 @@
 import java.io.IOException;
 import java.util.List;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
 
 //import org.biojava.nbio.structure.scop.RemoteScopInstallation;
 
@@ -43,7 +40,7 @@
 
 public class ScopTest {
 
-	boolean debug = false;
+	final boolean debug = false;
 
 	@Test
 	public void testLocalScop() throws IOException, StructureException{
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java
index b244c864ab..9ceec479d9 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java
@@ -20,11 +20,6 @@
  */
 package org.biojava.nbio.structure.test.symmetry;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-import java.util.*;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
@@ -45,6 +40,14 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import static org.junit.Assert.*;
+
 /**
  * Test the {@link QuatSymmetryDetector} algorithm for symmetry detection on a
  * variety of structures with different symmetries.
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/xtal/TestCrystalBuilder.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/xtal/TestCrystalBuilder.java
index 898e108a8e..710cac54f6 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/xtal/TestCrystalBuilder.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/xtal/TestCrystalBuilder.java
@@ -33,7 +33,7 @@
 import java.util.HashMap;
 import java.util.Map;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
 
 public class TestCrystalBuilder {
 
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ComponentXMLConverter.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ComponentXMLConverter.java
index 87e0314d50..45ce14a428 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ComponentXMLConverter.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ComponentXMLConverter.java
@@ -20,8 +20,8 @@
  */
 package org.biojava.nbio.protmod.io;
 
-import org.biojava.nbio.protmod.Component;
 import org.biojava.nbio.core.util.PrettyXMLWriter;
+import org.biojava.nbio.protmod.Component;
 import org.w3c.dom.NamedNodeMap;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java
index df0d78e6d2..6867d454e1 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java
@@ -20,10 +20,10 @@
  */
 package org.biojava.nbio.protmod.io;
 
+import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.biojava.nbio.protmod.ProteinModification;
 import org.biojava.nbio.protmod.ProteinModificationRegistry;
 import org.biojava.nbio.protmod.structure.*;
-import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.w3c.dom.Document;
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/StructureAtomXMLConverter.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/StructureAtomXMLConverter.java
index 08f69725bf..8419c97dd8 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/StructureAtomXMLConverter.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/StructureAtomXMLConverter.java
@@ -20,9 +20,9 @@
  */
 package org.biojava.nbio.protmod.io;
 
+import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.biojava.nbio.protmod.structure.StructureAtom;
 import org.biojava.nbio.protmod.structure.StructureGroup;
-import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.w3c.dom.NamedNodeMap;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/StructureGroupXMLConverter.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/StructureGroupXMLConverter.java
index def283f6ab..71cec2c619 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/StructureGroupXMLConverter.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/StructureGroupXMLConverter.java
@@ -20,9 +20,9 @@
  */
 package org.biojava.nbio.protmod.io;
 
+import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.biojava.nbio.protmod.structure.StructureGroup;
 import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.w3c.dom.NamedNodeMap;
 import org.w3c.dom.Node;
 
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java
index 8e407f9cbd..a5ffff2bc3 100644
--- a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java
+++ b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java
@@ -22,7 +22,9 @@
 
 import org.biojava.nbio.protmod.ProteinModification;
 import org.biojava.nbio.protmod.ProteinModificationRegistry;
-import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.ResidueNumber;
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureException;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/TmpAtomCache.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/TmpAtomCache.java
index 8d757a74a8..95ddb12e95 100644
--- a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/TmpAtomCache.java
+++ b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/TmpAtomCache.java
@@ -30,8 +30,8 @@
 
 public class TmpAtomCache
 {
-	static String tmpDir = System.getProperty("java.io.tmpdir");
-	public static AtomCache cache = new AtomCache(tmpDir, tmpDir);
+	static final String tmpDir = System.getProperty("java.io.tmpdir");
+	public static final AtomCache cache = new AtomCache(tmpDir, tmpDir);
 	static {
 		FileParsingParameters params = new FileParsingParameters();
 		params.setAlignSeqRes(true);
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java
index 55471c7926..e7f3a8ab8c 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java
@@ -25,7 +25,6 @@
 
 import java.io.BufferedReader;
 import java.io.IOException;
-import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.StringTokenizer;
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/OboParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/OboParser.java
index 093f292d66..1f03130185 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/OboParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/OboParser.java
@@ -23,7 +23,9 @@
 
 package org.biojava.nbio.ontology.io;
 
-import org.biojava.nbio.ontology.*;
+import org.biojava.nbio.ontology.OntoTools;
+import org.biojava.nbio.ontology.Ontology;
+import org.biojava.nbio.ontology.OntologyFactory;
 import org.biojava.nbio.ontology.obo.OboFileHandler;
 import org.biojava.nbio.ontology.obo.OboFileParser;
 
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java
index c70d9f58e3..a064859684 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java
@@ -43,7 +43,7 @@ public class OboFileHandler implements OboFileEventListener {
 
 	private static final Logger logger = LoggerFactory.getLogger(OboFileEventListener.class);
 
-	Ontology ontology;
+	final Ontology ontology;
 	List<Term> termStack ;
 
 	public static final String TERM        = "Term";
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
index 06d79205fd..76dd2d7819 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
@@ -53,10 +53,10 @@ public class OboFileParser {
 	List<OboFileEventListener> listeners;
 
 	protected String line;
-	protected int linenum = 0;
+	protected final int linenum = 0;
 	protected int totalSize = 0;
 	protected int bytesRead = 0;
-	protected StringBuffer tempBuffer = new StringBuffer();
+	protected final StringBuffer tempBuffer = new StringBuffer();
 	protected SimpleDateFormat dateFormat = new SimpleDateFormat("dd:MM:yyyy HH:mm", Locale.US);
 
 
@@ -89,11 +89,11 @@ public class OboFileParser {
 	}
 
 	public static class SOPair {
-		public String str;
+		public final String str;
 
-		public int index;
+		public final int index;
 
-		public int endIndex;
+		public final int endIndex;
 
 		public SOPair(String str, int index) {
 			this(str, index, -1);
@@ -606,7 +606,7 @@ else if (str.charAt(startIndex) == ',') {
 
 class NestedValue {
 
-	protected Properties propertyValues = new Properties();
+	protected final Properties propertyValues = new Properties();
 	protected String name;
 	protected String suggestedComment;
 
diff --git a/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestOboFileParsing.java b/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestOboFileParsing.java
index e7f1e7ab91..ed9ab28709 100644
--- a/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestOboFileParsing.java
+++ b/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestOboFileParsing.java
@@ -25,6 +25,7 @@
 package org.biojava.nbio.ontology;
 
 import org.biojava.nbio.ontology.io.OboParser;
+import org.biojava.nbio.ontology.utils.Annotation;
 import org.junit.Assert;
 import org.junit.Test;
 import org.slf4j.Logger;
@@ -35,8 +36,6 @@
 import java.io.InputStreamReader;
 import java.util.Set;
 
-import org.biojava.nbio.ontology.utils.Annotation;
-
 public class TestOboFileParsing {
 
 	private static final Logger logger = LoggerFactory.getLogger(TestOboFileParsing.class);
diff --git a/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java b/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java
index cb12e10109..dcc7871f34 100644
--- a/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java
+++ b/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java
@@ -27,7 +27,6 @@
 import org.junit.Test;
 
 import java.io.*;
-import java.text.ParseException;
 import java.util.Set;
 
 import static org.biojava.nbio.ontology.obo.OboFileHandler.NAMESPACE;
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java
index 345fb20cd5..7e6bc4e872 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java
@@ -95,8 +95,8 @@ public static class Model {
 	 */
 	final float[] W;// = new float[RonnConstraint.maxD];
 
-	int numOfDBAAseq;
-	int modelNum;
+	final int numOfDBAAseq;
+	final int modelNum;
 
 	public Model(final int modelNum, final int numberofSequence) {
 		this.modelNum = modelNum;
diff --git a/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java b/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
index 8535e7c0a9..bd0a2f6533 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
@@ -20,11 +20,6 @@
  */
 package demo;
 
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
@@ -32,11 +27,7 @@
 import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
 import org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface;
 import org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AlignmentTools;
@@ -44,6 +35,11 @@
 import org.biojava.nbio.structure.io.FastaStructureParser;
 import org.biojava.nbio.structure.io.StructureSequenceMatcher;
 
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
 /**
  * Demo of how to use the {@link FastaStructureParser} class to read protein
  * structures from a FASTA file.
diff --git a/biojava-structure-gui/src/main/java/demo/DemoCeSymm.java b/biojava-structure-gui/src/main/java/demo/DemoCeSymm.java
index a7fc6eeacd..a120793c96 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoCeSymm.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoCeSymm.java
@@ -20,7 +20,6 @@
  */
 package demo;
 
-import java.io.IOException;
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
@@ -33,6 +32,8 @@
 import org.biojava.nbio.structure.symmetry.internal.CeSymm;
 import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
 
+import java.io.IOException;
+
 /**
  * Quick demo of how to call CE-Symm programmatically.
  * Some examples of different symmetry types are proposed.
diff --git a/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java b/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java
index 8fa4594ee2..d365e4242c 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java
@@ -20,11 +20,6 @@
  */
 package demo;
 
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.List;
-import java.util.ArrayList;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIdentifier;
@@ -37,6 +32,11 @@
 import org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters;
 import org.biojava.nbio.structure.align.util.AtomCache;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
 /**
  * Demo for running the CEMC Algorithm on a protein family and
  * visualizing the results.
diff --git a/biojava-structure-gui/src/main/java/demo/DemoShowBiolAssembly.java b/biojava-structure-gui/src/main/java/demo/DemoShowBiolAssembly.java
index 1293af91a6..273da76812 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoShowBiolAssembly.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoShowBiolAssembly.java
@@ -21,8 +21,8 @@
 package demo;
 
 import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
 import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
 
 public class DemoShowBiolAssembly {
 
diff --git a/biojava-structure-gui/src/main/java/demo/DemoShowCATHDomain.java b/biojava-structure-gui/src/main/java/demo/DemoShowCATHDomain.java
index 7ddf7671f6..00d5a7e7fd 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoShowCATHDomain.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoShowCATHDomain.java
@@ -23,6 +23,7 @@
 
 package demo;
 
+import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.align.client.StructureName;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
 import org.biojava.nbio.structure.cath.CathDatabase;
@@ -30,7 +31,6 @@
 import org.biojava.nbio.structure.cath.CathInstallation;
 import org.biojava.nbio.structure.cath.CathSegment;
 import org.biojava.nbio.structure.gui.BiojavaJmol;
-import org.biojava.nbio.structure.StructureIO;
 
 import java.util.List;
 
diff --git a/biojava-structure-gui/src/main/java/demo/DemoShowLargeAssembly.java b/biojava-structure-gui/src/main/java/demo/DemoShowLargeAssembly.java
index aa0c4ea87c..7719d32442 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoShowLargeAssembly.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoShowLargeAssembly.java
@@ -1,10 +1,10 @@
 package demo;
 
 import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
-import org.biojava.nbio.structure.StructureIO;
 
 /*
  *                    BioJava development code
diff --git a/biojava-structure-gui/src/main/java/demo/DemoShowValidationResults.java b/biojava-structure-gui/src/main/java/demo/DemoShowValidationResults.java
index b88eac875a..b695ca5fe2 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoShowValidationResults.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoShowValidationResults.java
@@ -24,8 +24,8 @@
 package demo;
 
 import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
 import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
 import org.biojava.nbio.structure.validation.*;
 
 import javax.xml.bind.JAXBContext;
diff --git a/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java b/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java
index 238c85b9f4..11bfb74fa4 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java
@@ -20,12 +20,6 @@
  */
 package demo;
 
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.align.util.AtomCache;
-import org.biojava.nbio.structure.gui.BiojavaJmol;
-import org.biojava.nbio.structure.io.FastaStructureParser;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
@@ -33,6 +27,12 @@
 import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
 import org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface;
 import org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface;
+import org.biojava.nbio.structure.ResidueNumber;
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.biojava.nbio.structure.gui.BiojavaJmol;
+import org.biojava.nbio.structure.io.FastaStructureParser;
 
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
diff --git a/biojava-structure-gui/src/main/java/demo/ShowStructureInJmol.java b/biojava-structure-gui/src/main/java/demo/ShowStructureInJmol.java
index adeda7dac1..b451f32a9f 100644
--- a/biojava-structure-gui/src/main/java/demo/ShowStructureInJmol.java
+++ b/biojava-structure-gui/src/main/java/demo/ShowStructureInJmol.java
@@ -21,8 +21,8 @@
 package demo;
 
 import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
 import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
 
 
 /** Demo how to load and display a structure in Jmol
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java
index 98ed76f7a4..4bda6f155f 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java
@@ -52,8 +52,8 @@ public class AlignmentCalc implements AlignmentCalculationRunnable {
 	String pdb1;
 	String pdb2;
 
-	String name1;
-	String name2;
+	final String name1;
+	final String name2;
 
 	Structure structure1;
 	Structure structure2;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalcDB.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalcDB.java
index 61ab28273b..b0b8899410 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalcDB.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalcDB.java
@@ -40,11 +40,11 @@
 public class AlignmentCalcDB implements AlignmentCalculationRunnable {
 
 
-	public static String SCOP_VERSION =  "1.75";
+	public static final String SCOP_VERSION =  "1.75";
 
 	//private static final Logger logger = LoggerFactory.getLogger(AlignmentCalcDB.class);
 
-	AtomicBoolean interrupted ;
+	final AtomicBoolean interrupted ;
 
 
 	String name1;
@@ -56,10 +56,10 @@ public class AlignmentCalcDB implements AlignmentCalculationRunnable {
 	UserConfiguration config;
 
 
-	String outFile;
+	final String outFile;
 
 	int nrCPUs;
-	Boolean domainSplit ;
+	final Boolean domainSplit ;
 
 	StructureAlignment customAlgorithm;
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java
index e57d3ce862..c3d9813f67 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java
@@ -22,23 +22,6 @@
  */
 package org.biojava.nbio.structure.align.gui;
 
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.io.File;
-import java.io.IOException;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.Box;
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JMenuBar;
-import javax.swing.JOptionPane;
-import javax.swing.JProgressBar;
-import javax.swing.JTabbedPane;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.StructureAlignment;
@@ -52,6 +35,12 @@
 import org.biojava.nbio.structure.gui.util.ScopSelectPanel;
 import org.biojava.nbio.structure.gui.util.StructurePairSelector;
 
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.io.File;
+import java.io.IOException;
+
 /** A JFrame that allows to trigger a pairwise structure alignment,
  * either from files in a directory,
  * or after manual upload.
@@ -71,14 +60,14 @@ public class AlignmentGui extends JFrame{
 
 	JButton abortB;
 
-	SelectPDBPanel  tab1 ;
-	PDBUploadPanel  tab2;
-	ScopSelectPanel tab3;
+	final SelectPDBPanel  tab1 ;
+	final PDBUploadPanel  tab2;
+	final ScopSelectPanel tab3;
 
 	Thread thread;
 	AlignmentCalculationRunnable alicalc;
-	JTabbedPane masterPane;
-	JTabbedPane tabPane;
+	final JTabbedPane masterPane;
+	final JTabbedPane tabPane;
 	JProgressBar progress;
 
 
@@ -548,7 +537,7 @@ private void updateAlgorithm(String algorithmName) {
 class ProgressThreadDrawer extends Thread {
 
 	JProgressBar progress;
-	static int interval = 300;
+	static final int interval = 300;
 
 	public ProgressThreadDrawer(JProgressBar progress) {
 		this.progress = progress;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentTextPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentTextPanel.java
index d5aea38c5d..caee4ee93d 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentTextPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentTextPanel.java
@@ -33,7 +33,7 @@ public class AlignmentTextPanel extends JPrintPanel {
 	 *
 	 */
 	private static final long serialVersionUID = 5092386365924879073L;
-	JEditorPane tp;
+	final JEditorPane tp;
 
 	public AlignmentTextPanel(){
 		super();
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java
index 1e79061d78..cdf02e8154 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java
@@ -39,7 +39,7 @@
  */
 public class ChooseDirAction extends AbstractAction{
 
-	JTextField textField;
+	final JTextField textField;
 	UserConfiguration config;
 	public ChooseDirAction (JTextField textField, UserConfiguration config){
 		super("Choose");
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.java
index 32dd0d4b2c..028e464591 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.java
@@ -44,7 +44,7 @@ public class ConfigPDBInstallPanel extends JPanel
 	private static final long serialVersionUID = -1055193854675583808L;
 
 	JCheckBox fromFtp;
-	JComboBox fileType;
+	final JComboBox fileType;
 
 	JTextField pdbDir;
 
@@ -198,7 +198,7 @@ public void setPDBDirField(JTextField dir){
 }
 
 class MyAction implements ActionListener{
-	JDialog dialog;
+	final JDialog dialog;
 
 	public MyAction(JDialog dialog) {
 		this.dialog= dialog;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBSearchGUI.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBSearchGUI.java
index b1dbd9dfcb..6b982cb872 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBSearchGUI.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBSearchGUI.java
@@ -42,13 +42,13 @@ public class DBSearchGUI extends JPanel {
 
 
 	StructureAlignment algorithm;
-	SelectPDBPanel tab1;
+	final SelectPDBPanel tab1;
 	JTabbedPane tabPane;
 
-	PDBUploadPanel tab2;
-	ScopSelectPanel tab3;
+	final PDBUploadPanel tab2;
+	final ScopSelectPanel tab3;
 
-	JPanel listPane;
+	final JPanel listPane;
 	JButton abortB;
 	AlignmentCalcDB alicalc;
 	JProgressBar progress;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
index 43acfb5108..e0a0e128c4 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
@@ -19,21 +19,7 @@
 
 package org.biojava.nbio.structure.align.gui;
 
-import java.awt.Dimension;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import javax.swing.Box;
-import javax.swing.JFrame;
-import javax.swing.JMenuBar;
-import javax.swing.JScrollPane;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.gui.aligpanel.AligPanel;
 import org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay;
 import org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol;
@@ -44,6 +30,12 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.swing.*;
+import java.awt.*;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
 /** A utility class for visualistion of structure alignments
  *
  * @author Andreas Prlic
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIAlignmentProgressListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIAlignmentProgressListener.java
index 8f2e6865f0..cc42f42fb4 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIAlignmentProgressListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIAlignmentProgressListener.java
@@ -45,7 +45,7 @@ public class GUIAlignmentProgressListener extends JPanel implements AlignmentPro
 
 	int alignmentsProcessed;
 
-	JProgressBar progressBar;
+	final JProgressBar progressBar;
 	private final JTextArea taskOutput;
 	private final JButton stopButton;
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIFarmJobRunnable.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIFarmJobRunnable.java
index 9120909128..80b10c183a 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIFarmJobRunnable.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIFarmJobRunnable.java
@@ -27,7 +27,7 @@
 import java.awt.*;
 
 public class GUIFarmJobRunnable implements Runnable{
-	FarmJobParameters params;
+	final FarmJobParameters params;
 	GUIAlignmentProgressListener progressListener ;
 	public GUIFarmJobRunnable(FarmJobParameters params){
 		this.params = params;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java
index 307ddf3337..6b6f160441 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java
@@ -55,11 +55,11 @@
  */
 public class MemoryMonitor extends JPanel {
 
-	static JCheckBox dateStampCB = new JCheckBox("Output Date Stamp");
-	public Surface surf;
-	JPanel controls;
+	static final JCheckBox dateStampCB = new JCheckBox("Output Date Stamp");
+	public final Surface surf;
+	final JPanel controls;
 	boolean doControls;
-	JTextField tf;
+	final JTextField tf;
 
 	public static final long serialVersionUID = 56289234782130L;
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java
index 0abf5f2c52..133bb59b43 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java
@@ -29,7 +29,6 @@
 import org.biojava.nbio.structure.align.webstart.WebStartMain;
 
 import javax.swing.*;
-
 import java.awt.*;
 import java.awt.event.*;
 import java.io.File;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.java
index d3b2af0c6d..37ffe36517 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.java
@@ -22,19 +22,15 @@
  */
 package org.biojava.nbio.structure.align.gui;
 
-import java.util.ArrayList;
-import java.util.List;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIdentifier;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.MultipleStructureAligner;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  *  A class that obtains structures via DAS and aligns them.
  *  This is done in a separate thread.
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.java
index 9b4a848b89..2cf8e7503f 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.java
@@ -22,22 +22,6 @@
  */
 package org.biojava.nbio.structure.align.gui;
 
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.util.List;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.Box;
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JMenuBar;
-import javax.swing.JOptionPane;
-import javax.swing.JProgressBar;
-import javax.swing.JTabbedPane;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIdentifier;
@@ -50,6 +34,11 @@
 import org.biojava.nbio.structure.align.webstart.AligUIManager;
 import org.biojava.nbio.structure.gui.util.SelectMultiplePanel;
 
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.util.List;
+
 /**
  * A JFrame that allows to trigger a multiple structure alignment,
  * either from files in a directory or after manual upload.
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java
index 44c000a2f4..d746a83aea 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java
@@ -20,15 +20,6 @@
  */
 package org.biojava.nbio.structure.align.gui;
 
-import java.awt.Dimension;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.Box;
-import javax.swing.JFrame;
-import javax.swing.JMenuBar;
-import javax.swing.JScrollPane;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel;
@@ -39,6 +30,11 @@
 import org.biojava.nbio.structure.align.multiple.Block;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay;
+
+import javax.swing.*;
+import java.awt.*;
+import java.util.ArrayList;
+import java.util.List;
 //import org.slf4j.Logger;
 //import org.slf4j.LoggerFactory;
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyAlignmentLoadListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyAlignmentLoadListener.java
index 366996b5fd..bd11a5af1b 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyAlignmentLoadListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyAlignmentLoadListener.java
@@ -20,6 +20,7 @@
  */
 package org.biojava.nbio.structure.align.gui;
 
+import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
 import org.biojava.nbio.structure.align.model.AFPChain;
@@ -30,10 +31,8 @@
 import org.biojava.nbio.structure.align.webstart.WebStartMain;
 import org.biojava.nbio.structure.align.xml.AFPChainXMLParser;
 import org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser;
-import org.biojava.nbio.core.util.InputStreamProvider;
 
 import javax.swing.*;
-
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.io.BufferedReader;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyDistMaxListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyDistMaxListener.java
index 9faf74cfe7..87152b52c7 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyDistMaxListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyDistMaxListener.java
@@ -24,7 +24,6 @@
 import org.biojava.nbio.structure.jama.Matrix;
 
 import javax.swing.*;
-
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.WindowAdapter;
@@ -35,7 +34,7 @@
  */
 public class MyDistMaxListener implements ActionListener{
 
-	AbstractAlignmentJmol parent;
+	final AbstractAlignmentJmol parent;
 
 	public MyDistMaxListener(AbstractAlignmentJmol parent){
 		this.parent = parent;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyExportListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyExportListener.java
index 77a550c57c..88d24421d7 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyExportListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyExportListener.java
@@ -21,8 +21,8 @@
 
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol;
-import javax.swing.*;
 
+import javax.swing.*;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.io.File;
@@ -32,7 +32,7 @@
 
 public class MyExportListener implements ActionListener{
 
-	AbstractAlignmentJmol parent;
+	final AbstractAlignmentJmol parent;
 	MyExportListener(AbstractAlignmentJmol parent){
 		this.parent = parent;
 	}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MySaveFileListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MySaveFileListener.java
index 3655a21b16..1704f82061 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MySaveFileListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MySaveFileListener.java
@@ -30,7 +30,6 @@
 import org.biojava.nbio.structure.align.xml.AFPChainXMLConverter;
 
 import javax.swing.*;
-
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.io.BufferedWriter;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyTableRowSorter.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyTableRowSorter.java
index a8f141e76a..5d0745108e 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyTableRowSorter.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyTableRowSorter.java
@@ -50,7 +50,7 @@ public Comparator<?> getComparator(int column)
 class MyComparator implements Comparator<String>, Serializable {
 	private static final long serialVersionUID = 1;
 
-	int column;
+	final int column;
 	public MyComparator(int column){
 		this.column = column;
 	}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java
index d8eb946e4d..2099eac80f 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java
@@ -20,26 +20,16 @@
  */
 package org.biojava.nbio.structure.align.gui;
 
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.io.IOException;
-
-import javax.swing.Box;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.JTabbedPane;
-import javax.swing.JTextField;
-
-import org.biojava.nbio.structure.ResidueRange;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIdentifier;
-import org.biojava.nbio.structure.SubstructureIdentifier;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
 import org.biojava.nbio.structure.align.webstart.WebStartMain;
 import org.biojava.nbio.structure.gui.util.StructurePairSelector;
 
+import javax.swing.*;
+import java.awt.*;
+import java.io.IOException;
+
 
 /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
  *
@@ -52,12 +42,12 @@ public class SelectPDBPanel
 
 	boolean debug = true;
 
-	JTextField f1;
-	JTextField f2;
-	JTextField c1;
-	JTextField c2;
-	JTextField r1;
-	JTextField r2;
+	final JTextField f1;
+	final JTextField f2;
+	final JTextField c1;
+	final JTextField c2;
+	final JTextField r1;
+	final JTextField r2;
 
 	UserConfiguration config;
 	JTabbedPane configPane;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/StructureAlignmentDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/StructureAlignmentDisplay.java
index 266abef138..90ec47afca 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/StructureAlignmentDisplay.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/StructureAlignmentDisplay.java
@@ -20,8 +20,6 @@
  */
 package org.biojava.nbio.structure.align.gui;
 
-import java.util.List;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.StructureException;
@@ -30,6 +28,8 @@
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AlignmentTools;
 
+import java.util.List;
+
 public class StructureAlignmentDisplay {
 
 	/** Display an AFPChain alignment
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/StructureLoaderThread.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/StructureLoaderThread.java
index 813866c8ad..bb350bbc81 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/StructureLoaderThread.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/StructureLoaderThread.java
@@ -34,10 +34,10 @@
 
 public class StructureLoaderThread extends SwingWorker<String, Object> {
 
-	String name;
-	boolean showBiolAssembly;
+	final String name;
+	final boolean showBiolAssembly;
 
-	UserConfiguration config;
+	final UserConfiguration config;
 
 	StructureLoaderThread(UserConfiguration config, String name, boolean showBiolAssembly){
 		this.name = name;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SystemInfo.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SystemInfo.java
index 7e6d26fa1d..dacf98c759 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SystemInfo.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SystemInfo.java
@@ -69,7 +69,7 @@ public class SystemInfo
 		+ "user.dir "
 		+ "user.home "
 		+ "user.name ";
-	EtchedBorder        border;
+	final EtchedBorder        border;
 
 	public SystemInfo()
 	{
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.java
index 83f1dda632..8cbe50f689 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.java
@@ -34,7 +34,7 @@ public class AligPanelMouseMotionListener implements MouseMotionListener, MouseL
 
 	AligPanel parent;
 
-	List<AlignmentPositionListener> aligPosListeners;
+	final List<AlignmentPositionListener> aligPosListeners;
 	int prevPos;
 
 	boolean isDragging ;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
index 78a6dc2b8f..84ccbe53dd 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
@@ -20,20 +20,6 @@
  */
 package org.biojava.nbio.structure.align.gui.aligpanel;
 
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.awt.Point;
-import java.awt.Rectangle;
-import java.awt.RenderingHints;
-import java.awt.event.ActionEvent;
-import java.awt.event.WindowEvent;
-import java.awt.event.WindowListener;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.List;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.align.gui.JPrintPanel;
 import org.biojava.nbio.structure.align.gui.MenuCreator;
@@ -49,6 +35,14 @@
 import org.biojava.nbio.structure.gui.events.AlignmentPositionListener;
 import org.biojava.nbio.structure.gui.util.AlignedPosition;
 
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.List;
+
 /**
  * A JPanel that can display the sequence alignment of a
  * {@link MultipleAlignment} in a nice way and interact with Jmol by
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleStatusDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleStatusDisplay.java
index e87ad5817c..4ea5893b8f 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleStatusDisplay.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleStatusDisplay.java
@@ -20,19 +20,17 @@
  */
 package org.biojava.nbio.structure.align.gui.aligpanel;
 
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.event.WindowEvent;
-import java.awt.event.WindowListener;
-
-import javax.swing.JTextField;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.align.gui.jmol.JmolTools;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools;
 import org.biojava.nbio.structure.gui.events.AlignmentPositionListener;
 import org.biojava.nbio.structure.gui.util.AlignedPosition;
 
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+
 /**
  * This class provides information of the selected positions in the
  * {@link MultipleAligPanel}.
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java
index 24c47bb544..662f9bd3a5 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java
@@ -36,11 +36,11 @@
 
 public class SCOPAutoSuggestProvider implements AutoSuggestProvider{
 
-	boolean DEBUG = false;
+	final boolean DEBUG = false;
 
 	int maxResults = 20;
 
-	AtomicBoolean stop = new AtomicBoolean(false);
+	final AtomicBoolean stop = new AtomicBoolean(false);
 
 	@Override
 	public Vector<String> getSuggestion(String userInput) {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java
index 4663505797..b6cdf1f0fc 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java
@@ -20,23 +20,7 @@
  */
 package org.biojava.nbio.structure.align.gui.jmol;
 
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.awt.event.WindowEvent;
-import java.awt.event.WindowListener;
-import java.util.List;
-
-import javax.swing.JFrame;
-import javax.swing.JTextField;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureImpl;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.ResourceManager;
 import org.biojava.nbio.structure.jama.Matrix;
 import org.jcolorbrewer.ColorBrewer;
@@ -45,6 +29,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.swing.*;
+import java.awt.event.*;
+import java.util.List;
+
 /**
  * An Abstract Class to generalize the visualization of AFP and
  * MultipleAlignment structure alignments in Jmol.
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfoParser.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfoParser.java
index ff8561276f..8cef15b12b 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfoParser.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AtomInfoParser.java
@@ -33,7 +33,7 @@ public class AtomInfoParser {
 
 	private static final Logger logger = LoggerFactory.getLogger(AtomInfoParser.class);
 
-	static Pattern pattern;
+	static final Pattern pattern;
 
 	static {
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java
index 54df47a0ed..8ee76173b1 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java
@@ -24,27 +24,7 @@
 
 package org.biojava.nbio.structure.align.gui.jmol;
 
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.Graphics;
-import java.awt.Rectangle;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.BufferedInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.PipedInputStream;
-import java.io.PipedOutputStream;
-import java.text.DecimalFormat;
-import java.util.List;
-
-import javax.swing.JComboBox;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.gui.JPrintPanel;
 import org.biojava.nbio.structure.domain.LocalProteinDomainParser;
 import org.biojava.nbio.structure.domain.pdp.Domain;
@@ -63,6 +43,14 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.*;
+import java.text.DecimalFormat;
+import java.util.List;
+
 import static org.jmol.util.Logger.LEVEL_FATAL;
 
 
@@ -76,7 +64,7 @@ public class JmolPanel
 
 	private JmolViewer viewer;
 	private JmolAdapter adapter;
-	JmolStatusListener statusListener;
+	final JmolStatusListener statusListener;
 	final Dimension currentSize = new Dimension();
 	final Rectangle rectClip = new Rectangle();
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
index 1962a7657b..90e74be6e6 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
@@ -20,31 +20,8 @@
  */
 package org.biojava.nbio.structure.align.gui.jmol;
 
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ItemEvent;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.StringWriter;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.Box;
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JMenuBar;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.gui.MenuCreator;
 import org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI;
 import org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay;
@@ -62,6 +39,16 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.StringWriter;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * A class that provides a 3D visualization Frame in Jmol for
  * {@link MultipleAlignment}s.
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.java
index f0a5a5864d..00243ec366 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.java
@@ -24,15 +24,14 @@
 
 package org.biojava.nbio.structure.align.gui.jmol;
 
-import java.util.Map;
-
-import javax.swing.JTextField;
-
 import org.jmol.api.JmolStatusListener;
 import org.jmol.c.CBK;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.swing.*;
+import java.util.Map;
+
 public class MyJmolStatusListener implements JmolStatusListener {
 	private static final Logger logger = LoggerFactory.getLogger(MyJmolStatusListener.class);
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java
index ef230064c3..e890e90274 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java
@@ -41,10 +41,10 @@ public class RasmolCommandListener
 implements ActionListener,
 MouseListener {
 
-	JTextField textfield;
-	JmolPanel jmolPanel;
+	final JTextField textfield;
+	final JmolPanel jmolPanel;
 
-	List<String> history;
+	final List<String> history;
 	int historyPosition;
 
 	public RasmolCommandListener(JmolPanel panel, JTextField field){
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java
index 8e04e2cee3..a24d560901 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java
@@ -23,7 +23,9 @@
  */
 package org.biojava.nbio.structure.align.gui.jmol;
 
-import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.PDBHeader;
+import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.align.gui.AlignmentGui;
 import org.biojava.nbio.structure.align.gui.DisplayAFP;
 import org.biojava.nbio.structure.align.gui.MenuCreator;
@@ -40,9 +42,11 @@
 import javax.swing.*;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
-
 import java.awt.*;
-import java.awt.event.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
 import java.io.StringWriter;
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/ConfigXMLHandler.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/ConfigXMLHandler.java
index 78d43fe862..b0659c861c 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/ConfigXMLHandler.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/ConfigXMLHandler.java
@@ -35,7 +35,7 @@
  */
 public class ConfigXMLHandler extends DefaultHandler {
 
-	UserConfiguration config ;
+	final UserConfiguration config ;
 
 	/**
 	 *
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java
index 9a778d7664..eab0bd83c0 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java
@@ -41,7 +41,6 @@
 import org.biojava.nbio.structure.align.util.UserConfiguration;
 
 import javax.swing.*;
-
 import java.io.File;
 
 public class WebStartMain
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java
index 46b20d38f4..d2542e9240 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java
@@ -32,7 +32,9 @@
 
 import javax.swing.*;
 import java.awt.*;
-import java.awt.event.*;
+import java.awt.event.ItemEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
 
 
 /** A class that provides a simple GUI for Jmol
@@ -51,8 +53,8 @@ public class BiojavaJmol  {
 
 	Structure structure;
 
-	JmolPanel jmolPanel;
-	JFrame frame ;
+	final JmolPanel jmolPanel;
+	final JFrame frame ;
 
 
 	public static void main(String[] args){
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JMatrixPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JMatrixPanel.java
index 4f2fbd160b..3f6a889ce5 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JMatrixPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JMatrixPanel.java
@@ -63,7 +63,7 @@ public class JMatrixPanel extends JPanel{
 	int selectedAlignmentPos;
 
 	final static BasicStroke stroke = new BasicStroke(2.0f);
-	StrucAligParameters params;
+	final StrucAligParameters params;
 
 	public JMatrixPanel(){
 		scale = 1;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JmolViewerImpl.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JmolViewerImpl.java
index 2c89da3895..e7763c3269 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JmolViewerImpl.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JmolViewerImpl.java
@@ -42,7 +42,7 @@ public class JmolViewerImpl implements StructureViewer {
 	public static final String smartAdapter = "org.jmol.adapter.smarter.SmarterJmolAdapter";
 	Structure structure;
 	JmolPanel jmolPanel;
-	JFrame frame;
+	final JFrame frame;
 
 	public JmolViewerImpl() {
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java
index 33662abe61..cc33a5b106 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java
@@ -63,12 +63,12 @@ public class ScaleableMatrixPanel
 	 */
 	private static final long serialVersionUID = -8082261434322968652L;
 
-	protected JMatrixPanel mPanel;
-	protected JSlider slider;
-	protected JScrollPane scroll;
-	protected JComboBox coloring;
+	protected final JMatrixPanel mPanel;
+	protected final JSlider slider;
+	protected final JScrollPane scroll;
+	protected final JComboBox coloring;
 
-	protected Map<String,ContinuousColorMapper> gradients;
+	protected final Map<String,ContinuousColorMapper> gradients;
 
 	protected static final int SLIDER_STEPS = 8; // Number of minor ticks per unit scaled
 
@@ -381,8 +381,8 @@ protected class GradientRenderer extends JPanel
 		private static final long serialVersionUID = -2000575579184232365L;
 		private final int min;
 		private final int max;
-		JLabel title;
-		JPanel gradientContainer;
+		final JLabel title;
+		final JPanel gradientContainer;
 
 		public GradientRenderer() {
 			this.setPreferredSize(new Dimension(100,25));
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java
index d6eb415cc8..22f6781502 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java
@@ -57,11 +57,11 @@ public class SequenceDisplay extends JPanel implements ChangeListener {
 	Structure structure2;
 	AlternativeAlignment alig;
 	StructurePairAligner structurePairAligner;
-	SequenceScalePanel panel1;
-	SequenceScalePanel panel2;
+	final SequenceScalePanel panel1;
+	final SequenceScalePanel panel2;
 
-	JSlider  residueSizeSlider;
-	JLabel  percentageDisplay;
+	final JSlider  residueSizeSlider;
+	final JLabel  percentageDisplay;
 
 	int[] idx1;
 	int[] idx2;
@@ -73,15 +73,15 @@ public class SequenceDisplay extends JPanel implements ChangeListener {
 
 	//private static final Logger logger = LoggerFactory.getLogger(SequenceDisplay.class);
 
-	List<AlignedPosition> apos;
+	final List<AlignedPosition> apos;
 
 	float scale;
-	SequenceMouseListener mouseListener1;
-	SequenceMouseListener mouseListener2;
+	final SequenceMouseListener mouseListener1;
+	final SequenceMouseListener mouseListener2;
 
 
-	JLabel label1;
-	JLabel label2;
+	final JLabel label1;
+	final JLabel label2;
 
 	public static void main(String[] args){
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/WrapLayout.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/WrapLayout.java
index 7694632a9b..73ee69513a 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/WrapLayout.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/WrapLayout.java
@@ -20,9 +20,8 @@
  */
 package org.biojava.nbio.structure.gui;
 
+import javax.swing.*;
 import java.awt.*;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
 
 /**
  *  FlowLayout subclass that fully supports wrapping of components.
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/JmolAlignedPositionListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/JmolAlignedPositionListener.java
index e346fc9813..97f2cc3fc1 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/JmolAlignedPositionListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/JmolAlignedPositionListener.java
@@ -33,10 +33,10 @@
 
 public class JmolAlignedPositionListener implements AlignmentPositionListener{
 
-	BiojavaJmol parent;
+	final BiojavaJmol parent;
 	Atom[] ca1;
 	Atom[] ca2;
-	StructurePairAligner structurePairAligner;
+	final StructurePairAligner structurePairAligner;
 
 	public JmolAlignedPositionListener(BiojavaJmol parent, StructurePairAligner alig){
 		this.parent = parent;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java
index 54e1b341e5..462c715bcf 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java
@@ -61,10 +61,10 @@ public class AlternativeAlignmentFrame
 	private static final String[] columnNames = new String[]{"#","eqr","score", "rms", "gaps","cluster", "show distance matrix","show alignment"};
 
 	AlternativeAlignment[] aligs;
-	JPanel panel;
+	final JPanel panel;
 
-	Structure structure1;
-	Structure structure2;
+	final Structure structure1;
+	final Structure structure2;
 	StructurePairAligner structurePairAligner;
 
 	public AlternativeAlignmentFrame(Structure s1, Structure s2) {
@@ -322,8 +322,8 @@ private String[] createRasmolScripts(AlternativeAlignment alig){
 }
 
 class MyButtonMouseListener implements MouseListener{
-	AlternativeAlignmentFrame parent;
-	int pos;
+	final AlternativeAlignmentFrame parent;
+	final int pos;
 	public MyButtonMouseListener(AlternativeAlignmentFrame parent, int position){
 
 		this.parent = parent;
@@ -362,8 +362,8 @@ public void mouseExited(MouseEvent arg0) {
 }
 
 class MatrixMouseListener implements MouseListener{
-	AlternativeAlignmentFrame parent;
-	int pos;
+	final AlternativeAlignmentFrame parent;
+	final int pos;
 	public MatrixMouseListener( AlternativeAlignmentFrame parent, int position){
 
 		this.parent = parent;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JTableDataButtonModel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JTableDataButtonModel.java
index 23e877d88d..af19bbaf42 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JTableDataButtonModel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/JTableDataButtonModel.java
@@ -28,8 +28,8 @@ class JTableDataButtonModel extends AbstractTableModel {
 
 		public static final long serialVersionUID = 0L;
 
-		Object[][] __rows;
-		String[]   __columns;
+		final Object[][] __rows;
+		final String[]   __columns;
 
 		public JTableDataButtonModel(Object[][] rows, String[] columns){
 				__rows = rows;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBDirPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBDirPanel.java
index 8bb3d57230..67663657ee 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBDirPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBDirPanel.java
@@ -52,12 +52,12 @@ public class PDBDirPanel
 	 */
 	private static final long serialVersionUID = -5682120627824627408L;
 
-	boolean debug = true;
-	JTextField pdbDir;
-	JTextField f1;
-	JTextField f2;
-	JTextField c1;
-	JTextField c2;
+	final boolean debug = true;
+	final JTextField pdbDir;
+	final JTextField f1;
+	final JTextField f2;
+	final JTextField c1;
+	final JTextField c2;
 
 	private static final Logger logger = LoggerFactory.getLogger(StructurePairSelector.class);
 
@@ -220,7 +220,7 @@ private JPanel getPDBFilePanel(int pos ,JTextField f, JTextField c){
 
 class ChooseDirAction extends AbstractAction{
 
-	JTextField textField;
+	final JTextField textField;
 	public ChooseDirAction (JTextField textField){
 		super("Choose");
 		this.textField = textField;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBServerPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBServerPanel.java
index 22d0157021..6860f8e5c2 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBServerPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBServerPanel.java
@@ -50,12 +50,12 @@ public class PDBServerPanel
 	 */
 	private static final long serialVersionUID = -5682120627824627408L;
 
-	boolean debug = true;
+	final boolean debug = true;
 	JTextField pdbDir;
-	JTextField f1;
-	JTextField f2;
-	JTextField c1;
-	JTextField c2;
+	final JTextField f1;
+	final JTextField f2;
+	final JTextField c1;
+	final JTextField c2;
 
 
 	private static final Logger logger = LoggerFactory.getLogger(PDBServerPanel.class);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java
index 05795bc91a..35f12703d3 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java
@@ -61,10 +61,10 @@ public class PDBUploadPanel
 
 	private final JComboBox fileType ;
 
-	JTextField filePath1;
-	JTextField filePath2;
-	JTextField chain1;
-	JTextField chain2;
+	final JTextField filePath1;
+	final JTextField filePath2;
+	final JTextField chain1;
+	final JTextField chain2;
 
 	public static JComboBox getFileFormatSelect(){
 		JComboBox fileType = new JComboBox();
@@ -201,7 +201,7 @@ private JPanel getLocalFilePanel(int pos ,JTextField filePath, JTextField  chain
 
 class ChooseAction extends AbstractAction{
 
-	JTextField textField;
+	final JTextField textField;
 	public ChooseAction (JTextField textField){
 		super("Choose");
 		this.textField = textField;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopInstallationInstance.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopInstallationInstance.java
index f76fd5ff67..566c0ac33d 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopInstallationInstance.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopInstallationInstance.java
@@ -33,8 +33,8 @@ public class ScopInstallationInstance
 {
 
 
-	static ScopInstallationInstance me = new ScopInstallationInstance();
-	ScopDatabase install;
+	static final ScopInstallationInstance me = new ScopInstallationInstance();
+	final ScopDatabase install;
 	private ScopInstallationInstance(){
 		UserConfiguration config = WebStartMain.getWebStartConfig();
 		String cacheLocation = config.getPdbFilePath();
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopSelectPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopSelectPanel.java
index 4c9c7d6d0f..2ce7594388 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopSelectPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopSelectPanel.java
@@ -25,7 +25,6 @@
 package org.biojava.nbio.structure.gui.util;
 
 import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider;
 import org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest;
 import org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider;
@@ -47,8 +46,8 @@ public class ScopSelectPanel
 	 *
 	 */
 	private static final long serialVersionUID = 757947454156959178L;
-	JAutoSuggest dom1;
-	JAutoSuggest dom2;
+	final JAutoSuggest dom1;
+	final JAutoSuggest dom2;
 
 	//private static final Logger logger = LoggerFactory.getLogger(ScopSelectPanel.class);
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java
index b9e0d528ac..254d26369e 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java
@@ -23,24 +23,18 @@
  */
 package org.biojava.nbio.structure.gui.util;
 
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.Box;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-
 import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIdentifier;
 import org.biojava.nbio.structure.align.client.StructureName;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
 import org.biojava.nbio.structure.align.webstart.WebStartMain;
 
+import javax.swing.*;
+import java.awt.*;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * A Text Panel that allows the user to specify multiple structure
  * identifiers, space separated.
@@ -53,7 +47,7 @@ public class SelectMultiplePanel extends JPanel {
 
 	private static final long serialVersionUID = 757947454156959178L;
 
-	JTextField input;
+	final JTextField input;
 
 	public SelectMultiplePanel(){
 		this(true);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceMouseListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceMouseListener.java
index 11d7f2fd31..09b3ed03fd 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceMouseListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceMouseListener.java
@@ -50,7 +50,7 @@ public class SequenceMouseListener implements
 {
 
 
-	boolean selectionLocked;
+	final boolean selectionLocked;
 	boolean dragging;
 
 	int selectionStart;
@@ -61,13 +61,13 @@ public class SequenceMouseListener implements
 	int chainLength;
 
 
-	CoordManager coordManager;
+	final CoordManager coordManager;
 
 	//private static final Logger logger = LoggerFactory.getLogger(SequenceMouseListener.class);
 
-	SequenceDisplay parent;
+	final SequenceDisplay parent;
 
-	List<AlignmentPositionListener> alignmentPositionListeners;
+	final List<AlignmentPositionListener> alignmentPositionListeners;
 
 	public SequenceMouseListener(SequenceDisplay parent) {
 		super();
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/StructurePairSelector.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/StructurePairSelector.java
index 89710a6140..74a9352861 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/StructurePairSelector.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/StructurePairSelector.java
@@ -21,11 +21,11 @@
  */
 package org.biojava.nbio.structure.gui.util;
 
-import java.io.IOException;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 
+import java.io.IOException;
+
 /** To be implemented by JPanels that are part of the GUI to trigger structure aligmnents.
  *
  *
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ColorUtils.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ColorUtils.java
index 0d253a054d..cfbedfdb17 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ColorUtils.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ColorUtils.java
@@ -29,9 +29,9 @@
 public class ColorUtils
 {
 
-	public static Color orange =   Color.decode("#FFA500");
-	public static Color cyan   =   Color.decode("#00FFFF");
-	public static Color gold   =   Color.decode("#FFD700");
+	public static final Color orange =   Color.decode("#FFA500");
+	public static final Color cyan   =   Color.decode("#00FFFF");
+	public static final Color gold   =   Color.decode("#FFD700");
 
 
 	static final Color c1 = Color.decode("#228B22"); // green
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java
index 5cd010b356..d8a884cc24 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java
@@ -36,7 +36,7 @@
  */
 public abstract class ContinuousColorMapperTransform implements ContinuousColorMapper {
 
-	protected ContinuousColorMapper mapper;
+	protected final ContinuousColorMapper mapper;
 
 	/**
 	 * Creates a transform.
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
index 91e570d6d1..32da60da20 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
@@ -20,15 +20,6 @@
  */
 package org.biojava.nbio.structure.symmetry.gui;
 
-import java.awt.event.KeyEvent;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.swing.JMenu;
-import javax.swing.JMenuBar;
-import javax.swing.JMenuItem;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.StructureException;
@@ -50,6 +41,12 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.swing.*;
+import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
 /**
  * Class that provides visualizations methods for symmetry alignments. Call the
  * display() method for the default visualization of symmetry.
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryGui.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryGui.java
index 8447d35702..df8b5d4323 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryGui.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryGui.java
@@ -20,22 +20,6 @@
  */
 package org.biojava.nbio.structure.symmetry.gui;
 
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.io.IOException;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.Box;
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JMenuBar;
-import javax.swing.JOptionPane;
-import javax.swing.JProgressBar;
-import javax.swing.JTabbedPane;
-
 import org.biojava.nbio.structure.PassthroughIdentifier;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
@@ -53,6 +37,11 @@
 import org.biojava.nbio.structure.symmetry.internal.CESymmParameters;
 import org.biojava.nbio.structure.symmetry.internal.CeSymm;
 
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.io.IOException;
+
 /**
  * A JFrame that allows to trigger a symmetry analysis, either from files
  * in a directory or after manual upload
@@ -332,7 +321,7 @@ public CESymmParameters getParameters() {
 class ProgressThreadDrawer extends Thread {
 
 	JProgressBar progress;
-	static int interval = 300;
+	static final int interval = 300;
 
 	public ProgressThreadDrawer(JProgressBar progress) {
 		this.progress = progress;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java
index 1edb84d550..f14c6c69b1 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java
@@ -20,9 +20,6 @@
  */
 package org.biojava.nbio.structure.symmetry.gui;
 
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay;
@@ -33,6 +30,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
 /**
  * Action Listener for the symmetry menu. Trigger various internal symmetry
  * specific analysis.
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java
index dd2401b2c8..1aa07aa747 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java
@@ -27,7 +27,6 @@
 import javax.vecmath.Color4f;
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Tuple3d;
-
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java
index 7873a454e3..7b45bfe811 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java
@@ -28,10 +28,9 @@
 import org.jcolorbrewer.ColorBrewer;
 
 import javax.vecmath.*;
-
 import java.awt.*;
-import java.util.*;
 import java.util.List;
+import java.util.*;
 
 
 /**
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
index 902b6cc867..80123eab84 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
@@ -24,17 +24,16 @@
 package org.biojava.nbio.structure.symmetry.jmolScript;
 
 import org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner;
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
 import org.biojava.nbio.structure.symmetry.core.Rotation;
 import org.biojava.nbio.structure.symmetry.core.RotationGroup;
-import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
 import org.biojava.nbio.structure.symmetry.geometry.Polyhedron;
 import org.jcolorbrewer.ColorBrewer;
 
 import javax.vecmath.*;
-
 import java.awt.*;
-import java.util.*;
 import java.util.List;
+import java.util.*;
 
 /**
  * @author Peter
diff --git a/biojava-structure/src/main/java/demo/DemoAtomCache.java b/biojava-structure/src/main/java/demo/DemoAtomCache.java
index 460332c3ae..2e112acb36 100644
--- a/biojava-structure/src/main/java/demo/DemoAtomCache.java
+++ b/biojava-structure/src/main/java/demo/DemoAtomCache.java
@@ -22,9 +22,9 @@
 
 
 import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
-import org.biojava.nbio.structure.StructureIO;
 
 
 /** Example of how to load PDB files using the AtomCache class.
diff --git a/biojava-structure/src/main/java/demo/DemoBioAssemblies.java b/biojava-structure/src/main/java/demo/DemoBioAssemblies.java
index 4427bf3eea..c362a82b97 100644
--- a/biojava-structure/src/main/java/demo/DemoBioAssemblies.java
+++ b/biojava-structure/src/main/java/demo/DemoBioAssemblies.java
@@ -20,8 +20,6 @@
  */
 package demo;
 
-import java.util.List;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
@@ -29,6 +27,8 @@
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
 
+import java.util.List;
+
 public class DemoBioAssemblies {
 
 	public static void main(String[] args) throws Exception {
diff --git a/biojava-structure/src/main/java/demo/DemoCeSymm.java b/biojava-structure/src/main/java/demo/DemoCeSymm.java
index 996c889a9a..9720409837 100644
--- a/biojava-structure/src/main/java/demo/DemoCeSymm.java
+++ b/biojava-structure/src/main/java/demo/DemoCeSymm.java
@@ -20,8 +20,6 @@
  */
 package demo;
 
-import java.io.IOException;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
@@ -36,6 +34,8 @@
 import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
 import org.biojava.nbio.structure.symmetry.utils.SymmetryTools;
 
+import java.io.IOException;
+
 /**
  * Quick demo of how to call CE-Symm programmatically.
  * Some examples of different symmetry types are proposed.
diff --git a/biojava-structure/src/main/java/demo/DemoCrystalInterfaces.java b/biojava-structure/src/main/java/demo/DemoCrystalInterfaces.java
index caeef006ed..e6ac5f8da3 100644
--- a/biojava-structure/src/main/java/demo/DemoCrystalInterfaces.java
+++ b/biojava-structure/src/main/java/demo/DemoCrystalInterfaces.java
@@ -23,13 +23,13 @@
 
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.contact.*;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.xtal.CrystalBuilder;
 import org.biojava.nbio.structure.xtal.CrystalTransform;
 import org.biojava.nbio.structure.xtal.SpaceGroup;
-import org.biojava.nbio.structure.StructureIO;
 
 import javax.vecmath.AxisAngle4d;
 import javax.vecmath.Vector3d;
diff --git a/biojava-structure/src/main/java/demo/DemoLoadSecStruc.java b/biojava-structure/src/main/java/demo/DemoLoadSecStruc.java
index 8684ba1257..62d47033a3 100644
--- a/biojava-structure/src/main/java/demo/DemoLoadSecStruc.java
+++ b/biojava-structure/src/main/java/demo/DemoLoadSecStruc.java
@@ -20,9 +20,6 @@
  */
 package demo;
 
-import java.io.IOException;
-import java.util.List;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.util.AtomCache;
@@ -32,6 +29,9 @@
 import org.biojava.nbio.structure.secstruc.SecStrucInfo;
 import org.biojava.nbio.structure.secstruc.SecStrucTools;
 
+import java.io.IOException;
+import java.util.List;
+
 /**
  * Demonstration of how to load a Structure with the SS information, either from
  * the PDB file annotation (Author's assignment) or from the DSSP file in the
diff --git a/biojava-structure/src/main/java/demo/DemoLoadStructure.java b/biojava-structure/src/main/java/demo/DemoLoadStructure.java
index 276eccaaf3..900db3e4bd 100644
--- a/biojava-structure/src/main/java/demo/DemoLoadStructure.java
+++ b/biojava-structure/src/main/java/demo/DemoLoadStructure.java
@@ -24,11 +24,11 @@
 
 package demo;
 
+import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.io.PDBFileReader;
-import org.biojava.nbio.core.util.InputStreamProvider;
 
 
 
diff --git a/biojava-structure/src/main/java/demo/DemoMmcifToPdbConverter.java b/biojava-structure/src/main/java/demo/DemoMmcifToPdbConverter.java
index 5a5c1a222f..4d73017afe 100644
--- a/biojava-structure/src/main/java/demo/DemoMmcifToPdbConverter.java
+++ b/biojava-structure/src/main/java/demo/DemoMmcifToPdbConverter.java
@@ -27,12 +27,7 @@
 import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
 import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.PrintWriter;
+import java.io.*;
 
 /**
  * An example of how to convert mmCIF file to PDB file
diff --git a/biojava-structure/src/main/java/demo/DemoMmtfReader.java b/biojava-structure/src/main/java/demo/DemoMmtfReader.java
index e7cdce5283..95611353ad 100644
--- a/biojava-structure/src/main/java/demo/DemoMmtfReader.java
+++ b/biojava-structure/src/main/java/demo/DemoMmtfReader.java
@@ -20,11 +20,11 @@
  */
 package demo;
 
-import java.io.IOException;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.io.mmtf.MmtfActions;
 
+import java.io.IOException;
+
 /**
  * Class to show how to read a Biojava structure using MMTF
  * @author Anthony Bradley
diff --git a/biojava-structure/src/main/java/demo/DemoMmtfWriter.java b/biojava-structure/src/main/java/demo/DemoMmtfWriter.java
index c9fcd8166c..6aefaa0986 100644
--- a/biojava-structure/src/main/java/demo/DemoMmtfWriter.java
+++ b/biojava-structure/src/main/java/demo/DemoMmtfWriter.java
@@ -20,15 +20,15 @@
  */
 package demo;
 
-import java.io.IOException;
-import java.nio.file.Paths;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.io.mmtf.MmtfActions;
 import org.biojava.nbio.structure.io.mmtf.MmtfUtils;
 
+import java.io.IOException;
+import java.nio.file.Paths;
+
 public class DemoMmtfWriter {
 
 	public static void main(String[] args) throws IOException, StructureException {
diff --git a/biojava-structure/src/main/java/demo/DemoMultipleMC.java b/biojava-structure/src/main/java/demo/DemoMultipleMC.java
index 9f91a913fa..aa8c7f6f0b 100644
--- a/biojava-structure/src/main/java/demo/DemoMultipleMC.java
+++ b/biojava-structure/src/main/java/demo/DemoMultipleMC.java
@@ -20,11 +20,6 @@
  */
 package demo;
 
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.List;
-import java.util.ArrayList;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIdentifier;
@@ -36,6 +31,11 @@
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
 import org.biojava.nbio.structure.align.util.AtomCache;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
 /**
  * Demo for running the MultipleMC Algorithm on a protein family.
  * For visualizing the results in jmol use the same Demo in the GUI module.
diff --git a/biojava-structure/src/main/java/demo/DemoQsAlign.java b/biojava-structure/src/main/java/demo/DemoQsAlign.java
index 5c52aeb58b..a85d722fe3 100644
--- a/biojava-structure/src/main/java/demo/DemoQsAlign.java
+++ b/biojava-structure/src/main/java/demo/DemoQsAlign.java
@@ -20,8 +20,6 @@
  */
 package demo;
 
-import java.io.IOException;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
@@ -30,6 +28,8 @@
 import org.biojava.nbio.structure.align.quaternary.QsAlignResult;
 import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
 
+import java.io.IOException;
+
 /**
  * Demo on how to use programatically {@link QsAlign} for the alignment of
  * quaternary structures.
diff --git a/biojava-structure/src/main/java/demo/DemoSecStrucCalc.java b/biojava-structure/src/main/java/demo/DemoSecStrucCalc.java
index 9cadf0f854..782dfef100 100644
--- a/biojava-structure/src/main/java/demo/DemoSecStrucCalc.java
+++ b/biojava-structure/src/main/java/demo/DemoSecStrucCalc.java
@@ -20,16 +20,16 @@
  */
 package demo;
 
-import java.io.IOException;
-import java.util.List;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.util.AtomCache;
-import org.biojava.nbio.structure.secstruc.SecStrucElement;
 import org.biojava.nbio.structure.secstruc.SecStrucCalc;
+import org.biojava.nbio.structure.secstruc.SecStrucElement;
 import org.biojava.nbio.structure.secstruc.SecStrucTools;
 
+import java.io.IOException;
+import java.util.List;
+
 /**
  * Demonstration on how to use the Secondary Structure Prediction (DSSP)
  * implementation in BioJava and obtain different SS representations and
diff --git a/biojava-structure/src/main/java/demo/DemoSymmetry.java b/biojava-structure/src/main/java/demo/DemoSymmetry.java
index 4edc3cdc20..d86f56c6a8 100644
--- a/biojava-structure/src/main/java/demo/DemoSymmetry.java
+++ b/biojava-structure/src/main/java/demo/DemoSymmetry.java
@@ -20,8 +20,6 @@
  */
 package demo;
 
-import java.util.List;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
@@ -33,6 +31,8 @@
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
 
+import java.util.List;
+
 /**
  * A demo on how to use the quaternary symmetry detection algorithms.
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
index 23a401e0d0..dfbc5d326d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
@@ -23,9 +23,8 @@
  */
 package org.biojava.nbio.structure;
 
-import java.util.List;
-
 import javax.vecmath.Point3d;
+import java.util.List;
 
 /**
  * A simple interface for an Atom.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomImpl.java
index 36ccf49efb..1cdaf3dbf2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomImpl.java
@@ -25,11 +25,10 @@
 
 import org.biojava.nbio.structure.io.FileConvert;
 
+import javax.vecmath.Point3d;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.vecmath.Point3d;
-
 
 /**
  * Implementation of an Atom of a PDB file.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java
index 5330f3fe54..a9c44d1644 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java
@@ -23,21 +23,15 @@
 
 package org.biojava.nbio.structure;
 
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.NavigableMap;
-import java.util.TreeMap;
-
 import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
 import org.biojava.nbio.structure.io.mmcif.chem.ResidueType;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.Serializable;
+import java.util.*;
+
 /**
  * A map from {@link ResidueNumber ResidueNumbers} to ATOM record positions in a PDB file.
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
index 42c7e4116c..8f91832bbd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
@@ -20,13 +20,13 @@
  */
 package org.biojava.nbio.structure;
 
+import org.biojava.nbio.structure.align.util.AtomCache;
+
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.biojava.nbio.structure.align.util.AtomCache;
-
 public class BioAssemblyIdentifier implements StructureIdentifier {
 
 	private static final long serialVersionUID = -356206725119993449L;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
index f4cfd1bba3..5f0bd137e4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -22,15 +22,6 @@
  */
 package org.biojava.nbio.structure ;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import javax.vecmath.Matrix3d;
-import javax.vecmath.Matrix4d;
-import javax.vecmath.Point3d;
-import javax.vecmath.Vector3d;
-
 import org.biojava.nbio.structure.geometry.CalcPoint;
 import org.biojava.nbio.structure.geometry.Matrices;
 import org.biojava.nbio.structure.geometry.SuperPositionSVD;
@@ -38,6 +29,14 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix3d;
+import javax.vecmath.Matrix4d;
+import javax.vecmath.Point3d;
+import javax.vecmath.Vector3d;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
 /**
  * Utility operations on Atoms, AminoAcids, Matrices, Point3d, etc.
  * <p>
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java
index c763b5767e..ab1540c057 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java
@@ -24,18 +24,21 @@
 package org.biojava.nbio.structure;
 
 
-import org.biojava.nbio.structure.io.FileConvert;
-import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
-import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
-import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
 import org.biojava.nbio.core.sequence.template.Sequence;
+import org.biojava.nbio.structure.io.FileConvert;
+import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
+import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
+import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 
 /**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java
index cca63ffc8f..e99f1ef523 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java
@@ -28,14 +28,7 @@
 import org.slf4j.LoggerFactory;
 
 import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeSet;
+import java.util.*;
 
 /**
  * An object to contain the info from the PDB header for a Molecule.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupType.java
index 0e9ef84860..304b9ac52b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupType.java
@@ -95,7 +95,7 @@ public Set<ResidueType> getResidueTypes() {
 	 * @return
 	 */
 	private static Set<ResidueType> matchPolymerTypes(Set<PolymerType> allowedTypes) {
-		Set<ResidueType> matched = new HashSet<>();
+		Set<ResidueType> matched = EnumSet.noneOf(ResidueType.class);
 		for(ResidueType restype : ResidueType.values()) {
 			if(allowedTypes.contains(restype.polymerType)) {
 				matched.add(restype);
@@ -109,7 +109,7 @@ private static Set<ResidueType> matchPolymerTypes(Set<PolymerType> allowedTypes)
 	 * @return
 	 */
 	private static Set<ResidueType> getHetatmTypes() {
-		Set<ResidueType> unmatched = new HashSet<>();
+		Set<ResidueType> unmatched = EnumSet.noneOf(ResidueType.class);
 		for(ResidueType restype : ResidueType.values()) {
 			if(!AMINOACID.getResidueTypes().contains(restype) &&
 					!NUCLEOTIDE.getResidueTypes().contains(restype) ) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Model.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Model.java
index 4ff903814a..1951d82e07 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Model.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Model.java
@@ -20,13 +20,13 @@
  */
 package org.biojava.nbio.structure;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 /**
  * An internal utility class for StructureImpl to make it easier to manage poly and nonpoly chains.
  * Not to exposed to users through API.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java
index 16dfe6a0fa..c9223e18f2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java
@@ -20,8 +20,6 @@
 
 package org.biojava.nbio.structure;
 
-import org.biojava.nbio.structure.io.PDBParseException;
-
 import java.util.ArrayList;
 import java.util.List;
 
@@ -56,7 +54,7 @@
  * @version %I% %G%
  */
 public class Mutator{
-	List<String> supportedAtoms;
+	final List<String> supportedAtoms;
 
 	public Mutator(){
 		supportedAtoms = new ArrayList<>();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PassthroughIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PassthroughIdentifier.java
index f5acaa639f..78abd1a6d5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/PassthroughIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/PassthroughIdentifier.java
@@ -20,10 +20,10 @@
  */
 package org.biojava.nbio.structure;
 
-import java.util.ArrayList;
-
 import org.biojava.nbio.structure.align.util.AtomCache;
 
+import java.util.ArrayList;
+
 /**
  * A stub StructureIdentifier, representing the full structure in all cases.
  * @author Spencer Bliven
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java
index f93670e532..1e0e9a95d7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java
@@ -20,13 +20,13 @@
  */
 package org.biojava.nbio.structure;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 /**
  * A chain, a start residue, and an end residue.
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureFiletype.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureFiletype.java
new file mode 100644
index 0000000000..b94fcb546c
--- /dev/null
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureFiletype.java
@@ -0,0 +1,27 @@
+package org.biojava.nbio.structure;
+
+import org.biojava.nbio.structure.io.MMCIFFileReader;
+import org.biojava.nbio.structure.io.PDBFileReader;
+
+import java.util.Collections;
+import java.util.List;
+
+public enum StructureFiletype {
+    PDB( (new PDBFileReader()).getExtensions()),
+    CIF( new MMCIFFileReader().getExtensions()),
+    UNKNOWN(Collections.emptyList());
+
+    private final List<String> extensions;
+    /**
+     * @param extensions List of supported extensions, including leading period
+     */
+    StructureFiletype(List<String> extensions) {
+        this.extensions = extensions;
+    }
+    /**
+     * @return a list of file extensions associated with this type
+     */
+    public List<String> getExtensions() {
+        return extensions;
+    }
+}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
index ee331abe8c..d0564d60fe 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
@@ -20,14 +20,11 @@
  */
 package org.biojava.nbio.structure;
 
+import org.biojava.nbio.structure.align.util.AtomCache;
+
 import java.io.IOException;
-import java.util.Collections;
 import java.util.List;
 
-import org.biojava.nbio.structure.align.util.AtomCache;
-import org.biojava.nbio.structure.io.MMCIFFileReader;
-import org.biojava.nbio.structure.io.PDBFileReader;
-
 /**
  * A class that provides static access methods for easy lookup of protein structure related components
  *
@@ -39,7 +36,7 @@ public class StructureIO {
 
 	//private static final Logger logger = LoggerFactory.getLogger(StructureIO.class);
 
-	private static AtomCache cache ;
+	@Deprecated private static ThreadLocal<AtomCache> caches = ThreadLocal.withInitial(()->null) ;
 
 
 	/**
@@ -95,30 +92,27 @@ public class StructureIO {
 	 */
 	public static Structure getStructure(String name) throws IOException, StructureException{
 
-		checkInitAtomCache();
 
 		// delegate this functionality to AtomCache...
 
-		return cache.getStructure(name);
+		return getAtomCache().getStructure(name);
 
 	}
 
 
-	private static void checkInitAtomCache() {
-		if ( cache == null){
-			cache = new AtomCache();
-		}
-
+	@Deprecated public static void setAtomCache(AtomCache c){
+		caches.set(c);
 	}
 
-	public static void setAtomCache(AtomCache c){
-		cache = c;
+	@Deprecated public static AtomCache getAtomCache() {
+		//synchronized (StructureIO.class) {
+			AtomCache cache = caches.get();
+			if ( cache == null)
+				setAtomCache(cache = new AtomCache());
+			return cache;
+		//}
 	}
 
-	public static AtomCache getAtomCache() {
-		checkInitAtomCache();
-		return cache;
-	}
 
 
 	/**
@@ -147,13 +141,7 @@ public static AtomCache getAtomCache() {
 	 */
 	public static Structure getBiologicalAssembly(String pdbId, boolean multiModel) throws IOException, StructureException{
 
-		checkInitAtomCache();
-
-		pdbId = pdbId.toLowerCase();
-
-		Structure s = cache.getBiologicalAssembly(pdbId, multiModel);
-
-		return s;
+		return getAtomCache().getBiologicalAssembly(pdbId.toLowerCase(), multiModel);
 	}
 
 	/**
@@ -194,14 +182,7 @@ public static Structure getBiologicalAssembly(String pdbId) throws IOException,
 	 * @throws IOException
 	 */
 	public static Structure getBiologicalAssembly(String pdbId, int biolAssemblyNr, boolean multiModel) throws IOException, StructureException {
-
-		checkInitAtomCache();
-
-		pdbId = pdbId.toLowerCase();
-
-		Structure s = cache.getBiologicalAssembly(pdbId, biolAssemblyNr, multiModel);
-
-		return s;
+		return getAtomCache().getBiologicalAssembly(pdbId.toLowerCase(), biolAssemblyNr, multiModel);
 	}
 
 	/**
@@ -241,13 +222,8 @@ public static Structure getBiologicalAssembly(String pdbId, int biolAssemblyNr)
 	 */
 	public static List<Structure> getBiologicalAssemblies(String pdbId, boolean multiModel) throws IOException, StructureException {
 
-		checkInitAtomCache();
-
-		pdbId = pdbId.toLowerCase();
 
-		List<Structure> s = cache.getBiologicalAssemblies(pdbId, multiModel);
-
-		return s;
+		return getAtomCache().getBiologicalAssemblies(pdbId.toLowerCase(), multiModel);
 
 	}
 
@@ -267,39 +243,19 @@ public static List<Structure> getBiologicalAssemblies(String pdbId) throws IOExc
 	}
 
 
-	private static final String FILE_SEPARATOR = System.getProperty("file.separator");
+//	private static final String FILE_SEPARATOR = System.getProperty("file.separator");
 
-	/**
-	 * Utility method to set the location where PDB files can be found
-	 *
-	 * @param pathToPDBFiles
-	 */
-	public static void setPdbPath(String pathToPDBFiles){
+//	/**
+//	 * Utility method to set the location where PDB files can be found
+//	 *
+//	 * @param pathToPDBFiles
+//	 */
+//	public static void setPdbPath(String pathToPDBFiles){
+//
+//		if ( ! pathToPDBFiles.endsWith(FILE_SEPARATOR))
+//			pathToPDBFiles += FILE_SEPARATOR;
+//	}
 
-		if ( ! pathToPDBFiles.endsWith(FILE_SEPARATOR))
-			pathToPDBFiles += FILE_SEPARATOR;
-	}
-
-
-	public enum StructureFiletype {
-		PDB( (new PDBFileReader()).getExtensions()),
-		CIF( new MMCIFFileReader().getExtensions()),
-		UNKNOWN(Collections.emptyList());
-
-		private final List<String> extensions;
-		/**
-		 * @param extensions List of supported extensions, including leading period
-		 */
-		StructureFiletype(List<String> extensions) {
-			this.extensions = extensions;
-		}
-		/**
-		 * @return a list of file extensions associated with this type
-		 */
-		public List<String> getExtensions() {
-			return extensions;
-		}
-	}
 
 	/**
 	 * Attempts to guess the type of a structure file based on the extension
@@ -310,9 +266,8 @@ public static StructureFiletype guessFiletype(String filename) {
 		String lower = filename.toLowerCase();
 		for(StructureFiletype type : StructureFiletype.values()) {
 			for(String ext : type.getExtensions()) {
-				if(lower.endsWith(ext.toLowerCase())) {
+				if(lower.endsWith(ext.toLowerCase()))
 					return type;
-				}
 			}
 		}
 		return StructureFiletype.UNKNOWN;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java
index cc7d8109b2..f79c8f0733 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java
@@ -23,11 +23,11 @@
 
 package org.biojava.nbio.structure;
 
+import org.biojava.nbio.structure.align.util.AtomCache;
+
 import java.io.IOException;
 import java.io.Serializable;
 
-import org.biojava.nbio.structure.align.util.AtomCache;
-
 
 /**
  * An identifier that <em>uniquely</em> identifies a whole {@link Structure} or
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
index 4acb36c41c..24cf1ea093 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
@@ -23,14 +23,14 @@
  */
 package org.biojava.nbio.structure;
 
-import java.util.ArrayList;
-import java.util.List;
-import java.util.ListIterator;
-
 import org.biojava.nbio.structure.io.FileConvert;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.ArrayList;
+import java.util.List;
+import java.util.ListIterator;
+
 /**
  * Implementation of a PDB Structure. This class
  * provides the data contained in a PDB file.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
index 892fbe113a..4edab66c14 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -22,23 +22,22 @@
  */
 package org.biojava.nbio.structure;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.*;
-
-import javax.vecmath.Point3d;
-
+import org.biojava.nbio.core.util.FileDownloadUtils;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.contact.AtomContactSet;
 import org.biojava.nbio.structure.contact.Grid;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.io.PDBFileParser;
-import org.biojava.nbio.core.util.FileDownloadUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Point3d;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.*;
+
 /**
  * A class that provides some tool methods.
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
index a6681c69b5..d3016e5679 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
@@ -23,17 +23,17 @@
 
 package org.biojava.nbio.structure;
 
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.biojava.nbio.structure.contact.Grid;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.LinkedList;
 import java.util.List;
 
-import org.biojava.nbio.structure.align.util.AtomCache;
-import org.biojava.nbio.structure.contact.Grid;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 /**
  * This is the canonical way to identify a part of a structure.
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
index ee1bb75f42..0282de7e31 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
@@ -20,11 +20,16 @@
  */
 package org.biojava.nbio.structure;
 
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.UnsupportedEncodingException;
+import org.biojava.nbio.core.util.InputStreamProvider;
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.biojava.nbio.structure.io.PDBFileReader;
+import org.biojava.nbio.structure.io.mmcif.MMcifParser;
+import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
+import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.*;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLDecoder;
@@ -35,16 +40,6 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.biojava.nbio.core.util.InputStreamProvider;
-import org.biojava.nbio.structure.StructureIO.StructureFiletype;
-import org.biojava.nbio.structure.align.util.AtomCache;
-import org.biojava.nbio.structure.io.PDBFileReader;
-import org.biojava.nbio.structure.io.mmcif.MMcifParser;
-import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
-import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 /**
  * Represents a structure loaded from a URL (including a file URL)
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
index cae663df67..a62b6edcb6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
@@ -35,11 +35,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix4d;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.vecmath.Matrix4d;
-
 //import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
 
 public class AFPTwister {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/FarmJob.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/FarmJob.java
index 9452fad207..bad1657cb1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/FarmJob.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/FarmJob.java
@@ -20,6 +20,7 @@
  */
 package org.biojava.nbio.structure.align;
 
+import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.align.client.FarmJobParameters;
 import org.biojava.nbio.structure.align.client.FarmJobRunnable;
 import org.biojava.nbio.structure.align.events.AlignmentProgressListener;
@@ -29,7 +30,6 @@
 import org.biojava.nbio.structure.scop.CachedRemoteScopInstallation;
 import org.biojava.nbio.structure.scop.ScopDatabase;
 import org.biojava.nbio.structure.scop.ScopFactory;
-import org.biojava.nbio.core.util.InputStreamProvider;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java
index 6af2a2a1e8..7312fe5144 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java
@@ -24,6 +24,7 @@
  *
  */
 
+import org.biojava.nbio.core.util.ConcurrencyTools;
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
@@ -41,7 +42,6 @@
 import org.biojava.nbio.structure.domain.RemoteDomainProvider;
 import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
 import org.biojava.nbio.structure.io.PDBFileReader;
-import org.biojava.nbio.core.util.ConcurrencyTools;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -63,7 +63,7 @@ public class MultiThreadedDBSearch {
 
 	private final static Logger logger = LoggerFactory.getLogger(MultiThreadedDBSearch.class);
 
-	AtomicBoolean interrupted  ;
+	final AtomicBoolean interrupted  ;
 
 	StructureAlignment algorithm;
 
@@ -71,13 +71,13 @@ public class MultiThreadedDBSearch {
 
 	String name1;
 
-	int nrCPUs;
+	final int nrCPUs;
 
 	AtomCache cache;
 	File resultList;
 	SortedSet<String> representatives;
 
-	boolean domainSplit;
+	final boolean domainSplit;
 
 	Structure structure1;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultipleStructureAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultipleStructureAligner.java
index 18e814caac..950123c4ac 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultipleStructureAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultipleStructureAligner.java
@@ -20,13 +20,13 @@
  */
 package org.biojava.nbio.structure.align;
 
-import java.util.List;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.ce.ConfigStrucAligParams;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
 
+import java.util.List;
+
 /**
  * Interface for the Multiple Structure Alignment Algorithms. The Pairwise Alignment Algorithms can also
  * implement this class to be able to return {@link MultipleAlignment} Objects.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
index d8a2d4b506..b41eaae021 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
@@ -35,6 +35,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix4d;
 import java.io.FileOutputStream;
 import java.io.InputStream;
 import java.io.PrintStream;
@@ -43,8 +44,6 @@
 import java.util.Comparator;
 import java.util.List;
 
-import javax.vecmath.Matrix4d;
-
 /**
  * Perform a pairwise protein structure superimposition.
  *
@@ -142,7 +141,7 @@ public class StructurePairAligner {
 	StrucAligParameters params;
 	FragmentPair[] fragPairs;
 
-	List<AlignmentProgressListener> listeners = new ArrayList<>();
+	final List<AlignmentProgressListener> listeners = new ArrayList<>();
 
 	public StructurePairAligner() {
 		super();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
index f3469c1f1e..2bbb8b6964 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
@@ -78,9 +78,9 @@
  */
 public abstract class AbstractUserArgumentProcessor implements UserArgumentProcessor {
 
-	public static String newline = System.getProperty("line.separator");
+	public static final String newline = System.getProperty("line.separator");
 
-	protected StartupParameters params ;
+	protected final StartupParameters params ;
 
 	public static final List<String> mandatoryArgs= new ArrayList<>();
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
index c3b5dd959a..af229f73d8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
@@ -26,11 +26,9 @@
 
 import org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.model.AFP;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AFPAlignmentDisplay;
@@ -38,14 +36,11 @@
 import org.biojava.nbio.structure.geometry.Matrices;
 import org.biojava.nbio.structure.geometry.SuperPositions;
 import org.biojava.nbio.structure.jama.Matrix;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
 
+import javax.vecmath.Matrix4d;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.vecmath.Matrix4d;
-
 
 
 /** This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3),
@@ -85,7 +80,7 @@ public class CECalculator {
 
 	protected static final 	double  zThr=-0.1;
 
-	long timeStart ;
+	final long timeStart ;
 	long timeEnd;
 	private int nAtom;
 
@@ -103,13 +98,13 @@ public class CECalculator {
 	private double z;
 	private int[] traceIndexContainer;
 
-	protected CeParameters params;
+	protected final CeParameters params;
 	// SHOULD these fields be PARAMETERS?
 
 	protected static final int nIter = 1;
 	private static final boolean distAll = false;
 
-	List<MatrixListener> matrixListeners;
+	final List<MatrixListener> matrixListeners;
 
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
index e0b6893991..2c2ac90e82 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
@@ -32,13 +32,12 @@
 import org.biojava.nbio.structure.geometry.SuperPositions;
 import org.biojava.nbio.structure.jama.Matrix;
 
+import javax.vecmath.Matrix4d;
 import java.lang.reflect.InvocationTargetException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
-import javax.vecmath.Matrix4d;
-
 /**
  * A wrapper for {@link CeMain} which sets default parameters to be appropriate for finding
  * circular permutations.
@@ -113,13 +112,11 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureExce
 		case LEFT:
 			duplicateRight = false;
 			break;
-		case RIGHT:
-			duplicateRight = true;
-			break;
-		case SHORTER:
+            case SHORTER:
 			duplicateRight = ca1.length >= ca2.length;
 			break;
-		default:
+            case RIGHT:
+            default:
 			duplicateRight = true;
 		}
 
@@ -580,8 +577,8 @@ private static int[] countNtermResidues(int[] block, int nStart,
 	 * @see #filterDuplicateAFPs()
 	 */
 	private static class ResiduePair {
-		public int a;
-		public int b;
+		public final int a;
+		public final int b;
 		public ResiduePair(int a, int b) {
 			this.a=a;
 			this.b=b;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
index 198813783d..c5efd0076a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
@@ -26,6 +26,8 @@
 
 import org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
 import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.model.AFP;
 import org.biojava.nbio.structure.align.model.AFPChain;
@@ -33,14 +35,11 @@
 import org.biojava.nbio.structure.geometry.Matrices;
 import org.biojava.nbio.structure.geometry.SuperPositions;
 import org.biojava.nbio.structure.jama.Matrix;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
 
+import javax.vecmath.Matrix4d;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.vecmath.Matrix4d;
-
 
 
 /** This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3),
@@ -83,7 +82,7 @@ public class CeCalculatorEnhanced {
 
 	protected static final 	double  zThr=-0.1;
 
-	long timeStart ;
+	final long timeStart ;
 	long timeEnd;
 	private int nAtom;
 
@@ -101,13 +100,13 @@ public class CeCalculatorEnhanced {
 	private double z;
 	private int[] traceIndexContainer;
 
-	protected CeParameters params;
+	protected final CeParameters params;
 	// SHOULD these fields be PARAMETERS?
 
 	protected static final int nIter = 1;
 	private static final boolean distAll = false;
 
-	List<MatrixListener> matrixListeners;
+	final List<MatrixListener> matrixListeners;
 
 	public static final boolean GLOBAL_ALIGN1 = false;
 	public static final boolean GLOBAL_ALIGN2 = false;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
index 7253a7be9c..6ed2601fa8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
@@ -26,8 +26,8 @@
 
 import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
-import org.biojava.nbio.structure.align.util.CliTools;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+import org.biojava.nbio.structure.align.util.CliTools;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -52,7 +52,7 @@ public enum ScoringStrategy {
 		SIDE_CHAIN_ANGLE_SCORING("Angle between sidechains"),
 		CA_AND_SIDE_CHAIN_ANGLE_SCORING("CA distance+Angle between sidechains"),
 		SEQUENCE_CONSERVATION("Sequence Conservation");
-		public static ScoringStrategy DEFAULT_SCORING_STRATEGY = CA_SCORING;
+		public static final ScoringStrategy DEFAULT_SCORING_STRATEGY = CA_SCORING;
 
 		private final String name;
 		ScoringStrategy(String name) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java
index c19b840c08..8f2d394319 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java
@@ -20,6 +20,8 @@
  */
 package org.biojava.nbio.structure.align.client;
 
+import org.biojava.nbio.core.util.FlatFileCache;
+import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.StructureAlignment;
@@ -40,8 +42,6 @@
 import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
 import org.biojava.nbio.structure.scop.RemoteScopInstallation;
 import org.biojava.nbio.structure.scop.ScopFactory;
-import org.biojava.nbio.core.util.FlatFileCache;
-import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -75,7 +75,7 @@ public class FarmJobRunnable implements Runnable {
 
 	//private static DateFormat dateFormat = new SimpleDateFormat("MMMM dd, yyyy h:mm a",Locale.US);
 
-	FarmJobParameters params;
+	final FarmJobParameters params;
 
 	String prevName1;
 	Atom[] ca1 ;
@@ -93,10 +93,10 @@ public class FarmJobRunnable implements Runnable {
 	boolean terminated ;
 
 	List<AlignmentProgressListener> progressListeners;
-	CountProgressListener counter ;
+	final CountProgressListener counter ;
 
-	String userName;
-	protected AtomCache cache;
+	final String userName;
+	protected final AtomCache cache;
 
 	boolean verbose; // TODO dmyersturnbull: we should probably remove this in favor of SLF4J
 	String version = null;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
index 6759265628..5e5217d569 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
@@ -21,18 +21,19 @@
 package org.biojava.nbio.structure.align.client;
 
 import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.fatcat.FatCatRigid;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AtomCache;
-import org.biojava.nbio.structure.align.util.URLConnectionTools;
 import org.biojava.nbio.structure.align.util.ResourceManager;
+import org.biojava.nbio.structure.align.util.URLConnectionTools;
 import org.biojava.nbio.structure.align.xml.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.*;
-import java.net.MalformedURLException;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.net.URL;
 import java.net.URLEncoder;
 import java.util.Random;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
index d6b8962da1..e3bd7f7949 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
@@ -21,26 +21,8 @@
 package org.biojava.nbio.structure.align.client;
 
 
-import java.io.File;
-import java.io.IOException;
-import java.io.Serializable;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Set;
-import java.util.TreeSet;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.biojava.nbio.structure.BioAssemblyIdentifier;
-import org.biojava.nbio.structure.ResidueRange;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIdentifier;
-import org.biojava.nbio.structure.SubstructureIdentifier;
-import org.biojava.nbio.structure.URLIdentifier;
+import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.cath.CathDomain;
 import org.biojava.nbio.structure.cath.CathFactory;
@@ -48,13 +30,21 @@
 import org.biojava.nbio.structure.domain.PDPProvider;
 import org.biojava.nbio.structure.domain.RemotePDPProvider;
 import org.biojava.nbio.structure.ecod.EcodFactory;
-import org.biojava.nbio.core.util.FileDownloadUtils;
 import org.biojava.nbio.structure.scop.ScopDatabase;
 import org.biojava.nbio.structure.scop.ScopDomain;
 import org.biojava.nbio.structure.scop.ScopFactory;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.File;
+import java.io.IOException;
+import java.io.Serializable;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
 
 /**
  * A utility class that makes working with names of structures, domains and ranges easier.
@@ -74,7 +64,7 @@ public class StructureName implements Comparable<StructureName>, Serializable, S
 	private static final long serialVersionUID = 4021229518711762957L;
 	private static final Logger logger = LoggerFactory.getLogger(StructureName.class);
 
-	protected String name;
+	protected final String name;
 	protected String pdbId;
 	protected String chainName;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatUserArgumentProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatUserArgumentProcessor.java
index e047d876c9..43272df12a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatUserArgumentProcessor.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatUserArgumentProcessor.java
@@ -34,7 +34,7 @@
 
 
 public class FatCatUserArgumentProcessor extends AbstractUserArgumentProcessor {
-	Logger logger = LoggerFactory.getLogger(FatCatUserArgumentProcessor.class);
+	final Logger logger = LoggerFactory.getLogger(FatCatUserArgumentProcessor.class);
 
 	protected static class FatCatStartupParams extends StartupParameters {
 		int fragLen;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
index eba0840f89..ed93796c66 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
@@ -26,7 +26,9 @@
 
 package org.biojava.nbio.structure.align.fatcat.calc;
 
-import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.AtomImpl;
+import org.biojava.nbio.structure.Calc;
 import org.biojava.nbio.structure.align.model.AFP;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.geometry.SuperPositions;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
index a2775962e7..764d260f23 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
@@ -34,9 +34,8 @@
 import org.biojava.nbio.structure.geometry.SuperPositions;
 import org.biojava.nbio.structure.jama.Matrix;
 
-import java.util.List;
-
 import javax.vecmath.Matrix4d;
+import java.util.List;
 
 /** a class to chain AFPs to an alignment
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
index 203c004b91..1913558747 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
@@ -27,11 +27,14 @@
 package org.biojava.nbio.structure.align.fatcat.calc;
 
 
-import javax.vecmath.Matrix4d;
-
-import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Calc;
+import org.biojava.nbio.structure.Group;
+import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.geometry.SuperPositions;
 
+import javax.vecmath.Matrix4d;
+
 
 
 public class StructureAlignmentOptimizer
@@ -39,13 +42,13 @@ public class StructureAlignmentOptimizer
 
 	//private static final boolean showAlig = false;
 
-	int pro1Len;
-	int pro2Len;
-	int maxLen;
-	Atom[] cod1;
-	Atom[] cod2;
+	final int pro1Len;
+	final int pro2Len;
+	final int maxLen;
+	final Atom[] cod1;
+	final Atom[] cod2;
 
-	int[][] equSet;
+	final int[][] equSet;
 	int equLen;
 	int equLen0;
 	double[][]sij;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java
index 965bd590a8..dcf65c11c9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java
@@ -36,7 +36,7 @@ public class JointFragments {
 
 		double rms;
 
-		List<int[]> idxlist;
+		final List<int[]> idxlist;
 		public JointFragments(){
 			idxlist = new ArrayList<>();
 			rms = 999;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
index 0ab5aa64a9..4e0675f236 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
@@ -20,12 +20,12 @@
  */
 package org.biojava.nbio.structure.align.multiple;
 
+import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools;
+
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools;
-
 /**
  * General implementation of a {@link Block} that supports any type of
  * sequential alignment with gaps.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java
index aa531a8f01..a6bf88dfcc 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java
@@ -20,9 +20,8 @@
  */
 package org.biojava.nbio.structure.align.multiple;
 
-import java.util.List;
-
 import javax.vecmath.Matrix4d;
+import java.util.List;
 
 /**
  * A BlockSet is a Data Structure to store a flexible alignment part of a
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
index 6b2bbfad86..5246e8a3ad 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
@@ -20,12 +20,11 @@
  */
 package org.biojava.nbio.structure.align.multiple;
 
+import javax.vecmath.Matrix4d;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.vecmath.Matrix4d;
-
 /**
  * A general implementation of a BlockSet to store a flexible part of a multiple
  * alignment.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignment.java
index b4130a3498..5a5157c51a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignment.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignment.java
@@ -20,11 +20,11 @@
  */
 package org.biojava.nbio.structure.align.multiple;
 
-import java.util.List;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureIdentifier;
 
+import java.util.List;
+
 /**
  * A MultipleAlignment is a Data Structure to store the core information of a
  * multiple structure alignment, as a return type.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java
index 24a52d1562..4e754b20d0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java
@@ -20,12 +20,12 @@
  */
 package org.biojava.nbio.structure.align.multiple;
 
-import java.util.List;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureIdentifier;
 import org.biojava.nbio.structure.jama.Matrix;
 
+import java.util.List;
+
 /**
  * A MultipleAlignmentEnsemble is a collection of {@link MultipleAlignment}s
  * that share the same structures (Atoms) and creation properties (algorithm,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
index 484df94c85..aba7567b38 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
@@ -20,14 +20,6 @@
  */
 package org.biojava.nbio.structure.align.multiple;
 
-import java.io.IOException;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.vecmath.Matrix4d;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Calc;
 import org.biojava.nbio.structure.StructureException;
@@ -39,6 +31,13 @@
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.jama.Matrix;
 
+import javax.vecmath.Matrix4d;
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
 /**
  * A general implementation of a {@link MultipleAlignmentEnsemble}.
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
index d2ccafb320..a38d40b232 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
@@ -20,14 +20,14 @@
  */
 package org.biojava.nbio.structure.align.multiple;
 
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIdentifier;
 
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * A general implementation of a {@link MultipleAlignment}.
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/ScoresCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/ScoresCache.java
index c96bbf416d..480255ab53 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/ScoresCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/ScoresCache.java
@@ -20,10 +20,10 @@
  */
 package org.biojava.nbio.structure.align.multiple;
 
-import java.util.Set;
-
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
 
+import java.util.Set;
+
 /**
  * Interface for classes which implement a temporary cache for various numeric
  * scores, e.g. RMSD, TM-Score, etc.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
index 3a87e917d1..c5cb07847d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
@@ -20,17 +20,6 @@
  */
 package org.biojava.nbio.structure.align.multiple.mc;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.SortedSet;
-import java.util.TreeSet;
-import java.util.concurrent.Callable;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.CallableStructureAlignment;
@@ -39,17 +28,13 @@
 import org.biojava.nbio.structure.align.ce.CeCPMain;
 import org.biojava.nbio.structure.align.ce.ConfigStrucAligParams;
 import org.biojava.nbio.structure.align.model.AFPChain;
-import org.biojava.nbio.structure.align.multiple.Block;
-import org.biojava.nbio.structure.align.multiple.BlockImpl;
-import org.biojava.nbio.structure.align.multiple.BlockSet;
-import org.biojava.nbio.structure.align.multiple.BlockSetImpl;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
+import org.biojava.nbio.structure.align.multiple.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.*;
+import java.util.concurrent.*;
+
 /**
  * Main class of the Java implementation of the Combinatorial Extension -
  * Monte Carlo (CEMC) Algorithm,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
index 5b331f7ae5..d154faa95d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -20,16 +20,6 @@
  */
 package org.biojava.nbio.structure.align.multiple.mc;
 
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.Random;
-import java.util.SortedSet;
-import java.util.TreeSet;
-import java.util.concurrent.Callable;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.multiple.Block;
@@ -44,6 +34,11 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.*;
+import java.util.concurrent.Callable;
+
 /**
  * This class takes a MultipleAlignment seed previously generated and runs a
  * Monte Carlo optimization in order to improve the overall score and highlight
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcParameters.java
index d70ce9ceff..d56f16ed3c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcParameters.java
@@ -20,12 +20,12 @@
  */
 package org.biojava.nbio.structure.align.multiple.mc;
 
+import org.biojava.nbio.structure.align.ce.ConfigStrucAligParams;
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Random;
 
-import org.biojava.nbio.structure.align.ce.ConfigStrucAligParams;
-
 /**
  * Contains the parameters to be sent to the MC optimization.
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java
index de74dc2549..79a80089a7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java
@@ -20,11 +20,6 @@
  */
 package org.biojava.nbio.structure.align.multiple.util;
 
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.vecmath.Matrix4d;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Calc;
 import org.biojava.nbio.structure.StructureTools;
@@ -34,6 +29,10 @@
 import org.biojava.nbio.structure.geometry.SuperPositionSVD;
 import org.biojava.nbio.structure.geometry.SuperPositions;
 
+import javax.vecmath.Matrix4d;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Superimposes the core aligned residues of every structure in a
  * {@link MultipleAlignment} onto a reference structure. This method
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.java
index d3fe14ba20..e7cc54f711 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.java
@@ -26,7 +26,6 @@
 import org.slf4j.LoggerFactory;
 
 import javax.vecmath.Matrix4d;
-
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
index d3f91cf501..3f0827edd3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
@@ -20,16 +20,16 @@
  */
 package org.biojava.nbio.structure.align.multiple.util;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Calc;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
 import org.biojava.nbio.structure.jama.Matrix;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
 /**
  * Utility class for calculating common scores of {@link MultipleAlignment}s.
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
index bb67cbc64a..2a01044f85 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
@@ -20,17 +20,6 @@
  */
 package org.biojava.nbio.structure.align.multiple.util;
 
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import javax.vecmath.Matrix4d;
-
 import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.AccessionID;
@@ -40,17 +29,7 @@
 import org.biojava.nbio.phylo.DistanceMatrixCalculator;
 import org.biojava.nbio.phylo.TreeConstructor;
 import org.biojava.nbio.phylo.TreeConstructorType;
-import org.biojava.nbio.structure.AminoAcid;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.PDBHeader;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIdentifier;
-import org.biojava.nbio.structure.StructureImpl;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.multiple.Block;
 import org.biojava.nbio.structure.align.multiple.BlockSet;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
@@ -59,6 +38,10 @@
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.phylogeny.Phylogeny;
 
+import javax.vecmath.Matrix4d;
+import java.io.IOException;
+import java.util.*;
+
 /**
  * Utility functions for working with {@link MultipleAlignment}.
  * <p>
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
index ffd7408a04..8f7e4cd6c5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
@@ -20,25 +20,20 @@
  */
 package org.biojava.nbio.structure.align.multiple.util;
 
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.io.StringWriter;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.vecmath.Matrix4d;
-
 import org.biojava.nbio.core.util.PrettyXMLWriter;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.ResidueRange;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIdentifier;
-import org.biojava.nbio.structure.SubstructureIdentifier;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.multiple.Block;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble;
 import org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter;
 
+import javax.vecmath.Matrix4d;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * This class contains functions for the conversion of {@link MultipleAlignment}
  * to various String outputs.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.java
index 9a0a32ea37..815e50c055 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.java
@@ -20,11 +20,11 @@
  */
 package org.biojava.nbio.structure.align.multiple.util;
 
-import java.util.List;
-
 import org.biojava.nbio.structure.align.multiple.BlockSet;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
 
+import java.util.List;
+
 /**
  * Interface for Multiple Alignment superposition algorithms.
  * <p>
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java
index c7b0c57192..080b38144c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java
@@ -20,11 +20,6 @@
  */
 package org.biojava.nbio.structure.align.multiple.util;
 
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.vecmath.Matrix4d;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Calc;
 import org.biojava.nbio.structure.StructureTools;
@@ -34,6 +29,10 @@
 import org.biojava.nbio.structure.geometry.SuperPositionSVD;
 import org.biojava.nbio.structure.geometry.SuperPositions;
 
+import javax.vecmath.Matrix4d;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Superimposes each structure in a {@link MultipleAlignment} onto a reference
  * structure.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
index e8fe142693..e3592d0491 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
@@ -34,13 +34,11 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix4d;
 import java.io.Serializable;
 import java.text.DecimalFormat;
 import java.util.List;
 
-
-import javax.vecmath.Matrix4d;
-
 /**
  * Implements a class which handles one possible (alternative) solution.
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java
index 83ed3ffaae..5f0125acd6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java
@@ -37,9 +37,9 @@
  * @version %I% %G%
  */
 public class Gotoh {
-	public static int ALIGFACTOR = 1000; // constant to shift floats to ints
+	public static final int ALIGFACTOR = 1000; // constant to shift floats to ints
 
-	Alignable a;
+	final Alignable a;
 
 	int k,openPen,elgPen,rowDim,colDim,openVal,elgVal;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java
index 295820deed..516ab3cbce 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java
@@ -20,40 +20,21 @@
  */
 package org.biojava.nbio.structure.align.quaternary;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import javax.vecmath.Matrix4d;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureTools;
-import org.biojava.nbio.structure.align.multiple.Block;
-import org.biojava.nbio.structure.align.multiple.BlockImpl;
-import org.biojava.nbio.structure.align.multiple.BlockSet;
-import org.biojava.nbio.structure.align.multiple.BlockSetImpl;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.align.multiple.*;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
 import org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer;
-import org.biojava.nbio.structure.cluster.Subunit;
-import org.biojava.nbio.structure.cluster.SubunitCluster;
-import org.biojava.nbio.structure.cluster.SubunitClusterer;
-import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
-import org.biojava.nbio.structure.cluster.SubunitExtractor;
+import org.biojava.nbio.structure.cluster.*;
 import org.biojava.nbio.structure.contact.Pair;
 import org.biojava.nbio.structure.geometry.SuperPositions;
 import org.biojava.nbio.structure.geometry.UnitQuaternions;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix4d;
+import java.util.*;
+import java.util.Map.Entry;
+
 /**
  * Quaternary Structure Alignment (QS-Align). The algorithm takes as input two
  * protein structures at the quaternary structure level (multiple chains or
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
index 086928bc72..a4d4663b86 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
@@ -20,20 +20,19 @@
  */
 package org.biojava.nbio.structure.align.quaternary;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
-import java.util.stream.Collectors;
-
-import javax.vecmath.Matrix4d;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
 import org.biojava.nbio.structure.cluster.Subunit;
 import org.biojava.nbio.structure.cluster.SubunitCluster;
 
+import javax.vecmath.Matrix4d;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
 /**
  * Result of a Quaternary Structure Alignment {@link QsAlign}. The QsAlignResult
  * holds the original inputs of the algorithm and the results and scores of the
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java
index ed127b7529..f050b855d4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java
@@ -23,11 +23,16 @@
 import org.biojava.nbio.alignment.Alignments;
 import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
 import org.biojava.nbio.alignment.SimpleGapPenalty;
-import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.alignment.template.GapPenalty;
 import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
+import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.SequencePair;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
+import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
+import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
+import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.StructureException;
@@ -41,11 +46,6 @@
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AFPAlignmentDisplay;
 import org.biojava.nbio.structure.align.util.AlignmentTools;
-import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
-import org.biojava.nbio.core.sequence.ProteinSequence;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
-import org.biojava.nbio.core.sequence.template.Compound;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
index 6f53fd69c3..c24cdfefb5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
@@ -28,11 +28,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix4d;
 import java.lang.reflect.InvocationTargetException;
 import java.util.*;
 
-import javax.vecmath.Matrix4d;
-
 
 public class AFPAlignmentDisplay
 {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPChainScorer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPChainScorer.java
index 7453a38813..e711f3f4a9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPChainScorer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPChainScorer.java
@@ -25,8 +25,6 @@
 package org.biojava.nbio.structure.align.util;
 
 
-import javax.vecmath.Matrix4d;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Calc;
 import org.biojava.nbio.structure.StructureException;
@@ -35,6 +33,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix4d;
+
 public class AFPChainScorer {
 
 	private static final Logger logger = LoggerFactory.getLogger(AFPChainScorer.class);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
index aa52b671c2..cd80048cbb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -33,6 +33,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix4d;
 import java.io.IOException;
 import java.io.Writer;
 import java.util.*;
@@ -40,8 +41,6 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import javax.vecmath.Matrix4d;
-
 /**
  * Methods for analyzing and manipulating AFPChains and for
  * other pairwise alignment utilities. <p>
@@ -57,7 +56,7 @@ public class AlignmentTools {
 	private static final Logger logger = LoggerFactory.getLogger(AlignmentTools.class);
 
 
-	public static boolean debug = false;
+	public static final boolean debug = false;
 
 	/**
 	 * Checks that the alignment given by afpChain is sequential. This means
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index 8584c901b1..4b6112c72c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -20,13 +20,7 @@
  */
 package org.biojava.nbio.structure.align.util;
 
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.List;
-import java.util.TreeSet;
-
+import org.biojava.nbio.core.util.FileDownloadUtils;
 import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.client.StructureName;
@@ -41,17 +35,18 @@
 import org.biojava.nbio.structure.io.MMCIFFileReader;
 import org.biojava.nbio.structure.io.MMTFFileReader;
 import org.biojava.nbio.structure.io.PDBFileReader;
-import org.biojava.nbio.core.util.FileDownloadUtils;
 import org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder;
 import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
-import org.biojava.nbio.structure.scop.CachedRemoteScopInstallation;
-import org.biojava.nbio.structure.scop.ScopDatabase;
-import org.biojava.nbio.structure.scop.ScopDescription;
-import org.biojava.nbio.structure.scop.ScopDomain;
-import org.biojava.nbio.structure.scop.ScopFactory;
+import org.biojava.nbio.structure.scop.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.ConcurrentHashMap;
+
 /**
  * A utility class that provides easy access to Structure objects. If you are running a script that is frequently
  * re-using the same PDB structures, the AtomCache keeps an in-memory cache of the files for quicker access. The cache
@@ -92,7 +87,8 @@ public class AtomCache {
 	private String cachePath;
 
 	// make sure IDs are loaded uniquely
-	private final Collection<String> currentlyLoading = Collections.synchronizedCollection(new TreeSet<>());
+	//private final Collection<String> currentlyLoading = Collections.newSetFromMap(new ConcurrentHashMap());
+	private final Map<String,Structure> map = new ConcurrentHashMap();
 
 	private String path;
 
@@ -147,7 +143,7 @@ public AtomCache(String pdbFilePath, String cachePath) {
 		fetchBehavior = FetchBehavior.DEFAULT;
 		obsoleteBehavior = ObsoleteBehavior.DEFAULT;
 
-		currentlyLoading.clear();
+//		currentlyLoading.clear();
 		params = new FileParsingParameters();
 
 		setUseMmCif(false);
@@ -778,22 +774,23 @@ public boolean isUseMmCif() {
 	 * @param useMmCif
 	 *            the useMmCif to set
 	 */
-	public void setUseMmCif(boolean useMmCif) {
+	@Deprecated public void setUseMmCif(boolean useMmCif) {
 		this.useMmCif = useMmCif;
 		// Either way the user wants to use PDB or MMCIF
 		this.useMmtf = false;
+		map.clear();
 	}
 
 	/**
 	 * Set whether to use mmtf.
 	 * @param useMmtf the input boolean to set
 	 */
-	public void setUseMmtf(boolean useMmtf) {
+	@Deprecated public void setUseMmtf(boolean useMmtf) {
 		this.useMmtf = useMmtf;
 		if(useMmtf){
 			useMmCif=false;
 		}
-
+		map.clear();
 	}
 
 	/** Returns useMmtf flag
@@ -804,10 +801,9 @@ public boolean isUseMmtf(){
 		return this.useMmtf;
 	}
 
-	private boolean checkLoading(String name) {
-		return currentlyLoading.contains(name);
-
-	}
+//	private boolean checkLoading(String name) {
+//		return currentlyLoading.contains(name);
+//	}
 
 	/**
 	 * Returns a {@link Structure} corresponding to the CATH identifier supplied in {@code structureName}, using the the {@link CathDatabase}
@@ -844,17 +840,13 @@ public Structure getStructureForCathDomain(StructureName structureName, CathData
 		return n;
 	}
 
-	protected void flagLoading(String name) {
-		if (!currentlyLoading.contains(name)) {
-
-			currentlyLoading.add(name);
-		}
-	}
-
-	protected void flagLoadingFinished(String name) {
-
-		currentlyLoading.remove(name);
-	}
+//	protected void flagLoading(String name) {
+//		currentlyLoading.add(name);
+//	}
+//
+//	protected void flagLoadingFinished(String name) {
+//		currentlyLoading.remove(name);
+//	}
 
 	/**
 	 * Loads a structure directly by PDB ID
@@ -864,35 +856,40 @@ protected void flagLoadingFinished(String name) {
 	 * @throws StructureException
 	 */
 	public Structure getStructureForPdbId(String pdbId) throws IOException, StructureException {
+
 		if(pdbId == null)
 			return null;
-		if(pdbId.length() != 4) {
+
+		if(pdbId.length() != 4)
 			throw new StructureException("Unrecognized PDB ID: "+pdbId);
-		}
-		while (checkLoading(pdbId)) {
-			// waiting for loading to be finished...
 
-			try {
-				Thread.sleep(100);
-			} catch (InterruptedException e) {
-				logger.error(e.getMessage());
-			}
+//		while (checkLoading(pdbId)) {
+//			// waiting for loading to be finished...
+//
+//			try {
+//				Thread.sleep(100);
+//			} catch (InterruptedException e) {
+//				logger.error(e.getMessage());
+//			}
+//
+//		}
 
-		}
 
-		Structure s;
-		if (useMmtf) {
-			logger.debug("loading from mmtf");
-			s = loadStructureFromMmtfByPdbId(pdbId);
-		}
-		else if (useMmCif) {
-			logger.debug("loading from mmcif");
-			s = loadStructureFromCifByPdbId(pdbId);
-		} else {
-			logger.debug("loading from pdb");
-			s = loadStructureFromPdbByPdbId(pdbId);
-		}
-		return s;
+		return map.computeIfAbsent(pdbId, p->{
+			try {
+				if (useMmtf)
+					return loadStructureFromMmtfByPdbId(pdbId);
+				else if (useMmCif)
+					return loadStructureFromCifByPdbId(pdbId);
+				else
+					return loadStructureFromPdbByPdbId(pdbId);
+			} catch (Exception e) {
+				//TODO wrap exception e as a structure for storage in the cache
+
+				e.printStackTrace();
+				return null;
+			}
+		});
 	}
 
 	/**
@@ -906,25 +903,24 @@ private Structure loadStructureFromMmtfByPdbId(String pdbId) throws IOException
 		MMTFFileReader reader = new MMTFFileReader();
 		reader.setFetchBehavior(fetchBehavior);
 		reader.setObsoleteBehavior(obsoleteBehavior);
-		Structure structure = reader.getStructureById(pdbId.toLowerCase());
-		return structure;
+		return reader.getStructureById(pdbId.toLowerCase());
 	}
 
 	protected Structure loadStructureFromCifByPdbId(String pdbId) throws IOException {
 
 		logger.debug("Loading structure {} from mmCIF file {}.", pdbId, path);
 		Structure s;
-		flagLoading(pdbId);
-		try {
+//		flagLoading(pdbId);
+//		try {
 			MMCIFFileReader reader = new MMCIFFileReader(path);
 			reader.setFetchBehavior(fetchBehavior);
 			reader.setObsoleteBehavior(obsoleteBehavior);
 			reader.setFileParsingParameters(params);
 			s = reader.getStructureById(pdbId.toLowerCase());
 
-		} finally {
-			flagLoadingFinished(pdbId);
-		}
+//		} finally {
+//			flagLoadingFinished(pdbId);
+//		}
 
 		return s;
 	}
@@ -933,8 +929,8 @@ protected Structure loadStructureFromPdbByPdbId(String pdbId) throws IOException
 
 		logger.debug("Loading structure {} from PDB file {}.", pdbId, path);
 		Structure s;
-		flagLoading(pdbId);
-		try {
+//		flagLoading(pdbId);
+//		try {
 			PDBFileReader reader = new PDBFileReader(path);
 			reader.setFetchBehavior(fetchBehavior);
 			reader.setObsoleteBehavior(obsoleteBehavior);
@@ -943,9 +939,9 @@ protected Structure loadStructureFromPdbByPdbId(String pdbId) throws IOException
 
 			s = reader.getStructureById(pdbId.toLowerCase());
 
-		} finally {
-			flagLoadingFinished(pdbId);
-		}
+//		} finally {
+//			flagLoadingFinished(pdbId);
+//		}
 
 		return s;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/RotationAxis.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/RotationAxis.java
index 74b361ba87..1f53ff9fcf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/RotationAxis.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/RotationAxis.java
@@ -20,13 +20,6 @@
  */
 package org.biojava.nbio.structure.align.util;
 
-import java.io.StringWriter;
-
-import javax.vecmath.AxisAngle4d;
-import javax.vecmath.Matrix3d;
-import javax.vecmath.Matrix4d;
-import javax.vecmath.Vector3d;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.AtomImpl;
 import org.biojava.nbio.structure.Calc;
@@ -36,6 +29,12 @@
 import org.biojava.nbio.structure.geometry.Matrices;
 import org.biojava.nbio.structure.jama.Matrix;
 
+import javax.vecmath.AxisAngle4d;
+import javax.vecmath.Matrix3d;
+import javax.vecmath.Matrix4d;
+import javax.vecmath.Vector3d;
+import java.io.StringWriter;
+
 /**
  * Calculates the rotation axis for an alignment
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/SynchronizedOutFile.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/SynchronizedOutFile.java
index 7160005bca..3c3f79b973 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/SynchronizedOutFile.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/SynchronizedOutFile.java
@@ -30,7 +30,7 @@ public class SynchronizedOutFile {
 
 	String[] tmp;
 
-	int ARR_SIZE=100;
+	final int ARR_SIZE=100;
 	Integer counter;
 
 	boolean useGzipCompression;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
index 021c461c1e..b1e1635937 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
@@ -19,11 +19,11 @@
 
 package org.biojava.nbio.structure.align.util;
 
+import org.biojava.nbio.core.util.PrettyXMLWriter;
+import org.biojava.nbio.core.util.XMLWriter;
 import org.biojava.nbio.structure.align.ce.StartupParameters;
 import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
 import org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior;
-import org.biojava.nbio.core.util.PrettyXMLWriter;
-import org.biojava.nbio.core.util.XMLWriter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java
index 10b973cb0f..9de9e327c8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java
@@ -20,12 +20,12 @@
  */
 package org.biojava.nbio.structure.align.xml;
 
+import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AlignmentTools;
 import org.biojava.nbio.structure.jama.Matrix;
-import org.biojava.nbio.core.util.PrettyXMLWriter;
 
 import java.io.IOException;
 import java.io.PrintWriter;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLConverter.java
index 84c53f1c39..ce286f52ee 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLConverter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLConverter.java
@@ -20,20 +20,15 @@
  */
 package org.biojava.nbio.structure.align.xml;
 
-import java.io.IOException;
-import java.util.List;
-
-import javax.vecmath.Matrix4d;
-
 import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.biojava.nbio.structure.StructureIdentifier;
-import org.biojava.nbio.structure.align.multiple.Block;
-import org.biojava.nbio.structure.align.multiple.BlockSet;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble;
-import org.biojava.nbio.structure.align.multiple.ScoresCache;
+import org.biojava.nbio.structure.align.multiple.*;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
 
+import javax.vecmath.Matrix4d;
+import java.io.IOException;
+import java.util.List;
+
 /**
  * Helper methods to convert all the hierarchy levels of a MultipleAlignment
  * into an XML format.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java
index a8526fd6cd..8bc695a9f8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java
@@ -20,27 +20,9 @@
  */
 package org.biojava.nbio.structure.align.xml;
 
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.vecmath.Matrix4d;
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-
 import org.biojava.nbio.structure.StructureIdentifier;
 import org.biojava.nbio.structure.align.client.StructureName;
-import org.biojava.nbio.structure.align.multiple.Block;
-import org.biojava.nbio.structure.align.multiple.BlockImpl;
-import org.biojava.nbio.structure.align.multiple.BlockSet;
-import org.biojava.nbio.structure.align.multiple.BlockSetImpl;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
-import org.biojava.nbio.structure.align.multiple.ScoresCache;
+import org.biojava.nbio.structure.align.multiple.*;
 import org.w3c.dom.Document;
 import org.w3c.dom.NamedNodeMap;
 import org.w3c.dom.Node;
@@ -48,6 +30,15 @@
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
+import javax.vecmath.Matrix4d;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import java.io.IOException;
+import java.io.StringReader;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Parse an XML file representing a {@link MultipleAlignmentEnsemble}, so
  * that the original alignment can be recovered.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.java
index afcc4f95ac..ca7292356f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.java
@@ -20,9 +20,9 @@
  */
 package org.biojava.nbio.structure.align.xml;
 
+import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.biojava.nbio.structure.align.client.PdbPair;
 import org.biojava.nbio.structure.align.fatcat.FatCatRigid;
-import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.w3c.dom.Document;
 import org.w3c.dom.NamedNodeMap;
 import org.w3c.dom.Node;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java
index 031b635628..e0e17466c1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java
@@ -21,34 +21,25 @@
  */
 package org.biojava.nbio.structure.basepairs;
 
-import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Chain;
 import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.contact.Pair;
 import org.biojava.nbio.structure.geometry.SuperPosition;
 import org.biojava.nbio.structure.geometry.SuperPositionQCP;
 import org.biojava.nbio.structure.io.PDBFileReader;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.Serializable;
-import java.util.List;
-import java.util.Arrays;
-import java.util.ArrayList;
-import java.util.Map;
-import java.util.HashMap;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+import java.util.*;
 
-import static java.lang.Math.sin;
-import static java.lang.Math.cos;
-import static java.lang.Math.atan2;
-import static java.lang.Math.acos;
-import static java.lang.Math.PI;
+import static java.lang.Math.*;
 
 /**
  * This module calculates the el Hassan-Calladine Base Pairing and Base-pair Step Parameters for any nucleic
@@ -154,8 +145,8 @@ public class BasePairParameters implements Serializable {
 	protected String pairSequence = "";
 	protected double[][] pairingParameters;
 	protected double[][] stepParameters;
-	protected List<String> pairingNames = new ArrayList<>();
-	protected List<Matrix4d> referenceFrames = new ArrayList<>();
+	protected final List<String> pairingNames = new ArrayList<>();
+	protected final List<Matrix4d> referenceFrames = new ArrayList<>();
 
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathDomain.java
index 891b9ec1bc..57657de8d5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathDomain.java
@@ -27,20 +27,12 @@
  * @author Daniel Asarnow
  */
 
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.align.util.AtomCache;
+
 import java.io.IOException;
 import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.biojava.nbio.structure.ResidueRange;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIdentifier;
-import org.biojava.nbio.structure.SubstructureIdentifier;
-import org.biojava.nbio.structure.align.util.AtomCache;
+import java.util.*;
 
 /**
  * A class which represents a single CATH domain.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
index ba6017cffb..07ff9b3ffd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
@@ -23,11 +23,11 @@
 
 package org.biojava.nbio.structure.cath;
 
-import org.biojava.nbio.structure.align.util.UserConfiguration;
 import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.InputStreamProvider;
+import org.biojava.nbio.structure.align.util.UserConfiguration;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.biojava.nbio.core.util.InputStreamProvider;
 
 import java.io.*;
 import java.net.URL;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
index 9ea7474b5f..428d1d62a2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
@@ -30,23 +30,12 @@
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.EntityInfo;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.StructureAlignment;
 import org.biojava.nbio.structure.align.StructureAlignmentFactory;
 import org.biojava.nbio.structure.align.ce.ConfigStrucAligParams;
 import org.biojava.nbio.structure.align.model.AFPChain;
-import org.biojava.nbio.structure.align.multiple.Block;
-import org.biojava.nbio.structure.align.multiple.BlockImpl;
-import org.biojava.nbio.structure.align.multiple.BlockSet;
-import org.biojava.nbio.structure.align.multiple.BlockSetImpl;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
+import org.biojava.nbio.structure.align.multiple.*;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
 import org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
@@ -58,7 +47,10 @@
 
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
 import java.util.stream.Collectors;
 
 /**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
index 6295f8fdf0..8de30076dd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
@@ -20,9 +20,6 @@
  */
 package org.biojava.nbio.structure.cluster;
 
-import java.util.ArrayList;
-import java.util.List;
-
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
@@ -30,6 +27,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * The SubunitClusterer takes as input a collection of {@link Subunit} and
  * returns a collection of {@link SubunitCluster}.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java
index 7071a028ad..e3b7928cd6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java
@@ -20,7 +20,10 @@
  */
 package org.biojava.nbio.structure.cluster;
 
-import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Chain;
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureTools;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomContact.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomContact.java
index 042ae7cc83..bb657cd80c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomContact.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomContact.java
@@ -20,10 +20,10 @@
  */
 package org.biojava.nbio.structure.contact;
 
-import java.io.Serializable;
-
 import org.biojava.nbio.structure.Atom;
 
+import java.io.Serializable;
+
 /**
  * A pair of atoms that are in contact
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java
index 9a9b9a613e..316ed8c1ca 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java
@@ -140,8 +140,8 @@ public BoundingBox(BoundingBox[] boxes) {
 	}
 
 	private static class Bound implements Comparable<Bound> {
-		int cardinal;
-		double value;
+		final int cardinal;
+		final double value;
 		public Bound(int cardinal,double value) {
 			this.cardinal = cardinal;
 			this.value = value;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java
index 9fa884df10..52ab85f48d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java
@@ -21,16 +21,15 @@
 package org.biojava.nbio.structure.contact;
 
 
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Calc;
+
+import javax.vecmath.Point3d;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
 
-import javax.vecmath.Point3d;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Calc;
-
 
 /**
  * A grid to be used for calculating atom contacts through a spatial hashing algorithm.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java
index f025ac5fda..05b6033a00 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java
@@ -20,11 +20,10 @@
  */
 package org.biojava.nbio.structure.contact;
 
+import javax.vecmath.Point3d;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.vecmath.Point3d;
-
 
 /**
  * A grid cell to be used in contact calculation via spatial hashing algorithm.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/ResidueIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/ResidueIdentifier.java
index 5fa0dbd179..073e4b4016 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/ResidueIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/ResidueIdentifier.java
@@ -20,14 +20,14 @@
  */
 package org.biojava.nbio.structure.contact;
 
-import java.io.Serializable;
-
 import org.biojava.nbio.structure.Chain;
 import org.biojava.nbio.structure.EntityInfo;
 import org.biojava.nbio.structure.Group;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.Serializable;
+
 /**
  * A bean for identifying groups in GroupContactSets.
  * Used only within the contact package to be able to compare
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
index cd29c164e0..05165bf825 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
@@ -20,20 +20,7 @@
  */
 package org.biojava.nbio.structure.contact;
 
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Element;
-import org.biojava.nbio.structure.EntityInfo;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.GroupType;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.asa.AsaCalculator;
 import org.biojava.nbio.structure.asa.GroupAsa;
 import org.biojava.nbio.structure.io.FileConvert;
@@ -47,6 +34,12 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
 
 /**
  * An interface between 2 molecules (2 sets of atoms).
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
index 8211c61688..319de6b279 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
@@ -20,16 +20,6 @@
  */
 package org.biojava.nbio.structure.contact;
 
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Optional;
-import java.util.Set;
-import java.util.TreeMap;
-
 import org.biojava.nbio.core.util.SingleLinkageClusterer;
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Structure;
@@ -38,6 +28,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.Serializable;
+import java.util.*;
+
 
 /**
  * A list of interfaces between 2 molecules (2 sets of atoms)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/DomainProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/DomainProvider.java
index c736af4eb3..81fb6f2754 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/DomainProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/DomainProvider.java
@@ -20,11 +20,11 @@
  */
 package org.biojava.nbio.structure.domain;
 
+import org.biojava.nbio.structure.StructureException;
+
 import java.io.IOException;
 import java.util.SortedSet;
 
-import org.biojava.nbio.structure.StructureException;
-
 /**
  * Decomposes a structure from the PDB into representative domains
  */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java
index 947557eef6..6ca44efaa1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java
@@ -20,18 +20,14 @@
  */
 package org.biojava.nbio.structure.domain;
 
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.align.util.AtomCache;
+
 import java.io.IOException;
 import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.biojava.nbio.structure.ResidueRange;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIdentifier;
-import org.biojava.nbio.structure.SubstructureIdentifier;
-import org.biojava.nbio.structure.align.util.AtomCache;
-
 public class PDPDomain implements StructureIdentifier {
 	private static final long serialVersionUID = 6894463080739943026L;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPProvider.java
index 79e91bc835..12b9569860 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPProvider.java
@@ -24,13 +24,13 @@
  */
 package org.biojava.nbio.structure.domain;
 
-import java.io.IOException;
-import java.util.SortedSet;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.util.AtomCache;
 
+import java.io.IOException;
+import java.util.SortedSet;
+
 /**
  * Decomposes a structure into representative PDP domains.
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java
index 541ae282f2..c997360ce5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java
@@ -20,12 +20,6 @@
  */
 package org.biojava.nbio.structure.domain;
 
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.*;
-
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.client.JFatCatClient;
 import org.biojava.nbio.structure.align.client.StructureName;
@@ -37,6 +31,12 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.*;
+
 
 /**
  * A DomainProvider that uses a mixture of SCOP and PDP domains.
@@ -50,7 +50,7 @@
 public class RemoteDomainProvider extends SerializableCache<String,SortedSet<String>> implements DomainProvider{
 	private static final Logger logger = LoggerFactory.getLogger(RemoteDomainProvider.class);
 
-	public String url = RemotePDPProvider.DEFAULT_SERVER;
+	public final String url = RemotePDPProvider.DEFAULT_SERVER;
 
 	ScopDatabase scop;
 	PDPProvider pdp;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
index 0e92516846..05824c3483 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
@@ -24,12 +24,6 @@
  */
 package org.biojava.nbio.structure.domain;
 
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.*;
-
 import org.biojava.nbio.structure.ResidueRange;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
@@ -41,6 +35,12 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.*;
+
 
 /** A class that provided PDP assignments that are loaded from a remote web server
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/SerializableCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/SerializableCache.java
index 7377f82a7f..33472d468d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/SerializableCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/SerializableCache.java
@@ -42,7 +42,7 @@ public class SerializableCache <K,V>{
 
 	private static final Logger logger = LoggerFactory.getLogger(SerializableCache.class);
 
-	protected String cacheFileName;
+	protected final String cacheFileName;
 	protected Map<K,V> serializedCache ;
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Cut.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Cut.java
index a845ce1304..03a849100e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Cut.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Cut.java
@@ -26,7 +26,7 @@
 
 public class Cut {
 
-	static boolean verbose = CutDomain.verbose;
+	static final boolean verbose = CutDomain.verbose;
 
 	public static int cut(Atom[] ca, Domain dom, CutValues val, int[][] dist, PDPDistanceMatrix pdpMatrix) {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/CutDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/CutDomain.java
index 870882fe75..be07f49992 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/CutDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/CutDomain.java
@@ -30,12 +30,12 @@ public class CutDomain {
 
 	int ndom;
 
-	List<Domain> domains;
+	final List<Domain> domains;
 
-	public static boolean verbose = true;
+	public static final boolean verbose = true;
 
-	int[][] dist;
-	Atom[] ca;
+	final int[][] dist;
+	final Atom[] ca;
 
 	public CutDomain(Atom[]ca, PDPDistanceMatrix pdpMatrix){
 		dist = pdpMatrix.getDist();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java
index f2038754b8..cdabc26922 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java
@@ -20,7 +20,10 @@
  */
 package org.biojava.nbio.structure.domain.pdp;
 
-import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.AminoAcid;
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Calc;
+import org.biojava.nbio.structure.Group;
 
 
 public class GetDistanceMatrix {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
index 1ecf094845..34121ac9cf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
@@ -20,6 +20,12 @@
  */
 package org.biojava.nbio.structure.ecod;
 
+import org.biojava.nbio.structure.align.util.UserConfiguration;
+import org.biojava.nbio.structure.cath.CathFactory;
+import org.biojava.nbio.structure.scop.ScopFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import java.io.IOException;
 import java.lang.ref.SoftReference;
 import java.util.Collections;
@@ -28,12 +34,6 @@
 import java.util.Map;
 import java.util.Map.Entry;
 
-import org.biojava.nbio.structure.align.util.UserConfiguration;
-import org.biojava.nbio.structure.cath.CathFactory;
-import org.biojava.nbio.structure.scop.ScopFactory;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 /**
  * Controls global {@link EcodDatabase EcodDatabases} being used.
  * Implements a multiton pattern through {@link #getEcodDatabase(String)},
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
index e229da576e..214d22fe7b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
@@ -20,33 +20,20 @@
 
 package org.biojava.nbio.structure.ecod;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.Reader;
+import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.structure.align.util.UserConfiguration;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.*;
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Collections;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.LinkedHashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
 import java.util.concurrent.locks.ReadWriteLock;
 import java.util.concurrent.locks.ReentrantReadWriteLock;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.biojava.nbio.structure.align.util.UserConfiguration;
-import org.biojava.nbio.core.util.FileDownloadUtils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 /**
  * Provides access to the Evolutionary Classification of Protein Domains (ECOD).
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java
index c1cfeb73e1..894a6a9178 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java
@@ -20,12 +20,12 @@
  */
 package org.biojava.nbio.structure.geometry;
 
+import org.biojava.nbio.structure.jama.Matrix;
+
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
 
-import org.biojava.nbio.structure.jama.Matrix;
-
 /**
  * Utility operations on Point3d.
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/Matrices.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/Matrices.java
index a00af40fd8..949347da46 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/Matrices.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/Matrices.java
@@ -20,12 +20,12 @@
  */
 package org.biojava.nbio.structure.geometry;
 
+import org.biojava.nbio.structure.jama.Matrix;
+
 import javax.vecmath.Matrix3d;
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Vector3d;
 
-import org.biojava.nbio.structure.jama.Matrix;
-
 /**
  * Matrices contains static methods to operate and transform matrices used in 3D
  * geometry (transformation matrices and rotation matrices).
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
index 10d6d224a2..f33d85516e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
@@ -27,7 +27,6 @@
 import javax.vecmath.Matrix3d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
-
 import java.util.ArrayList;
 import java.util.List;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
index 8b7c2a65dc..9ce2bdad6f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
@@ -21,14 +21,14 @@
 
 package org.biojava.nbio.structure.geometry;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import javax.vecmath.Matrix3d;
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 /**
  * Implementation of the Quaternion-Based Characteristic Polynomial algorithm
  * for RMSD and Superposition calculations.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQuat.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQuat.java
index 6003530a39..9311dca32e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQuat.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQuat.java
@@ -20,7 +20,10 @@
  */
 package org.biojava.nbio.structure.geometry;
 
-import javax.vecmath.*;
+import javax.vecmath.Matrix4d;
+import javax.vecmath.Point3d;
+import javax.vecmath.Quat4d;
+import javax.vecmath.Vector3d;
 
 /**
  * The SuperPositionQuat implements a quaternion based algorithm to superpose
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionSVD.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionSVD.java
index d0fbb6adca..2a12d2dc11 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionSVD.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionSVD.java
@@ -22,13 +22,13 @@
  */
 package org.biojava.nbio.structure.geometry;
 
+import org.biojava.nbio.structure.jama.Matrix;
+import org.biojava.nbio.structure.jama.SingularValueDecomposition;
+
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
 
-import org.biojava.nbio.structure.jama.Matrix;
-import org.biojava.nbio.structure.jama.SingularValueDecomposition;
-
 /**
  * A class that calculates the superposition between two sets of points using an
  * SVD Matrix Decomposition. It was introduced by Wolfgang Kabsch, hence the
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/UnitQuaternions.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/UnitQuaternions.java
index 0e31e101a5..5ab2cb8788 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/UnitQuaternions.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/UnitQuaternions.java
@@ -20,13 +20,13 @@
  */
 package org.biojava.nbio.structure.geometry;
 
+import org.biojava.nbio.structure.jama.EigenvalueDecomposition;
+import org.biojava.nbio.structure.jama.Matrix;
+
 import javax.vecmath.AxisAngle4d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Quat4d;
 
-import org.biojava.nbio.structure.jama.EigenvalueDecomposition;
-import org.biojava.nbio.structure.jama.Matrix;
-
 /**
  * UnitQuaternions is a static Class that contains methods for calculating and
  * using unit quaternions. It assumes the use of {@link Quat4d} Class from
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
index ad28c5550b..22e523a64a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
@@ -32,12 +32,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
 
 /**
  * Adds polymer bonds for peptides and nucleotides based on distance cutoffs and
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/ChargeAdder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/ChargeAdder.java
index 28fbddb9a9..3d52c88c55 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/ChargeAdder.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/ChargeAdder.java
@@ -22,8 +22,6 @@
  */
 package org.biojava.nbio.structure.io;
 
-import java.util.List;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Chain;
 import org.biojava.nbio.structure.Group;
@@ -34,6 +32,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.List;
+
 /**
  * A class to add appropriate charge information to a structure.
  * @author Anthony Bradley
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java
index c91a573b5c..eda9cd9baf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java
@@ -23,9 +23,9 @@
 import org.biojava.nbio.alignment.Alignments;
 import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
 import org.biojava.nbio.alignment.SimpleGapPenalty;
-import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.alignment.template.GapPenalty;
 import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
+import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 import org.biojava.nbio.core.alignment.template.SequencePair;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
@@ -38,14 +38,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-import java.util.TreeSet;
+import java.util.*;
 
 /**
  * Heuristical finding of Entities (called Compounds in legacy PDB format)
@@ -130,7 +123,7 @@ public static void createPurelyNonPolyEntities(List<List<Chain>> nonPolyModels,
 		// let's find first the max entity id to assign entity ids to the newly found entities
 		int maxMolId = 0;
 		if (!entities.isEmpty()) {
-			maxMolId = Collections.max(entities, (o1, o2) -> Integer.compare(o1.getMolId(), o2.getMolId())).getMolId();
+			maxMolId = Collections.max(entities, Comparator.comparingInt(EntityInfo::getMolId)).getMolId();
 		}
 		// we go one over the max
 		int molId = maxMolId + 1;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
index f69c3d7580..f736185867 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
@@ -26,10 +26,6 @@
 
 import org.biojava.nbio.core.alignment.template.AlignedSequence;
 import org.biojava.nbio.core.alignment.template.SequencePair;
-import org.biojava.nbio.structure.*;
-import org.biojava.nbio.structure.align.model.AFPChain;
-import org.biojava.nbio.structure.align.util.AlignmentTools;
-import org.biojava.nbio.structure.align.xml.AFPChainXMLConverter;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
@@ -41,6 +37,10 @@
 import org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface;
 import org.biojava.nbio.core.sequence.template.Sequence;
 import org.biojava.nbio.core.util.SequenceTools;
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.align.model.AFPChain;
+import org.biojava.nbio.structure.align.util.AlignmentTools;
+import org.biojava.nbio.structure.align.xml.AFPChainXMLConverter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaStructureParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaStructureParser.java
index 7507d7df8d..35f3836ddf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaStructureParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaStructureParser.java
@@ -20,15 +20,15 @@
  */
 package org.biojava.nbio.structure.io;
 
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
 import org.biojava.nbio.core.sequence.io.FastaReader;
 import org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface;
 import org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface;
+import org.biojava.nbio.structure.ResidueNumber;
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.align.util.AtomCache;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java
index df6c66de50..7201f9c05b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java
@@ -21,6 +21,14 @@
  */
 package org.biojava.nbio.structure.io;
 
+import org.biojava.nbio.core.util.XMLWriter;
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.io.mmcif.MMCIFFileTools;
+import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
+import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import java.io.IOException;
 import java.text.DateFormat;
 import java.text.DecimalFormat;
@@ -29,23 +37,6 @@
 import java.util.List;
 import java.util.Locale;
 
-import org.biojava.nbio.core.util.XMLWriter;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Bond;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.DBRef;
-import org.biojava.nbio.structure.Element;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.GroupType;
-import org.biojava.nbio.structure.PDBHeader;
-import org.biojava.nbio.structure.Site;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.io.mmcif.MMCIFFileTools;
-import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
-import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 
 /**
  * Methods to convert a structure object into different file formats.
@@ -63,14 +54,14 @@ public class FileConvert {
 	private boolean printConnections;
 
 	// Locale should be english, e.g. in DE separator is "," -> PDB files have "." !
-	public static DecimalFormat d3 = (DecimalFormat)NumberFormat.getInstance(Locale.US);
+	public static final DecimalFormat d3 = (DecimalFormat)NumberFormat.getInstance(Locale.US);
 	static {
 		d3.setMaximumIntegerDigits(4);
 		d3.setMinimumFractionDigits(3);
 		d3.setMaximumFractionDigits(3);
 		d3.setGroupingUsed(false);
 	}
-	public static DecimalFormat d2 = (DecimalFormat)NumberFormat.getInstance(Locale.US);
+	public static final DecimalFormat d2 = (DecimalFormat)NumberFormat.getInstance(Locale.US);
 	static {
 		d2.setMaximumIntegerDigits(3);
 		d2.setMinimumFractionDigits(2);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileParsingParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileParsingParameters.java
index 4f28294287..b39d4d5e70 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileParsingParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileParsingParameters.java
@@ -24,10 +24,10 @@
 
 package org.biojava.nbio.structure.io;
 
-import java.io.Serializable;
-
 import org.biojava.nbio.structure.AminoAcid;
 
+import java.io.Serializable;
+
 /**
  * A class that configures parameters that can be sent to the PDB file parsers
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java
index 1ab5e3d3fc..c14ac578ac 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java
@@ -20,13 +20,14 @@
  */
 package org.biojava.nbio.structure.io;
 
-import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.List;
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Bond;
 import org.biojava.nbio.structure.Group;
 
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.List;
+
 
 public class GroupToSDF {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
index f22a2bcdfe..1504cf8f1d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
@@ -21,14 +21,14 @@
  */
 package org.biojava.nbio.structure.io;
 
+import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.PDBStatus;
 import org.biojava.nbio.structure.PDBStatus.Status;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
-import org.biojava.nbio.core.util.FileDownloadUtils;
 import org.rcsb.mmtf.utils.CodecUtils;
-import org.biojava.nbio.core.util.InputStreamProvider;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/MMTFFileReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/MMTFFileReader.java
index e410d9f538..1d321c2cb7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/MMTFFileReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/MMTFFileReader.java
@@ -20,13 +20,13 @@
  */
 package org.biojava.nbio.structure.io;
 
-import java.io.IOException;
-import java.io.InputStream;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
 import org.biojava.nbio.structure.io.mmtf.MmtfActions;
 
+import java.io.IOException;
+import java.io.InputStream;
+
 /**
  * A class to read MMTF files and cache them locally.
  * @author Anthony Bradley
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java
index fd2439b37b..064993dd42 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java
@@ -23,11 +23,12 @@
 import org.biojava.nbio.structure.jama.Matrix;
 import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
 import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
-//import org.slf4j.Logger;
-//import org.slf4j.LoggerFactory;
 
 import java.util.*;
 
+//import org.slf4j.Logger;
+//import org.slf4j.LoggerFactory;
+
 /**
  * Parses REMARK 350 records in a PDB file and creates transformations to
  * construct the quaternary structure of a protein from an asymmetric unit
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
index ae8474b990..824df1443d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -21,8 +21,19 @@
  */
 package org.biojava.nbio.structure.io;
 
-import static java.lang.Math.min;
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
+import org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom;
+import org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord;
+import org.biojava.nbio.structure.secstruc.SecStrucInfo;
+import org.biojava.nbio.structure.secstruc.SecStrucType;
+import org.biojava.nbio.structure.xtal.CrystalCell;
+import org.biojava.nbio.structure.xtal.SpaceGroup;
+import org.biojava.nbio.structure.xtal.SymoplibParser;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix4d;
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStream;
@@ -30,55 +41,11 @@
 import java.text.DateFormat;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Locale;
-import java.util.Map;
-import java.util.StringTokenizer;
+import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import javax.vecmath.Matrix4d;
-
-import org.biojava.nbio.structure.AminoAcid;
-import org.biojava.nbio.structure.AminoAcidImpl;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.AtomImpl;
-import org.biojava.nbio.structure.Author;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.DBRef;
-import org.biojava.nbio.structure.Element;
-import org.biojava.nbio.structure.EntityInfo;
-import org.biojava.nbio.structure.EntityType;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.GroupIterator;
-import org.biojava.nbio.structure.HetatomImpl;
-import org.biojava.nbio.structure.JournalArticle;
-import org.biojava.nbio.structure.NucleotideImpl;
-import org.biojava.nbio.structure.PDBCrystallographicInfo;
-import org.biojava.nbio.structure.PDBHeader;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.Site;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureImpl;
-import org.biojava.nbio.structure.StructureTools;
-import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
-import org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom;
-import org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord;
-import org.biojava.nbio.structure.secstruc.SecStrucInfo;
-import org.biojava.nbio.structure.secstruc.SecStrucType;
-import org.biojava.nbio.structure.xtal.CrystalCell;
-import org.biojava.nbio.structure.xtal.SpaceGroup;
-import org.biojava.nbio.structure.xtal.SymoplibParser;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+import static java.lang.Math.min;
 
 
 /**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
index 5591fbdd84..ae04756d9d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
@@ -26,6 +26,7 @@
 
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
+
 import java.io.IOException;
 import java.io.InputStream;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SSBondImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SSBondImpl.java
index ae3aaab9ae..2392e8ac3f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SSBondImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SSBondImpl.java
@@ -23,12 +23,12 @@
 
 package org.biojava.nbio.structure.io;
 
-import java.util.ArrayList;
-import java.util.List;
-
 import org.biojava.nbio.structure.Bond;
 import org.biojava.nbio.structure.PDBRecord;
 
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.
  * The two residues specified here are CYS residues that form a Disulfide bridge.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SandboxStyleStructureProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SandboxStyleStructureProvider.java
index 84bce020b6..fe7cc98034 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SandboxStyleStructureProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SandboxStyleStructureProvider.java
@@ -20,10 +20,10 @@
  */
 package org.biojava.nbio.structure.io;
 
+import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
-import org.biojava.nbio.core.util.InputStreamProvider;
 
 import java.io.File;
 import java.io.IOException;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java
index 68e9b14000..c0296d6fc6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java
@@ -24,11 +24,6 @@
 package org.biojava.nbio.structure.io;
 
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
 import org.biojava.nbio.alignment.Alignments;
 import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
 import org.biojava.nbio.alignment.SimpleGapPenalty;
@@ -41,30 +36,21 @@
 import org.biojava.nbio.core.sequence.DNASequence;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.RNASequence;
-import org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet;
-import org.biojava.nbio.core.sequence.compound.AmbiguityDNARNAHybridCompoundSet;
-import org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
-import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
-import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
+import org.biojava.nbio.core.sequence.compound.*;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
-import org.biojava.nbio.structure.AminoAcid;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.GroupType;
-import org.biojava.nbio.structure.HetatomImpl;
-import org.biojava.nbio.structure.NucleotideImpl;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
 import org.biojava.nbio.structure.io.mmcif.chem.ResidueType;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
 
 /**
  * Aligns the SEQRES residues to the ATOM residues.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
index 7f02f20e33..e71e4dd19f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
@@ -29,12 +29,12 @@
 import org.biojava.nbio.core.alignment.template.AlignedSequence;
 import org.biojava.nbio.core.alignment.template.SequencePair;
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
-import org.biojava.nbio.structure.*;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
 import org.biojava.nbio.core.sequence.template.CompoundSet;
+import org.biojava.nbio.structure.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumer.java
index 0a0c0e3fb5..4a58833f38 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumer.java
@@ -1,50 +1,6 @@
 package org.biojava.nbio.structure.io.cif;
 
-import org.rcsb.cif.model.generated.AtomSite;
-import org.rcsb.cif.model.generated.AtomSites;
-import org.rcsb.cif.model.generated.AuditAuthor;
-import org.rcsb.cif.model.generated.Cell;
-import org.rcsb.cif.model.generated.ChemComp;
-import org.rcsb.cif.model.generated.ChemCompBond;
-import org.rcsb.cif.model.generated.DatabasePDBRemark;
-import org.rcsb.cif.model.generated.DatabasePDBRev;
-import org.rcsb.cif.model.generated.DatabasePDBRevRecord;
-import org.rcsb.cif.model.generated.Entity;
-import org.rcsb.cif.model.generated.EntityPoly;
-import org.rcsb.cif.model.generated.EntityPolySeq;
-import org.rcsb.cif.model.generated.EntitySrcGen;
-import org.rcsb.cif.model.generated.EntitySrcNat;
-import org.rcsb.cif.model.generated.Exptl;
-import org.rcsb.cif.model.generated.PdbxAuditRevisionHistory;
-import org.rcsb.cif.model.generated.PdbxChemCompIdentifier;
-import org.rcsb.cif.model.generated.PdbxDatabaseStatus;
-import org.rcsb.cif.model.generated.PdbxEntityDescriptor;
-import org.rcsb.cif.model.generated.PdbxEntitySrcSyn;
-import org.rcsb.cif.model.generated.PdbxMolecule;
-import org.rcsb.cif.model.generated.PdbxMoleculeFeatures;
-import org.rcsb.cif.model.generated.PdbxNonpolyScheme;
-import org.rcsb.cif.model.generated.PdbxReferenceEntityLink;
-import org.rcsb.cif.model.generated.PdbxReferenceEntityList;
-import org.rcsb.cif.model.generated.PdbxReferenceEntityPolyLink;
-import org.rcsb.cif.model.generated.PdbxStructAssembly;
-import org.rcsb.cif.model.generated.PdbxStructAssemblyGen;
-import org.rcsb.cif.model.generated.PdbxStructModResidue;
-import org.rcsb.cif.model.generated.PdbxStructOperList;
-import org.rcsb.cif.model.generated.Refine;
-import org.rcsb.cif.model.generated.Struct;
-import org.rcsb.cif.model.generated.StructAsym;
-import org.rcsb.cif.model.generated.StructConf;
-import org.rcsb.cif.model.generated.StructConn;
-import org.rcsb.cif.model.generated.StructConnType;
-import org.rcsb.cif.model.generated.StructKeywords;
-import org.rcsb.cif.model.generated.StructNcsOper;
-import org.rcsb.cif.model.generated.StructRef;
-import org.rcsb.cif.model.generated.StructRefSeq;
-import org.rcsb.cif.model.generated.StructRefSeqDif;
-import org.rcsb.cif.model.generated.StructSheetRange;
-import org.rcsb.cif.model.generated.StructSite;
-import org.rcsb.cif.model.generated.StructSiteGen;
-import org.rcsb.cif.model.generated.Symmetry;
+import org.rcsb.cif.model.generated.*;
 
 /**
  * Defines a rather generic interface which allows to populate some data structure with data parsed from a CIF file.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java
index b5d6fa8143..82cc9c076b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java
@@ -1,34 +1,7 @@
 package org.biojava.nbio.structure.io.cif;
 
-import org.biojava.nbio.structure.AminoAcid;
-import org.biojava.nbio.structure.AminoAcidImpl;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.AtomImpl;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.DBRef;
-import org.biojava.nbio.structure.Element;
-import org.biojava.nbio.structure.EntityInfo;
-import org.biojava.nbio.structure.EntityType;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.GroupType;
-import org.biojava.nbio.structure.HetatomImpl;
-import org.biojava.nbio.structure.NucleotideImpl;
-import org.biojava.nbio.structure.PDBCrystallographicInfo;
-import org.biojava.nbio.structure.PDBHeader;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.SeqMisMatch;
-import org.biojava.nbio.structure.SeqMisMatchImpl;
-import org.biojava.nbio.structure.Site;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureImpl;
-import org.biojava.nbio.structure.StructureTools;
-import org.biojava.nbio.structure.io.BondMaker;
-import org.biojava.nbio.structure.io.ChargeAdder;
-import org.biojava.nbio.structure.io.EntityFinder;
-import org.biojava.nbio.structure.io.FileParsingParameters;
-import org.biojava.nbio.structure.io.SeqRes2AtomAligner;
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.io.*;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
 import org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord;
 import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
@@ -40,51 +13,7 @@
 import org.rcsb.cif.model.FloatColumn;
 import org.rcsb.cif.model.IntColumn;
 import org.rcsb.cif.model.StrColumn;
-import org.rcsb.cif.model.generated.AtomSite;
-import org.rcsb.cif.model.generated.AtomSites;
-import org.rcsb.cif.model.generated.AuditAuthor;
-import org.rcsb.cif.model.generated.Cell;
-import org.rcsb.cif.model.generated.ChemComp;
-import org.rcsb.cif.model.generated.ChemCompBond;
-import org.rcsb.cif.model.generated.DatabasePDBRemark;
-import org.rcsb.cif.model.generated.DatabasePDBRev;
-import org.rcsb.cif.model.generated.DatabasePDBRevRecord;
-import org.rcsb.cif.model.generated.Entity;
-import org.rcsb.cif.model.generated.EntityPoly;
-import org.rcsb.cif.model.generated.EntityPolySeq;
-import org.rcsb.cif.model.generated.EntitySrcGen;
-import org.rcsb.cif.model.generated.EntitySrcNat;
-import org.rcsb.cif.model.generated.Exptl;
-import org.rcsb.cif.model.generated.PdbxAuditRevisionHistory;
-import org.rcsb.cif.model.generated.PdbxChemCompIdentifier;
-import org.rcsb.cif.model.generated.PdbxDatabaseStatus;
-import org.rcsb.cif.model.generated.PdbxEntityDescriptor;
-import org.rcsb.cif.model.generated.PdbxEntitySrcSyn;
-import org.rcsb.cif.model.generated.PdbxMolecule;
-import org.rcsb.cif.model.generated.PdbxMoleculeFeatures;
-import org.rcsb.cif.model.generated.PdbxNonpolyScheme;
-import org.rcsb.cif.model.generated.PdbxReferenceEntityLink;
-import org.rcsb.cif.model.generated.PdbxReferenceEntityList;
-import org.rcsb.cif.model.generated.PdbxReferenceEntityPolyLink;
-import org.rcsb.cif.model.generated.PdbxStructAssembly;
-import org.rcsb.cif.model.generated.PdbxStructAssemblyGen;
-import org.rcsb.cif.model.generated.PdbxStructModResidue;
-import org.rcsb.cif.model.generated.PdbxStructOperList;
-import org.rcsb.cif.model.generated.Refine;
-import org.rcsb.cif.model.generated.Struct;
-import org.rcsb.cif.model.generated.StructAsym;
-import org.rcsb.cif.model.generated.StructConf;
-import org.rcsb.cif.model.generated.StructConn;
-import org.rcsb.cif.model.generated.StructConnType;
-import org.rcsb.cif.model.generated.StructKeywords;
-import org.rcsb.cif.model.generated.StructNcsOper;
-import org.rcsb.cif.model.generated.StructRef;
-import org.rcsb.cif.model.generated.StructRefSeq;
-import org.rcsb.cif.model.generated.StructRefSeqDif;
-import org.rcsb.cif.model.generated.StructSheetRange;
-import org.rcsb.cif.model.generated.StructSite;
-import org.rcsb.cif.model.generated.StructSiteGen;
-import org.rcsb.cif.model.generated.Symmetry;
+import org.rcsb.cif.model.generated.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImpl.java
index 9d839de4f2..1f8e069a3e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImpl.java
@@ -1,22 +1,11 @@
 package org.biojava.nbio.structure.io.cif;
 
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Element;
-import org.biojava.nbio.structure.EntityType;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.GroupType;
-import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.xtal.CrystalCell;
 import org.biojava.nbio.structure.xtal.SpaceGroup;
 import org.rcsb.cif.model.Category;
 import org.rcsb.cif.model.CifFile;
-import org.rcsb.cif.model.builder.BlockBuilder;
-import org.rcsb.cif.model.builder.CategoryBuilder;
-import org.rcsb.cif.model.builder.CifBuilder;
-import org.rcsb.cif.model.builder.FloatColumnBuilder;
-import org.rcsb.cif.model.builder.IntColumnBuilder;
-import org.rcsb.cif.model.builder.StrColumnBuilder;
+import org.rcsb.cif.model.builder.*;
 
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java
index 4cb3e397c4..bedb4d0673 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java
@@ -21,10 +21,10 @@
  */
 package org.biojava.nbio.structure.io.mmcif;
 
+import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
 import org.biojava.nbio.structure.io.LocalPDBDirectory;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
-import org.biojava.nbio.core.util.InputStreamProvider;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -57,8 +57,8 @@ public class AllChemCompProvider implements ChemCompProvider, Runnable{
 	static ChemicalComponentDictionary dict;
 
 	// flags to make sure there is only one thread running that is loading the dictionary
-	static AtomicBoolean loading       = new AtomicBoolean(false);
-	static AtomicBoolean isInitialized = new AtomicBoolean(false);
+	static final AtomicBoolean loading       = new AtomicBoolean(false);
+	static final AtomicBoolean isInitialized = new AtomicBoolean(false);
 
 	public AllChemCompProvider(){
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompConsumer.java
index f2d043a5b9..b6cd7bfad4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompConsumer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompConsumer.java
@@ -32,7 +32,7 @@ public class ChemCompConsumer implements MMcifConsumer {
 
 	private static final Logger logger = LoggerFactory.getLogger(ChemCompConsumer.class);
 
-	ChemicalComponentDictionary dictionary;
+	final ChemicalComponentDictionary dictionary;
 
 	String latestChemCompId;
 	public ChemCompConsumer(){
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java
index 64b29ad38b..86de7e11a5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java
@@ -23,11 +23,7 @@
 package org.biojava.nbio.structure.io.mmcif;
 
 import org.biojava.nbio.core.util.SoftHashMap;
-import org.biojava.nbio.structure.AminoAcid;
-import org.biojava.nbio.structure.AminoAcidImpl;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.HetatomImpl;
-import org.biojava.nbio.structure.NucleotideImpl;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.slf4j.Logger;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
index 00fc056555..c4a1228aea 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
@@ -20,15 +20,15 @@
  */
 package org.biojava.nbio.structure.io.mmcif;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.FilenameFilter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.PrintWriter;
-import java.io.StringWriter;
+import org.biojava.nbio.core.util.InputStreamProvider;
+import org.biojava.nbio.structure.align.util.URLConnectionTools;
+import org.biojava.nbio.structure.align.util.UserConfiguration;
+import org.biojava.nbio.structure.io.LocalPDBDirectory;
+import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.*;
 import java.net.URL;
 import java.net.URLConnection;
 import java.nio.file.Files;
@@ -39,14 +39,6 @@
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.zip.GZIPOutputStream;
 
-import org.biojava.nbio.core.util.InputStreamProvider;
-import org.biojava.nbio.structure.align.util.URLConnectionTools;
-import org.biojava.nbio.structure.align.util.UserConfiguration;
-import org.biojava.nbio.structure.io.LocalPDBDirectory;
-import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 
 
 /**
@@ -85,7 +77,7 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 
 
 	// flags to make sure there is only one thread running that is loading the dictionary
-	static AtomicBoolean loading = new AtomicBoolean(false);
+	static final AtomicBoolean loading = new AtomicBoolean(false);
 
 	static final List<String> protectedIDs = new ArrayList<>();
 	static {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
index 39a6dd1050..82c4dde9ce 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
@@ -21,28 +21,17 @@
 package org.biojava.nbio.structure.io.mmcif;
 
 
-import java.lang.reflect.Field;
-import java.util.*;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Element;
-import org.biojava.nbio.structure.EntityType;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.GroupType;
-import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.io.FileConvert;
-import org.biojava.nbio.structure.io.mmcif.model.AbstractBean;
-import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
-import org.biojava.nbio.structure.io.mmcif.model.CIFLabel;
-import org.biojava.nbio.structure.io.mmcif.model.Cell;
-import org.biojava.nbio.structure.io.mmcif.model.IgnoreField;
-import org.biojava.nbio.structure.io.mmcif.model.Symmetry;
+import org.biojava.nbio.structure.io.mmcif.model.*;
 import org.biojava.nbio.structure.xtal.CrystalCell;
 import org.biojava.nbio.structure.xtal.SpaceGroup;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.lang.reflect.Field;
+import java.util.*;
+
 /**
  * Some tools for mmCIF file writing.
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java
index 4438de1470..19b6a35ffb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java
@@ -35,7 +35,7 @@
 public class MetalBondConsumer implements MMcifConsumer{
 
 
-	Map<String,List<MetalBondDistance>> definitions = new HashMap<>();
+	final Map<String,List<MetalBondDistance>> definitions = new HashMap<>();
 
 	@Override
 	public void documentStart() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondParser.java
index 03d6789c5c..3fbd0cd2f6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondParser.java
@@ -25,8 +25,8 @@
 import org.slf4j.LoggerFactory;
 
 import java.io.InputStream;
-import java.util.*;
-
+import java.util.List;
+import java.util.Map;
 import java.util.zip.GZIPInputStream;
 
 /**
@@ -39,7 +39,7 @@ public class MetalBondParser  {
 	private static final String BONDS_FILE = "org/biojava/nbio/structure/bond_distance_limits.cif.gz";
 
 
-	static Map<String,List<MetalBondDistance>> definitions;
+	static final Map<String,List<MetalBondDistance>> definitions;
 
 	static {
 		 definitions = init();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ReducedChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ReducedChemCompProvider.java
index 0d752cea04..cef70f04cd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ReducedChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ReducedChemCompProvider.java
@@ -20,16 +20,16 @@
  */
 package org.biojava.nbio.structure.io.mmcif;
 
+import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.util.zip.GZIPInputStream;
 
-import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 
 /** Unlike the {@link DownloadChemCompProvider}, this  {@link ChemCompProvider} does not download any chem comp definitions.
  * It has access to a limited set of files that are part of the biojava distribution.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
index 860ba62a52..4461ab4b01 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
@@ -21,87 +21,9 @@
  */
 package org.biojava.nbio.structure.io.mmcif;
 
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Locale;
-import java.util.Map;
-
-import javax.vecmath.Matrix4d;
-
-import org.biojava.nbio.structure.AminoAcid;
-import org.biojava.nbio.structure.AminoAcidImpl;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.AtomImpl;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.EntityInfo;
-import org.biojava.nbio.structure.EntityType;
-import org.biojava.nbio.structure.DBRef;
-import org.biojava.nbio.structure.Element;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.GroupType;
-import org.biojava.nbio.structure.HetatomImpl;
-import org.biojava.nbio.structure.NucleotideImpl;
-import org.biojava.nbio.structure.PDBCrystallographicInfo;
-import org.biojava.nbio.structure.PDBHeader;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.SeqMisMatch;
-import org.biojava.nbio.structure.SeqMisMatchImpl;
-import org.biojava.nbio.structure.Site;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureImpl;
-import org.biojava.nbio.structure.StructureTools;
-import org.biojava.nbio.structure.io.BondMaker;
-import org.biojava.nbio.structure.io.ChargeAdder;
-import org.biojava.nbio.structure.io.EntityFinder;
-import org.biojava.nbio.structure.io.FileParsingParameters;
-import org.biojava.nbio.structure.io.SeqRes2AtomAligner;
-import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
-import org.biojava.nbio.structure.io.mmcif.model.AtomSites;
-import org.biojava.nbio.structure.io.mmcif.model.AuditAuthor;
-import org.biojava.nbio.structure.io.mmcif.model.Cell;
-import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
-import org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom;
-import org.biojava.nbio.structure.io.mmcif.model.ChemCompBond;
-import org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor;
-import org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark;
-import org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev;
-import org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord;
-import org.biojava.nbio.structure.io.mmcif.model.Entity;
-import org.biojava.nbio.structure.io.mmcif.model.EntityPoly;
-import org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq;
-import org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen;
-import org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat;
-import org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn;
-import org.biojava.nbio.structure.io.mmcif.model.Exptl;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxAuditRevisionHistory;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxDatabaseStatus;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList;
-import org.biojava.nbio.structure.io.mmcif.model.Refine;
-import org.biojava.nbio.structure.io.mmcif.model.Struct;
-import org.biojava.nbio.structure.io.mmcif.model.StructAsym;
-import org.biojava.nbio.structure.io.mmcif.model.StructConn;
-import org.biojava.nbio.structure.io.mmcif.model.StructKeywords;
-import org.biojava.nbio.structure.io.mmcif.model.StructNcsOper;
-import org.biojava.nbio.structure.io.mmcif.model.StructRef;
-import org.biojava.nbio.structure.io.mmcif.model.StructRefSeq;
-import org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif;
-import org.biojava.nbio.structure.io.mmcif.model.StructSite;
-import org.biojava.nbio.structure.io.mmcif.model.StructSiteGen;
-import org.biojava.nbio.structure.io.mmcif.model.Symmetry;
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.io.*;
+import org.biojava.nbio.structure.io.mmcif.model.*;
 import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
 import org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder;
 import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
@@ -111,6 +33,11 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix4d;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.*;
+
 /**
  * A MMcifConsumer implementation that builds an in-memory representation of the
  * content of a mmcif file as a BioJava Structure object.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
index 5c9267ccfc..981e265f2c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
@@ -21,6 +21,13 @@
  */
 package org.biojava.nbio.structure.io.mmcif;
 
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.io.MMCIFFileReader;
+import org.biojava.nbio.structure.io.StructureIOFile;
+import org.biojava.nbio.structure.io.mmcif.model.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStream;
@@ -28,61 +35,7 @@
 import java.lang.reflect.Field;
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.io.MMCIFFileReader;
-import org.biojava.nbio.structure.io.StructureIOFile;
-import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
-import org.biojava.nbio.structure.io.mmcif.model.AtomSites;
-import org.biojava.nbio.structure.io.mmcif.model.AuditAuthor;
-import org.biojava.nbio.structure.io.mmcif.model.CIFLabel;
-import org.biojava.nbio.structure.io.mmcif.model.Cell;
-import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
-import org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom;
-import org.biojava.nbio.structure.io.mmcif.model.ChemCompBond;
-import org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor;
-import org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark;
-import org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev;
-import org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord;
-import org.biojava.nbio.structure.io.mmcif.model.Entity;
-import org.biojava.nbio.structure.io.mmcif.model.EntityPoly;
-import org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq;
-import org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen;
-import org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat;
-import org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn;
-import org.biojava.nbio.structure.io.mmcif.model.Exptl;
-import org.biojava.nbio.structure.io.mmcif.model.IgnoreField;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxAuditRevisionHistory;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxDatabaseStatus;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen;
-import org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList;
-import org.biojava.nbio.structure.io.mmcif.model.Refine;
-import org.biojava.nbio.structure.io.mmcif.model.Struct;
-import org.biojava.nbio.structure.io.mmcif.model.StructAsym;
-import org.biojava.nbio.structure.io.mmcif.model.StructConn;
-import org.biojava.nbio.structure.io.mmcif.model.StructKeywords;
-import org.biojava.nbio.structure.io.mmcif.model.StructNcsOper;
-import org.biojava.nbio.structure.io.mmcif.model.StructRef;
-import org.biojava.nbio.structure.io.mmcif.model.StructRefSeq;
-import org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif;
-import org.biojava.nbio.structure.io.mmcif.model.StructSite;
-import org.biojava.nbio.structure.io.mmcif.model.StructSiteGen;
-import org.biojava.nbio.structure.io.mmcif.model.Symmetry;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+import java.util.*;
 
 /**
  * A simple mmCif file parser
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
index 5ffa87abf1..d9c7c79330 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
@@ -20,29 +20,21 @@
  */
 package org.biojava.nbio.structure.io.mmcif;
 
-import java.io.BufferedOutputStream;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
+import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
+import org.biojava.nbio.structure.io.mmcif.chem.ResidueType;
+import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.*;
 import java.nio.file.FileSystem;
-import java.nio.file.FileSystems;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.nio.file.StandardCopyOption;
+import java.nio.file.*;
 import java.util.HashSet;
 import java.util.Set;
 import java.util.zip.GZIPInputStream;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipOutputStream;
 
-import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
-import org.biojava.nbio.structure.io.mmcif.chem.ResidueType;
-import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 /** This chemical component provider retrieves and caches chemical component definition files from a
  * zip archive specified in its construction.  If the archive does not contain the record, an attempt is
  * made to download it using DownloadChemCompProvider. The downloaded file is then added to the archive.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/PolymerType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/PolymerType.java
index 1ab4dad31a..a309ff5cf1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/PolymerType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/PolymerType.java
@@ -90,7 +90,7 @@ public enum PolymerType implements Serializable
 	 */
 	unknown(null);
 
-	static Map<String,PolymerType> lookupTable = new HashMap<>();
+	static final Map<String,PolymerType> lookupTable = new HashMap<>();
 
 	static {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ResidueType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ResidueType.java
index e1d7e55b25..5680120dd2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ResidueType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ResidueType.java
@@ -75,7 +75,7 @@ public enum ResidueType implements Serializable {
 	otherChemComp(null, "other");
 
 
-	static Map<String,ResidueType> lookupTable = new HashMap<>();
+	static final Map<String,ResidueType> lookupTable = new HashMap<>();
 
 	static {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemCompBond.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemCompBond.java
index be33fed0f3..0c502c743d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemCompBond.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemCompBond.java
@@ -24,11 +24,11 @@
  */
 package org.biojava.nbio.structure.io.mmcif.model;
 
-import java.io.Serializable;
-
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.Serializable;
+
 
 /*
  * _chem_comp_bond.comp_id
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfActions.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfActions.java
index 7b9cd4642f..4e9da53e67 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfActions.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfActions.java
@@ -20,18 +20,18 @@
  */
 package org.biojava.nbio.structure.io.mmtf;
 
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.nio.file.Path;
-
 import org.biojava.nbio.structure.Structure;
 import org.rcsb.mmtf.decoder.GenericDecoder;
-import org.rcsb.mmtf.decoder.StructureDataToAdapter;
 import org.rcsb.mmtf.decoder.ReaderUtils;
+import org.rcsb.mmtf.decoder.StructureDataToAdapter;
 import org.rcsb.mmtf.encoder.AdapterToStructureData;
 import org.rcsb.mmtf.encoder.WriterUtils;
 
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.nio.file.Path;
+
 /**
  * A class of functions for reading and writing Biojava structures using MMTF
  * @author Anthony Bradley
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
index f15a639c2c..39e9f7a240 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
@@ -20,36 +20,7 @@
  */
 package org.biojava.nbio.structure.io.mmtf;
 
-import java.io.Serializable;
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.vecmath.Matrix4d;
-
-import org.biojava.nbio.structure.AminoAcid;
-import org.biojava.nbio.structure.AminoAcidImpl;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.AtomImpl;
-import org.biojava.nbio.structure.BondImpl;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.Element;
-import org.biojava.nbio.structure.EntityInfo;
-import org.biojava.nbio.structure.EntityType;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.HetatomImpl;
-import org.biojava.nbio.structure.NucleotideImpl;
-import org.biojava.nbio.structure.PDBCrystallographicInfo;
-import org.biojava.nbio.structure.PDBHeader;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureImpl;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
 import org.biojava.nbio.structure.io.mmcif.chem.ResidueType;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
@@ -62,6 +33,12 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix4d;
+import java.io.Serializable;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.*;
+
 
 /**
  * A biojava specific structure inflator for MMTF.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java
index 05a56340f4..272f6b1a9b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java
@@ -20,24 +20,16 @@
  */
 package org.biojava.nbio.structure.io.mmtf;
 
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Bond;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.EntityInfo;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.PDBCrystallographicInfo;
-import org.biojava.nbio.structure.PDBHeader;
-import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
 import org.rcsb.mmtf.api.StructureAdapterInterface;
 import org.rcsb.mmtf.dataholders.MmtfStructure;
 
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
 /**
  * Class to take Biojava structure data and covert to the DataApi for encoding.
  * Must implement all the functions in {@link StructureAdapterInterface}.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfSummaryDataBean.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfSummaryDataBean.java
index 45b702657c..cbb63345e2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfSummaryDataBean.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfSummaryDataBean.java
@@ -20,12 +20,12 @@
  */
 package org.biojava.nbio.structure.io.mmtf;
 
-import java.util.List;
-import java.util.Map;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Chain;
 
+import java.util.List;
+import java.util.Map;
+
 /**
  * Class to store the summary data for a given structure.
  * @author Anthony Bradley
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
index 59b0b45742..d20636c12e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
@@ -20,32 +20,7 @@
  */
 package org.biojava.nbio.structure.io.mmtf;
 
-import java.text.DateFormat;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import javax.vecmath.Matrix4d;
-
-import org.biojava.nbio.structure.AminoAcid;
-import org.biojava.nbio.structure.AminoAcidImpl;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Bond;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ExperimentalTechnique;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.GroupType;
-import org.biojava.nbio.structure.NucleotideImpl;
-import org.biojava.nbio.structure.PDBCrystallographicInfo;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
@@ -65,6 +40,12 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix4d;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.*;
+import java.util.Map.Entry;
+
 /**
  * A utils class of functions needed for Biojava to read and write to mmtf.
  * @author Anthony Bradley
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java
index 9dae6e5091..6a487a9a44 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java
@@ -23,8 +23,8 @@
  */
 package org.biojava.nbio.structure.io.sifts;
 
-import org.biojava.nbio.structure.align.util.UserConfiguration;
 import org.biojava.nbio.core.sequence.io.util.IOUtils;
+import org.biojava.nbio.structure.align.util.UserConfiguration;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.java
index 7c67305f3c..b55b449f5b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.java
@@ -24,9 +24,9 @@
  */
 package org.biojava.nbio.structure.io.sifts;
 
-import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.core.util.FileDownloadUtils;
 import org.biojava.nbio.core.util.InputStreamProvider;
+import org.biojava.nbio.structure.align.util.AtomCache;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java
index 05e1784dc9..1f5b835c22 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java
@@ -34,7 +34,6 @@
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
-
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayList;
@@ -49,7 +48,7 @@ public class SiftsXMLParser {
 	Document dom;
 	List<SiftsEntity> entities;
 
-	static boolean debug = false;
+	static final boolean debug = false;
 	public SiftsXMLParser(){
 		entities = new ArrayList<>();
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
index 8c457e15dd..24f57e0381 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
@@ -22,12 +22,11 @@
 
 import org.biojava.nbio.structure.*;
 
+import javax.vecmath.Point3d;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
-import javax.vecmath.Point3d;
-
 
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
index 457a639d6c..44413c260e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
@@ -32,7 +32,10 @@
 import org.slf4j.LoggerFactory;
 
 import javax.vecmath.Matrix4d;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 /**
  * Reconstructs the quaternary structure of a protein from an asymmetric unit
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java
index 8a57be4dac..40164e2d39 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java
@@ -20,9 +20,9 @@
  */
 package org.biojava.nbio.structure.quaternary;
 
+import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.biojava.nbio.structure.xtal.CrystalCell;
 import org.biojava.nbio.structure.xtal.CrystalTransform;
-import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.w3c.dom.Document;
 import org.w3c.dom.NamedNodeMap;
 import org.w3c.dom.Node;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/PdbIdLists.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/PdbIdLists.java
index 94b4df0b23..1827dc6188 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/PdbIdLists.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/PdbIdLists.java
@@ -24,7 +24,8 @@
 import java.net.URL;
 import java.net.URLConnection;
 import java.net.URLEncoder;
-import java.util.*;
+import java.util.Set;
+import java.util.TreeSet;
 
 /**
  *  Utility classes for retrieving lists of PDB IDs.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.java
index 598a99d513..1beaac2811 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.java
@@ -38,8 +38,8 @@
 public class BerkeleyScopInstallation extends ScopInstallation {
 
 
-	String defaultBerkeleyDownloadURL = "http://scop.berkeley.edu/downloads/parse/";
-	String defaultBerkeleyScopVersion=ScopFactory.LATEST_VERSION;
+	final String defaultBerkeleyDownloadURL = "http://scop.berkeley.edu/downloads/parse/";
+	final String defaultBerkeleyScopVersion=ScopFactory.LATEST_VERSION;
 
 	/**
 	 * A map from SCOP version names which the Berkeley server offers as a
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/CachedRemoteScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/CachedRemoteScopInstallation.java
index 8c2c49df91..aec7572600 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/CachedRemoteScopInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/CachedRemoteScopInstallation.java
@@ -50,9 +50,9 @@ public class CachedRemoteScopInstallation extends SerializableCache<String,ScopD
 
 	private static final String CACHE_FILE_NAME = "remotescopinstallation.ser";
 
-	RemoteScopInstallation proxy ;
+	final RemoteScopInstallation proxy ;
 
-	SerializableCache<Integer,ScopDescription> scopDescriptionCache ;
+	final SerializableCache<Integer,ScopDescription> scopDescriptionCache ;
 
 	public CachedRemoteScopInstallation() throws IOException {
 		this(true);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java
index 23de56d73b..794da93911 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java
@@ -20,23 +20,18 @@
  */
 package org.biojava.nbio.structure.scop;
 
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.align.util.AtomCache;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlRootElement;
 import java.io.IOException;
 import java.io.Serializable;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlRootElement;
-
-import org.biojava.nbio.structure.ResidueRange;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIdentifier;
-import org.biojava.nbio.structure.SubstructureIdentifier;
-import org.biojava.nbio.structure.align.util.AtomCache;
-
 
 /** Container for the information for a domain. Contains a line in the file
  * dir.cla.scop.txt_1.75
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java
index e2a6eb1f35..1e2443549b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java
@@ -23,7 +23,6 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.util.HashMap;
 import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
index d295cfdc7c..eef68dc348 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
@@ -24,15 +24,18 @@
 
 package org.biojava.nbio.structure.scop;
 
+import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
-import org.biojava.nbio.core.util.FileDownloadUtils;
-import org.biojava.nbio.core.util.InputStreamProvider;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
 import java.net.URL;
 import java.util.*;
 import java.util.concurrent.atomic.AtomicBoolean;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ListStringWrapper.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ListStringWrapper.java
index 6f8b4e5174..0f3ea6f6bb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ListStringWrapper.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ListStringWrapper.java
@@ -50,7 +50,7 @@ public class ListStringWrapper implements Serializable{
 	private static final long serialVersionUID = 4193799052494327416L;
 	List<String> data;
 
-	static JAXBContext jaxbContext;
+	static final JAXBContext jaxbContext;
 	static {
 		try {
 			jaxbContext= JAXBContext.newInstance(ListStringWrapper.class);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDescriptions.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDescriptions.java
index a175add7c2..74925bf5dd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDescriptions.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDescriptions.java
@@ -47,7 +47,7 @@ public class ScopDescriptions implements Serializable{
 
 	private static final long serialVersionUID = 4924350548761431852L;
 
-	static JAXBContext jaxbContext;
+	static final JAXBContext jaxbContext;
 	static {
 		try {
 			jaxbContext= JAXBContext.newInstance(ScopDescriptions.class);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDomains.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDomains.java
index f648d0ed3c..3c42467b5b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDomains.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDomains.java
@@ -49,7 +49,7 @@ public class ScopDomains implements Serializable{
 
 	List<ScopDomain> domains ;
 
-	static JAXBContext jaxbContext;
+	static final JAXBContext jaxbContext;
 	static {
 		try {
 			jaxbContext= JAXBContext.newInstance(ScopDomains.class);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopNodes.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopNodes.java
index 57277bb54a..cdd5c99ca4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopNodes.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopNodes.java
@@ -50,7 +50,7 @@ public class ScopNodes implements Serializable {
 
 	List<ScopNode> scopNodes ;
 
-	static JAXBContext jaxbContext;
+	static final JAXBContext jaxbContext;
 	static {
 		try {
 			jaxbContext= JAXBContext.newInstance(ScopNodes.class);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/TreeSetStringWrapper.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/TreeSetStringWrapper.java
index 6f3123e364..d81ae886ce 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/TreeSetStringWrapper.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/TreeSetStringWrapper.java
@@ -49,7 +49,7 @@ public class TreeSetStringWrapper implements Serializable{
 	private static final long serialVersionUID = 4193799052494327416L;
 	TreeSet<String> data;
 
-	static JAXBContext jaxbContext;
+	static final JAXBContext jaxbContext;
 	static {
 		try {
 			jaxbContext= JAXBContext.newInstance(TreeSetStringWrapper.class);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/XMLUtil.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/XMLUtil.java
index f206813b41..df5d7bca02 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/XMLUtil.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/XMLUtil.java
@@ -49,7 +49,7 @@
  */
 public class XMLUtil {
 
-	static JAXBContext jaxbContextScopDescription;
+	static final JAXBContext jaxbContextScopDescription;
 	static {
 		try {
 			jaxbContextScopDescription= JAXBContext.newInstance(ScopDescription.class);
@@ -58,7 +58,7 @@ public class XMLUtil {
 		}
 	}
 
-	static JAXBContext jaxbContextScopDomain;
+	static final JAXBContext jaxbContextScopDomain;
 	static {
 		try {
 			jaxbContextScopDomain= JAXBContext.newInstance(ScopDomain.class);
@@ -67,7 +67,7 @@ public class XMLUtil {
 		}
 	}
 
-	static JAXBContext jaxbContextScopNode;
+	static final JAXBContext jaxbContextScopNode;
 	static {
 		try {
 			jaxbContextScopNode= JAXBContext.newInstance(ScopNode.class);
@@ -76,7 +76,7 @@ public class XMLUtil {
 		}
 	}
 
-	static JAXBContext jaxbContextDomains;
+	static final JAXBContext jaxbContextDomains;
 	static {
 		try {
 			jaxbContextDomains= JAXBContext.newInstance(TreeSet.class);
@@ -85,7 +85,7 @@ public class XMLUtil {
 		}
 	}
 
-	static JAXBContext jaxbContextStringSortedSet;
+	static final JAXBContext jaxbContextStringSortedSet;
 	static {
 		try {
 			jaxbContextStringSortedSet= JAXBContext.newInstance(TreeSetStringWrapper.class);
@@ -94,7 +94,7 @@ public class XMLUtil {
 		}
 	}
 
-	static JAXBContext jaxbContextComments;
+	static final JAXBContext jaxbContextComments;
 	static {
 		try {
 			jaxbContextComments = JAXBContext.newInstance(ListStringWrapper.class);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BetaBridge.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BetaBridge.java
index 552b509a23..066d7e38a3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BetaBridge.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BetaBridge.java
@@ -34,9 +34,9 @@ public class BetaBridge implements Serializable {
 
 	private static final long serialVersionUID = -5097435425455958487L;
 
-	BridgeType type;
-	int partner1;
-	int partner2;
+	final BridgeType type;
+	final int partner1;
+	final int partner2;
 
 	public BetaBridge(int i, int j, BridgeType t) {
 		partner1 = Math.min(i, j);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java
index aa06a9b641..897618ce9e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java
@@ -20,19 +20,6 @@
  */
 package org.biojava.nbio.structure.secstruc;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.StringReader;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.zip.GZIPInputStream;
-
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.ResidueNumber;
 import org.biojava.nbio.structure.Structure;
@@ -40,6 +27,12 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.*;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.zip.GZIPInputStream;
+
 /**
  * Class to parse a DSSP file (output of the DSSP program),
  * that contains the secondary structure assignment of a structure.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java
index cc66c9a4a2..c70f3f3cb5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java
@@ -28,12 +28,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 /**
  * Calculate and assign the secondary structure (SS) to the
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucElement.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucElement.java
index 7c08b9100d..38815aa570 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucElement.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucElement.java
@@ -20,11 +20,11 @@
  */
 package org.biojava.nbio.structure.secstruc;
 
-import java.io.Serializable;
-
 import org.biojava.nbio.structure.ResidueNumber;
 import org.biojava.nbio.structure.ResidueRangeAndLength;
 
+import java.io.Serializable;
+
 /**
  * A secondary structure element (SSE) is an object representing a block of
  * sequential residues that share the same secondary structure type.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucInfo.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucInfo.java
index 88654724d2..51271a314b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucInfo.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucInfo.java
@@ -20,10 +20,10 @@
  */
 package org.biojava.nbio.structure.secstruc;
 
-import java.io.Serializable;
-
 import org.biojava.nbio.structure.Group;
 
+import java.io.Serializable;
+
 /**
  * Container for the secondary structure information of a single residue. This
  * class is designed to be stored inside an Amino Acid object. It can also
@@ -47,8 +47,8 @@ public class SecStrucInfo implements Serializable {
 	public static final String BIOJAVA_ASSIGNMENT = "BIOJAVA_ASSIGNMENT";
 
 	protected SecStrucType type;
-	protected String assignment;
-	protected Group parent;
+	protected final String assignment;
+	protected final Group parent;
 
 	public SecStrucInfo(Group g, String ass, SecStrucType t) {
 		type = t;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
index 93f248768c..17d32cc224 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
@@ -20,13 +20,16 @@
  */
 package org.biojava.nbio.structure.secstruc;
 
-import java.util.*;
-
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.GroupIterator;
 import org.biojava.nbio.structure.ResidueNumber;
 import org.biojava.nbio.structure.Structure;
 
+import java.util.ArrayList;
+import java.util.EnumMap;
+import java.util.List;
+import java.util.Map;
+
 /**
  * This class contains methods for obtaining and converting secondary structure
  * information from BioJava {@link Structure}s.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/AxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/AxisAligner.java
index 4721f101b3..8d44a0ef14 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/AxisAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/AxisAligner.java
@@ -20,14 +20,13 @@
  */
 package org.biojava.nbio.structure.symmetry.axis;
 
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
+
 import javax.vecmath.Matrix3d;
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
-
-import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
-import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
-
 import java.util.List;
 
 public abstract class AxisAligner {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java
index 1c8159dde7..a52fba61fe 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java
@@ -30,7 +30,6 @@
 import org.slf4j.LoggerFactory;
 
 import javax.vecmath.*;
-
 import java.util.*;
 
 public class HelixAxisAligner extends AxisAligner {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java
index 950429401e..bb0631d577 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java
@@ -23,14 +23,13 @@
 import org.biojava.nbio.structure.geometry.CalcPoint;
 import org.biojava.nbio.structure.geometry.MomentsOfInertia;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
 import org.biojava.nbio.structure.symmetry.core.Rotation;
 import org.biojava.nbio.structure.symmetry.core.RotationGroup;
-import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import javax.vecmath.*;
-
 import java.util.*;
 
 public class RotationAxisAligner extends AxisAligner{
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java
index 0101c9d189..276944fa40 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java
@@ -24,12 +24,7 @@
 import org.biojava.nbio.structure.geometry.CalcPoint;
 import org.biojava.nbio.structure.geometry.UnitQuaternions;
 
-import javax.vecmath.AxisAngle4d;
-import javax.vecmath.Matrix4d;
-import javax.vecmath.Point3d;
-import javax.vecmath.Quat4d;
-import javax.vecmath.Vector3d;
-
+import javax.vecmath.*;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
index 9d6850f5e5..0a679c33e4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
@@ -21,8 +21,8 @@
 package org.biojava.nbio.structure.symmetry.core;
 
 import org.biojava.nbio.structure.geometry.CalcPoint;
-import javax.vecmath.Point3d;
 
+import javax.vecmath.Point3d;
 import java.util.*;
 import java.util.Map.Entry;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java
index 7a5af85d39..ee035a2ee6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java
@@ -21,9 +21,9 @@
 package org.biojava.nbio.structure.symmetry.core;
 
 import org.biojava.nbio.structure.geometry.CalcPoint;
+
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
-
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
index 39ca6dcd94..df9f4c29f8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
@@ -29,7 +29,6 @@
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
-
 import java.util.*;
 import java.util.Map.Entry;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
index ed0ab1636d..5d286c9bcd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
@@ -21,18 +21,14 @@
 
 package org.biojava.nbio.structure.symmetry.core;
 
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
 
 /**
  *
  * @author Peter
  */
 public class PermutationGroup implements Iterable<List<Integer>> {
-	List<List<Integer>> permutations = new ArrayList<>();
+	final List<List<Integer>> permutations = new ArrayList<>();
 
 	public void addPermutation(List<Integer> permutation) {
 		if (!permutations.contains(permutation)) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
index 5df1278563..ed4569d522 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
@@ -25,7 +25,6 @@
 
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
-
 import java.util.List;
 
 /**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
index 4a9642efc2..da2199b7f2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
@@ -24,18 +24,20 @@
 
 import org.biojava.nbio.structure.Calc;
 import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.cluster.*;
+import org.biojava.nbio.structure.cluster.Subunit;
+import org.biojava.nbio.structure.cluster.SubunitCluster;
+import org.biojava.nbio.structure.cluster.SubunitClusterer;
+import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
 import org.biojava.nbio.structure.contact.BoundingBox;
 import org.biojava.nbio.structure.contact.Grid;
+import org.jgrapht.Graph;
+import org.jgrapht.alg.clique.CliqueMinimalSeparatorDecomposition;
+import org.jgrapht.graph.AsSubgraph;
+import org.jgrapht.graph.DefaultEdge;
 import org.jgrapht.graph.SimpleGraph;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import org.jgrapht.alg.clique.CliqueMinimalSeparatorDecomposition;
-import org.jgrapht.graph.DefaultEdge;
-import org.jgrapht.graph.AsSubgraph;
-import org.jgrapht.Graph;
-
 import javax.vecmath.Point3d;
 import java.util.*;
 import java.util.stream.Collectors;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
index 63452a9f76..47f9b3fa68 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
@@ -30,8 +30,8 @@
 
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
-
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.stream.Collectors;
 
 /**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
index 6f451d0097..07cbdc1067 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
@@ -21,25 +21,15 @@
 
 package org.biojava.nbio.structure.symmetry.core;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import javax.vecmath.AxisAngle4d;
-import javax.vecmath.Matrix4d;
-import javax.vecmath.Point3d;
-import javax.vecmath.Quat4d;
-import javax.vecmath.Vector3d;
-
 import org.biojava.nbio.structure.geometry.CalcPoint;
 import org.biojava.nbio.structure.geometry.MomentsOfInertia;
 import org.biojava.nbio.structure.geometry.UnitQuaternions;
 import org.biojava.nbio.structure.symmetry.geometry.DistanceBox;
 import org.biojava.nbio.structure.symmetry.geometry.SphereSampler;
 
+import javax.vecmath.*;
+import java.util.*;
+
 
 /**
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java
index dc6a09053f..435dfce949 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java
@@ -204,17 +204,12 @@ private String generateAlpha(int clusterInd) {
 				}
 				break;
 
-			case QUESTIONMARK:
-				key = "?";
-				if(clusterInd<alphabet.length()) {
-					key = alphabet.substring(clusterInd, clusterInd + 1);
-				}
-				break;
-
-			case CUSTOM:
+            case CUSTOM:
 				throw new IllegalStateException("Alphas should be handled by the custom generator function.");
 
-			default:
+            case QUESTIONMARK:
+
+            default:
 				key = "?";
 				if(clusterInd<alphabet.length()) {
 					key = alphabet.substring(clusterInd, clusterInd + 1);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
index 4ae3d06a54..6e3c2cdc1b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
@@ -25,12 +25,7 @@
 import org.biojava.nbio.structure.geometry.UnitQuaternions;
 import org.biojava.nbio.structure.symmetry.utils.PermutationGenerator;
 
-import javax.vecmath.AxisAngle4d;
-import javax.vecmath.Matrix4d;
-import javax.vecmath.Point3d;
-import javax.vecmath.Quat4d;
-import javax.vecmath.Vector3d;
-
+import javax.vecmath.*;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java
index c6a4d49594..38a848805b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java
@@ -20,10 +20,10 @@
  */
 package org.biojava.nbio.structure.symmetry.geometry;
 
+import org.biojava.nbio.structure.geometry.CalcPoint;
+
 import javax.vecmath.Matrix3d;
 import javax.vecmath.Point3d;
-
-import org.biojava.nbio.structure.geometry.CalcPoint;
 import java.util.Arrays;
 import java.util.List;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java
index 52be30f224..f971d0bdd8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java
@@ -20,13 +20,12 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
-import static java.lang.Math.*;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.RotationAxis;
-import org.biojava.nbio.structure.symmetry.internal.OrderDetector;
-import org.biojava.nbio.structure.symmetry.internal.RefinerFailedException;
+
+import static java.lang.Math.PI;
+import static java.lang.Math.abs;
 
 /**
  * Guesses an order of rotational symmetry from the angle.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java
index 2548d7ef8d..f12bf4ec0d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java
@@ -20,11 +20,11 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
+import org.biojava.nbio.structure.align.ce.CeParameters;
+
 import java.util.List;
 import java.util.Random;
 
-import org.biojava.nbio.structure.align.ce.CeParameters;
-
 /**
  * Provides parameters to {@link CeSymm}.
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
index 0403f71439..24dba870bd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
@@ -20,16 +20,7 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.vecmath.Matrix4d;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIdentifier;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.ce.CECalculator;
 import org.biojava.nbio.structure.align.ce.CeCPMain;
 import org.biojava.nbio.structure.align.ce.MatrixListener;
@@ -44,6 +35,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix4d;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Identify the symmetries in a structure by running an alignment of the
  * structure against itself disabling the diagonal of the identity alignment.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
index 21ae1ad30f..3362b502df 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
@@ -20,22 +20,9 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-import java.util.Set;
-
-import javax.vecmath.Matrix4d;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.align.multiple.Block;
-import org.biojava.nbio.structure.align.multiple.BlockImpl;
-import org.biojava.nbio.structure.align.multiple.BlockSet;
-import org.biojava.nbio.structure.align.multiple.BlockSetImpl;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
+import org.biojava.nbio.structure.align.multiple.*;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
 import org.biojava.nbio.structure.secstruc.SecStrucElement;
 import org.biojava.nbio.structure.secstruc.SecStrucTools;
@@ -50,6 +37,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix4d;
+import java.util.*;
+
 /**
  * Iterative version of CeSymm that aims at identifying all symmetry axis of a
  * structure.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java
index fac56358f5..b3111e47cd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java
@@ -20,16 +20,7 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.ResidueRange;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIdentifier;
-import org.biojava.nbio.structure.SubstructureIdentifier;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.multiple.Block;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
@@ -38,6 +29,10 @@
 import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType;
 import org.biojava.nbio.structure.symmetry.utils.SymmetryTools;
 
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
 /**
  * This Class stores all the relevant information of an internal symmetry result
  * obtained with CeSymm. The purpose is to carry all the information packed
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java
index 0c77cfce07..3b310c8869 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java
@@ -20,11 +20,6 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.symmetry.utils.SymmetryTools;
@@ -32,6 +27,11 @@
 import org.jgrapht.alg.connectivity.ConnectivityInspector;
 import org.jgrapht.graph.DefaultEdge;
 
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
 /**
  * The GraphOrderDetector transforms the self-alignment into a Graph and
  * extracts its maximally connected Components.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java
index e4a682b35a..99ef318557 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java
@@ -20,14 +20,6 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.Set;
-
-import javax.vecmath.GMatrix;
-import javax.vecmath.GVector;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.model.AFPChain;
@@ -38,6 +30,13 @@
 import org.jgrapht.alg.connectivity.ConnectivityInspector;
 import org.jgrapht.graph.DefaultEdge;
 
+import javax.vecmath.GMatrix;
+import javax.vecmath.GVector;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Set;
+
 /**
  * The GraphRefiner transforms the self-alignment into a Graph and extracts its
  * maximally connected Components. It then refines the alignment by combining
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionOrderDetector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionOrderDetector.java
index 8a5e0aff81..1d9e05b031 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionOrderDetector.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionOrderDetector.java
@@ -20,13 +20,13 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
-import java.util.Map;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AlignmentTools;
 
+import java.util.Map;
+
 /**
  * Calls Spencer's method for determining order.
  * This method uses the sequence alignment information
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
index 8672f68b76..2272406d5d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
@@ -20,15 +20,6 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.NavigableSet;
-import java.util.TreeSet;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.model.AFPChain;
@@ -36,6 +27,8 @@
 import org.biojava.nbio.structure.align.util.AlignmentTools;
 import org.biojava.nbio.structure.symmetry.utils.SymmetryTools;
 
+import java.util.*;
+
 /**
  * Creates a refined alignment with the CE-Symm alternative self-alignment.
  * Needs the order of symmetry and assumes that the last repeat aligns
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
index fded24ae09..71c5e73009 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
@@ -20,13 +20,6 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.Random;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.multiple.Block;
@@ -39,6 +32,13 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Random;
+
 /**
  * Optimizes a symmetry alignment by a Monte Carlo score optimization of the
  * repeat multiple alignment. The superposition of the repeats is not free
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java
index cd8509e50b..6f69aef4b9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java
@@ -20,17 +20,16 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
+import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
+import org.biojava.nbio.structure.align.util.RotationAxis;
+import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType;
+
+import javax.vecmath.Matrix4d;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
 
-import javax.vecmath.Matrix4d;
-
-import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
-import org.biojava.nbio.structure.align.util.RotationAxis;
-import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType;
-
 /**
  * Data Structure that stores all the symmetry axis that describe
  * the symmetry of a structure. Generalizes to all types of symmetry,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java
index d827a03f48..fb5975c0d7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java
@@ -23,11 +23,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Serializable;
+import java.io.*;
 import java.net.URL;
 import java.util.*;
 
@@ -162,8 +158,7 @@ private void loadClusters(int sequenceIdentity) {
 				String line;
 				while ((line = reader.readLine()) != null) {
 					line = line.replaceAll("_", ".");
-					List<String> cluster = Arrays.asList(line.split(" "));
-					clusters.add(cluster);
+					clusters.add(Arrays.asList(line.split(" ")));
 				}
 				reader.close();
 				stream.close();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PowerSet.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PowerSet.java
index 9a0f154d6d..03bae032f2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PowerSet.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PowerSet.java
@@ -20,13 +20,13 @@
  */
 package org.biojava.nbio.structure.symmetry.utils;
 
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector;
+
 import java.util.ArrayList;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Set;
 
-import org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector;
-
 /**
  * In mathematics, the power set (or powerset) of any set S, written P(S), is
  * the set of all subsets of S, including the empty set and S itself.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
index db5ebb04cf..27a62291e1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
@@ -20,37 +20,11 @@
  */
 package org.biojava.nbio.structure.symmetry.utils;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-import java.util.Set;
-import java.util.TreeSet;
-import java.util.stream.Collectors;
-
-import javax.vecmath.Matrix4d;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.GroupType;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIdentifier;
-import org.biojava.nbio.structure.StructureImpl;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.ce.CECalculator;
 import org.biojava.nbio.structure.align.helper.AlignUtils;
 import org.biojava.nbio.structure.align.model.AFPChain;
-import org.biojava.nbio.structure.align.multiple.Block;
-import org.biojava.nbio.structure.align.multiple.BlockImpl;
-import org.biojava.nbio.structure.align.multiple.BlockSet;
-import org.biojava.nbio.structure.align.multiple.BlockSetImpl;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
+import org.biojava.nbio.structure.align.multiple.*;
 import org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
 import org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer;
@@ -70,6 +44,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.vecmath.Matrix4d;
+import java.util.*;
+import java.util.stream.Collectors;
+
 /**
  * Utility methods for symmetry (quaternary and internal) detection and result
  * manipulation.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/WwPDBValidationInformation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/WwPDBValidationInformation.java
index 7bcf3a9a13..3a2a043b48 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/WwPDBValidationInformation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/validation/WwPDBValidationInformation.java
@@ -29,7 +29,6 @@
 package org.biojava.nbio.structure.validation;
 
 import javax.xml.bind.annotation.*;
-
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
index 4573ddbd5b..4ac9ba66b5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
@@ -37,7 +37,6 @@
 import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
-
 import java.io.ByteArrayOutputStream;
 import java.io.PrintStream;
 import java.io.Serializable;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/UnitCellBoundingBox.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/UnitCellBoundingBox.java
index 25e5ebe76a..33963396f4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/UnitCellBoundingBox.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/UnitCellBoundingBox.java
@@ -26,10 +26,9 @@
 import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.contact.BoundingBox;
 
-import java.util.List;
-
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Vector3d;
+import java.util.List;
 
 /**
  * A class to contain the BoundingBoxes of all polymeric molecules in a full unit cell.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/AtomPositionMapTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/AtomPositionMapTest.java
index 45929ad5c1..31b92dd39f 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/AtomPositionMapTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/AtomPositionMapTest.java
@@ -33,7 +33,7 @@
 import java.util.NavigableMap;
 
 import static org.junit.Assert.*;
-import static org.junit.Assume.*;
+import static org.junit.Assume.assumeTrue;
 
 /**
  * A unit test for {@link org.biojava.nbio.structure.AtomPositionMap}.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/PdbFileFormat30Test.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/PdbFileFormat30Test.java
index a2351cfa71..c1398dbeb1 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/PdbFileFormat30Test.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/PdbFileFormat30Test.java
@@ -27,13 +27,12 @@
 import org.biojava.nbio.structure.io.PDBFileParser;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
 import org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider;
+import org.junit.Test;
 
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.List;
 
-import org.junit.Test;
-
 import static org.junit.Assert.*;
 
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java
index 8d42461300..172cd9b5a3 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java
@@ -20,14 +20,14 @@
  */
 package org.biojava.nbio.structure;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.junit.Test;
 
+import java.io.IOException;
+
+import static org.junit.Assert.*;
+
 /**
  * Created by andreas on 9/16/15.
  */
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomIterator.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomIterator.java
index 7d4fea963d..e4bcf8b874 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomIterator.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomIterator.java
@@ -20,18 +20,13 @@
  */
 package org.biojava.nbio.structure;
 
-import static org.junit.Assert.*;
+import org.junit.Test;
 
 import java.io.IOException;
 import java.util.NoSuchElementException;
 
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.AtomIterator;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.StructureTools;
-import org.junit.Test;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
 
 public class TestAtomIterator {
 	@Test
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBioAssemblyIdentifier.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBioAssemblyIdentifier.java
index 845ea0f51c..332a4e0a07 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBioAssemblyIdentifier.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBioAssemblyIdentifier.java
@@ -20,12 +20,13 @@
  */
 package org.biojava.nbio.structure;
 
-import static org.junit.Assert.*;
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.junit.Test;
 
 import java.io.IOException;
 
-import org.biojava.nbio.structure.align.util.AtomCache;
-import org.junit.Test;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
 
 public class TestBioAssemblyIdentifier {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java
index 1140a14738..260b7307a9 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java
@@ -20,10 +20,6 @@
  */
 package org.biojava.nbio.structure;
 
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
@@ -33,7 +29,12 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import static org.junit.Assert.*;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 
 public class TestBond {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
index 5a9838cc2e..ae31b9911a 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
@@ -20,15 +20,16 @@
  */
 package org.biojava.nbio.structure;
 
-import static org.junit.Assert.*;
+import org.biojava.nbio.structure.geometry.Matrices;
+import org.biojava.nbio.structure.jama.Matrix;
+import org.junit.Test;
 
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
 
-import org.biojava.nbio.structure.geometry.Matrices;
-import org.biojava.nbio.structure.jama.Matrix;
-import org.junit.Test;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 public class TestCalc {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestChargeAdder.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestChargeAdder.java
index f814a600db..c22442f213 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestChargeAdder.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestChargeAdder.java
@@ -20,12 +20,12 @@
  */
 package org.biojava.nbio.structure;
 
-import static org.junit.Assert.assertEquals;
+import org.biojava.nbio.structure.io.ChargeAdder;
+import org.junit.Test;
 
 import java.io.IOException;
 
-import org.biojava.nbio.structure.io.ChargeAdder;
-import org.junit.Test;
+import static org.junit.Assert.assertEquals;
 
 /**
  * Class of functions to test the charge adder.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java
index 0b9d7f7860..fb314939cc 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java
@@ -24,14 +24,14 @@
  */
 package org.biojava.nbio.structure;
 
-import java.io.IOException;
-import java.util.Iterator;
-import java.util.List;
-
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.junit.Test;
 
+import java.io.IOException;
+import java.util.Iterator;
+import java.util.List;
+
 import static org.junit.Assert.*;
 
 public class TestCloning {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDNAAlignment.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDNAAlignment.java
index 1324832866..3a22386273 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDNAAlignment.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDNAAlignment.java
@@ -24,15 +24,16 @@
 
 package org.biojava.nbio.structure;
 
-import java.io.IOException;
-
-import static org.junit.Assert.*;
-
 import org.biojava.nbio.structure.align.ce.CeMain;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.junit.Test;
 
+import java.io.IOException;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
 /** make sure DNA alignments fail gracefully
  *
  * @author Andreas Prlic
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDownloadChemCompProvider.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDownloadChemCompProvider.java
index 96508dc551..53e6fe5510 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDownloadChemCompProvider.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDownloadChemCompProvider.java
@@ -24,7 +24,6 @@
 import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.junit.Test;
-import static org.junit.Assert.*;
 
 import java.io.File;
 import java.io.FileOutputStream;
@@ -32,6 +31,8 @@
 import java.io.PrintWriter;
 import java.util.zip.GZIPOutputStream;
 
+import static org.junit.Assert.*;
+
 public class TestDownloadChemCompProvider {
 
 	@Test
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java
index c457bc3db4..9913e3dd92 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java
@@ -26,10 +26,12 @@
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.util.Comparator;
 import java.util.List;
 import java.util.zip.GZIPInputStream;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
 
 public class TestEntityHeuristics {
 
@@ -243,7 +245,7 @@ private Structure getStructure(String fileName, boolean setAlignSeqRes) throws I
 
 	private void checkEntitiesNumbered(List<EntityInfo> entities) {
 
-		entities.sort((o1, o2) -> Integer.compare(o1.getMolId(), o2.getMolId()));
+		entities.sort(Comparator.comparingInt(EntityInfo::getMolId));
 
 		int id = 1;
 		for (EntityInfo compound:entities) {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityResIndexMapping.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityResIndexMapping.java
index f0926364b9..c336834eb6 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityResIndexMapping.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityResIndexMapping.java
@@ -20,7 +20,11 @@
  */
 package org.biojava.nbio.structure;
 
-import static org.junit.Assert.*;
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.biojava.nbio.structure.io.FileParsingParameters;
+import org.biojava.nbio.structure.io.PDBFileParser;
+import org.junit.Ignore;
+import org.junit.Test;
 
 import java.io.IOException;
 import java.io.InputStream;
@@ -28,11 +32,7 @@
 import java.util.List;
 import java.util.zip.GZIPInputStream;
 
-import org.biojava.nbio.structure.align.util.AtomCache;
-import org.biojava.nbio.structure.io.FileParsingParameters;
-import org.biojava.nbio.structure.io.PDBFileParser;
-import org.junit.Ignore;
-import org.junit.Test;
+import static org.junit.Assert.*;
 
 /**
  * Various tests for functionality in {@link EntityInfo} and {@link org.biojava.nbio.structure.io.EntityFinder}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java
index a448d327b8..0f31936360 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java
@@ -20,15 +20,6 @@
  */
 package org.biojava.nbio.structure;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNotSame;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
-
-import java.io.IOException;
-import java.util.List;
-
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.contact.StructureInterface;
 import org.biojava.nbio.structure.contact.StructureInterfaceList;
@@ -38,6 +29,11 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.IOException;
+import java.util.List;
+
+import static org.junit.Assert.*;
+
 public class TestStructureCrossReferences {
 
 	private static final Logger logger = LoggerFactory.getLogger(TestStructureCrossReferences.class);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureImpl.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureImpl.java
index 14ab6e6abf..446d69fbbc 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureImpl.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureImpl.java
@@ -20,11 +20,11 @@
  */
 package org.biojava.nbio.structure;
 
-import static org.junit.Assert.*;
+import org.junit.Test;
 
 import java.util.ArrayList;
 
-import org.junit.Test;
+import static org.junit.Assert.assertEquals;
 
 /**
  * This tests the correctness of the {@link Structure} data structure, in terms
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureSerialization.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureSerialization.java
index 8eb7d584a8..fae48c638e 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureSerialization.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureSerialization.java
@@ -23,13 +23,9 @@
 import org.biojava.nbio.structure.io.PDBFileReader;
 import org.junit.Test;
 
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
+import java.io.*;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
 
 /**
  * Test the serialization and deserialization of BioJava structure objects.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java
index 41f4ff5def..8252b8c04d 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java
@@ -20,17 +20,17 @@
  */
 package org.biojava.nbio.structure;
 
-import static org.junit.Assert.*;
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
 import java.net.URL;
 import java.net.UnknownHostException;
 import java.util.Arrays;
 
-import org.biojava.nbio.structure.align.util.AtomCache;
-import org.junit.Test;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+import static org.junit.Assert.*;
 
 public class TestURLIdentifier {
 	private static final Logger logger = LoggerFactory.getLogger(TestURLIdentifier.class);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/TestAlignmentConsistency.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/TestAlignmentConsistency.java
index 4cdd29eae9..0d1da5b6d1 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/TestAlignmentConsistency.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/TestAlignmentConsistency.java
@@ -29,12 +29,13 @@
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.junit.Test;
-import static org.junit.Assert.*;
 
 import java.io.IOException;
 import java.util.Arrays;
 import java.util.List;
 
+import static org.junit.Assert.assertEquals;
+
 public class TestAlignmentConsistency {
 
 	// Check that indices of the aligned residues are unique
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java
index 5118756f3a..87d95dc57b 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java
@@ -28,7 +28,6 @@
 import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AtomCache;
-import org.biojava.nbio.structure.io.PDBParseException;
 import org.junit.Assert;
 import org.junit.Test;
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestWebStartClient.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestWebStartClient.java
index c8c79077cf..2884534205 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestWebStartClient.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestWebStartClient.java
@@ -24,6 +24,7 @@
 
 package org.biojava.nbio.structure.align.ce;
 
+import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.StructureAlignment;
@@ -34,7 +35,6 @@
 import org.biojava.nbio.structure.align.xml.AFPChainFlipper;
 import org.biojava.nbio.structure.align.xml.AFPChainXMLConverter;
 import org.biojava.nbio.structure.align.xml.AFPChainXMLParser;
-import org.biojava.nbio.core.util.PrettyXMLWriter;
 import org.junit.Assert;
 import org.junit.Test;
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/client/TestStructureName.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/client/TestStructureName.java
index c40bfa84f2..dc61324d0b 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/client/TestStructureName.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/client/TestStructureName.java
@@ -20,16 +20,16 @@
  */
 package org.biojava.nbio.structure.align.client;
 
-import static org.biojava.nbio.structure.align.client.StructureName.Source.*;
-import static org.junit.Assert.*;
+import org.biojava.nbio.structure.StructureException;
+import org.junit.Ignore;
+import org.junit.Test;
 
 import java.io.File;
 import java.net.MalformedURLException;
 import java.net.URL;
 
-import org.biojava.nbio.structure.StructureException;
-import org.junit.Ignore;
-import org.junit.Test;
+import static org.biojava.nbio.structure.align.client.StructureName.Source.*;
+import static org.junit.Assert.*;
 
 public class TestStructureName {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestAFPChainConversion.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestAFPChainConversion.java
index 425c88b2f4..49ce1102df 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestAFPChainConversion.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestAFPChainConversion.java
@@ -28,7 +28,7 @@
 import org.biojava.nbio.structure.jama.Matrix;
 import org.junit.Test;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
 
 /**
  * Test that all relevant information (except scores and cache) is correctly
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestSampleGenerator.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestSampleGenerator.java
index d9decd149b..10256da06a 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestSampleGenerator.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/TestSampleGenerator.java
@@ -20,17 +20,7 @@
  */
 package org.biojava.nbio.structure.align.multiple;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIdentifier;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.client.StructureName;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
 import org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer;
@@ -39,6 +29,12 @@
 import org.biojava.nbio.structure.io.PDBFileReader;
 import org.biojava.nbio.structure.io.StructureIOFile;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
 /**
  * This class is a helper for all the other MultipleAlignment test classes.
  * It contains methods for generating sample MultipleAlignments with known
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java
index 86b3874888..8610f1f3fb 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java
@@ -20,31 +20,16 @@
  */
 package org.biojava.nbio.structure.align.multiple.util;
 
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.align.multiple.*;
+import org.junit.Test;
+
+import javax.vecmath.Matrix4d;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
-import javax.vecmath.Matrix4d;
-
-import org.biojava.nbio.structure.AminoAcidImpl;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.AtomImpl;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.align.multiple.Block;
-import org.biojava.nbio.structure.align.multiple.BlockImpl;
-import org.biojava.nbio.structure.align.multiple.BlockSet;
-import org.biojava.nbio.structure.align.multiple.BlockSetImpl;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
-import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
-import org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer;
-import org.junit.Test;
-
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
 
 /**
  * Test the correctness of various Score calculations for
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentTools.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentTools.java
index a0b0b30287..ea660480ed 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentTools.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentTools.java
@@ -20,19 +20,14 @@
  */
 package org.biojava.nbio.structure.align.multiple.util;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
+import org.biojava.nbio.structure.align.multiple.*;
+import org.junit.Test;
 
 import java.util.Arrays;
 import java.util.List;
 
-import org.biojava.nbio.structure.align.multiple.Block;
-import org.biojava.nbio.structure.align.multiple.BlockImpl;
-import org.biojava.nbio.structure.align.multiple.BlockSet;
-import org.biojava.nbio.structure.align.multiple.BlockSetImpl;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
-import org.junit.Test;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
 
 /**
  *
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentWriter.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentWriter.java
index 064643ff6d..3f89012228 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentWriter.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentWriter.java
@@ -20,17 +20,16 @@
  */
 package org.biojava.nbio.structure.align.multiple.util;
 
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
-
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
 import org.biojava.nbio.structure.align.multiple.TestSampleGenerator;
-import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
 import org.junit.Test;
 
-import static org.junit.Assert.*;
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+
+import static org.junit.Assert.assertEquals;
 
 /**
  * Test the correctness of various Text outputs for {@link MultipleAlignment}s.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentXMLParser.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentXMLParser.java
index 195e1015c8..343f719b32 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentXMLParser.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentXMLParser.java
@@ -20,25 +20,19 @@
  */
 package org.biojava.nbio.structure.align.multiple.util;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-import java.util.List;
-
-import javax.vecmath.Matrix4d;
-import javax.xml.parsers.ParserConfigurationException;
-
 import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.align.multiple.Block;
-import org.biojava.nbio.structure.align.multiple.BlockSet;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
-import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble;
-import org.biojava.nbio.structure.align.multiple.TestSampleGenerator;
-import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
+import org.biojava.nbio.structure.align.multiple.*;
 import org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser;
 import org.junit.Test;
 import org.xml.sax.SAXException;
 
+import javax.vecmath.Matrix4d;
+import javax.xml.parsers.ParserConfigurationException;
+import java.io.IOException;
+import java.util.List;
+
+import static org.junit.Assert.assertTrue;
+
 /**
  * Test the correctness of converting and parsing a MultipleAlignment
  * into an XML format. It checks that the alignments before converting
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
index 505c5e852b..255b925c4d 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
@@ -20,37 +20,8 @@
  */
 package org.biojava.nbio.structure.align.util;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.net.URL;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.Date;
-import java.util.List;
-import java.util.Locale;
-import java.util.zip.GZIPOutputStream;
-
 import org.biojava.nbio.core.util.FileDownloadUtils;
-import org.biojava.nbio.structure.AtomPositionMap;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.ResidueRangeAndLength;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.StructureIdentifier;
-import org.biojava.nbio.structure.StructureTools;
-import org.biojava.nbio.structure.SubstructureIdentifier;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.io.LocalPDBDirectory;
 import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
 import org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior;
@@ -67,6 +38,22 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.net.URL;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+import java.util.List;
+import java.util.Locale;
+import java.util.zip.GZIPOutputStream;
+
+import static org.junit.Assert.*;
+
 
 /**
  * A test for {@link AtomCache}.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/RotationAxisTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/RotationAxisTest.java
index 24e1513946..85ba3cf6cf 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/RotationAxisTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/RotationAxisTest.java
@@ -51,12 +51,12 @@
 import org.biojava.nbio.structure.AtomImpl;
 import org.junit.Test;
 
-import static org.junit.Assert.assertArrayEquals;
-import static org.junit.Assert.assertEquals;
-
 import javax.vecmath.AxisAngle4d;
 import javax.vecmath.Matrix4d;
 
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+
 /**
  * @author blivens
  *
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java
index 79598bd410..2774f4ca3e 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java
@@ -20,24 +20,17 @@
  */
 package org.biojava.nbio.structure.asa;
 
-import org.biojava.nbio.structure.AminoAcidImpl;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.AtomImpl;
-import org.biojava.nbio.structure.Element;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
 import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
-import static org.junit.Assert.*;
-
 import org.junit.Test;
 
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
+import static org.junit.Assert.*;
+
 /**
  * Testing of Accessible Surface Area calculations
  *
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/basepairs/TestBasePairParameters.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/basepairs/TestBasePairParameters.java
index 0b5c3d0349..f430fd40af 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/basepairs/TestBasePairParameters.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/basepairs/TestBasePairParameters.java
@@ -24,12 +24,11 @@
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.basepairs.BasePairParameters;
 import org.junit.Test;
 
 import java.io.IOException;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
 
 /**
  * This class tests the implementations of the search for base pairs for different RCSB structures
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitCluster.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitCluster.java
index 4b6e55ee28..b1da8919c1 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitCluster.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitCluster.java
@@ -20,27 +20,15 @@
  */
 package org.biojava.nbio.structure.cluster;
 
-import static org.junit.Assert.*;
+import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
+import org.biojava.nbio.structure.*;
+import org.junit.Test;
 
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
-import org.biojava.nbio.structure.AminoAcidImpl;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.AtomImpl;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.EntityInfo;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.StructureImpl;
-import org.biojava.nbio.structure.StructureTools;
-import org.junit.Test;
+import static org.junit.Assert.*;
 
 /**
  * Test the {@link SubunitCluster} merge and divide methods, one test specific
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitExtractor.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitExtractor.java
index e80f4c3b1d..c0ea6c45f9 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitExtractor.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitExtractor.java
@@ -20,16 +20,17 @@
  */
 package org.biojava.nbio.structure.cluster;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-import java.util.List;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.align.util.AtomCache;
 import org.junit.Test;
 
+import java.io.IOException;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+
 /**
  * Test the {@link SubunitExtractor} correctness on different real structures
  * with different types of difficulties.
@@ -85,6 +86,7 @@ public void testHistone() throws StructureException, IOException {
 	@Test
 	public void testBioAssembly() throws StructureException, IOException {
 
+		StructureIO.setAtomCache(new AtomCache());
 		Structure s = StructureIO.getStructure("BIO:4E3E:1");
 
 		List<Subunit> subunits = SubunitExtractor.extractSubunits(s, 5, 0.75, 20);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java
index 96c261e927..1f697aabe2 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java
@@ -30,7 +30,6 @@
 
 import java.io.IOException;
 
-
 import static org.junit.Assert.*;
 
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPosition.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPosition.java
index d963d5872f..09f0447b5a 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPosition.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPosition.java
@@ -20,24 +20,22 @@
  */
 package org.biojava.nbio.structure.geometry;
 
-import static org.junit.Assert.*;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Random;
+import org.junit.Before;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.vecmath.AxisAngle4d;
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Random;
 
-import org.biojava.nbio.structure.geometry.SuperPositionQuat;
-import org.biojava.nbio.structure.geometry.SuperPositionQCP;
-import org.junit.Before;
-import org.junit.Test;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 /**
  * Test and compare the different superposition methods implemented in BioJava.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPositionQCP.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPositionQCP.java
index 8928c26cbd..d86ecd1d6e 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPositionQCP.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestSuperPositionQCP.java
@@ -20,20 +20,18 @@
  */
 package org.biojava.nbio.structure.geometry;
 
-import static org.junit.Assert.*;
-
-import java.util.Random;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.vecmath.AxisAngle4d;
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
+import java.util.Random;
 
-import org.biojava.nbio.structure.geometry.SuperPositionQuat;
-import org.biojava.nbio.structure.geometry.SuperPositionQCP;
-import org.junit.Test;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 /**
  * Test the Quaternion-Based Characteristic Polynomial {@link SuperPositionQCP}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestUnitQuaternions.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestUnitQuaternions.java
index b7456dde1f..1357f9d713 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestUnitQuaternions.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestUnitQuaternions.java
@@ -20,23 +20,15 @@
  */
 package org.biojava.nbio.structure.geometry;
 
-import static org.junit.Assert.*;
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.junit.Test;
 
+import javax.vecmath.*;
 import java.io.IOException;
 
-import javax.vecmath.AxisAngle4d;
-import javax.vecmath.Matrix4d;
-import javax.vecmath.Point3d;
-import javax.vecmath.Quat4d;
-import javax.vecmath.Vector3d;
-
-import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.StructureTools;
-import org.biojava.nbio.structure.geometry.UnitQuaternions;
-import org.junit.Test;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 /**
  * Test the methods in the {@link UnitQuaternions} class.
@@ -170,6 +162,7 @@ public void testOrientationMetricIncrement() throws IOException,
 		transform.rotZ(Math.PI / 15);
 
 		// Get points from a structure.
+		StructureIO.setAtomCache(new AtomCache());
 		Structure pdb = StructureIO.getStructure("4hhb.A");
 		Point3d[] cloud = Calc.atomsToPoints(StructureTools
 				.getRepresentativeAtomArray(pdb));
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java
index ad30f29e3b..75e1d9c31a 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java
@@ -24,6 +24,8 @@
  */
 package org.biojava.nbio.structure.io;
 
+import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
+import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureTools;
@@ -31,8 +33,6 @@
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.align.xml.AFPChainXMLConverter;
 import org.biojava.nbio.structure.scop.ScopFactory;
-import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
-import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.custommonkey.xmlunit.DetailedDiff;
 import org.custommonkey.xmlunit.Diff;
 import org.custommonkey.xmlunit.Difference;
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/StructureSequenceMatcherTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/StructureSequenceMatcherTest.java
index d13975714e..44434bc6e2 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/StructureSequenceMatcherTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/StructureSequenceMatcherTest.java
@@ -23,10 +23,10 @@
 package org.biojava.nbio.structure.io;
 
 
-import org.biojava.nbio.structure.*;
-import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.align.util.AtomCache;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java
index 1368649f61..350bff61e3 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java
@@ -20,14 +20,14 @@
  */
 package org.biojava.nbio.structure.io;
 
-import static org.junit.Assert.assertEquals;
+import org.biojava.nbio.structure.Structure;
+import org.junit.Test;
 
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 
-import org.biojava.nbio.structure.Structure;
-import org.junit.Test;
+import static org.junit.Assert.assertEquals;
 
 public class TestDBRefParsing {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDifficultMmCIFFiles.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDifficultMmCIFFiles.java
index 71ba72ed6e..1982839130 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDifficultMmCIFFiles.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDifficultMmCIFFiles.java
@@ -20,29 +20,7 @@
  */
 package org.biojava.nbio.structure.io;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assume.assumeNotNull;
-import static org.junit.Assume.assumeTrue;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.URISyntaxException;
-import java.net.URL;
-import java.util.List;
-import java.util.Map;
-
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.mmcif.MMcifParser;
 import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
@@ -50,6 +28,16 @@
 import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
 import org.junit.Test;
 
+import java.io.*;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.util.List;
+import java.util.Map;
+
+import static org.junit.Assert.*;
+import static org.junit.Assume.assumeNotNull;
+import static org.junit.Assume.assumeTrue;
+
 /**
  * Testing parsing of some difficult mmCIF files.
  * For instance those containing multi-line quoting using ";\n" as delimiters
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHardBioUnits.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHardBioUnits.java
index 047f1e7b29..f583889a2c 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHardBioUnits.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHardBioUnits.java
@@ -20,27 +20,21 @@
  */
 package org.biojava.nbio.structure.io;
 
-import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.geometry.CalcPoint;
 import org.biojava.nbio.structure.geometry.SuperPosition;
 import org.biojava.nbio.structure.geometry.SuperPositionQCP;
 import org.junit.Test;
 
-import static org.junit.Assert.*;
-
+import javax.vecmath.Matrix4d;
+import javax.vecmath.Point3d;
 import java.io.IOException;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
-import javax.vecmath.Matrix4d;
-import javax.vecmath.Point3d;
+import static org.junit.Assert.*;
 
 public class TestHardBioUnits {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java
index fb685de8d3..2e23c803f4 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java
@@ -20,18 +20,7 @@
  */
 package org.biojava.nbio.structure.io;
 
-import static org.junit.Assert.assertNotNull;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.List;
-import java.util.zip.GZIPInputStream;
-
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
 import org.biojava.nbio.structure.io.mmcif.MMcifParser;
@@ -43,6 +32,13 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
+import java.util.zip.GZIPInputStream;
+
+import static org.junit.Assert.assertNotNull;
+
 public class TestHeaderOnly {
 
 	private static final Logger logger = LoggerFactory.getLogger(TestHeaderOnly.class);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java
index f64d5595a5..9f63489022 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java
@@ -20,29 +20,7 @@
  */
 package org.biojava.nbio.structure.io;
 
-import static org.junit.Assert.*;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.Arrays;
-
-import org.biojava.nbio.structure.AminoAcidImpl;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.AtomImpl;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.Element;
-import org.biojava.nbio.structure.EntityInfo;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.StructureImpl;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.mmcif.MMCIFFileTools;
 import org.biojava.nbio.structure.io.mmcif.MMcifParser;
@@ -52,6 +30,12 @@
 import org.biojava.nbio.structure.io.mmcif.model.IgnoreField;
 import org.junit.Test;
 
+import java.io.*;
+import java.util.Arrays;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
 public class TestMMCIFWriting {
 
 	@Test
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java
index d8dd6100ae..c3e24df943 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java
@@ -24,20 +24,14 @@
 package org.biojava.nbio.structure.io;
 
 
-import org.biojava.nbio.structure.EntityInfo;
-import org.biojava.nbio.structure.EntityType;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
 import java.io.IOException;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
 
 
 public class TestMMcifOrganismParsing {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMmCIFSpecialCases.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMmCIFSpecialCases.java
index 95bb0c29b9..83bab6f865 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMmCIFSpecialCases.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMmCIFSpecialCases.java
@@ -22,13 +22,13 @@
 
 //import static org.junit.Assert.*;
 
+import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
+import org.junit.Test;
+
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.StringReader;
 
-import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
-import org.junit.Test;
-
 public class TestMmCIFSpecialCases {
 
 	/**
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java
index be3b2afe6b..86b6e57832 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java
@@ -20,22 +20,7 @@
  */
 package org.biojava.nbio.structure.io;
 
-import static org.junit.Assert.*;
-
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.List;
-import java.util.zip.GZIPInputStream;
-
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.EntityInfo;
-import org.biojava.nbio.structure.EntityType;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.mmcif.MMcifParser;
 import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
@@ -43,6 +28,12 @@
 import org.biojava.nbio.structure.xtal.CrystalCell;
 import org.junit.Test;
 
+import java.io.*;
+import java.util.List;
+import java.util.zip.GZIPInputStream;
+
+import static org.junit.Assert.*;
+
 /**
  * Tests for non-deposited PDB/mmCIF files, i.e. any kind of "raw" file
  * lacking significant parts of the headers.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFFeatures.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFFeatures.java
index f0c10f5e17..197d9dc854 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFFeatures.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFFeatures.java
@@ -20,20 +20,14 @@
  */
 package org.biojava.nbio.structure.io;
 
-import static org.junit.Assert.*;
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.junit.Test;
 
 import java.io.IOException;
 import java.util.List;
 
-import org.biojava.nbio.structure.Bond;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.Site;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.align.util.AtomCache;
-import org.junit.Test;
+import static org.junit.Assert.*;
 
 /**
  * Created by larsonmattr on 10/31/2015.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFLigands.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFLigands.java
index c97aed8d88..239ad05b9a 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFLigands.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFLigands.java
@@ -20,22 +20,17 @@
  */
 package org.biojava.nbio.structure.io;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
 import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
 import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
 import org.junit.Test;
 
+import java.io.IOException;
+
+import static org.junit.Assert.assertEquals;
+
 /**
  * Created by edlunde-dnastar
  * @since 10/30/2015.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseOnAsymId.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseOnAsymId.java
index 448aed4750..8d92429b18 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseOnAsymId.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseOnAsymId.java
@@ -20,10 +20,6 @@
  */
 package org.biojava.nbio.structure.io;
 
-import java.io.IOException;
-import java.util.List;
-import static org.junit.Assert.*;
-
 import org.biojava.nbio.structure.Chain;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
@@ -31,6 +27,12 @@
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.junit.Test;
 
+import java.io.IOException;
+import java.util.List;
+
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+
 public class TestParseOnAsymId {
 
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestShortLines.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestShortLines.java
index 6f16f478fe..bd1dbbba80 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestShortLines.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestShortLines.java
@@ -20,19 +20,19 @@
  */
 package org.biojava.nbio.structure.io;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Chain;
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.Structure;
 import org.junit.Test;
 
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
 /**
  * This class will test parsing short CONECT lines.
  * @since Nov 30, 2016
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestURLBasedFileParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestURLBasedFileParsing.java
index 0d07e77c6e..b61434e63a 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestURLBasedFileParsing.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestURLBasedFileParsing.java
@@ -21,13 +21,14 @@
 package org.biojava.nbio.structure.io;
 
 
-import java.io.IOException;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
 import org.junit.Test;
-import static org.junit.Assert.*;
+
+import java.io.IOException;
+
+import static org.junit.Assert.assertNotNull;
 
 /**
  * Created by ap3 on 31/07/2015.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestWriteLargeCoordinatePDB.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestWriteLargeCoordinatePDB.java
index 78137f73e2..8bf3ec9bf9 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestWriteLargeCoordinatePDB.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestWriteLargeCoordinatePDB.java
@@ -20,17 +20,13 @@
  */
 package org.biojava.nbio.structure.io;
 
-import static org.junit.Assert.fail;
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.junit.Test;
 
 import java.io.IOException;
 
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.align.util.AtomCache;
-import org.junit.Test;
+import static org.junit.Assert.fail;
 
 public class TestWriteLargeCoordinatePDB {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestChemCompProvider.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestChemCompProvider.java
index 24197868a1..288d850589 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestChemCompProvider.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestChemCompProvider.java
@@ -20,14 +20,6 @@
  */
 package org.biojava.nbio.structure.io.mmcif;
 
-import static org.junit.Assert.assertEquals;
-
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
@@ -39,6 +31,14 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+import static org.junit.Assert.assertEquals;
+
 public class TestChemCompProvider {
 	private static final Logger s_logger = LoggerFactory.getLogger(TestChemCompProvider.class);
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestEntityNameAndType.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestEntityNameAndType.java
index 780aad41c4..9900b69174 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestEntityNameAndType.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestEntityNameAndType.java
@@ -20,18 +20,14 @@
  */
 package org.biojava.nbio.structure.io.mmcif;
 
-import static org.junit.Assert.assertArrayEquals;
-
-import java.io.IOException;
-
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.EntityInfo;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.junit.Test;
+
+import java.io.IOException;
+
+import static org.junit.Assert.assertArrayEquals;
 /**
  * Test to ensure the entity name and type
  * @author Anthony Bradley
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestMmcifV5Changes.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestMmcifV5Changes.java
index 3a1aeef824..2dfc1077f4 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestMmcifV5Changes.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestMmcifV5Changes.java
@@ -20,7 +20,11 @@
  */
 package org.biojava.nbio.structure.io.mmcif;
 
-import static org.junit.Assert.*;
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureIO;
+import org.junit.Before;
+import org.junit.Test;
 
 import java.io.IOException;
 import java.text.ParseException;
@@ -28,11 +32,7 @@
 import java.util.Date;
 import java.util.Locale;
 
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
-import org.junit.Before;
-import org.junit.Test;
+import static org.junit.Assert.assertEquals;
 
 /**
  * Test date related changes in mmCIF 5.0 format.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseInternalChainId.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseInternalChainId.java
index 0132d29de4..98ead0071b 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseInternalChainId.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseInternalChainId.java
@@ -21,14 +21,16 @@
 package org.biojava.nbio.structure.io.mmcif;
 
 
-import java.io.IOException;
-
 import org.biojava.nbio.structure.Chain;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.junit.Test;
-import static org.junit.Assert.*;
+
+import java.io.IOException;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
 
 /**
  * Created by andreas on 5/3/16.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseMmcifHeader.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseMmcifHeader.java
index 52c76422ec..7e4e902de3 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseMmcifHeader.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseMmcifHeader.java
@@ -20,7 +20,12 @@
  */
 package org.biojava.nbio.structure.io.mmcif;
 
-import static org.junit.Assert.assertEquals;
+import org.biojava.nbio.structure.PDBHeader;
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.junit.Test;
 
 import java.io.IOException;
 import java.text.ParseException;
@@ -28,12 +33,7 @@
 import java.util.Date;
 import java.util.Locale;
 
-import org.biojava.nbio.structure.PDBHeader;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.align.util.AtomCache;
-import org.junit.Test;
+import static org.junit.Assert.assertEquals;
 
 /**
  * Test parsing header information from MmCif files.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestBondFinding.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestBondFinding.java
index ab5268578c..6c75e70742 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestBondFinding.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestBondFinding.java
@@ -20,24 +20,18 @@
  */
 package org.biojava.nbio.structure.io.mmtf;
 
-import org.junit.Test;
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-import java.util.List;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Bond;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
 import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
+import org.junit.Test;
+
+import java.io.IOException;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
 
 /**
  * Test bond finding in BioJava
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java
index e0b576d79a..303f58a81d 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java
@@ -25,7 +25,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.*;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
 import java.net.URL;
 import java.util.zip.GZIPInputStream;
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
index a4acb727ee..b80b4dc62e 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
@@ -20,24 +20,7 @@
  */
 package org.biojava.nbio.structure.io.mmtf;
 
-import static org.junit.Assert.assertArrayEquals;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Map;
-
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Bond;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
@@ -48,6 +31,14 @@
 import org.rcsb.mmtf.decoder.StructureDataToAdapter;
 import org.rcsb.mmtf.encoder.AdapterToStructureData;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Map;
+
+import static org.junit.Assert.*;
+
 /**
  * Tests to see if roundtripping of MMTF can be done.
  *
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureReader.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureReader.java
index 17e9d42d32..7f45ffb884 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureReader.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureReader.java
@@ -1,9 +1,5 @@
 package org.biojava.nbio.structure.io.mmtf;
 
-import java.io.IOException;
-import java.nio.file.Paths;
-import java.util.List;
-
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
@@ -14,7 +10,13 @@
 import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
 import org.junit.Ignore;
 import org.junit.Test;
-import static org.junit.Assert.*;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
 
 /**
  * Test the Biojava MMTF reader.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureWriter.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureWriter.java
index 2ef83527c2..84a9f1a9f7 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureWriter.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureWriter.java
@@ -20,27 +20,18 @@
  */
 package org.biojava.nbio.structure.io.mmtf;
 
+import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 
-import org.biojava.nbio.structure.AminoAcidImpl;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.AtomImpl;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.Element;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.PDBHeader;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureImpl;
-import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
-import org.junit.Rule;
-import org.junit.Test;
-import static org.junit.Assert.*;
-import org.junit.rules.TemporaryFolder;
+import static org.junit.Assert.assertEquals;
 
 /**
  * Test the Biojava MMTF writer.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfUtils.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfUtils.java
index 859e24548a..e3f3692da0 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfUtils.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfUtils.java
@@ -20,43 +20,19 @@
  */
 package org.biojava.nbio.structure.io.mmtf;
 
-import org.junit.Test;
-
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import javax.vecmath.Matrix4d;
-
-import org.biojava.nbio.structure.AminoAcidImpl;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.AtomImpl;
-import org.biojava.nbio.structure.BondImpl;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.ExperimentalTechnique;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.HetatomImpl;
-import org.biojava.nbio.structure.NucleotideImpl;
-import org.biojava.nbio.structure.PDBCrystallographicInfo;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.StructureImpl;
-import org.biojava.nbio.structure.io.mmtf.MmtfUtils;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
 import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
 import org.biojava.nbio.structure.xtal.BravaisLattice;
 import org.biojava.nbio.structure.xtal.CrystalCell;
 import org.biojava.nbio.structure.xtal.SpaceGroup;
+import org.junit.Test;
+
+import javax.vecmath.Matrix4d;
+import java.io.IOException;
+import java.util.*;
+
+import static org.junit.Assert.*;
 
 /**
  * Test the MMTF utils class.
@@ -185,7 +161,7 @@ public void testGetUnitCellAsArray() {
 	 */
 	@Test
 	public void testGetExperimentalMethods() {
-		Set<ExperimentalTechnique> experimentalTechniques = new HashSet<>();
+		Set<ExperimentalTechnique> experimentalTechniques = EnumSet.noneOf(ExperimentalTechnique.class);
 		experimentalTechniques.add(ExperimentalTechnique.XRAY_DIFFRACTION);
 		experimentalTechniques.add(ExperimentalTechnique.ELECTRON_MICROSCOPY);
 		String[] techniques = MmtfUtils.techniquesToStringArray(experimentalTechniques);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMappingTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMappingTest.java
index 66f3485248..563e2c0614 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMappingTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMappingTest.java
@@ -25,11 +25,7 @@
 
 import org.junit.Test;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.PrintWriter;
+import java.io.*;
 
 import static org.junit.Assert.assertEquals;
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/redmine/Test1DARSeqAlign.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/redmine/Test1DARSeqAlign.java
index d65bb41abe..defe255958 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/redmine/Test1DARSeqAlign.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/redmine/Test1DARSeqAlign.java
@@ -28,10 +28,11 @@
 import org.biojava.nbio.structure.io.mmcif.ChemCompProvider;
 import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
 import org.junit.Test;
-import static org.junit.Assert.*;
 
 import java.io.IOException;
 
+import static org.junit.Assert.*;
+
 /** test for https://redmine.open-bio.org/issues/3282
  *
  * @author Andreas Prlic
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java
index 6eb2c43a01..bc46d01ba8 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java
@@ -20,17 +20,18 @@
  */
 package org.biojava.nbio.structure.secstruc;
 
-import java.io.IOException;
-import java.util.Collections;
-import java.util.List;
-import java.util.zip.GZIPInputStream;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.junit.Test;
 
-import static org.junit.Assert.*;
+import java.io.IOException;
+import java.util.Collections;
+import java.util.List;
+import java.util.zip.GZIPInputStream;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 /**
  * Test all the options for writting and fetching DSSP file formats. Also
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestSecStrucCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestSecStrucCalc.java
index a2d2708448..7448b888bf 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestSecStrucCalc.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestSecStrucCalc.java
@@ -20,17 +20,17 @@
  */
 package org.biojava.nbio.structure.secstruc;
 
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.List;
-import java.util.zip.GZIPInputStream;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.junit.Test;
 
-import static org.junit.Assert.*;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.zip.GZIPInputStream;
+
+import static org.junit.Assert.assertEquals;
 
 /**
  * Test the correctness of the DSSP implementation in BioJava
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestCeSymm.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestCeSymm.java
index f9d829b5c3..349ffaa95e 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestCeSymm.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestCeSymm.java
@@ -20,17 +20,17 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureTools;
-import org.biojava.nbio.structure.symmetry.internal.CeSymm;
 import org.junit.Test;
 
+import java.io.IOException;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
 /**
  * Run two easy cases of internal symmetry and test that results are significant
  * and order is correct.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSequenceFunctionOrderDetector.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSequenceFunctionOrderDetector.java
index 2dfb680fc6..f5cb5589d4 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSequenceFunctionOrderDetector.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSequenceFunctionOrderDetector.java
@@ -20,22 +20,19 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.Map;
-
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AtomCache;
-import org.biojava.nbio.structure.symmetry.internal.CeSymm;
-import org.biojava.nbio.structure.symmetry.internal.RefinerFailedException;
-import org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector;
 import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod;
 import org.junit.Test;
 
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+
+import static org.junit.Assert.assertEquals;
+
 /**
  * Originally part of {@link CeSymmTest}.
  * @author Spencer Bliven
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSingleRefiner.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSingleRefiner.java
index fa160be574..d31a94f2ad 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSingleRefiner.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSingleRefiner.java
@@ -20,17 +20,16 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.util.AlignmentTools;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
 
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
 /**
  * @author blivens
  *
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSymmetryAxes.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSymmetryAxes.java
index e3c5e6b9bb..b3a2c57ff9 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSymmetryAxes.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSymmetryAxes.java
@@ -20,20 +20,19 @@
  */
 package org.biojava.nbio.structure.symmetry.internal;
 
-import static org.junit.Assert.*;
-
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
+import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType;
+import org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis;
+import org.junit.Test;
 
 import javax.vecmath.AxisAngle4d;
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
 
-import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType;
-import org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis;
-import org.junit.Test;
+import static org.junit.Assert.*;
 
 
 public class TestSymmetryAxes {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/utils/TestSymmetryTools.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/utils/TestSymmetryTools.java
index 543d2322e5..a230c84e3b 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/utils/TestSymmetryTools.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/utils/TestSymmetryTools.java
@@ -20,13 +20,13 @@
  */
 package org.biojava.nbio.structure.symmetry.utils;
 
-import static org.junit.Assert.*;
+import org.junit.Test;
 
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 
-import org.junit.Test;
+import static org.junit.Assert.assertEquals;
 
 /**
  * Test the methods in {@link SymmetryTools} class.
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/test/util/GlobalsHelper.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/test/util/GlobalsHelper.java
index 84884f03f2..c769fa771b 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/test/util/GlobalsHelper.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/test/util/GlobalsHelper.java
@@ -20,10 +20,6 @@
  */
 package org.biojava.nbio.structure.test.util;
 
-import java.util.Deque;
-import java.util.LinkedList;
-import java.util.NoSuchElementException;
-
 import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
@@ -33,6 +29,10 @@
 import org.biojava.nbio.structure.scop.ScopDatabase;
 import org.biojava.nbio.structure.scop.ScopFactory;
 
+import java.util.Deque;
+import java.util.LinkedList;
+import java.util.NoSuchElementException;
+
 /**
  * Helper class to manage all the global state changes in BioJava.
  * For instance, this should be used in tests before modifying PDB_PATH.
@@ -78,7 +78,7 @@ private GlobalsHelper() {}
 	/**
 	 * Save current global state to the stack
 	 */
-	public static void pushState() {
+	public synchronized static void pushState() {
 		PathInfo paths = new PathInfo();
 		stack.addFirst(paths);
 	}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalCell.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalCell.java
index 57bc703d10..d0194d8140 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalCell.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalCell.java
@@ -20,16 +20,17 @@
  */
 package org.biojava.nbio.structure.xtal;
 
-import static org.junit.Assert.*;
+import org.junit.Before;
+import org.junit.Test;
 
 import javax.vecmath.AxisAngle4d;
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Point3i;
-import static java.lang.Math.sqrt;
 
-import org.junit.Before;
-import org.junit.Test;
+import static java.lang.Math.sqrt;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 public class TestCrystalCell {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestInterfaceClustering.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestInterfaceClustering.java
index 313d8ac334..1dfee68774 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestInterfaceClustering.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestInterfaceClustering.java
@@ -20,16 +20,6 @@
  */
 package org.biojava.nbio.structure.xtal;
 
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.zip.GZIPInputStream;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
@@ -43,6 +33,15 @@
 import org.junit.Test;
 
 import javax.vecmath.Matrix4d;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.zip.GZIPInputStream;
+
+import static org.junit.Assert.*;
 
 public class TestInterfaceClustering {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
index 1eb0bcd867..80b5929c5a 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
@@ -61,7 +61,7 @@ public class CoxInfo {
 	int numEvents = 0;
 	private LinkedHashMap<String, String> metaDataFilter = null;
 	private final LinkedHashMap<String, CoxCoefficient> coefficientsList = new LinkedHashMap<>();
-	LinkedHashMap<Double, Double> baselineSurvivorFunction = new LinkedHashMap<>();
+	final LinkedHashMap<Double, Double> baselineSurvivorFunction = new LinkedHashMap<>();
 	ArrayList<SurvivalInfo> survivalInfoList = new ArrayList<>();
 	/**
 	 *
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java
index 57d7b016f3..3725ffdb91 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java
@@ -44,7 +44,7 @@ public class StrataInfo {
 	private final ArrayList<Double> upper = new ArrayList<>();
 	private final ArrayList<Double> lower = new ArrayList<>();
 	private final LinkedHashMap<Double, Integer> ndead = new LinkedHashMap<>();
-	DecimalFormat df = new DecimalFormat("#.######");
+	final DecimalFormat df = new DecimalFormat("#.######");
 	DecimalFormat dfe = new DecimalFormat("0.000000E0");
 
 	/**
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java
index 67a46b9802..9c7e475107 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java
@@ -46,12 +46,12 @@ public class SurvivalInfo implements Comparable<SurvivalInfo> {
 	private double residual = 0.0;
 	private String clusterValue = "";
 
-	LinkedHashMap<String,Double> residualVariableMap = new LinkedHashMap<>();
+	final LinkedHashMap<String,Double> residualVariableMap = new LinkedHashMap<>();
 
 	LinkedHashMap<String, Double> data = new LinkedHashMap<>();
 	//    LinkedHashMap<String, Double> discreteData = new LinkedHashMap<String, Double>();
-	LinkedHashMap<String, String> unknownDataType = new LinkedHashMap<>();
-	LinkedHashMap<String, String> originalMetaData = new LinkedHashMap<>();
+    final LinkedHashMap<String, String> unknownDataType = new LinkedHashMap<>();
+	final LinkedHashMap<String, String> originalMetaData = new LinkedHashMap<>();
 
 	/**
 	 *
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java
index cccbae421b..0f6df69bb8 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java
@@ -33,7 +33,7 @@
 public class CoxVariablesOverallModelFitComparator implements Comparator<CoxVariables>, Serializable {
 	private static final long serialVersionUID = 1;
 
-	String variables;
+	final String variables;
 
 	/**
 	 * Variables are stored as a string representation of an ArrayList
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java
index aab32d5721..445fb7d21c 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java
@@ -29,8 +29,8 @@
  */
 public class CoxVariablesVariableComparator implements CoxComparatorInterface {
 
-	String variables;
-	String variable;
+	final String variables;
+	final String variable;
 
 	/**
 	 *
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java
index 65aef84fb6..b962d399d2 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java
@@ -33,7 +33,7 @@
 public class MeanModelComparator implements Comparator<CoxVariables>, Serializable {
 	private static final long serialVersionUID = 1;
 
-	String variable;
+	final String variable;
 
 	/**
 	 *
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java
index 583283e88f..d0418db509 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java
@@ -32,7 +32,7 @@
 public class SurvivalInfoValueComparator implements Comparator<SurvivalInfo>, Serializable {
 	private static final long serialVersionUID = 1;
 
-	String variable;
+	final String variable;
 
 	/**
 	 *
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
index c31c93ae5a..24573c3b4f 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
@@ -34,7 +34,7 @@ public class WorkSheet {
 	private final LinkedHashMap<String, HeaderInfo> columnLookup = new LinkedHashMap<>();
 	private final LinkedHashMap<String, HeaderInfo> rowLookup = new LinkedHashMap<>();
 	private CompactCharSequence[][] data = new CompactCharSequence[1][1];
-	HashMap<String, String> dataGrid = new HashMap<>();
+	final HashMap<String, String> dataGrid = new HashMap<>();
 	private String indexColumnName = "";
 
 	/**
@@ -808,7 +808,7 @@ public boolean isValidColumn(String col) {
 		}
 	}
 	//When we do gene signatures we ask for the same data value often. This method took up 50% of the time.
-	HashMap<String, Double> doubleValues = new HashMap<>();
+    final HashMap<String, Double> doubleValues = new HashMap<>();
 	boolean cacheDoubleValues = false;
 
 	/**
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
index 11f3ae57d9..933ee57d95 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
@@ -149,7 +149,7 @@ public void setSurvivalInfo(ArrayList<String> title, ArrayList<SurvivalInfo> _si
 
 		this.repaint();
 	}
-	DecimalFormat df = new DecimalFormat("#.#");
+	final DecimalFormat df = new DecimalFormat("#.#");
 
 	private void setRenderingHints(Graphics2D g) {
 		RenderingHints rh = new RenderingHints(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java
index cae28fe6e2..9545f2b185 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java
@@ -34,31 +34,31 @@ public class KMFigureInfo {
 	/**
 	 *
 	 */
-	public int titleHeight = 40;
+	public final int titleHeight = 40;
 	/**
 	 *
 	 */
-	public int padding = 20;
+	public final int padding = 20;
 	/**
 	 *
 	 */
-	public Integer width = 600;
+	public final Integer width = 600;
 	/**
 	 *
 	 */
-	public Integer height = 400;
+	public final Integer height = 400;
 	/**
 	 *
 	 */
-	public double timeScale = 1.0; //multiplier to change time from days to months etc
+	public final double timeScale = 1.0; //multiplier to change time from days to months etc
 	/**
 	 *
 	 */
-	public double yaxisPercentIncrement = .2;
+	public final double yaxisPercentIncrement = .2;
 	/**
 	 *
 	 */
-	public double xaxisPercentIncrement = .25;
+	public final double xaxisPercentIncrement = .25;
 	/**
 	 *
 	 */
@@ -70,24 +70,24 @@ public class KMFigureInfo {
 	/**
 	 *
 	 */
-	public double figureLineInfoLowerPercentX = .01;
+	public final double figureLineInfoLowerPercentX = .01;
 	/**
 	 *
 	 */
-	public double figureLineInfoLowerPercentY = .01;
+	public final double figureLineInfoLowerPercentY = .01;
 	/**
 	 *
 	 */
-	public BasicStroke axisStroke = new BasicStroke(2);
+	public final BasicStroke axisStroke = new BasicStroke(2);
 	/**
 	 *
 	 */
-	public BasicStroke kmStroke = new BasicStroke(3);
+	public final BasicStroke kmStroke = new BasicStroke(3);
 	/**
 	 *
 	 */
-	public Color[] legendColor = {Color.RED, Color.BLUE, Color.GREEN, Color.CYAN, Color.ORANGE, Color.YELLOW, Color.MAGENTA, Color.PINK};
-	public ArrayList<Double> xAxisLabels = new ArrayList<>();//new ArrayList<Double>(Arrays.asList(0.0, 5.0, 10.0, 15.0, 20.0));
+	public final Color[] legendColor = {Color.RED, Color.BLUE, Color.GREEN, Color.CYAN, Color.ORANGE, Color.YELLOW, Color.MAGENTA, Color.PINK};
+	public final ArrayList<Double> xAxisLabels = new ArrayList<>();//new ArrayList<Double>(Arrays.asList(0.0, 5.0, 10.0, 15.0, 20.0));
 	public String xAxisLegend = "";
 	public String yAxisLegend = "";
 	public Color getColor(int index) {
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java
index f48116d832..7206b1b036 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java
@@ -65,8 +65,8 @@ public class KaplanMeierFigure extends JPanel {
 	int labelWidth;
 	double minTime = 0.0;
 	double maxTime = 10.0;
-	double minPercentage = 0.0;
-	double maxPercentage = 1.0;
+	final double minPercentage = 0.0;
+	final double maxPercentage = 1.0;
 	FontMetrics fm;
 	KMFigureInfo kmfi = new KMFigureInfo();
 	LinkedHashMap<String, ArrayList<CensorStatus>> survivalData = new LinkedHashMap<>();
@@ -346,7 +346,7 @@ public void saveSurvivalData(String fileName) throws Exception {
 		}
 		fw.close();
 	}
-	DecimalFormat df = new DecimalFormat("#.#");
+	final DecimalFormat df = new DecimalFormat("#.#");
 
 	@Override
 	public void paintComponent(Graphics g) // draw graphics in the panel
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java
index d3edd72143..25bd425632 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java
@@ -33,7 +33,7 @@ public class MetaDataInfo {
 	/**
 	 *
 	 */
-	public String column;
+	public final String column;
 	/**
 	 *
 	 */
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
index 1811f6fb15..225386cc50 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
@@ -316,8 +316,7 @@ public void setBlastMatrix(BlastMatrixEnum matrix) {
 				setBlastGapCosts(13, 2);
 				break;
                 case BLOSUM62:
-				break;
-			default:
+                default:
 				break;
 			}
 		}
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
index bac977b6d5..b5d178e90c 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
@@ -26,7 +26,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.DataOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
 import java.net.HttpURLConnection;
 import java.net.URL;
 import java.util.SortedSet;
diff --git a/biojava-ws/src/test/java/org/biojava/nbio/ws/hmmer/TestRemoteHmmerScan.java b/biojava-ws/src/test/java/org/biojava/nbio/ws/hmmer/TestRemoteHmmerScan.java
index 59686a2de0..0076052f5c 100644
--- a/biojava-ws/src/test/java/org/biojava/nbio/ws/hmmer/TestRemoteHmmerScan.java
+++ b/biojava-ws/src/test/java/org/biojava/nbio/ws/hmmer/TestRemoteHmmerScan.java
@@ -20,11 +20,12 @@
  */
 package org.biojava.nbio.ws.hmmer;
 
-import java.util.SortedSet;
-
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.junit.Ignore;
 import org.junit.Test;
+
+import java.util.SortedSet;
+
 import static org.junit.Assert.*;
 
 public class TestRemoteHmmerScan {
diff --git a/pom.xml b/pom.xml
index b680b89f62..f24a2df92f 100644
--- a/pom.xml
+++ b/pom.xml
@@ -164,7 +164,7 @@
 				</plugin>
 				<plugin>
 					<artifactId>maven-compiler-plugin</artifactId>
-					<version>3.8.0</version>
+					<version>3.8.1</version>
 					<configuration>
 						<source>${jdk.version}</source>
 						<target>${jdk.version}</target>
@@ -180,11 +180,11 @@
 				</plugin>
 				<plugin>
 					<artifactId>maven-scm-plugin</artifactId>
-					<version>1.10.0</version>
+					<version>1.11.2</version>
 				</plugin>
 				<plugin>
 					<artifactId>maven-source-plugin</artifactId>
-					<version>3.0.1</version>
+					<version>3.2.1</version>
 				</plugin>
 				<plugin>
 					<artifactId>maven-failsafe-plugin</artifactId>
@@ -239,7 +239,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-shade-plugin</artifactId>
-					<version>3.2.0</version>
+					<version>3.2.2</version>
 				</plugin>
 				<plugin>
 					<artifactId>maven-assembly-plugin</artifactId>
@@ -313,7 +313,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-surefire-plugin</artifactId>
-					<version>3.0.0-M3</version>
+					<version>3.0.0-M4</version>
 				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
@@ -368,8 +368,8 @@
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
 					<argLine>-Xmx1500M</argLine>
-					<reuseForks>false</reuseForks>
-					<forkCount>1</forkCount>
+<!--					<reuseForks>false</reuseForks>-->
+<!--					<forkCount>1</forkCount>-->
 				</configuration>
 			</plugin>
 

From 7b660ff61c1f74a4b25e3c8b9af2b07bd9b3540d Mon Sep 17 00:00:00 2001
From: me <seh@internet.earth>
Date: Sat, 7 Mar 2020 20:32:35 -0500
Subject: [PATCH 10/18] updates

---
 .../core/alignment/SimpleAlignedSequence.java |  2 +-
 .../nbio/core/sequence/AccessionID.java       |  1 +
 .../core/sequence/io/GenbankWriterHelper.java | 10 +--
 .../location/template/AbstractLocation.java   |  3 +-
 .../storage/JoiningSequenceReader.java        |  2 +-
 .../sequence/template/AbstractSequence.java   |  2 +-
 .../sequence/template/SequenceProxyView.java  |  2 +-
 .../core/sequence/transcription/Table.java    | 14 +--
 .../org/biojava/nbio/core/util/Equals.java    | 10 ++-
 .../nbio/core/util/PrettyXMLWriter.java       |  8 +-
 .../org/biojava/nbio/core/util/XMLWriter.java |  4 +-
 .../GeneChromosomePositionParser.java         | 11 +--
 .../genome/util/ChromosomeMappingTools.java   | 61 +++++--------
 .../nbio/genome/TestGenomeMapping.java        | 24 +++--
 .../fatcat/TestFlexibleRotationMatrices.java  |  6 +-
 .../java/demo/DemoAlignmentFromFasta.java     |  2 +-
 .../nbio/structure/align/gui/DisplayAFP.java  |  6 +-
 .../align/webstart/AligUIManager.java         |  7 +-
 .../symmetry/gui/SymmetryDisplay.java         |  2 +-
 .../java/org/biojava/nbio/structure/Atom.java |  5 +-
 .../nbio/structure/AtomPositionMap.java       | 34 +++----
 .../java/org/biojava/nbio/structure/Calc.java |  7 +-
 .../org/biojava/nbio/structure/Chain.java     |  2 +
 .../org/biojava/nbio/structure/ChainImpl.java |  8 +-
 .../biojava/nbio/structure/StructureIO.java   |  2 +-
 .../nbio/structure/StructureTools.java        | 37 ++++----
 .../nbio/structure/align/AFPTwister.java      |  5 +-
 .../align/CallableStructureAlignment.java     |  6 +-
 .../nbio/structure/align/ce/CECalculator.java | 90 ++++++++-----------
 .../align/ce/CeCalculatorEnhanced.java        | 22 ++---
 .../calc/StructureAlignmentOptimizer.java     |  3 +-
 .../multiple/mc/MultipleMcOptimizer.java      |  3 +-
 .../align/multiple/util/CoreSuperimposer.java |  4 +-
 .../multiple/util/ReferenceSuperimposer.java  |  4 +-
 .../align/pairwise/AltAligComparator.java     | 25 +++---
 .../align/pairwise/FragmentJoiner.java        |  2 +-
 .../structure/align/quaternary/QsAlign.java   |  8 +-
 .../align/seq/SmithWaterman3Daligner.java     |  3 +-
 .../align/util/AFPAlignmentDisplay.java       |  6 +-
 .../structure/align/util/AlignmentTools.java  |  3 +-
 .../nbio/structure/align/util/AtomCache.java  | 67 +++++---------
 .../basepairs/BasePairParameters.java         | 24 +++--
 .../structure/contact/StructureInterface.java |  2 +-
 .../domain/LocalProteinDomainParser.java      | 10 ++-
 .../biojava/nbio/structure/jama/Matrix.java   |  2 +
 .../structure/symmetry/internal/CeSymm.java   |  2 +-
 .../symmetry/utils/SymmetryTools.java         |  8 +-
 .../util/TestMultipleAlignmentScorer.java     |  6 +-
 .../nbio/structure/asa/TestAsaCalc.java       |  2 +-
 .../structure/cluster/TestSubunitCluster.java |  2 +-
 50 files changed, 270 insertions(+), 311 deletions(-)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
index 81ab206cde..27bf026225 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
@@ -297,7 +297,7 @@ public List<C> getAsList() {
 
 	@Override
 	public boolean equals(Object o){
-
+		if (this == o) return true;
 		if(! Equals.classEqual(this, o)) {
 			return false;
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java
index ebbca86a2a..d145a13035 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java
@@ -93,6 +93,7 @@ public DataSource getDataSource() {
 
 	@Override
 	public boolean equals(Object o) {
+		if (this == o) return true;
 		boolean equals = false;
 		if (Equals.classEqual(this, o)) {
 			AccessionID l = (AccessionID) o;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java
index 4480cab662..dc2a2768ec 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java
@@ -105,11 +105,10 @@ public static void writeNucleotideSequence(File file,
 	 *
 	 * @param outputStream
 	 * @param dnaSequences
-	 * @throws Exception
-	 */
+     */
 
 	public static void writeNucleotideSequence(OutputStream outputStream,
-			Collection<DNASequence> dnaSequences) throws Exception {
+			Collection<DNASequence> dnaSequences) {
 		writeNucleotideSequence(outputStream, dnaSequences, LINEAR_DNA);
 	}
 
@@ -153,10 +152,9 @@ public static void writeSequence(File file, Sequence<?> sequence)
 	 *
 	 * @param outputStream
 	 * @param sequence
-	 * @throws Exception
-	 */
+     */
 	public static void writeSequence(OutputStream outputStream,
-			Sequence<?> sequence) throws Exception {
+			Sequence<?> sequence) {
 		writeSequences(outputStream, singleSeqToCollection(sequence));
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
index 9e5d842cfe..7f07d8bc22 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
@@ -260,8 +260,7 @@ private List<Location> getAllSubLocations(Location location) {
 
 	@Override
 	public boolean equals(Object obj) {
-		if (this == obj)
-			return true;
+		if (this == obj) return true;
 
 		boolean equals = false;
 		if (classEqual(this, obj)) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
index ecd8ac3faf..eaa2c15dc5 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
@@ -303,7 +303,7 @@ public List<C> getAsList() {
 
 	@Override
 	public boolean equals(Object o) {
-
+		if (this == o) return true;
 		if(! Equals.classEqual(this, o)) {
 			return false;
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
index a2e3b145ca..87f0ef34dd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
@@ -545,7 +545,7 @@ public void setCompoundSet(CompoundSet<C> compoundSet) {
 
 	@Override
 	public boolean equals(Object o){
-
+		if (this == o) return true;
 		if(! Equals.classEqual(this, o)) {
 			return false;
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java
index 57c0d5cbc3..15100c8cf5 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java
@@ -74,7 +74,7 @@ public List<C> getAsList() {
 
 	@Override
 	public boolean equals(Object o) {
-
+		if (this == o) return true;
 		if(! Equals.classEqual(this, o)) {
 			return false;
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
index 6bfd4215b2..32d6e4f5dd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
@@ -114,10 +114,11 @@ public CaseInsensitiveTriplet getTriplet() {
 		}
 
 		@Override
-		public boolean equals(Object obj) {
+		public boolean equals(Object o) {
+			if (this == o) return true;
 			boolean equals = false;
-			if(Equals.classEqual(this, obj)) {
-				Codon casted = (Codon) obj;
+			if(Equals.classEqual(this, o)) {
+				Codon casted = (Codon) o;
 				equals =   Equals.equal(getTriplet(), casted.getTriplet()) &&
 							Equals.equal(isStart(), casted.isStart()) &&
 							Equals.equal(isStop(), casted.isStop()) &&
@@ -223,10 +224,11 @@ public NucleotideCompound getThree() {
 		}
 
 		@Override
-		public boolean equals(Object obj) {
+		public boolean equals(Object o) {
+			if (this == o) return true;
 			boolean equals = false;
-			if(Equals.classEqual(this, obj)) {
-				CaseInsensitiveTriplet casted = (CaseInsensitiveTriplet) obj;
+			if(Equals.classEqual(this, o)) {
+				CaseInsensitiveTriplet casted = (CaseInsensitiveTriplet) o;
 				return toString().equals(casted.toString());
 			}
 			return equals;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
index 85beddf1de..335793df75 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
@@ -20,6 +20,8 @@
  */
 package org.biojava.nbio.core.util;
 
+import java.util.Objects;
+
 /**
  * A set of helper methods which return true if the two parameters are
  * equal to each other.
@@ -46,8 +48,9 @@ public static boolean equal(boolean one, boolean two) {
 	 * Does not compare class types.
 	 * @see #classEqual(Object, Object)
 	 */
-	public static boolean equal(Object one, Object two) {
-		return one == null && two == null || !(one == null || two == null) && (one == two || one.equals(two));
+	@Deprecated public static boolean equal(Object one, Object two) {
+		return Objects.equals(one, two);
+		//return one == null && two == null || !(one == null || two == null) && (one == two || one.equals(two));
 	}
 
 	/**
@@ -82,6 +85,7 @@ public static boolean equal(Object one, Object two) {
 	 *         equal at the class level
 	 */
 	public static boolean classEqual(Object one, Object two) {
-		return one == two || !(one == null || two == null) && one.getClass() == two.getClass();
+		return one == two ||
+				(!(one == null || two == null) && one.getClass() == two.getClass());
 	}
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java
index dc06da9683..eeca840485 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java
@@ -238,9 +238,7 @@ public void closeTag(String qName) {
 	}
 
 	@Override
-	public void println(String data)
-		throws IOException
-	{
+	public void println(String data) {
 	if (isOpeningTag) {
 		writer.println('>');
 		isOpeningTag = false;
@@ -251,9 +249,7 @@ public void println(String data)
 	}
 
 	@Override
-	public void print(String data)
-		throws IOException
-	{
+	public void print(String data) {
 	if (isOpeningTag) {
 		writer.print('>');
 		isOpeningTag = false;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
index d17193cc0e..3a448292b0 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
@@ -83,13 +83,13 @@ public interface XMLWriter {
 	 * Prints some textual content in an element.
 	 */
 
-    void print(String data) throws IOException;
+    void print(String data);
 
 	/**
 	 * Prints some textual content, terminated with a newline character.
 	 */
 
-    void println(String data) throws IOException;
+    void println(String data);
 
 	/**
 	 * Closes an element
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
index d79caf1ac0..eb6d9682c6 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
@@ -66,20 +66,13 @@ public static void main(String[] args){
 	}
 
 	public static List<GeneChromosomePosition> getChromosomeMappings() throws IOException {
-
-		URL url = new URL(DEFAULT_MAPPING_URL);
-
-		InputStreamProvider prov = new InputStreamProvider();
-
-		InputStream inStream = prov.getInputStream(url);
-
-		return getChromosomeMappings(inStream);
+		return getChromosomeMappings(new InputStreamProvider().getInputStream(new URL(DEFAULT_MAPPING_URL)));
 	}
 
 	public static List<GeneChromosomePosition> getChromosomeMappings(InputStream inStream) throws IOException {
 		BufferedReader reader = new BufferedReader(new InputStreamReader(inStream));
 
-		ArrayList<GeneChromosomePosition> gcps = new ArrayList<>();
+		ArrayList<GeneChromosomePosition> gcps = new ArrayList<>(1024);
 
 		String line;
 		while ((line = reader.readLine()) != null) {
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
index 0805920bae..0c03ce9c2e 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
@@ -586,9 +586,9 @@ public static List<Range<Integer>> getCDSExonRanges(GeneChromosomePosition chrom
 	 * @return
 	 */
 	public static List<Range<Integer>> getChromosomalRangesForCDS(GeneChromosomePosition chromPos){
-		if ( chromPos.getOrientation() == '+')
-			return getCDSExonRangesForward(chromPos,CHROMOSOME);
-		return getCDSExonRangesReverse(chromPos,CHROMOSOME);
+		return chromPos.getOrientation() == '+' ?
+				getCDSExonRangesForward(chromPos, CHROMOSOME) :
+				getCDSExonRangesReverse(chromPos, CHROMOSOME);
 	}
 
 	private static List<Range<Integer>> getCDSExonRangesReverse(GeneChromosomePosition chromPos, String responseType) {
@@ -657,24 +657,17 @@ private static List<Range<Integer>> getCDSExonRangesReverse(GeneChromosomePositi
 				}
 
 
-				Range<Integer> r ;
-				if ( responseType.equals(CDS))
-					r = Range.closed(0,codingLength);
-				else
-					r = Range.closed(tmpstart,cdsEnd);
 
-				data.add(r);
+				data.add(responseType.equals(CDS) ?
+						Range.closed(0, codingLength) :
+						Range.closed(tmpstart, cdsEnd));
 
 			} else if (start <= cdsStart && end >= cdsStart) {
 				inCoding = false;
 
-				Range<Integer> r;
-				if ( responseType.equals(CDS))
-					r = Range.closed(codingLength,codingLength+(end-cdsStart));
-				else
-					r = Range.closed(cdsStart+1,end);
-
-				data.add(r);
+				data.add(responseType.equals(CDS) ?
+						Range.closed(codingLength, codingLength + (end - cdsStart)) :
+						Range.closed(cdsStart + 1, end));
 
 				codingLength += (end - cdsStart);
 				if  (debug) {
@@ -685,12 +678,9 @@ private static List<Range<Integer>> getCDSExonRangesReverse(GeneChromosomePositi
 				}
 			} else if (inCoding) {
 				// full exon is coding
-				Range<Integer> r;
-				if ( responseType.equals(CDS))
-					r = Range.closed(codingLength,codingLength+(end-start));
-				else
-					r = Range.closed(start,end);
-				data.add(r);
+				data.add(responseType.equals(CDS) ?
+						Range.closed(codingLength, codingLength + (end - start)) :
+						Range.closed(start, end));
 
 				codingLength += (end - start);
 				if  (debug) {
@@ -736,33 +726,24 @@ private static List<Range<Integer>> getCDSExonRangesForward(GeneChromosomePositi
 				inCoding = true;
 				codingLength += (end - cdsStart);
 
-				Range<Integer> r;
-				if ( responseType.equals(CDS))
-					r = Range.closed(0,codingLength);
-				else
-					r = Range.closed(cdsStart,end);
-				data.add(r);
+				data.add(responseType.equals(CDS) ?
+						Range.closed(0, codingLength) :
+						Range.closed(cdsStart, end));
 
 			} else if (start <= cdsEnd && end >= cdsEnd) {
 				//logger.debug(" <-- CDS end at: " + cdsEnd );
 				inCoding = false;
 
-				Range<Integer> r;
-				if ( responseType.equals(CDS))
-					r = Range.closed(codingLength,codingLength+(cdsEnd-start));
-				else
-					r = Range.closed(start,cdsEnd);
-				data.add(r);
+				data.add(responseType.equals(CDS) ?
+						Range.closed(codingLength, codingLength + (cdsEnd - start)) :
+						Range.closed(start, cdsEnd));
 				codingLength += (cdsEnd - start);
 
 			} else if (inCoding) {
 				// full exon is coding
-				Range<Integer> r;
-				if ( responseType.equals(CDS))
-					r = Range.closed(codingLength,codingLength+(end-start));
-				else
-					r = Range.closed(start,end);
-				data.add(r);
+				data.add(responseType.equals(CDS) ?
+						Range.closed(codingLength, codingLength + (end - start)) :
+						Range.closed(start, end));
 				codingLength += (end - start);
 			}
 		}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
index ba68ae3917..395a66c401 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
@@ -26,10 +26,9 @@
 import org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser;
 import org.biojava.nbio.genome.util.ChromosomeMappingTools;
 import org.junit.Assert;
-import org.junit.Before;
 import org.junit.Test;
 
-import java.io.InputStream;
+import java.io.IOException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -43,14 +42,25 @@ public class TestGenomeMapping {
 
 	private static final String geneChromosomeFile = "http://cdn.rcsb.org/gene/hg38/geneChromosome38.tsf.gz";
 
-	private List<GeneChromosomePosition> gcps = null;
+	private static final List<GeneChromosomePosition> gcps;
 
-	@Before
-	public void setUp() throws Exception {
-		InputStream input = new GZIPInputStream(new URL(geneChromosomeFile).openStream());
-		gcps = GeneChromosomePositionParser.getChromosomeMappings(input);
+	static {
+		List<GeneChromosomePosition> g;
+		try {
+			g = GeneChromosomePositionParser.getChromosomeMappings(
+					new GZIPInputStream(new URL(geneChromosomeFile).openStream()));
+		} catch (IOException e) {
+			e.printStackTrace();
+			g = null;
+		}
+		gcps = g;
 	}
 
+//	@Before
+//	public void setUp() throws Exception {
+//
+//	}
+
 	@Test
 	public void testAK1() {
 		String geneName = "AK1";
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java
index 9b2b380e00..e4e7cac756 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java
@@ -183,9 +183,9 @@ private void compareBlock(int blockNr, AFPChain afpChain, AFPChain newChain,
 
 		// THIS IS ROTATING the coordinates according to what is in the file.
 
-		Atom[] blockSet1 = eqrPos1.toArray(new Atom[0]);
-		Atom[] blockSet2 = eqrPos2.toArray(new Atom[0]);
-		Atom[] blockSet2copy = eqrPos2copy.toArray(new Atom[0]);
+		Atom[] blockSet1 = eqrPos1.toArray(Atom.EmptyAtomArray);
+		Atom[] blockSet2 = eqrPos2.toArray(Atom.EmptyAtomArray);
+		Atom[] blockSet2copy = eqrPos2copy.toArray(Atom.EmptyAtomArray);
 
 
 		//System.out.println(shift );
diff --git a/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java b/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
index bd0a2f6533..8cf8fafc44 100644
--- a/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
+++ b/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
@@ -121,7 +121,7 @@ public static void getAlignmentFromFasta() {
 	}
 
 
-	public static void main(String[] args) throws StructureException {
+	public static void main(String[] args) {
 		getAlignmentFromFasta();
 	}
 }
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
index e0a0e128c4..aac4af81f7 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
@@ -415,7 +415,7 @@ public static Atom[] getAtomArray(Atom[] ca, List<Group> hetatms ) {
 			atoms.add(a);
 		}
 
-		Atom[] arr = atoms.toArray(new Atom[0]);
+		Atom[] arr = atoms.toArray(Atom.EmptyAtomArray);
 
 		return arr;
 	}
@@ -436,7 +436,7 @@ public static StructureAlignmentJmol display(AFPChain afpChain, Group[] twistedG
 			Atom a = g.getAtom(0);
 			twistedAs.add(a);
 		}
-		Atom[] twistedAtoms = twistedAs.toArray(new Atom[0]);
+		Atom[] twistedAtoms = twistedAs.toArray(Atom.EmptyAtomArray);
 		twistedAtoms = StructureTools.cloneAtomArray(twistedAtoms);
 
 		Atom[] arr1 = getAtomArray(ca1, hetatms1);
@@ -560,7 +560,7 @@ public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1,
 			Atom a = g.getAtom(0);
 			twistedAs.add(a);
 		}
-		Atom[] twistedAtoms = twistedAs.toArray(new Atom[0]);
+		Atom[] twistedAtoms = twistedAs.toArray(Atom.EmptyAtomArray);
 
 		List<Group> hetatms  = StructureTools.getUnalignedGroups(ca1);
 		List<Group> hetatms2 = StructureTools.getUnalignedGroups(ca2);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/AligUIManager.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/AligUIManager.java
index 7767b948fa..a86fd15062 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/AligUIManager.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/AligUIManager.java
@@ -25,7 +25,6 @@
 package org.biojava.nbio.structure.align.webstart;
 
 import javax.swing.*;
-import javax.swing.UIManager.LookAndFeelInfo;
 
 
 public class AligUIManager
@@ -43,13 +42,13 @@ public static void setLookAndFeel(){
 			}
 
 			//System.out.println("Installed Look And Feels:");
-			LookAndFeelInfo[] feels = UIManager.getInstalledLookAndFeels();
+			//LookAndFeelInfo[] feels = UIManager.getInstalledLookAndFeels();
 
-			if ( feels != null){
+			//if ( feels != null){
 				//for ( LookAndFeelInfo info: feels){
 					//System.out.println(info.getName() + " " + info.getClassName());
 			  // }
-			}
+			//}
 
 
 			//System.out.println("Auxiliary Look And Feels:");
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
index 32da60da20..486ec431af 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
@@ -244,7 +244,7 @@ public static String printSymmetryAxes(CeSymmResult symm,boolean allAxes)
 			}
 
 			script += rot.getJmolScript(
-					repAtoms.toArray(new Atom[0]), id);
+					repAtoms.toArray(Atom.EmptyAtomArray), id);
 			id++;
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
index dfbc5d326d..893866a6e6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
@@ -42,7 +42,10 @@
  */
 public interface Atom extends Cloneable, PDBRecord {
 
-	/**
+	Atom[] EmptyAtomArray = new Atom[0];
+
+
+    /**
 	 * Set atom name, e.g. "CA".
 	 * @param s  a trimmed String specifying the name value
 	 * @see #getName
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java
index a9c44d1644..a79d024a92 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java
@@ -144,9 +144,9 @@ public AtomPositionMap(Atom[] atoms, GroupMatcher matcher) {
 			Group group = atoms[i].getGroup();
 			ResidueNumber rn = group.getResidueNumber();
 			if (matcher.matches(group)) {
-				if (!hashMap.containsKey(rn)) {
-					hashMap.put(rn, i);
-				}
+				//if (!hashMap.containsKey(rn)) {
+				hashMap.putIfAbsent(rn, i);
+				//}
 			}
 		}
 		Comparator<ResidueNumber> vc = new ValueComparator<>(hashMap);
@@ -205,11 +205,7 @@ public int getLength(int positionA, int positionB, String startingChain) {
 	 */
 	public int getLengthDirectional(int positionStart, int positionEnd, String startingChain) {
 		int count = getLength(positionStart,positionEnd,startingChain);
-		if(positionStart <= positionEnd) {
-			return count;
-		} else {
-			return -count;
-		}
+		return positionStart <= positionEnd ? count : -count;
 	}
 
 	/**
@@ -287,8 +283,9 @@ public Integer getPosition(ResidueNumber residueNumber) {
 	public ResidueNumber getFirst(String chainId) {
 		Map.Entry<ResidueNumber,Integer> entry = treeMap.firstEntry();
 		while (true) {
-			if (entry.getKey().getChainName().equals(chainId)) return entry.getKey();
-			entry = treeMap.higherEntry(entry.getKey());
+			ResidueNumber k = entry.getKey();
+			if (k.getChainName().equals(chainId)) return k;
+			entry = treeMap.higherEntry(k);
 			if (entry == null) return null;
 		}
 	}
@@ -300,8 +297,9 @@ public ResidueNumber getFirst(String chainId) {
 	public ResidueNumber getLast(String chainId) {
 		Map.Entry<ResidueNumber,Integer> entry = treeMap.lastEntry();
 		while (true) {
-			if (entry.getKey().getChainName().equals(chainId)) return entry.getKey();
-			entry = treeMap.lowerEntry(entry.getKey());
+			ResidueNumber k = entry.getKey();
+			if (k.getChainName().equals(chainId)) return k;
+			entry = treeMap.lowerEntry(k);
 			if (entry == null) return null;
 		}
 	}
@@ -331,16 +329,20 @@ public List<ResidueRangeAndLength> getRanges() {
 		for (ResidueNumber rn : treeMap.keySet()) {
 			if (!rn.getChainName().equals(currentChain)) {
 				if (first != null) {
-					ResidueRangeAndLength newRange = new ResidueRangeAndLength(currentChain, first, prev, this.getLength(first, prev));
-					ranges.add(newRange);
+					ranges.add(new ResidueRangeAndLength(
+							currentChain, first, prev,
+							getLength(first, prev)));
 				}
 				first = rn;
 			}
 			prev = rn;
 			currentChain = rn.getChainName();
 		}
-		ResidueRangeAndLength newRange = new ResidueRangeAndLength(currentChain, first, prev, this.getLength(first, prev));
-		ranges.add(newRange);
+
+		ranges.add(new ResidueRangeAndLength(
+				currentChain, first, prev,
+				getLength(first, prev)));
+
 		return ranges;
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
index 5f0bd137e4..541150c519 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -445,8 +445,7 @@ public static void rotate(Atom atom, Matrix m){
 		double z = atom.getZ();
 		double[][] ad = new double[][]{{x,y,z}};
 
-		Matrix am = new Matrix(ad);
-		Matrix na = am.times(m);
+		Matrix na = new Matrix(ad).times(m);
 
 		atom.setX(na.get(0,0));
 		atom.setY(na.get(0,1));
@@ -468,9 +467,7 @@ public static void rotate(Group group, Matrix m){
 		AtomIterator iter = new AtomIterator(group) ;
 
 		while (iter.hasNext()) {
-			Atom atom = iter.next() ;
-			rotate(atom,m);
-
+			rotate(iter.next(), m);
 		}
 
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
index 3c694acc4c..3297c4c8e2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
@@ -163,6 +163,8 @@ public interface Chain extends Serializable {
 	 */
 	Group getGroupByPDB(ResidueNumber resNum) throws StructureException;
 
+	boolean hasGroupByPDB(ResidueNumber resNum);
+
 	/**
 	 * Get all groups that are located between two PDB residue numbers.
 	 *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java
index ab1540c057..046ee4244a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java
@@ -429,14 +429,18 @@ public Group[] getGroupsByPDB(ResidueNumber start, ResidueNumber end, boolean ig
 	@Override
 	public Group getGroupByPDB(ResidueNumber resNum) throws StructureException {
 		String pdbresnum = resNum.toString();
-		if ( pdbResnumMap.containsKey(pdbresnum)) {
-			Integer pos = pdbResnumMap.get(pdbresnum);
+		Integer pos = pdbResnumMap.get(pdbresnum);
+		if ( pos!=null ) {
 			return groups.get(pos);
 		} else {
 			throw new StructureException("unknown PDB residue number " + pdbresnum + " in chain " + authId);
 		}
 	}
 
+	public boolean hasGroupByPDB(ResidueNumber resNum)  {
+		return pdbResnumMap.containsKey(resNum);
+	}
+
 	/**
 	 * {@inheritDoc}
 	 *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
index d0564d60fe..ff97afc1f8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
@@ -36,7 +36,7 @@ public class StructureIO {
 
 	//private static final Logger logger = LoggerFactory.getLogger(StructureIO.class);
 
-	@Deprecated private static ThreadLocal<AtomCache> caches = ThreadLocal.withInitial(()->null) ;
+	@Deprecated private static final ThreadLocal<AtomCache> caches = ThreadLocal.withInitial(()->null) ;
 
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
index 4edab66c14..83115b0ffb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -307,7 +307,7 @@ public static Atom[] getAtomArray(Structure s, String[] atomNames) {
 		List<Atom> atoms = new ArrayList<>();
 
 		extractAtoms(atomNames, chains, atoms);
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 
 	}
 
@@ -336,7 +336,7 @@ public static Atom[] getAtomArrayAllModels(Structure s,
 			List<Chain> chains = s.getModel(i);
 			extractAtoms(atomNames, chains, atoms);
 		}
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 
 	}
 
@@ -355,7 +355,7 @@ public static Atom[] getAllAtomArray(Structure s) {
 			Atom a = iter.next();
 			atoms.add(a);
 		}
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 	/**
 	 * Convert all atoms of the structure (specified model) into an Atom array
@@ -372,7 +372,7 @@ public static Atom[] getAllAtomArray(Structure s, int model) {
 			Atom a = iter.next();
 			atoms.add(a);
 		}
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 
 	}
 
@@ -392,7 +392,7 @@ public static Atom[] getAllAtomArray(Chain c) {
 				continue;
 			atoms.addAll(g.getAtoms());
 		}
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 
 	/**
@@ -693,7 +693,7 @@ private static Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, AtomIte
 
 			atoms.add(a);
 		}
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 
 	/**
@@ -722,7 +722,7 @@ public static Atom[] getAllNonHAtomArray(Chain c, boolean hetAtoms) {
 				atoms.add(a);
 			}
 		}
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 
 	/**
@@ -836,7 +836,7 @@ public static Atom[] getAtomArray(Chain c, String[] atomNames) {
 			}
 
 		}
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 
 	}
 
@@ -859,7 +859,7 @@ public static Atom[] getAtomCAArray(Chain c) {
 			}
 		}
 
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 
 	/**
@@ -898,7 +898,7 @@ public static Atom[] getRepresentativeAtomArray(Chain c) {
 			}
 		}
 
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 
 	}
 
@@ -939,13 +939,10 @@ public static Atom[] cloneAtomArray(Atom[] ca) {
 			Group parentN = (Group) parentG.clone();
 
 			newCA[apos] = parentN.getAtom(a.getName());
-			try {
-				// if the group doesn't exist yet, this produces a StructureException
-				newChain.getGroupByPDB(parentN.getResidueNumber());
-			} catch (StructureException e) {
-				// the group doesn't exist yet in the newChain, let's add it
-				newChain.addGroup(parentN);
-			}
+
+			// if the group doesn't exist yet, this produces a StructureException
+			if (!newChain.hasGroupByPDB(parentN.getResidueNumber()))
+				newChain.addGroup(parentN); // the group doesn't exist yet in the newChain, let's add it
 
 		}
 		return newCA;
@@ -1080,7 +1077,7 @@ public static Atom[] getAtomCAArray(Structure s) {
 			}
 		}
 
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 
 	/**
@@ -1107,7 +1104,7 @@ public static Atom[] getRepresentativeAtomArray(Structure s) {
 			atoms.addAll(Arrays.asList(chainAtoms));
 		}
 
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 
 	/**
@@ -1175,7 +1172,7 @@ public static Atom[] getBackboneAtomArray(Structure s) {
 
 		}
 
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
index a62b6edcb6..ff2b1ae4bd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
@@ -54,8 +54,7 @@ public class AFPTwister {
 	 *
 	 * @return twisted Groups
 	 */
-	public static Group[] twistPDB(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
-			throws StructureException {
+	public static Group[] twistPDB(AFPChain afpChain, Atom[] ca1, Atom[] ca2) {
 		// --------------------------------------------------------
 
 		if (afpChain.isShortAlign())
@@ -306,7 +305,7 @@ private static Atom[] getAtoms(Atom[] ca, int[] positions, int length,
 			}
 			atoms.add(a);
 		}
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/CallableStructureAlignment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/CallableStructureAlignment.java
index 80087f8e3c..1d74107a06 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/CallableStructureAlignment.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/CallableStructureAlignment.java
@@ -103,13 +103,15 @@ public AFPChain call() throws Exception {
 			if (ca1 == null) {
 				Structure structure1 = cache.getStructure(pair.getName1());
 				ca1 =  StructureTools.getRepresentativeAtomArray(structure1);
-			} else ca1 = StructureTools.cloneAtomArray(ca1);
+			} else
+				ca1 = StructureTools.cloneAtomArray(ca1);
 
 			Structure structure2 = null;
 			if (ca2 == null) {
 				structure2 = cache.getStructure(pair.getName2());
 				ca2 = StructureTools.getRepresentativeAtomArray(structure2);
-			} else ca2 = StructureTools.cloneAtomArray(ca2);
+			} else
+				ca2 = StructureTools.cloneAtomArray(ca2);
 
 			afpChain = algorithm.align(ca1, ca2);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
index af229f73d8..a5ead9a8dd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
@@ -59,6 +59,8 @@ public class CECalculator {
 	protected static final boolean isPrint = false;
 	private static final boolean debug = false;
 
+	public static final double strLenThreshold = 0.95;
+
 	int[] f1;
 	int[] f2;
 	double[][]dist1;
@@ -107,11 +109,12 @@ public class CECalculator {
 	final List<MatrixListener> matrixListeners;
 
 
+	static final double[][] EMPTY_DOUBLE_SQUARE = new double[0][0];
 
 	public CECalculator(CeParameters params){
 		timeStart = System.currentTimeMillis();
-		dist1= new double[0][0];
-		dist2= new double[0][0];
+
+		dist1 = dist2 = EMPTY_DOUBLE_SQUARE;
 		this.params = params;
 		matrixListeners = new ArrayList<>();
 
@@ -123,10 +126,9 @@ public CECalculator(CeParameters params){
 	 * @param ca1
 	 * @param ca2
 	 * @return afpChain
-	 * @throws StructureException
 	 */
 	public AFPChain extractFragments(AFPChain afpChain,
-			Atom[] ca1, Atom[] ca2) throws StructureException{
+			Atom[] ca1, Atom[] ca2) {
 
 		int nse1 = ca1.length;
 		int nse2 = ca2.length;
@@ -804,11 +806,11 @@ protected double getScore2(int jse1, int jse2, double[][] traceScore, int traceI
 		else
 			val = score0;
 
-		double score2 =  (val * traceIndexContainer[nTrace-1]+score1*(traceIndexContainer[nTrace]-traceIndexContainer[nTrace-1]))/traceIndexContainer[nTrace];
+		return  (val * traceIndexContainer[nTrace-1]+score1*(traceIndexContainer[nTrace]-traceIndexContainer[nTrace-1]))/traceIndexContainer[nTrace];
 
 		//System.out.println("check: score0 " + score0 + " score 1 " + score1 + " sc2: " + score2 + " val: " + val + " nTrace:" + nTrace+ " " +  traceIndexContainer[nTrace-1] + " " +  traceIndexContainer[nTrace-1] + " " + traceIndexContainer[nTrace] );
 
-		return score2;
+
 
 
 	}
@@ -914,8 +916,7 @@ public void nextStep( AFPChain afpChain,
 
 		convertAfpChain(afpChain, ca1, ca2);
 		AFPAlignmentDisplay.getAlign(afpChain, ca1, ca2);
-		double tmScore = AFPChainScorer.getTMScore(afpChain, ca1, ca2,false);
-		afpChain.setTMScore(tmScore);
+		afpChain.setTMScore(AFPChainScorer.getTMScore(afpChain, ca1, ca2,false));
 	}
 
 
@@ -923,7 +924,7 @@ public void nextStep( AFPChain afpChain,
 	// this part is modified from the original CeCalculator
 	@SuppressWarnings("unused")
 	private void checkBestTraces( AFPChain afpChain,
-			Atom[] ca1, Atom[] ca2) throws StructureException{
+			Atom[] ca1, Atom[] ca2) {
 
 		z=0.0;
 
@@ -1135,7 +1136,7 @@ private void checkBestTraces( AFPChain afpChain,
 		}
 
 		// start to convert CE internal datastructure to generic AFPChain one...
-		List<AFP> afpSet = new ArrayList<>();
+		List<AFP> afpSet = new ArrayList<>(nBestTrace);
 		for (int afp=0;afp<nBestTrace;afp++){
 			// fill in data from nBestTrace into AFP
 
@@ -1238,7 +1239,7 @@ private void checkBestTraces( AFPChain afpChain,
 	 * @param ca
 	 * @param j
 	 */
-	private void setStrBuf(Atom[] strBuf, int i, Atom[] ca, int j) {
+	private static void setStrBuf(Atom[] strBuf, int i, Atom[] ca, int j) {
 		// TODO Auto-generated method stub
 		//TODO
 		Group parent = ca[j].getGroup();
@@ -1264,7 +1265,7 @@ private void setStrBuf(Atom[] strBuf, int i, Atom[] ca, int j) {
 	// TODO:  consider all requested Atoms?
 	private double getRMSDForBestTrace(int ir, Atom[] strBuf1, Atom[] strBuf2,
 			int[] bestTracesN2, int[][] bestTraces12, int[] bestTrace22,
-			int winSize,Atom[] ca1, Atom[] ca2 ) throws StructureException {
+			int winSize,Atom[] ca1, Atom[] ca2 ) {
 		int is=0;
 		for(int jt=0; jt<bestTracesN[ir]; jt++) {
 			for(int i=0; i<winSize; i++) {
@@ -1275,8 +1276,8 @@ private double getRMSDForBestTrace(int ir, Atom[] strBuf1, Atom[] strBuf2,
 			is+=winSize;
 		}
 		//sup_str(strBuf1, strBuf2, bestTracesN[ir]*winSize, d_);
-		double rmsdNew=calc_rmsd(strBuf1, strBuf2, bestTracesN[ir]*winSize, true);
-		return rmsdNew;
+		return calc_rmsd(strBuf1, strBuf2, bestTracesN[ir]*winSize, true);
+
 
 	}
 
@@ -1288,7 +1289,7 @@ private double getRMSDForBestTrace(int ir, Atom[] strBuf1, Atom[] strBuf2,
 	/** calc initial RMSD for bestTrace1 in debug only
 	 *
 	 */
-	private void checkPrintRmsdNew(int traceMaxSize, int winSize, Atom[] ca1, Atom[] ca2) throws StructureException{
+	private void checkPrintRmsdNew(int traceMaxSize, int winSize, Atom[] ca1, Atom[] ca2) {
 
 		int is = 0;
 		// calc initial RMSD for bestTrace1
@@ -1336,7 +1337,7 @@ private static char getOneLetter(Group g){
 
 
 	private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int strLen, double rmsd, Atom[] ca1, Atom[] ca2,int nGaps,
-			Atom[] strBuf1, Atom[] strBuf2 ) throws StructureException {
+			Atom[] strBuf1, Atom[] strBuf2 ) {
 
 		//System.out.println("optimizing Superimposition...");
 
@@ -1417,17 +1418,16 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str
 
 			nAtom=0; nGaps=0;
 			for(int ia=0; ia<lcmp; ia++) {
-				if(align_se1[ia]!=-1 && align_se2[ia]!=-1) {
+				int seia1, seia2;
+				if((seia1 = align_se1[ia]) !=-1 && (seia2 = align_se2[ia]) !=-1) {
 
-					strBuf1[nAtom]=ca1[align_se1[ia]];
-					strBuf2[nAtom]=ca2[align_se2[ia]];
+					strBuf1[nAtom]=ca1[seia1];
+					strBuf2[nAtom]=ca2[seia2];
 
 					nAtom++;
 
-				}
-				else {
+				} else
 					nGaps++;
-				}
 			}
 
 
@@ -1442,7 +1442,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str
 			//afpChain.setTotalRmsdOpt(rmsd);
 			//System.out.println("rmsd: " + rmsd);
 
-			if(!(nAtom<strLen*0.95) && (!isRmsdLenAssigned)) {
+			if(!isRmsdLenAssigned && nAtom >= strLen * strLenThreshold) {
 				rmsdLen=rmsd;
 				isRmsdLenAssigned=true;
 			}
@@ -1842,7 +1842,7 @@ private double dpAlign(int nSeq1, int nSeq2, double gapI, double gapE,
 	}
 
 
-	private void rot_mol(Atom[] caA, Atom[] caB, int nse2, Matrix m , Atom shift) {
+	private static void rot_mol(Atom[] caA, Atom[] caB, int nse2, Matrix m, Atom shift) {
 
 		for(int l=0; l<nse2; l++) {
 			Atom a = caA[l];
@@ -1911,22 +1911,17 @@ public double calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen,
 	 * @param clone If true, preform a deep copy, cloning the underlying Groups
 	 * @return An array with the first length items of ca, possibly cloning the Atoms.
 	 */
-	private Atom[] getAtoms(Atom[] ca,  int length, boolean clone) {
+	private static Atom[] getAtoms(Atom[] ca, int length, boolean clone) {
 
-		List<Atom> atoms = new ArrayList<>();
+		List<Atom> atoms = new ArrayList<>(length); //TODO avoid ArrayList, just craete Atom[]
 		for ( int i = 0 ; i < length ; i++){
-
-			Atom a;
-			if ( clone ){
-				Group g = (Group)ca[i].getGroup().clone();
-				a = g.getAtom(ca[i].getName());
-			}
-			else {
-				a = ca[i];
-			}
-			atoms.add(a);
+			atoms.add(clone ?
+				((Group) ca[i].getGroup().clone()).getAtom(ca[i].getName()) :
+				ca[i]
+			);
 		}
-		return atoms.toArray(new Atom[0]);
+
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 
 
@@ -1944,21 +1939,21 @@ private void noBestTrace(){
 
 
 
-	private double zToP(double z) {
+	private static double zToP(double z) {
 		int ind=(int)(z/0.1);
 		if(ind<0) ind=0;
 		if(ind>149) ind=149;
 		return(tableZtoP[ind]);
 	}
 	///////////////////////////////////////////////////////////////////////////
-	private		double pToZ(double p) {
+	private static double pToZ(double p) {
 		int ind=(int)(-Math.log10(p)*3.0);
 		if(ind<0) ind=0;
 		if(ind>149) ind=149;
 		return(tablePtoZ[ind]);
 	}
 	///////////////////////////////////////////////////////////////////////////
-	private	double zByZ(double z1, double z2) {
+	private static double zByZ(double z1, double z2) {
 		double p1=zToP(z1);
 		double p2=zToP(z2);
 		return(pToZ(p1*p2));
@@ -1970,7 +1965,7 @@ protected double zStrAlign(int winSize, int nTrace, double score, int nGaps) {
 		return(zByZ(z1, z2));
 	}
 
-	double zScore(int winSize, int nTrace, double score) {
+	static double zScore(int winSize, int nTrace, double score) {
 
 		if(winSize==8) {
 
@@ -2010,7 +2005,7 @@ protected double zStrAlign(int winSize, int nTrace, double score, int nGaps) {
 
 	}
 	///////////////////////////////////////////////////////////////////////////
-	double zGaps(int winSize, int nTrace, int nGaps) {
+	static double zGaps(int winSize, int nTrace, int nGaps) {
 
 		if(nTrace<2) return(0.0);
 		double scoreAv_, scoreSd_;
@@ -2109,21 +2104,14 @@ public void convertAfpChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2) {
 
 		 afpChain.setBlockNum(1);
 		 //afpChain.setAlignScore(z);
-		 Matrix[] m ;
-
-		 if ( r != null ) {
-			 m = new Matrix[1];
-			 m[0] = r;
-		 } else  {
-			 m = new Matrix[0];
-		 }
+		 Matrix[] m = r != null ? new Matrix[]{r} : Matrix.EmptyMatrixArray;
 
 		 Atom[] as ;
 		 if ( t != null) {
 			 as = new Atom[1];
 			 as[0] = t;
 		 } else {
-			 as = new Atom[0];
+			 as = Atom.EmptyAtomArray;
 		 }
 
 		 afpChain.setBlockRotationMatrix(m);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
index c5efd0076a..9efaa42e0d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
@@ -126,10 +126,9 @@ public CeCalculatorEnhanced(CeParameters params){
 	 * @param ca1
 	 * @param ca2
 	 * @return afpChain
-	 * @throws StructureException
 	 */
 	public AFPChain extractFragments(AFPChain afpChain,
-			Atom[] ca1, Atom[] ca2) throws StructureException{
+			Atom[] ca1, Atom[] ca2) {
 
 		int nse1 = ca1.length;
 		int nse2 = ca2.length;
@@ -1260,7 +1259,7 @@ private void setStrBuf(Atom[] strBuf, int i, Atom[] ca, int j) {
 	// TODO:  consider all requested Atoms?
 	private double getRMSDForBestTrace(int ir, Atom[] strBuf1, Atom[] strBuf2,
 			int[] bestTracesN2, int[][] bestTraces12, int[] bestTrace22,
-			int winSize,Atom[] ca1, Atom[] ca2 ) throws StructureException {
+			int winSize,Atom[] ca1, Atom[] ca2 ) {
 		int is=0;
 		for(int jt=0; jt<bestTracesN[ir]; jt++) {
 			for(int i=0; i<winSize; i++) {
@@ -1284,7 +1283,7 @@ private double getRMSDForBestTrace(int ir, Atom[] strBuf1, Atom[] strBuf2,
 	/** calc initial RMSD for bestTrace1 in debug only
 	 *
 	 */
-	private void checkPrintRmsdNew(int traceMaxSize, int winSize, Atom[] ca1, Atom[] ca2) throws StructureException{
+	private void checkPrintRmsdNew(int traceMaxSize, int winSize, Atom[] ca1, Atom[] ca2) {
 
 		int is = 0;
 		// calc initial RMSD for bestTrace1
@@ -1332,7 +1331,7 @@ private static char getOneLetter(Group g){
 
 
 	private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int strLen, double rmsd, Atom[] ca1, Atom[] ca2,int nGaps,
-			Atom[] strBuf1, Atom[] strBuf2 ) throws StructureException {
+			Atom[] strBuf1, Atom[] strBuf2 ) {
 
 		//System.out.println("optimizing Superimposition...");
 
@@ -2020,7 +2019,7 @@ private Atom[] getAtoms(Atom[] ca,  int length, boolean clone) {
 			}
 			atoms.add(a);
 		}
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 
 
@@ -2203,21 +2202,14 @@ public void convertAfpChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2) {
 
 		afpChain.setBlockNum(1);
 		//afpChain.setAlignScore(z);
-		Matrix[] m ;
-
-		if ( r != null ) {
-			m = new Matrix[1];
-			m[0] = r;
-		} else  {
-			m = new Matrix[0];
-		}
+		Matrix[] m = r != null ? new Matrix[]{r} : Matrix.EmptyMatrixArray;
 
 		Atom[] as ;
 		if ( t != null) {
 			as = new Atom[1];
 			as[0] = t;
 		} else {
-			as = new Atom[0];
+			as = Atom.EmptyAtomArray;
 		}
 
 		afpChain.setBlockRotationMatrix(m);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
index 1913558747..43669368e6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
@@ -285,8 +285,7 @@ private void superimposeBySet () {
 	}
 
 
-	private void optimize(int maxi) throws StructureException
-	{
+	private void optimize(int maxi) {
 		long optStart = System.currentTimeMillis();
 		if ( debug)
 			System.out.println("Optimizing up to " + maxi + " iterations.. ");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
index d154faa95d..d1caf74991 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -173,9 +173,8 @@ public MultipleAlignment call() throws Exception {
 	 * Initialize the freePool and all the variables needed for the
 	 * optimization.
 	 *
-	 * @throws StructureException
 	 */
-	private void initialize() throws StructureException {
+	private void initialize() {
 
 		// Initialize alignment variables
 		freePool = new ArrayList<>();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java
index 79a80089a7..0853b78382 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java
@@ -153,8 +153,8 @@ public void superimpose(MultipleAlignment alignment) {
 						atomSet2.add(curr[pos2]);
 					}
 				}
-				Atom[] array1 = atomSet1.toArray(new Atom[0]);
-				Atom[] array2 = atomSet2.toArray(new Atom[0]);
+				Atom[] array1 = atomSet1.toArray(Atom.EmptyAtomArray);
+				Atom[] array2 = atomSet2.toArray(Atom.EmptyAtomArray);
 
 				array2 = StructureTools.cloneAtomArray(array2);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java
index 080b38144c..b569b72973 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java
@@ -142,8 +142,8 @@ public void superimpose(MultipleAlignment alignment) {
 						atomSet2.add(curr[pos2]);
 					}
 				}
-				Atom[] array1 = atomSet1.toArray(new Atom[0]);
-				Atom[] array2 = atomSet2.toArray(new Atom[0]);
+				Atom[] array1 = atomSet1.toArray(Atom.EmptyAtomArray);
+				Atom[] array2 = atomSet2.toArray(Atom.EmptyAtomArray);
 
 				array2 = StructureTools.cloneAtomArray(array2);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AltAligComparator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AltAligComparator.java
index 1ac6c90e78..2608ab4f87 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AltAligComparator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AltAligComparator.java
@@ -37,31 +37,32 @@ public class AltAligComparator implements Comparator<AlternativeAlignment>, Seri
 
 	public AltAligComparator() {
 		super();
-
 	}
 
 	@Override
 	public int compare(AlternativeAlignment a, AlternativeAlignment b) {
+		if (a==b) return 0;
 
 		int s1 = a.getIdx1().length;
 		int s2 = b.getIdx1().length;
 
 		if ( s1 > s2)
 			return 1;
-		if ( s1 < s2)
+		else if ( s1 < s2)
 			return -1;
+		else {
 
-		// seem to have the same length
-
-		double rms1 = a.getRmsd();
-		double rms2 = b.getRmsd();
-
-		if ( rms1 < rms2)
-			return 1;
-		if ( rms1 < rms2)
-			return -1;
+			double rms1 = a.getRmsd();
+			double rms2 = b.getRmsd();
+			return Double.compare(rms1, rms2);
 
-		return 0;
+//			if (rms1 < rms2)
+//				return 1;
+//			if (rms1 < rms2)
+//				return -1;
+//
+//			return 0;
+		}
 	}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
index 4ceecdf37a..4766d472d3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
@@ -292,7 +292,7 @@ private double rmsCheck(Atom[] a1, Atom[] a2,List<int[]> idxlist, int p2i, int p
 	 * @param frag the JointFragments object that contains the list of identical positions
 	 * @return the rms
 	 */
-	public static double getRMS(Atom[] ca1, Atom[]ca2,JointFragments frag) throws StructureException {
+	public static double getRMS(Atom[] ca1, Atom[]ca2,JointFragments frag) {
 		//      now svd ftmp and check if the rms is < X ...
 		AlternativeAlignment ali = new AlternativeAlignment();
 		ali.apairs_from_idxlst(frag);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java
index 516ab3cbce..55fd3d3342 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java
@@ -250,8 +250,8 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 			MultipleAlignment msa = new MultipleAlignmentImpl();
 			msa.setEnsemble(new MultipleAlignmentEnsembleImpl());
 			msa.getEnsemble().setAtomArrays(
-					Arrays.asList(atomArray1.toArray(new Atom[0]),
-							atomArray2.toArray(new Atom[0])));
+					Arrays.asList(atomArray1.toArray(Atom.EmptyAtomArray),
+							atomArray2.toArray(Atom.EmptyAtomArray)));
 
 			// Fill in the alignment information
 			BlockSet bs = new BlockSetImpl(msa);
@@ -331,8 +331,8 @@ private static Pair<Atom[]> getAlignedAtomsForClusterSubunitMap(
 
 		}
 		return new Pair<>(
-				atomArray1.toArray(new Atom[0]),
-				atomArray2.toArray(new Atom[0]));
+				atomArray1.toArray(Atom.EmptyAtomArray),
+				atomArray2.toArray(Atom.EmptyAtomArray));
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java
index f050b855d4..69a8a0769d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java
@@ -161,10 +161,9 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object parameters)
 	 * @param smithWaterman pairwise Sequence aligner
 	 * @param pair The sequence alignment calculated by aligner
 	 * @return an AFPChain encapsulating the alignment in aligPair
-	 * @throws StructureException
 	 */
 	private AFPChain convert(Atom[] ca1, Atom[] ca2,  SequencePair<ProteinSequence,
-			AminoAcidCompound> pair, PairwiseSequenceAligner<ProteinSequence, AminoAcidCompound> smithWaterman) throws StructureException {
+			AminoAcidCompound> pair, PairwiseSequenceAligner<ProteinSequence, AminoAcidCompound> smithWaterman) {
 		AFPChain afpChain = new AFPChain(algorithmName);
 		int ca1Length = ca1.length;
 		int ca2Length = ca2.length;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
index c24cdfefb5..9e2c58402a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
@@ -106,7 +106,7 @@ public static Atom[] getAlignedAtoms1(AFPChain afpChain,Atom[] ca1){
 			}
 
 		}
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 	public static Atom[] getAlignedAtoms2(AFPChain afpChain,Atom[] ca2){
 
@@ -127,7 +127,7 @@ public static Atom[] getAlignedAtoms2(AFPChain afpChain,Atom[] ca2){
 			}
 
 		}
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 
 
@@ -409,7 +409,7 @@ public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1,
 			Atom a = g.getAtom(0);
 			twistedAs.add(a);
 		}
-		Atom[] twistedAtoms = twistedAs.toArray(new Atom[0]);
+		Atom[] twistedAtoms = twistedAs.toArray(Atom.EmptyAtomArray);
 
 		List<Group> hetatms  = new ArrayList<>();
 		List<Group> nucs1    = new ArrayList<>();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
index cd80048cbb..8763b19f8e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -1258,9 +1258,8 @@ public static Structure getAlignedStructure(Atom[] ca1, Atom[] ca2) {
 	 * @param ca1
 	 * @param ca2
 	 * @return an array of Groups that are transformed for 3D display
-	 * @throws StructureException
 	 */
-	public static Group[] prepareGroupsForDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException{
+	public static Group[] prepareGroupsForDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2) {
 
 
 		if ( afpChain.getBlockRotationMatrix().length == 0 ) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index 4b6112c72c..6a2f32b839 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -35,6 +35,7 @@
 import org.biojava.nbio.structure.io.MMCIFFileReader;
 import org.biojava.nbio.structure.io.MMTFFileReader;
 import org.biojava.nbio.structure.io.PDBFileReader;
+import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
 import org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder;
 import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
 import org.biojava.nbio.structure.scop.*;
@@ -183,19 +184,8 @@ public Atom[] getAtoms(String name) throws IOException, StructureException {
 		return getAtoms(new StructureName(name));
 	}
 	public Atom[] getAtoms(StructureIdentifier name) throws IOException, StructureException {
-
-		Atom[] atoms;
-
 		// System.out.println("loading " + name);
-		Structure s = getStructure(name);
-
-		atoms = StructureTools.getAtomCAArray(s);
-
-		/*
-		 * synchronized (cache){ cache.put(name, atoms); }
-		 */
-
-		return atoms;
+		return StructureTools.getAtomCAArray(getStructure(name));
 	}
 	/**
 	 * Returns the representative atoms for the provided name.
@@ -212,18 +202,7 @@ public Atom[] getRepresentativeAtoms(String name) throws IOException, StructureE
 	}
 
 	public Atom[] getRepresentativeAtoms(StructureIdentifier name) throws IOException, StructureException {
-
-		Atom[] atoms;
-
-		Structure s = getStructure(name);
-
-		atoms = StructureTools.getRepresentativeAtomArray(s);
-
-		/*
-		 * synchronized (cache){ cache.put(name, atoms); }
-		 */
-
-		return atoms;
+		return StructureTools.getRepresentativeAtomArray(getStructure(name));
 	}
 
 	/**
@@ -271,7 +250,7 @@ public Structure getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean
 
 		// 0 ... asym unit
 		if ( bioAssemblyId == 0) {
-			logger.info("Requested biological assembly 0 for PDB id "+pdbId+", returning asymmetric unit");
+			logger.info("Requested biological assembly 0 for PDB id {} returning asymmetric unit", pdbId);
 			return asymUnit;
 		}
 		// does it exist?
@@ -315,15 +294,16 @@ public Structure getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean
 	 */
 	public Structure getBiologicalAssembly(String pdbId, boolean multiModel) throws StructureException, IOException {
 
-		boolean prevIsParseBioAssembly = getFileParsingParams().isParseBioAssembly();
+		FileParsingParameters params = getFileParsingParams();
+		boolean prevIsParseBioAssembly = params.isParseBioAssembly();
 
-		if (!getFileParsingParams().isParseBioAssembly()) {
-			getFileParsingParams().setParseBioAssembly(true);
+		if (!params.isParseBioAssembly()) {
+			params.setParseBioAssembly(true);
 		}
 
 		Structure asymUnit = getStructureForPdbId(pdbId);
 
-		getFileParsingParams().setParseBioAssembly(prevIsParseBioAssembly);
+		params.setParseBioAssembly(prevIsParseBioAssembly);
 
 
 		if (asymUnit.getPDBHeader() == null || asymUnit.getPDBHeader().getBioAssemblies()==null) {
@@ -383,32 +363,30 @@ public List<Structure> getBiologicalAssemblies(String pdbId, boolean multiModel)
 		getFileParsingParams().setParseBioAssembly(prevIsParseBioAssembly);
 
 
-		if (asymUnit.getPDBHeader() == null || asymUnit.getPDBHeader().getBioAssemblies()==null) {
+		Map<Integer, BioAssemblyInfo> basms = asymUnit.getPDBHeader().getBioAssemblies();
+		if (asymUnit.getPDBHeader() == null || basms ==null) {
 			logger.info("No bioassembly information found for {}, returning asymmetric unit as the only biological assembly", pdbId);
 			assemblies.add(asymUnit);
 			return assemblies;
 		}
 
 
-		for (int bioAssemblyId : asymUnit.getPDBHeader().getBioAssemblies().keySet()) {
+		for (Map.Entry<Integer,BioAssemblyInfo> e : basms.entrySet()) {
 			List<BiologicalAssemblyTransformation> transformations =
-					asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms();
+					e.getValue().getTransforms(); //assemblies.get(bioAssemblyId).getTransforms();
 
 
 			if ( transformations == null || transformations.size() == 0){
-
-				logger.info("Could not load transformations to recreate biological assembly id " + bioAssemblyId + " of " + pdbId+". Assembly id will be missing in biological assemblies.");
+				if (logger.isInfoEnabled())
+					logger.info("Could not load transformations to recreate biological assembly id " + assemblies + " of " + pdbId+". Assembly id will be missing in biological assemblies.");
 				continue;
 			}
 
-			BiologicalAssemblyBuilder builder = new BiologicalAssemblyBuilder();
-
 			// if we use mmcif or mmtf, then we need to pass useAsymIds=true
-			boolean useAsymIds = false;
-			if (useMmCif) useAsymIds = true;
-			if (useMmtf) useAsymIds = true;
-			Structure s = builder.rebuildQuaternaryStructure(asymUnit, transformations, useAsymIds, multiModel);
-			assemblies.add(s);
+			assemblies.add(new BiologicalAssemblyBuilder()
+					.rebuildQuaternaryStructure(
+						asymUnit, transformations,
+						useMmCif || useMmtf, multiModel));
 		}
 		return assemblies;
 	}
@@ -488,9 +466,7 @@ public PDPProvider getPdpprovider() {
 	 *             errors, eg for poorly formatted subranges.
 	 */
 	public Structure getStructure(String name) throws IOException, StructureException {
-		StructureName structureName = new StructureName(name);
-
-		return getStructure(structureName);
+		return getStructure(new StructureName(name));
 	}
 
 	/**
@@ -852,10 +828,9 @@ public Structure getStructureForCathDomain(StructureName structureName, CathData
 	 * Loads a structure directly by PDB ID
 	 * @param pdbId
 	 * @return
-	 * @throws IOException
 	 * @throws StructureException
 	 */
-	public Structure getStructureForPdbId(String pdbId) throws IOException, StructureException {
+	public Structure getStructureForPdbId(String pdbId) throws StructureException {
 
 		if(pdbId == null)
 			return null;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java
index e0e17466c1..826fcf648a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java
@@ -430,11 +430,25 @@ public List<Chain> getNucleicChains(boolean removeDups) {
 				result.add(c);
 			}
 		}
-		if (removeDups) for (int i = 0; i < result.size(); i++) {
-			for (int j = i+2; j < result.size(); j++) {
-				// remove duplicate sequences (structures with two or more identical units)
-				if (result.get(i).getAtomSequence().equals(result.get(j).getAtomSequence())) {
-					result.remove(j);
+		if (removeDups) {
+			int s = result.size();
+			BitSet toRemove = new BitSet();
+			for (int i = 0; i < s; i++) {
+				for (int j = i + 2; j < s; j++) {
+					// remove duplicate sequences (structures with two or more identical units)
+					if (result.get(i).getAtomSequence().equals(result.get(j).getAtomSequence())) {
+						toRemove.set(j);
+					}
+				}
+			}
+			if (!toRemove.isEmpty()) {
+				Iterator<Chain> r = result.iterator();
+				int i = 0;
+				while (r.hasNext()) {
+					Chain rr = r.next();
+					if (toRemove.get(i++)) {
+						r.remove();
+					}
 				}
 			}
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
index 05165bf825..46293edf86 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
@@ -310,7 +310,7 @@ private static Atom[] getAllNonHAtomArray(Atom[] m, int minSizeHetAtomToInclude)
 			atoms.add(a);
 
 		}
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java
index 28ff97bd7c..ce2db4a3f4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java
@@ -23,7 +23,10 @@
  */
 package org.biojava.nbio.structure.domain;
 
-import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Chain;
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.domain.pdp.*;
 
 import java.util.List;
@@ -60,9 +63,8 @@ private LocalProteinDomainParser(){
 	 *
 	 * @param s the protein structure
 	 * @return a list of possible domains
-	 * @throws StructureException
-	 */
-	public static List<Domain> suggestDomains(Structure s) throws StructureException{
+     */
+	public static List<Domain> suggestDomains(Structure s) {
 
 		Atom[] ca = StructureTools.getRepresentativeAtomArray(s);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
index 1df157ee5a..164f211f44 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
@@ -82,6 +82,8 @@ public class Matrix implements Cloneable, java.io.Serializable {
 
 	 static final long serialVersionUID = 8492558293015348719L;
 
+	public static final Matrix[] EmptyMatrixArray = new Matrix[0];
+
 
 /* ------------------------
 	Class variables
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
index 24dba870bd..bf75f843a3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
@@ -424,7 +424,7 @@ public static CeSymmResult analyzeLevel(Atom[] atoms,
 					msa = optimizer.optimize();
 					result.setMultipleAlignment(msa);
 				} catch (RefinerFailedException e) {
-					logger.debug("Optimization failed:" + e.getMessage());
+					logger.debug("Optimization failed {}", e.getMessage());
 				}
 			}
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
index 27a62291e1..75283deba8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
@@ -520,7 +520,7 @@ public static List<Structure> divideStructure(CeSymmResult symmetry)
 
 			List<Group> ligands = StructureTools.getLigandsByProximity(
 					allGroups,
-					repeat.toArray(new Atom[0]),
+					repeat.toArray(Atom.EmptyAtomArray),
 					StructureTools.DEFAULT_LIGAND_PROXIMITY_CUTOFF);
 
 			logger.warn("Adding {} ligands to {}",ligands.size(), symmetry.getMultipleAlignment().getStructureIdentifier(i));
@@ -783,8 +783,8 @@ public static void updateSymmetryTransformation(SymmetryAxes axes,
 					}
 				}
 
-				Atom[] arr1 = list1.toArray(new Atom[0]);
-				Atom[] arr2 = list2.toArray(new Atom[0]);
+				Atom[] arr1 = list1.toArray(Atom.EmptyAtomArray);
+				Atom[] arr2 = list2.toArray(Atom.EmptyAtomArray);
 
 				// Calculate the new transformation information
 				if (arr1.length > 0 && arr2.length > 0) {
@@ -850,7 +850,7 @@ public static Atom[] getRepresentativeAtoms(Structure structure) {
 					atomList.addAll(Arrays.asList(StructureTools
 							.getRepresentativeAtomArray(c)));
 			}
-			return atomList.toArray(new Atom[0]);
+			return atomList.toArray(Atom.EmptyAtomArray);
 		}
 
 	}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java
index 8610f1f3fb..8f271acadc 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java
@@ -47,7 +47,7 @@
 public class TestMultipleAlignmentScorer {
 
 	@Test
-	public void testRefRMSD() throws Exception{
+	public void testRefRMSD() {
 
 		//Identity Test: RefRMSD has to be equal to 0.0
 		MultipleAlignment identMSA = identityMSTA();
@@ -66,7 +66,7 @@ public void testRefRMSD() throws Exception{
 	}
 
 	@Test
-	public void testRMSD() throws Exception{
+	public void testRMSD() {
 
 		//Identity Test: RMSD has to be equal to 0.0
 		MultipleAlignment identMSA = identityMSTA();
@@ -123,7 +123,7 @@ public void testAvgTMScore() throws Exception{
 	}
 
 	@Test
-	public void testMCScore() throws Exception {
+	public void testMCScore() {
 
 		//Identity Test: MultipleMC-Score has to be equal to 576.21
 		MultipleAlignment identMSA = identityMSTA();
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java
index 2774f4ca3e..eef49daeb3 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java
@@ -241,7 +241,7 @@ private Atom getAtom(double x, double y, double z) {
 	public void testNoAtomsAsaCalc() {
 
 		// in case of no atoms at all, the calculation should not fail and return an empty array
-		Atom[] atoms = new Atom[0];
+		Atom[] atoms = Atom.EmptyAtomArray;
 
 		AsaCalculator asaCalc = new AsaCalculator(atoms,
 				AsaCalculator.DEFAULT_PROBE_SIZE,
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitCluster.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitCluster.java
index b1da8919c1..ebb2d11ccf 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitCluster.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitCluster.java
@@ -293,7 +293,7 @@ private Atom[] mockAtomArray(int size1, String type1, int size2, String type2) {
 				atoms.add(a);
 			}
 		}
-		return atoms.toArray(new Atom[0]);
+		return atoms.toArray(Atom.EmptyAtomArray);
 	}
 
 	/**

From 75e9c2079422ec924a384ec5f39346d304d7d415 Mon Sep 17 00:00:00 2001
From: me <seh@internet.earth>
Date: Sat, 7 Mar 2020 22:21:57 -0500
Subject: [PATCH 11/18] updates

---
 .../xml/CaseFreeAminoAcidCompoundSet.java     |  2 +-
 .../xml/ModifiedAminoAcidCompoundSet.java     |  2 +-
 .../AbstractProfileProfileAligner.java        | 17 ++++---
 .../nbio/core/alignment/SimpleProfile.java    | 23 +++++----
 .../matrices/SimpleSubstitutionMatrix.java    | 15 +++---
 .../nbio/core/sequence/AccessionID.java       | 10 ++--
 .../compound/AminoAcidCompoundSet.java        | 21 ++++----
 .../core/sequence/location/FuzzyPoint.java    | 10 ++--
 .../core/sequence/location/SimplePoint.java   |  6 +--
 .../location/template/AbstractLocation.java   | 20 ++++----
 .../storage/ArrayListSequenceReader.java      |  5 +-
 .../sequence/storage/BitSequenceReader.java   | 14 +++---
 .../storage/SingleCompoundSequenceReader.java | 13 ++---
 .../template/AbstractCompoundSet.java         | 25 ++++++----
 .../core/sequence/template/CompoundSet.java   |  6 ++-
 .../core/sequence/transcription/Table.java    |  9 ++--
 .../org/biojava/nbio/core/util/Equals.java    | 21 --------
 .../core/util/SingleLinkageClusterer.java     | 18 +++----
 .../biojava/nbio/core/util/SoftHashMap.java   |  2 +-
 .../nbio/structure/ecod/EcodFactory.java      |  4 +-
 .../io/mmcif/ChemCompGroupFactory.java        | 29 +++++------
 .../io/mmcif/chem/ChemCompTools.java          | 41 ++++++++--------
 .../nbio/structure/io/mmtf/MmtfUtils.java     | 48 +++++++++----------
 23 files changed, 177 insertions(+), 184 deletions(-)

diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
index d9082a1ca4..e830453233 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
@@ -185,7 +185,7 @@ public boolean hasCompound(AminoAcidCompound compound) {
 	}
 
 	@Override
-	public List<AminoAcidCompound> getAllCompounds() {
+	public Collection<AminoAcidCompound> getAllCompounds() {
 		return new ArrayList<>(aminoAcidCompoundCache.values());
 	}
 
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java
index b1c63e9655..82061e14e6 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java
@@ -83,7 +83,7 @@ public boolean hasCompound(AminoAcidCompound compound) {
 	}
 
 	@Override
-	public List<AminoAcidCompound> getAllCompounds() {
+	public Collection<AminoAcidCompound> getAllCompounds() {
 		return new ArrayList<>(aminoAcidCompoundCache.values());
 	}
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
index 0f2662d571..95af0ea5ff 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
@@ -236,7 +236,7 @@ protected void reset() {
 		if (query != null && target != null && getGapPenalty() != null && getSubstitutionMatrix() != null &&
 				query.getCompoundSet().equals(target.getCompoundSet())) {
 			int maxq = 0, maxt = 0;
-			cslist = query.getCompoundSet().getAllCompounds();
+			cslist = new ArrayList(query.getCompoundSet().getAllCompounds());
 			qfrac = new float[query.getLength()][];
 			for (int i = 0; i < qfrac.length; i++) {
 				qfrac[i] = query.getCompoundWeightsAt(i + 1, cslist);
@@ -255,17 +255,20 @@ protected void reset() {
 
 	// helper method that scores alignment of two column vectors
 	private int getSubstitutionScore(float[] qv, float[] tv) {
-		float score = 0.0f;
+		double score = 0.0;
+		SubstitutionMatrix<C> s = getSubstitutionMatrix();
 		for (int q = 0; q < qv.length; q++) {
-			if (qv[q] > 0.0f) {
+			float qvq = qv[q];
+			if (qvq > 0.0) {
+				C cq = cslist.get(q);
 				for (int t = 0; t < tv.length; t++) {
-					if (tv[t] > 0.0f) {
-						score += qv[q]*tv[t]*getSubstitutionMatrix().getValue(cslist.get(q), cslist.get(t));
-					}
+					float tvt = tv[t];
+					if (tvt > 0.0)
+						score += qvq * tvt * s.getValue(cq, cslist.get(t));
 				}
 			}
 		}
-		return Math.round(score);
+		return (int) Math.round(score); //TODO return double?
 	}
 
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
index 3614777b36..d7438af53d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
@@ -243,17 +243,18 @@ public C getCompoundAt(S sequence, int alignmentIndex) {
 
 	@Override
 	public int[] getCompoundCountsAt(int alignmentIndex) {
-		return getCompoundCountsAt(alignmentIndex, getCompoundSet().getAllCompounds());
+		return getCompoundCountsAt(alignmentIndex, new ArrayList(getCompoundSet().getAllCompounds()));
 	}
 
 	@Override
 	public int[] getCompoundCountsAt(int alignmentIndex, List<C> compounds) {
 		int[] counts = new int[compounds.size()];
-		C gap = getCompoundSet().getCompoundForString("-");
+		CompoundSet<C> s = getCompoundSet();
+		C gap = s.getCompoundForString("-");
 		int igap = compounds.indexOf(gap);
 		for (C compound : getCompoundsAt(alignmentIndex)) {
 			int i = compounds.indexOf(compound);
-			if (i >= 0 && i != igap && !getCompoundSet().compoundsEquivalent(compound, gap)) {
+			if (i >= 0 && i != igap && !s.compoundsEquivalent(compound, gap)) {
 				counts[i]++;
 			}
 		}
@@ -277,19 +278,20 @@ public CompoundSet<C> getCompoundSet() {
 
 	@Override
 	public float[] getCompoundWeightsAt(int alignmentIndex) {
-		return getCompoundWeightsAt(alignmentIndex, getCompoundSet().getAllCompounds());
+		return getCompoundWeightsAt(alignmentIndex, new ArrayList(getCompoundSet().getAllCompounds()));
 	}
 
 	@Override
 	public float[] getCompoundWeightsAt(int alignmentIndex, List<C> compounds) {
-		float[] weights = new float[compounds.size()];
+		int N = compounds.size();
+		float[] weights = new float[N];
 		int[] counts = getCompoundCountsAt(alignmentIndex, compounds);
 		float total = 0.0f;
-		for (int i : counts) {
+		for (int i : counts)
 			total += i;
-		}
+
 		if (total > 0.0f) {
-			for (int i = 0; i < weights.length; i++) {
+			for (int i = 0; i < N; i++) {
 				weights[i] = counts[i]/total;
 			}
 		}
@@ -352,9 +354,10 @@ public ProfileView<S, C> getSubProfile(Location location) {
 
 	@Override
 	public boolean hasGap(int alignmentIndex) {
-		C gap = getCompoundSet().getCompoundForString("-");
+		CompoundSet<C> s = getCompoundSet();
+		C gap = s.getCompoundForString("-");
 		for (C compound : getCompoundsAt(alignmentIndex)) {
-			if (getCompoundSet().compoundsEquivalent(compound, gap)) {
+			if (s.compoundsEquivalent(compound, gap)) {
 				return true;
 			}
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java
index 99d9fd33ab..cb8f23d8dd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java
@@ -108,10 +108,11 @@ public SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, short match, short r
 		name = "IDENTITY_" + match + "_" + replace;
 		max = (match > replace) ? match : replace;
 		min = (match < replace) ? match : replace;
-		rows = cols = compoundSet.getAllCompounds();
-		matrix = new short[rows.size()][cols.size()];
-		for (int r = 0; r < rows.size(); r++) {
-			for (int c = 0; c < cols.size(); c++) {
+		rows = cols = new ArrayList<>(compoundSet.getAllCompounds());
+		int N = rows.size();
+		matrix = new short[N][N];
+		for (int r = 0; r < N; r++) {
+			for (int c = 0; c < N; c++) {
 				try {
 					matrix[r][c] = (compoundSet.compoundsEquivalent(rows.get(r), cols.get(c))) ? match : replace;
 				} catch (UnsupportedOperationException e) {
@@ -230,7 +231,8 @@ public String getName() {
 	private static <C extends Compound> int getIndexOfCompound(List<C> list, C compound) {
 		int index = list.indexOf(compound);
 		if (index == -1) {
-			for (int i = 0; i < list.size(); i++) {
+			int N = list.size();
+			for (int i = 0; i < N; i++) {
 				if (compound.equalsIgnoreCase(list.get(i))) {
 					index = i;
 					break;
@@ -290,7 +292,8 @@ public String toString() {
 	public Map<C, Short> getRow(C row) {
 		int rowIndex = rows.indexOf(row);
 		Map<C, Short> map = new HashMap<>();
-		for (int colIndex = 0; colIndex < matrix[rowIndex].length; colIndex++) {
+		int N = matrix[rowIndex].length;
+		for (int colIndex = 0; colIndex < N; colIndex++) {
 			map.put(cols.get(colIndex), matrix[rowIndex][colIndex]);
 		}
 		return map;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java
index d145a13035..c929fc6015 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java
@@ -25,6 +25,8 @@
 import org.biojava.nbio.core.util.Equals;
 import org.biojava.nbio.core.util.Hashcoder;
 
+import java.util.Objects;
+
 /**
  * Used in Sequences as the unique indentifier. If possible, set the {@link DataSource} to know the
  * source of the id. This allows a SequenceProxy to gather features or related sequences
@@ -97,10 +99,10 @@ public boolean equals(Object o) {
 		boolean equals = false;
 		if (Equals.classEqual(this, o)) {
 			AccessionID l = (AccessionID) o;
-			equals = (Equals.equal(getID(), l.getID())
-					&& Equals.equal(getDataSource(), l.getDataSource())
-					&& Equals.equal(getIdentifier(), l.getIdentifier())
-					&& Equals.equal(getVersion(), l.getVersion()));
+            equals = (Objects.equals(getID(), l.getID())
+					&& Objects.equals(getDataSource(), l.getDataSource())
+					&& Objects.equals(getIdentifier(), l.getIdentifier())
+					&& Objects.equals(getVersion(), l.getVersion()));
 	}
 		return equals;
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java
index 22c766c39a..a59a9557b2 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java
@@ -145,7 +145,7 @@ public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound)
 			addAmbiguousEquivalents("I", "L", "J");
 			// ambiguous gaps
 			AminoAcidCompound gap1, gap2, gap3;
-			Set<AminoAcidCompound> gaps = new HashSet<>();
+			Set<AminoAcidCompound> gaps = new HashSet<>(3);
 			gaps.add(gap1 = aminoAcidCompoundCache.get("-"));
 			gaps.add(gap2 = aminoAcidCompoundCache.get("."));
 			gaps.add(gap3 = aminoAcidCompoundCache.get("_"));
@@ -153,7 +153,7 @@ public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound)
 			equivalentsCache.put(gap2, gaps);
 			equivalentsCache.put(gap3, gaps);
 			// X is never equivalent, even to itself
-			equivalentsCache.put(aminoAcidCompoundCache.get("X"), new HashSet<>());
+			equivalentsCache.put(aminoAcidCompoundCache.get("X"), Collections.EMPTY_SET);
 		}
 		return equivalentsCache.get(compound);
 	}
@@ -163,18 +163,18 @@ private void addAmbiguousEquivalents(String one, String two, String either) {
 		Set<AminoAcidCompound> equivalents;
 		AminoAcidCompound cOne, cTwo, cEither;
 
-		equivalents = new HashSet<>();
+		equivalents = new HashSet<>(3);
 		equivalents.add(cOne = aminoAcidCompoundCache.get(one));
 		equivalents.add(cTwo = aminoAcidCompoundCache.get(two));
 		equivalents.add(cEither = aminoAcidCompoundCache.get(either));
 		equivalentsCache.put(cEither, equivalents);
 
-		equivalents = new HashSet<>();
+		equivalents = new HashSet<>(2);
 		equivalents.add(cOne);
 		equivalents.add(cEither);
 		equivalentsCache.put(cOne, equivalents);
 
-		equivalents = new HashSet<>();
+		equivalents = new HashSet<>(2);
 		equivalents.add(cTwo);
 		equivalents.add(cEither);
 		equivalentsCache.put(cTwo, equivalents);
@@ -188,16 +188,19 @@ public boolean hasCompound(AminoAcidCompound compound) {
 	@Override
 	public boolean isValidSequence(Sequence<AminoAcidCompound> sequence) {
 		for (AminoAcidCompound compound: sequence) {
-			if (!hasCompound(compound)) {
+			if (!hasCompound(compound))
 				return false;
-			}
 		}
 		return true;
 	}
 
 	@Override
-	public List<AminoAcidCompound> getAllCompounds() {
-		return new ArrayList<>(aminoAcidCompoundCache.values());
+	public Collection<AminoAcidCompound> getAllCompounds() {
+		return
+			//new ArrayList<>(
+			Collections.unmodifiableCollection(
+				aminoAcidCompoundCache.values()
+			);
 	}
 
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java
index b6a8963685..ea3ccad87d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java
@@ -25,6 +25,8 @@
 import org.biojava.nbio.core.util.Equals;
 import org.biojava.nbio.core.util.Hashcoder;
 
+import java.util.Objects;
+
 /**
  * Implementation for resolving fuzzy locations. Caches the calculated
  * value.
@@ -113,10 +115,10 @@ public boolean equals(Object obj) {
 		boolean equals = false;
 		if (Equals.classEqual(this, obj)) {
 			FuzzyPoint p = (FuzzyPoint) obj;
-			equals = (Equals.equal(getMin(), p.getMin())
-					&& Equals.equal(getMax(), p.getMax())
-					&& Equals.equal(isUnknown(), p.isUnknown())
-					&& Equals.equal(isUncertain(), p.isUncertain())
+			equals = (Objects.equals(getMin(), p.getMin())
+					&& Objects.equals(getMax(), p.getMax())
+					&& isUnknown() == p.isUnknown()
+					&& isUncertain() == p.isUncertain()
 					);
 		}
 		return equals;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java
index 517c1414fd..c4ccb8510f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java
@@ -104,9 +104,9 @@ public boolean equals(Object obj) {
 		boolean equals = false;
 		if (Equals.classEqual(this, obj)) {
 			SimplePoint p = (SimplePoint) obj;
-			equals = (Equals.equal(getPosition(), p.getPosition())
-					&& Equals.equal(isUncertain(), p.isUncertain())
-					&& Equals.equal(isUnknown(), p.isUnknown()));
+			equals = (getPosition() == p.getPosition()
+					&& isUncertain() == p.isUncertain()
+					&& isUnknown() == p.isUnknown());
 		}
 		return equals;
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
index 7f07d8bc22..4e0b23bc0e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
@@ -33,14 +33,10 @@
 import org.biojava.nbio.core.util.Hashcoder;
 
 import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
+import java.util.*;
 
 import static java.lang.String.format;
 import static org.biojava.nbio.core.util.Equals.classEqual;
-import static org.biojava.nbio.core.util.Equals.equal;
 
 /**
  * Base abstraction of a location which encodes for the majority of important
@@ -265,13 +261,13 @@ public boolean equals(Object obj) {
 		boolean equals = false;
 		if (classEqual(this, obj)) {
 			AbstractLocation l = (AbstractLocation) obj;
-			equals = (equal(getStart(), l.getStart())
-					&& equal(getEnd(), l.getEnd())
-					&& equal(getStrand(), l.getStrand())
-					&& equal(isCircular(), l.isCircular())
-					&& equal(isBetweenCompounds(), l.isBetweenCompounds())
-					&& equal(getSubLocations(), l.getSubLocations())
-					&& equal(getAccession(), l.getAccession()));
+			equals = (Objects.equals(getStart(), l.getStart())
+					&& Objects.equals(getEnd(), l.getEnd())
+					&& Objects.equals(getStrand(), l.getStrand())
+					&& isCircular() == l.isCircular()
+					&& isBetweenCompounds() == l.isBetweenCompounds()
+					&& Objects.equals(getSubLocations(), l.getSubLocations())
+					&& Objects.equals(getAccession(), l.getAccession()));
 		}
 		return equals;
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java
index aa4356cd25..3c7e4c9a79 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java
@@ -35,6 +35,7 @@
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Objects;
 
 /**
  * Stores a Sequence as a collection of compounds in an ArrayList
@@ -277,8 +278,8 @@ public int hashCode() {
 	public boolean equals(Object o) {
 		if(Equals.classEqual(this, o)) {
 			ArrayListSequenceReader<C> that = (ArrayListSequenceReader<C>)o;
-			return  Equals.equal(parsedCompounds, that.parsedCompounds) &&
-					Equals.equal(compoundSet, that.compoundSet);
+            return  Objects.equals(parsedCompounds, that.parsedCompounds) &&
+                    Objects.equals(compoundSet, that.compoundSet);
 		}
 		return false;
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
index 6ee1e2177e..c410c982c9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
@@ -29,6 +29,7 @@
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 
 /**
  * An implementation of the popular bit encodings. This class provides the
@@ -193,8 +194,8 @@ public boolean equals(Object o) {
 		if(Equals.classEqual(this, o)) {
 			@SuppressWarnings("unchecked")
 			BitSequenceReader<C> that = (BitSequenceReader<C>)o;
-			return  Equals.equal(this.accession, that.accession) &&
-					Equals.equal(this.worker, that.worker);
+			return  Objects.equals(this.accession, that.accession) &&
+					Objects.equals(this.worker, that.worker);
 		}
 		return false;
 	}
@@ -287,9 +288,8 @@ public int seqArraySize(int length) {
 		 */
 		public void populate(Sequence<C> sequence) {
 			int position = 1;
-			for (C c : sequence) {
+			for (C c : sequence)
 				setCompoundAt(c, position++);
-			}
 		}
 
 		/**
@@ -460,9 +460,9 @@ public int hashCode() {
 		public boolean equals(Object o) {
 			if(Equals.classEqual(this, o)) {
 				BitArrayWorker<C> that = (BitArrayWorker<C>)o;
-				return  Equals.equal(compoundSet, that.compoundSet) &&
-						Equals.equal(indexToCompoundsLookup, that.indexToCompoundsLookup) &&
-						Equals.equal(sequence, that.sequence);
+				return  Objects.equals(compoundSet, that.compoundSet) &&
+						Objects.equals(indexToCompoundsLookup, that.indexToCompoundsLookup) &&
+						Objects.equals(sequence, that.sequence);
 			}
 			return false;
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
index 09e695914f..d523e1f817 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
@@ -27,6 +27,7 @@
 
 import java.util.Iterator;
 import java.util.List;
+import java.util.Objects;
 
 /**
  * An implementation of the SequenceReader interface which for every
@@ -204,9 +205,9 @@ public int hashCode() {
 	public boolean equals(Object o) {
 		if(Equals.classEqual(this, o)) {
 			SingleCompoundSequenceReader<C> that = (SingleCompoundSequenceReader<C>)o;
-			return  Equals.equal(compound, that.compound) &&
-					Equals.equal(compoundSet, that.compoundSet) &&
-					Equals.equal(length, that.length);
+			return  Objects.equals(compound, that.compound) &&
+                    Objects.equals(compoundSet, that.compoundSet) &&
+					length == that.length;
 		}
 		return false;
 	}
@@ -214,9 +215,9 @@ public boolean equals(Object o) {
 	public boolean equals(Sequence<C> o) {
 		if(Equals.classEqual(this, o)) {
 			SingleCompoundSequenceReader<C> that = (SingleCompoundSequenceReader<C>)o;
-			return  Equals.equal(compound, that.compound) &&
-					Equals.equal(compoundSet, that.compoundSet) &&
-					Equals.equal(length, that.length);
+			return  Objects.equals(compound, that.compound) &&
+                    Objects.equals(compoundSet, that.compoundSet) &&
+					length == that.length;
 		}
 		return false;
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
index c8790da2f8..6533fabc9f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
@@ -21,6 +21,7 @@
  */
 package org.biojava.nbio.core.sequence.template;
 
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
 import org.biojava.nbio.core.util.Equals;
 import org.biojava.nbio.core.util.Hashcoder;
 import org.slf4j.Logger;
@@ -155,19 +156,22 @@ public boolean compoundsEqual(C compoundOne, C compoundTwo) {
 
 		@Override
 		public boolean isValidSequence(Sequence<C> sequence) {
-				for (C compound: sequence) {
-						if (!hasCompound(compound)) {
-								return false;
-						}
-				}
-				return true;
+			for (C compound: sequence) {
+				if (!hasCompound(compound))
+					return false;
+			}
+			return true;
 		}
 
 
 
 	@Override
-	public List<C> getAllCompounds() {
-		return new ArrayList<>(charSeqToCompound.values());
+	public Collection<C> getAllCompounds() {
+		return
+			Collections.unmodifiableCollection(
+			//new ArrayList<>(
+				charSeqToCompound.values()
+			);
 	}
 
 	private void assertCompound(C compound) {
@@ -197,11 +201,12 @@ public int hashCode() {
 		@Override
 		@SuppressWarnings("unchecked")
 		public boolean equals(Object o) {
+				if (this == o) return true;
 				if (! (o instanceof AbstractCompoundSet)) return false;
 				if(Equals.classEqual(this, o)) {
 						AbstractCompoundSet<C> that = (AbstractCompoundSet<C>)o;
-						return  Equals.equal(charSeqToCompound, that.charSeqToCompound) &&
-										Equals.equal(equivalentsMap, that.equivalentsMap);
+                    return  Objects.equals(charSeqToCompound, that.charSeqToCompound) &&
+                            Objects.equals(equivalentsMap, that.equivalentsMap);
 				}
 				return false;
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/CompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/CompoundSet.java
index 1710d0c358..4708d72d0b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/CompoundSet.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/CompoundSet.java
@@ -25,7 +25,9 @@
  */
 package org.biojava.nbio.core.sequence.template;
 
-import java.util.List;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+
+import java.util.Collection;
 import java.util.Set;
 
 
@@ -58,7 +60,7 @@ public interface CompoundSet<C extends Compound> {
 
 	boolean hasCompound(C compound);
 
-	List<C> getAllCompounds();
+	Collection<C> getAllCompounds();
 
 	boolean isComplementable();
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
index 32d6e4f5dd..f765c6ea2e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
@@ -30,6 +30,7 @@
 import org.biojava.nbio.core.util.Hashcoder;
 
 import java.util.List;
+import java.util.Objects;
 
 /**
  * Provides a way of separating us from the specific {@link IUPACTable} even
@@ -119,10 +120,10 @@ public boolean equals(Object o) {
 			boolean equals = false;
 			if(Equals.classEqual(this, o)) {
 				Codon casted = (Codon) o;
-				equals =   Equals.equal(getTriplet(), casted.getTriplet()) &&
-							Equals.equal(isStart(), casted.isStart()) &&
-							Equals.equal(isStop(), casted.isStop()) &&
-							Equals.equal(getAminoAcid(), casted.getAminoAcid());
+				equals =   Objects.equals(getTriplet(), casted.getTriplet()) &&
+						isStart() == casted.isStart() &&
+						isStop() == casted.isStop() &&
+                        Objects.equals(getAminoAcid(), casted.getAminoAcid());
 			}
 			return equals;
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
index 335793df75..e2733818fe 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
@@ -32,27 +32,6 @@
  */
 public class Equals {
 
-	public static boolean equal(int one, int two) {
-		return one == two;
-	}
-
-	public static boolean equal(long one, long two) {
-		return (one == two);
-	}
-
-	public static boolean equal(boolean one, boolean two) {
-		return one == two;
-	}
-
-	/**
-	 * Does not compare class types.
-	 * @see #classEqual(Object, Object)
-	 */
-	@Deprecated public static boolean equal(Object one, Object two) {
-		return Objects.equals(one, two);
-		//return one == null && two == null || !(one == null || two == null) && (one == two || one.equals(two));
-	}
-
 	/**
 	 * This method should be called before beginning any equals methods. In order
 	 * to return true the method:
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java
index b946a43f1f..1a62a232bb 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java
@@ -135,7 +135,7 @@ private void clusterIt() {
 		dendrogram = new LinkedPair[numItems-1];
 
 
-		logger.debug("Initial matrix: \n"+matrixToString());
+		//logger.debug("Initial matrix: \n"+matrixToString());
 
 
 		for (int m=0;m<numItems-1;m++) {
@@ -176,11 +176,7 @@ private void merge(LinkedPair closestPair) {
 	 * @return
 	 */
 	private double link(double d1, double d2) {
-		if (isScoreMatrix) {
-			return Math.max(d1,d2);
-		} else {
-			return Math.min(d1,d2);
-		}
+		return isScoreMatrix ? Math.max(d1, d2) : Math.min(d1, d2);
 	}
 
 	private double getDistance(int first, int second) {
@@ -293,23 +289,23 @@ public Map<Integer, Set<Integer>> getClusters(double cutoff) {
 					Set<Integer> firstCluster = clusters.get(firstClusterId);
 					Set<Integer> secondCluster = clusters.get(secondClusterId);
 					if (firstCluster.size()<secondCluster.size()) {
-						logger.debug("Joining cluster "+firstClusterId+" to cluster "+secondClusterId);
+						//logger.debug("Joining cluster "+firstClusterId+" to cluster "+secondClusterId);
 						// we join first onto second
 						secondCluster.addAll(firstCluster);
 						clusters.remove(firstClusterId);
 					} else {
-						logger.debug("Joining cluster "+secondClusterId+" to cluster "+firstClusterId);
+						//logger.debug("Joining cluster "+secondClusterId+" to cluster "+firstClusterId);
 						// we join second onto first
 						firstCluster.addAll(secondCluster);
 						clusters.remove(secondClusterId);
 					}
 				}
 
-				logger.debug("Within cutoff:     "+dendrogram[i]);
+				//logger.debug("Within cutoff:     "+dendrogram[i]);
 
 			} else {
 
-				logger.debug("Not within cutoff: "+dendrogram[i]);
+				//logger.debug("Not within cutoff: "+dendrogram[i]);
 
 			}
 		}
@@ -340,7 +336,7 @@ public Map<Integer, Set<Integer>> getClusters(double cutoff) {
 
 		}
 
-		logger.debug("Clusters: \n"+clustersToString(finalClusters));
+		//logger.debug("Clusters: \n"+clustersToString(finalClusters));
 
 		return finalClusters;
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
index d26e1144c5..48eaca4409 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
@@ -37,7 +37,7 @@ public class SoftHashMap<K, V> extends AbstractMap<K, V> {
 
 	private final static Logger logger = LoggerFactory.getLogger(SoftHashMap.class);
 
-	public static final int DEFAULT_LIMIT = 1;
+	//public static final int DEFAULT_LIMIT = 1;
 
 	/** The internal HashMap that stores SoftReference to actual data. */
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
index 34121ac9cf..1feaa533a9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
@@ -33,6 +33,7 @@
 import java.util.Iterator;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.concurrent.ConcurrentHashMap;
 
 /**
  * Controls global {@link EcodDatabase EcodDatabases} being used.
@@ -50,7 +51,8 @@ public class EcodFactory {
 	public static final String DEFAULT_VERSION = EcodInstallation.DEFAULT_VERSION;
 
 	private static final Map<String, SoftReference<EcodDatabase>> versionedEcodDBs =
-			Collections.synchronizedMap(new HashMap<>());
+			//Collections.synchronizedMap(new HashMap<>());
+			new ConcurrentHashMap();
 	private static String defaultVersion = EcodInstallation.DEFAULT_VERSION;
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java
index 86de7e11a5..34de9704f8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java
@@ -39,23 +39,15 @@ public class ChemCompGroupFactory {
 	private static final SoftHashMap<String, ChemComp> cache = new SoftHashMap<>(0);
 
 	public static ChemComp getChemComp(String recordName){
-
-		recordName = recordName.toUpperCase().trim();
-
 		// we are using the cache, to avoid hitting the file system too often.
-		ChemComp cc = cache.get(recordName);
-		if ( cc != null) {
-			logger.debug("Chem comp "+cc.getThree_letter_code()+" read from cache");
-			return cc;
-		}
-
-		// not cached, get the chem comp from the provider
-		logger.debug("Chem comp "+recordName+" read from provider "+chemCompProvider.getClass().getCanonicalName());
-		cc = chemCompProvider.getChemComp(recordName);
-
 		// Note that this also caches null or empty responses
-		cache.put(recordName, cc);
-		return cc;
+		return cache.computeIfAbsent(recordName.toUpperCase().trim(), r -> {
+			// not cached, get the chem comp from the provider
+			if (logger.isDebugEnabled())
+				logger.debug("Chem comp " + r + " read from provider " + chemCompProvider.getClass().getCanonicalName());
+
+			return chemCompProvider.getChemComp(r);
+		});
 	}
 
 	/**
@@ -117,7 +109,8 @@ public static Group getGroupFromChemCompDictionary(String recordName) {
 
 			if ( one_letter == null || one_letter.length()==0 || one_letter.equals("?")) {
 				// e.g. problem with PRR, which probably should have a parent of ALA, but as of 20110127 does not.
-				logger.warn("Problem with chemical component: " + recordName + "  Did not find one letter code! Setting it to 'X'");
+				if (logger.isWarnEnabled())
+					logger.warn("Problem with chemical component: " + recordName + "  Did not find one letter code! Setting it to 'X'");
 				aa.setAminoType('X');
 
 			} else  {
@@ -127,9 +120,9 @@ public static Group getGroupFromChemCompDictionary(String recordName) {
 
 			g = aa;
 		} else if ( PolymerType.POLYNUCLEOTIDE_ONLY.contains(cc.getPolymerType())) {
-			NucleotideImpl nuc = new NucleotideImpl();
 
-			g = nuc;
+
+			g = new NucleotideImpl();
 
 
 		} else {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java
index 44da26cd85..c964722053 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java
@@ -44,6 +44,7 @@ public class ChemCompTools {
 
 	/**
 	 * Lookup table to convert standard amino acid's one-letter-codes to monomer ids
+	 * TODO use an array since there are only alphabetic keys
 	 */
 	private static final Map<Character, String> AMINO_ACID_LOOKUP_1TO3;
 
@@ -52,10 +53,8 @@ public class ChemCompTools {
 	 */
 	private static final Map<String, Character> DNA_LOOKUP_2TO1;
 
-	/**
-	 * Lookup table to convert standard nucleic acid's one-letter-codes to monomer ids
-	 */
-	private static final Map<Character, String> DNA_LOOKUP_1TO2;
+
+
 
 	/**
 	 * Static block that initializes lookup maps and initializes their <tt>ResidueInfo</tt> instances
@@ -85,7 +84,7 @@ public class ChemCompTools {
 		foo.put("TRP", 'W');
 		foo.put("TYR", 'Y');
 		foo.put("VAL", 'V');
-		AMINO_ACID_LOOKUP_3TO1 = Collections.unmodifiableMap((Collections.synchronizedMap(foo)));
+		AMINO_ACID_LOOKUP_3TO1 = Collections.unmodifiableMap(foo);
 
 		Map<Character, String> bar = new HashMap<>();
 		bar.put('A', "ALA");
@@ -110,7 +109,7 @@ public class ChemCompTools {
 		bar.put('W', "TRP");
 		bar.put('Y', "TYR");
 		bar.put('V', "VAL");
-		AMINO_ACID_LOOKUP_1TO3 = Collections.unmodifiableMap(Collections.synchronizedMap(bar));
+		AMINO_ACID_LOOKUP_1TO3 = Collections.unmodifiableMap(bar);
 
 		foo = new HashMap<>();
 		foo.put("DA",'A');
@@ -119,16 +118,8 @@ public class ChemCompTools {
 		foo.put("DI",'I');
 		foo.put("DU",'U');
 		foo.put("DT",'T');
-		DNA_LOOKUP_2TO1 = Collections.unmodifiableMap((Collections.synchronizedMap(foo)));
+		DNA_LOOKUP_2TO1 = Collections.unmodifiableMap(foo);
 
-		bar = new HashMap<>();
-		bar.put('A',"DA");
-		bar.put('C',"DC");
-		bar.put('G',"DG");
-		bar.put('I',"DI");
-		bar.put('U',"DU");
-		bar.put('T',"DT");
-		DNA_LOOKUP_1TO2 = Collections.unmodifiableMap(Collections.synchronizedMap(bar));
 
 
 		// initialise standard chemical components
@@ -153,8 +144,20 @@ public static String getAminoThreeLetter(Character c){
 		return AMINO_ACID_LOOKUP_1TO3.get(c);
 	}
 
-	public static String getDNATwoLetter(Character c){
-		return DNA_LOOKUP_1TO2.get(c);
+	/**
+	 * Lookup table to convert standard nucleic acid's one-letter-codes to monomer ids
+	 * TODO use an array since there are only alphabetic keys
+	 */
+	public static String getDNATwoLetter(char c){
+		switch (c) {
+			case 'A': return "DA";
+			case 'C': return "DC";
+			case 'G': return "DG";
+			case 'I': return "DI";
+			case 'U': return "DU";
+			case 'T': return "DT";
+			default: return null;
+		}
 	}
 
 	public static boolean isStandardChemComp(ChemComp cc){
@@ -168,7 +171,7 @@ public static boolean isStandardChemComp(ChemComp cc){
 		if ((pid == null) || (pid.equals("?"))){
 
 			// and they have a one letter code
-			if ( ( one != null) && ( ! one.equals("?") )){
+			if ( ( one != null) && ( !one.equals("?") )){
 
 				// peptides and dpeptides must not have X
 				if ( (polymerType == PolymerType.peptide) ||
@@ -180,9 +183,7 @@ public static boolean isStandardChemComp(ChemComp cc){
 					return performRNACheck(cc);
 				}
 				if (polymerType == PolymerType.dna) {
-
 					return performDNACheck(cc);
-
 				}
 
 				//System.err.println("Non standard chem comp: " + cc);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
index d20636c12e..d991f174ca 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
@@ -520,30 +520,30 @@ private static <T> void addGroupAtId(List<T> seqResGroups, T group, int sequence
 
 	private static Group getSeqResGroup(char singleLetterCode, GroupType type) {
 
-		if(type==GroupType.AMINOACID){
-			String threeLetter = ChemCompTools.getAminoThreeLetter(singleLetterCode);
-			if (threeLetter == null) return null;
-			ChemComp chemComp = ChemCompGroupFactory.getChemComp(threeLetter);
-
-			AminoAcidImpl a = new AminoAcidImpl();
-			a.setRecordType(AminoAcid.SEQRESRECORD);
-			a.setAminoType(singleLetterCode);
-			a.setPDBName(threeLetter);
-			a.setChemComp(chemComp);
-			return a;
-
-		} else if (type==GroupType.NUCLEOTIDE) {
-			String twoLetter = ChemCompTools.getDNATwoLetter(singleLetterCode);
-			if (twoLetter == null) return null;
-			ChemComp chemComp = ChemCompGroupFactory.getChemComp(twoLetter);
-
-			NucleotideImpl n = new NucleotideImpl();
-			n.setPDBName(twoLetter);
-			n.setChemComp(chemComp);
-			return n;
-		}
-		else{
-			return null;
+		switch (type) {
+			case AMINOACID:
+				String threeLetter = ChemCompTools.getAminoThreeLetter(singleLetterCode);
+				if (threeLetter != null) {
+					AminoAcidImpl a = new AminoAcidImpl();
+					a.setRecordType(AminoAcid.SEQRESRECORD);
+					a.setAminoType(singleLetterCode);
+					a.setPDBName(threeLetter);
+					a.setChemComp(ChemCompGroupFactory.getChemComp(threeLetter));
+					return a;
+				}
+
+				break;
+			case NUCLEOTIDE:
+				String twoLetter = ChemCompTools.getDNATwoLetter(singleLetterCode);
+				if (twoLetter != null) {
+					NucleotideImpl n = new NucleotideImpl();
+					n.setPDBName(twoLetter);
+					n.setChemComp(ChemCompGroupFactory.getChemComp(twoLetter));
+					return n;
+				}
+				break;
 		}
+		return null;
+
 	}
 }
\ No newline at end of file

From a875504adae94bbcdf9e1403691f3e01d0c20131 Mon Sep 17 00:00:00 2001
From: me <seh@internet.earth>
Date: Sun, 8 Mar 2020 09:03:24 -0400
Subject: [PATCH 12/18] updates

---
 .../biojava/nbio/core/search/io/Result.java   |   14 +-
 .../sequence/io/GenbankSequenceParser.java    |    2 +-
 .../location/template/AbstractLocation.java   |    7 +-
 .../sequence/storage/BitSequenceReader.java   |    7 +-
 .../template/AbstractCompoundSet.java         |    1 -
 .../core/sequence/template/CompoundSet.java   |    2 -
 .../org/biojava/nbio/core/util/Equals.java    |    2 -
 .../homology/GFF3FromUniprotBlastHits.java    |   71 +-
 .../nbio/genome/parsers/gff/Location.java     |   15 +-
 .../nbio/protmod/structure/StructureAtom.java |    7 +-
 .../protmod/structure/StructureGroup.java     |    5 +-
 .../java/org/biojava/nbio/ontology/Term.java  |    2 +-
 .../nbio/data/sequence/FastaSequence.java     |  316 +-
 .../nbio/data/sequence/SequenceUtil.java      |  496 ++-
 .../java/org/biojava/nbio/ronn/ORonn.java     |   23 +-
 .../org/biojava/nbio/ronn/ORonnModel.java     |  278 +-
 .../nbio/structure/align/gui/DisplayAFP.java  |    5 +-
 .../align/gui/jmol/MultipleAlignmentJmol.java |    8 +-
 .../nbio/structure/BioAssemblyIdentifier.java |    4 +-
 .../java/org/biojava/nbio/structure/Calc.java |    9 +-
 .../java/org/biojava/nbio/structure/Site.java |   15 +-
 .../biojava/nbio/structure/StructureIO.java   |   13 +-
 .../nbio/structure/StructureTools.java        | 3521 ++++++++---------
 .../structure/SubstructureIdentifier.java     |    6 +-
 .../structure/align/StructurePairAligner.java |    2 +-
 .../ce/AbstractUserArgumentProcessor.java     |    6 +-
 .../nbio/structure/align/ce/CECalculator.java |    6 +-
 .../align/ce/CeCalculatorEnhanced.java        |    9 +-
 .../align/fatcat/calc/AFPOptimizer.java       |    4 +-
 .../calc/StructureAlignmentOptimizer.java     |    6 +-
 .../nbio/structure/align/model/AFPChain.java  |   14 +-
 .../align/pairwise/AlternativeAlignment.java  |    5 +-
 .../align/pairwise/FragmentJoiner.java        |   22 +-
 .../align/util/AFPAlignmentDisplay.java       |    6 +-
 .../nbio/structure/align/util/AtomCache.java  |   21 +-
 .../nbio/structure/asa/AsaCalculator.java     |   21 +-
 .../structure/contact/AtomIdentifier.java     |   21 +-
 .../nbio/structure/contact/BoundingBox.java   |    4 +-
 .../biojava/nbio/structure/contact/Grid.java  |   20 +-
 .../domain/LocalProteinDomainParser.java      |    4 +-
 .../nbio/structure/domain/PDPDomain.java      |    4 +-
 .../domain/pdp/GetDistanceMatrix.java         |    4 +-
 .../nbio/structure/ecod/EcodDomain.java       |    4 +-
 .../nbio/structure/ecod/EcodFactory.java      |    2 -
 .../nbio/structure/ecod/EcodInstallation.java |    2 +-
 .../io/mmcif/AllChemCompProvider.java         |    2 +-
 .../io/mmcif/chem/ChemCompTools.java          |   47 +-
 .../structure/io/mmcif/model/ChemComp.java    |   13 +-
 .../nbio/structure/io/mmtf/MmtfUtils.java     |    1 -
 .../nbio/structure/scop/ScopDomain.java       |    4 +-
 .../structure/secstruc/SecStrucTools.java     |    4 +-
 .../symmetry/core/C2RotationSolver.java       |    2 +-
 .../structure/symmetry/core/HelixSolver.java  |    2 +-
 .../symmetry/core/QuatSymmetryDetector.java   |   37 +-
 .../symmetry/core/RotationSolver.java         |    2 +-
 .../symmetry/core/SystematicSolver.java       |    2 +-
 56 files changed, 2477 insertions(+), 2655 deletions(-)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java
index d547e002da..aeab300342 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java
@@ -83,6 +83,7 @@ public int hashCode() {
 	 */
 	@Override
 	public boolean equals(Object obj) {
+		if (this == obj) return true;
 		if (obj == null) {
 			return false;
 		}
@@ -90,16 +91,9 @@ public boolean equals(Object obj) {
 			return false;
 		}
 		final Result other = (Result) obj;
-		if (!Objects.equals(this.queryID, other.queryID)) {
-			return false;
-		}
-		if (!Objects.equals(this.queryDef, other.queryDef)) {
-			return false;
-		}
-		if (!Objects.equals(this.hits, other.hits)) {
-			return false;
-		}
-		return true;
+		return Objects.equals(this.queryID, other.queryID) &&
+				Objects.equals(this.queryDef, other.queryDef) &&
+				Objects.equals(this.hits, other.hits);
 	}
 
 	public int getIterationNumber() {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
index e016068652..97829fc547 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
@@ -146,7 +146,7 @@ private String parse(BufferedReader bufferedReader) {
 			sectionKey = section.get(0)[0];
 			if (sectionKey == null) {
 				//if we reach the end of the file, section contains empty strings
-				if(section.get(0)[1]==null || section.get(0)[1]=="" ||
+				if(section.get(0)[1]==null || section.get(0)[1].equals("") ||
 						section.get(0)[1].length()==0) {
 					throw new ParserException(Messages.ENDOFFILE);
 				}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
index 4e0b23bc0e..10de177683 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java
@@ -240,13 +240,12 @@ public List<Location> getRelevantSubLocations() {
 	/**
 	 * Here to allow for recursion
 	 */
-	private List<Location> getAllSubLocations(Location location) {
+	private static List<Location> getAllSubLocations(Location location) {
 		List<Location> flatSubLocations = new ArrayList<>();
 		for (Location l : location.getSubLocations()) {
 			if (l.isComplex()) {
 				flatSubLocations.addAll(getAllSubLocations(l));
-			}
-			else {
+			} else {
 				flatSubLocations.add(l);
 			}
 		}
@@ -358,7 +357,7 @@ protected <C extends Compound> Sequence<C> reverseSequence(Sequence<C> sequence)
 	 * Uses the Sequence's CompoundSet to decide if a compound can
 	 * be assgined to ComplementCompound meaning it can complement
 	 */
-	protected <C extends Compound> boolean canComplement(Sequence<C> sequence) {
+	protected static <C extends Compound> boolean canComplement(Sequence<C> sequence) {
 		CompoundSet<C> compoundSet = sequence.getCompoundSet();
 		Compound c = compoundSet.getAllCompounds().iterator().next();
 		return ComplementCompound.class.isAssignableFrom(c.getClass());
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
index c410c982c9..608e95c53b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
@@ -26,10 +26,7 @@
 import org.biojava.nbio.core.util.Equals;
 import org.biojava.nbio.core.util.Hashcoder;
 
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
+import java.util.*;
 
 /**
  * An implementation of the popular bit encodings. This class provides the
@@ -462,7 +459,7 @@ public boolean equals(Object o) {
 				BitArrayWorker<C> that = (BitArrayWorker<C>)o;
 				return  Objects.equals(compoundSet, that.compoundSet) &&
 						Objects.equals(indexToCompoundsLookup, that.indexToCompoundsLookup) &&
-						Objects.equals(sequence, that.sequence);
+						Arrays.equals(sequence, that.sequence);
 			}
 			return false;
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
index 6533fabc9f..edc8bd1096 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
@@ -21,7 +21,6 @@
  */
 package org.biojava.nbio.core.sequence.template;
 
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
 import org.biojava.nbio.core.util.Equals;
 import org.biojava.nbio.core.util.Hashcoder;
 import org.slf4j.Logger;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/CompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/CompoundSet.java
index 4708d72d0b..a0a6e91ab1 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/CompoundSet.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/CompoundSet.java
@@ -25,8 +25,6 @@
  */
 package org.biojava.nbio.core.sequence.template;
 
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
-
 import java.util.Collection;
 import java.util.Set;
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
index e2733818fe..b335791b7f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
@@ -20,8 +20,6 @@
  */
 package org.biojava.nbio.core.util;
 
-import java.util.Objects;
-
 /**
  * A set of helper methods which return true if the two parameters are
  * equal to each other.
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
index 2ceae673c4..4a51dfebc8 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
@@ -48,15 +48,18 @@
  *
  * @author Scooter Willis <willishf at gmail dot com>
  * @author Mark Chapman
+ *
+ * TODO test
+ *
  */
 public class GFF3FromUniprotBlastHits {
 
 	private static final Logger logger = LoggerFactory.getLogger(GFF3FromUniprotBlastHits.class);
 
-	public void process(File xmlBlastHits, double ecutoff, LinkedHashMap<String, GeneSequence> geneSequenceHashMap, OutputStream gff3Output) throws Exception {
-		LinkedHashMap<String, ArrayList<String>> hits = BlastHomologyHits.getMatches(xmlBlastHits, ecutoff);
-		process(hits, geneSequenceHashMap, gff3Output);
-	}
+//	public void process(File xmlBlastHits, double ecutoff, LinkedHashMap<String, GeneSequence> geneSequenceHashMap, OutputStream gff3Output) throws Exception {
+//		LinkedHashMap<String, ArrayList<String>> hits = BlastHomologyHits.getMatches(xmlBlastHits, ecutoff);
+//		process(hits, geneSequenceHashMap, gff3Output);
+//	}
 
 	public void process(LinkedHashMap<String, ArrayList<String>> hits, LinkedHashMap<String, GeneSequence> geneSequenceHashMap, OutputStream gff3Output) {
 		int size = hits.size();
@@ -117,30 +120,28 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
 					//   System.out.println(new Pair().format(alignment));
 					int proteinIndex = 0;
 					int gff3Index = 0;
-					for (int i = 0; i < cdsProteinList.size(); i++) {
+					int cdsProteins = cdsProteinList.size();
+					for (int i = 0; i < cdsProteins; i++) {
 						ProteinSequence peptideSequence = cdsProteinList.get(i);
-						String seq = peptideSequence.getSequenceAsString();
-						int startIndex = -1;
+						final String seq = peptideSequence.getSequenceAsString();
+						int startIndex;
 						int offsetStartIndex = 0;
-						for (int s = 0; s < seq.length(); s++) {
-							startIndex = alignment.getIndexInTargetForQueryAt(proteinIndex + s);
+						int seqLen = seq.length();
+						//for (int s = 0; s < seqLen; s++) {
+							startIndex = alignment.getIndexInTargetForQueryAt(proteinIndex);
 							startIndex = startIndex + 1;
-							offsetStartIndex = s;
-							break;
-						}
-						int endIndex = -1;
+//							offsetStartIndex = 0;
+						//}
+						int endIndex;
 
 						int offsetEndIndex = 0;
-						for (int e = 0; e < seq.length(); e++) {
-							endIndex = alignment.getIndexInTargetForQueryAt(proteinIndex + seq.length() - 1 - e);
-							{
-								endIndex = endIndex + 1;
-								offsetEndIndex = e;
-								break;
-							}
-						}
+//						for (int e = 0; e < seqLen; e++) {
+							endIndex = alignment.getIndexInTargetForQueryAt(proteinIndex + seqLen - 1);
+							endIndex = endIndex + 1;
+//							offsetEndIndex = 0;
+//						}
 
-						proteinIndex = proteinIndex + seq.length();
+						proteinIndex = proteinIndex + seqLen;
 						if (startIndex != endIndex) {
 							CDSSequence cdsSequence = cdsSequenceList.get(i);
 							String hitLabel;
@@ -167,15 +168,16 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
 									if (keyWords.size() > 0) {
 										notes = ";Note=";
 										for (String note : keyWords) {
-											if (note.equals("Complete proteome")) {
-												continue;
-											}
-											if (note.equals("Direct protein sequencing")) {
-												continue;
-											}
+											switch (note) {
+												case "Complete proteome":
+												case "Direct protein sequencing":
+													continue;
+												default:
+													notes = notes + " " + note;
+													geneSequence.addNote(note); // add note/keyword which can be output in fasta header if needed
+													break;
 
-											notes = notes + " " + note;
-											geneSequence.addNote(note); // add note/keyword which can be output in fasta header if needed
+											}
 										}
 									}
 
@@ -231,14 +233,13 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(),
 											geneSequence.addNote(note.getId()); // add note/keyword which can be output in fasta header if needed
 											LinkedHashMap<String, String> properties = note.getProperties();
 											for (Map.Entry<String, String> entry : properties.entrySet()) {
-												if (entry.getKey().equals("evidence")) {
+												if (entry.getKey().equals("evidence"))
 													continue;
-												}
-												String property = entry.getValue();
 
-												if (property.startsWith("C:")) {
+												String property = entry.getValue();
+												if (property.startsWith("C:"))
 													continue; // skip over the location
-												}
+
 												if (property.endsWith("...")) {
 													property = property.substring(0, property.length() - 3);
 												}
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
index 96b0ed6b18..43463b92fb 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
@@ -857,24 +857,17 @@ public int hashCode() {
 	public boolean equals(Object obj) {
 		if (this == obj)
 			return true;
-		if (obj == null)
-			return false;
-		if (getClass() != obj.getClass())
+		if (obj == null || getClass() != obj.getClass())
 			return false;
 		Location other = (Location) obj;
-		if (mEnd != other.mEnd)
-			return false;
-		if (mStart != other.mStart)
-			return false;
-		return true;
+		return mStart == other.mStart && mEnd == other.mEnd;
 	}
 
 	/**
 	 *
 	 */
-	private boolean isHealthy()
-	{
-		return ( mStart <= mEnd ) && (( mStart <= 0 && mEnd <= 0 ) || (mStart >= 0 && mEnd >= 0));
+	private boolean isHealthy() {
+		return ( mStart <= mEnd ) && (( mStart <= 0 && mEnd <= 0 ) || (mStart >= 0 /*&& mEnd >= 0*/));
 	}
 
 }
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureAtom.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureAtom.java
index 42e43f3247..c4dd3dffc5 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureAtom.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureAtom.java
@@ -60,13 +60,8 @@ public boolean equals(Object obj) {
 
 		StructureAtom anAtom = (StructureAtom)obj;
 
-		if (!anAtom.getGroup().equals(group))
-			return false;
-
-		if (!anAtom.getAtomName().equals(atomName))
-			return false;
+		return anAtom.getGroup().equals(group) && anAtom.getAtomName().equals(atomName);
 
-		return true;
 	}
 
 	@Override
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureGroup.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureGroup.java
index 21fe1d87eb..cec71f2faa 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureGroup.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureGroup.java
@@ -117,10 +117,7 @@ public boolean equals(Object obj) {
 			return false;
 
 		StructureGroup aGroup = (StructureGroup) obj;
-		if (!resNum.equals(aGroup.resNum))
-			return false;
-
-		return true;
+		return resNum.equals(aGroup.resNum);
 	}
 
 	@Override
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java
index dee4691177..ad20f570bf 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java
@@ -227,7 +227,7 @@ public boolean equals(Object obj)
 		Term that = (Term) obj;
 
 		return this.getOntology() == that.getOntology() &&
-				this.getName() == that.getName();
+                this.getName().equals(that.getName());
 	  }
 	}
 }
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/FastaSequence.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/FastaSequence.java
index 6af6f13712..b915989ebb 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/FastaSequence.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/FastaSequence.java
@@ -26,8 +26,7 @@
 
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
+import java.util.Objects;
 
 /**
  * A FASTA formatted sequence. Please note that this class does not make any
@@ -41,173 +40,150 @@
  */
 
 @XmlAccessorType(XmlAccessType.FIELD)
-public final class FastaSequence implements Comparable<FastaSequence>{
-
-	/**
-	 * Sequence id
-	 */
-	private String id;
-
-	// TODO what about gapped sequence here! should be indicated
-	/**
-	 * Returns the string representation of sequence
-	 */
-	private String sequence;
-
-	@SuppressWarnings("unused")
-	private FastaSequence() {
-	// Default constructor for JaxB
-	}
-
-	/**
-	 * Upon construction the any whitespace characters are removed from the
-	 * sequence
-	 *
-	 * @param id
-	 * @param sequence
-	 */
-	public FastaSequence(final String id, final String sequence) {
-	this.id = id.trim();
-	this.sequence = SequenceUtil.cleanSequence(sequence);
-	}
-
-	/**
-	 * Gets the value of id
-	 *
-	 * @return the value of id
-	 */
-	public String getId() {
-	return id;
-	}
-
-	/**
-	 * Gets the value of sequence
-	 *
-	 * @return the value of sequence
-	 */
-	public String getSequence() {
-	return sequence;
-	}
-
-	public static int countMatchesInSequence(final String theString,
-		final String theRegExp) {
-	final Pattern p = Pattern.compile(theRegExp);
-	final Matcher m = p.matcher(theString);
-	int cnt = 0;
-	while (m.find()) {
-		cnt++;
-	}
-	return cnt;
-	}
-
-	public String getFormattedFasta() {
-	return getFormatedSequence(80);
-	}
-
-	/**
-	 *
-	 * @return one line name, next line sequence, no matter what the sequence
-	 *         length is
-	 */
-	public String getOnelineFasta() {
-	String fasta = ">" + getId() + "\n";
-	fasta += getSequence() + "\n";
-	return fasta;
-	}
-
-	/**
-	 * Format sequence per width letter in one string. Without spaces.
-	 *
-	 * @return multiple line formated sequence, one line width letters length
-	 *
-	 */
-	public String getFormatedSequence(final int width) {
-	if (sequence == null) {
-		return "";
-	}
-
-	assert width >= 0 : "Wrong width parameter ";
-
-	final StringBuilder sb = new StringBuilder(sequence);
-	int nchunks = sequence.length() / width;
-	// add up inserted new line chars
-	nchunks = (nchunks + sequence.length()) / width;
-	int nlineCharcounter = 0;
-	for (int i = 1; i <= nchunks; i++) {
-		final int insPos = width * i + nlineCharcounter;
-		// to prevent inserting new line in the very end of a sequence then
-		// it would have failed.
-		// Also covers the case when the sequences shorter than width
-		if (sb.length() <= insPos) {
-		break;
-		}
-		sb.insert(insPos, "\n");
-		nlineCharcounter++;
-	}
-	return sb.toString();
-	}
-
-	/**
-	 *
-	 * @return sequence length
-	 */
-	public int getLength() {
-	return sequence.length();
-	}
-
-	/**
-	 * Same as oneLineFasta
-	 */
-	@Override
-	public String toString() {
-	return this.getOnelineFasta();
-	}
-
-	@Override
-	public int hashCode() {
-	final int prime = 31;
-	int result = 1;
-	result = prime * result + ((id == null) ? 0 : id.hashCode());
-	result = prime * result
-		+ ((sequence == null) ? 0 : sequence.hashCode());
-	return result;
-	}
-
-	@Override
-	public boolean equals(final Object obj) {
-	if (this == obj) {
-		return true;
-	}
-	if (obj == null) {
-		return false;
-	}
-	if (getClass() != obj.getClass()) {
-		return false;
-	}
-	final FastaSequence other = (FastaSequence) obj;
-	if (id == null) {
-		if (other.id != null) {
-		return false;
-		}
-	} else if (!id.equals(other.id)) {
-		return false;
-	}
-	if (sequence == null) {
-		if (other.sequence != null) {
-		return false;
-		}
-	} else if (!sequence.equals(other.sequence)) {
-		return false;
-	}
-	return true;
-	}
-
-	@Override
-	public int compareTo(FastaSequence o) {
-		if(o==null || o.id==null)
-			return 1;
-
-		return this.getId().compareTo(o.id);
-	}
+public final class FastaSequence implements Comparable<FastaSequence> {
+
+    /**
+     * Sequence id
+     */
+    private String id;
+
+    // TODO what about gapped sequence here! should be indicated
+    /**
+     * Returns the string representation of sequence
+     */
+    private String sequence;
+
+    @SuppressWarnings("unused")
+    private FastaSequence() {
+        // Default constructor for JaxB
+    }
+
+    /**
+     * Upon construction the any whitespace characters are removed from the
+     * sequence
+     *
+     * @param id
+     * @param sequence
+     */
+    public FastaSequence(final String id, final String sequence) {
+        this.id = id.trim();
+        this.sequence = SequenceUtil.cleanSequence(sequence);
+    }
+
+    /**
+     * Gets the value of id
+     *
+     * @return the value of id
+     */
+    public String getId() {
+        return id;
+    }
+
+    /**
+     * Gets the value of sequence
+     *
+     * @return the value of sequence
+     */
+    public String getSequence() {
+        return sequence;
+    }
+
+//    public static int countMatchesInSequence(final String theString,
+//                                             final String theRegExp) {
+//        final Pattern p = Pattern.compile(theRegExp);
+//        final Matcher m = p.matcher(theString);
+//        int cnt = 0;
+//        while (m.find()) {
+//            cnt++;
+//        }
+//        return cnt;
+//    }
+
+    public String getFormattedFasta() {
+        return getFormatedSequence(80);
+    }
+
+    /**
+     * @return one line name, next line sequence, no matter what the sequence
+     * length is
+     */
+    public String getOnelineFasta() {
+		return ">" + getId() + "\n" + (getSequence() + "\n");
+    }
+
+    /**
+     * Format sequence per width letter in one string. Without spaces.
+     *
+     * @return multiple line formated sequence, one line width letters length
+     */
+    public String getFormatedSequence(final int width) {
+        if (sequence == null) {
+            return "";
+        }
+
+        assert width >= 0 : "Wrong width parameter ";
+
+        final StringBuilder sb = new StringBuilder(sequence);
+        int nchunks = sequence.length() / width;
+        // add up inserted new line chars
+        nchunks = (nchunks + sequence.length()) / width;
+        int nlineCharcounter = 0;
+        for (int i = 1; i <= nchunks; i++) {
+            final int insPos = width * i + nlineCharcounter;
+            // to prevent inserting new line in the very end of a sequence then
+            // it would have failed.
+            // Also covers the case when the sequences shorter than width
+            if (sb.length() <= insPos) {
+                break;
+            }
+            sb.insert(insPos, "\n");
+            nlineCharcounter++;
+        }
+        return sb.toString();
+    }
+
+    /**
+     * @return sequence length
+     */
+    public int getLength() {
+        return sequence.length();
+    }
+
+    /**
+     * Same as oneLineFasta
+     */
+    @Override
+    public String toString() {
+        return this.getOnelineFasta();
+    }
+
+    @Override
+    public int hashCode() {
+        final int prime = 31;
+        int result = 1;
+        result = prime * result + ((id == null) ? 0 : id.hashCode());
+        result = prime * result + ((sequence == null) ? 0 : sequence.hashCode());
+        return result;
+    }
+
+    @Override
+    public boolean equals(final Object obj) {
+        if (this == obj)
+            return true;
+
+        if (obj == null || getClass() != obj.getClass())
+            return false;
+
+        final FastaSequence other = (FastaSequence) obj;
+        return Objects.equals(id, other.id) && Objects.equals(sequence, other.sequence);
+    }
+
+    @Override
+    public int compareTo(FastaSequence o) {
+        if (o == null || o.id == null)
+            return 1;
+
+        return this.getId().compareTo(o.id);
+    }
 
 }
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java
index 19aa512e88..096927f51d 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java
@@ -44,255 +44,251 @@
  */
 public final class SequenceUtil {
 
-	private static final Logger logger = LoggerFactory.getLogger(SequenceUtil.class);
-
-	/**
-	 * A whitespace character: [\t\n\x0B\f\r]
-	 */
-	public static final Pattern WHITE_SPACE = Pattern.compile("\\s");
-
-	/**
-	 * A digit
-	 */
-	public static final Pattern DIGIT = Pattern.compile("\\d");
-
-	/**
-	 * Non word
-	 */
-	public static final Pattern NONWORD = Pattern.compile("\\W");
-
-	/**
-	 * Valid Amino acids
-	 */
-	public static final Pattern AA = Pattern.compile("[ARNDCQEGHILKMFPSTWYVUO]+",
-		Pattern.CASE_INSENSITIVE);
-
-	/**
-	 * inversion of AA pattern
-	 */
-	public static final Pattern NON_AA = Pattern.compile(
-		"[^ARNDCQEGHILKMFPSTWYVXUO]+", Pattern.CASE_INSENSITIVE);
-
-	/**
-	 * Same as AA pattern but with one additional letters - X
-	 */
-	public static final Pattern AMBIGUOUS_AA = Pattern.compile(
-		"[ARNDCQEGHILKMFPSTWYVXUO]+", Pattern.CASE_INSENSITIVE);
-
-	/**
-	 * Nucleotides a, t, g, c, u
-	 */
-	public static final Pattern NUCLEOTIDE = Pattern.compile("[AGTCU]+",
-		Pattern.CASE_INSENSITIVE);
-
-	/**
-	 * Ambiguous nucleotide
-	 */
-	public static final Pattern AMBIGUOUS_NUCLEOTIDE = Pattern.compile(
-		"[AGTCRYMKSWHBVDNU]+", Pattern.CASE_INSENSITIVE); // see IUPAC
-	/**
-	 * Non nucleotide
-	 */
-	public static final Pattern NON_NUCLEOTIDE = Pattern.compile("[^AGTCU]+",
-		Pattern.CASE_INSENSITIVE);
-
-	private SequenceUtil() {
-	} // utility class, no instantiation
-
-	/*
-	 * public static void write_PirSeq(OutputStream os, FastaSequence seq)
-	 * throws IOException { BufferedWriter pir_out = new BufferedWriter(new
-	 * OutputStreamWriter(os)); pir_out.write(">P1;" + seq.getId() +
-	 * SysPrefs.newlinechar); pir_out.write(seq.getSequence() +
-	 * SysPrefs.newlinechar); pir_out.close(); }
-	 *
-	 * public static void write_FastaSeq(OutputStream os, FastaSequence seq)
-	 * throws IOException { BufferedWriter fasta_out = new BufferedWriter( new
-	 * OutputStreamWriter(os)); fasta_out.write(">" + seq.getId() +
-	 * SysPrefs.newlinechar); fasta_out.write(seq.getSequence() +
-	 * SysPrefs.newlinechar); fasta_out.close(); }
-	 */
-
-	/**
-	 * @return true is the sequence contains only letters a,c, t, g, u
-	 */
-	public static boolean isNucleotideSequence(final FastaSequence s) {
-	return SequenceUtil.isNonAmbNucleotideSequence(s.getSequence());
-	}
-
-	/**
-	 * Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
-	 * (!) - B char
-	 */
-	public static boolean isNonAmbNucleotideSequence(String sequence) {
-	sequence = SequenceUtil.cleanSequence(sequence);
-	if (SequenceUtil.DIGIT.matcher(sequence).find()) {
-		return false;
-	}
-	if (SequenceUtil.NON_NUCLEOTIDE.matcher(sequence).find()) {
-		return false;
-		/*
-		 * System.out.format("I found the text starting at " +
-		 * "index %d and ending at index %d.%n", nonDNAmatcher .start(),
-		 * nonDNAmatcher.end());
-		 */
-	}
-	final Matcher DNAmatcher = SequenceUtil.NUCLEOTIDE.matcher(sequence);
-	return DNAmatcher.find();
-	}
-
-	/**
-	 * Removes all whitespace chars in the sequence string
-	 *
-	 * @param sequence
-	 * @return cleaned up sequence
-	 */
-	public static String cleanSequence(String sequence) {
-	assert sequence != null;
-	final Matcher m = SequenceUtil.WHITE_SPACE.matcher(sequence);
-	sequence = m.replaceAll("").toUpperCase();
-	return sequence;
-	}
-
-	/**
-	 * Removes all special characters and digits as well as whitespace chars
-	 * from the sequence
-	 *
-	 * @param sequence
-	 * @return cleaned up sequence
-	 */
-	public static String deepCleanSequence(String sequence) {
-	sequence = SequenceUtil.cleanSequence(sequence);
-	sequence = SequenceUtil.DIGIT.matcher(sequence).replaceAll("");
-	sequence = SequenceUtil.NONWORD.matcher(sequence).replaceAll("");
-	final Pattern othernonSeqChars = Pattern.compile("[_-]+");
-	sequence = othernonSeqChars.matcher(sequence).replaceAll("");
-	return sequence;
-	}
-
-	/**
-	 *
-	 * @param sequence
-	 * @return true is the sequence is a protein sequence, false overwise
-	 */
-	public static boolean isProteinSequence(String sequence) {
-	sequence = SequenceUtil.cleanSequence(sequence);
-	if (SequenceUtil.isNonAmbNucleotideSequence(sequence)) {
-		return false;
-	}
-	if (SequenceUtil.DIGIT.matcher(sequence).find()) {
-		return false;
-	}
-	if (SequenceUtil.NON_AA.matcher(sequence).find()) {
-		logger.info("Found non aa: {}", sequence);
-		return false;
-	}
-	final Matcher protmatcher = SequenceUtil.AA.matcher(sequence);
-	return protmatcher.find();
-	}
-
-	/**
-	 * Check whether the sequence confirms to amboguous protein sequence
-	 *
-	 * @param sequence
-	 * @return return true only if the sequence if ambiguous protein sequence
-	 *         Return false otherwise. e.g. if the sequence is non-ambiguous
-	 *         protein or DNA
-	 */
-	public static boolean isAmbiguosProtein(String sequence) {
-	sequence = SequenceUtil.cleanSequence(sequence);
-	if (SequenceUtil.isNonAmbNucleotideSequence(sequence)) {
-		return false;
-	}
-	if (SequenceUtil.DIGIT.matcher(sequence).find()) {
-		return false;
-	}
-	if (SequenceUtil.NON_AA.matcher(sequence).find()) {
-		return false;
-	}
-	if (SequenceUtil.AA.matcher(sequence).find()) {
-		return false;
-	}
-	final Matcher amb_prot = SequenceUtil.AMBIGUOUS_AA.matcher(sequence);
-	return amb_prot.find();
-	}
-
-	/**
-	 * Writes list of FastaSequeces into the outstream formatting the sequence
-	 * so that it contains width chars on each line
-	 *
-	 * @param outstream
-	 * @param sequences
-	 * @param width
-	 *            - the maximum number of characters to write in one line
-	 * @throws IOException
-	 */
-	public static void writeFasta(final OutputStream outstream,
-		final List<FastaSequence> sequences, final int width)
-		throws IOException {
-	final OutputStreamWriter writer = new OutputStreamWriter(outstream);
-	final BufferedWriter fastawriter = new BufferedWriter(writer);
-	for (final FastaSequence fs : sequences) {
-		fastawriter.write(fs.getFormatedSequence(width));
-	}
-	outstream.flush();
-	fastawriter.close();
-	writer.close();
-	}
-
-	/**
-	 * Reads fasta sequences from inStream into the list of FastaSequence
-	 * objects
-	 *
-	 * @param inStream
-	 *            from
-	 * @return list of FastaSequence objects
-	 * @throws IOException
-	 */
-	public static List<FastaSequence> readFasta(final InputStream inStream)
-		throws IOException {
-	final List<FastaSequence> seqs = new ArrayList<>();
-
-	final BufferedReader infasta = new BufferedReader(
-		new InputStreamReader(inStream, StandardCharsets.UTF_8), 16000);
-	final Pattern pattern = Pattern.compile("//s+");
-
-	String line;
-	String sname = "", seqstr = null;
-	do {
-		line = infasta.readLine();
-		if ((line == null) || line.startsWith(">")) {
-		if (seqstr != null) {
-			seqs.add(new FastaSequence(sname.substring(1), seqstr));
-		}
-		sname = line; // remove >
-		seqstr = "";
-		} else {
-		final String subseq = pattern.matcher(line).replaceAll("");
-		seqstr += subseq;
-		}
-	} while (line != null);
-
-	infasta.close();
-	return seqs;
-	}
-
-	/**
-	 * Writes FastaSequence in the file, each sequence will take one line only
-	 *
-	 * @param os
-	 * @param sequences
-	 * @throws IOException
-	 */
-	public static void writeFasta(final OutputStream os,
-		final List<FastaSequence> sequences) throws IOException {
-	final OutputStreamWriter outWriter = new OutputStreamWriter(os);
-	final BufferedWriter fasta_out = new BufferedWriter(outWriter);
-	for (final FastaSequence fs : sequences) {
-		fasta_out.write(fs.getOnelineFasta());
-	}
-	fasta_out.close();
-	outWriter.close();
-	}
+    private static final Logger logger = LoggerFactory.getLogger(SequenceUtil.class);
+
+    /**
+     * A whitespace character: [\t\n\x0B\f\r]
+     */
+    public static final Pattern WHITE_SPACE = Pattern.compile("\\s");
+
+    /**
+     * A digit
+     */
+    public static final Pattern DIGIT = Pattern.compile("\\d");
+
+    /**
+     * Non word
+     */
+    public static final Pattern NONWORD = Pattern.compile("\\W");
+
+    /**
+     * Valid Amino acids
+     */
+    public static final Pattern AA = Pattern.compile("[ARNDCQEGHILKMFPSTWYVUO]+",
+            Pattern.CASE_INSENSITIVE);
+
+    /**
+     * inversion of AA pattern
+     */
+    public static final Pattern NON_AA = Pattern.compile(
+            "[^ARNDCQEGHILKMFPSTWYVXUO]+", Pattern.CASE_INSENSITIVE);
+
+    /**
+     * Same as AA pattern but with one additional letters - X
+     */
+    public static final Pattern AMBIGUOUS_AA = Pattern.compile(
+            "[ARNDCQEGHILKMFPSTWYVXUO]+", Pattern.CASE_INSENSITIVE);
+
+    /**
+     * Nucleotides a, t, g, c, u
+     */
+    public static final Pattern NUCLEOTIDE = Pattern.compile("[AGTCU]+",
+            Pattern.CASE_INSENSITIVE);
+
+    /**
+     * Ambiguous nucleotide
+     */
+    public static final Pattern AMBIGUOUS_NUCLEOTIDE = Pattern.compile(
+            "[AGTCRYMKSWHBVDNU]+", Pattern.CASE_INSENSITIVE); // see IUPAC
+    /**
+     * Non nucleotide
+     */
+    public static final Pattern NON_NUCLEOTIDE = Pattern.compile("[^AGTCU]+",
+            Pattern.CASE_INSENSITIVE);
+
+    private SequenceUtil() {
+    } // utility class, no instantiation
+
+    /*
+     * public static void write_PirSeq(OutputStream os, FastaSequence seq)
+     * throws IOException { BufferedWriter pir_out = new BufferedWriter(new
+     * OutputStreamWriter(os)); pir_out.write(">P1;" + seq.getId() +
+     * SysPrefs.newlinechar); pir_out.write(seq.getSequence() +
+     * SysPrefs.newlinechar); pir_out.close(); }
+     *
+     * public static void write_FastaSeq(OutputStream os, FastaSequence seq)
+     * throws IOException { BufferedWriter fasta_out = new BufferedWriter( new
+     * OutputStreamWriter(os)); fasta_out.write(">" + seq.getId() +
+     * SysPrefs.newlinechar); fasta_out.write(seq.getSequence() +
+     * SysPrefs.newlinechar); fasta_out.close(); }
+     */
+
+    /**
+     * @return true is the sequence contains only letters a,c, t, g, u
+     */
+    public static boolean isNucleotideSequence(final FastaSequence s) {
+        return SequenceUtil.isNonAmbNucleotideSequence(s.getSequence());
+    }
+
+    /**
+     * Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
+     * (!) - B char
+     */
+    public static boolean isNonAmbNucleotideSequence(String sequence) {
+
+    	sequence = SequenceUtil.cleanSequence(sequence);
+
+        if (SequenceUtil.DIGIT.matcher(sequence).find())
+            return false;
+
+        if (SequenceUtil.NON_NUCLEOTIDE.matcher(sequence).find())
+            return false;
+            /*
+             * System.out.format("I found the text starting at " +
+             * "index %d and ending at index %d.%n", nonDNAmatcher .start(),
+             * nonDNAmatcher.end());
+             */
+
+        return SequenceUtil.NUCLEOTIDE.matcher(sequence).find();
+    }
+
+    /**
+     * Removes all whitespace chars in the sequence string
+     *
+     * @param sequence
+     * @return cleaned up sequence
+     */
+    public static String cleanSequence(String sequence) {
+        assert sequence != null;
+        return SequenceUtil.WHITE_SPACE.matcher(sequence).replaceAll("").toUpperCase();
+    }
+
+    /**
+     * Removes all special characters and digits as well as whitespace chars
+     * from the sequence
+     *
+     * @param sequence
+     * @return cleaned up sequence
+     */
+    public static String deepCleanSequence(String sequence) {
+        sequence = SequenceUtil.cleanSequence(sequence);
+        sequence = SequenceUtil.DIGIT.matcher(sequence).replaceAll("");
+        sequence = SequenceUtil.NONWORD.matcher(sequence).replaceAll("");
+        final Pattern othernonSeqChars = Pattern.compile("[_-]+");
+        sequence = othernonSeqChars.matcher(sequence).replaceAll("");
+        return sequence;
+    }
+
+    /**
+     * @param sequence
+     * @return true is the sequence is a protein sequence, false overwise
+     */
+    public static boolean isProteinSequence(String sequence) {
+        sequence = SequenceUtil.cleanSequence(sequence);
+        if (SequenceUtil.isNonAmbNucleotideSequence(sequence)) {
+            return false;
+        }
+        if (SequenceUtil.DIGIT.matcher(sequence).find()) {
+            return false;
+        }
+        if (SequenceUtil.NON_AA.matcher(sequence).find()) {
+            logger.info("Found non aa: {}", sequence);
+            return false;
+        }
+        final Matcher protmatcher = SequenceUtil.AA.matcher(sequence);
+        return protmatcher.find();
+    }
+
+    /**
+     * Check whether the sequence confirms to amboguous protein sequence
+     *
+     * @param sequence
+     * @return return true only if the sequence if ambiguous protein sequence
+     * Return false otherwise. e.g. if the sequence is non-ambiguous
+     * protein or DNA
+     */
+    public static boolean isAmbiguosProtein(String sequence) {
+        sequence = SequenceUtil.cleanSequence(sequence);
+        if (SequenceUtil.isNonAmbNucleotideSequence(sequence)) {
+            return false;
+        }
+        if (SequenceUtil.DIGIT.matcher(sequence).find()) {
+            return false;
+        }
+        if (SequenceUtil.NON_AA.matcher(sequence).find()) {
+            return false;
+        }
+        if (SequenceUtil.AA.matcher(sequence).find()) {
+            return false;
+        }
+        final Matcher amb_prot = SequenceUtil.AMBIGUOUS_AA.matcher(sequence);
+        return amb_prot.find();
+    }
+
+    /**
+     * Writes list of FastaSequeces into the outstream formatting the sequence
+     * so that it contains width chars on each line
+     *
+     * @param outstream
+     * @param sequences
+     * @param width     - the maximum number of characters to write in one line
+     * @throws IOException
+     */
+    public static void writeFasta(final OutputStream outstream,
+                                  final List<FastaSequence> sequences, final int width)
+            throws IOException {
+        final OutputStreamWriter writer = new OutputStreamWriter(outstream);
+        final BufferedWriter fastawriter = new BufferedWriter(writer);
+        for (final FastaSequence fs : sequences) {
+            fastawriter.write(fs.getFormatedSequence(width));
+        }
+        outstream.flush();
+        fastawriter.close();
+        writer.close();
+    }
+
+    /**
+     * Reads fasta sequences from inStream into the list of FastaSequence
+     * objects
+     *
+     * @param inStream from
+     * @return list of FastaSequence objects
+     * @throws IOException
+     */
+    public static List<FastaSequence> readFasta(final InputStream inStream)
+            throws IOException {
+        final List<FastaSequence> seqs = new ArrayList<>();
+
+        final BufferedReader infasta = new BufferedReader(
+                new InputStreamReader(inStream, StandardCharsets.UTF_8), 16000);
+        final Pattern pattern = Pattern.compile("//s+");
+
+        String line;
+        String sname = "", seqstr = null;
+        do {
+            line = infasta.readLine();
+            if ((line == null) || line.startsWith(">")) {
+                if (seqstr != null) {
+                    seqs.add(new FastaSequence(sname.substring(1), seqstr));
+                }
+                sname = line; // remove >
+                seqstr = "";
+            } else {
+                final String subseq = pattern.matcher(line).replaceAll("");
+                seqstr += subseq;
+            }
+        } while (line != null);
+
+        infasta.close();
+        return seqs;
+    }
+
+    /**
+     * Writes FastaSequence in the file, each sequence will take one line only
+     *
+     * @param os
+     * @param sequences
+     * @throws IOException
+     */
+    public static void writeFasta(final OutputStream os,
+                                  final List<FastaSequence> sequences) throws IOException {
+        final OutputStreamWriter outWriter = new OutputStreamWriter(os);
+        final BufferedWriter fasta_out = new BufferedWriter(outWriter);
+        for (final FastaSequence fs : sequences) {
+            fasta_out.write(fs.getOnelineFasta());
+        }
+        fasta_out.close();
+        outWriter.close();
+    }
 
 }
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonn.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonn.java
index 8f5122eefd..0440e56b06 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonn.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonn.java
@@ -26,7 +26,6 @@
 
 import org.biojava.nbio.data.sequence.FastaSequence;
 import org.biojava.nbio.data.sequence.SequenceUtil;
-import org.biojava.nbio.ronn.ModelLoader.Model;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -138,20 +137,13 @@ static boolean isValidSequence(final FastaSequence fsequence) {
 	public ORonn call() throws NumberFormatException {
 		final String seq = sequence.getSequence();
 		// Calculate for each model
-		for (int m = 0; m < ORonn.NUMBER_OF_MODELS; m++) {
-			final Model model = mloader.getModel(m);
-			final ORonnModel rmodel = new ORonnModel(seq, model, disorder);
-			final float[] scores = rmodel.detect();
-			addScore(scores);
-		}
+		for (int m = 0; m < ORonn.NUMBER_OF_MODELS; m++)
+			addScore(new ORonnModel(seq, mloader.getModel(m), disorder).detect());
 
-		final char[] ch = seq.toCharArray();
 		final float[] meanScores = getMeanScores();
-		assert meanScores.length == seq.length() : "Scores are not calculated for "
-				+ "all residues!";
-		writeResults(meanScores, ch);
-		stat.println(timer.getTotalTime() + "ms prediction completed for "
-				+ sequence.getId());
+		assert meanScores.length == seq.length() : "Scores are not calculated for all residues!";
+		writeResults(meanScores, seq.toCharArray());
+		stat.println(timer.getTotalTime() + "ms prediction completed for " + sequence.getId());
 		return this;
 	}
 
@@ -171,8 +163,9 @@ private void addScore(final float[] scores) {
 	}
 
 	float[] getMeanScores() {
-		final float[] meanScores = new float[cummulativeScore.length];
-		for (int i = 0; i < cummulativeScore.length; i++) {
+		int n = cummulativeScore.length;
+		final float[] meanScores = new float[n];
+		for (int i = 0; i < n; i++) {
 			meanScores[i] = cummulativeScore[i] / ORonn.NUMBER_OF_MODELS;
 		}
 		return meanScores;
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java
index fe4dcaef12..0f6dfca151 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java
@@ -34,7 +34,6 @@
 import java.io.PrintWriter;
 
 
-
 /**
  * Fully re-factored version of RONN model. Based on the code in C version of
  * RONN.
@@ -45,142 +44,143 @@
  */
 public final class ORonnModel {
 
-	private static final Logger logger = LoggerFactory.getLogger(ORonnModel.class);
-
-	/**
-	 * Order probability, corresponds to disorder as 1-order
-	 */
-	private final float disorder_weight;
-
-	private final static int AA_ALPHABET = 19;
-	private final static int maxR = 110;
-	//private final static float coef = 1.0f;
-	/**
-	 * Holds encoded query sequence
-	 */
-	private final short[] seqAA;
-	/**
-	 * Holds query sequence
-	 */
-	private final char[] query;
-
-	private final Model model;
-
-	/**
-	 * Disorder scores for all residues
-	 */
-	private float[] scores = null;
-
-	final float[] detect() {
-
-	scores = new float[query.length];
-	int sResidue;
-	int dIndex;
-	int r;
-	float est, fOrder, pDisor, fDisor;
-	final float[][] Z = new float[seqAA.length][ORonnModel.maxR];
-	final int[] Q = new int[seqAA.length];
-	final Threshold thold = new ModelLoader.Threshold(model.modelNum);
-
-	/*
-	 * 19 looks like a size of the sliding window. So for any sequences
-	 * shorted than 19 AA the score will be NaN. Original RONN segfault in
-	 * such condition
-	 */
-	for (sResidue = 0; sResidue <= query.length - ORonnModel.AA_ALPHABET; sResidue++) {
-		est = 0.0f;
-
-		for (dIndex = 0; dIndex < model.numOfDBAAseq; dIndex++) {
-		final float[] rho = align(sResidue, dIndex);// search for the
-		// maximum alignment between ith peptide from the
-		// query and the dIndex-th database sequence
-		est += model.W[dIndex] * Math.exp((rho[1] - rho[0]) / rho[0]);
-		}
-
-		fOrder = (float) (Math.exp(-0.5 * Math.pow(est - thold.mu0, 2.0)
-			/ thold.sigma0) / (Math.sqrt(6.28) * thold.sigma0));
-
-		fDisor = (float) (Math.exp(-0.5 * Math.pow(est - thold.mu1, 2.0)
-			/ thold.sigma1) / (Math.sqrt(6.28) * thold.sigma1));
-
-		pDisor = (float) (disorder_weight * fDisor / ((1.0 - disorder_weight)
-			* fOrder + disorder_weight * fDisor));
-		for (r = sResidue; r < sResidue + ORonnModel.AA_ALPHABET; r++) {
-		Z[r][Q[r]] = pDisor;
-		Q[r]++;
-		}
-	}
-
-	for (sResidue = 0; sResidue < query.length; sResidue++) {
-		est = 0.0f;
-		float[] zRow = Z[sResidue];
-		int numOfIterations = Q[sResidue];
-		for (r = 0; r < numOfIterations; r++) {
-		est += zRow[r];
-		}
-		scores[sResidue] = est / numOfIterations;
-	}
-	return scores;
-	}
-
-	public void getScores(final File outfile) throws FileNotFoundException {
-	final PrintWriter output = new PrintWriter(outfile);
-	if (scores == null) {
-		synchronized (this) {
-		if (scores == null) {
-			detect();
-		}
-		}
-	}
-	for (int i = 0; i < scores.length; i++) {
-		output.printf("%c\t%f\n", query[i], scores[i]);
-	}
-	output.close();
-	}
-
-	// sResidue query sequence index and dIndex database sequence index
-	private float[] align(final int sResidue, final int dIndex) {
-	int dResidue, r;
-	float maxScore = -1000000;
-	float rho1;
-	int maxIdx = 0;
-	float rho0 = 0;
-	short[] dbAARow = model.dbAA[dIndex];
-	int numOfIterations = model.Length[dIndex] - ORonnModel.AA_ALPHABET;
-	for (dResidue = 0; dResidue <= numOfIterations; dResidue++) {
-		// go though the database sequence for maximised alignment
-		rho1 = 0.0f;
-		for (r = 0; r < ORonnModel.AA_ALPHABET; r++) {
-		// go through the query sequence for one alignment
-		rho1 += RonnConstraint.Blosum62[seqAA[sResidue + r]][dbAARow[dResidue
-			+ r]];
-		}
-		if (rho1 > maxScore) {
-		maxScore = rho1;
-		maxIdx = dResidue;
-		}
-	}
-	for (r = 0; r < ORonnModel.AA_ALPHABET; r++) {
-		rho0 += RonnConstraint.Blosum62[dbAARow[maxIdx + r]][dbAARow[maxIdx
-			+ r]];
-	}
-	return new float[] { rho0, maxScore };
-	}
-
-	public ORonnModel(final String sequence, final Model model,
-		final float disorder) throws NumberFormatException {
-	this.disorder_weight = disorder;
-	this.model = model;
-	query = sequence.toCharArray();
-	seqAA = new short[query.length];
-	assert model != null;
-	assert model.numOfDBAAseq > 0;
-	for (int sResidue = 0; sResidue < sequence.length(); sResidue++) {
-		seqAA[sResidue] = RonnConstraint.INDEX[query[sResidue] - 'A'];
-		if ((seqAA[sResidue] < 0) || (seqAA[sResidue] > 19)) {
-			logger.error("seqAA[sResidue]={}({})", seqAA[sResidue], query[sResidue]);
-			System.exit(1);
-		}
-	}
-	}
+    private static final Logger logger = LoggerFactory.getLogger(ORonnModel.class);
+
+    /**
+     * Order probability, corresponds to disorder as 1-order
+     */
+    private final float disorder_weight;
+
+    private final static int AA_ALPHABET = 19;
+    private final static int maxR = 110;
+    //private final static float coef = 1.0f;
+    /**
+     * Holds encoded query sequence
+     */
+    private final short[] seqAA;
+    /**
+     * Holds query sequence
+     */
+    private final char[] query;
+
+    private final Model model;
+
+    /**
+     * Disorder scores for all residues
+     */
+    private float[] scores = null;
+
+    final float[] detect() {
+
+        scores = new float[query.length];
+        int sResidue;
+        int dIndex;
+        int r;
+        float est, fOrder, pDisor, fDisor;
+        final float[][] Z = new float[seqAA.length][ORonnModel.maxR];
+        final int[] Q = new int[seqAA.length];
+        final Threshold thold = new ModelLoader.Threshold(model.modelNum);
+
+        /*
+         * 19 looks like a size of the sliding window. So for any sequences
+         * shorted than 19 AA the score will be NaN. Original RONN segfault in
+         * such condition
+         */
+        for (sResidue = 0; sResidue <= query.length - ORonnModel.AA_ALPHABET; sResidue++) {
+            est = 0.0f;
+
+            for (dIndex = 0; dIndex < model.numOfDBAAseq; dIndex++) {
+                final float[] rho = align(sResidue, dIndex);// search for the
+                // maximum alignment between ith peptide from the
+                // query and the dIndex-th database sequence
+                est += model.W[dIndex] * Math.exp((rho[1] - rho[0]) / rho[0]);
+            }
+
+            fOrder = (float) (Math.exp(-0.5 * Math.pow(est - thold.mu0, 2.0)
+                    / thold.sigma0) / (Math.sqrt(6.28) * thold.sigma0));
+
+            fDisor = (float) (Math.exp(-0.5 * Math.pow(est - thold.mu1, 2.0)
+                    / thold.sigma1) / (Math.sqrt(6.28) * thold.sigma1));
+
+            pDisor = (float) (disorder_weight * fDisor / ((1.0 - disorder_weight)
+                    * fOrder + disorder_weight * fDisor));
+            for (r = sResidue; r < sResidue + ORonnModel.AA_ALPHABET; r++) {
+                Z[r][Q[r]] = pDisor;
+                Q[r]++;
+            }
+        }
+
+        for (sResidue = 0; sResidue < query.length; sResidue++) {
+            est = 0.0f;
+            float[] zRow = Z[sResidue];
+            int numOfIterations = Q[sResidue];
+            for (r = 0; r < numOfIterations; r++) {
+                est += zRow[r];
+            }
+            scores[sResidue] = est / numOfIterations;
+        }
+        return scores;
+    }
+
+    public void getScores(final File outfile) throws FileNotFoundException {
+        final PrintWriter output = new PrintWriter(outfile);
+        if (scores == null) {
+            synchronized (this) {
+                if (scores == null) {
+                    detect();
+                }
+            }
+        }
+        for (int i = 0; i < scores.length; i++) {
+            output.printf("%c\t%f\n", query[i], scores[i]);
+        }
+        output.close();
+    }
+
+    // sResidue query sequence index and dIndex database sequence index
+    private float[] align(final int sResidue, final int dIndex) {
+        int dResidue, r;
+        float maxScore = Float.NEGATIVE_INFINITY;
+        float rho1;
+        int maxIdx = 0;
+        float rho0 = 0;
+        short[] dbAARow = model.dbAA[dIndex];
+        int numOfIterations = model.Length[dIndex] - ORonnModel.AA_ALPHABET;
+        for (dResidue = 0; dResidue <= numOfIterations; dResidue++) {
+            // go though the database sequence for maximised alignment
+            rho1 = 0.0f;
+            for (r = 0; r < ORonnModel.AA_ALPHABET; r++) {
+                // go through the query sequence for one alignment
+                rho1 += RonnConstraint.Blosum62[seqAA[sResidue + r]][dbAARow[dResidue
+                        + r]];
+            }
+            if (rho1 > maxScore) {
+                maxScore = rho1;
+                maxIdx = dResidue;
+            }
+        }
+        for (r = 0; r < ORonnModel.AA_ALPHABET; r++) {
+            rho0 += RonnConstraint.Blosum62[dbAARow[maxIdx + r]][dbAARow[maxIdx + r]];
+        }
+        return new float[]{rho0, maxScore};
+    }
+
+    public ORonnModel(final String sequence, final Model model,
+                      final float disorder) throws NumberFormatException {
+        this.disorder_weight = disorder;
+        this.model = model;
+        query = sequence.toCharArray();
+        seqAA = new short[query.length];
+        assert model != null;
+        assert model.numOfDBAAseq > 0;
+        int sLen = sequence.length();
+        for (int sResidue = 0; sResidue < sLen; sResidue++) {
+            short r = RonnConstraint.INDEX[query[sResidue] - 'A'];
+            if ((r < 0) || (r > 19)) {
+                logger.error("seqAA[sResidue]={}({})", r, query[sResidue]);
+                System.exit(1);
+            }
+            seqAA[sResidue] = r;
+        }
+    }
 }
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
index aac4af81f7..5ce33ee02c 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java
@@ -538,10 +538,9 @@ public static void showAlignmentImage(AFPChain afpChain, String result) {
 	 * @param ca1 atoms for protein 1
 	 * @param ca2 atoms for protein 2
 	 * @return a protein structure with 2 models.
-	 * @throws StructureException
-	 */
+     */
 	public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1,
-			Atom[] ca2) throws StructureException{
+			Atom[] ca2) {
 
 
 		if ( afpChain.getNrEQR() < 1){
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
index 90e74be6e6..6d49cd3b18 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
@@ -217,13 +217,13 @@ public void windowClosing(WindowEvent e) {
 			evalString("save selection; select *; color grey; "
 					+ "select ligand; color CPK;");
 
-			if (value == "Set1") {
+			if (value.equals("Set1")) {
 				colorPalette = ColorBrewer.Set1;
-			} else if (value == "Set2") {
+			} else if (value.equals("Set2")) {
 				colorPalette = ColorBrewer.Set2;
-			} else if (value == "Spectral") {
+			} else if (value.equals("Spectral")) {
 				colorPalette = ColorBrewer.Spectral;
-			} else if (value == "Pastel") {
+			} else if (value.equals("Pastel")) {
 				colorPalette = ColorBrewer.Pastel1;
 			}
 			String script = getJmolString(multAln, transformedAtoms,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
index 8f91832bbd..6ef3f7693f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
@@ -22,7 +22,6 @@
 
 import org.biojava.nbio.structure.align.util.AtomCache;
 
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -68,8 +67,7 @@ public String toString() {
 	}
 
 	@Override
-	public Structure loadStructure(AtomCache cache) throws StructureException,
-			IOException {
+	public Structure loadStructure(AtomCache cache) throws StructureException {
 		return cache.getBiologicalAssembly(pdbCode, biolNr, AtomCache.DEFAULT_BIOASSEMBLY_STYLE);
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
index 541150c519..ff5fb8589b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -767,23 +767,18 @@ public static void shift(Group group , Atom a ){
 	public static Atom getCentroid(Atom[] atomSet){
 
 		// if we don't catch this case, the centroid returned is (NaN,NaN,NaN), which can cause lots of problems down the line
-		if (atomSet.length==0)
+		int n = atomSet.length;
+		if (n==0)
 			throw new IllegalArgumentException("Atom array has length 0, can't calculate centroid!");
 
-
 		double[] coords = new double[3];
 
-		coords[0] = 0;
-		coords[1] = 0;
-		coords[2] = 0 ;
-
 		for (Atom a : atomSet) {
 			coords[0] += a.getX();
 			coords[1] += a.getY();
 			coords[2] += a.getZ();
 		}
 
-		int n = atomSet.length;
 		coords[0] = coords[0] / n;
 		coords[1] = coords[1] / n;
 		coords[2] = coords[2] / n;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java
index 8a0dfc839c..488107e8b0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java
@@ -227,6 +227,7 @@ public void setEvCode(String evCode) {
 
 	@Override
 	public boolean equals(Object obj) {
+		if (this == obj) return true;
 		if (obj == null) {
 			return false;
 		}
@@ -234,19 +235,7 @@ public boolean equals(Object obj) {
 			return false;
 		}
 		final Site other = (Site) obj;
-		if (!Objects.equals(this.siteID, other.siteID)) {
-			return false;
-		}
-		if (!Objects.equals(this.groups, other.groups)) {
-			return false;
-		}
-		if (!Objects.equals(this.evCode, other.evCode)) {
-			return false;
-		}
-		if (!Objects.equals(this.description, other.description)) {
-			return false;
-		}
-		return true;
+		return Objects.equals(this.siteID, other.siteID) && Objects.equals(this.groups, other.groups) && Objects.equals(this.evCode, other.evCode) && Objects.equals(this.description, other.description);
 	}
 
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
index ff97afc1f8..a04deed335 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
@@ -137,9 +137,8 @@ public static Structure getStructure(String name) throws IOException, StructureE
 	 * if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).
 	 * @return a Structure object or null if that assembly is not available
 	 * @throws StructureException
-	 * @throws IOException
-	 */
-	public static Structure getBiologicalAssembly(String pdbId, boolean multiModel) throws IOException, StructureException{
+     */
+	public static Structure getBiologicalAssembly(String pdbId, boolean multiModel) throws StructureException{
 
 		return getAtomCache().getBiologicalAssembly(pdbId.toLowerCase(), multiModel);
 	}
@@ -179,9 +178,8 @@ public static Structure getBiologicalAssembly(String pdbId) throws IOException,
 	 * if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).
 	 * @return a Structure object or null if that assembly is not available
 	 * @throws StructureException if there is no bioassembly available for given biolAssemblyNr or some other problems encountered while loading it
-	 * @throws IOException
-	 */
-	public static Structure getBiologicalAssembly(String pdbId, int biolAssemblyNr, boolean multiModel) throws IOException, StructureException {
+     */
+	public static Structure getBiologicalAssembly(String pdbId, int biolAssemblyNr, boolean multiModel) throws StructureException {
 		return getAtomCache().getBiologicalAssembly(pdbId.toLowerCase(), biolAssemblyNr, multiModel);
 	}
 
@@ -216,11 +214,10 @@ public static Structure getBiologicalAssembly(String pdbId, int biolAssemblyNr)
 	 * @param multiModel if true the output Structure will be a multi-model one with one transformId per model,
 	 * if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).
 	 * @return
-	 * @throws IOException
 	 * @throws StructureException
 	 * @since 5.0
 	 */
-	public static List<Structure> getBiologicalAssemblies(String pdbId, boolean multiModel) throws IOException, StructureException {
+	public static List<Structure> getBiologicalAssemblies(String pdbId, boolean multiModel) throws StructureException {
 
 
 		return getAtomCache().getBiologicalAssemblies(pdbId.toLowerCase(), multiModel);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
index 83115b0ffb..cbeb137ba7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -47,447 +47,437 @@
  */
 public class StructureTools {
 
-	private static final Logger logger = LoggerFactory
-			.getLogger(StructureTools.class);
-
-	// Amino Acid backbone
-	/**
-	 * The atom name of the backbone C-alpha atom. Note that this can be
-	 * ambiguous depending on the context since Calcium atoms use the same name
-	 * in PDB.
-	 */
-	public static final String CA_ATOM_NAME = "CA";
-
-	/**
-	 * The atom name for the backbone amide nitrogen
-	 */
-	public static final String N_ATOM_NAME = "N";
-
-	/**
-	 * The atom name for the backbone carbonyl
-	 */
-	public static final String C_ATOM_NAME = "C";
-
-	/**
-	 * The atom name for the backbone carbonyl oxygen
-	 */
-	public static final String O_ATOM_NAME = "O";
-
-	/**
-	 * The atom name of the side-chain C-beta atom
-	 */
-	public static final String CB_ATOM_NAME = "CB";
-
-	// Nucleotide backbone
-	/**
-	 * The atom name of the backbone C1' in RNA
-	 */
-	public static final String C1_ATOM_NAME = "C1'";
-	/**
-	 * The atom name of the backbone C2' in RNA
-	 */
-	public static final String C2_ATOM_NAME = "C2'";
-	/**
-	 * The atom name of the backbone C3' in RNA
-	 */
-	public static final String C3_ATOM_NAME = "C3'";
-	/**
-	 * The atom name of the backbone C4' in RNA
-	 */
-	public static final String C4_ATOM_NAME = "C4'";
-	/**
-	 * The atom name of the backbone O2' in RNA
-	 */
-	public static final String O2_ATOM_NAME = "O2'";
-	/**
-	 * The atom name of the backbone O3' in RNA
-	 */
-	public static final String O3_ATOM_NAME = "O3'";
-	/**
-	 * The atom name of the backbone O4' in RNA
-	 */
-	public static final String O4_ATOM_NAME = "O4'";
-	/**
-	 * The atom name of the backbone O4' in RNA
-	 */
-	public static final String O5_ATOM_NAME = "O5'";
-	/**
-	 * The atom name of the backbone O4' in RNA
-	 */
-	public static final String OP1_ATOM_NAME = "OP1";
-	/**
-	 * The atom name of the backbone O4' in RNA
-	 */
-	public static final String OP2_ATOM_NAME = "OP2";
-	/**
-	 * The atom name of the backbone phosphate in RNA
-	 */
-	public static final String P_ATOM_NAME = "P";
-
-	/**
-	 * The atom used as representative for nucleotides, equivalent to
-	 * {@link #CA_ATOM_NAME} for proteins
-	 */
-	public static final String NUCLEOTIDE_REPRESENTATIVE = P_ATOM_NAME;
-
-	/**
-	 * The character to use for unknown compounds in sequence strings
-	 */
-	public static final char UNKNOWN_GROUP_LABEL = 'X';
-
-	/**
-	 * Below this ratio of aminoacid/nucleotide residues to the sequence total,
-	 * we use simple majority of aminoacid/nucleotide residues to decide the
-	 * character of the chain (protein/nucleotide)
-	 */
-	public static final double RATIO_RESIDUES_TO_TOTAL = 0.95;
-
-	/**
-	 * Threshold for plausible binding of a ligand to the selected substructure
-	 */
-	public static final double DEFAULT_LIGAND_PROXIMITY_CUTOFF = 5;
-
-	// there is a file format change in PDB 3.0 and nucleotides are being
-	// renamed
-	private static final Map<String, Character> nucleotides30;
-	private static final Map<String, Character> nucleotides23;
-
-	// amino acid 3 and 1 letter code definitions
-	private static final Map<String, Character> aminoAcids;
-
-	private static final Set<Element> hBondDonorAcceptors;
-
-	static {
-		nucleotides30 = new HashMap<>();
-		nucleotides30.put("DA", 'A');
-		nucleotides30.put("DC", 'C');
-		nucleotides30.put("DG", 'G');
-		nucleotides30.put("DT", 'T');
-		nucleotides30.put("DI", 'I');
-		nucleotides30.put("A", 'A');
-		nucleotides30.put("G", 'G');
-		nucleotides30.put("C", 'C');
-		nucleotides30.put("U", 'U');
-		nucleotides30.put("I", 'I');
-
-		// the DNA linkers - the +C , +G, +A +T +U and +I have been replaced
-		// with these:
-		nucleotides30.put("TAF", UNKNOWN_GROUP_LABEL); // Fluorinated Thymine
-		nucleotides30.put("TC1", UNKNOWN_GROUP_LABEL); // Furanosyl
-		nucleotides30.put("TFE", UNKNOWN_GROUP_LABEL); // Fluorinated Thymine
-		nucleotides30.put("TFO", UNKNOWN_GROUP_LABEL); // Tenofovir (3'
-		// terminator)
-		nucleotides30.put("TGP", UNKNOWN_GROUP_LABEL); // Guanine variant
-		nucleotides30.put("THX", UNKNOWN_GROUP_LABEL); // 5' terminator
-		nucleotides30.put("TLC", UNKNOWN_GROUP_LABEL); // Thymine with dicyclic
-		// sugar
-		nucleotides30.put("TLN", UNKNOWN_GROUP_LABEL); // locked Thymine
-		nucleotides30.put("LCG", UNKNOWN_GROUP_LABEL); // locked Guanine
-		nucleotides30.put("TP1", UNKNOWN_GROUP_LABEL); // Thymine peptide
-		// nucleic acid, with
-		// added methyl
-		nucleotides30.put("CP1", UNKNOWN_GROUP_LABEL); // Cytidine peptide
-		// nucleic acid, with
-		// added methyl
-		nucleotides30.put("TPN", UNKNOWN_GROUP_LABEL); // Thymine peptide
-		// nucleic acid
-		nucleotides30.put("CPN", UNKNOWN_GROUP_LABEL); // Cytidine peptide
-		// nucleic acid
-		nucleotides30.put("GPN", UNKNOWN_GROUP_LABEL); // Guanine peptide
-		// nucleic acid
-		nucleotides30.put("APN", UNKNOWN_GROUP_LABEL); // Adenosine peptide
-		// nucleic acid
-		nucleotides30.put("TPC", UNKNOWN_GROUP_LABEL); // Thymine variant
-
-		// store nucleic acids (C, G, A, T, U, and I), and
-		// the modified versions of nucleic acids (+C, +G, +A, +T, +U, and +I),
-		// and
-		nucleotides23 = new HashMap<>();
-		String[] names = { "C", "G", "A", "T", "U", "I", "+C", "+G", "+A",
-				"+T", "+U", "+I" };
-		for (String n : names) {
-			nucleotides23.put(n, n.charAt(n.length() - 1));
-		}
-
-		aminoAcids = new HashMap<>();
-		aminoAcids.put("GLY", 'G');
-		aminoAcids.put("ALA", 'A');
-		aminoAcids.put("VAL", 'V');
-		aminoAcids.put("LEU", 'L');
-		aminoAcids.put("ILE", 'I');
-		aminoAcids.put("PHE", 'F');
-		aminoAcids.put("TYR", 'Y');
-		aminoAcids.put("TRP", 'W');
-		aminoAcids.put("PRO", 'P');
-		aminoAcids.put("HIS", 'H');
-		aminoAcids.put("LYS", 'K');
-		aminoAcids.put("ARG", 'R');
-		aminoAcids.put("SER", 'S');
-		aminoAcids.put("THR", 'T');
-		aminoAcids.put("GLU", 'E');
-		aminoAcids.put("GLN", 'Q');
-		aminoAcids.put("ASP", 'D');
-		aminoAcids.put("ASN", 'N');
-		aminoAcids.put("CYS", 'C');
-		aminoAcids.put("MET", 'M');
-		// MSE is only found as a molecular replacement for MET
-		aminoAcids.put("MSE", 'M');
-		// 'non-standard', genetically encoded
-		// http://www.chem.qmul.ac.uk/iubmb/newsletter/1999/item3.html
-		// IUBMB recommended name is 'SEC' but the wwPDB currently use 'CSE'
-		// likewise 'PYL' (IUBMB) and 'PYH' (PDB)
-		aminoAcids.put("CSE", 'U');
-		aminoAcids.put("SEC", 'U');
-		aminoAcids.put("PYH", 'O');
-		aminoAcids.put("PYL", 'O');
-
-		hBondDonorAcceptors = new HashSet<>();
-		hBondDonorAcceptors.add(Element.N);
-		hBondDonorAcceptors.add(Element.O);
-		hBondDonorAcceptors.add(Element.S);
-
-	}
-
-	/**
-	 * Count how many Atoms are contained within a Structure object.
-	 *
-	 * @param s
-	 *            the structure object
-	 * @return the number of Atoms in this Structure
-	 */
-	public static int getNrAtoms(Structure s) {
-
-		int nrAtoms = 0;
-
-		Iterator<Group> iter = new GroupIterator(s);
-
-		while (iter.hasNext()) {
-			Group g = iter.next();
-			nrAtoms += g.size();
-		}
-
-		return nrAtoms;
-	}
-
-	/**
-	 * Count how many groups are contained within a structure object.
-	 *
-	 * @param s
-	 *            the structure object
-	 * @return the number of groups in the structure
-	 */
-	public static int getNrGroups(Structure s) {
-		int nrGroups = 0;
-
-		List<Chain> chains = s.getChains(0);
-		for (Chain c : chains) {
-			nrGroups += c.getAtomLength();
-		}
-		return nrGroups;
-	}
-
-	/**
-	 * Returns an array of the requested Atoms from the Structure object.
-	 * Iterates over all groups and checks if the requested atoms are in this
-	 * group, no matter if this is a {@link AminoAcid} or {@link HetatomImpl}
-	 * group. If the group does not contain all requested atoms then no atoms
-	 * are added for that group. For structures with more than one model, only
-	 * model 0 will be used.
-	 *
-	 * @param s
-	 *            the structure to get the atoms from
-	 *
-	 * @param atomNames
-	 *            contains the atom names to be used.
-	 * @return an Atom[] array
-	 */
-	public static Atom[] getAtomArray(Structure s, String[] atomNames) {
-		List<Chain> chains = s.getModel(0);
-
-		List<Atom> atoms = new ArrayList<>();
-
-		extractAtoms(atomNames, chains, atoms);
-		return atoms.toArray(Atom.EmptyAtomArray);
-
-	}
-
-	/**
-	 * Returns an array of the requested Atoms from the Structure object. In
-	 * contrast to {@link #getAtomArray(Structure, String[])} this method
-	 * iterates over all chains. Iterates over all chains and groups and checks
-	 * if the requested atoms are in this group, no matter if this is a
-	 * {@link AminoAcid} or {@link HetatomImpl} group. If the group does not
-	 * contain all requested atoms then no atoms are added for that group. For
-	 * structures with more than one model, only model 0 will be used.
-	 *
-	 * @param s
-	 *            the structure to get the atoms from
-	 *
-	 * @param atomNames
-	 *            contains the atom names to be used.
-	 * @return an Atom[] array
-	 */
-	public static Atom[] getAtomArrayAllModels(Structure s,
-											   String[] atomNames) {
-
-		List<Atom> atoms = new ArrayList<>();
-
-		for (int i = 0; i < s.nrModels(); i++) {
-			List<Chain> chains = s.getModel(i);
-			extractAtoms(atomNames, chains, atoms);
-		}
-		return atoms.toArray(Atom.EmptyAtomArray);
-
-	}
-
-	/**
-	 * Convert all atoms of the structure (all models) into an Atom array
-	 *
-	 * @param s
-	 *            input structure
-	 * @return all atom array
-	 */
-	public static Atom[] getAllAtomArray(Structure s) {
-		List<Atom> atoms = new ArrayList<>();
-
-		AtomIterator iter = new AtomIterator(s);
-		while (iter.hasNext()) {
-			Atom a = iter.next();
-			atoms.add(a);
-		}
-		return atoms.toArray(Atom.EmptyAtomArray);
-	}
-	/**
-	 * Convert all atoms of the structure (specified model) into an Atom array
-	 *
-	 * @param s
-	 *            input structure
-	 * @return all atom array
-	 */
-	public static Atom[] getAllAtomArray(Structure s, int model) {
-		List<Atom> atoms = new ArrayList<>();
-
-		AtomIterator iter = new AtomIterator(s,model);
-		while (iter.hasNext()) {
-			Atom a = iter.next();
-			atoms.add(a);
-		}
-		return atoms.toArray(Atom.EmptyAtomArray);
-
-	}
-
-	/**
-	 * Returns and array of all atoms of the chain, including
-	 * Hydrogens (if present) and all HETATOMs. Waters are not included.
-	 *
-	 * @param c
-	 *            input chain
-	 * @return all atom array
-	 */
-	public static Atom[] getAllAtomArray(Chain c) {
-		List<Atom> atoms = new ArrayList<>();
-
-		for (Group g : c.getAtomGroups()) {
-			if (g.isWater())
-				continue;
-			atoms.addAll(g.getAtoms());
-		}
-		return atoms.toArray(Atom.EmptyAtomArray);
-	}
-
-	/**
-	 * List of groups from the structure not included in ca (e.g. ligands).
-	 *
-	 * Unaligned groups are searched from all chains referenced in ca, as well
-	 * as any chains in the first model of the structure from ca[0], if any.
-	 *
-	 * @param ca an array of atoms
-	 * @return
-	 */
-	public static List<Group> getUnalignedGroups(Atom[] ca) {
-		Set<Chain> chains = new HashSet<>();
-		Set<Group> caGroups = new HashSet<>();
-
-		// Create list of all chains in this structure
-		Structure s = null;
-		if (ca.length > 0) {
-			Group g = ca[0].getGroup();
-			if (g != null) {
-				Chain c = g.getChain();
-				if (c != null) {
-					s = c.getStructure();
-				}
-			}
-		}
-		if (s != null) {
-			// Add all chains from the structure
-			chains.addAll(s.getChains(0));
-		}
-
-		// Add groups and chains from ca
-		for (Atom a : ca) {
-			Group g = a.getGroup();
-			if (g != null) {
-				caGroups.add(g);
-
-				Chain c = g.getChain();
-				if (c != null) {
-					chains.add(c);
-				}
-			}
-		}
-
-		// Iterate through all chains, finding groups not in ca
-		List<Group> unadded = new ArrayList<>();
-		for (Chain c : chains) {
-			for (Group g : c.getAtomGroups()) {
-				if (!caGroups.contains(g)) {
-					unadded.add(g);
-				}
-			}
-		}
-		return unadded;
-	}
-
-	/**
-	 * Finds all ligand groups from the target which fall within the cutoff distance
-	 * of some atom from the query set.
-	 *
-	 * @param target Set of groups including the ligands
-	 * @param query Atom selection
-	 * @param cutoff Distance from query atoms to consider, in angstroms
-	 * @return All groups from the target with at least one atom within cutoff of a query atom
-	 * @see StructureTools#DEFAULT_LIGAND_PROXIMITY_CUTOFF
-	 */
-	public static List<Group> getLigandsByProximity(Collection<Group> target, Atom[] query, double cutoff) {
-		// Geometric hashing of the reduced structure
-		Grid grid = new Grid(cutoff);
-		grid.addAtoms(query);
-
-		List<Group> ligands = new ArrayList<>();
-		for(Group g :target ) {
-			// don't worry about waters
-			if(g.isWater()) {
-				continue;
-			}
-
-			if(g.isPolymeric() ) {
-				// Polymers aren't ligands
-				continue;
-			}
-
-			// It is a ligand!
-
-			// Check that it's within cutoff of something in reduced
-			List<Atom> groupAtoms = g.getAtoms();
-			if( ! grid.hasAnyContact(Calc.atomsToPoints(groupAtoms))) {
-				continue;
-			}
-
-			ligands.add(g);
-		}
-		return ligands;
-	}
+    private static final Logger logger = LoggerFactory
+            .getLogger(StructureTools.class);
+
+    // Amino Acid backbone
+    /**
+     * The atom name of the backbone C-alpha atom. Note that this can be
+     * ambiguous depending on the context since Calcium atoms use the same name
+     * in PDB.
+     */
+    public static final String CA_ATOM_NAME = "CA";
+
+    /**
+     * The atom name for the backbone amide nitrogen
+     */
+    public static final String N_ATOM_NAME = "N";
+
+    /**
+     * The atom name for the backbone carbonyl
+     */
+    public static final String C_ATOM_NAME = "C";
+
+    /**
+     * The atom name for the backbone carbonyl oxygen
+     */
+    public static final String O_ATOM_NAME = "O";
+
+    /**
+     * The atom name of the side-chain C-beta atom
+     */
+    public static final String CB_ATOM_NAME = "CB";
+
+    // Nucleotide backbone
+    /**
+     * The atom name of the backbone C1' in RNA
+     */
+    public static final String C1_ATOM_NAME = "C1'";
+    /**
+     * The atom name of the backbone C2' in RNA
+     */
+    public static final String C2_ATOM_NAME = "C2'";
+    /**
+     * The atom name of the backbone C3' in RNA
+     */
+    public static final String C3_ATOM_NAME = "C3'";
+    /**
+     * The atom name of the backbone C4' in RNA
+     */
+    public static final String C4_ATOM_NAME = "C4'";
+    /**
+     * The atom name of the backbone O2' in RNA
+     */
+    public static final String O2_ATOM_NAME = "O2'";
+    /**
+     * The atom name of the backbone O3' in RNA
+     */
+    public static final String O3_ATOM_NAME = "O3'";
+    /**
+     * The atom name of the backbone O4' in RNA
+     */
+    public static final String O4_ATOM_NAME = "O4'";
+    /**
+     * The atom name of the backbone O4' in RNA
+     */
+    public static final String O5_ATOM_NAME = "O5'";
+    /**
+     * The atom name of the backbone O4' in RNA
+     */
+    public static final String OP1_ATOM_NAME = "OP1";
+    /**
+     * The atom name of the backbone O4' in RNA
+     */
+    public static final String OP2_ATOM_NAME = "OP2";
+    /**
+     * The atom name of the backbone phosphate in RNA
+     */
+    public static final String P_ATOM_NAME = "P";
+
+    /**
+     * The atom used as representative for nucleotides, equivalent to
+     * {@link #CA_ATOM_NAME} for proteins
+     */
+    public static final String NUCLEOTIDE_REPRESENTATIVE = P_ATOM_NAME;
+
+    /**
+     * The character to use for unknown compounds in sequence strings
+     */
+    public static final char UNKNOWN_GROUP_LABEL = 'X';
+
+    /**
+     * Below this ratio of aminoacid/nucleotide residues to the sequence total,
+     * we use simple majority of aminoacid/nucleotide residues to decide the
+     * character of the chain (protein/nucleotide)
+     */
+    public static final double RATIO_RESIDUES_TO_TOTAL = 0.95;
+
+    /**
+     * Threshold for plausible binding of a ligand to the selected substructure
+     */
+    public static final double DEFAULT_LIGAND_PROXIMITY_CUTOFF = 5;
+
+    // there is a file format change in PDB 3.0 and nucleotides are being
+    // renamed
+    private static final Map<String, Character> nucleotides30;
+    private static final Map<String, Character> nucleotides23;
+
+    // amino acid 3 and 1 letter code definitions
+    private static final Map<String, Character> aminoAcids;
+
+    private static final Set<Element> hBondDonorAcceptors;
+
+    static {
+        nucleotides30 = new HashMap<>();
+        nucleotides30.put("DA", 'A');
+        nucleotides30.put("DC", 'C');
+        nucleotides30.put("DG", 'G');
+        nucleotides30.put("DT", 'T');
+        nucleotides30.put("DI", 'I');
+        nucleotides30.put("A", 'A');
+        nucleotides30.put("G", 'G');
+        nucleotides30.put("C", 'C');
+        nucleotides30.put("U", 'U');
+        nucleotides30.put("I", 'I');
+
+        // the DNA linkers - the +C , +G, +A +T +U and +I have been replaced
+        // with these:
+        nucleotides30.put("TAF", UNKNOWN_GROUP_LABEL); // Fluorinated Thymine
+        nucleotides30.put("TC1", UNKNOWN_GROUP_LABEL); // Furanosyl
+        nucleotides30.put("TFE", UNKNOWN_GROUP_LABEL); // Fluorinated Thymine
+        nucleotides30.put("TFO", UNKNOWN_GROUP_LABEL); // Tenofovir (3'
+        // terminator)
+        nucleotides30.put("TGP", UNKNOWN_GROUP_LABEL); // Guanine variant
+        nucleotides30.put("THX", UNKNOWN_GROUP_LABEL); // 5' terminator
+        nucleotides30.put("TLC", UNKNOWN_GROUP_LABEL); // Thymine with dicyclic
+        // sugar
+        nucleotides30.put("TLN", UNKNOWN_GROUP_LABEL); // locked Thymine
+        nucleotides30.put("LCG", UNKNOWN_GROUP_LABEL); // locked Guanine
+        nucleotides30.put("TP1", UNKNOWN_GROUP_LABEL); // Thymine peptide
+        // nucleic acid, with
+        // added methyl
+        nucleotides30.put("CP1", UNKNOWN_GROUP_LABEL); // Cytidine peptide
+        // nucleic acid, with
+        // added methyl
+        nucleotides30.put("TPN", UNKNOWN_GROUP_LABEL); // Thymine peptide
+        // nucleic acid
+        nucleotides30.put("CPN", UNKNOWN_GROUP_LABEL); // Cytidine peptide
+        // nucleic acid
+        nucleotides30.put("GPN", UNKNOWN_GROUP_LABEL); // Guanine peptide
+        // nucleic acid
+        nucleotides30.put("APN", UNKNOWN_GROUP_LABEL); // Adenosine peptide
+        // nucleic acid
+        nucleotides30.put("TPC", UNKNOWN_GROUP_LABEL); // Thymine variant
+
+        // store nucleic acids (C, G, A, T, U, and I), and
+        // the modified versions of nucleic acids (+C, +G, +A, +T, +U, and +I),
+        // and
+        nucleotides23 = new HashMap<>();
+        String[] names = {"C", "G", "A", "T", "U", "I", "+C", "+G", "+A",
+                "+T", "+U", "+I"};
+        for (String n : names) {
+            nucleotides23.put(n, n.charAt(n.length() - 1));
+        }
+
+        aminoAcids = new HashMap<>();
+        aminoAcids.put("GLY", 'G');
+        aminoAcids.put("ALA", 'A');
+        aminoAcids.put("VAL", 'V');
+        aminoAcids.put("LEU", 'L');
+        aminoAcids.put("ILE", 'I');
+        aminoAcids.put("PHE", 'F');
+        aminoAcids.put("TYR", 'Y');
+        aminoAcids.put("TRP", 'W');
+        aminoAcids.put("PRO", 'P');
+        aminoAcids.put("HIS", 'H');
+        aminoAcids.put("LYS", 'K');
+        aminoAcids.put("ARG", 'R');
+        aminoAcids.put("SER", 'S');
+        aminoAcids.put("THR", 'T');
+        aminoAcids.put("GLU", 'E');
+        aminoAcids.put("GLN", 'Q');
+        aminoAcids.put("ASP", 'D');
+        aminoAcids.put("ASN", 'N');
+        aminoAcids.put("CYS", 'C');
+        aminoAcids.put("MET", 'M');
+        // MSE is only found as a molecular replacement for MET
+        aminoAcids.put("MSE", 'M');
+        // 'non-standard', genetically encoded
+        // http://www.chem.qmul.ac.uk/iubmb/newsletter/1999/item3.html
+        // IUBMB recommended name is 'SEC' but the wwPDB currently use 'CSE'
+        // likewise 'PYL' (IUBMB) and 'PYH' (PDB)
+        aminoAcids.put("CSE", 'U');
+        aminoAcids.put("SEC", 'U');
+        aminoAcids.put("PYH", 'O');
+        aminoAcids.put("PYL", 'O');
+
+        hBondDonorAcceptors = new HashSet<>();
+        hBondDonorAcceptors.add(Element.N);
+        hBondDonorAcceptors.add(Element.O);
+        hBondDonorAcceptors.add(Element.S);
+
+    }
+
+    /**
+     * Count how many Atoms are contained within a Structure object.
+     *
+     * @param s the structure object
+     * @return the number of Atoms in this Structure
+     */
+    public static int getNrAtoms(Structure s) {
+
+        int nrAtoms = 0;
+
+        Iterator<Group> iter = new GroupIterator(s);
+
+        while (iter.hasNext()) {
+            Group g = iter.next();
+            nrAtoms += g.size();
+        }
+
+        return nrAtoms;
+    }
+
+    /**
+     * Count how many groups are contained within a structure object.
+     *
+     * @param s the structure object
+     * @return the number of groups in the structure
+     */
+    public static int getNrGroups(Structure s) {
+        int nrGroups = 0;
+
+        List<Chain> chains = s.getChains(0);
+        for (Chain c : chains) {
+            nrGroups += c.getAtomLength();
+        }
+        return nrGroups;
+    }
+
+    /**
+     * Returns an array of the requested Atoms from the Structure object.
+     * Iterates over all groups and checks if the requested atoms are in this
+     * group, no matter if this is a {@link AminoAcid} or {@link HetatomImpl}
+     * group. If the group does not contain all requested atoms then no atoms
+     * are added for that group. For structures with more than one model, only
+     * model 0 will be used.
+     *
+     * @param s         the structure to get the atoms from
+     * @param atomNames contains the atom names to be used.
+     * @return an Atom[] array
+     */
+    public static Atom[] getAtomArray(Structure s, String[] atomNames) {
+        List<Chain> chains = s.getModel(0);
+
+        List<Atom> atoms = new ArrayList<>();
+
+        extractAtoms(atomNames, chains, atoms);
+        return atoms.toArray(Atom.EmptyAtomArray);
+
+    }
+
+    /**
+     * Returns an array of the requested Atoms from the Structure object. In
+     * contrast to {@link #getAtomArray(Structure, String[])} this method
+     * iterates over all chains. Iterates over all chains and groups and checks
+     * if the requested atoms are in this group, no matter if this is a
+     * {@link AminoAcid} or {@link HetatomImpl} group. If the group does not
+     * contain all requested atoms then no atoms are added for that group. For
+     * structures with more than one model, only model 0 will be used.
+     *
+     * @param s         the structure to get the atoms from
+     * @param atomNames contains the atom names to be used.
+     * @return an Atom[] array
+     */
+    public static Atom[] getAtomArrayAllModels(Structure s,
+                                               String[] atomNames) {
+
+        List<Atom> atoms = new ArrayList<>();
+
+        for (int i = 0; i < s.nrModels(); i++) {
+            List<Chain> chains = s.getModel(i);
+            extractAtoms(atomNames, chains, atoms);
+        }
+        return atoms.toArray(Atom.EmptyAtomArray);
+
+    }
+
+    /**
+     * Convert all atoms of the structure (all models) into an Atom array
+     *
+     * @param s input structure
+     * @return all atom array
+     */
+    public static Atom[] getAllAtomArray(Structure s) {
+        List<Atom> atoms = new ArrayList<>();
+
+        AtomIterator iter = new AtomIterator(s);
+        while (iter.hasNext()) {
+            Atom a = iter.next();
+            atoms.add(a);
+        }
+        return atoms.toArray(Atom.EmptyAtomArray);
+    }
+
+    /**
+     * Convert all atoms of the structure (specified model) into an Atom array
+     *
+     * @param s input structure
+     * @return all atom array
+     */
+    public static Atom[] getAllAtomArray(Structure s, int model) {
+        List<Atom> atoms = new ArrayList<>();
+
+        AtomIterator iter = new AtomIterator(s, model);
+        while (iter.hasNext()) {
+            Atom a = iter.next();
+            atoms.add(a);
+        }
+        return atoms.toArray(Atom.EmptyAtomArray);
+
+    }
+
+    /**
+     * Returns and array of all atoms of the chain, including
+     * Hydrogens (if present) and all HETATOMs. Waters are not included.
+     *
+     * @param c input chain
+     * @return all atom array
+     */
+    public static Atom[] getAllAtomArray(Chain c) {
+        List<Atom> atoms = new ArrayList<>();
+
+        for (Group g : c.getAtomGroups()) {
+            if (g.isWater())
+                continue;
+            atoms.addAll(g.getAtoms());
+        }
+        return atoms.toArray(Atom.EmptyAtomArray);
+    }
+
+    /**
+     * List of groups from the structure not included in ca (e.g. ligands).
+     * <p>
+     * Unaligned groups are searched from all chains referenced in ca, as well
+     * as any chains in the first model of the structure from ca[0], if any.
+     *
+     * @param ca an array of atoms
+     * @return
+     */
+    public static List<Group> getUnalignedGroups(Atom[] ca) {
+        Set<Chain> chains = new HashSet<>();
+        Set<Group> caGroups = new HashSet<>();
+
+        // Create list of all chains in this structure
+        Structure s = null;
+        if (ca.length > 0) {
+            Group g = ca[0].getGroup();
+            if (g != null) {
+                Chain c = g.getChain();
+                if (c != null) {
+                    s = c.getStructure();
+                }
+            }
+        }
+        if (s != null) {
+            // Add all chains from the structure
+            chains.addAll(s.getChains(0));
+        }
+
+        // Add groups and chains from ca
+        for (Atom a : ca) {
+            Group g = a.getGroup();
+            if (g != null) {
+                caGroups.add(g);
+
+                Chain c = g.getChain();
+                if (c != null) {
+                    chains.add(c);
+                }
+            }
+        }
+
+        // Iterate through all chains, finding groups not in ca
+        List<Group> unadded = new ArrayList<>();
+        for (Chain c : chains) {
+            for (Group g : c.getAtomGroups()) {
+                if (!caGroups.contains(g)) {
+                    unadded.add(g);
+                }
+            }
+        }
+        return unadded;
+    }
+
+    /**
+     * Finds all ligand groups from the target which fall within the cutoff distance
+     * of some atom from the query set.
+     *
+     * @param target Set of groups including the ligands
+     * @param query  Atom selection
+     * @param cutoff Distance from query atoms to consider, in angstroms
+     * @return All groups from the target with at least one atom within cutoff of a query atom
+     * @see StructureTools#DEFAULT_LIGAND_PROXIMITY_CUTOFF
+     */
+    public static List<Group> getLigandsByProximity(Collection<Group> target, Atom[] query, double cutoff) {
+        // Geometric hashing of the reduced structure
+        Grid grid = new Grid(cutoff);
+        grid.addAtoms(query);
+
+        List<Group> ligands = new ArrayList<>();
+        for (Group g : target) {
+            // don't worry about waters
+            if (g.isWater()) {
+                continue;
+            }
+
+            if (g.isPolymeric()) {
+                // Polymers aren't ligands
+                continue;
+            }
+
+            // It is a ligand!
+
+            // Check that it's within cutoff of something in reduced
+            List<Atom> groupAtoms = g.getAtoms();
+            if (!grid.hasAnyContact(Calc.atomsToPoints(groupAtoms))) {
+                continue;
+            }
+
+            ligands.add(g);
+        }
+        return ligands;
+    }
 
 	/**
 	 * Adds a particular group to a structure. A new chain will be created if necessary.
@@ -514,7 +504,7 @@ public static Chain addGroupToStructure(Structure s, Group g, int model, Chain c
 			String chainId = g.getChainId();
 			assert !chainId.isEmpty();
 			Chain chain;
-			if(chainGuess != null && chainGuess.getId() == chainId) {
+			if(chainGuess != null && chainGuess.getId().equals(chainId)) {
 				// previously guessed chain
 				chain = chainGuess;
 			} else {
@@ -577,1343 +567,1312 @@ public static void addGroupsToStructure(Structure s, Collection<Group> groups, i
 		}
 	}
 
-	/**
-	 * Expand a set of atoms into all groups from the same structure.
-	 *
-	 * If the structure is set, only the first atom is used (assuming all
-	 * atoms come from the same original structure).
-	 * If the atoms aren't linked to a structure (for instance, for cloned atoms),
-	 * searches all chains of all atoms for groups.
-	 * @param atoms Sample of atoms
-	 * @return All groups from all chains accessible from the input atoms
-	 */
-	public static Set<Group> getAllGroupsFromSubset(Atom[] atoms) {
-		return getAllGroupsFromSubset(atoms,null);
-	}
-	/**
-	 * Expand a set of atoms into all groups from the same structure.
-	 *
-	 * If the structure is set, only the first atom is used (assuming all
-	 * atoms come from the same original structure).
-	 * If the atoms aren't linked to a structure (for instance, for cloned atoms),
-	 * searches all chains of all atoms for groups.
-	 * @param atoms Sample of atoms
-	 * @param types Type of groups to return (useful for getting only ligands, for instance).
-	 *  Null gets all groups.
-	 * @return All groups from all chains accessible from the input atoms
-	 */
-	public static Set<Group> getAllGroupsFromSubset(Atom[] atoms,GroupType types) {
-		// Get the full structure
-		Structure s = null;
-		if (atoms.length > 0) {
-			Group g = atoms[0].getGroup();
-			if (g != null) {
-				Chain c = g.getChain();
-				if (c != null) {
-					s = c.getStructure();
-				}
-			}
-		}
-		// Collect all groups from the structure
-		Set<Chain> allChains = new HashSet<>();
-		if( s != null ) {
-			allChains.addAll(s.getChains());
-		}
-		// In case the structure wasn't set, need to use ca chains too
-		for(Atom a : atoms) {
-			Group g = a.getGroup();
-			if(g != null) {
-				Chain c = g.getChain();
-				if( c != null ) {
-					allChains.add(c);
-				}
-			}
-		}
-
-		if(allChains.isEmpty() ) {
-			return Collections.emptySet();
-		}
-
-		// Extract all ligand groups
-		Set<Group> full = new HashSet<>();
-		for(Chain c : allChains) {
-			if(types == null) {
-				full.addAll(c.getAtomGroups());
-			} else {
-				full.addAll(c.getAtomGroups(types));
-			}
-		}
-
-		return full;
-	}
-
-
-	/**
-	 * Returns and array of all non-Hydrogen atoms in the given Structure,
-	 * optionally including HET atoms or not. Waters are not included.
-	 *
-	 * @param s
-	 * @param hetAtoms
-	 *            if true HET atoms are included in array, if false they are not
-	 * @return
-	 */
-	public static Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms) {
-		AtomIterator iter = new AtomIterator(s);
-		return getAllNonHAtomArray(s, hetAtoms, iter);
-	}
-	/**
-	 * Returns and array of all non-Hydrogen atoms in the given Structure,
-	 * optionally including HET atoms or not. Waters are not included.
-	 *
-	 * @param s
-	 * @param hetAtoms
-	 *            if true HET atoms are included in array, if false they are not
-	 * @param modelNr Model number to draw atoms from
-	 * @return
-	 */
-	public static Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, int modelNr) {
-		AtomIterator iter = new AtomIterator(s,modelNr);
-		return getAllNonHAtomArray(s, hetAtoms, iter);
-	}
-	private static Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, AtomIterator iter) {
-		List<Atom> atoms = new ArrayList<>();
-
-		while (iter.hasNext()) {
-			Atom a = iter.next();
-			if (a.getElement() == Element.H)
-				continue;
-
-			Group g = a.getGroup();
-
-			if (g.isWater())
-				continue;
-
-			if (!hetAtoms && g.getType().equals(GroupType.HETATM))
-				continue;
-
-			atoms.add(a);
-		}
-		return atoms.toArray(Atom.EmptyAtomArray);
-	}
-
-	/**
-	 * Returns and array of all non-Hydrogen atoms in the given Chain,
-	 * optionally including HET atoms or not Waters are not included.
-	 *
-	 * @param c
-	 * @param hetAtoms
-	 *            if true HET atoms are included in array, if false they are not
-	 * @return
-	 */
-	public static Atom[] getAllNonHAtomArray(Chain c, boolean hetAtoms) {
-		List<Atom> atoms = new ArrayList<>();
-
-		for (Group g : c.getAtomGroups()) {
-			if (g.isWater())
-				continue;
-			for (Atom a : g.getAtoms()) {
-
-				if (a.getElement() == Element.H)
-					continue;
-
-				if (!hetAtoms && g.getType().equals(GroupType.HETATM))
-					continue;
-
-				atoms.add(a);
-			}
-		}
-		return atoms.toArray(Atom.EmptyAtomArray);
-	}
-
-	/**
-	 * Returns and array of all non-Hydrogen atoms coordinates in the given Chain,
-	 * optionally including HET atoms or not Waters are not included.
-	 *
-	 * @param c
-	 * @param hetAtoms
-	 *            if true HET atoms are included in array, if false they are not
-	 * @return
-	 */
-	public static Point3d[] getAllNonHCoordsArray(Chain c, boolean hetAtoms) {
-		List<Point3d> atoms = new ArrayList<>();
-
-		for (Group g : c.getAtomGroups()) {
-			if (g.isWater())
-				continue;
-			for (Atom a : g.getAtoms()) {
-
-				if (a.getElement() == Element.H)
-					continue;
-
-				if (!hetAtoms && g.getType().equals(GroupType.HETATM))
-					continue;
-
-				atoms.add(a.getCoordsAsPoint3d());
-			}
-		}
-		return atoms.toArray(new Point3d[0]);
-	}
-
-	/**
-	 * Adds to the given atoms list, all atoms of groups that contained all
-	 * requested atomNames, i.e. if a group does not contain all of the
-	 * requested atom names, its atoms won't be added.
-	 *
-	 * @param atomNames
-	 * @param chains
-	 * @param atoms
-	 */
-	private static void extractAtoms(String[] atomNames, List<Chain> chains,
-			List<Atom> atoms) {
-
-		for (Chain c : chains) {
-
-			for (Group g : c.getAtomGroups()) {
-
-				// a temp container for the atoms of this group
-				List<Atom> thisGroupAtoms = new ArrayList<>();
-				// flag to check if this group contains all the requested atoms.
-				boolean thisGroupAllAtoms = true;
-				for (String atomName : atomNames) {
-					Atom a = g.getAtom(atomName);
-
-					if (a == null) {
-						// this group does not have a required atom, skip it...
-						thisGroupAllAtoms = false;
-						break;
-					}
-					thisGroupAtoms.add(a);
-				}
-				if (thisGroupAllAtoms) {
-					// add the atoms of this group to the array.
-					atoms.addAll(thisGroupAtoms);
-				}
-
-			}
-		}
-	}
-
-	/**
-	 * Returns an array of the requested Atoms from the Chain object. Iterates
-	 * over all groups and checks if the requested atoms are in this group, no
-	 * matter if this is a AminoAcid or Hetatom group. If the group does not
-	 * contain all requested atoms then no atoms are added for that group.
-	 *
-	 * @param c
-	 *            the Chain to get the atoms from
-	 *
-	 * @param atomNames
-	 *            contains the atom names to be used.
-	 * @return an Atom[] array
-	 */
-	public static Atom[] getAtomArray(Chain c, String[] atomNames) {
-
-		List<Atom> atoms = new ArrayList<>();
-
-		for (Group g : c.getAtomGroups()) {
-
-			// a temp container for the atoms of this group
-			List<Atom> thisGroupAtoms = new ArrayList<>();
-			// flag to check if this group contains all the requested atoms.
-			boolean thisGroupAllAtoms = true;
-			for (String atomName : atomNames) {
-				Atom a = g.getAtom(atomName);
-				if (a == null) {
-					logger.debug("Group " + g.getResidueNumber() + " ("
-							+ g.getPDBName()
-							+ ") does not have the required atom '" + atomName
-							+ "'");
-					// this group does not have a required atom, skip it...
-					thisGroupAllAtoms = false;
-					break;
-				}
-				thisGroupAtoms.add(a);
-			}
-
-			if (thisGroupAllAtoms) {
-				// add the atoms of this group to the array.
-				atoms.addAll(thisGroupAtoms);
-			}
-
-		}
-		return atoms.toArray(Atom.EmptyAtomArray);
-
-	}
-
-	/**
-	 * Returns an Atom array of the C-alpha atoms. Any atom that is a carbon and
-	 * has CA name will be returned.
-	 *
-	 * @param c
-	 *            the structure object
-	 * @return an Atom[] array
-	 * @see #getRepresentativeAtomArray(Chain)
-	 */
-	public static Atom[] getAtomCAArray(Chain c) {
-		List<Atom> atoms = new ArrayList<>();
-
-		for (Group g : c.getAtomGroups()) {
-			if (g.hasAtom(CA_ATOM_NAME)
-					&& g.getAtom(CA_ATOM_NAME).getElement() == Element.C) {
-				atoms.add(g.getAtom(CA_ATOM_NAME));
-			}
-		}
-
-		return atoms.toArray(Atom.EmptyAtomArray);
-	}
-
-	/**
-	 * Gets a representative atom for each group that is part of the chain
-	 * backbone. Note that modified aminoacids won't be returned as part of the
-	 * backbone if the {@link org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider} was used to load the
-	 * structure.
-	 *
-	 * For amino acids, the representative is a CA carbon. For nucleotides, the
-	 * representative is the {@value #NUCLEOTIDE_REPRESENTATIVE}. Other group
-	 * types will be ignored.
-	 *
-	 * @param c
-	 * @return representative Atoms of the chain backbone
-	 * @since Biojava 4.1.0
-	 */
-	public static Atom[] getRepresentativeAtomArray(Chain c) {
-		List<Atom> atoms = new ArrayList<>();
-
-		for (Group g : c.getAtomGroups()) {
-
-			switch (g.getType()) {
-			case AMINOACID:
-				if (g.hasAtom(CA_ATOM_NAME)
-						&& g.getAtom(CA_ATOM_NAME).getElement() == Element.C) {
-					atoms.add(g.getAtom(CA_ATOM_NAME));
-				}
-				break;
-			case NUCLEOTIDE:
-				if (g.hasAtom(NUCLEOTIDE_REPRESENTATIVE)) {
-					atoms.add(g.getAtom(NUCLEOTIDE_REPRESENTATIVE));
-				}
-				break;
-			default:
-				// don't add
-			}
-		}
-
-		return atoms.toArray(Atom.EmptyAtomArray);
-
-	}
-
-	/**
-	 * Provides an equivalent copy of Atoms in a new array. Clones everything,
-	 * starting with parent groups and chains. The chain will only contain
-	 * groups that are part of the input array.
-	 *
-	 * @param ca
-	 *            array of representative atoms, e.g. CA atoms
-	 * @return Atom array
-	 * @since Biojava 4.1.0
-	 */
-	public static Atom[] cloneAtomArray(Atom[] ca) {
-		Atom[] newCA = new Atom[ca.length];
-
-		List<Chain> model = new ArrayList<>();
-		int apos = -1;
-		for (Atom a : ca) {
-			apos++;
-			Group parentG = a.getGroup();
-			Chain parentC = parentG.getChain();
-
-			Chain newChain = null;
-			for (Chain c : model) {
-				if (c.getName().equals(parentC.getName())) {
-					newChain = c;
-					break;
-				}
-			}
-			if (newChain == null) {
-				newChain = new ChainImpl();
-				newChain.setId(parentC.getId());
-				newChain.setName(parentC.getName());
-				model.add(newChain);
-			}
-
-			Group parentN = (Group) parentG.clone();
-
-			newCA[apos] = parentN.getAtom(a.getName());
-
-			// if the group doesn't exist yet, this produces a StructureException
-			if (!newChain.hasGroupByPDB(parentN.getResidueNumber()))
-				newChain.addGroup(parentN); // the group doesn't exist yet in the newChain, let's add it
-
-		}
-		return newCA;
-	}
-
-	/**
-	 * Clone a set of representative Atoms, but returns the parent groups
-	 *
-	 * @param ca
-	 *            Atom array
-	 * @return Group array
-	 */
-	public static Group[] cloneGroups(Atom[] ca) {
-		Group[] newGroup = new Group[ca.length];
-
-		List<Chain> model = new ArrayList<>();
-		int apos = -1;
-		for (Atom a : ca) {
-			apos++;
-			Group parentG = a.getGroup();
-			Chain parentC = parentG.getChain();
-
-			Chain newChain = null;
-			for (Chain c : model) {
-				if (c.getName().equals(parentC.getName())) {
-					newChain = c;
-					break;
-				}
-			}
-			if (newChain == null) {
-				newChain = new ChainImpl();
-				newChain.setName(parentC.getName());
-				model.add(newChain);
-			}
-
-			Group ng = (Group) parentG.clone();
-			newGroup[apos] = ng;
-			newChain.addGroup(ng);
-		}
-		return newGroup;
-	}
-
-	/**
-	 * Utility method for working with circular permutations. Creates a
-	 * duplicated and cloned set of Calpha atoms from the input array.
-	 *
-	 * @param ca2
-	 *            atom array
-	 * @return cloned and duplicated set of input array
-	 */
-	public static Atom[] duplicateCA2(Atom[] ca2) {
-		// we don't want to rotate input atoms, do we?
-		Atom[] ca2clone = new Atom[ca2.length * 2];
-
-		int pos = 0;
-
-		Chain c = null;
-		String prevChainId = "";
-		for (Atom a : ca2) {
-			Group g = (Group) a.getGroup().clone(); // works because each group
-			// has only a single atom
-
-			if (c == null) {
-				c = new ChainImpl();
-				Chain orig = a.getGroup().getChain();
-				c.setId(orig.getId());
-				c.setName(orig.getName());
-			} else {
-				Chain orig = a.getGroup().getChain();
-				if (!orig.getId().equals(prevChainId)) {
-					c = new ChainImpl();
-					c.setId(orig.getId());
-					c.setName(orig.getName());
-				}
-			}
-
-			c.addGroup(g);
-			ca2clone[pos] = g.getAtom(a.getName());
-
-			pos++;
-		}
-
-		// Duplicate ca2!
-		c = null;
-		prevChainId = "";
-		for (Atom a : ca2) {
-			Group g = (Group) a.getGroup().clone();
-
-			if (c == null) {
-				c = new ChainImpl();
-				Chain orig = a.getGroup().getChain();
-				c.setId(orig.getId());
-				c.setName(orig.getName());
-			} else {
-				Chain orig = a.getGroup().getChain();
-				if (!orig.getId().equals(prevChainId)) {
-					c = new ChainImpl();
-					c.setId(orig.getId());
-					c.setName(orig.getName());
-				}
-			}
-
-			c.addGroup(g);
-			ca2clone[pos] = g.getAtom(a.getName());
-
-			pos++;
-		}
-
-		return ca2clone;
-
-	}
-
-	/**
-	 * Return an Atom array of the C-alpha atoms. Any atom that is a carbon and
-	 * has CA name will be returned.
-	 *
-	 * @param s
-	 *            the structure object
-	 * @return an Atom[] array
-	 * @see #getRepresentativeAtomArray(Structure)
-	 */
-	public static Atom[] getAtomCAArray(Structure s) {
-
-		List<Atom> atoms = new ArrayList<>();
-
-		for (Chain c : s.getChains()) {
-			for (Group g : c.getAtomGroups()) {
-				if (g.hasAtom(CA_ATOM_NAME)
-						&& g.getAtom(CA_ATOM_NAME).getElement() == Element.C) {
-					atoms.add(g.getAtom(CA_ATOM_NAME));
-				}
-			}
-		}
-
-		return atoms.toArray(Atom.EmptyAtomArray);
-	}
-
-	/**
-	 * Gets a representative atom for each group that is part of the chain
-	 * backbone. Note that modified aminoacids won't be returned as part of the
-	 * backbone if the {@link org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider} was used to load the
-	 * structure.
-	 *
-	 * For amino acids, the representative is a CA carbon. For nucleotides, the
-	 * representative is the {@value #NUCLEOTIDE_REPRESENTATIVE}. Other group
-	 * types will be ignored.
-	 *
-	 * @param s
-	 *            Input structure
-	 * @return representative Atoms of the structure backbone
-	 * @since Biojava 4.1.0
-	 */
-	public static Atom[] getRepresentativeAtomArray(Structure s) {
-
-		List<Atom> atoms = new ArrayList<>();
-
-		for (Chain c : s.getChains()) {
-			Atom[] chainAtoms = getRepresentativeAtomArray(c);
-			atoms.addAll(Arrays.asList(chainAtoms));
-		}
-
-		return atoms.toArray(Atom.EmptyAtomArray);
-	}
-
-	/**
-	 * Return an Atom array of the main chain atoms: CA, C, N, O Any group that
-	 * contains those atoms will be included, be it a standard aminoacid or not
-	 *
-	 * @param s
-	 *            the structure object
-	 * @return an Atom[] array
-	 */
-	public static Atom[] getBackboneAtomArray(Structure s) {
-
-		List<Atom> atoms = new ArrayList<>();
-
-		for (Chain c : s.getChains()) {
-			for (Group g : c.getAtomGroups()) {
-				if (g.hasAminoAtoms()) {
-					// this means we will only take atoms grom groups that have
-					// complete backbones
-					for (Atom a : g.getAtoms()) {
-						switch (g.getType()) {
-						case NUCLEOTIDE:
-							// Nucleotide backbone
-							if (a.getName().equals(C1_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(C2_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(C3_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(C4_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(O2_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(O3_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(O4_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(O5_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(OP1_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(OP2_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(P_ATOM_NAME))
-								atoms.add(a);
-							// TODO Allow C4* names as well as C4'? -SB 3/2015
-							break;
-						case AMINOACID:
-						default:
-							// we do it this way instead of with g.getAtom() to
-							// be sure we always use the same order as original
-							if (a.getName().equals(CA_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(C_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(N_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(O_ATOM_NAME))
-								atoms.add(a);
-							break;
-						}
-					}
-				}
-			}
-
-		}
-
-		return atoms.toArray(Atom.EmptyAtomArray);
-	}
-
-	/**
-	 * Convert three character amino acid codes into single character e.g.
-	 * convert CYS to C. Valid 3-letter codes will be those of the standard 20
-	 * amino acids plus MSE, CSE, SEC, PYH, PYL (see the {@link #aminoAcids}
-	 * map)
-	 *
-	 * @return the 1 letter code, or null if the given 3 letter code does not
-	 *         correspond to an amino acid code
-	 * @param groupCode3
-	 *            a three character amino acid representation String
-	 * @see {@link #get1LetterCode(String)}
-	 */
-	public static Character get1LetterCodeAmino(String groupCode3) {
-		return aminoAcids.get(groupCode3);
-	}
-
-	/**
-	 * Convert a three letter amino acid or nucleotide code into a single
-	 * character code. If the code does not correspond to an amino acid or
-	 * nucleotide, returns {@link #UNKNOWN_GROUP_LABEL}.
-	 *
-	 * Returned null for nucleotides prior to version 4.0.1.
-	 *
-	 * @param groupCode3
-	 *            three letter representation
-	 * @return The 1-letter abbreviation
-	 */
-	public static Character get1LetterCode(String groupCode3) {
-
-		Character code1;
-
-		// is it a standard amino acid ?
-		code1 = get1LetterCodeAmino(groupCode3);
-
-		if (code1 == null) {
-			// hm groupCode3 is not standard
-			// perhaps it is a nucleotide?
-			groupCode3 = groupCode3.trim();
-			if (isNucleotide(groupCode3)) {
-				code1 = nucleotides30.get(groupCode3);
-				if (code1 == null) {
-					code1 = nucleotides23.get(groupCode3);
-				}
-				if (code1 == null) {
-					code1 = UNKNOWN_GROUP_LABEL;
-				}
-			} else {
-				// does not seem to be so let's assume it is
-				// nonstandard aminoacid and label it "X"
-				// logger.warning("unknown group name "+groupCode3 );
-				code1 = UNKNOWN_GROUP_LABEL;
-			}
-		}
-
-		return code1;
-
-	}
-
-	/**
-	 * Test if the three-letter code of an ATOM entry corresponds to a
-	 * nucleotide or to an aminoacid.
-	 *
-	 * @param groupCode3
-	 *            3-character code for a group.
-	 *
-	 */
-	public static boolean isNucleotide(String groupCode3) {
-		String code = groupCode3.trim();
-		return nucleotides30.containsKey(code)
-				|| nucleotides23.containsKey(code);
-	}
-
-	/**
-	 * Reduce a structure to provide a smaller representation . Only takes the
-	 * first model of the structure. If chainName is provided only return a
-	 * structure containing that Chain ID. Converts lower case chain IDs to
-	 * upper case if structure does not contain a chain with that ID.
-	 *
-	 * @param s
-	 * @param chainId
-	 * @return Structure
-	 * @since 3.0
-	 * @deprecated Use {@link StructureIdentifier#reduce(Structure)} instead (v. 4.2.0)
-	 */
-	@Deprecated
-	public static Structure getReducedStructure(Structure s,
-			String chainId) throws StructureException {
-		// since we deal here with structure alignments,
-		// only use Model 1...
-
-		Structure newS = new StructureImpl();
-		newS.setPDBCode(s.getPDBCode());
-		newS.setPDBHeader(s.getPDBHeader());
-		newS.setName(s.getName());
-		newS.setSSBonds(s.getSSBonds());
-		newS.setDBRefs(s.getDBRefs());
-		newS.setSites(s.getSites());
-		newS.setBiologicalAssembly(s.isBiologicalAssembly());
-		newS.setEntityInfos(s.getEntityInfos());
-		newS.setSSBonds(s.getSSBonds());
-		newS.setSites(s.getSites());
-
-		if (chainId != null)
-			chainId = chainId.trim();
-
-		if (chainId == null || chainId.isEmpty()) {
-			// only get model 0
-			List<Chain> model0 = s.getModel(0);
-			for (Chain c : model0) {
-				newS.addChain(c);
-			}
-			return newS;
-
-		}
-
-		Chain c;
-		try {
-			c = s.getChainByPDB(chainId);
-		} catch (StructureException e) {
-			logger.warn(e.getMessage() + ". Chain id " + chainId
-					+ " did not match, trying upper case Chain id.");
-			c = s.getChainByPDB(chainId.toUpperCase());
-
-		}
-		if (c != null) {
-			newS.addChain(c);
-			for (EntityInfo comp : s.getEntityInfos()) {
-				if (comp.getChainIds() != null
-						&& comp.getChainIds().contains(c.getChainID())) {
-					// found matching entity info. set description...
-					newS.getPDBHeader().setDescription(
-							"Chain " + c.getChainID() + " of " + s.getPDBCode()
-							+ " " + comp.getDescription());
-				}
-			}
-		}
-
-		return newS;
-	}
-
-	public static String convertAtomsToSeq(Atom[] atoms) {
-
-		StringBuilder buf = new StringBuilder();
-		Group prevGroup = null;
-		for (Atom a : atoms) {
-			Group g = a.getGroup();
-			if (prevGroup != null) {
-				if (prevGroup.equals(g)) {
-					// we add each group only once.
-					continue;
-				}
-			}
-			String code3 = g.getPDBName();
-			Character code1 = get1LetterCodeAmino(code3);
-			if (code1 == null)
-				code1 = UNKNOWN_GROUP_LABEL;
-
-			buf.append(code1);
-
-			prevGroup = g;
-
-		}
-		return buf.toString();
-	}
-
-	/**
-	 * Get a group represented by a ResidueNumber.
-	 *
-	 * @param struc
-	 *            a {@link Structure}
-	 * @param pdbResNum
-	 *            a {@link ResidueNumber}
-	 * @return a group in the structure that is represented by the pdbResNum.
-	 * @throws StructureException
-	 *             if the group cannot be found.
-	 */
-	public static Group getGroupByPDBResidueNumber(Structure struc,
-			ResidueNumber pdbResNum) throws StructureException {
-		if (struc == null || pdbResNum == null) {
-			throw new IllegalArgumentException("Null argument(s).");
-		}
-
-		Chain chain = struc.getPolyChainByPDB(pdbResNum.getChainName());
-
-		return chain.getGroupByPDB(pdbResNum);
-	}
-
-	/**
-	 * Returns the set of intra-chain contacts for the given chain for given
-	 * atom names, i.e. the contact map. Uses a geometric hashing algorithm that
-	 * speeds up the calculation without need of full distance matrix. The
-	 * parsing mode {@link FileParsingParameters#setAlignSeqRes(boolean)} needs
-	 * to be set to true for this to work.
-	 *
-	 * @param chain
-	 * @param atomNames
-	 *            the array with atom names to be used. Beware: CA will do both
-	 *            C-alphas an Calciums if null all non-H atoms of non-hetatoms
-	 *            will be used
-	 * @param cutoff
-	 * @return
-	 */
-	public static AtomContactSet getAtomsInContact(Chain chain,
-			String[] atomNames, double cutoff) {
-		Grid grid = new Grid(cutoff);
-
-		Atom[] atoms;
-		if (atomNames == null) {
-			atoms = getAllNonHAtomArray(chain, false);
-		} else {
-			atoms = getAtomArray(chain, atomNames);
-		}
-		// If tha
-		if(atoms.length==0){
-			logger.warn("No atoms found for buidling grid!");
-			return new AtomContactSet(cutoff);
-		}
-		grid.addAtoms(atoms);
-
-		return grid.getAtomContacts();
-	}
-
-	/**
-	 * Returns the set of intra-chain contacts for the given chain for all non-H
-	 * atoms of non-hetatoms, i.e. the contact map. Uses a geometric hashing
-	 * algorithm that speeds up the calculation without need of full distance
-	 * matrix. The parsing mode
-	 * {@link FileParsingParameters#setAlignSeqRes(boolean)} needs to be set to
-	 * true for this to work.
-	 *
-	 * @param chain
-	 * @param cutoff
-	 * @return
-	 */
-	public static AtomContactSet getAtomsInContact(Chain chain, double cutoff) {
-		return getAtomsInContact(chain, null, cutoff);
-	}
-
-	/**
-	 * Returns the set of intra-chain contacts for the given chain for C-alpha
-	 * atoms (including non-standard aminoacids appearing as HETATM groups),
-	 * i.e. the contact map. Uses a geometric hashing algorithm that speeds up
-	 * the calculation without need of full distance matrix. The parsing mode
-	 * {@link FileParsingParameters#setAlignSeqRes(boolean)} needs to be set to
-	 * true for this to work.
-	 *
-	 * @param chain
-	 * @param cutoff
-	 * @return
-	 * @see #getRepresentativeAtomsInContact(Chain, double)
-	 */
-	public static AtomContactSet getAtomsCAInContact(Chain chain, double cutoff) {
-		Grid grid = new Grid(cutoff);
-
-		Atom[] atoms = getAtomCAArray(chain);
-
-		grid.addAtoms(atoms);
-
-		return grid.getAtomContacts();
-	}
-
-	/**
-	 * Returns the set of intra-chain contacts for the given chain for C-alpha
-	 * or C3' atoms (including non-standard aminoacids appearing as HETATM
-	 * groups), i.e. the contact map. Uses a geometric hashing algorithm that
-	 * speeds up the calculation without need of full distance matrix.
-	 *
-	 * @param chain
-	 * @param cutoff
-	 * @return
-	 * @since Biojava 4.1.0
-	 */
-	public static AtomContactSet getRepresentativeAtomsInContact(Chain chain,
-			double cutoff) {
-		Grid grid = new Grid(cutoff);
-
-		Atom[] atoms = getRepresentativeAtomArray(chain);
-
-		grid.addAtoms(atoms);
-
-		return grid.getAtomContacts();
-	}
-
-	/**
-	 * Returns the set of inter-chain contacts between the two given chains for
-	 * the given atom names. Uses a geometric hashing algorithm that speeds up
-	 * the calculation without need of full distance matrix. The parsing mode
-	 * {@link FileParsingParameters#setAlignSeqRes(boolean)} needs to be set to
-	 * true for this to work.
-	 *
-	 * @param chain1
-	 * @param chain2
-	 * @param atomNames
-	 *            the array with atom names to be used. For Calphas use {"CA"},
-	 *            if null all non-H atoms will be used. Note HET atoms are
-	 *            ignored unless this parameter is null.
-	 * @param cutoff
-	 * @param hetAtoms
-	 *            if true HET atoms are included, if false they are not
-	 * @return
-	 */
-	public static AtomContactSet getAtomsInContact(Chain chain1, Chain chain2,
-			String[] atomNames, double cutoff, boolean hetAtoms) {
-		Grid grid = new Grid(cutoff);
-		Atom[] atoms1;
-		Atom[] atoms2;
-		if (atomNames == null) {
-			atoms1 = getAllNonHAtomArray(chain1, hetAtoms);
-			atoms2 = getAllNonHAtomArray(chain2, hetAtoms);
-		} else {
-			atoms1 = getAtomArray(chain1, atomNames);
-			atoms2 = getAtomArray(chain2, atomNames);
-		}
-		grid.addAtoms(atoms1, atoms2);
-
-		return grid.getAtomContacts();
-	}
-
-	/**
-	 * Returns the set of inter-chain contacts between the two given chains for
-	 * all non-H atoms. Uses a geometric hashing algorithm that speeds up the
-	 * calculation without need of full distance matrix. The parsing mode
-	 * {@link FileParsingParameters#setAlignSeqRes(boolean)} needs to be set to
-	 * true for this to work.
-	 *
-	 * @param chain1
-	 * @param chain2
-	 * @param cutoff
-	 * @param hetAtoms
-	 *            if true HET atoms are included, if false they are not
-	 * @return
-	 */
-	public static AtomContactSet getAtomsInContact(Chain chain1, Chain chain2,
-			double cutoff, boolean hetAtoms) {
-		return getAtomsInContact(chain1, chain2, null, cutoff, hetAtoms);
-	}
-
-	/**
-	 * Finds Groups in {@code structure} that contain at least one Atom that is
-	 * within {@code radius} Angstroms of {@code centroid}.
-	 *
-	 * @param structure
-	 *            The structure from which to find Groups
-	 * @param centroid
-	 *            The centroid of the shell
-	 * @param excludeResidues
-	 *            A list of ResidueNumbers to exclude
-	 * @param radius
-	 *            The radius from {@code centroid}, in Angstroms
-	 * @param includeWater
-	 *            Whether to include Groups whose <em>only</em> atoms are water
-	 * @param useAverageDistance
-	 *            When set to true, distances are the arithmetic mean (1-norm)
-	 *            of the distances of atoms that belong to the group and that
-	 *            are within the shell; otherwise, distances are the minimum of
-	 *            these values
-	 * @return A map of Groups within (or partially within) the shell, to their
-	 *         distances in Angstroms
-	 */
-	public static Map<Group, Double> getGroupDistancesWithinShell(
-			Structure structure, Atom centroid,
-			Set<ResidueNumber> excludeResidues, double radius,
-			boolean includeWater, boolean useAverageDistance) {
-
-		// for speed, we avoid calculating square roots
-		radius = radius * radius;
-
-		Map<Group, Double> distances = new HashMap<>();
-
-		// we only need this if we're averaging distances
-		// note that we can't use group.getAtoms().size() because some the
-		// group's atoms be outside the shell
-		Map<Group, Integer> atomCounts = new HashMap<>();
-
-		for (Chain chain : structure.getChains()) {
-			groupLoop: for (Group chainGroup : chain.getAtomGroups()) {
-
-				// exclude water
-				if (!includeWater && chainGroup.isWater())
-					continue;
-
-				// check blacklist of residue numbers
-				for (ResidueNumber rn : excludeResidues) {
-					if (rn.equals(chainGroup.getResidueNumber()))
-						continue groupLoop;
-				}
-
-				for (Atom testAtom : chainGroup.getAtoms()) {
-
-					// use getDistanceFast as we are doing a lot of comparisons
-					double dist = Calc.getDistanceFast(centroid, testAtom);
-
-					// if we're the shell
-					if (dist <= radius) {
-						if (!distances.containsKey(chainGroup))
-							distances.put(chainGroup, Double.POSITIVE_INFINITY);
-						if (useAverageDistance) {
-							// sum the distance; we'll divide by the total
-							// number later
-							// here, we CANNOT use fastDistance (distance
-							// squared) because we want the arithmetic mean
-							distances.put(chainGroup, distances.get(chainGroup)
-									+ Math.sqrt(dist));
-							if (!atomCounts.containsKey(chainGroup))
-								atomCounts.put(chainGroup, 0);
-							atomCounts.put(chainGroup,
-									atomCounts.get(chainGroup) + 1);
-						} else {
-							// take the minimum distance among all atoms of
-							// chainGroup
-							// note that we can't break here because we might
-							// find a smaller distance
-							if (dist < distances.get(chainGroup)) {
-								distances.put(chainGroup, dist);
-							}
-						}
-					}
-
-				}
-			}
-		}
-
-		if (useAverageDistance) {
-			for (Map.Entry<Group, Double> entry : distances.entrySet()) {
-				int count = atomCounts.get(entry.getKey());
-				distances.put(entry.getKey(), entry.getValue() / count);
-			}
-		} else {
-			// in this case we used getDistanceFast
-			distances.replaceAll((k, v) -> Math.sqrt(v));
-		}
-
-		return distances;
-
-	}
-
-	public static Set<Group> getGroupsWithinShell(Structure structure,
-			Atom atom, Set<ResidueNumber> excludeResidues, double distance,
-			boolean includeWater) {
-
-		// square the distance to use as a comparison against getDistanceFast
-		// which returns the square of a distance.
-		distance = distance * distance;
-
-		Set<Group> returnSet = new LinkedHashSet<>();
-		for (Chain chain : structure.getChains()) {
-			groupLoop: for (Group chainGroup : chain.getAtomGroups()) {
-				if (!includeWater && chainGroup.isWater())
-					continue;
-				for (ResidueNumber rn : excludeResidues) {
-					if (rn.equals(chainGroup.getResidueNumber()))
-						continue groupLoop;
-				}
-				for (Atom atomB : chainGroup.getAtoms()) {
-
-					// use getDistanceFast as we are doing a lot of comparisons
-					double dist = Calc.getDistanceFast(atom, atomB);
-					if (dist <= distance) {
-						returnSet.add(chainGroup);
-						break;
-					}
-
-				}
-			}
-		}
-		return returnSet;
-	}
-
-	/**
-	 * <p>
-	 * Returns a Set of Groups in a structure within the distance specified of a
-	 * given group.
-	 * </p>
-	 * <p>
-	 * Updated 18-Sep-2015 sroughley to return a Set so only a unique set of
-	 * Groups returned
-	 *
-	 * @param structure
-	 *            The structure to work with
-	 * @param group
-	 *            The 'query' group
-	 * @param distance
-	 *            The cutoff distance
-	 * @param includeWater
-	 *            Should water residues be included in the output?
-	 * @return {@link LinkedHashSet} of {@link Group}s within at least one atom
-	 *         with {@code distance} of at least one atom in {@code group}
-	 */
-	public static Set<Group> getGroupsWithinShell(Structure structure,
-			Group group, double distance, boolean includeWater) {
-
-		Set<Group> returnList = new LinkedHashSet<>();
-
-		Set<ResidueNumber> excludeGroups = new HashSet<>();
-		excludeGroups.add(group.getResidueNumber());
-		for (Atom atom : group.getAtoms()) {
-			Set<Group> set = getGroupsWithinShell(structure, atom,
-					excludeGroups, distance, includeWater);
-			returnList.addAll(set);
-		}
-
-		return returnList;
-	}
-
-	/**
-	 * Remove all models from a Structure and keep only the first
-	 *
-	 * @param s
-	 *            original Structure
-	 * @return a structure that contains only the first model
-	 * @since 3.0.5
-	 */
-	public static Structure removeModels(Structure s) {
-		if (s.nrModels() == 1)
-			return s;
-
-		Structure n = new StructureImpl();
-		// go through whole substructure and clone ...
-
-		// copy structure data
-
-		n.setPDBCode(s.getPDBCode());
-		n.setName(s.getName());
-
-		// TODO: do deep copying of data!
-		n.setPDBHeader(s.getPDBHeader());
-		n.setDBRefs(s.getDBRefs());
-
-		n.setSites(s.getSites());
-
-		n.setChains(s.getModel(0));
-
-		return n;
-
-	}
-
-	/**
-	 * Removes all polymeric and solvent groups from a list of groups
-	 *
-	 */
-	public static List<Group> filterLigands(List<Group> allGroups) {
-
-		List<Group> groups = new ArrayList<>();
-		for (Group g : allGroups) {
-
-			if ( g.isPolymeric())
-				continue;
-
-			if (!g.isWater()) {
-				groups.add(g);
-			}
-		}
-
-		return groups;
-	}
-
-	/**
-	 * Short version of {@link #getStructure(String, PDBFileParser, AtomCache)}
-	 * which creates new parsers when needed
-	 *
-	 * @param name
-	 * @return
-	 * @throws IOException
-	 * @throws StructureException
-	 */
-	public static Structure getStructure(String name) throws IOException,
-	StructureException {
-		return StructureTools.getStructure(name, null, null);
-	}
-
-	/**
-	 * Flexibly get a structure from an input String. The intent of this method
-	 * is to allow any reasonable string which could refer to a structure to be
-	 * correctly parsed. The following are currently supported:
-	 * <ol>
-	 * <li>Filename (if name refers to an existing file)
-	 * <li>PDB ID
-	 * <li>SCOP domains
-	 * <li>PDP domains
-	 * <li>Residue ranges
-	 * <li>Other formats supported by AtomCache
-	 * </ol>
-	 *
-	 * @param name
-	 *            Some reference to the protein structure
-	 * @param parser
-	 *            A clean PDBFileParser to use if it is a file. If null, a
-	 *            PDBFileParser will be instantiated if needed.
-	 * @param cache
-	 *            An AtomCache to use if the structure can be fetched from the
-	 *            PDB. If null, a AtomCache will be instantiated if needed.
-	 * @return A Structure object
-	 * @throws IOException
-	 *             if name is an existing file, but doesn't parse correctly
-	 * @throws StructureException
-	 *             if the format is unknown, or if AtomCache throws an
-	 *             exception.
-	 */
-	public static Structure getStructure(String name, PDBFileParser parser,
-			AtomCache cache) throws IOException, StructureException {
-		File f = new File(FileDownloadUtils.expandUserHome(name));
-		if (f.exists()) {
-			if (parser == null) {
-				parser = new PDBFileParser();
-			}
-			InputStream inStream = new FileInputStream(f);
-			return parser.parsePDBFile(inStream);
-		} else {
-			if (cache == null) {
-				cache = new AtomCache();
-			}
-			return cache.getStructure(name);
-		}
-	}
-
-	/**
-	 * @deprecated  use {@link Chain#isProtein()} instead.
-	 */
-	@Deprecated
-	public static boolean isProtein(Chain c) {
-
-		return c.isProtein();
-	}
-
-	/**
-	 * @deprecated use {@link Chain#isNucleicAcid()} instead.
-	 */
-	@Deprecated
-	public static boolean isNucleicAcid(Chain c) {
-		return c.isNucleicAcid();
-	}
-
-	/**
-	 * @deprecated use {@link Chain#getPredominantGroupType()} instead.
-	 */
-	@Deprecated
-	public static GroupType getPredominantGroupType(Chain c) {
-		return c.getPredominantGroupType();
-	}
-
-	/**
-	 * @deprecated use {@link Chain#isWaterOnly()} instead.
-	 */
-	@Deprecated
-	public static boolean isChainWaterOnly(Chain c) {
-		return c.isWaterOnly();
-	}
-
-	/**
-	 * @deprecated  use {@link Chain#isPureNonPolymer()} instead.
-	 */
-	@Deprecated
-	public static boolean isChainPureNonPolymer(Chain c) {
-
-		return c.isPureNonPolymer();
-	}
-
-	/**
-	 * Cleans up the structure's alternate location (altloc) groups. All alternate location groups should have all atoms (except
-	 * in the case of microheterogenity) or when a deuterium exists.
-	 * Ensure that all the alt loc groups have all the atoms in the main group.
-	 * @param structure The Structure to be cleaned up
-	 */
-	public static void cleanUpAltLocs(Structure structure) {
-		for (int i =0; i< structure.nrModels() ; i++){
-			for (Chain chain : structure.getModel(i)) {
-				for (Group group : chain.getAtomGroups()) {
-					for (Group altLocGroup : group.getAltLocs()) {
-						for ( Atom groupAtom : group.getAtoms()) {
-							// If this alt loc doesn't have this atom
-							if (! altLocGroup.hasAtom(groupAtom.getName())) {
-								// Fix for microheterogenity
-								if (altLocGroup.getPDBName().equals(group.getPDBName())) {
-									// If it's a Hydrogen then we check for it's Deuterated brother
-									if(!hasDeuteratedEquiv(groupAtom, altLocGroup)){
-										altLocGroup.addAtom(groupAtom);
-									}
-								}
-							}
-						}
-					}
-				}
-			}
-		}
-	}
-
-	/**
-	 * Check to see if an Deuterated atom has a non deuterated brother in the group.
-	 * @param atom the input atom that is putatively deuterium
-	 * @param currentGroup the group the atom is in
-	 * @return true if the atom is deuterated and it's hydrogen equive exists.
-	 */
-	public static boolean hasNonDeuteratedEquiv(Atom atom, Group currentGroup) {
-		if(atom.getElement()==Element.D && currentGroup.hasAtom(replaceFirstChar(atom.getName(),'D', 'H'))) {
-			// If it's deuterated and has a non-deuterated brother
-			return true;
-		}
-		return false;
-	}
-
-	/**
-	 * Check to see if a Hydrogen has a  Deuterated brother in the group.
-	 * @param atom the input atom that is putatively hydorgen
-	 * @param currentGroup the group the atom is in
-	 * @return true if the atom is hydrogen and it's Deuterium equiv exists.
-	 */
-	public static boolean hasDeuteratedEquiv(Atom atom, Group currentGroup) {
-		if(atom.getElement()==Element.H && currentGroup.hasAtom(replaceFirstChar(atom.getName(),'H', 'D'))) {
-			// If it's hydrogen and has a deuterated brother
-			return true;
-		}
-		return false;
-	}
-
-	private static String replaceFirstChar(String name, char c, char d) {
-		if(name.charAt(0)==c){
-			return name.replaceFirst(String.valueOf(c), String.valueOf(d));
-		}
-		return name;
-	}
-
-	/**
-	 * Remove all atoms but the representative atoms (C alphas or phosphates) from the given structure.
-	 * @param structure the structure
-	 * @since 5.4.0
-	 */
-	public static void reduceToRepresentativeAtoms(Structure structure) {
-		for (int modelIdx = 0; modelIdx<structure.nrModels(); modelIdx++) {
-			for (Chain c : structure.getPolyChains(modelIdx)) {
-				for (Group g : c.getAtomGroups()) {
-					List<Atom> atoms = g.getAtoms();
-					if (g.isAminoAcid()) {
-						atoms.removeIf(a->!a.getName().equals(CA_ATOM_NAME));
-					} else if (g.isNucleotide()) {
-						atoms.removeIf(a->!a.getName().equals(NUCLEOTIDE_REPRESENTATIVE));
-					}
-					// else we keep all other atoms. We are concerned only about aminoacids and nucleotides that make up the bulk of the structures
-				}
-			}
-		}
-	}
+    /**
+     * Expand a set of atoms into all groups from the same structure.
+     * <p>
+     * If the structure is set, only the first atom is used (assuming all
+     * atoms come from the same original structure).
+     * If the atoms aren't linked to a structure (for instance, for cloned atoms),
+     * searches all chains of all atoms for groups.
+     *
+     * @param atoms Sample of atoms
+     * @return All groups from all chains accessible from the input atoms
+     */
+    public static Set<Group> getAllGroupsFromSubset(Atom[] atoms) {
+        return getAllGroupsFromSubset(atoms, null);
+    }
+
+    /**
+     * Expand a set of atoms into all groups from the same structure.
+     * <p>
+     * If the structure is set, only the first atom is used (assuming all
+     * atoms come from the same original structure).
+     * If the atoms aren't linked to a structure (for instance, for cloned atoms),
+     * searches all chains of all atoms for groups.
+     *
+     * @param atoms Sample of atoms
+     * @param types Type of groups to return (useful for getting only ligands, for instance).
+     *              Null gets all groups.
+     * @return All groups from all chains accessible from the input atoms
+     */
+    public static Set<Group> getAllGroupsFromSubset(Atom[] atoms, GroupType types) {
+        // Get the full structure
+        Structure s = null;
+        if (atoms.length > 0) {
+            Group g = atoms[0].getGroup();
+            if (g != null) {
+                Chain c = g.getChain();
+                if (c != null) {
+                    s = c.getStructure();
+                }
+            }
+        }
+        // Collect all groups from the structure
+        Set<Chain> allChains = new HashSet<>();
+        if (s != null) {
+            allChains.addAll(s.getChains());
+        }
+        // In case the structure wasn't set, need to use ca chains too
+        for (Atom a : atoms) {
+            Group g = a.getGroup();
+            if (g != null) {
+                Chain c = g.getChain();
+                if (c != null) {
+                    allChains.add(c);
+                }
+            }
+        }
+
+        if (allChains.isEmpty()) {
+            return Collections.emptySet();
+        }
+
+        // Extract all ligand groups
+        Set<Group> full = new HashSet<>();
+        for (Chain c : allChains) {
+            if (types == null) {
+                full.addAll(c.getAtomGroups());
+            } else {
+                full.addAll(c.getAtomGroups(types));
+            }
+        }
+
+        return full;
+    }
+
+
+    /**
+     * Returns and array of all non-Hydrogen atoms in the given Structure,
+     * optionally including HET atoms or not. Waters are not included.
+     *
+     * @param s
+     * @param hetAtoms if true HET atoms are included in array, if false they are not
+     * @return
+     */
+    public static Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms) {
+        AtomIterator iter = new AtomIterator(s);
+        return getAllNonHAtomArray(s, hetAtoms, iter);
+    }
+
+    /**
+     * Returns and array of all non-Hydrogen atoms in the given Structure,
+     * optionally including HET atoms or not. Waters are not included.
+     *
+     * @param s
+     * @param hetAtoms if true HET atoms are included in array, if false they are not
+     * @param modelNr  Model number to draw atoms from
+     * @return
+     */
+    public static Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, int modelNr) {
+        AtomIterator iter = new AtomIterator(s, modelNr);
+        return getAllNonHAtomArray(s, hetAtoms, iter);
+    }
+
+    private static Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, AtomIterator iter) {
+        List<Atom> atoms = new ArrayList<>();
+
+        while (iter.hasNext()) {
+            Atom a = iter.next();
+            if (a.getElement() == Element.H)
+                continue;
+
+            Group g = a.getGroup();
+
+            if (g.isWater())
+                continue;
+
+            if (!hetAtoms && g.getType().equals(GroupType.HETATM))
+                continue;
+
+            atoms.add(a);
+        }
+        return atoms.toArray(Atom.EmptyAtomArray);
+    }
+
+    /**
+     * Returns and array of all non-Hydrogen atoms in the given Chain,
+     * optionally including HET atoms or not Waters are not included.
+     *
+     * @param c
+     * @param hetAtoms if true HET atoms are included in array, if false they are not
+     * @return
+     */
+    public static Atom[] getAllNonHAtomArray(Chain c, boolean hetAtoms) {
+        List<Atom> atoms = new ArrayList<>();
+
+        for (Group g : c.getAtomGroups()) {
+            if (g.isWater())
+                continue;
+            for (Atom a : g.getAtoms()) {
+
+                if (a.getElement() == Element.H)
+                    continue;
+
+                if (!hetAtoms && g.getType().equals(GroupType.HETATM))
+                    continue;
+
+                atoms.add(a);
+            }
+        }
+        return atoms.toArray(Atom.EmptyAtomArray);
+    }
+
+    /**
+     * Returns and array of all non-Hydrogen atoms coordinates in the given Chain,
+     * optionally including HET atoms or not Waters are not included.
+     *
+     * @param c
+     * @param hetAtoms if true HET atoms are included in array, if false they are not
+     * @return
+     */
+    public static Point3d[] getAllNonHCoordsArray(Chain c, boolean hetAtoms) {
+        List<Point3d> atoms = new ArrayList<>();
+
+        for (Group g : c.getAtomGroups()) {
+            if (g.isWater())
+                continue;
+            for (Atom a : g.getAtoms()) {
+
+                if (a.getElement() == Element.H)
+                    continue;
+
+                if (!hetAtoms && g.getType().equals(GroupType.HETATM))
+                    continue;
+
+                atoms.add(a.getCoordsAsPoint3d());
+            }
+        }
+        return atoms.toArray(new Point3d[0]);
+    }
+
+    /**
+     * Adds to the given atoms list, all atoms of groups that contained all
+     * requested atomNames, i.e. if a group does not contain all of the
+     * requested atom names, its atoms won't be added.
+     *
+     * @param atomNames
+     * @param chains
+     * @param atoms
+     */
+    private static void extractAtoms(String[] atomNames, List<Chain> chains,
+                                     List<Atom> atoms) {
+
+        for (Chain c : chains) {
+
+            for (Group g : c.getAtomGroups()) {
+
+                // a temp container for the atoms of this group
+                List<Atom> thisGroupAtoms = new ArrayList<>();
+                // flag to check if this group contains all the requested atoms.
+                boolean thisGroupAllAtoms = true;
+                for (String atomName : atomNames) {
+                    Atom a = g.getAtom(atomName);
+
+                    if (a == null) {
+                        // this group does not have a required atom, skip it...
+                        thisGroupAllAtoms = false;
+                        break;
+                    }
+                    thisGroupAtoms.add(a);
+                }
+                if (thisGroupAllAtoms) {
+                    // add the atoms of this group to the array.
+                    atoms.addAll(thisGroupAtoms);
+                }
+
+            }
+        }
+    }
+
+    /**
+     * Returns an array of the requested Atoms from the Chain object. Iterates
+     * over all groups and checks if the requested atoms are in this group, no
+     * matter if this is a AminoAcid or Hetatom group. If the group does not
+     * contain all requested atoms then no atoms are added for that group.
+     *
+     * @param c         the Chain to get the atoms from
+     * @param atomNames contains the atom names to be used.
+     * @return an Atom[] array
+     */
+    public static Atom[] getAtomArray(Chain c, String[] atomNames) {
+
+        List<Atom> atoms = new ArrayList<>();
+
+        for (Group g : c.getAtomGroups()) {
+
+            // a temp container for the atoms of this group
+            List<Atom> thisGroupAtoms = new ArrayList<>();
+            // flag to check if this group contains all the requested atoms.
+            boolean thisGroupAllAtoms = true;
+            for (String atomName : atomNames) {
+                Atom a = g.getAtom(atomName);
+                if (a == null) {
+                    logger.debug("Group " + g.getResidueNumber() + " ("
+                            + g.getPDBName()
+                            + ") does not have the required atom '" + atomName
+                            + "'");
+                    // this group does not have a required atom, skip it...
+                    thisGroupAllAtoms = false;
+                    break;
+                }
+                thisGroupAtoms.add(a);
+            }
+
+            if (thisGroupAllAtoms) {
+                // add the atoms of this group to the array.
+                atoms.addAll(thisGroupAtoms);
+            }
+
+        }
+        return atoms.toArray(Atom.EmptyAtomArray);
+
+    }
+
+    /**
+     * Returns an Atom array of the C-alpha atoms. Any atom that is a carbon and
+     * has CA name will be returned.
+     *
+     * @param c the structure object
+     * @return an Atom[] array
+     * @see #getRepresentativeAtomArray(Chain)
+     */
+    public static Atom[] getAtomCAArray(Chain c) {
+        List<Atom> atoms = new ArrayList<>();
+
+        for (Group g : c.getAtomGroups()) {
+            if (g.hasAtom(CA_ATOM_NAME)
+                    && g.getAtom(CA_ATOM_NAME).getElement() == Element.C) {
+                atoms.add(g.getAtom(CA_ATOM_NAME));
+            }
+        }
+
+        return atoms.toArray(Atom.EmptyAtomArray);
+    }
+
+    /**
+     * Gets a representative atom for each group that is part of the chain
+     * backbone. Note that modified aminoacids won't be returned as part of the
+     * backbone if the {@link org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider} was used to load the
+     * structure.
+     * <p>
+     * For amino acids, the representative is a CA carbon. For nucleotides, the
+     * representative is the {@value #NUCLEOTIDE_REPRESENTATIVE}. Other group
+     * types will be ignored.
+     *
+     * @param c
+     * @return representative Atoms of the chain backbone
+     * @since Biojava 4.1.0
+     */
+    public static Atom[] getRepresentativeAtomArray(Chain c) {
+        List<Atom> atoms = new ArrayList<>();
+
+        for (Group g : c.getAtomGroups()) {
+
+            switch (g.getType()) {
+                case AMINOACID:
+                    if (g.hasAtom(CA_ATOM_NAME)
+                            && g.getAtom(CA_ATOM_NAME).getElement() == Element.C) {
+                        atoms.add(g.getAtom(CA_ATOM_NAME));
+                    }
+                    break;
+                case NUCLEOTIDE:
+                    if (g.hasAtom(NUCLEOTIDE_REPRESENTATIVE)) {
+                        atoms.add(g.getAtom(NUCLEOTIDE_REPRESENTATIVE));
+                    }
+                    break;
+                default:
+                    // don't add
+            }
+        }
+
+        return atoms.toArray(Atom.EmptyAtomArray);
+
+    }
+
+    /**
+     * Provides an equivalent copy of Atoms in a new array. Clones everything,
+     * starting with parent groups and chains. The chain will only contain
+     * groups that are part of the input array.
+     *
+     * @param ca array of representative atoms, e.g. CA atoms
+     * @return Atom array
+     * @since Biojava 4.1.0
+     */
+    public static Atom[] cloneAtomArray(Atom[] ca) {
+        Atom[] newCA = new Atom[ca.length];
+
+        List<Chain> model = new ArrayList<>();
+        int apos = -1;
+        for (Atom a : ca) {
+            apos++;
+            Group parentG = a.getGroup();
+            Chain parentC = parentG.getChain();
+
+            Chain newChain = null;
+            for (Chain c : model) {
+                if (c.getName().equals(parentC.getName())) {
+                    newChain = c;
+                    break;
+                }
+            }
+            if (newChain == null) {
+                newChain = new ChainImpl();
+                newChain.setId(parentC.getId());
+                newChain.setName(parentC.getName());
+                model.add(newChain);
+            }
+
+            Group parentN = (Group) parentG.clone();
+
+            newCA[apos] = parentN.getAtom(a.getName());
+
+            // if the group doesn't exist yet, this produces a StructureException
+            if (!newChain.hasGroupByPDB(parentN.getResidueNumber()))
+                newChain.addGroup(parentN); // the group doesn't exist yet in the newChain, let's add it
+
+        }
+        return newCA;
+    }
+
+    /**
+     * Clone a set of representative Atoms, but returns the parent groups
+     *
+     * @param ca Atom array
+     * @return Group array
+     */
+    public static Group[] cloneGroups(Atom[] ca) {
+        Group[] newGroup = new Group[ca.length];
+
+        List<Chain> model = new ArrayList<>();
+        int apos = -1;
+        for (Atom a : ca) {
+            apos++;
+            Group parentG = a.getGroup();
+            Chain parentC = parentG.getChain();
+
+            Chain newChain = null;
+            for (Chain c : model) {
+                if (c.getName().equals(parentC.getName())) {
+                    newChain = c;
+                    break;
+                }
+            }
+            if (newChain == null) {
+                newChain = new ChainImpl();
+                newChain.setName(parentC.getName());
+                model.add(newChain);
+            }
+
+            Group ng = (Group) parentG.clone();
+            newGroup[apos] = ng;
+            newChain.addGroup(ng);
+        }
+        return newGroup;
+    }
+
+    /**
+     * Utility method for working with circular permutations. Creates a
+     * duplicated and cloned set of Calpha atoms from the input array.
+     *
+     * @param ca2 atom array
+     * @return cloned and duplicated set of input array
+     */
+    public static Atom[] duplicateCA2(Atom[] ca2) {
+        // we don't want to rotate input atoms, do we?
+        Atom[] ca2clone = new Atom[ca2.length * 2];
+
+        int pos = 0;
+
+        Chain c = null;
+        String prevChainId = "";
+        for (Atom a : ca2) {
+            Group g = (Group) a.getGroup().clone(); // works because each group
+            // has only a single atom
+
+            if (c == null) {
+                c = new ChainImpl();
+                Chain orig = a.getGroup().getChain();
+                c.setId(orig.getId());
+                c.setName(orig.getName());
+            } else {
+                Chain orig = a.getGroup().getChain();
+                if (!orig.getId().equals(prevChainId)) {
+                    c = new ChainImpl();
+                    c.setId(orig.getId());
+                    c.setName(orig.getName());
+                }
+            }
+
+            c.addGroup(g);
+            ca2clone[pos] = g.getAtom(a.getName());
+
+            pos++;
+        }
+
+        // Duplicate ca2!
+        c = null;
+        prevChainId = "";
+        for (Atom a : ca2) {
+            Group g = (Group) a.getGroup().clone();
+
+            if (c == null) {
+                c = new ChainImpl();
+                Chain orig = a.getGroup().getChain();
+                c.setId(orig.getId());
+                c.setName(orig.getName());
+            } else {
+                Chain orig = a.getGroup().getChain();
+                if (!orig.getId().equals(prevChainId)) {
+                    c = new ChainImpl();
+                    c.setId(orig.getId());
+                    c.setName(orig.getName());
+                }
+            }
+
+            c.addGroup(g);
+            ca2clone[pos] = g.getAtom(a.getName());
+
+            pos++;
+        }
+
+        return ca2clone;
+
+    }
+
+    /**
+     * Return an Atom array of the C-alpha atoms. Any atom that is a carbon and
+     * has CA name will be returned.
+     *
+     * @param s the structure object
+     * @return an Atom[] array
+     * @see #getRepresentativeAtomArray(Structure)
+     */
+    public static Atom[] getAtomCAArray(Structure s) {
+
+        List<Atom> atoms = new ArrayList<>();
+
+        for (Chain c : s.getChains()) {
+            for (Group g : c.getAtomGroups()) {
+                if (g.hasAtom(CA_ATOM_NAME)
+                        && g.getAtom(CA_ATOM_NAME).getElement() == Element.C) {
+                    atoms.add(g.getAtom(CA_ATOM_NAME));
+                }
+            }
+        }
+
+        return atoms.toArray(Atom.EmptyAtomArray);
+    }
+
+    /**
+     * Gets a representative atom for each group that is part of the chain
+     * backbone. Note that modified aminoacids won't be returned as part of the
+     * backbone if the {@link org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider} was used to load the
+     * structure.
+     * <p>
+     * For amino acids, the representative is a CA carbon. For nucleotides, the
+     * representative is the {@value #NUCLEOTIDE_REPRESENTATIVE}. Other group
+     * types will be ignored.
+     *
+     * @param s Input structure
+     * @return representative Atoms of the structure backbone
+     * @since Biojava 4.1.0
+     */
+    public static Atom[] getRepresentativeAtomArray(Structure s) {
+
+        List<Atom> atoms = new ArrayList<>();
+
+        for (Chain c : s.getChains()) {
+            Atom[] chainAtoms = getRepresentativeAtomArray(c);
+            atoms.addAll(Arrays.asList(chainAtoms));
+        }
+
+        return atoms.toArray(Atom.EmptyAtomArray);
+    }
+
+    /**
+     * Return an Atom array of the main chain atoms: CA, C, N, O Any group that
+     * contains those atoms will be included, be it a standard aminoacid or not
+     *
+     * @param s the structure object
+     * @return an Atom[] array
+     */
+    public static Atom[] getBackboneAtomArray(Structure s) {
+
+        List<Atom> atoms = new ArrayList<>();
+
+        for (Chain c : s.getChains()) {
+            for (Group g : c.getAtomGroups()) {
+                if (g.hasAminoAtoms()) {
+                    // this means we will only take atoms grom groups that have
+                    // complete backbones
+                    for (Atom a : g.getAtoms()) {
+                        switch (g.getType()) {
+                            case NUCLEOTIDE:
+                                // Nucleotide backbone
+                                if (a.getName().equals(C1_ATOM_NAME))
+                                    atoms.add(a);
+                                if (a.getName().equals(C2_ATOM_NAME))
+                                    atoms.add(a);
+                                if (a.getName().equals(C3_ATOM_NAME))
+                                    atoms.add(a);
+                                if (a.getName().equals(C4_ATOM_NAME))
+                                    atoms.add(a);
+                                if (a.getName().equals(O2_ATOM_NAME))
+                                    atoms.add(a);
+                                if (a.getName().equals(O3_ATOM_NAME))
+                                    atoms.add(a);
+                                if (a.getName().equals(O4_ATOM_NAME))
+                                    atoms.add(a);
+                                if (a.getName().equals(O5_ATOM_NAME))
+                                    atoms.add(a);
+                                if (a.getName().equals(OP1_ATOM_NAME))
+                                    atoms.add(a);
+                                if (a.getName().equals(OP2_ATOM_NAME))
+                                    atoms.add(a);
+                                if (a.getName().equals(P_ATOM_NAME))
+                                    atoms.add(a);
+                                // TODO Allow C4* names as well as C4'? -SB 3/2015
+                                break;
+                            case AMINOACID:
+                            default:
+                                // we do it this way instead of with g.getAtom() to
+                                // be sure we always use the same order as original
+                                if (a.getName().equals(CA_ATOM_NAME))
+                                    atoms.add(a);
+                                if (a.getName().equals(C_ATOM_NAME))
+                                    atoms.add(a);
+                                if (a.getName().equals(N_ATOM_NAME))
+                                    atoms.add(a);
+                                if (a.getName().equals(O_ATOM_NAME))
+                                    atoms.add(a);
+                                break;
+                        }
+                    }
+                }
+            }
+
+        }
+
+        return atoms.toArray(Atom.EmptyAtomArray);
+    }
+
+    /**
+     * Convert three character amino acid codes into single character e.g.
+     * convert CYS to C. Valid 3-letter codes will be those of the standard 20
+     * amino acids plus MSE, CSE, SEC, PYH, PYL (see the {@link #aminoAcids}
+     * map)
+     *
+     * @param groupCode3 a three character amino acid representation String
+     * @return the 1 letter code, or null if the given 3 letter code does not
+     * correspond to an amino acid code
+     * @see {@link #get1LetterCode(String)}
+     */
+    public static Character get1LetterCodeAmino(String groupCode3) {
+        return aminoAcids.get(groupCode3);
+    }
+
+    /**
+     * Convert a three letter amino acid or nucleotide code into a single
+     * character code. If the code does not correspond to an amino acid or
+     * nucleotide, returns {@link #UNKNOWN_GROUP_LABEL}.
+     * <p>
+     * Returned null for nucleotides prior to version 4.0.1.
+     *
+     * @param groupCode3 three letter representation
+     * @return The 1-letter abbreviation
+     */
+    public static Character get1LetterCode(String groupCode3) {
+
+        Character code1;
+
+        // is it a standard amino acid ?
+        code1 = get1LetterCodeAmino(groupCode3);
+
+        if (code1 == null) {
+            // hm groupCode3 is not standard
+            // perhaps it is a nucleotide?
+            groupCode3 = groupCode3.trim();
+            if (isNucleotide(groupCode3)) {
+                code1 = nucleotides30.get(groupCode3);
+                if (code1 == null) {
+                    code1 = nucleotides23.get(groupCode3);
+                }
+                if (code1 == null) {
+                    code1 = UNKNOWN_GROUP_LABEL;
+                }
+            } else {
+                // does not seem to be so let's assume it is
+                // nonstandard aminoacid and label it "X"
+                // logger.warning("unknown group name "+groupCode3 );
+                code1 = UNKNOWN_GROUP_LABEL;
+            }
+        }
+
+        return code1;
+
+    }
+
+    /**
+     * Test if the three-letter code of an ATOM entry corresponds to a
+     * nucleotide or to an aminoacid.
+     *
+     * @param groupCode3 3-character code for a group.
+     */
+    public static boolean isNucleotide(String groupCode3) {
+        String code = groupCode3.trim();
+        return nucleotides30.containsKey(code)
+                || nucleotides23.containsKey(code);
+    }
+
+    /**
+     * Reduce a structure to provide a smaller representation . Only takes the
+     * first model of the structure. If chainName is provided only return a
+     * structure containing that Chain ID. Converts lower case chain IDs to
+     * upper case if structure does not contain a chain with that ID.
+     *
+     * @param s
+     * @param chainId
+     * @return Structure
+     * @since 3.0
+     * @deprecated Use {@link StructureIdentifier#reduce(Structure)} instead (v. 4.2.0)
+     */
+    @Deprecated
+    public static Structure getReducedStructure(Structure s,
+                                                String chainId) throws StructureException {
+        // since we deal here with structure alignments,
+        // only use Model 1...
+
+        Structure newS = new StructureImpl();
+        newS.setPDBCode(s.getPDBCode());
+        newS.setPDBHeader(s.getPDBHeader());
+        newS.setName(s.getName());
+        newS.setSSBonds(s.getSSBonds());
+        newS.setDBRefs(s.getDBRefs());
+        newS.setSites(s.getSites());
+        newS.setBiologicalAssembly(s.isBiologicalAssembly());
+        newS.setEntityInfos(s.getEntityInfos());
+        newS.setSSBonds(s.getSSBonds());
+        newS.setSites(s.getSites());
+
+        if (chainId != null)
+            chainId = chainId.trim();
+
+        if (chainId == null || chainId.isEmpty()) {
+            // only get model 0
+            List<Chain> model0 = s.getModel(0);
+            for (Chain c : model0) {
+                newS.addChain(c);
+            }
+            return newS;
+
+        }
+
+        Chain c;
+        try {
+            c = s.getChainByPDB(chainId);
+        } catch (StructureException e) {
+            logger.warn(e.getMessage() + ". Chain id " + chainId
+                    + " did not match, trying upper case Chain id.");
+            c = s.getChainByPDB(chainId.toUpperCase());
+
+        }
+        if (c != null) {
+            newS.addChain(c);
+            for (EntityInfo comp : s.getEntityInfos()) {
+                if (comp.getChainIds() != null
+                        && comp.getChainIds().contains(c.getChainID())) {
+                    // found matching entity info. set description...
+                    newS.getPDBHeader().setDescription(
+                            "Chain " + c.getChainID() + " of " + s.getPDBCode()
+                                    + " " + comp.getDescription());
+                }
+            }
+        }
+
+        return newS;
+    }
+
+    public static String convertAtomsToSeq(Atom[] atoms) {
+
+        StringBuilder buf = new StringBuilder();
+        Group prevGroup = null;
+        for (Atom a : atoms) {
+            Group g = a.getGroup();
+            if (prevGroup != null) {
+                if (prevGroup.equals(g)) {
+                    // we add each group only once.
+                    continue;
+                }
+            }
+            String code3 = g.getPDBName();
+            Character code1 = get1LetterCodeAmino(code3);
+            if (code1 == null)
+                code1 = UNKNOWN_GROUP_LABEL;
+
+            buf.append(code1);
+
+            prevGroup = g;
+
+        }
+        return buf.toString();
+    }
+
+    /**
+     * Get a group represented by a ResidueNumber.
+     *
+     * @param struc     a {@link Structure}
+     * @param pdbResNum a {@link ResidueNumber}
+     * @return a group in the structure that is represented by the pdbResNum.
+     * @throws StructureException if the group cannot be found.
+     */
+    public static Group getGroupByPDBResidueNumber(Structure struc,
+                                                   ResidueNumber pdbResNum) throws StructureException {
+        if (struc == null || pdbResNum == null) {
+            throw new IllegalArgumentException("Null argument(s).");
+        }
+
+        Chain chain = struc.getPolyChainByPDB(pdbResNum.getChainName());
+
+        return chain.getGroupByPDB(pdbResNum);
+    }
+
+    /**
+     * Returns the set of intra-chain contacts for the given chain for given
+     * atom names, i.e. the contact map. Uses a geometric hashing algorithm that
+     * speeds up the calculation without need of full distance matrix. The
+     * parsing mode {@link FileParsingParameters#setAlignSeqRes(boolean)} needs
+     * to be set to true for this to work.
+     *
+     * @param chain
+     * @param atomNames the array with atom names to be used. Beware: CA will do both
+     *                  C-alphas an Calciums if null all non-H atoms of non-hetatoms
+     *                  will be used
+     * @param cutoff
+     * @return
+     */
+    public static AtomContactSet getAtomsInContact(Chain chain,
+                                                   String[] atomNames, double cutoff) {
+        Grid grid = new Grid(cutoff);
+
+        Atom[] atoms;
+        if (atomNames == null) {
+            atoms = getAllNonHAtomArray(chain, false);
+        } else {
+            atoms = getAtomArray(chain, atomNames);
+        }
+        // If tha
+        if (atoms.length == 0) {
+            logger.warn("No atoms found for buidling grid!");
+            return new AtomContactSet(cutoff);
+        }
+        grid.addAtoms(atoms);
+
+        return grid.getAtomContacts();
+    }
+
+    /**
+     * Returns the set of intra-chain contacts for the given chain for all non-H
+     * atoms of non-hetatoms, i.e. the contact map. Uses a geometric hashing
+     * algorithm that speeds up the calculation without need of full distance
+     * matrix. The parsing mode
+     * {@link FileParsingParameters#setAlignSeqRes(boolean)} needs to be set to
+     * true for this to work.
+     *
+     * @param chain
+     * @param cutoff
+     * @return
+     */
+    public static AtomContactSet getAtomsInContact(Chain chain, double cutoff) {
+        return getAtomsInContact(chain, null, cutoff);
+    }
+
+    /**
+     * Returns the set of intra-chain contacts for the given chain for C-alpha
+     * atoms (including non-standard aminoacids appearing as HETATM groups),
+     * i.e. the contact map. Uses a geometric hashing algorithm that speeds up
+     * the calculation without need of full distance matrix. The parsing mode
+     * {@link FileParsingParameters#setAlignSeqRes(boolean)} needs to be set to
+     * true for this to work.
+     *
+     * @param chain
+     * @param cutoff
+     * @return
+     * @see #getRepresentativeAtomsInContact(Chain, double)
+     */
+    public static AtomContactSet getAtomsCAInContact(Chain chain, double cutoff) {
+        Grid grid = new Grid(cutoff);
+
+        Atom[] atoms = getAtomCAArray(chain);
+
+        grid.addAtoms(atoms);
+
+        return grid.getAtomContacts();
+    }
+
+    /**
+     * Returns the set of intra-chain contacts for the given chain for C-alpha
+     * or C3' atoms (including non-standard aminoacids appearing as HETATM
+     * groups), i.e. the contact map. Uses a geometric hashing algorithm that
+     * speeds up the calculation without need of full distance matrix.
+     *
+     * @param chain
+     * @param cutoff
+     * @return
+     * @since Biojava 4.1.0
+     */
+    public static AtomContactSet getRepresentativeAtomsInContact(Chain chain,
+                                                                 double cutoff) {
+        Grid grid = new Grid(cutoff);
+
+        Atom[] atoms = getRepresentativeAtomArray(chain);
+
+        grid.addAtoms(atoms);
+
+        return grid.getAtomContacts();
+    }
+
+    /**
+     * Returns the set of inter-chain contacts between the two given chains for
+     * the given atom names. Uses a geometric hashing algorithm that speeds up
+     * the calculation without need of full distance matrix. The parsing mode
+     * {@link FileParsingParameters#setAlignSeqRes(boolean)} needs to be set to
+     * true for this to work.
+     *
+     * @param chain1
+     * @param chain2
+     * @param atomNames the array with atom names to be used. For Calphas use {"CA"},
+     *                  if null all non-H atoms will be used. Note HET atoms are
+     *                  ignored unless this parameter is null.
+     * @param cutoff
+     * @param hetAtoms  if true HET atoms are included, if false they are not
+     * @return
+     */
+    public static AtomContactSet getAtomsInContact(Chain chain1, Chain chain2,
+                                                   String[] atomNames, double cutoff, boolean hetAtoms) {
+        Grid grid = new Grid(cutoff);
+        Atom[] atoms1;
+        Atom[] atoms2;
+        if (atomNames == null) {
+            atoms1 = getAllNonHAtomArray(chain1, hetAtoms);
+            atoms2 = getAllNonHAtomArray(chain2, hetAtoms);
+        } else {
+            atoms1 = getAtomArray(chain1, atomNames);
+            atoms2 = getAtomArray(chain2, atomNames);
+        }
+        grid.addAtoms(atoms1, atoms2);
+
+        return grid.getAtomContacts();
+    }
+
+    /**
+     * Returns the set of inter-chain contacts between the two given chains for
+     * all non-H atoms. Uses a geometric hashing algorithm that speeds up the
+     * calculation without need of full distance matrix. The parsing mode
+     * {@link FileParsingParameters#setAlignSeqRes(boolean)} needs to be set to
+     * true for this to work.
+     *
+     * @param chain1
+     * @param chain2
+     * @param cutoff
+     * @param hetAtoms if true HET atoms are included, if false they are not
+     * @return
+     */
+    public static AtomContactSet getAtomsInContact(Chain chain1, Chain chain2,
+                                                   double cutoff, boolean hetAtoms) {
+        return getAtomsInContact(chain1, chain2, null, cutoff, hetAtoms);
+    }
+
+    /**
+     * Finds Groups in {@code structure} that contain at least one Atom that is
+     * within {@code radius} Angstroms of {@code centroid}.
+     *
+     * @param structure          The structure from which to find Groups
+     * @param centroid           The centroid of the shell
+     * @param excludeResidues    A list of ResidueNumbers to exclude
+     * @param radius             The radius from {@code centroid}, in Angstroms
+     * @param includeWater       Whether to include Groups whose <em>only</em> atoms are water
+     * @param useAverageDistance When set to true, distances are the arithmetic mean (1-norm)
+     *                           of the distances of atoms that belong to the group and that
+     *                           are within the shell; otherwise, distances are the minimum of
+     *                           these values
+     * @return A map of Groups within (or partially within) the shell, to their
+     * distances in Angstroms
+     */
+    public static Map<Group, Double> getGroupDistancesWithinShell(
+            Structure structure, Atom centroid,
+            Set<ResidueNumber> excludeResidues, double radius,
+            boolean includeWater, boolean useAverageDistance) {
+
+        // for speed, we avoid calculating square roots
+        radius = radius * radius;
+
+        Map<Group, Double> distances = new HashMap<>();
+
+        // we only need this if we're averaging distances
+        // note that we can't use group.getAtoms().size() because some the
+        // group's atoms be outside the shell
+        Map<Group, Integer> atomCounts = new HashMap<>();
+
+        for (Chain chain : structure.getChains()) {
+            groupLoop:
+            for (Group chainGroup : chain.getAtomGroups()) {
+
+                // exclude water
+                if (!includeWater && chainGroup.isWater())
+                    continue;
+
+                // check blacklist of residue numbers
+                for (ResidueNumber rn : excludeResidues) {
+                    if (rn.equals(chainGroup.getResidueNumber()))
+                        continue groupLoop;
+                }
+
+                for (Atom testAtom : chainGroup.getAtoms()) {
+
+                    // use getDistanceFast as we are doing a lot of comparisons
+                    double dist = Calc.getDistanceFast(centroid, testAtom);
+
+                    // if we're the shell
+                    if (dist <= radius) {
+                        if (!distances.containsKey(chainGroup))
+                            distances.put(chainGroup, Double.POSITIVE_INFINITY);
+                        if (useAverageDistance) {
+                            // sum the distance; we'll divide by the total
+                            // number later
+                            // here, we CANNOT use fastDistance (distance
+                            // squared) because we want the arithmetic mean
+                            distances.put(chainGroup, distances.get(chainGroup)
+                                    + Math.sqrt(dist));
+                            if (!atomCounts.containsKey(chainGroup))
+                                atomCounts.put(chainGroup, 0);
+                            atomCounts.put(chainGroup,
+                                    atomCounts.get(chainGroup) + 1);
+                        } else {
+                            // take the minimum distance among all atoms of
+                            // chainGroup
+                            // note that we can't break here because we might
+                            // find a smaller distance
+                            if (dist < distances.get(chainGroup)) {
+                                distances.put(chainGroup, dist);
+                            }
+                        }
+                    }
+
+                }
+            }
+        }
+
+        if (useAverageDistance) {
+            for (Map.Entry<Group, Double> entry : distances.entrySet()) {
+                int count = atomCounts.get(entry.getKey());
+                distances.put(entry.getKey(), entry.getValue() / count);
+            }
+        } else {
+            // in this case we used getDistanceFast
+            distances.replaceAll((k, v) -> Math.sqrt(v));
+        }
+
+        return distances;
+
+    }
+
+    public static Set<Group> getGroupsWithinShell(Structure structure,
+                                                  Atom atom, Set<ResidueNumber> excludeResidues, double distance,
+                                                  boolean includeWater) {
+
+        // square the distance to use as a comparison against getDistanceFast
+        // which returns the square of a distance.
+        distance = distance * distance;
+
+        Set<Group> returnSet = new LinkedHashSet<>();
+        for (Chain chain : structure.getChains()) {
+            groupLoop:
+            for (Group chainGroup : chain.getAtomGroups()) {
+                if (!includeWater && chainGroup.isWater())
+                    continue;
+                for (ResidueNumber rn : excludeResidues) {
+                    if (rn.equals(chainGroup.getResidueNumber()))
+                        continue groupLoop;
+                }
+                for (Atom atomB : chainGroup.getAtoms()) {
+
+                    // use getDistanceFast as we are doing a lot of comparisons
+                    double dist = Calc.getDistanceFast(atom, atomB);
+                    if (dist <= distance) {
+                        returnSet.add(chainGroup);
+                        break;
+                    }
+
+                }
+            }
+        }
+        return returnSet;
+    }
+
+    /**
+     * <p>
+     * Returns a Set of Groups in a structure within the distance specified of a
+     * given group.
+     * </p>
+     * <p>
+     * Updated 18-Sep-2015 sroughley to return a Set so only a unique set of
+     * Groups returned
+     *
+     * @param structure    The structure to work with
+     * @param group        The 'query' group
+     * @param distance     The cutoff distance
+     * @param includeWater Should water residues be included in the output?
+     * @return {@link LinkedHashSet} of {@link Group}s within at least one atom
+     * with {@code distance} of at least one atom in {@code group}
+     */
+    public static Set<Group> getGroupsWithinShell(Structure structure,
+                                                  Group group, double distance, boolean includeWater) {
+
+        Set<Group> returnList = new LinkedHashSet<>();
+
+        Set<ResidueNumber> excludeGroups = new HashSet<>();
+        excludeGroups.add(group.getResidueNumber());
+        for (Atom atom : group.getAtoms()) {
+            Set<Group> set = getGroupsWithinShell(structure, atom,
+                    excludeGroups, distance, includeWater);
+            returnList.addAll(set);
+        }
+
+        return returnList;
+    }
+
+    /**
+     * Remove all models from a Structure and keep only the first
+     *
+     * @param s original Structure
+     * @return a structure that contains only the first model
+     * @since 3.0.5
+     */
+    public static Structure removeModels(Structure s) {
+        if (s.nrModels() == 1)
+            return s;
+
+        Structure n = new StructureImpl();
+        // go through whole substructure and clone ...
+
+        // copy structure data
+
+        n.setPDBCode(s.getPDBCode());
+        n.setName(s.getName());
+
+        // TODO: do deep copying of data!
+        n.setPDBHeader(s.getPDBHeader());
+        n.setDBRefs(s.getDBRefs());
+
+        n.setSites(s.getSites());
+
+        n.setChains(s.getModel(0));
+
+        return n;
+
+    }
+
+    /**
+     * Removes all polymeric and solvent groups from a list of groups
+     */
+    public static List<Group> filterLigands(List<Group> allGroups) {
+
+        List<Group> groups = new ArrayList<>();
+        for (Group g : allGroups) {
+
+            if (g.isPolymeric())
+                continue;
+
+            if (!g.isWater()) {
+                groups.add(g);
+            }
+        }
+
+        return groups;
+    }
+
+    /**
+     * Short version of {@link #getStructure(String, PDBFileParser, AtomCache)}
+     * which creates new parsers when needed
+     *
+     * @param name
+     * @return
+     * @throws IOException
+     * @throws StructureException
+     */
+    public static Structure getStructure(String name) throws IOException,
+            StructureException {
+        return StructureTools.getStructure(name, null, null);
+    }
+
+    /**
+     * Flexibly get a structure from an input String. The intent of this method
+     * is to allow any reasonable string which could refer to a structure to be
+     * correctly parsed. The following are currently supported:
+     * <ol>
+     * <li>Filename (if name refers to an existing file)
+     * <li>PDB ID
+     * <li>SCOP domains
+     * <li>PDP domains
+     * <li>Residue ranges
+     * <li>Other formats supported by AtomCache
+     * </ol>
+     *
+     * @param name   Some reference to the protein structure
+     * @param parser A clean PDBFileParser to use if it is a file. If null, a
+     *               PDBFileParser will be instantiated if needed.
+     * @param cache  An AtomCache to use if the structure can be fetched from the
+     *               PDB. If null, a AtomCache will be instantiated if needed.
+     * @return A Structure object
+     * @throws IOException        if name is an existing file, but doesn't parse correctly
+     * @throws StructureException if the format is unknown, or if AtomCache throws an
+     *                            exception.
+     */
+    public static Structure getStructure(String name, PDBFileParser parser,
+                                         AtomCache cache) throws IOException, StructureException {
+        File f = new File(FileDownloadUtils.expandUserHome(name));
+        if (f.exists()) {
+            if (parser == null) {
+                parser = new PDBFileParser();
+            }
+            InputStream inStream = new FileInputStream(f);
+            return parser.parsePDBFile(inStream);
+        } else {
+            if (cache == null) {
+                cache = new AtomCache();
+            }
+            return cache.getStructure(name);
+        }
+    }
+
+    /**
+     * @deprecated use {@link Chain#isProtein()} instead.
+     */
+    @Deprecated
+    public static boolean isProtein(Chain c) {
+
+        return c.isProtein();
+    }
+
+    /**
+     * @deprecated use {@link Chain#isNucleicAcid()} instead.
+     */
+    @Deprecated
+    public static boolean isNucleicAcid(Chain c) {
+        return c.isNucleicAcid();
+    }
+
+    /**
+     * @deprecated use {@link Chain#getPredominantGroupType()} instead.
+     */
+    @Deprecated
+    public static GroupType getPredominantGroupType(Chain c) {
+        return c.getPredominantGroupType();
+    }
+
+    /**
+     * @deprecated use {@link Chain#isWaterOnly()} instead.
+     */
+    @Deprecated
+    public static boolean isChainWaterOnly(Chain c) {
+        return c.isWaterOnly();
+    }
+
+    /**
+     * @deprecated use {@link Chain#isPureNonPolymer()} instead.
+     */
+    @Deprecated
+    public static boolean isChainPureNonPolymer(Chain c) {
+
+        return c.isPureNonPolymer();
+    }
+
+    /**
+     * Cleans up the structure's alternate location (altloc) groups. All alternate location groups should have all atoms (except
+     * in the case of microheterogenity) or when a deuterium exists.
+     * Ensure that all the alt loc groups have all the atoms in the main group.
+     *
+     * @param structure The Structure to be cleaned up
+     */
+    public static void cleanUpAltLocs(Structure structure) {
+        for (int i = 0; i < structure.nrModels(); i++) {
+            for (Chain chain : structure.getModel(i)) {
+                for (Group group : chain.getAtomGroups()) {
+                    for (Group altLocGroup : group.getAltLocs()) {
+                        for (Atom groupAtom : group.getAtoms()) {
+                            // If this alt loc doesn't have this atom
+                            if (!altLocGroup.hasAtom(groupAtom.getName())) {
+                                // Fix for microheterogenity
+                                if (altLocGroup.getPDBName().equals(group.getPDBName())) {
+                                    // If it's a Hydrogen then we check for it's Deuterated brother
+                                    if (!hasDeuteratedEquiv(groupAtom, altLocGroup)) {
+                                        altLocGroup.addAtom(groupAtom);
+                                    }
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+
+    /**
+     * Check to see if an Deuterated atom has a non deuterated brother in the group.
+     *
+     * @param atom         the input atom that is putatively deuterium
+     * @param currentGroup the group the atom is in
+     * @return true if the atom is deuterated and it's hydrogen equive exists.
+     */
+    public static boolean hasNonDeuteratedEquiv(Atom atom, Group currentGroup) {
+        if (atom.getElement() == Element.D && currentGroup.hasAtom(replaceFirstChar(atom.getName(), 'D', 'H'))) {
+            // If it's deuterated and has a non-deuterated brother
+            return true;
+        }
+        return false;
+    }
+
+    /**
+     * Check to see if a Hydrogen has a  Deuterated brother in the group.
+     *
+     * @param atom         the input atom that is putatively hydorgen
+     * @param currentGroup the group the atom is in
+     * @return true if the atom is hydrogen and it's Deuterium equiv exists.
+     */
+    public static boolean hasDeuteratedEquiv(Atom atom, Group currentGroup) {
+        if (atom.getElement() == Element.H && currentGroup.hasAtom(replaceFirstChar(atom.getName(), 'H', 'D'))) {
+            // If it's hydrogen and has a deuterated brother
+            return true;
+        }
+        return false;
+    }
+
+    private static String replaceFirstChar(String name, char c, char d) {
+        if (name.charAt(0) == c) {
+            return name.replaceFirst(String.valueOf(c), String.valueOf(d));
+        }
+        return name;
+    }
+
+    /**
+     * Remove all atoms but the representative atoms (C alphas or phosphates) from the given structure.
+     *
+     * @param structure the structure
+     * @since 5.4.0
+     */
+    public static void reduceToRepresentativeAtoms(Structure structure) {
+        for (int modelIdx = 0; modelIdx < structure.nrModels(); modelIdx++) {
+            for (Chain c : structure.getPolyChains(modelIdx)) {
+                for (Group g : c.getAtomGroups()) {
+                    List<Atom> atoms = g.getAtoms();
+                    if (g.isAminoAcid()) {
+                        atoms.removeIf(a -> !a.getName().equals(CA_ATOM_NAME));
+                    } else if (g.isNucleotide()) {
+                        atoms.removeIf(a -> !a.getName().equals(NUCLEOTIDE_REPRESENTATIVE));
+                    }
+                    // else we keep all other atoms. We are concerned only about aminoacids and nucleotides that make up the bulk of the structures
+                }
+            }
+        }
+    }
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
index d3016e5679..39a294869c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
@@ -28,7 +28,6 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.LinkedList;
@@ -286,10 +285,9 @@ public Structure reduce(Structure s) throws StructureException {
 	 * @return A Structure containing at least the atoms identified by this,
 	 *  or null if no PDB ID is set
 	 * @throws StructureException For errors loading and parsing the structure
-	 * @throws IOException Errors reading the structure from disk
-	 */
+     */
 	@Override
-	public Structure loadStructure(AtomCache cache) throws IOException, StructureException {
+	public Structure loadStructure(AtomCache cache) throws StructureException {
 		String pdb = pdbId;
 		return pdb == null ? null : cache.getStructureForPdbId(pdb);
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
index b41eaae021..7eeabb1d89 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
@@ -519,7 +519,7 @@ public void align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)
 
 		} else if (params.isJoinPlo()) {
 			// this approach by StrComPy (peter lackner):
-			frags = joiner.frag_pairwise_compat(fp, params.getAngleDiff(),
+			frags = FragmentJoiner.frag_pairwise_compat(fp, params.getAngleDiff(),
 					params.getFragCompat(), params.getMaxrefine());
 
 		} else {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
index 2bbb8b6964..c40ee3f76f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
@@ -563,10 +563,8 @@ private void runPairwise() throws ConfigurationException{
 	 * @throws NoSuchMethodException If an error occurs when invoking jmol
 	 * @throws InvocationTargetException If an error occurs when invoking jmol
 	 * @throws IllegalAccessException If an error occurs when invoking jmol
-	 * @throws StructureException
-	 */
-	private void checkWriteFile( AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean dbsearch) throws IOException, ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException, StructureException
-			{
+     */
+	private void checkWriteFile( AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean dbsearch) throws IOException, ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException {
 		String output = null;
 		if ( params.isOutputPDB()){
 			if (! GuiWrapper.isGuiModuleInstalled()) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
index a5ead9a8dd..a9bb046229 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
@@ -1956,13 +1956,13 @@ private static double pToZ(double p) {
 	private static double zByZ(double z1, double z2) {
 		double p1=zToP(z1);
 		double p2=zToP(z2);
-		return(pToZ(p1*p2));
+		return pToZ(p1*p2);
 	}
 
-	protected double zStrAlign(int winSize, int nTrace, double score, int nGaps) {
+	protected static double zStrAlign(int winSize, int nTrace, double score, int nGaps) {
 		double z1=zScore(winSize, nTrace, score);
 		double z2=zGaps(winSize, nTrace, nGaps);
-		return(zByZ(z1, z2));
+		return zByZ(z1, z2);
 	}
 
 	static double zScore(int winSize, int nTrace, double score) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
index 9efaa42e0d..77c57f2a29 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
@@ -28,7 +28,10 @@
 import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
-import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Calc;
+import org.biojava.nbio.structure.Group;
+import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.model.AFP;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AFPAlignmentDisplay;
@@ -905,7 +908,7 @@ protected double getScoreFromDistanceMatrices(int mse1, int mse2,int winSize) {
 	}
 
 	public void nextStep( AFPChain afpChain,
-			Atom[] ca1, Atom[] ca2) throws StructureException{
+			Atom[] ca1, Atom[] ca2) {
 
 
 		if(nBestTrace>0) {
@@ -923,7 +926,7 @@ public void nextStep( AFPChain afpChain,
 	// this part is modified from the original CeCalculator
 	@SuppressWarnings("unused")
 	private void checkBestTraces( AFPChain afpChain,
-			Atom[] ca1, Atom[] ca2) throws StructureException{
+			Atom[] ca1, Atom[] ca2) {
 
 		z=0.0;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java
index f701268c9f..a77e8ad6cf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java
@@ -27,7 +27,6 @@
 package org.biojava.nbio.structure.align.fatcat.calc;
 
 import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.model.AFP;
 import org.biojava.nbio.structure.align.model.AFPChain;
 
@@ -41,8 +40,7 @@ public class AFPOptimizer
 	/**
 	 * optimize the alignment by dynamic programming
 	 */
-	public static void optimizeAln(FatCatParameters params, AFPChain afpChain,Atom[] ca1, Atom[] ca2) throws StructureException
-	{
+	public static void optimizeAln(FatCatParameters params, AFPChain afpChain,Atom[] ca1, Atom[] ca2) {
 
 		int minLen = afpChain.getMinLen();
 		int fragLen = params.getFragLen();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
index 43669368e6..5874fe8acb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
@@ -30,7 +30,6 @@
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Calc;
 import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.geometry.SuperPositions;
 
 import javax.vecmath.Matrix4d;
@@ -197,9 +196,8 @@ public StructureAlignmentOptimizer(int b1, int end1, Atom[] c1, int b2, int end2
 	/** run the optimization
 	 *
 	 * @param maxi maximum nr. of iterations
-	 * @throws StructureException
-	 */
-	public void runOptimization(int maxi) throws StructureException{
+     */
+	public void runOptimization(int maxi) {
 		superimposeBySet();
 		if ( debug)
 			System.err.println("   initial rmsd " + rmsd);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
index 877ee8f4bf..5448091f84 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
@@ -400,13 +400,10 @@ public String toString(){
 
 	public boolean isSignificantResult(){
 		if ( algorithmName.equalsIgnoreCase(CeMain.algorithmName) || algorithmName.equalsIgnoreCase(CeSideChainMain.algorithmName)){
-			if (probability >= 3.5)
-				return true;
+			return probability >= 3.5;
 		} else {
-			if (probability < 0.01)
-				return true;
+			return probability < 0.01;
 		}
-		return false;
 	}
 
 
@@ -1392,8 +1389,7 @@ public int hashCode() {
 	 */
 	@Override
 	public boolean equals(Object obj) {
-		if (this == obj)
-			return true;
+		if (this == obj) return true;
 		if (obj == null)
 			return false;
 		if (getClass() != obj.getClass())
@@ -1409,9 +1405,7 @@ public boolean equals(Object obj) {
 			return false;
 		if (!Arrays.equals(optLen, other.optLen))
 			return false;
-		if (optLength != other.optLength)
-			return false;
-		return true;
+		return optLength == other.optLength;
 	}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
index e3592d0491..01a3ec22a7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
@@ -710,14 +710,13 @@ public void setPDBresnum2(String[] pdbresnum2) {
 	 * @param i2
 	 * @return the number of gaps in this alignment
 	 */
-	private int count_gaps(int[] i1, int[] i2){
+	private static int count_gaps(int[] i1, int[] i2){
 
 		int i0 = i1[0];
 		int j0 = i2[0];
 		int gaps = 0;
 		for (int i =1 ; i<i1.length;i++ ){
-			if ( Math.abs(i1[i]-i0) != 1 ||
-					( Math.abs(i2[i]-j0) != 1)){
+			if (Math.abs(i1[i]-i0) != 1 || Math.abs(i2[i]-j0) != 1){
 				gaps +=1;
 			}
 			i0 = i1[i];
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
index 4766d472d3..520e73d169 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
@@ -115,7 +115,7 @@ public static boolean reduceFragments(List<FragmentPair> fragments, FragmentPair
 
 
 	public JointFragments[] approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst,
-													 StrucAligParameters params) throws StructureException {
+													 StrucAligParameters params) {
 
 		//the final list of joined fragments stores as apairs
 		List<JointFragments> fll = new ArrayList<>();
@@ -213,9 +213,9 @@ public JointFragments[] approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] frag
 
 	}
 
-	private boolean densityCheckOk(Atom[] aa1, Atom[] aa2, List<int[]> idxlist,
-											 int p2i, int p2j, int l2,
-											 double densityCutoff) {
+	private static boolean densityCheckOk(Atom[] aa1, Atom[] aa2, List<int[]> idxlist,
+										  int p2i, int p2j, int l2,
+										  double densityCutoff) {
 		JointFragments ftmp = new JointFragments();
 		ftmp.setIdxlist(idxlist);
 		ftmp.add(p2i,p2j,0,l2);
@@ -245,7 +245,7 @@ private boolean densityCheckOk(Atom[] aa1, Atom[] aa2, List<int[]> idxlist,
 	 * @param ca2subset
 	 * @return a double
 	 */
-	private double getDensity(Atom[] ca1subset, Atom[] ca2subset ) {
+	private static double getDensity(Atom[] ca1subset, Atom[] ca2subset) {
 
 		Atom centroid1 =  Calc.getCentroid(ca1subset);
 		Atom centroid2 = Calc.getCentroid(ca2subset);
@@ -270,7 +270,7 @@ private double getDensity(Atom[] ca1subset, Atom[] ca2subset ) {
 		return Math.min(avd1,avd2);
 	}
 
-	private double rmsCheck(Atom[] a1, Atom[] a2,List<int[]> idxlist, int p2i, int p2j, int l2) throws StructureException {
+	private static double rmsCheck(Atom[] a1, Atom[] a2, List<int[]> idxlist, int p2i, int p2j, int l2) {
 
 		//System.out.println(dd);
 		// check if a joint fragment has low rms ...
@@ -320,7 +320,7 @@ public static double getRMS(Atom[] ca1, Atom[]ca2,JointFragments frag) {
 		return rms;
 	}
 
-	public boolean angleCheckOk(FragmentPair a, FragmentPair b, float distcutoff){
+	public static boolean angleCheckOk(FragmentPair a, FragmentPair b, float distcutoff){
 
 		double dist;
 
@@ -331,7 +331,7 @@ public boolean angleCheckOk(FragmentPair a, FragmentPair b, float distcutoff){
 		return dist <= distcutoff;
 	}
 
-	private boolean distanceCheckOk(FragmentPair a, FragmentPair b, float fragCompatDist){
+	private static boolean distanceCheckOk(FragmentPair a, FragmentPair b, float fragCompatDist){
 
 		double dd ;
 
@@ -357,7 +357,7 @@ private boolean distanceCheckOk(FragmentPair a, FragmentPair b, float fragCompat
 	 * @param maxRefine max number of solutions to keep
 	 * @return JointFragments[]
 	 */
-	public JointFragments[] frag_pairwise_compat(FragmentPair[] fraglst, int angleDiff, float fragCompatDist, int maxRefine  ){
+	public static JointFragments[] frag_pairwise_compat(FragmentPair[] fraglst, int angleDiff, float fragCompatDist, int maxRefine){
 
 
 		FragmentPair[] tmpfidx = new FragmentPair[fraglst.length];
@@ -461,7 +461,7 @@ public void extendFragments(Atom[] ca1, Atom[] ca2 ,JointFragments[] fragments,
 
 	}
 
-	public void extendFragments(Atom[] ca1, Atom[] ca2 , JointFragments fragments, StrucAligParameters params) throws StructureException {
+	public static void extendFragments(Atom[] ca1, Atom[] ca2, JointFragments fragments, StrucAligParameters params) {
 
 		List<int[]> pos = fragments.getIdxlist();
 
@@ -518,7 +518,7 @@ public void extendFragments(Atom[] ca1, Atom[] ca2 , JointFragments fragments, S
 	}
 
 
-	private double testAdd(Atom[] ca1, Atom[] ca2, JointFragments fragments, int pstart1, int pstart2) throws StructureException {
+	private static double testAdd(Atom[] ca1, Atom[] ca2, JointFragments fragments, int pstart1, int pstart2) {
 
 		JointFragments frag = new JointFragments();
 		frag.setIdxlist(fragments.getIdxlist());
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
index 9e2c58402a..a7ff29dc9d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
@@ -386,12 +386,10 @@ public static Map<String,Double> calcIdSimilarity(char[] seq1, char[] seq2, int
 	 * @throws NoSuchMethodException If an error occurs when invoking jmol
 	 * @throws InvocationTargetException If an error occurs when invoking jmol
 	 * @throws IllegalAccessException If an error occurs when invoking jmol
-	 * @throws StructureException
-	 */
+     */
 	public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1,
 													 Atom[] ca2) throws ClassNotFoundException, NoSuchMethodException,
-			InvocationTargetException, IllegalAccessException, StructureException
-	{
+			InvocationTargetException, IllegalAccessException {
 
 		if ( afpChain.getNrEQR() < 1){
 			return GuiWrapper.getAlignedStructure(ca1, ca2);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index 6a2f32b839..173887f1ee 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -220,13 +220,12 @@ public Atom[] getRepresentativeAtoms(StructureIdentifier name) throws IOExceptio
 	 * @param multiModel if true the output Structure will be a multi-model one with one transformId per model,
 	 * if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).
 	 * @return a structure object
-	 * @throws IOException
 	 * @throws StructureException if biassemblyId < 0 or other problems while loading structure
 	 * @author Peter Rose
 	 * @since 3.2
 	 */
 	public Structure getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean multiModel)
-			throws StructureException, IOException {
+			throws StructureException {
 
 		if (bioAssemblyId < 0) {
 			throw new StructureException("bioAssemblyID must be nonnegative: " + pdbId + " bioAssemblyId "
@@ -288,11 +287,10 @@ public Structure getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean
 	 * @param multiModel if true the output Structure will be a multi-model one with one transformId per model,
 	 * if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).
 	 * @return a structure object
-	 * @throws IOException
 	 * @throws StructureException
 	 * @since 4.2
 	 */
-	public Structure getBiologicalAssembly(String pdbId, boolean multiModel) throws StructureException, IOException {
+	public Structure getBiologicalAssembly(String pdbId, boolean multiModel) throws StructureException {
 
 		FileParsingParameters params = getFileParsingParams();
 		boolean prevIsParseBioAssembly = params.isParseBioAssembly();
@@ -345,10 +343,9 @@ public Structure getBiologicalAssembly(String pdbId, boolean multiModel) throws
 	 * if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).
 	 * @return
 	 * @throws StructureException
-	 * @throws IOException
 	 * @since 5.0
 	 */
-	public List<Structure> getBiologicalAssemblies(String pdbId, boolean multiModel) throws StructureException, IOException {
+	public List<Structure> getBiologicalAssemblies(String pdbId, boolean multiModel) throws StructureException {
 
 		List<Structure> assemblies = new ArrayList<>();
 
@@ -508,11 +505,10 @@ public Structure getStructureForDomain(ScopDomain domain) throws IOException, St
 	 * @param scopDatabase
 	 *            A {@link ScopDatabase} to use
 	 * @return a Structure object
-	 * @throws IOException
 	 * @throws StructureException
 	 */
-	public Structure getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase) throws IOException,
-			StructureException {
+	public Structure getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase) throws
+            StructureException {
 		return getStructureForDomain(domain, scopDatabase, false);
 	}
 
@@ -528,11 +524,10 @@ public Structure getStructureForDomain(ScopDomain domain, ScopDatabase scopDatab
 	 *            domain belongs; if set to true, hetero-atoms are included if and only if they are strictly within the
 	 *            definition (residue numbers) of the SCOP domain
 	 * @return a Structure object
-	 * @throws IOException
 	 * @throws StructureException
 	 */
 	public Structure getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase, boolean strictLigandHandling)
-			throws IOException, StructureException {
+			throws StructureException {
 
 		String pdbId = domain.getPdbId();
 		Structure fullStructure = getStructureForPdbId(pdbId);
@@ -785,14 +780,14 @@ public boolean isUseMmtf(){
 	 * Returns a {@link Structure} corresponding to the CATH identifier supplied in {@code structureName}, using the the {@link CathDatabase}
 	 * at {@link CathFactory#getCathDatabase()}.
 	 */
-	public Structure getStructureForCathDomain(StructureName structureName) throws IOException, StructureException {
+	public Structure getStructureForCathDomain(StructureName structureName) throws StructureException {
 		return getStructureForCathDomain(structureName, CathFactory.getCathDatabase());
 	}
 
 	/**
 	 * Returns a {@link Structure} corresponding to the CATH identifier supplied in {@code structureName}, using the specified {@link CathDatabase}.
 	 */
-	public Structure getStructureForCathDomain(StructureName structureName, CathDatabase cathInstall) throws IOException, StructureException {
+	public Structure getStructureForCathDomain(StructureName structureName, CathDatabase cathInstall) throws StructureException {
 
 		CathDomain cathDomain = cathInstall.getDomainByCathId(structureName.getIdentifier());
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
index 493ab25733..02a2581fcc 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
@@ -59,9 +59,9 @@ public class AsaCalculator {
 	 * The default value for number of sphere points to sample.
 	 * See this paper for a nice study on the effect of this parameter: https://f1000research.com/articles/5-189/v1
 	 */
-	public static final int DEFAULT_N_SPHERE_POINTS = 1000;
+//	public static final int DEFAULT_N_SPHERE_POINTS = 1000;
 	public static final double DEFAULT_PROBE_SIZE = 1.4;
-	public static final int DEFAULT_NTHREADS = 1;
+//	public static final int DEFAULT_NTHREADS = 1;
 
 	private static final boolean DEFAULT_USE_SPATIAL_HASHING = true;
 
@@ -458,7 +458,7 @@ Point3d[] getAtomCoords() {
 
 	private List<Contact> calcContacts() {
 		if (atomCoords.length == 0)
-			return new ArrayList<>();
+			return Collections.EMPTY_LIST;//new ArrayList<>();
 		double maxRadius = 0;
 		OptionalDouble optionalDouble = Arrays.stream(radii).max();
 		if (optionalDouble.isPresent())
@@ -480,11 +480,14 @@ private double calcSingleAsa(int i) {
 
 		int n_accessible_point = 0;
 
+		Point3d test_point = new Point3d();
+
 		for (Point3d point: spherePoints){
 			boolean is_accessible = true;
-			Point3d test_point = new Point3d(point.x*radius + atom_i.x,
-					point.y*radius + atom_i.y,
-					point.z*radius + atom_i.z);
+			test_point.set(
+			 point.x*radius + atom_i.x,
+			point.y*radius + atom_i.y,
+			point.z*radius + atom_i.z);
 
 			int[] cycled_indices = new int[n_neighbor];
 			int arind = 0;
@@ -498,9 +501,9 @@ private double calcSingleAsa(int i) {
 			}
 
 			for (int j: cycled_indices) {
-				Point3d atom_j = atomCoords[neighbor_indices[j]];
-				double r = radii[neighbor_indices[j]] + probe;
-				double diff_sq = test_point.distanceSquared(atom_j);
+				int jj = neighbor_indices[j];
+				double r = radii[jj] + probe;
+				double diff_sq = test_point.distanceSquared(atomCoords[jj]);
 				if (diff_sq < r*r) {
 					j_closest_neighbor = j;
 					is_accessible = false;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomIdentifier.java
index edf7bec54e..1226d951b3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomIdentifier.java
@@ -21,6 +21,7 @@
 package org.biojava.nbio.structure.contact;
 
 import java.io.Serializable;
+import java.util.Objects;
 
 public class AtomIdentifier implements Serializable {
 
@@ -63,25 +64,17 @@ public int hashCode() {
 	public boolean equals(Object obj) {
 		if (this == obj)
 			return true;
-		if (obj == null)
+		if (obj==null || getClass() != obj.getClass())
 			return false;
-		if (getClass() != obj.getClass())
-			return false;
-		AtomIdentifier other = (AtomIdentifier) obj;
-		if (chainId == null) {
-			if (other.chainId != null)
-				return false;
-		} else if (!chainId.equals(other.chainId))
-			return false;
-		if (pdbSerial != other.pdbSerial)
-			return false;
-		return true;
+		else {
+			AtomIdentifier other = (AtomIdentifier) obj;
+			return pdbSerial == other.pdbSerial && Objects.equals(chainId, other.chainId);
+		}
 	}
 
 	@Override
 	public String toString() {
-		return " [" + pdbSerial + " - "
-				+ chainId + "]";
+		return " [" + pdbSerial + " - " + chainId + "]";
 	}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java
index 316ed8c1ca..7d293b3045 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java
@@ -179,7 +179,7 @@ public boolean overlaps(BoundingBox o, double cutoff) {
 		return true;
 	}
 
-	private boolean areOverlapping(double imin, double imax, double jmin, double jmax, double cutoff) {
+	private static boolean areOverlapping(double imin, double imax, double jmin, double jmax, double cutoff) {
 
 		Bound[] bounds = {new Bound(0, imin), new Bound(1, imax),
                 new Bound(2, jmin), new Bound(3, jmax)};
@@ -228,7 +228,7 @@ public void translate(Vector3d translation) {
 	 * @param array
 	 * @return
 	 */
-	public double[] getMinMax(double[] array) {
+	public static double[] getMinMax(double[] array) {
 		double[] minmax = new double[2];
 
 		double max = Double.MIN_VALUE;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java
index 52ab85f48d..943daacc38 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java
@@ -30,6 +30,8 @@
 import java.util.Collection;
 import java.util.List;
 
+import static java.util.Collections.EMPTY_LIST;
+
 
 /**
  * A grid to be used for calculating atom contacts through a spatial hashing algorithm.
@@ -417,11 +419,11 @@ public AtomContactSet getContacts() {
 	 */
 	public List<Contact> getIndicesContacts() {
 
-		List<Contact> list = new ArrayList<>();
-
 		// if the 2 sets of atoms are not overlapping they are too far away and no need to calculate anything
 		// this won't apply if there's only one set of atoms (iAtoms), where we would want all-to-all contacts
-		if (noOverlap) return list;
+		if (noOverlap) return EMPTY_LIST;
+
+		List<Contact> list = new ArrayList<>();
 
 
 		for (int xind=0;xind<cells.length;xind++) {
@@ -451,7 +453,7 @@ public List<Contact> getIndicesContacts() {
 			}
 		}
 
-		return list;
+		return list.isEmpty() ? EMPTY_LIST : list;
 	}
 
 	/**
@@ -476,14 +478,16 @@ public boolean hasAnyContact(Collection<Point3d> atoms) {
 				if( x<0 || cells.length<=x) continue;
 				for (int y=yind-1;y<=yind+1;y++) {
 					if( y<0 || cells[x].length<=y ) continue;
+
+					GridCell[] cxy = cells[x][y];
+
 					for (int z=zind-1;z<=zind+1;z++) {
-						if( z<0 || cells[x][y].length<=z ) continue;
+						if( z<0 || cxy.length<=z ) continue;
 
-						GridCell cell = cells[x][y][z];
 						// Check for contacts in this cell
-						if(cell != null && cell.hasContactToAtom(iAtoms, jAtoms, atom, cutoff)) {
+						GridCell cell = cxy[z];
+						if(cell != null && cell.hasContactToAtom(iAtoms, jAtoms, atom, cutoff))
 							return true;
-						}
 					}
 				}
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java
index ce2db4a3f4..17a318e5b9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java
@@ -79,9 +79,9 @@ public static List<Domain> suggestDomains(Structure s) {
      */
 	public static List<Domain> suggestDomains(Atom[] ca) {
 
-		GetDistanceMatrix distMaxCalculator = new GetDistanceMatrix();
+		//GetDistanceMatrix distMaxCalculator = new GetDistanceMatrix();
 
-		PDPDistanceMatrix pdpMatrix = distMaxCalculator.getDistanceMatrix(ca);
+		PDPDistanceMatrix pdpMatrix = GetDistanceMatrix.getDistanceMatrix(ca);
 
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java
index 6ca44efaa1..7c45030995 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java
@@ -23,7 +23,6 @@
 import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 
-import java.io.IOException;
 import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -71,8 +70,7 @@ public String toString() {
 	}
 
 	@Override
-	public Structure loadStructure(AtomCache cache) throws StructureException,
-			IOException {
+	public Structure loadStructure(AtomCache cache) throws StructureException {
 		return canonical.loadStructure(cache);
 	}
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java
index cdabc26922..149bf65430 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java
@@ -38,7 +38,7 @@ public class GetDistanceMatrix {
      *
      * @param protein
      */
-    public PDPDistanceMatrix getDistanceMatrix(final Atom[] protein) {
+    public static PDPDistanceMatrix getDistanceMatrix(final Atom[] protein) {
         int n = protein.length;
         int[][] dist = new int[n + 3][n + 3];
         int i, j;
@@ -147,7 +147,7 @@ else if (i > 2 && j < n - 2) {
     }
 
 
-    private Atom getCBeta(Group g1) {
+    private static Atom getCBeta(Group g1) {
         Atom cb;
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java
index d09a906343..ae2d296f85 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java
@@ -22,7 +22,6 @@
 import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 
-import java.io.IOException;
 import java.io.Serializable;
 import java.util.HashSet;
 import java.util.List;
@@ -454,8 +453,7 @@ public Structure reduce(Structure input) throws StructureException {
 	}
 
 	@Override
-	public Structure loadStructure(AtomCache cache) throws StructureException,
-			IOException {
+	public Structure loadStructure(AtomCache cache) throws StructureException {
 		return cache.getStructureForPdbId(pdbId);
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
index 1feaa533a9..f70fde2f6f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
@@ -28,8 +28,6 @@
 
 import java.io.IOException;
 import java.lang.ref.SoftReference;
-import java.util.Collections;
-import java.util.HashMap;
 import java.util.Iterator;
 import java.util.Map;
 import java.util.Map.Entry;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
index 214d22fe7b..c216bace32 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
@@ -355,7 +355,7 @@ private boolean domainsAvailable() {
 				return false;
 
 			// Re-download old copies of "latest"
-			if(updateFrequency != null && requestedVersion == DEFAULT_VERSION ) {
+			if(updateFrequency != null && requestedVersion.equals(DEFAULT_VERSION)) {
 				long mod = f.lastModified();
 				// Time of last update
 				Date lastUpdate = new Date();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java
index bedb4d0673..6c1301e9f0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java
@@ -168,7 +168,7 @@ private static String getLocalFileName(){
 	 */
 	private void loadAllChemComps() throws IOException {
 		String fileName = getLocalFileName();
-		logger.debug("Loading " + fileName);
+		logger.debug("Loading {}", fileName);
 		InputStreamProvider isp = new InputStreamProvider();
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java
index c964722053..d04eeb3ba5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.java
@@ -131,13 +131,13 @@ public class ChemCompTools {
 
 	}
 
-	public static Character getAminoOneLetter(String chemCompId){
-		return  AMINO_ACID_LOOKUP_3TO1.get(chemCompId);
+	public static char getAminoOneLetter(String chemCompId){
+		return  AMINO_ACID_LOOKUP_3TO1.getOrDefault(chemCompId, (char)0);
 	}
 
 
-	public static Character getDNAOneLetter(String chemCompId){
-		return  DNA_LOOKUP_2TO1.get(chemCompId) ;
+	public static char getDNAOneLetter(String chemCompId){
+		return DNA_LOOKUP_2TO1.getOrDefault(chemCompId, (char)0) ;
 	}
 
 	public static String getAminoThreeLetter(Character c){
@@ -195,10 +195,7 @@ public static boolean isStandardChemComp(ChemComp cc){
 
 
 	private static boolean performRNACheck(ChemComp cc) {
-		if (cc.getId().length() == 1)
-			return true;
-		else
-			return false;
+		return cc.getId().length() == 1;
 	}
 
 
@@ -206,25 +203,19 @@ private static boolean performDNACheck(ChemComp cc) {
 		if ( cc.getId().equals(UNKNOWN_NUCLEOTIDE.toString()))
 			return false;
 
-		Character c = getDNAOneLetter(cc.getId());
-		if ( c==null){
-			// we did not find it in the list of standard nucleotides
-			return false;
-		}
-		return true;
+		char c = getDNAOneLetter(cc.getId());
+		// we did not find it in the list of standard nucleotides?
+		return c != 0;
 	}
 
 
 	private static boolean performPeptideCheck(ChemComp cc, String one) {
-		if (one.equals(UNKNOWN_ONE_LETTER_CODE.toString())) {
+		if (one.equals(UNKNOWN_ONE_LETTER_CODE.toString()))
 			return false;
-		}
-		Character c =  getAminoOneLetter(cc.getId());
-		if ( c==null){
-			// we did not find it in the list of standard aminos
-			return false;
-		}
-		return true;
+
+		char c =  getAminoOneLetter(cc.getId());
+		// we did not find it in the list of standard aminos?
+		return c != 0;
 	}
 
 
@@ -245,16 +236,12 @@ public static Character getOneLetterCode(ChemComp cc, ChemicalComponentDictionar
 		}
 		PolymerType poly = cc.getPolymerType();
 		if (( poly == PolymerType.peptide) || ( poly == PolymerType.dpeptide)){
-			Character c = getAminoOneLetter(parent.getId());
-			if ( c == null)
-				c = UNKNOWN_ONE_LETTER_CODE;
-			return c;
+			char c = getAminoOneLetter(parent.getId());
+			return c == 0 ? UNKNOWN_ONE_LETTER_CODE : Character.valueOf(c);
 		}
 		if ( poly == PolymerType.dna){
-			Character c = getDNAOneLetter(parent.getId());
-			if (c == null)
-				c = UNKNOWN_NUCLEOTIDE;
-			return c;
+			char c = getDNAOneLetter(parent.getId());
+			return c == 0 ? UNKNOWN_NUCLEOTIDE : Character.valueOf(c);
 
 		}
 		return cc.getMon_nstd_parent_comp_id().charAt(0);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemComp.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemComp.java
index f30e3a6ff8..292c63df3a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemComp.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemComp.java
@@ -27,6 +27,7 @@
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Objects;
 
 /** A definition for a Chemical Component, as maintained by the wwPDB. For access to all definitions,
  * please download the components.cif.gz file from the wwPDB website.
@@ -111,10 +112,7 @@ public String toString(){
 
 	public boolean hasParent(){
 		String pid = mon_nstd_parent_comp_id;
-		if ((pid != null ) && (! pid.equals("?"))){
-			return true;
-		}
-		return false;
+		return (pid != null) && (!pid.equals("?"));
 	}
 
 	public boolean isStandard(){
@@ -584,12 +582,7 @@ public boolean equals(Object obj) {
 				return false;
 		} else if (!three_letter_code.equals(other.three_letter_code))
 			return false;
-		if (type == null) {
-			if (other.type != null)
-				return false;
-		} else if (!type.equals(other.type))
-			return false;
-		return true;
+		return Objects.equals(type, other.type);
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
index d991f174ca..3b4121cbc8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
@@ -26,7 +26,6 @@
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
 import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
 import org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools;
-import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
 import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
 import org.biojava.nbio.structure.secstruc.DSSPParser;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java
index 794da93911..723c21b3a6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java
@@ -26,7 +26,6 @@
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlRootElement;
-import java.io.IOException;
 import java.io.Serializable;
 import java.util.HashSet;
 import java.util.List;
@@ -235,8 +234,7 @@ public Structure reduce(Structure input) throws StructureException {
 	}
 
 	@Override
-	public Structure loadStructure(AtomCache cache) throws StructureException,
-	IOException {
+	public Structure loadStructure(AtomCache cache) throws StructureException {
 		return cache.getStructureForPdbId(pdbId);
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
index 17d32cc224..05736aeb62 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
@@ -114,7 +114,7 @@ public static List<SecStrucElement> getSecStrucElements(Structure s) {
 
 				if (count > 0) {
 					// If chain and type are equal increment counter
-					if (ss.type == type && chainId == g.getChainId()) {
+					if (ss.type == type && chainId.equals(g.getChainId())) {
 						previous = g.getResidueNumber();
 						count++;
 						continue;
@@ -185,7 +185,7 @@ public static List<SecStrucElement> getSecStrucElements(List<Group> groups) {
 
 				if (count > 0) {
 					// If chain and type are equal increment counter
-					if (ss.type == type && chainId == g.getChainId()) {
+					if (ss.type == type && chainId.equals(g.getChainId())) {
 						previous = g.getResidueNumber();
 						count++;
 						continue;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java
index 276944fa40..a9ed913875 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java
@@ -148,7 +148,7 @@ private void combineWithTranslation(Matrix4d rotation) {
 		rotation.mul(rotation, centroidInverse);
 	}
 
-	private Rotation createSymmetryOperation(List<Integer> permutation, Matrix4d transformation, AxisAngle4d axisAngle, int fold, QuatSymmetryScores scores) {
+	private static Rotation createSymmetryOperation(List<Integer> permutation, Matrix4d transformation, AxisAngle4d axisAngle, int fold, QuatSymmetryScores scores) {
 		Rotation s = new Rotation();
 		s.setPermutation(new ArrayList<>(permutation));
 		s.setTransformation(new Matrix4d(transformation));
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
index df9f4c29f8..e591fae1e0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
@@ -365,7 +365,7 @@ private List<Integer> getPermutation(Matrix4d transformation) {
 			int permutation = -1;
 			double minDistSq = Double.MAX_VALUE;
 			for (int j = 0; j < centers.size(); j++) {
-				if (seqClusterId.get(i) == seqClusterId.get(j)) {
+				if (seqClusterId.get(i).equals(seqClusterId.get(j))) {
 					if (!used[j]) {
 						double dSq = tCenter.distanceSquared(centers.get(j));
 						if (dSq < minDistSq && dSq <= rmsdThresholdSq) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
index da2199b7f2..56b1576aba 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
@@ -342,9 +342,9 @@ private static List<QuatSymmetryResults> calcLocalSymmetriesCluster(Stoichiometr
 							map(QuatSymmetryResults::getStoichiometry).
 								reduce(Stoichiometry::combineWith).get();
 
-				if (groupComposition.numberOfComponents() < 2) {
+				if (groupComposition.numberOfComponents() < 2)
 					continue;
-				}
+
 				//check if grouped clusters also have symmetry
 				QuatSymmetryResults localResult = calcQuatSymmetry(groupComposition,symmParams);
 
@@ -353,10 +353,11 @@ private static List<QuatSymmetryResults> calcLocalSymmetriesCluster(Stoichiometr
 					clusterSymmetries.add(localResult);
 					// find subunit ids in this cluster list
 					Set<Integer> knownResult = new HashSet<>();
-					for (SubunitCluster cluster: groupComposition.getClusters()) {
-						int i = nontrivialComposition.getClusters().indexOf(cluster);
-						knownResult.addAll(clusterIdToSubunitIds.get(i));
-					}
+					List<SubunitCluster> nc = nontrivialComposition.getClusters();
+					for (SubunitCluster cluster: groupComposition.getClusters())
+						knownResult.addAll(clusterIdToSubunitIds.get(nc.indexOf(cluster)));
+					if (knownResult.isEmpty())
+						knownResult = Collections.EMPTY_SET;
 					// since symmetry is found,
 					// do not try graph decomposition of this set of subunits later
 					knownCombinations.add(knownResult);
@@ -374,12 +375,13 @@ private static List<QuatSymmetryResults> calcLocalSymmetriesGraph(final Stoichio
 	                                                                  Set<Set<Integer>> knownCombinations,
 	                                                                  Graph<Integer, DefaultEdge> graph) {
 
-		List<QuatSymmetryResults> localSymmetries = new ArrayList<>();
-
 		// do not go any deeper into recursion if over the time/combinations limit
 		if(symmParams.isLocalLimitsExceeded(knownCombinations)) {
-			return localSymmetries;
+			return Collections.EMPTY_LIST;
 		}
+
+		List<QuatSymmetryResults> localSymmetries = new ArrayList<>();
+
 		// extract components of a (sub-)graph
 		CliqueMinimalSeparatorDecomposition<Integer, DefaultEdge> cmsd =
 				new CliqueMinimalSeparatorDecomposition<>(graph);
@@ -402,20 +404,16 @@ private static List<QuatSymmetryResults> calcLocalSymmetriesGraph(final Stoichio
 			Stoichiometry localStoichiometry =
 					trimSubunitClusters(globalComposition, allSubunitClusterIds, clusterIdToSubunitIds, usedSubunitIds);
 
-			if (localStoichiometry.numberOfComponents()==0) {
+			if (localStoichiometry.numberOfComponents()==0)
 				continue;
-			}
+
 
 			//NB: usedSubunitIds might have changed when trimming clusters
 			// if a subunit belongs to a cluster with no other subunits,
 			// it is removed inside trimSubunitClusters
 			Set<Integer> usedSubunitIdsSet = new HashSet<>(usedSubunitIds);
-			if(!graphComponent.equals(usedSubunitIdsSet)) {
-				if(knownCombinations.contains(usedSubunitIdsSet)) {
-					continue;
-				} else {
-					knownCombinations.add(usedSubunitIdsSet);
-				}
+			if (!graphComponent.equals(usedSubunitIdsSet) && !knownCombinations.add(usedSubunitIdsSet)) {
+				continue;
 			}
 
 			QuatSymmetryResults localResult = calcQuatSymmetry(localStoichiometry,symmParams);
@@ -434,10 +432,9 @@ private static List<QuatSymmetryResults> calcLocalSymmetriesGraph(final Stoichio
 				// try removing subunits one by one and decompose the sub-graph recursively
 				Set<Integer> prunedGraphVertices = new HashSet<>(usedSubunitIds);
 				prunedGraphVertices.remove(removeSubunitId);
-				if (knownCombinations.contains(prunedGraphVertices)) {
+				if (!knownCombinations.add(prunedGraphVertices))
 					continue;
-				}
-				knownCombinations.add(prunedGraphVertices);
+
 
 				Graph<Integer, DefaultEdge> subGraph = new AsSubgraph<>(graph,prunedGraphVertices);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
index 07cbdc1067..19b136c2db 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
@@ -324,7 +324,7 @@ private boolean isAllowedPermutation(List<Integer> permutation) {
 		int selfaligned = 0;
 		for (int i = 0; i < permutation.size(); i++) {
 			int j = permutation.get(i);
-			if ( seqClusterId.get(i) != seqClusterId.get(j)) {
+			if (!seqClusterId.get(i).equals(seqClusterId.get(j))) {
 				return false;
 			}
 			if(i == j ) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
index 6e3c2cdc1b..650ba181c8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
@@ -171,7 +171,7 @@ private boolean isAllowedPermuation(List<Integer> permutation) {
 		List<Integer> seqClusterId = subunits.getClusterIds();
 		for (int i = 0; i < permutation.size(); i++) {
 			int j = permutation.get(i);
-			if (seqClusterId.get(i) != seqClusterId.get(j)) {
+			if (!seqClusterId.get(i).equals(seqClusterId.get(j))) {
 				return false;
 			}
 		}

From 5607faa1ee7ee22c5424557f462c9688ac1481ae Mon Sep 17 00:00:00 2001
From: me <seh@internet.earth>
Date: Sun, 8 Mar 2020 17:25:03 -0400
Subject: [PATCH 13/18] central URL cache using OKHttp3, partially working

---
 biojava-core/pom.xml                          |   9 +
 .../nbio/core/sequence/ProteinSequence.java   |   3 +-
 .../nbio/core/util/FileDownloadUtils.java     | 256 ++++++++++++------
 .../biojava/nbio/structure/StructureIO.java   |   3 +-
 .../align/MultiThreadedDBSearch.java          |  19 +-
 .../nbio/structure/align/util/AtomCache.java  |  11 +-
 .../align/util/URLConnectionTools.java        |  41 +--
 .../nbio/structure/io/LocalPDBDirectory.java  | 196 +++++++-------
 8 files changed, 291 insertions(+), 247 deletions(-)

diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index b465a40a36..a7aa8be1e4 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -62,6 +62,15 @@
     		<groupId>org.apache.logging.log4j</groupId>
     		<artifactId>log4j-core</artifactId>
   		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/com.squareup.okhttp3/okhttp -->
+		<dependency>
+			<!-- v3 doesnt have the huge kotlin dep -->
+			<groupId>com.squareup.okhttp3</groupId>
+			<artifactId>okhttp</artifactId>
+			<version>3.14.7</version>
+		</dependency>
+
 	</dependencies>
 </project>
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
index 94016b7a81..a2d5f06029 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
@@ -35,6 +35,7 @@
 import org.biojava.nbio.core.sequence.template.AbstractSequence;
 import org.biojava.nbio.core.sequence.template.CompoundSet;
 import org.biojava.nbio.core.sequence.template.ProxySequenceReader;
+import org.biojava.nbio.core.util.FileDownloadUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -158,7 +159,7 @@ private DNASequence getRawParentSequence(String accessId) throws IOException {
 
 		logger.trace("Getting parent DNA sequence from URL: {}", url.toString());
 
-		InputStream is = url.openConnection().getInputStream();
+		InputStream is = FileDownloadUtils.downloadStream(url, 60000); //url.openConnection().getInputStream();
 
 		FastaReader<DNASequence, NucleotideCompound> parentReader
 				= new FastaReader<>(is,
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
index a0caca5964..31f284209e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
@@ -21,22 +21,17 @@
  */
 package org.biojava.nbio.core.util;
 
+import okhttp3.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.net.HttpURLConnection;
-import java.net.SocketTimeoutException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.nio.channels.Channels;
+import java.io.*;
+import java.net.*;
 import java.nio.channels.FileChannel;
-import java.nio.channels.ReadableByteChannel;
 import java.nio.file.*;
 import java.nio.file.attribute.BasicFileAttributes;
+import java.util.concurrent.TimeUnit;
+import java.util.zip.GZIPInputStream;
 
 public class FileDownloadUtils {
 
@@ -66,73 +61,35 @@ public static void copy(File src, File dst) throws IOException {
 
 	public static String getFileExtension(File f) {
 		String fileName = f.getName();
-		String ext;
-		int mid = fileName.lastIndexOf('.');
-		ext = fileName.substring(mid + 1);
-		return ext;
+		return fileName.substring(fileName.lastIndexOf('.') + 1);
 	}
 
 	public static String getFilePrefix(File f) {
 		String fileName = f.getName();
-		String fname;
-
-		int mid = fileName.indexOf('.');
-		fname = fileName.substring(0, mid);
-
-		return fname;
+		return fileName.substring(0, fileName.indexOf('.'));
 	}
 
-	/**
-	 * Download the content provided at URL url and store the result to a local
-	 * file, using a temp file to cache the content in case something goes wrong
-	 * in download
-	 *
-	 * @param url
-	 * @param destination
-	 * @throws IOException
-	 */
-	public static void downloadFile(URL url, File destination) throws IOException {
-		int count = 0;
-		int maxTries = 10;
-		int timeout = 60000; //60 sec
-
-		File tempFile = File.createTempFile(getFilePrefix(destination), "." + getFileExtension(destination));
-
-		// Took following recipe from stackoverflow:
-		// http://stackoverflow.com/questions/921262/how-to-download-and-save-a-file-from-internet-using-java
-		// It seems to be the most efficient way to transfer a file
-		// See: http://docs.oracle.com/javase/7/docs/api/java/nio/channels/FileChannel.html
-		ReadableByteChannel rbc = null;
-		FileOutputStream fos = null;
-		while (true) {
-			try {
-				URLConnection connection = prepareURLConnection(url.toString(), timeout);
-				connection.connect();
-
-				rbc = Channels.newChannel(connection.getInputStream());
-				fos = new FileOutputStream(tempFile);
-				fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
-				break;
-			} catch (SocketTimeoutException e) {
-				if (++count == maxTries) throw e;
-			} finally {
-				if (rbc != null) {
-					rbc.close();
-				}
-				if (fos != null) {
-					fos.close();
-				}
-			}
-		}
-
-		logger.debug("Copying temp file {} to final location {}", tempFile, destination);
-		copy(tempFile, destination);
+	static final OkHttpClient.Builder clients;
+	static {
+		/** https://square.github.io/okhttp/recipes/#response-caching-kt-java */
+		int cacheSize = 512 * 1024 * 1024; //512m
+		OkHttpClient.Builder bb = new OkHttpClient.Builder();
+		bb.followRedirects(true);
+		bb.followSslRedirects(true);
 
-		// delete the tmp file
-		tempFile.delete();
+//		try {
+			File cacheDir = Paths.get(System.getProperty("java.io.tmpdir"), "biojava").toFile();
+			cacheDir.mkdirs();
+			Cache cache = new Cache(cacheDir, cacheSize);
+			bb.cache(cache);
 
+//		} catch (IOException e) {
+//			e.printStackTrace();
+//		}
+		clients = bb;
 	}
 
+
 	/**
 	 * Converts path to Unix convention and adds a terminating slash if it was
 	 * omitted
@@ -247,36 +204,163 @@ public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IO
 
 	        @Override
 	        public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOException {
-	            if (e != null) {
+	            if (e != null)
 	                throw e;
-	            }
 	            Files.delete(dir);
 	            return FileVisitResult.CONTINUE;
 	        }
 	    });
 	}
+
 	/**
-	 * Recursively delete a folder & contents
-	 *
-	 * @param dir directory to delete
+	 * Open a URL and return an InputStream to it
+	 * if acceptGzipEncoding == true, use GZIPEncoding to
+	 * compress communication.
+	 * <p>
+	 * The caller is responsible to close the returned InputStream not to cause
+	 * resource leaks.
+	 * @param url the input URL to be read
+	 * @param timeoutMS
+	 * @return an {@link InputStream} of response
+	 * @throws IOException due to an error opening the URL
 	 */
-	public static void deleteDirectory(String dir) throws IOException {
-		deleteDirectory(Paths.get(dir));
+	public static InputStream downloadStream(URL url, int timeoutMS) throws IOException {
+//		InputStream inStream;
+//		URLConnection huc = URLConnectionTools.openURLConnection(url,timeout);
+//
+//		if ( acceptGzipEncoding) huc.setRequestProperty("Accept-Encoding", "gzip");
+//
+//		String contentEncoding = huc.getContentEncoding();
+//
+//		inStream = huc.getInputStream();
+
+		OkHttpClient client = clients.build(); //TODO ThreadLocal
+
+		Call c = client.newCall(new Request.Builder().url(url).cacheControl(CacheControl.FORCE_CACHE).build());
+
+		c.timeout().deadline(timeoutMS, TimeUnit.MILLISECONDS);
+		try (Response r = c.execute()) {
+			if (!r.isSuccessful()) {
+				//throw new IOException("Unexpected code " + r);
+				return new ByteArrayInputStream(new byte[] { } ); //HACK
+			}
+
+			ResponseBody b = r.body();
+
+			InputStream inStream = new ByteArrayInputStream(b.bytes()); //b.byteStream();
+
+			if (b.contentType().toString().contains("gzip")) {
+				return new GZIPInputStream(inStream);
+			}
+
+//			if (acceptGzipEncoding) {
+////				if (contentEncoding != null) {
+////					if (contentEncoding.contains("gzip")) {
+
+////					}
+////				}
+//			}
+
+			return inStream;
+		}
+
+
 	}
 
+	/**
+	 * Download the content provided at URL url and store the result to a local
+	 * file, using a temp file to cache the content in case something goes wrong
+	 * in download
+	 *
+	 * @param url
+	 * @param destination
+	 * @throws IOException
+	 */
+	public static void downloadFile(URL url, File destination) throws IOException {
+
+
+		OkHttpClient client = clients.build(); //TODO ThreadLocal
+
+		try (Response r = client.newCall(new Request.Builder().url(url).build()).execute()) {
+			if (!r.isSuccessful()) {
+				//throw new IOException("Unexpected code " + r);
+				return;
+			}
+
+			ResponseBody b = r.body();
+
+			FileChannel dst = new FileOutputStream(destination).getChannel();
+			dst.transferFrom(b.source(), 0, b.contentLength());
+
+			System.out.println("Response 1 response:          " + r);
+			System.out.println("Response 1 cache response:    " + r.cacheResponse());
+			System.out.println("Response 1 network response:  " + r.networkResponse());
+		}
+
+
+//		int count = 0;
+//		int maxTries = 10;
+//		int timeout = 60000; //60 sec
+//
+//		File tempFile = File.createTempFile(getFilePrefix(destination), "." + getFileExtension(destination));
+//
+//		// Took following recipe from stackoverflow:
+//		// http://stackoverflow.com/questions/921262/how-to-download-and-save-a-file-from-internet-using-java
+//		// It seems to be the most efficient way to transfer a file
+//		// See: http://docs.oracle.com/javase/7/docs/api/java/nio/channels/FileChannel.html
+//		ReadableByteChannel rbc = null;
+//		FileOutputStream fos = null;
+//		while (true) {
+//			try {
+//				URLConnection connection = prepareURLConnection(url.toString(), timeout);
+//				connection.connect();
+//
+//				rbc = Channels.newChannel(connection.getInputStream());
+//				fos = new FileOutputStream(tempFile);
+//				fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
+//				break;
+//			} catch (SocketTimeoutException e) {
+//				if (++count == maxTries) throw e;
+//			} finally {
+//				if (rbc != null) {
+//					rbc.close();
+//				}
+//				if (fos != null) {
+//					fos.close();
+//				}
+//			}
+//		}
+//
+//		logger.debug("Copying temp file {} to final location {}", tempFile, destination);
+//		copy(tempFile, destination);
+//
+//		// delete the tmp file
+//		tempFile.delete();
 
-	public static void main(String[] args) {
-		String url;
-		url = "http://scop.mrc-lmb.cam.ac.uk/scop/parse/";
-		System.out.format("%s\t%s%n", ping(url, 200), url);
-		url = "http://scop.mrc-lmb.cam.ac.uk/scop/parse/foo";
-		System.out.format("%s\t%s%n", ping(url, 200), url);
-		url = "http://scopzzz.mrc-lmb.cam.ac.uk/scop/parse/";
-		System.out.format("%s\t%s%n", ping(url, 200), url);
-		url = "scop.mrc-lmb.cam.ac.uk";
-		System.out.format("%s\t%s%n", ping(url, 200), url);
-		url = "http://scop.mrc-lmb.cam.ac.uk";
-		System.out.format("%s\t%s%n", ping(url, 200), url);
 	}
 
+//	/**
+//	 * Recursively delete a folder & contents
+//	 *
+//	 * @param dir directory to delete
+//	 */
+//	public static void deleteDirectory(String dir) throws IOException {
+//		deleteDirectory(Paths.get(dir));
+//	}
+//
+//
+//	public static void main(String[] args) {
+//		String url;
+//		url = "http://scop.mrc-lmb.cam.ac.uk/scop/parse/";
+//		System.out.format("%s\t%s%n", ping(url, 200), url);
+//		url = "http://scop.mrc-lmb.cam.ac.uk/scop/parse/foo";
+//		System.out.format("%s\t%s%n", ping(url, 200), url);
+//		url = "http://scopzzz.mrc-lmb.cam.ac.uk/scop/parse/";
+//		System.out.format("%s\t%s%n", ping(url, 200), url);
+//		url = "scop.mrc-lmb.cam.ac.uk";
+//		System.out.format("%s\t%s%n", ping(url, 200), url);
+//		url = "http://scop.mrc-lmb.cam.ac.uk";
+//		System.out.format("%s\t%s%n", ping(url, 200), url);
+//	}
+
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
index a04deed335..6ba01d7e48 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
@@ -154,9 +154,8 @@ public static Structure getBiologicalAssembly(String pdbId, boolean multiModel)
 	 * @param pdbId
 	 * @return a Structure object or null if that assembly is not available
 	 * @throws StructureException
-	 * @throws IOException
 	 */
-	public static Structure getBiologicalAssembly(String pdbId) throws IOException, StructureException{
+	public static Structure getBiologicalAssembly(String pdbId) throws StructureException{
 		return getBiologicalAssembly(pdbId, AtomCache.DEFAULT_BIOASSEMBLY_STYLE);
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java
index 7312fe5144..6dcf3165c3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java
@@ -388,8 +388,7 @@ private void checkLocalFiles() throws IOException, StructureException {
 		}
 
 		if ( domainProvider instanceof RemoteDomainProvider ) {
-			RemoteDomainProvider remoteP = (RemoteDomainProvider) domainProvider;
-			remoteP.flushCache();
+			((RemoteDomainProvider) domainProvider).flushCache();
 		}
 
 		logger.info("done checking local files...");
@@ -397,15 +396,15 @@ private void checkLocalFiles() throws IOException, StructureException {
 	}
 
 
-	private void checkFile(String repre) throws IOException, StructureException {
+	@Deprecated private void checkFile(String repre) throws IOException, StructureException {
 
-		StructureName name = new StructureName(repre);
-
-		PDBFileReader reader = new PDBFileReader();
-		reader.setFetchBehavior(FetchBehavior.FETCH_REMEDIATED);
-		reader.setPath(cache.getPath());
-		reader.setFileParsingParameters(cache.getFileParsingParams());
-		reader.prefetchStructure(name.getPdbId());
+//		StructureName name = new StructureName(repre);
+//
+//		PDBFileReader reader = new PDBFileReader();
+//		reader.setFetchBehavior(FetchBehavior.FETCH_REMEDIATED);
+//		reader.setPath(cache.getPath());
+//		reader.setFileParsingParameters(cache.getFileParsingParams());
+//		reader.prefetchStructure(name.getPdbId());
 	}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index 173887f1ee..10c31f0b63 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -624,8 +624,7 @@ public Structure getStructureForDomain(String scopId) throws IOException, Struct
 	 */
 	public Structure getStructureForDomain(String scopId, ScopDatabase scopDatabase) throws IOException,
 			StructureException {
-		ScopDomain domain = scopDatabase.getDomainByScopID(scopId);
-		return getStructureForDomain(domain, scopDatabase);
+		return getStructureForDomain(scopDatabase.getDomainByScopID(scopId), scopDatabase);
 	}
 
 	/**
@@ -643,11 +642,9 @@ public void notifyShutdown() {
 
 		// todo: use a SCOP implementation that is backed by SerializableCache
 		ScopDatabase scopInstallation = ScopFactory.getSCOP();
-		if (scopInstallation != null) {
-			if (scopInstallation instanceof CachedRemoteScopInstallation) {
-				CachedRemoteScopInstallation cacheScop = (CachedRemoteScopInstallation) scopInstallation;
-				cacheScop.flushCache();
-			}
+		if (scopInstallation instanceof CachedRemoteScopInstallation) {
+			CachedRemoteScopInstallation cacheScop = (CachedRemoteScopInstallation) scopInstallation;
+			cacheScop.flushCache();
 		}
 
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java
index 8def86cfad..837a2e6b13 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java
@@ -27,13 +27,13 @@
 
 package org.biojava.nbio.structure.align.util;
 
+import org.biojava.nbio.core.util.FileDownloadUtils;
+
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStreamWriter;
 import java.net.URL;
 import java.net.URLConnection;
-import java.util.zip.GZIPInputStream;
-
 
 
 /**
@@ -90,7 +90,7 @@ public static URLConnection openURLConnection(URL url) throws IOException {
 	 */
 	public static InputStream getInputStream(URL url, int timeout) throws IOException
 	{
-		return getInputStream(url,true, timeout);
+		return FileDownloadUtils.downloadStream(url, timeout);
 	}
 
 
@@ -106,40 +106,7 @@ public static InputStream getInputStream(URL url, int timeout) throws IOExceptio
 	 */
 	public static InputStream getInputStream(URL url) throws IOException
 	{
-		return getInputStream(url,true, DEFAULT_CONNECTION_TIMEOUT);
-	}
-
-	/**
-	 * Open a URL and return an InputStream to it
-	 * if acceptGzipEncoding == true, use GZIPEncoding to
-	 * compress communication.
-	 * <p>
-	 * The caller is responsible to close the returned InputStream not to cause
-	 * resource leaks.
-	 * @param url the input URL to be read
-	 * @param acceptGzipEncoding whether to accept Gzip encoding
-	 * @param timeout
-	 * @return an {@link InputStream} of response
-	 * @throws IOException due to an error opening the URL
-	 */
-	public static InputStream getInputStream(URL url, boolean acceptGzipEncoding, int timeout) throws IOException {
-		InputStream inStream;
-		URLConnection huc = URLConnectionTools.openURLConnection(url,timeout);
-
-		if ( acceptGzipEncoding) huc.setRequestProperty("Accept-Encoding", "gzip");
-
-		String contentEncoding = huc.getContentEncoding();
-
-		inStream = huc.getInputStream();
-
-		if (contentEncoding != null) {
-			if (contentEncoding.contains("gzip")) {
-				inStream = new GZIPInputStream(inStream);
-			}
-		}
-
-		return inStream;
-
+		return FileDownloadUtils.downloadStream(url, DEFAULT_CONNECTION_TIMEOUT);
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
index 1504cf8f1d..dac28d7c86 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
@@ -51,7 +51,7 @@
  * @author Spencer Bliven
  *
  */
-public abstract class LocalPDBDirectory implements StructureIOFile {
+@Deprecated public abstract class LocalPDBDirectory implements StructureIOFile {
 
 	private static final Logger logger = LoggerFactory.getLogger(LocalPDBDirectory.class);
 
@@ -349,37 +349,27 @@ protected InputStream getInputStream(String pdbId) throws IOException{
 			throw new IOException("The provided ID does not look like a PDB ID : " + pdbId);
 
 		// Check existing
-		File file = downloadStructure(pdbId);
-
-		if(!file.exists()) {
-			throw new IOException("Structure "+pdbId+" not found and unable to download.");
-		}
-
-		InputStreamProvider isp = new InputStreamProvider();
-
-		InputStream inputStream = isp.getInputStream(file);
-
-		return inputStream;
+		return downloadStructure(pdbId);
 	}
 
-	/**
-	 * Download a structure, but don't parse it yet or store it in memory.
-	 *
-	 * Used to pre-fetch large numbers of structures.
-	 * @param pdbId
-	 * @throws IOException
-	 */
-	public void prefetchStructure(String pdbId) throws IOException {
-		if ( pdbId.length() != 4)
-			throw new IOException("The provided ID does not look like a PDB ID : " + pdbId);
-
-		// Check existing
-		File file = downloadStructure(pdbId);
-
-		if(!file.exists()) {
-			throw new IOException("Structure "+pdbId+" not found and unable to download.");
-		}
-	}
+//	/**
+//	 * Download a structure, but don't parse it yet or store it in memory.
+//	 *
+//	 * Used to pre-fetch large numbers of structures.
+//	 * @param pdbId
+//	 * @throws IOException
+//	 */
+//	public void prefetchStructure(String pdbId) throws IOException {
+//		if ( pdbId.length() != 4)
+//			throw new IOException("The provided ID does not look like a PDB ID : " + pdbId);
+//
+//		// Check existing
+//		File file = downloadStructure(pdbId);
+//
+//		if(!file.exists()) {
+//			throw new IOException("Structure "+pdbId+" not found and unable to download.");
+//		}
+//	}
 
 	/**
 	 * Attempts to delete all versions of a structure from the local directory.
@@ -434,52 +424,52 @@ public boolean deleteStructure(String pdbId) throws IOException{
 	 * @throws IOException for errors downloading or writing, or if the
 	 *  fetchBehavior is {@link FetchBehavior#LOCAL_ONLY}
 	 */
-	protected File downloadStructure(String pdbId) throws IOException{
+	protected InputStream downloadStructure(String pdbId) throws IOException{
 		if ( pdbId.length() != 4)
 			throw new IOException("The provided ID does not look like a PDB ID : " + pdbId);
 
 		// decide whether download is required
-		File existing =  getLocalFile(pdbId);
-		switch(fetchBehavior) {
-		case LOCAL_ONLY:
-			if( existing == null ) {
-				throw new IOException(String.format("Structure %s not found in %s "
-						+ "and configured not to download.",pdbId,getPath()));
-			} else {
-				return existing;
-			}
-		case FETCH_FILES:
-			// Use existing if present
-			if( existing != null) {
-				return existing;
-			}
-			// existing is null, downloadStructure(String,String,boolean,File) will download it
-			break;
-		case FETCH_IF_OUTDATED:
-			// here existing can be null or not:
-			// existing == null : downloadStructure(String,String,boolean,File) will download it
-			// existing != null : downloadStructure(String,String,boolean,File) will check its date and download if older
-			break;
-		case FETCH_REMEDIATED:
-			// Use existing if present and recent enough
-			if( existing != null) {
-				long lastModified = existing.lastModified();
-
-				if (lastModified < LAST_REMEDIATION_DATE) {
-					// the file is too old, replace with newer version
-					logger.warn("Replacing file {} with latest remediated (remediation of {}) file from PDB.",
-							existing, LAST_REMEDIATION_DATE_STRING);
-					existing = null;
-					break;
-				} else {
-					return existing;
-				}
-			}
-		case FORCE_DOWNLOAD:
-			// discard the existing file to force redownload
-			existing = null; // downloadStructure(String,String,boolean,File) will download it
-			break;
-		}
+//		File existing =  getLocalFile(pdbId);
+//		switch(fetchBehavior) {
+//		case LOCAL_ONLY:
+//			if( existing == null ) {
+//				throw new IOException(String.format("Structure %s not found in %s "
+//						+ "and configured not to download.",pdbId,getPath()));
+//			} else {
+//				return existing;
+//			}
+//		case FETCH_FILES:
+//			// Use existing if present
+//			if( existing != null) {
+//				return existing;
+//			}
+//			// existing is null, downloadStructure(String,String,boolean,File) will download it
+//			break;
+//		case FETCH_IF_OUTDATED:
+//			// here existing can be null or not:
+//			// existing == null : downloadStructure(String,String,boolean,File) will download it
+//			// existing != null : downloadStructure(String,String,boolean,File) will check its date and download if older
+//			break;
+//		case FETCH_REMEDIATED:
+//			// Use existing if present and recent enough
+//			if( existing != null) {
+//				long lastModified = existing.lastModified();
+//
+//				if (lastModified < LAST_REMEDIATION_DATE) {
+//					// the file is too old, replace with newer version
+//					logger.warn("Replacing file {} with latest remediated (remediation of {}) file from PDB.",
+//							existing, LAST_REMEDIATION_DATE_STRING);
+//					existing = null;
+//					break;
+//				} else {
+//					return existing;
+//				}
+//			}
+//		case FORCE_DOWNLOAD:
+//			// discard the existing file to force redownload
+//			existing = null; // downloadStructure(String,String,boolean,File) will download it
+//			break;
+//		}
 
 		// Force the download now
 		if(obsoleteBehavior == ObsoleteBehavior.FETCH_CURRENT) {
@@ -489,12 +479,12 @@ protected File downloadStructure(String pdbId) throws IOException{
 				// either an error or there is not current entry
 				current = pdbId;
 			}
-			return downloadStructure(current, splitDirURL,false, existing);
+			return downloadStructure(current, splitDirURL,false);
 		} else if(obsoleteBehavior == ObsoleteBehavior.FETCH_OBSOLETE
 				&& PDBStatus.getStatus(pdbId) == Status.OBSOLETE) {
-			return downloadStructure(pdbId, obsoleteDirURL, true, existing);
+			return downloadStructure(pdbId, obsoleteDirURL, true);
 		} else {
-			return downloadStructure(pdbId, splitDirURL, false, existing);
+			return downloadStructure(pdbId, splitDirURL, false);
 		}
 	}
 
@@ -508,45 +498,43 @@ protected File downloadStructure(String pdbId) throws IOException{
 	 * @return
 	 * @throws IOException
 	 */
-	private File downloadStructure(String pdbId, String pathOnServer, boolean obsolete, File existingFile)
-			throws IOException{
+	private InputStream downloadStructure(String pdbId, String pathOnServer, boolean obsolete) throws IOException{
 
-		File dir = getDir(pdbId,obsolete);
-		File realFile = new File(dir,getFilename(pdbId));
+//		File dir = getDir(pdbId,obsolete);
+//		File realFile = new File(dir,getFilename(pdbId));
 
 		String ftp;
 
 		if (getFilename(pdbId).endsWith(".mmtf.gz")){
 			ftp = CodecUtils.getMmtfEntryUrl(pdbId, true, false);
 		} else {
-			ftp = String.format("%s%s/%s/%s",
-			serverName, pathOnServer, pdbId.substring(1,3).toLowerCase(), getFilename(pdbId));
+			ftp = String.format("%s%s/%s/%s", serverName, pathOnServer, pdbId.substring(1,3).toLowerCase(), getFilename(pdbId));
 		}
 
 		URL url = new URL(ftp);
 
-		Date serverFileDate;
-		if (existingFile!=null) {
-
-			serverFileDate = getLastModifiedTime(url);
-
-			if (serverFileDate!=null) {
-				if (existingFile.lastModified()>=serverFileDate.getTime()) {
-					return existingFile;
-				} else {
-					// otherwise we go ahead and download, warning about it first
-					logger.warn("File {} is outdated, will download new one from PDB (updated on {})",
-							existingFile, serverFileDate.toString());
-				}
-			} else {
-				logger.warn("Could not determine if file {} is outdated (could not get timestamp from server). Will force redownload", existingFile);
-			}
-		}
-
-		logger.info("Fetching " + ftp);
-		logger.info("Writing to "+ realFile);
-
-		FileDownloadUtils.downloadFile(url, realFile);
+//		Date serverFileDate;
+//		if (existingFile!=null) {
+//
+//			serverFileDate = getLastModifiedTime(url);
+//
+//			if (serverFileDate!=null) {
+//				if (existingFile.lastModified()>=serverFileDate.getTime()) {
+//					return existingFile;
+//				} else {
+//					// otherwise we go ahead and download, warning about it first
+//					logger.warn("File {} is outdated, will download new one from PDB (updated on {})",
+//							existingFile, serverFileDate.toString());
+//				}
+//			} else {
+//				logger.warn("Could not determine if file {} is outdated (could not get timestamp from server). Will force redownload", existingFile);
+//			}
+//		}
+
+//		logger.info("Fetching " + ftp);
+//		logger.info("Writing to "+ realFile);
+
+		return FileDownloadUtils.downloadStream(url, 60000);
 
 		// Commented out following code used for setting the modified date to the downloaded file - JD 2015-01-15
 		// The only reason to have it was in order to get an rsync-like behavior, respecting the timestamps
@@ -563,7 +551,7 @@ private File downloadStructure(String pdbId, String pathOnServer, boolean obsole
 		//}
 
 
-		return realFile;
+//		return realFile;
 	}
 
 	/**

From 229fad4eed7810b173e48f8cbdd4cb0b78289136 Mon Sep 17 00:00:00 2001
From: Jim Northrup <jim@vsiwest.com>
Date: Wed, 11 Mar 2020 11:35:34 +0700
Subject: [PATCH 14/18] enable a non-signed build to run shellscripted demo in
 bin/;   or for that main class to be specified in bash.

---
 README.md                     | 11 ++++
 bin/biojava.sh                | 15 ++++++
 biojava-aa-prop/pom.xml       | 10 +---
 biojava-alignment/pom.xml     | 10 +---
 biojava-core/pom.xml          | 10 +---
 biojava-genome/pom.xml        | 10 +---
 biojava-modfinder/pom.xml     | 10 +---
 biojava-ontology/pom.xml      | 99 ++++++++++++++++-------------------
 biojava-structure-gui/pom.xml | 10 +---
 biojava-structure/pom.xml     | 10 +---
 biojava-survival/pom.xml      | 10 +---
 biojava-ws/pom.xml            | 10 +---
 pom.xml                       | 43 +++++++++++----
 13 files changed, 114 insertions(+), 144 deletions(-)
 create mode 100755 bin/biojava.sh

diff --git a/README.md b/README.md
index 9ff33d976b..bbd8d9b3e8 100644
--- a/README.md
+++ b/README.md
@@ -34,6 +34,17 @@ If you are using Maven you can add the BioJava repository by adding the followin
     </dependencies>
 ```
 
+### Quick Demo
+
+on Linux, Mac, or in (git-bash)[https://gitforwindows.org/] run 
+
+```bash
+
+mvn install
+bin/biojava.sh
+```
+
+
 ### Snapshot builds
 
 To use the latest builds from BioJava, you can add the following config your project's pom.xml:
diff --git a/bin/biojava.sh b/bin/biojava.sh
new file mode 100755
index 0000000000..b786b11915
--- /dev/null
+++ b/bin/biojava.sh
@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+# this runs any main function in the source tree.
+# to change the class to be run
+# EXECMAIN=org.biojava.not.demo.main bin/biojava.sh
+mkdir -p target/lib/                                          && {
+ln -s 2>/dev/null    $PWD/*/target{,/lib}/*jar  target/lib
+cp 2>/dev/null  -as  $PWD/*/src/main/resources/* target/
+}
+
+set -fx
+JDIR=$PWD/$(dirname $0)/../
+pushd target
+exec java  -classpath "$JDIR/target/*:$JDIR/target/lib/*"  ${EXECMAIN:=demo.DemoSixFrameTranslation} "$@"
+popd
\ No newline at end of file
diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index c8da170664..2869d2f272 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -20,15 +20,7 @@
 	<build>
 		<plugins>
 			<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <configuration>
-                    <excludes>
-                        <exclude>demo/**</exclude>
-                    </excludes>
-                </configuration>
-            </plugin>
+
 
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index 092dbc3d0b..494856db16 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -26,15 +26,7 @@
 
 			<!-- Excluding demo package is required for avoiding namespace clashes
 				(demo package is in all modules) for signing the jar. See issue #387 -->
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <configuration>
-                    <excludes>
-                        <exclude>demo/**</exclude>
-                    </excludes>
-                </configuration>
-            </plugin>
+
 
 		</plugins>
 	</build>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index a7aa8be1e4..ed5fd10f82 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -26,15 +26,7 @@
 		<plugins>
 
 			<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <configuration>
-                    <excludes>
-                        <exclude>demo/**</exclude>
-                    </excludes>
-                </configuration>
-            </plugin>
+
 
 		</plugins>
 	</build>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index da492a3a6f..d0ef1e08ae 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -35,15 +35,7 @@
 		<plugins>
 
 			<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <configuration>
-                    <excludes>
-                        <exclude>demo/**</exclude>
-                    </excludes>
-                </configuration>
-            </plugin>
+
 
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 5367030867..a7ba91e08a 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -58,15 +58,7 @@
   <plugins>
 
 			<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <configuration>
-                    <excludes>
-                        <exclude>demo/**</exclude>
-                    </excludes>
-                </configuration>
-            </plugin>
+
 
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index b6a4fa0967..9b75177d21 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -1,51 +1,52 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-  <modelVersion>4.0.0</modelVersion>
-  <parent>
-    <groupId>org.biojava</groupId>
-    <artifactId>biojava</artifactId>
-    <version>5.3.1-SNAPSHOT</version>
-  </parent>
+<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <groupId>org.biojava</groupId>
+        <artifactId>biojava</artifactId>
+        <version>5.3.1-SNAPSHOT</version>
+    </parent>
 
-  <artifactId>biojava-ontology</artifactId>
-  <name>biojava-ontology</name>
-  <url>http://www.biojava.org</url>
+    <artifactId>biojava-ontology</artifactId>
+    <name>biojava-ontology</name>
+    <url>http://www.biojava.org</url>
 
-  <licenses>
-    <license>
-      <name>GNU LGPL v2</name>
-      <url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
-      <distribution>repo</distribution>
-    </license>
-  </licenses>
+    <licenses>
+        <license>
+            <name>GNU LGPL v2</name>
+            <url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
+            <distribution>repo</distribution>
+        </license>
+    </licenses>
 
-  <dependencies>
-    <dependency>
-      <groupId>junit</groupId>
-      <artifactId>junit</artifactId>
-      <scope>test</scope>
-    </dependency>
-		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
-		<dependency>
-        	<groupId>org.slf4j</groupId>
-        	<artifactId>slf4j-api</artifactId>
-    	</dependency>
-    	<!-- binding for log4j2, scope=runTime set in parent pom -->
- 		<dependency>
-    		<groupId>org.apache.logging.log4j</groupId>
-    		<artifactId>log4j-slf4j-impl</artifactId>
-  		</dependency>
-  		<dependency>
-    		<groupId>org.apache.logging.log4j</groupId>
-    		<artifactId>log4j-api</artifactId>
-  		</dependency>
-  		<dependency>
-    		<groupId>org.apache.logging.log4j</groupId>
-    		<artifactId>log4j-core</artifactId>
-  		</dependency>
-  </dependencies>
+    <dependencies>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+        </dependency>
+        <!-- binding for log4j2, scope=runTime set in parent pom -->
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-slf4j-impl</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-core</artifactId>
+        </dependency>
+    </dependencies>
 
-      <properties>
+    <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.build.targetEncoding>UTF-8</project.build.targetEncoding>
 
@@ -56,16 +57,8 @@
     <build>
         <plugins>
 
-			<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <configuration>
-                    <excludes>
-                        <exclude>demo/**</exclude>
-                    </excludes>
-                </configuration>
-            </plugin>
+            <!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
+
 
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 8dfa407860..27bd24317e 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -78,15 +78,7 @@
 
 			<!-- Excluding demo package is required for avoiding namespace clashes
 				(demo package is in all modules) for signing the jar. See issue #387 -->
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <configuration>
-                    <excludes>
-                        <exclude>demo/**</exclude>
-                    </excludes>
-                </configuration>
-            </plugin>
+
 
         </plugins>
     </build>
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 78c0081f24..79e02b9d12 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -130,15 +130,7 @@
 
 			<!-- Excluding demo package is required for avoiding namespace clashes
 				(demo package is in all modules) for signing the jar. See issue #387 -->
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <configuration>
-                    <excludes>
-                        <exclude>demo/**</exclude>
-                    </excludes>
-                </configuration>
-            </plugin>
+
 
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 479b57276b..598c868930 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -60,15 +60,7 @@
     <build>
         <plugins>
 			<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <configuration>
-                    <excludes>
-                        <exclude>demo/**</exclude>
-                    </excludes>
-                </configuration>
-            </plugin>
+
 
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 8df54334cf..2c2b895319 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -56,15 +56,7 @@
         <plugins>
 
 			<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <configuration>
-                    <excludes>
-                        <exclude>demo/**</exclude>
-                    </excludes>
-                </configuration>
-            </plugin>
+
 
         </plugins>
     </build>
diff --git a/pom.xml b/pom.xml
index f24a2df92f..a3b33e121d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -455,6 +455,20 @@
 				<!--</executions>-->
 			<!--</plugin>-->
 
+			<plugin><!--the simplest possible deployment/bundling with the fewest jarfile collision risks-->
+				<artifactId>maven-dependency-plugin</artifactId>
+				<executions>
+					<execution>
+						<phase>install</phase>
+						<goals>
+							<goal>copy-dependencies</goal>
+						</goals>
+						<configuration>
+							<outputDirectory>${project.build.directory}/lib</outputDirectory>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
 		</plugins>
 
 		<extensions>
@@ -645,6 +659,15 @@
 			</activation>
 			<build>
 				<plugins>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-jar-plugin</artifactId>
+						<configuration>
+							<excludes>
+								<exclude>demo/**</exclude>
+							</excludes>
+						</configuration>
+					</plugin>
 					<plugin>
 						<groupId>org.apache.maven.plugins</groupId>
 						<artifactId>maven-gpg-plugin</artifactId>
@@ -658,28 +681,28 @@
 								</goals>
 							</execution>
 						</executions>
-					</plugin>
-				</plugins>
+					</plugin>			<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
+ 				</plugins>
 			</build>
+
 		</profile>
 
 	</profiles>
 
 	<modules>
 
-		<module>biojava-core</module>
+		<module>biojava-aa-prop</module>
 		<module>biojava-alignment</module>
-		<module>biojava-structure</module>
-		<module>biojava-structure-gui</module>
+		<module>biojava-core</module>
 		<module>biojava-genome</module>
+		<module>biojava-integrationtest</module>
 		<module>biojava-modfinder</module>
-		<module>biojava-ws</module>
+		<module>biojava-ontology</module>
 		<module>biojava-protein-disorder</module>
-		<module>biojava-aa-prop</module>
+		<module>biojava-structure-gui</module>
+		<module>biojava-structure</module>
 		<module>biojava-survival</module>
-		<module>biojava-ontology</module>
-		<!-- Keep integration tests last  -->
-		<module>biojava-integrationtest</module>
+		<module>biojava-ws</module>
 	</modules>
 	<inceptionYear>2000</inceptionYear>
 	<issueManagement>

From 80f097f61df4f7e7b8b6d804a352944840a0ee4a Mon Sep 17 00:00:00 2001
From: me <seh@internet.earth>
Date: Wed, 11 Mar 2020 12:33:59 -0400
Subject: [PATCH 15/18] updates

---
 .../nbio/core/util/FileDownloadUtils.java     |    4 +-
 .../org/biojava/nbio/structure/PDBStatus.java | 1200 ++++++++---------
 .../nbio/structure/io/LocalPDBDirectory.java  |  148 +-
 3 files changed, 667 insertions(+), 685 deletions(-)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
index 31f284209e..a451f60134 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
@@ -236,7 +236,9 @@ public static InputStream downloadStream(URL url, int timeoutMS) throws IOExcept
 
 		OkHttpClient client = clients.build(); //TODO ThreadLocal
 
-		Call c = client.newCall(new Request.Builder().url(url).cacheControl(CacheControl.FORCE_CACHE).build());
+		Call c = client.newCall(new Request.Builder().url(url)
+				//.cacheControl(CacheControl.FORCE_CACHE)
+				.build());
 
 		c.timeout().deadline(timeoutMS, TimeUnit.MILLISECONDS);
 		try (Response r = c.execute()) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java
index d22558d903..5a12b5b026 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java
@@ -77,615 +77,613 @@
  */
 public class PDBStatus {
 
-	private static final Logger logger = LoggerFactory.getLogger(PDBStatus.class);
-
-	public static final String DEFAULT_PDB_SERVER = "www.rcsb.org";
-	public static final String PDB_SERVER_PROPERTY = "PDB.SERVER";
-
-	/**
-	 * saves the returned results for further use.
-	 *
-	 */
-	//TODO Use SoftReferences to allow garbage collection
-	private static final Map<String, Map<String, String>> recordsCache= new Hashtable<>();
-
-	/**
-	 * Represents the status of PDB IDs. 'OBSOLETE' and 'CURRENT' are the most
-	 * common.
-	 * @author Spencer Bliven <sbliven@ucsd.edu>
-	 *
-	 */
-	public enum Status {
-		OBSOLETE,
-		CURRENT,
-		AUTH,
-		HOLD,
-		HPUB,
-		POLC,
-		PROC,
-		REFI,
-		REPL,
-		WAIT,
-		WDRN,
-		MODEL,
-		UNKNOWN;
-
-
-		/**
-		 *
-		 * @param statusStr
-		 * @return
-		 * @throws IllegalArgumentException If the string is not recognized
-		 */
-		public static Status fromString(String statusStr) {
-			Status status;
-			String statusStrUpper = statusStr.toUpperCase();
-			if(statusStrUpper.equalsIgnoreCase("OBSOLETE"))
-				status = Status.OBSOLETE;
-			else if(statusStrUpper.equalsIgnoreCase("CURRENT"))
-				status = Status.CURRENT;
-			else if(statusStrUpper.equalsIgnoreCase("AUTH"))
-				status = Status.AUTH;
-			else if(statusStrUpper.equalsIgnoreCase("HOLD"))
-				status = Status.HOLD;
-			else if(statusStrUpper.equalsIgnoreCase("HPUB"))
-				status = Status.HPUB;
-			else if(statusStrUpper.equalsIgnoreCase("POLC"))
-				status = Status.POLC;
-			else if(statusStrUpper.equalsIgnoreCase("PROC"))
-				status = Status.PROC;
-			else if(statusStrUpper.equalsIgnoreCase("REFI"))
-				status = Status.REFI;
-			else if(statusStrUpper.equalsIgnoreCase("REPL"))
-				status = Status.REPL;
-			else if(statusStrUpper.equalsIgnoreCase("WAIT"))
-				status = Status.WAIT;
-			else if(statusStrUpper.equalsIgnoreCase("WDRN"))
-				status = Status.WDRN;
-			else if(statusStrUpper.equalsIgnoreCase("MODEL"))
-				status = Status.MODEL;
-			else if(statusStrUpper.equalsIgnoreCase("UNKNOWN"))
-				status = Status.UNKNOWN;
-			else {
-				throw new IllegalArgumentException("Unable to parse status '"+statusStrUpper+"'.");
-			}
-			return status;
-		}
-	}
-
-	/**
-	 * Get the status of the PDB in question.
-	 *
-	 * @param pdbId
-	 * @return The status, or null if an error occurred.
-	 */
-	public static Status getStatus(String pdbId) {
-		Status[] statuses = getStatus(new String[] {pdbId});
-		if(statuses != null) {
-			assert(statuses.length == 1);
-			return statuses[0];
-		} else {
-			return null;
-		}
-	}
-
-	/**
-	 * Get the status of the a collection of PDBs in question in a single query.
-	 *
-	 * @see #getStatus(String)
-	 * @param pdbIds
-	 * @return The status array, or null if an error occurred.
-	 */
-	public static Status[] getStatus(String[] pdbIds) {
-		Status[] statuses = new Status[pdbIds.length];
-
-		List<Map<String,String>> attrList = getStatusIdRecords(pdbIds);
-		//Expect a single record
-		if(attrList == null || attrList.size() != pdbIds.length) {
-			logger.error("Error getting Status for {} from the PDB website.", Arrays.toString(pdbIds));
-			return null;
-		}
-
-
-		for(int pdbNum = 0;pdbNum<pdbIds.length;pdbNum++) {
-			//Locate first element of attrList with matching structureId.
-			//attrList is usually short, so don't worry about performance
-			boolean foundAttr = false;
-			for( Map<String,String> attrs : attrList) {
-
-				//Check that the record matches pdbId
-				String id = attrs.get("structureId");
-				if(id == null || !id.equalsIgnoreCase(pdbIds[pdbNum])) {
-					continue;
-				}
-
-				//Check that the status is given
-				String statusStr = attrs.get("status");
-				Status status = null;
-				if(statusStr == null ) {
-					logger.error("No status returned for {}", pdbIds[pdbNum]);
-					statuses[pdbNum] = null;
-				} else {
-					status = Status.fromString(statusStr);
-				}
-
-				if(status == null) {
-					logger.error("Unknown status '{}'", statusStr);
-					statuses[pdbNum] = null;
-				}
-
-				statuses[pdbNum] = status;
-				foundAttr = true;
-			}
-			if(!foundAttr) {
-				logger.error("No result found for {}", pdbIds[pdbNum]);
-				statuses[pdbNum] = null;
-			}
-		}
-
-		return statuses;
-	}
-
-	/**
-	 * Gets the current version of a PDB ID. This is equivalent to selecting
-	 * the first element from
-	 * {@link #getReplacement(String,boolean,boolean)
-	 *
-	 * @param oldPdbId
-	 * @return The replacement for oldPdbId, or null if none are found or if an error occurred.
-	 */
-	public static String getCurrent(String oldPdbId) {
-		List<String> replacements =  getReplacement(oldPdbId,true, false);
-		if(replacements != null && !replacements.isEmpty())
-			return replacements.get(0);
-		else
-			return null;
-	}
-
-	/**
-	 * Gets the PDB which superseded oldPdbId. For CURRENT IDs, this will
-	 * be itself. For obsolete IDs, the behavior depends on the recursion
-	 * parameter. If false, only IDs which directly supersede oldPdbId are
-	 * returned. If true, the replacements for obsolete records are recursively
-	 * fetched, yielding a list of all current replacements of oldPdbId.
-	 *
-	 *
-	 *
-	 * @param oldPdbId A pdb ID
-	 * @param recurse Indicates whether the replacements for obsolete records
-	 * 		should be fetched.
-	 * @param includeObsolete Indicates whether obsolete records should be
-	 * 		included in the results.
-	 * @return The PDB which replaced oldPdbId. This may be oldPdbId itself, for
-	 * 		current records. A return value of null indicates that the ID has
-	 * 		been removed from the PDB or that an error has occurred.
-	 */
-	public static List<String> getReplacement(String oldPdbId, boolean recurse, boolean includeObsolete) {
-		List<Map<String,String>> attrList = getStatusIdRecords(new String[] {oldPdbId});
-		//Expect a single record
-		if(attrList == null || attrList.size() != 1) {
-			logger.error("Error getting Status for {} from the PDB website.", oldPdbId);
-			return null;
-		}
-
-		Map<String,String> attrs = attrList.get(0);
-
-		//Check that the record matches pdbId
-		String id = attrs.get("structureId");
-		if(id == null || !id.equalsIgnoreCase(oldPdbId)) {
-			logger.error("Results returned from the query don't match {}", oldPdbId);
-			return null;
-		}
-
-		//Check that the status is given
-		String statusStr = attrs.get("status");
-		if(statusStr == null ) {
-			logger.error("No status returned for {}", oldPdbId);
-			return null;
-		}
-
-		Status status = Status.fromString(statusStr);
-		if(status == null ) {
-			logger.error("Unknown status '{}'", statusStr);
-			return null;
-		}
-
-		// If we're current, just return
-		LinkedList<String> results = new LinkedList<>();
-		switch(status) {
-			case CURRENT:
-				results.add(oldPdbId);
-				return results;
-			case OBSOLETE: {
-				String replacementStr = attrs.get("replacedBy");
-				if(replacementStr == null) {
-					logger.error("{} is OBSOLETE but lacks a replacedBy attribute.", oldPdbId);
-					return null;
-				}
-				replacementStr = replacementStr.toUpperCase();
-				//include this result
-				if(includeObsolete) {
-					results.add(oldPdbId);
-				}
-				// Some PDBs are not replaced.
-				if(replacementStr.equals("NONE")) {
-					return results; //empty
-				}
-
-				String[] replacements = replacementStr.split(" ");
-				Arrays.sort(replacements, (o1, o2) -> o2.compareToIgnoreCase(o1));
-				for(String replacement : replacements) {
-
-					// Return the replacement.
-					if(recurse) {
-						List<String> others = PDBStatus.getReplacement(replacement, recurse, includeObsolete);
-						mergeReversed(results,others);
+    private static final Logger logger = LoggerFactory.getLogger(PDBStatus.class);
+
+    public static final String DEFAULT_PDB_SERVER = "www.rcsb.org";
+    public static final String PDB_SERVER_PROPERTY = "PDB.SERVER";
+
+    /**
+     * saves the returned results for further use.
+     *
+     */
+    //TODO Use SoftReferences to allow garbage collection
+    private static final Map<String, Map<String, String>> recordsCache = new Hashtable<>();
+
+    /**
+     * Represents the status of PDB IDs. 'OBSOLETE' and 'CURRENT' are the most
+     * common.
+     * @author Spencer Bliven <sbliven@ucsd.edu>
+     *
+     */
+    public enum Status {
+        OBSOLETE,
+        CURRENT,
+        AUTH,
+        HOLD,
+        HPUB,
+        POLC,
+        PROC,
+        REFI,
+        REPL,
+        WAIT,
+        WDRN,
+        MODEL,
+        UNKNOWN;
+
+
+        /**
+         *
+         * @param statusStr
+         * @return
+         * @throws IllegalArgumentException If the string is not recognized
+         */
+        public static Status fromString(String statusStr) {
+            Status status;
+            String statusStrUpper = statusStr.toUpperCase();
+            if (statusStrUpper.equalsIgnoreCase("OBSOLETE"))
+                status = Status.OBSOLETE;
+            else if (statusStrUpper.equalsIgnoreCase("CURRENT"))
+                status = Status.CURRENT;
+            else if (statusStrUpper.equalsIgnoreCase("AUTH"))
+                status = Status.AUTH;
+            else if (statusStrUpper.equalsIgnoreCase("HOLD"))
+                status = Status.HOLD;
+            else if (statusStrUpper.equalsIgnoreCase("HPUB"))
+                status = Status.HPUB;
+            else if (statusStrUpper.equalsIgnoreCase("POLC"))
+                status = Status.POLC;
+            else if (statusStrUpper.equalsIgnoreCase("PROC"))
+                status = Status.PROC;
+            else if (statusStrUpper.equalsIgnoreCase("REFI"))
+                status = Status.REFI;
+            else if (statusStrUpper.equalsIgnoreCase("REPL"))
+                status = Status.REPL;
+            else if (statusStrUpper.equalsIgnoreCase("WAIT"))
+                status = Status.WAIT;
+            else if (statusStrUpper.equalsIgnoreCase("WDRN"))
+                status = Status.WDRN;
+            else if (statusStrUpper.equalsIgnoreCase("MODEL"))
+                status = Status.MODEL;
+            else if (statusStrUpper.equalsIgnoreCase("UNKNOWN"))
+                status = Status.UNKNOWN;
+            else {
+                throw new IllegalArgumentException("Unable to parse status '" + statusStrUpper + "'.");
+            }
+            return status;
+        }
+    }
+
+    /**
+     * Get the status of the PDB in question.
+     *
+     * @param pdbId
+     * @return The status, or null if an error occurred.
+     */
+    public static Status getStatus(String pdbId) {
+        Status[] statuses = getStatus(new String[]{pdbId});
+        if (statuses != null) {
+            assert (statuses.length == 1);
+            return statuses[0];
+        } else {
+            return null;
+        }
+    }
+
+    /**
+     * Get the status of the a collection of PDBs in question in a single query.
+     *
+     * @see #getStatus(String)
+     * @param pdbIds
+     * @return The status array, or null if an error occurred.
+     */
+    public static Status[] getStatus(String[] pdbIds) {
+        Status[] statuses = new Status[pdbIds.length];
+
+        List<Map<String, String>> attrList = getStatusIdRecords(pdbIds);
+        //Expect a single record
+        if (attrList == null || attrList.size() != pdbIds.length) {
+            logger.error("Error getting Status for {} from the PDB website.", Arrays.toString(pdbIds));
+            return null;
+        }
+
+
+        for (int pdbNum = 0; pdbNum < pdbIds.length; pdbNum++) {
+            //Locate first element of attrList with matching structureId.
+            //attrList is usually short, so don't worry about performance
+            boolean foundAttr = false;
+            for (Map<String, String> attrs : attrList) {
+
+                //Check that the record matches pdbId
+                String id = attrs.get("structureId");
+                if (id == null || !id.equalsIgnoreCase(pdbIds[pdbNum])) {
+                    continue;
+                }
+
+                //Check that the status is given
+                String statusStr = attrs.get("status");
+                Status status = null;
+                if (statusStr == null) {
+                    logger.error("No status returned for {}", pdbIds[pdbNum]);
+                    statuses[pdbNum] = null;
+                } else {
+                    status = Status.fromString(statusStr);
+                }
+
+                if (status == null) {
+                    logger.error("Unknown status '{}'", statusStr);
+                    statuses[pdbNum] = null;
+                }
+
+                statuses[pdbNum] = status;
+                foundAttr = true;
+            }
+            if (!foundAttr) {
+                logger.error("No result found for {}", pdbIds[pdbNum]);
+                statuses[pdbNum] = null;
+            }
+        }
+
+        return statuses;
+    }
+
+    /**
+     * Gets the current version of a PDB ID. This is equivalent to selecting
+     * the first element from
+     * {@link #getReplacement(String, boolean, boolean)
+     *
+     * @param oldPdbId
+     * @return The replacement for oldPdbId, or null if none are found or if an error occurred.
+     */
+    public static String getCurrent(String oldPdbId) {
+        List<String> replacements = getReplacement(oldPdbId, true, false);
+        if (replacements != null && !replacements.isEmpty())
+            return replacements.get(0);
+        else
+            return null;
+    }
+
+    /**
+     * Gets the PDB which superseded oldPdbId. For CURRENT IDs, this will
+     * be itself. For obsolete IDs, the behavior depends on the recursion
+     * parameter. If false, only IDs which directly supersede oldPdbId are
+     * returned. If true, the replacements for obsolete records are recursively
+     * fetched, yielding a list of all current replacements of oldPdbId.
+     *
+     *
+     *
+     * @param oldPdbId A pdb ID
+     * @param recurse Indicates whether the replacements for obsolete records
+     * 		should be fetched.
+     * @param includeObsolete Indicates whether obsolete records should be
+     * 		included in the results.
+     * @return The PDB which replaced oldPdbId. This may be oldPdbId itself, for
+     * 		current records. A return value of null indicates that the ID has
+     * 		been removed from the PDB or that an error has occurred.
+     */
+    public static List<String> getReplacement(String oldPdbId, boolean recurse, boolean includeObsolete) {
+        List<Map<String, String>> attrList = getStatusIdRecords(oldPdbId);
+        //Expect a single record
+        if (attrList == null || attrList.size() != 1) {
+            logger.error("Error getting Status for {} from the PDB website.", oldPdbId);
+            return null;
+        }
+
+        Map<String, String> attrs = attrList.get(0);
+
+        //Check that the record matches pdbId
+        String id = attrs.get("structureId");
+        if (id == null || !id.equalsIgnoreCase(oldPdbId)) {
+            logger.error("Results returned from the query don't match {}", oldPdbId);
+            return null;
+        }
+
+        //Check that the status is given
+        String statusStr = attrs.get("status");
+        if (statusStr == null) {
+            logger.error("No status returned for {}", oldPdbId);
+            return null;
+        }
+
+        Status status = Status.fromString(statusStr);
+        if (status == null) {
+            logger.error("Unknown status '{}'", statusStr);
+            return null;
+        }
+
+        // If we're current, just return
+        LinkedList<String> results = new LinkedList<>();
+        switch (status) {
+            case CURRENT:
+                results.add(oldPdbId);
+                return results;
+            case OBSOLETE: {
+                String replacementStr = attrs.get("replacedBy");
+                if (replacementStr == null) {
+                    logger.error("{} is OBSOLETE but lacks a replacedBy attribute.", oldPdbId);
+                    return null;
+                }
+                replacementStr = replacementStr.toUpperCase();
+                //include this result
+                if (includeObsolete) {
+                    results.add(oldPdbId);
+                }
+                // Some PDBs are not replaced.
+                if (replacementStr.equals("NONE")) {
+                    return results; //empty
+                }
+
+                String[] replacements = replacementStr.split(" ");
+                Arrays.sort(replacements, (o1, o2) -> o2.compareToIgnoreCase(o1));
+                for (String replacement : replacements) {
+
+                    // Return the replacement.
+                    if (recurse) {
+                        List<String> others = PDBStatus.getReplacement(replacement, recurse, includeObsolete);
+                        mergeReversed(results, others);
+                    } else {
+                        if (includeObsolete) {
+                            mergeReversed(results, Collections.singletonList(replacement));
+                        } else {
+                            // check status of replacement
+                            Status replacementStatus = getStatus(replacement);
+                            switch (replacementStatus) {
+                                case OBSOLETE:
+                                    //ignore obsolete
+                                    break;
+                                case CURRENT:
+                                default:
+                                    // include it
+                                    mergeReversed(results, Collections.singletonList(replacement));
+                            }
+                        }
+                    }
+                }
+
+
+                return results;
+            }
+            case UNKNOWN:
+                return null;
+            default: { //TODO handle other cases explicitly. They might have other syntax than "replacedBy"
+                String replacementStr = attrs.get("replacedBy");
+
+                if (replacementStr == null) {
+                    // If no "replacedBy" attribute, treat like we're current
+                    // TODO is this correct?
+                    results.add(oldPdbId);
+                    return results;
+                }
+
+                replacementStr = replacementStr.toUpperCase();
+                // Some PDBs are not replaced.
+                if (replacementStr.equals("NONE"))
+                    return null;
+
+
+                //include this result, since it's not obsolete
+                results.add(oldPdbId);
+
+                String[] replacements = replacementStr.split(" ");
+                Arrays.sort(replacements, (o1, o2) -> o2.compareToIgnoreCase(o1));
+                for (String replacement : replacements) {
+
+                    // Return the replacement.
+                    if (recurse) {
+                        mergeReversed(results, PDBStatus.getReplacement(replacement, recurse, includeObsolete));
+                    } else {
+                        mergeReversed(results, Collections.singletonList(replacement));
+                    }
+                }
+
+
+                return results;
+            }
+        }
+    }
+
+    /**
+     * Takes two reverse sorted lists of strings and merges the second into the
+     * first. Duplicates are removed.
+     *
+     * @param merged A reverse sorted list. Modified by this method to contain
+     * 		the contents of other.
+     * @param other A reverse sorted list. Not modified.
+     */
+    private static void mergeReversed(List<String> merged, final List<String> other) {
+
+        if (other.isEmpty())
+            return;
+
+        if (merged.isEmpty()) {
+            merged.addAll(other);
+            return;
+        }
+
+        ListIterator<String> o = other.listIterator();
+
+        if (o.hasNext()) {
+			String nextM, prevO;
+			ListIterator<String> m = merged.listIterator();
+			prevO = o.next();
+			while (m.hasNext()) {
+				// peek at m
+				nextM = m.next();
+				m.previous();
+
+				//insert from O until exhausted or occurs after nextM
+				while (prevO.compareTo(nextM) > 0) {
+					m.add(prevO);
+					if (!o.hasNext()) {
+						return;
 					}
-					else {
-						if(includeObsolete) {
-							mergeReversed(results, Collections.singletonList(replacement));
-						} else {
-							// check status of replacement
-							Status replacementStatus = getStatus(replacement);
-							switch(replacementStatus) {
-								case OBSOLETE:
-									//ignore obsolete
-									break;
-								case CURRENT:
-								default:
-									// include it
-									mergeReversed(results, Collections.singletonList(replacement));
-							}
-						}
-					}
-				}
-
-
-				return results;
-			}
-			case UNKNOWN:
-				return null;
-			default: { //TODO handle other cases explicitly. They might have other syntax than "replacedBy"
-				String replacementStr = attrs.get("replacedBy");
-
-				if(replacementStr == null) {
-					// If no "replacedBy" attribute, treat like we're current
-					// TODO is this correct?
-					results.add(oldPdbId);
-					return results;
-				}
-
-				replacementStr = replacementStr.toUpperCase();
-				// Some PDBs are not replaced.
-				if(replacementStr.equals("NONE")) {
-					return null;
+					prevO = o.next();
 				}
-
-
-				//include this result, since it's not obsolete
-				results.add(oldPdbId);
-
-				String[] replacements = replacementStr.split(" ");
-				Arrays.sort(replacements, (o1, o2) -> o2.compareToIgnoreCase(o1));
-				for(String replacement : replacements) {
-
-					// Return the replacement.
-					if(recurse) {
-						List<String> others = PDBStatus.getReplacement(replacement, recurse, includeObsolete);
-						mergeReversed(results,others);
-					}
-					else {
-						mergeReversed(results, Collections.singletonList(replacement));
+				//remove duplicates
+				if (prevO.equals(nextM)) {
+					if (!o.hasNext()) {
+						return;
 					}
+					prevO = o.next();
 				}
 
-
-				return results;
-			}
-		}
-	}
-
-	/**
-	 * Takes two reverse sorted lists of strings and merges the second into the
-	 * first. Duplicates are removed.
-	 *
-	 * @param merged A reverse sorted list. Modified by this method to contain
-	 * 		the contents of other.
-	 * @param other A reverse sorted list. Not modified.
-	 */
-	private static void mergeReversed(List<String> merged,
-	                                  final List<String> other) {
-
-		if(other.isEmpty())
-			return;
-
-		if(merged.isEmpty()) {
-			merged.addAll(other);
-			return;
-		}
-
-		ListIterator<String> m = merged.listIterator();
-		ListIterator<String> o = other.listIterator();
-
-		String nextM, prevO;
-		prevO = o.next();
-		while(m.hasNext()) {
-			// peek at m
-			nextM = m.next();
-			m.previous();
-
-			//insert from O until exhausted or occurs after nextM
-			while(prevO.compareTo(nextM) > 0) {
-				m.add(prevO);
-				if(!o.hasNext()) {
-					return;
-				}
-				prevO = o.next();
-			}
-			//remove duplicates
-			if(prevO.equals(nextM)) {
-				if(!o.hasNext()) {
-					return;
-				}
-				prevO = o.next();
-			}
-
-			m.next();
-		}
-		m.add(prevO);
-		while(o.hasNext()) {
-			m.add(o.next());
-		}
-
-	}
-
-
-	/**
-	 * Get the ID of the protein which was made obsolete by newPdbId.
-	 *
-	 * @param newPdbId PDB ID of the newer structure
-	 * @param recurse If true, return all ancestors of newPdbId.
-	 * 		Otherwise, just go one step newer than oldPdbId.
-	 * @return A (possibly empty) list of ID(s) of the ancestor(s) of
-	 * 		newPdbId, or <tt>null</tt> if an error occurred.
-	 */
-	public static List<String> getReplaces(String newPdbId, boolean recurse) {
-		List<Map<String,String>> attrList = getStatusIdRecords(new String[] {newPdbId});
-		//Expect a single record
-		if(attrList == null || attrList.size() != 1) {
-			//TODO Is it possible to have multiple record per ID?
-			// They seem to be combined into one record with space-delimited 'replaces'
-			logger.error("Error getting Status for {} from the PDB website.", newPdbId);
-			return null;
-		}
-
-		Map<String,String> attrs = attrList.get(0);
-
-		//Check that the record matches pdbId
-		String id = attrs.get("structureId");
-		if(id == null || !id.equals(newPdbId)) {
-			logger.error("Results returned from the query don't match {}", newPdbId);
-			return null;
-		}
-
-
-		String replacedList = attrs.get("replaces"); //space-delimited list
-		if(replacedList == null) {
-			// no replaces value; assume root
-			return new ArrayList<>();
-		}
-		String[] directDescendents = replacedList.split("\\s");
-
-		// Not the root! Return the replaced PDB.
-		if(recurse) {
-			// Note: Assumes a proper directed acyclic graph of revisions
-			// Cycles will cause infinite loops.
-			List<String> allDescendents = new LinkedList<>();
-			for(String replaced : directDescendents) {
-				List<String> roots = PDBStatus.getReplaces(replaced, recurse);
-				mergeReversed(allDescendents,roots);
-			}
-			mergeReversed(allDescendents,Arrays.asList(directDescendents));
-
-			return allDescendents;
-		} else {
-			return Arrays.asList(directDescendents);
-		}
-	}
-
-
-	/**
-	 * The status of PDB IDs are cached to reduce server overload.
-	 *
-	 * This method clears the cached records.
-	 */
-	public static void clearCache() {
-		recordsCache.clear();
-	}
-
-	/**
-	 * Fetches the status of one or more pdbIDs from the server.
-	 *
-	 * <p>Returns the results as a list of Attributes.
-	 * Each attribute should contain "structureId" and "status" attributes, and
-	 * possibly more.
-	 *
-	 * <p>Example:</br>
-	 * <tt>http://www.rcsb.org/pdb/rest/idStatus?structureID=1HHB,4HHB</tt></br>
-	 *<pre>&lt;idStatus&gt;
-	 *  &lt;record structureId="1HHB" status="OBSOLETE" replacedBy="4HHB"/&gt;
-	 *  &lt;record structureId="4HHB" status="CURRENT" replaces="1HHB"/&gt;
-	 *&lt;/idStatus&gt;
-	 * </pre>
-	 *
-	 * <p>Results are not guaranteed to be returned in the same order as pdbIDs.
-	 * Refer to the structureId property to match them.
-	 *
-	 * @param pdbIDs
-	 * @return A map between attributes and values
-	 */
-	private static List<Map<String, String>> getStatusIdRecords(String[] pdbIDs) {
-
-		List<Map<String,String>> result = new ArrayList<>(pdbIDs.length);
-
-		String serverName = System.getProperty(PDB_SERVER_PROPERTY);
-
-		if ( serverName == null)
-			serverName = DEFAULT_PDB_SERVER;
-		else
-			logger.info(String.format("Got System property %s=%s",PDB_SERVER_PROPERTY,serverName));
-
-		// Build REST query URL
-		if(pdbIDs.length < 1) {
-			throw new IllegalArgumentException("No pdbIDs specified");
-		}
-		String urlStr = String.format("http://%s/pdb/rest/idStatus?structureId=",serverName);
-		for(String pdbId : pdbIDs) {
-			pdbId = pdbId.toUpperCase();
-			//check the cache
-			if (recordsCache.containsKey(pdbId)) {
-				//logger.debug("Fetching "+pdbId+" from Cache");
-				result.add( recordsCache.get(pdbId) );
-			} else {
-				urlStr += pdbId + ",";
-			}
-		}
-
-		// check if any ids still need fetching
-		if(urlStr.charAt(urlStr.length()-1) == '=') {
-			return result;
-		}
-
-		try {
-			logger.info("Fetching {}", urlStr);
-
-			URL url = new URL(urlStr);
-
-			InputStream uStream = url.openStream();
-
-			InputSource source = new InputSource(uStream);
-			SAXParserFactory parserFactory = SAXParserFactory.newInstance();
-			SAXParser parser = parserFactory.newSAXParser();
-			XMLReader reader = parser.getXMLReader();
-
-			PDBStatusXMLHandler handler = new PDBStatusXMLHandler();
-
-			reader.setContentHandler(handler);
-			reader.parse(source);
-
-			// Fetch results of SAX parsing
-			List<Map<String,String>> records = handler.getRecords();
-
-			//add to cache
-			for(Map<String,String> record : records) {
-				String pdbId = record.get("structureId").toUpperCase();
-				if(pdbId != null) {
-					recordsCache.put(pdbId, record);
-				}
-			}
-
-			// return results
-			result.addAll(handler.getRecords());
-
-			// TODO should throw these forward and let the caller log
-		} catch (IOException | ParserConfigurationException | SAXException e){
-			logger.error("Problem getting status for {} from PDB server. Error: {}", Arrays.toString(pdbIDs), e.getMessage());
-			return null;
-		}
-
-		return result;
-	}
-
-	/**
-	 * Handles idStatus xml by storing attributes for all record elements.
-	 *
-	 * @author Spencer Bliven <sbliven@ucsd.edu>
-	 *
-	 */
-	private static class PDBStatusXMLHandler extends DefaultHandler {
-		private final List<Map<String,String>> records;
-
-		public PDBStatusXMLHandler() {
-			records = new ArrayList<>();
-		}
-
-		/**
-		 * @param uri
-		 * @param localName
-		 * @param qName
-		 * @param attributes
-		 * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)
-		 */
-		@Override
-		public void startElement(String uri, String localName, String qName,
-		                         Attributes attributes) {
-			//System.out.format("Starting element: uri='%s' localName='%s' qName='%s'\n", uri, localName, qName);
-			if(qName.equals("record")) {
-				//Convert attributes into a Map, as it should have been.
-				//Important since SAX reuses Attributes objects for different calls
-				Map<String,String> attrMap = new HashMap<>(attributes.getLength() * 2);
-				for(int i=0;i<attributes.getLength();i++) {
-					attrMap.put(attributes.getQName(i), attributes.getValue(i));
-				}
-				records.add(attrMap);
+				m.next();
 			}
-		}
-
-
-		/**
-		 * @param e
-		 * @throws SAXException
-		 * @see org.xml.sax.helpers.DefaultHandler#error(org.xml.sax.SAXParseException)
-		 */
-		@Override
-		public void error(SAXParseException e) throws SAXException {
-			logger.error(e.getMessage());
-			super.error(e);
-		}
-
-
-		public List<Map<String, String>> getRecords() {
-			return records;
-		}
-	}
-
-	/** Returns a list of current PDB IDs
-	 *
-	 * @return a list of PDB IDs, or null if a problem occurred
-	 */
-
-	public static SortedSet<String> getCurrentPDBIds() throws IOException {
-
-		SortedSet<String> allPDBs = new TreeSet<>();
-		String serverName = System.getProperty(PDB_SERVER_PROPERTY);
-
-		if ( serverName == null)
-			serverName = DEFAULT_PDB_SERVER;
-		else
-			logger.info(String.format("Got System property %s=%s",PDB_SERVER_PROPERTY,serverName));
-
-		// Build REST query URL
-
-		String urlStr = String.format("http://%s/pdb/rest/getCurrent",serverName);
-		URL u = new URL(urlStr);
-
-		InputStream stream = URLConnectionTools.getInputStream(u, 60000);
-
-		if (stream != null) {
-			BufferedReader reader = new BufferedReader(
-					new InputStreamReader(stream));
-
-			String line;
-
-			while ((line = reader.readLine()) != null) {
-				int index = line.lastIndexOf("structureId=");
-				if (index > 0) {
-					allPDBs.add(line.substring(index + 13, index + 17));
-				}
+			m.add(prevO);
+			while (o.hasNext()) {
+				m.add(o.next());
 			}
 		}
-		return allPDBs;
 
-	}
+    }
+
+
+    /**
+     * Get the ID of the protein which was made obsolete by newPdbId.
+     *
+     * @param newPdbId PDB ID of the newer structure
+     * @param recurse If true, return all ancestors of newPdbId.
+     * 		Otherwise, just go one step newer than oldPdbId.
+     * @return A (possibly empty) list of ID(s) of the ancestor(s) of
+     * 		newPdbId, or <tt>null</tt> if an error occurred.
+     */
+    public static List<String> getReplaces(String newPdbId, boolean recurse) {
+        List<Map<String, String>> attrList = getStatusIdRecords(new String[]{newPdbId});
+        //Expect a single record
+        if (attrList == null || attrList.size() != 1) {
+            //TODO Is it possible to have multiple record per ID?
+            // They seem to be combined into one record with space-delimited 'replaces'
+            logger.error("Error getting Status for {} from the PDB website.", newPdbId);
+            return null;
+        }
+
+        Map<String, String> attrs = attrList.get(0);
+
+        //Check that the record matches pdbId
+        String id = attrs.get("structureId");
+        if (id == null || !id.equals(newPdbId)) {
+            logger.error("Results returned from the query don't match {}", newPdbId);
+            return null;
+        }
+
+
+        String replacedList = attrs.get("replaces"); //space-delimited list
+        if (replacedList == null) {
+            // no replaces value; assume root
+            return new ArrayList<>();
+        }
+        String[] directDescendents = replacedList.split("\\s");
+
+        // Not the root! Return the replaced PDB.
+        if (recurse) {
+            // Note: Assumes a proper directed acyclic graph of revisions
+            // Cycles will cause infinite loops.
+            List<String> allDescendents = new LinkedList<>();
+            for (String replaced : directDescendents) {
+                List<String> roots = PDBStatus.getReplaces(replaced, recurse);
+                mergeReversed(allDescendents, roots);
+            }
+            mergeReversed(allDescendents, Arrays.asList(directDescendents));
+
+            return allDescendents;
+        } else {
+            return Arrays.asList(directDescendents);
+        }
+    }
+
+
+    /**
+     * The status of PDB IDs are cached to reduce server overload.
+     *
+     * This method clears the cached records.
+     */
+    public static void clearCache() {
+        recordsCache.clear();
+    }
+
+    /**
+     * Fetches the status of one or more pdbIDs from the server.
+     *
+     * <p>Returns the results as a list of Attributes.
+     * Each attribute should contain "structureId" and "status" attributes, and
+     * possibly more.
+     *
+     * <p>Example:</br>
+     * <tt>http://www.rcsb.org/pdb/rest/idStatus?structureID=1HHB,4HHB</tt></br>
+     *<pre>&lt;idStatus&gt;
+     *  &lt;record structureId="1HHB" status="OBSOLETE" replacedBy="4HHB"/&gt;
+     *  &lt;record structureId="4HHB" status="CURRENT" replaces="1HHB"/&gt;
+     *&lt;/idStatus&gt;
+     * </pre>
+     *
+     * <p>Results are not guaranteed to be returned in the same order as pdbIDs.
+     * Refer to the structureId property to match them.
+     *
+     * @param pdbIDs
+     * @return A map between attributes and values
+     */
+    private static List<Map<String, String>> getStatusIdRecords(String... pdbIDs) {
+
+        List<Map<String, String>> result = new ArrayList<>(pdbIDs.length);
+
+        String serverName = System.getProperty(PDB_SERVER_PROPERTY);
+
+        if (serverName == null)
+            serverName = DEFAULT_PDB_SERVER;
+        else
+            logger.info(String.format("Got System property %s=%s", PDB_SERVER_PROPERTY, serverName));
+
+        // Build REST query URL
+        if (pdbIDs.length < 1) {
+            throw new IllegalArgumentException("No pdbIDs specified");
+        }
+        String urlStr = String.format("http://%s/pdb/rest/idStatus?structureId=", serverName);
+        for (String pdbId : pdbIDs) {
+            pdbId = pdbId.toUpperCase();
+            //check the cache
+            Map<String, String> theResult = recordsCache.get(pdbId);
+            if (theResult != null) {
+                //logger.debug("Fetching "+pdbId+" from Cache");
+                result.add(theResult);
+            } else {
+                urlStr += pdbId + ",";
+            }
+        }
+
+        // check if any ids still need fetching
+        if (urlStr.charAt(urlStr.length() - 1) == '=')
+            return result;
+
+
+        try {
+            logger.info("Fetching {}", urlStr);
+
+            URL url = new URL(urlStr);
+
+            InputStream uStream = url.openStream();
+
+            InputSource source = new InputSource(uStream);
+            SAXParserFactory parserFactory = SAXParserFactory.newInstance();
+            SAXParser parser = parserFactory.newSAXParser();
+            XMLReader reader = parser.getXMLReader();
+
+            PDBStatusXMLHandler handler = new PDBStatusXMLHandler();
+
+            reader.setContentHandler(handler);
+            reader.parse(source);
+
+            // Fetch results of SAX parsing
+            List<Map<String, String>> records = handler.getRecords();
+
+            //add to cache
+            for (Map<String, String> record : records) {
+                String pdbId = record.get("structureId").toUpperCase();
+                if (pdbId != null) {
+                    recordsCache.put(pdbId, record);
+                }
+            }
+
+            // return results
+            result.addAll(handler.getRecords());
+
+            // TODO should throw these forward and let the caller log
+        } catch (IOException | ParserConfigurationException | SAXException e) {
+            logger.error("Problem getting status for {} from PDB server. Error: {}", Arrays.toString(pdbIDs), e.getMessage());
+            return null;
+        }
+
+        return result;
+    }
+
+    /**
+     * Handles idStatus xml by storing attributes for all record elements.
+     *
+     * @author Spencer Bliven <sbliven@ucsd.edu>
+     *
+     */
+    private static class PDBStatusXMLHandler extends DefaultHandler {
+        private final List<Map<String, String>> records;
+
+        public PDBStatusXMLHandler() {
+            records = new ArrayList<>();
+        }
+
+        /**
+         * @param uri
+         * @param localName
+         * @param qName
+         * @param attributes
+         * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)
+         */
+        @Override
+        public void startElement(String uri, String localName, String qName,
+                                 Attributes attributes) {
+            //System.out.format("Starting element: uri='%s' localName='%s' qName='%s'\n", uri, localName, qName);
+            if (qName.equals("record")) {
+                //Convert attributes into a Map, as it should have been.
+                //Important since SAX reuses Attributes objects for different calls
+                Map<String, String> attrMap = new HashMap<>(attributes.getLength() * 2);
+                for (int i = 0; i < attributes.getLength(); i++) {
+                    attrMap.put(attributes.getQName(i), attributes.getValue(i));
+                }
+                records.add(attrMap);
+            }
+        }
+
+
+        /**
+         * @param e
+         * @throws SAXException
+         * @see org.xml.sax.helpers.DefaultHandler#error(org.xml.sax.SAXParseException)
+         */
+        @Override
+        public void error(SAXParseException e) throws SAXException {
+            logger.error(e.getMessage());
+            super.error(e);
+        }
+
+
+        public List<Map<String, String>> getRecords() {
+            return records;
+        }
+    }
+
+    /** Returns a list of current PDB IDs
+     *
+     * @return a list of PDB IDs, or null if a problem occurred
+     */
+
+    public static SortedSet<String> getCurrentPDBIds() throws IOException {
+
+        SortedSet<String> allPDBs = new TreeSet<>();
+        String serverName = System.getProperty(PDB_SERVER_PROPERTY);
+
+        if (serverName == null)
+            serverName = DEFAULT_PDB_SERVER;
+        else
+            logger.info(String.format("Got System property %s=%s", PDB_SERVER_PROPERTY, serverName));
+
+        // Build REST query URL
+
+        String urlStr = String.format("http://%s/pdb/rest/getCurrent", serverName);
+        URL u = new URL(urlStr);
+
+        InputStream stream = URLConnectionTools.getInputStream(u, 60000);
+
+        if (stream != null) {
+            BufferedReader reader = new BufferedReader(
+                    new InputStreamReader(stream));
+
+            String line;
+
+            while ((line = reader.readLine()) != null) {
+                int index = line.lastIndexOf("structureId=");
+                if (index > 0) {
+                    allPDBs.add(line.substring(index + 13, index + 17));
+                }
+            }
+        }
+        return allPDBs;
+
+    }
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
index dac28d7c86..246ce2385b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
@@ -325,7 +325,7 @@ public Structure getStructure(File filename) throws IOException {
 	@Override
 	public Structure getStructureById(String pdbId) throws IOException {
 
-		return getStructure(getInputStream(pdbId));
+		return getStructure(structureInputStream(pdbId));
 	}
 
 	/**
@@ -343,13 +343,67 @@ public Structure getStructureById(String pdbId) throws IOException {
 	 * @return
 	 * @throws IOException
 	 */
-	protected InputStream getInputStream(String pdbId) throws IOException{
+	protected InputStream structureInputStream(String pdbId) throws IOException{
 
 		if ( pdbId.length() != 4)
-			throw new IOException("The provided ID does not look like a PDB ID : " + pdbId);
+			throw new IOException("Invalid PDB ID : " + pdbId);
 
-		// Check existing
-		return downloadStructure(pdbId);
+//		// Check existing
+//		if ( pdbId.length() != 4)
+//			throw new IOException("The provided ID does not look like a PDB ID : " + pdbId);
+
+		// decide whether download is required
+//		File existing =  getLocalFile(pdbId);
+//		switch(fetchBehavior) {
+//		case LOCAL_ONLY:
+//			if( existing == null ) {
+//				throw new IOException(String.format("Structure %s not found in %s "
+//						+ "and configured not to download.",pdbId,getPath()));
+//			} else {
+//				return existing;
+//			}
+//		case FETCH_FILES:
+//			// Use existing if present
+//			if( existing != null) {
+//				return existing;
+//			}
+//			// existing is null, downloadStructure(String,String,boolean,File) will download it
+//			break;
+//		case FETCH_IF_OUTDATED:
+//			// here existing can be null or not:
+//			// existing == null : downloadStructure(String,String,boolean,File) will download it
+//			// existing != null : downloadStructure(String,String,boolean,File) will check its date and download if older
+//			break;
+//		case FETCH_REMEDIATED:
+//			// Use existing if present and recent enough
+//			if( existing != null) {
+//				long lastModified = existing.lastModified();
+//
+//				if (lastModified < LAST_REMEDIATION_DATE) {
+//					// the file is too old, replace with newer version
+//					logger.warn("Replacing file {} with latest remediated (remediation of {}) file from PDB.",
+//							existing, LAST_REMEDIATION_DATE_STRING);
+//					existing = null;
+//					break;
+//				} else {
+//					return existing;
+//				}
+//			}
+//		case FORCE_DOWNLOAD:
+//			// discard the existing file to force redownload
+//			existing = null; // downloadStructure(String,String,boolean,File) will download it
+//			break;
+//		}
+
+		// Force the download now
+		if(obsoleteBehavior == ObsoleteBehavior.FETCH_CURRENT) {
+			String current = PDBStatus.getCurrent(pdbId); // either an error or there is not current entry
+			return structureInputStream(current == null ? pdbId : current, splitDirURL);
+		} else if(obsoleteBehavior == ObsoleteBehavior.FETCH_OBSOLETE && PDBStatus.getStatus(pdbId) == Status.OBSOLETE) {
+			return structureInputStream(pdbId, obsoleteDirURL);
+		} else {
+			return structureInputStream(pdbId, splitDirURL);
+		}
 	}
 
 //	/**
@@ -417,94 +471,22 @@ public boolean deleteStructure(String pdbId) throws IOException{
 		}
 	}
 
-	/**
-	 * Downloads an MMCIF file from the PDB to the local path
-	 * @param pdbId
-	 * @return The file, or null if it was unavailable for download
-	 * @throws IOException for errors downloading or writing, or if the
-	 *  fetchBehavior is {@link FetchBehavior#LOCAL_ONLY}
-	 */
-	protected InputStream downloadStructure(String pdbId) throws IOException{
-		if ( pdbId.length() != 4)
-			throw new IOException("The provided ID does not look like a PDB ID : " + pdbId);
-
-		// decide whether download is required
-//		File existing =  getLocalFile(pdbId);
-//		switch(fetchBehavior) {
-//		case LOCAL_ONLY:
-//			if( existing == null ) {
-//				throw new IOException(String.format("Structure %s not found in %s "
-//						+ "and configured not to download.",pdbId,getPath()));
-//			} else {
-//				return existing;
-//			}
-//		case FETCH_FILES:
-//			// Use existing if present
-//			if( existing != null) {
-//				return existing;
-//			}
-//			// existing is null, downloadStructure(String,String,boolean,File) will download it
-//			break;
-//		case FETCH_IF_OUTDATED:
-//			// here existing can be null or not:
-//			// existing == null : downloadStructure(String,String,boolean,File) will download it
-//			// existing != null : downloadStructure(String,String,boolean,File) will check its date and download if older
-//			break;
-//		case FETCH_REMEDIATED:
-//			// Use existing if present and recent enough
-//			if( existing != null) {
-//				long lastModified = existing.lastModified();
-//
-//				if (lastModified < LAST_REMEDIATION_DATE) {
-//					// the file is too old, replace with newer version
-//					logger.warn("Replacing file {} with latest remediated (remediation of {}) file from PDB.",
-//							existing, LAST_REMEDIATION_DATE_STRING);
-//					existing = null;
-//					break;
-//				} else {
-//					return existing;
-//				}
-//			}
-//		case FORCE_DOWNLOAD:
-//			// discard the existing file to force redownload
-//			existing = null; // downloadStructure(String,String,boolean,File) will download it
-//			break;
-//		}
-
-		// Force the download now
-		if(obsoleteBehavior == ObsoleteBehavior.FETCH_CURRENT) {
-			String current = PDBStatus.getCurrent(pdbId);
-
-			if(current == null) {
-				// either an error or there is not current entry
-				current = pdbId;
-			}
-			return downloadStructure(current, splitDirURL,false);
-		} else if(obsoleteBehavior == ObsoleteBehavior.FETCH_OBSOLETE
-				&& PDBStatus.getStatus(pdbId) == Status.OBSOLETE) {
-			return downloadStructure(pdbId, obsoleteDirURL, true);
-		} else {
-			return downloadStructure(pdbId, splitDirURL, false);
-		}
-	}
-
 	/**
 	 * Download a file from the ftp server, replacing any existing files if needed
 	 * @param pdbId PDB ID
 	 * @param pathOnServer Path on the FTP server, e.g. data/structures/divided/pdb
-	 * @param obsolete Whether or not file should be saved to the obsolete location locally
 	 * @param existingFile if not null and checkServerFileDate is true, the last modified date of the
 	 * server file and this file will be compared to decide whether to download or not
 	 * @return
 	 * @throws IOException
 	 */
-	private InputStream downloadStructure(String pdbId, String pathOnServer, boolean obsolete) throws IOException{
-
-//		File dir = getDir(pdbId,obsolete);
-//		File realFile = new File(dir,getFilename(pdbId));
-
+	private InputStream structureInputStream(String pdbId, String pathOnServer) throws IOException{
+//
+////		File dir = getDir(pdbId,obsolete);
+////		File realFile = new File(dir,getFilename(pdbId));
+//
 		String ftp;
-
+//
 		if (getFilename(pdbId).endsWith(".mmtf.gz")){
 			ftp = CodecUtils.getMmtfEntryUrl(pdbId, true, false);
 		} else {

From 1b6060129071a10ddcb85ee88dbcc37aaa3d75f1 Mon Sep 17 00:00:00 2001
From: me <me@internet.earth>
Date: Wed, 11 Mar 2020 12:58:22 -0400
Subject: [PATCH 16/18] url cache updates

---
 .../exceptions/CompoundNotFoundException.java |   4 +-
 .../nbio/core/sequence/ProteinSequence.java   |   6 +-
 .../sequence/features/FeatureRetriever.java   |   5 +-
 .../sequence/io/GenbankSequenceParser.java    |  49 ++++----
 .../io/template/SequenceParserInterface.java  |   1 +
 .../loader/GenbankProxySequenceReader.java    | 108 ++++++++----------
 .../loader/StringProxySequenceReader.java     |   7 +-
 .../{FileDownloadUtils.java => Download.java} |  77 +++++++------
 .../core/sequence/io/GenbankCookbookTest.java |   4 +-
 .../GenbankProxySequenceReaderTest.java       |   4 +-
 .../SimpleGenbankProxySequenceReaderTest.java |   4 +-
 .../twobit/SimpleTwoBitFileProvider.java      |   4 +-
 .../nbio/structure/StructureTools.java        |   4 +-
 .../structure/align/client/StructureName.java |   6 +-
 .../nbio/structure/align/util/AtomCache.java  |   4 +-
 .../align/util/URLConnectionTools.java        |   6 +-
 .../nbio/structure/cath/CathInstallation.java |   6 +-
 .../nbio/structure/ecod/EcodInstallation.java |   4 +-
 .../nbio/structure/io/LocalPDBDirectory.java  |  10 +-
 .../io/sifts/SiftsMappingProvider.java        |   4 +-
 .../nbio/structure/scop/ScopInstallation.java |   4 +-
 .../nbio/structure/scop/ScopMirror.java       |   6 +-
 .../structure/align/util/AtomCacheTest.java   |  14 +--
 .../io/mmtf/TestMmtfPerformance.java          |   1 +
 24 files changed, 169 insertions(+), 173 deletions(-)
 rename biojava-core/src/main/java/org/biojava/nbio/core/util/{FileDownloadUtils.java => Download.java} (88%)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/exceptions/CompoundNotFoundException.java b/biojava-core/src/main/java/org/biojava/nbio/core/exceptions/CompoundNotFoundException.java
index 4a16546a68..be5b6c5e7f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/exceptions/CompoundNotFoundException.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/exceptions/CompoundNotFoundException.java
@@ -25,7 +25,9 @@
  */
 package org.biojava.nbio.core.exceptions;
 
-public class CompoundNotFoundException extends Exception {
+import java.io.IOException;
+
+public class CompoundNotFoundException extends IOException {
 	/**
 	 *
 	 */
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
index a2d5f06029..c6ee24831d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
@@ -35,7 +35,7 @@
 import org.biojava.nbio.core.sequence.template.AbstractSequence;
 import org.biojava.nbio.core.sequence.template.CompoundSet;
 import org.biojava.nbio.core.sequence.template.ProxySequenceReader;
-import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.Download;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -157,9 +157,9 @@ private DNASequence getRawParentSequence(String accessId) throws IOException {
 		String seqUrlTemplate = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=%s&rettype=fasta&retmode=text";
 		URL url = new URL(String.format(seqUrlTemplate, accessId));
 
-		logger.trace("Getting parent DNA sequence from URL: {}", url.toString());
+		logger.trace("Getting parent DNA sequence from URL: {}", url);
 
-		InputStream is = FileDownloadUtils.downloadStream(url, 60000); //url.openConnection().getInputStream();
+		InputStream is = Download.stream(url); //url.openConnection().getInputStream();
 
 		FastaReader<DNASequence, NucleotideCompound> parentReader
 				= new FastaReader<>(is,
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureRetriever.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureRetriever.java
index bd2d48afee..fd47c00a44 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureRetriever.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureRetriever.java
@@ -23,12 +23,13 @@
 package org.biojava.nbio.core.sequence.features;
 
 import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.Map;
+
 /**
  * If a SequenceProxyReader implements this interface then that external source
  * has a list features
  * @author @author Paolo Pavan
  */
 public interface FeatureRetriever {
-	HashMap<String, ArrayList<AbstractFeature>> getFeatures();
+	Map<String, ArrayList<AbstractFeature>> getFeatures();
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
index 97829fc547..4cd9aa52d1 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
@@ -54,6 +54,7 @@
 
 import java.io.BufferedReader;
 import java.io.IOException;
+import java.io.Reader;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
@@ -143,11 +144,12 @@ private String parse(BufferedReader bufferedReader) {
 		// Get an ordered list of key->value pairs in array-tuples
 		do {
 			section = this.readSection(bufferedReader);
-			sectionKey = section.get(0)[0];
+			String[] s0 = section.get(0);
+			sectionKey = s0[0];
 			if (sectionKey == null) {
 				//if we reach the end of the file, section contains empty strings
-				if(section.get(0)[1]==null || section.get(0)[1].equals("") ||
-						section.get(0)[1].length()==0) {
+				if(s0[1]==null || s0[1].equals("") ||
+						s0[1].length()==0) {
 					throw new ParserException(Messages.ENDOFFILE);
 				}
 				throw new ParserException(Messages.SECTIONKEYNULL);
@@ -155,7 +157,7 @@ private String parse(BufferedReader bufferedReader) {
 			// process section-by-section
 			switch (sectionKey) {
 				case LOCUS_TAG: {
-					String loc = section.get(0)[1];
+					String loc = s0[1];
 					header = loc;
 					Matcher m = lp.matcher(loc);
 					if (m.matches()) {
@@ -169,7 +171,7 @@ private String parse(BufferedReader bufferedReader) {
 							compoundType = AminoAcidCompoundSet.aminoAcidCompoundSet;
 						} else if (lengthUnits.equalsIgnoreCase("bp")) {
 							if (type != null) {
-								if (type.contains("RNA")) {
+								if (type.contains("RNA")) { //HACK
 									compoundType = RNACompoundSet.getRNACompoundSet();
 								} else {
 									compoundType = DNACompoundSet.getDNACompoundSet();
@@ -179,7 +181,7 @@ private String parse(BufferedReader bufferedReader) {
 							}
 						}
 
-						log.debug("compound type: {}", compoundType.getClass().getSimpleName());
+						//log.debug("compound type: {}", compoundType.getClass().getSimpleName());
 
 					} else {
 						throw new ParserException("Bad locus line");
@@ -187,17 +189,17 @@ private String parse(BufferedReader bufferedReader) {
 					break;
 				}
 				case DEFINITION_TAG:
-					headerParser.setDescription(section.get(0)[1]);
+					headerParser.setDescription(s0[1]);
 					break;
 				case ACCESSION_TAG:
 					// if multiple accessions, store only first as accession,
 					// and store rest in annotation
-					String[] accs = section.get(0)[1].split("\\s+");
+					String[] accs = s0[1].split("\\s+");
 					accession = accs[0].trim();
 					headerParser.setAccession(accession);
 					break;
 				case VERSION_TAG: {
-					String ver = section.get(0)[1];
+					String ver = s0[1];
 					Matcher m = vp.matcher(ver);
 					if (m.matches()) {
 						String verAcc = m.group(1);
@@ -244,15 +246,16 @@ private String parse(BufferedReader bufferedReader) {
 					break;
 				case COMMENT_TAG:
 					// Set up some comments
-					headerParser.setComment(section.get(0)[1]);
+					headerParser.setComment(s0[1]);
 					break;
 				case FEATURE_TAG:
 					// starting from second line of input, start a new feature whenever we come across
 					// a key that does not start with /
 					AbstractFeature gbFeature = null;
 					for (int i = 1; i < section.size(); i++) {
-						String key = section.get(i)[0];
-						String val = section.get(i)[1];
+						String[] si = section.get(i);
+						String key = si[0];
+						String val = si[1];
 						if (key.startsWith("/")) {
 							if (gbFeature == null) {
 								throw new ParserException("Malformed GenBank file: found a qualifier without feature.");
@@ -271,7 +274,7 @@ private String parse(BufferedReader bufferedReader) {
 									DBReferenceInfo xref = new DBReferenceInfo(dbname, raccession);
 									gbFeature.addQualifier(key, xref);
 
-									ArrayList<DBReferenceInfo> listDBEntry = new ArrayList<>();
+									ArrayList<DBReferenceInfo> listDBEntry = new ArrayList<>(1);
 									listDBEntry.add(xref);
 									mapDB.put(key, listDBEntry);
 								} else {
@@ -284,24 +287,17 @@ private String parse(BufferedReader bufferedReader) {
 								if (key.equalsIgnoreCase("translation")) {
 									// strip spaces from sequence
 									val = val.replaceAll("\\s+", "");
-									Qualifier q = new Qualifier(key, val);
-									gbFeature.addQualifier(key, q);
+									gbFeature.addQualifier(key, new Qualifier(key, val));
 								} else {
-									Qualifier q = new Qualifier(key, val);
-									gbFeature.addQualifier(key, q);
+									gbFeature.addQualifier(key, new Qualifier(key, val));
 								}
 							}
 						} else {
 							// new feature!
 							gbFeature = new TextFeature(key, val, key, key);
-							Location l =
-									locationParser.parse(val);
-							gbFeature.setLocation((AbstractLocation) l);
+							gbFeature.setLocation((AbstractLocation) locationParser.parse(val));
 
-							if (!featureCollection.containsKey(key)) {
-								featureCollection.put(key, new ArrayList());
-							}
-							featureCollection.get(key).add(gbFeature);
+							featureCollection.computeIfAbsent(key, (x)->new ArrayList<>(1)).add(gbFeature);
 						}
 					}
 					break;
@@ -363,8 +359,7 @@ private List<String[]> readSection(BufferedReader bufferedReader) {
 					// having only white space characters
 					continue;
 				}
-				if (line == null
-						|| (!line.startsWith(" ") && linecount++ > 0 && (!firstSecKey
+				if (line == null || (!line.startsWith(" ") && linecount++ > 0 && (!firstSecKey
 						.equals(START_SEQUENCE_TAG) || line
 						.startsWith(END_SEQUENCE_TAG)))) {
 					// dump out last part of section
@@ -417,7 +412,7 @@ public String getSequence(BufferedReader bufferedReader, int sequenceLength) {
 		try {
 			parse(bufferedReader);
 		} catch (ParserException e) {
-			if(e.getMessage().equalsIgnoreCase(Messages.ENDOFFILE))	return null;
+			if (e.getMessage().equalsIgnoreCase(Messages.ENDOFFILE)) return null;
 			else throw new ParserException(e.getMessage());
 		}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
index af982f4846..bcdf19b550 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
@@ -24,6 +24,7 @@
 
 import java.io.BufferedReader;
 import java.io.IOException;
+import java.io.Reader;
 
 /**
  *
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
index b1b6ebfe4c..d9cfa03982 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
@@ -38,14 +38,15 @@
 import org.biojava.nbio.core.sequence.template.AbstractSequence;
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.CompoundSet;
+import org.biojava.nbio.core.util.Download;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.io.*;
 import java.net.URL;
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.LinkedHashMap;
+import java.util.Map;
 
 /**
  * @author Karl Nicholas <github:karlnicholas>
@@ -56,33 +57,47 @@ public class GenbankProxySequenceReader<C extends Compound> extends StringProxyS
 	private static final Logger logger = LoggerFactory.getLogger(GenbankProxySequenceReader.class);
 
 	private static final String eutilBaseURL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"; //
-	private String genbankDirectoryCache = null;
+//	private String genbankDirectoryCache = null;
 	private final GenbankSequenceParser<AbstractSequence<C>, C> genbankParser;
 	private final GenericGenbankHeaderParser<AbstractSequence<C>, C> headerParser;
 	private final String header;
-	private final HashMap<String, ArrayList<AbstractFeature>> features;
+	private final Map<String, ArrayList<AbstractFeature>> features;
 
 
 	/**
 	 *
-	 * @throws InterruptedException
 	 * @throws IOException
 	 * @throws CompoundNotFoundException
 	 */
-	public GenbankProxySequenceReader(
-			String genbankDirectoryCache,
-			String accessionID,
-			CompoundSet<C> compoundSet ) throws IOException, InterruptedException, CompoundNotFoundException {
+	public GenbankProxySequenceReader(String accessionID, CompoundSet<C> compoundSet) throws IOException, CompoundNotFoundException {
 
-		setGenbankDirectoryCache(genbankDirectoryCache);
+//		setGenbankDirectoryCache(genbankDirectoryCache);
 		setCompoundSet(compoundSet);
 
 		String db = compoundSet instanceof AminoAcidCompoundSet ? "protein" : "nuccore";
 
-		InputStream inStream = getBufferedInputStream(accessionID, db);
+		BufferedInputStream inStream1;
+//		if (genbankDirectoryCache != null && genbankDirectoryCache.length() > 0) {
+//			File f = new File(genbankDirectoryCache + File.separatorChar + accessionID + ".gb");
+//			if (f.exists()) {
+//				logger.debug("Reading: {}", f.toString());
+//				inStream1 = new BufferedInputStream(new FileInputStream(f));
+//			} else {
+//				InputStream in = getEutilsInputStream(accessionID, db);
+//				copyInputStreamToFile(in, f);
+//				inStream1 = new BufferedInputStream(new FileInputStream(f));
+//			}
+//		} else {
+		String genbankURL = eutilBaseURL + "efetch.fcgi?db=" + db + "&id=" + accessionID + "&rettype=gb&retmode=text";
+//		logger.trace("Loading: {}", genbankURL);
+//		URL genbank = new URL(genbankURL);
+//		inStream1 = new BufferedInputStream(genbank.openConnection().getInputStream());
+//		}
+		InputStream inStream = Download.stream(new URL(genbankURL));
 		genbankParser = new GenbankSequenceParser<>();
 
-		setContents(genbankParser.getSequence(new BufferedReader(new InputStreamReader(inStream)), 0));
+		String s = genbankParser.getSequence(new BufferedReader(new InputStreamReader(inStream)), 0);
+		setContents(s);
 		headerParser = genbankParser.getSequenceHeaderParser();
 		header = genbankParser.getHeader();
 		features = genbankParser.getFeatures();
@@ -97,24 +112,6 @@ public GenbankProxySequenceReader(
 		inStream.close();
 	}
 
-	private BufferedInputStream getBufferedInputStream(String accessionID, String db) throws IOException, InterruptedException {
-		BufferedInputStream inStream;
-		if (genbankDirectoryCache != null && genbankDirectoryCache.length() > 0) {
-			File f = new File(genbankDirectoryCache + File.separatorChar + accessionID + ".gb");
-			if (f.exists()) {
-				logger.debug("Reading: {}", f.toString());
-				inStream = new BufferedInputStream(new FileInputStream(f));
-			} else {
-				InputStream in = getEutilsInputStream(accessionID, db);
-				copyInputStreamToFile(in, f);
-				inStream = new BufferedInputStream(new FileInputStream(f));
-			}
-		} else {
-			inStream = new BufferedInputStream(getEutilsInputStream(accessionID, db));
-		}
-		return inStream;
-	}
-
 	private void copyInputStreamToFile(InputStream in, File f) throws IOException, InterruptedException {
 		FileOutputStream out = new FileOutputStream(f);
 		byte[] buffer = new byte[1024];
@@ -132,14 +129,7 @@ private void copyInputStreamToFile(InputStream in, File f) throws IOException, I
 		out.close();
 	}
 
-	private InputStream getEutilsInputStream(String accessionID, String db) throws IOException {
-		String genbankURL = eutilBaseURL + "efetch.fcgi?db=" + db + "&id=" + accessionID + "&rettype=gb&retmode=text";
-		logger.trace("Loading: {}", genbankURL);
-		URL genbank = new URL(genbankURL);
-		return genbank.openConnection().getInputStream();
-	}
-
-//	/**
+	//	/**
 //	 * Local directory cache of Genbank that can be downloaded
 //	 *
 //	 * @return the uniprotDirectoryCache
@@ -147,19 +137,19 @@ private InputStream getEutilsInputStream(String accessionID, String db) throws I
 //	public String getGenbankDirectoryCache() {
 //		return genbankDirectoryCache;
 //	}
-
-	/**
-	 * @param genbankDirectoryCache
-	 */
-	public void setGenbankDirectoryCache(String genbankDirectoryCache) {
-		if (genbankDirectoryCache != null) {
-			File f = new File(genbankDirectoryCache);
-			if (!f.exists()) {
-				f.mkdirs();
-			}
-		}
-		this.genbankDirectoryCache = genbankDirectoryCache;
-	}
+//
+//	/**
+//	 * @param genbankDirectoryCache
+//	 */
+//	public void setGenbankDirectoryCache(String genbankDirectoryCache) {
+//		if (genbankDirectoryCache != null) {
+//			File f = new File(genbankDirectoryCache);
+//			if (!f.exists()) {
+//				f.mkdirs();
+//			}
+//		}
+//		this.genbankDirectoryCache = genbankDirectoryCache;
+//	}
 
 	public String getHeader() {
 		return header;
@@ -169,7 +159,7 @@ public GenericGenbankHeaderParser<AbstractSequence<C>, C> getHeaderParser() {
 		return headerParser;
 	}
 	@Override
-	public HashMap<String, ArrayList<AbstractFeature>> getFeatures() {
+	public Map<String, ArrayList<AbstractFeature>> getFeatures() {
 		return features;
 	}
 
@@ -186,7 +176,7 @@ public ArrayList<String> getKeyWords() {
 	public static void main(String[] args) throws Throwable {
 
         GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
-				= new GenbankProxySequenceReader<>("/tmp", "NP_000257", AminoAcidCompoundSet.aminoAcidCompoundSet);
+				= new GenbankProxySequenceReader<>("NP_000257", AminoAcidCompoundSet.aminoAcidCompoundSet);
 		ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
 		genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
 		logger.info("Sequence ({},{})={}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
@@ -195,7 +185,7 @@ public static void main(String[] args) throws Throwable {
 		proteinSequence.getFeatures();
 
 		GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
-				= new GenbankProxySequenceReader<>("/tmp", "NM_001126", DNACompoundSet.getDNACompoundSet());
+				= new GenbankProxySequenceReader<>("NM_001126", DNACompoundSet.getDNACompoundSet());
 		DNASequence dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		dnaSequence.setAccession(new AccessionID("NM_001126"));
@@ -206,7 +196,7 @@ public static void main(String[] args) throws Throwable {
 		}
 
 		genbankDNAReader
-				= new GenbankProxySequenceReader<>("/tmp", "NM_000266", DNACompoundSet.getDNACompoundSet());
+				= new GenbankProxySequenceReader<>("NM_000266", DNACompoundSet.getDNACompoundSet());
 		dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
@@ -214,7 +204,7 @@ public static void main(String[] args) throws Throwable {
 		logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
 
 		genbankDNAReader
-				= new GenbankProxySequenceReader<>("/tmp", "AV254721", DNACompoundSet.getDNACompoundSet());
+				= new GenbankProxySequenceReader<>("AV254721", DNACompoundSet.getDNACompoundSet());
 		dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
@@ -222,7 +212,7 @@ public static void main(String[] args) throws Throwable {
 		logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
 
 		genbankDNAReader
-				= new GenbankProxySequenceReader<>("/tmp", "AV254721.2", DNACompoundSet.getDNACompoundSet());
+				= new GenbankProxySequenceReader<>("AV254721.2", DNACompoundSet.getDNACompoundSet());
 		dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
@@ -230,7 +220,7 @@ public static void main(String[] args) throws Throwable {
 		logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
 
 		genbankDNAReader
-				= new GenbankProxySequenceReader<>("/tmp", "U49845", DNACompoundSet.getDNACompoundSet());
+				= new GenbankProxySequenceReader<>("U49845", DNACompoundSet.getDNACompoundSet());
 		dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
@@ -238,7 +228,7 @@ public static void main(String[] args) throws Throwable {
 		logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
 
 		genbankDNAReader
-				= new GenbankProxySequenceReader<>("/tmp", "GI:1293613", DNACompoundSet.getDNACompoundSet());
+				= new GenbankProxySequenceReader<>("GI:1293613", DNACompoundSet.getDNACompoundSet());
 		dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
@@ -246,7 +236,7 @@ public static void main(String[] args) throws Throwable {
 		logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
 
 		genbankDNAReader
-				= new GenbankProxySequenceReader<>("/tmp", "14109166", DNACompoundSet.getDNACompoundSet());
+				= new GenbankProxySequenceReader<>("14109166", DNACompoundSet.getDNACompoundSet());
 		dnaSequence = new DNASequence(genbankDNAReader);
 		genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 		logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
index ee16f3c1d3..cd54b5823d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
@@ -32,6 +32,7 @@
 import org.biojava.nbio.core.sequence.template.*;
 import org.biojava.nbio.core.util.Equals;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
@@ -63,11 +64,15 @@ public void setCompoundSet(CompoundSet<C> compoundSet) {
 
 	@Override
 	public void setContents(String sequence) throws CompoundNotFoundException {
+		if (sequence == null)
+			throw new CompoundNotFoundException("null sequence: " +  sequence);
+
 		// Horrendously inefficient - pretty much the way the old BJ did things.
 		// TODO Should be optimised.
 		this.sequence = sequence;
 		this.parsedCompounds.clear();
-		for (int i = 0; i < sequence.length();) {
+		int l = sequence.length();
+		for (int i = 0; i < l;) {
 			String compoundStr = null;
 			C compound = null;
 			for (int compoundStrLength = 1; compound == null && compoundStrLength <= compoundSet.getMaxSingleCompoundStringLength(); compoundStrLength++) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/Download.java
similarity index 88%
rename from biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
rename to biojava-core/src/main/java/org/biojava/nbio/core/util/Download.java
index a451f60134..6465cd3e2b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/Download.java
@@ -33,9 +33,10 @@
 import java.util.concurrent.TimeUnit;
 import java.util.zip.GZIPInputStream;
 
-public class FileDownloadUtils {
+public class Download {
 
-	private static final Logger logger = LoggerFactory.getLogger(FileDownloadUtils.class);
+	private static final Logger logger = LoggerFactory.getLogger(Download.class);
+	private static final int DOWNLOAD_TIMEOUT_MS_DEFAULT = 60000;
 
 	/**
 	 * Copy the content of file src to dst TODO since java 1.7 this is provided
@@ -77,6 +78,7 @@ public static String getFilePrefix(File f) {
 		bb.followRedirects(true);
 		bb.followSslRedirects(true);
 
+
 //		try {
 			File cacheDir = Paths.get(System.getProperty("java.io.tmpdir"), "biojava").toFile();
 			cacheDir.mkdirs();
@@ -90,29 +92,29 @@ public static String getFilePrefix(File f) {
 	}
 
 
-	/**
-	 * Converts path to Unix convention and adds a terminating slash if it was
-	 * omitted
-	 *
-	 * @param path original platform dependent path
-	 * @return path in Unix convention
-	 * @author Peter Rose
-	 * @since 3.2
-	 */
-	public static String toUnixPath(String path) {
-		String uPath = path;
-		if (uPath.contains("\\")) {
-			uPath = uPath.replaceAll("\\\\", "/");
-		}
-		// this should be removed, it's need since "\" is added AtomCache code
-		if (uPath.endsWith("//")) {
-			uPath = uPath.substring(0, uPath.length() - 1);
-		}
-		if (!uPath.endsWith("/")) {
-			uPath = uPath + "/";
-		}
-		return uPath;
-	}
+//	/**
+//	 * Converts path to Unix convention and adds a terminating slash if it was
+//	 * omitted
+//	 *
+//	 * @param path original platform dependent path
+//	 * @return path in Unix convention
+//	 * @author Peter Rose
+//	 * @since 3.2
+//	 */
+//	public static String toUnixPath(String path) {
+//		String uPath = path;
+//		if (uPath.contains("\\")) {
+//			uPath = uPath.replaceAll("\\\\", "/");
+//		}
+//		// this should be removed, it's need since "\" is added AtomCache code
+//		if (uPath.endsWith("//")) {
+//			uPath = uPath.substring(0, uPath.length() - 1);
+//		}
+//		if (!uPath.endsWith("/")) {
+//			uPath = uPath + "/";
+//		}
+//		return uPath;
+//	}
 
 	/**
 	 * Expands ~ in paths to the user's home directory.
@@ -180,7 +182,7 @@ public static boolean ping(String url, int timeout) {
 	 * @throws IOException
 	 * @author Jacek Grzebyta
 	 */
-	public static URLConnection prepareURLConnection(String url, int timeout) throws IOException {
+	private static URLConnection prepareURLConnection(String url, int timeout) throws IOException {
 		URLConnection connection = new URL(url).openConnection();
 		connection.setReadTimeout(timeout);
 		connection.setConnectTimeout(timeout);
@@ -212,6 +214,10 @@ public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOExce
 	    });
 	}
 
+	public static InputStream stream(URL url) throws IOException {
+		return stream(url, DOWNLOAD_TIMEOUT_MS_DEFAULT);
+	}
+
 	/**
 	 * Open a URL and return an InputStream to it
 	 * if acceptGzipEncoding == true, use GZIPEncoding to
@@ -224,7 +230,7 @@ public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOExce
 	 * @return an {@link InputStream} of response
 	 * @throws IOException due to an error opening the URL
 	 */
-	public static InputStream downloadStream(URL url, int timeoutMS) throws IOException {
+	public static InputStream stream(URL url, int timeoutMS) throws IOException {
 //		InputStream inStream;
 //		URLConnection huc = URLConnectionTools.openURLConnection(url,timeout);
 //
@@ -248,21 +254,18 @@ public static InputStream downloadStream(URL url, int timeoutMS) throws IOExcept
 			}
 
 			ResponseBody b = r.body();
+//			if (b.contentLength()==0) {
+//				return new ByteArrayInputStream(new byte[] { } ); //HACK
+//			}
 
-			InputStream inStream = new ByteArrayInputStream(b.bytes()); //b.byteStream();
+			InputStream inStream =
+					//b.byteStream();
+					new ByteArrayInputStream(b.bytes()); //b.byteStream();
 
-			if (b.contentType().toString().contains("gzip")) {
+			if (b.contentType().toString().contains("-gzip")) {
 				return new GZIPInputStream(inStream);
 			}
 
-//			if (acceptGzipEncoding) {
-////				if (contentEncoding != null) {
-////					if (contentEncoding.contains("gzip")) {
-
-////					}
-////				}
-//			}
-
 			return inStream;
 		}
 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
index 1ce4df936d..77580fbaf8 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
@@ -71,13 +71,13 @@ public void testProcess() throws Throwable {
 		 */
 		//Try with the GenbankProxySequenceReader
         GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
-				= new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"), "NP_000257", AminoAcidCompoundSet.aminoAcidCompoundSet);
+				= new GenbankProxySequenceReader<>("NP_000257", AminoAcidCompoundSet.aminoAcidCompoundSet);
 		ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
 		genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
 		//logger.info("Sequence({},{}) = {}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
 
 	GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
-	= new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"), "NM_001126", DNACompoundSet.getDNACompoundSet());
+	= new GenbankProxySequenceReader<>("NM_001126", DNACompoundSet.getDNACompoundSet());
 	DNASequence dnaSequence = new DNASequence(genbankDNAReader);
 	genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
 	//logger.info("Sequence({},{}) = {}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
index a56cc6ecdd..57cb736ee0 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
@@ -125,7 +125,7 @@ private void copyTestFileToWorkingDirectory(String filename) throws IOException
 	public void testFeatures() throws IOException, InterruptedException, CompoundNotFoundException {
 		logger.info("run test for protein: {}", gi);
 		GenbankProxySequenceReader<AminoAcidCompound> genbankReader
-				= new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"),
+				= new GenbankProxySequenceReader<>(
 						this.gi,
 				AminoAcidCompoundSet.aminoAcidCompoundSet);
 
@@ -180,7 +180,7 @@ public void testProteinSequenceFactoring() throws Exception {
 		logger.info("create protein sequence test for target {}", gi);
 
 		GenbankProxySequenceReader<AminoAcidCompound> genbankReader
-				= new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"),
+				= new GenbankProxySequenceReader<>(
 						this.gi,
 				AminoAcidCompoundSet.aminoAcidCompoundSet);
 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
index 6bcd55360d..ecfc518b14 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
@@ -49,9 +49,7 @@ public void testWrongSequence() throws Exception {
 		String wrongGi = "34567";
 
         GenbankProxySequenceReader<AminoAcidCompound> genbankReader
-				= new GenbankProxySequenceReader<>(System.getProperty("java.io.tmpdir"),
-				wrongGi,
-                AminoAcidCompoundSet.aminoAcidCompoundSet);
+				= new GenbankProxySequenceReader<>(wrongGi, AminoAcidCompoundSet.aminoAcidCompoundSet);
 
 		ProteinSequence seq = new ProteinSequence(genbankReader);
 	}
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/SimpleTwoBitFileProvider.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/SimpleTwoBitFileProvider.java
index b587a5950f..a23e4a6d69 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/SimpleTwoBitFileProvider.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/SimpleTwoBitFileProvider.java
@@ -20,7 +20,7 @@
  */
 package org.biojava.nbio.genome.parsers.twobit;
 
-import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.Download;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -49,7 +49,7 @@ public static synchronized void downloadIfNoTwoBitFileExists(File twoBitFileLoca
 			logger.info("downloading " + twoBitFileURL + " to " + tmp.getAbsolutePath());
 
 			// 2bit files are large and take a while to download
-			FileDownloadUtils.downloadFile(twoBitFileURL, tmp);
+			Download.downloadFile(twoBitFileURL, tmp);
 
 			// check the parent directory exists
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
index a09ed5d8e9..1dabf61ddb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -22,7 +22,7 @@
  */
 package org.biojava.nbio.structure;
 
-import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.contact.AtomContactSet;
 import org.biojava.nbio.structure.contact.Grid;
@@ -1730,7 +1730,7 @@ public static Structure getStructure(String name) throws IOException,
      */
     public static Structure getStructure(String name, PDBFileParser parser,
                                          AtomCache cache) throws IOException, StructureException {
-        File f = new File(FileDownloadUtils.expandUserHome(name));
+        File f = new File(Download.expandUserHome(name));
         if (f.exists()) {
             if (parser == null) {
                 parser = new PDBFileParser();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
index e3bd7f7949..267059d591 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
@@ -21,7 +21,7 @@
 package org.biojava.nbio.structure.align.client;
 
 
-import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.cath.CathDomain;
@@ -218,7 +218,7 @@ private void init(){
 			return;
 
 		// Guess FILE based on file existence
-		File file = new File(FileDownloadUtils.expandUserHome(name));
+		File file = new File(Download.expandUserHome(name));
 		if( file.canRead() && !file.isDirectory() ) {
 			// an attempt to mitigate issue #398. It doesn't fix it but it catches the most common case of passing a pdb id and finding a file in working dir matching it
 			if (name.matches("\\d\\w\\w\\w")) {
@@ -478,7 +478,7 @@ public StructureIdentifier getBaseIdentifier() throws StructureException {
 					} else {
 						filename = name;
 					}
-					filename = FileDownloadUtils.expandUserHome(filename);
+					filename = Download.expandUserHome(filename);
 					base = new URLIdentifier(new File(filename).toURI().toURL());
 				} catch (MalformedURLException e) {
 					// Should never happen
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index 10c31f0b63..071b4d74cd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -20,7 +20,7 @@
  */
 package org.biojava.nbio.structure.align.util;
 
-import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.client.StructureName;
@@ -724,7 +724,7 @@ public void setFetchBehavior(FetchBehavior fetchBehavior) {
 	 *            to a directory
 	 */
 	public void setPath(String path) {
-		this.path = FileDownloadUtils.expandUserHome(path);
+		this.path = Download.expandUserHome(path);
 	}
 
 	public void setPdpprovider(PDPProvider pdpprovider) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java
index 837a2e6b13..12e461e01f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java
@@ -27,7 +27,7 @@
 
 package org.biojava.nbio.structure.align.util;
 
-import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.Download;
 
 import java.io.IOException;
 import java.io.InputStream;
@@ -90,7 +90,7 @@ public static URLConnection openURLConnection(URL url) throws IOException {
 	 */
 	public static InputStream getInputStream(URL url, int timeout) throws IOException
 	{
-		return FileDownloadUtils.downloadStream(url, timeout);
+		return Download.stream(url, timeout);
 	}
 
 
@@ -106,7 +106,7 @@ public static InputStream getInputStream(URL url, int timeout) throws IOExceptio
 	 */
 	public static InputStream getInputStream(URL url) throws IOException
 	{
-		return FileDownloadUtils.downloadStream(url, DEFAULT_CONNECTION_TIMEOUT);
+		return Download.stream(url, DEFAULT_CONNECTION_TIMEOUT);
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
index 07ff9b3ffd..868948051b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
@@ -23,7 +23,7 @@
 
 package org.biojava.nbio.structure.cath;
 
-import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
 import org.slf4j.Logger;
@@ -638,7 +638,7 @@ protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOEx
 		LOGGER.info("Downloading file {} to local file {}", remoteURL, localFile);
 
 		long timeS = System.currentTimeMillis();
-		File tempFile  = File.createTempFile(FileDownloadUtils.getFilePrefix(localFile), "."+ FileDownloadUtils.getFileExtension(localFile));
+		File tempFile  = File.createTempFile(Download.getFilePrefix(localFile), "."+ Download.getFileExtension(localFile));
 
 		FileOutputStream out = new FileOutputStream(tempFile);
 
@@ -651,7 +651,7 @@ protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOEx
 		in.close();
 		out.close();
 
-		FileDownloadUtils.copy(tempFile,localFile);
+		Download.copy(tempFile,localFile);
 
 		// delete the tmp file
 		tempFile.delete();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
index c216bace32..05635e578e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
@@ -20,7 +20,7 @@
 
 package org.biojava.nbio.structure.ecod;
 
-import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -388,7 +388,7 @@ private void downloadDomains() throws IOException {
 			File localFile = getDomainFile();
 
 			logger.info("Downloading {} to: {}",domainsURL, localFile);
-			FileDownloadUtils.downloadFile(domainsURL, localFile);
+			Download.downloadFile(domainsURL, localFile);
 		} catch (MalformedURLException e) {
 			logger.error("Malformed url: "+ url + DOMAINS_PATH + getDomainFilename(),e);
 		} finally {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
index 246ce2385b..83238fc0bb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
@@ -21,7 +21,7 @@
  */
 package org.biojava.nbio.structure.io;
 
-import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.PDBStatus;
 import org.biojava.nbio.structure.PDBStatus.Status;
@@ -172,7 +172,7 @@ public LocalPDBDirectory(String path) {
 			path = config.getPdbFilePath();
 			logger.debug("Initialising from system property/environment variable to path: {}", path);
 		} else {
-			path = FileDownloadUtils.expandUserHome(path);
+			path = Download.expandUserHome(path);
 			logger.debug("Initialising with path {}", path);
 		}
 		this.path = new File(path);
@@ -194,7 +194,7 @@ public LocalPDBDirectory() {
 	 * Sets the path for the directory where PDB files are read/written
 	 */
 	public void setPath(String p){
-		path = new File(FileDownloadUtils.expandUserHome(p)) ;
+		path = new File(Download.expandUserHome(p)) ;
 		initPaths();
 	}
 
@@ -300,7 +300,7 @@ public void setFetchBehavior(FetchBehavior fetchBehavior) {
 	@Override
 	public Structure getStructure(String filename) throws IOException
 	{
-		filename = FileDownloadUtils.expandUserHome(filename);
+		filename = Download.expandUserHome(filename);
 		File f = new File(filename);
 		return getStructure(f);
 
@@ -516,7 +516,7 @@ private InputStream structureInputStream(String pdbId, String pathOnServer) thro
 //		logger.info("Fetching " + ftp);
 //		logger.info("Writing to "+ realFile);
 
-		return FileDownloadUtils.downloadStream(url, 60000);
+		return Download.stream(url);
 
 		// Commented out following code used for setting the modified date to the downloaded file - JD 2015-01-15
 		// The only reason to have it was in order to get an rsync-like behavior, respecting the timestamps
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.java
index b55b449f5b..e878ef511b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.java
@@ -24,7 +24,7 @@
  */
 package org.biojava.nbio.structure.io.sifts;
 
-import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.slf4j.Logger;
@@ -88,7 +88,7 @@ public static List<SiftsEntity> getSiftsMapping(String pdbId) throws IOException
 			String u = String.format(fileLoc,pdbId);
 			URL url = new URL(u);
 			logger.debug("Downloading SIFTS file {} to {}",url,dest);
-			FileDownloadUtils.downloadFile(url, dest);
+			Download.downloadFile(url, dest);
 		}
 
 		InputStreamProvider prov = new InputStreamProvider();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
index eef68dc348..de9eb04962 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
@@ -24,7 +24,7 @@
 
 package org.biojava.nbio.structure.scop;
 
-import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureTools;
@@ -724,7 +724,7 @@ protected void downloadComFile() throws IOException{
 
 	protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOException{
 		logger.info("Downloading " + remoteURL + " to: " + localFile);
-		FileDownloadUtils.downloadFile(remoteURL, localFile);
+		Download.downloadFile(remoteURL, localFile);
 	}
 
 	private boolean claFileAvailable(){
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopMirror.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopMirror.java
index bd7ffa8175..5eff7e4db1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopMirror.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopMirror.java
@@ -20,7 +20,7 @@
  */
 package org.biojava.nbio.structure.scop;
 
-import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.Download;
 
 import java.net.URI;
 import java.net.URISyntaxException;
@@ -86,12 +86,12 @@ public String getComURL(String scopVersion) {
 	public boolean isReachable() {
 		final int timeout = 800;
 		if(rootURL != null) {
-			return FileDownloadUtils.ping(getRootURL(),timeout);
+			return Download.ping(getRootURL(),timeout);
 		} else {
 			try {
 				URI cla = new URI(getClaURL("VERSION"));
 				String host = cla.getHost();
-				return FileDownloadUtils.ping(host,timeout);
+				return Download.ping(host,timeout);
 			} catch (URISyntaxException e) {
 				return false;
 			}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
index 255b925c4d..73275bd149 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
@@ -20,7 +20,7 @@
  */
 package org.biojava.nbio.structure.align.util;
 
-import org.biojava.nbio.core.util.FileDownloadUtils;
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.io.LocalPDBDirectory;
 import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
@@ -354,7 +354,7 @@ public void testEmptyChemComp() throws IOException, StructureException {
 		System.setProperty(UserConfiguration.PDB_DIR, tmpCache.toString());
 		System.setProperty(UserConfiguration.PDB_CACHE_DIR, tmpCache.toString());
 
-		FileDownloadUtils.deleteDirectory(tmpCache);
+		Download.deleteDirectory(tmpCache);
 		Files.createDirectory(tmpCache);
 		try {
 			cache.setPath(tmpCache.toString());
@@ -374,7 +374,7 @@ public void testEmptyChemComp() throws IOException, StructureException {
 			Files.createDirectories(testCif.getParent());
 			URL resource = AtomCacheTest.class.getResource("/atp.cif.gz");
 			File src = new File(resource.getPath());
-			FileDownloadUtils.copy(src, testCif.toFile());
+			Download.copy(src, testCif.toFile());
 
 			// Load structure
 			Structure s = cache.getStructure("1ABC");
@@ -394,7 +394,7 @@ public void testEmptyChemComp() throws IOException, StructureException {
 			assertTrue(chem.getAtoms().size() > 0);
 			assertEquals("NON-POLYMER", chem.getType());
 		} finally {
-			FileDownloadUtils.deleteDirectory(tmpCache);
+			Download.deleteDirectory(tmpCache);
 		}
 	}
 
@@ -413,7 +413,7 @@ public void testEmptyGZChemComp() throws IOException, StructureException {
 		System.setProperty(UserConfiguration.PDB_DIR, tmpCache.toString());
 		System.setProperty(UserConfiguration.PDB_CACHE_DIR, tmpCache.toString());
 
-		FileDownloadUtils.deleteDirectory(tmpCache);
+		Download.deleteDirectory(tmpCache);
 		Files.createDirectory(tmpCache);
 		try {
 			cache.setPath(tmpCache.toString());
@@ -437,7 +437,7 @@ public void testEmptyGZChemComp() throws IOException, StructureException {
 			Files.createDirectories(testCif.getParent());
 			URL resource = AtomCacheTest.class.getResource("/atp.cif.gz");
 			File src = new File(resource.getPath());
-			FileDownloadUtils.copy(src, testCif.toFile());
+			Download.copy(src, testCif.toFile());
 
 			// Load structure
 			Structure s = cache.getStructure("1ABC");
@@ -457,7 +457,7 @@ public void testEmptyGZChemComp() throws IOException, StructureException {
 			assertTrue(chem.getAtoms().size() > 0);
 			assertEquals("NON-POLYMER", chem.getType());
 		} finally {
-			FileDownloadUtils.deleteDirectory(tmpCache);
+			Download.deleteDirectory(tmpCache);
 		}
 	}
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java
index 303f58a81d..26d9cbf202 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java
@@ -92,6 +92,7 @@ public void test3HBX() throws Exception{
 
 		// first make sure chemcomp cache is warmed up (chemcomp files are parsed). Like that we count the parsing time without the influence of chemcomp parsing
 		MmtfActions.readFromInputStream(new ByteArrayInputStream(mmtfdata));
+		
 		parser.parsePDBFile(new ByteArrayInputStream(pdbBytes));
 
 		for ( int i =0 ; i< NUMBER_OF_REPEATS ; i++) {

From 48fecfa73865dc283c98fe8cfe3870367b5b0593 Mon Sep 17 00:00:00 2001
From: me <me@internet.earth>
Date: Wed, 11 Mar 2020 16:48:27 -0400
Subject: [PATCH 17/18] updates

---
 .../sequence/io/GenbankSequenceParser.java    |   8 +-
 .../io/template/SequenceParserInterface.java  |   1 -
 .../loader/GenbankProxySequenceReader.java    |  64 +--
 .../loader/SequenceFileProxyLoader.java       |   2 +-
 .../loader/StringProxySequenceReader.java     |   1 -
 .../org/biojava/nbio/core/util/Download.java  |  31 +-
 .../core/sequence/io/GenbankReaderTest.java   |  14 +-
 .../GenbankProxySequenceReaderTest.java       |  13 +-
 .../nbio/genome/parsers/gff/Location.java     |  12 +-
 .../test/contact/TestInterfaceFinder.java     |   6 +-
 .../structure/test/io/TestBioassemblies.java  |  13 +-
 .../org/biojava/nbio/ontology/Ontology.java   |   3 +-
 .../org/biojava/nbio/ronn/ORonnModel.java     |  41 +-
 .../org/biojava/nbio/ronn/RonnConstraint.java | 391 +++++++-------
 .../ronn/NonstandardProteinCompoundTest.java  |   4 +-
 .../align/gui/jmol/MultipleAlignmentJmol.java |  21 +-
 .../java/org/biojava/nbio/structure/Calc.java |   2 +-
 .../biojava/nbio/structure/EntityInfo.java    |   6 +-
 .../org/biojava/nbio/structure/PDBHeader.java |   4 +-
 .../org/biojava/nbio/structure/PDBStatus.java |   2 +-
 .../biojava/nbio/structure/StructureIO.java   |   8 +-
 .../nbio/structure/StructureTools.java        |  60 +--
 .../align/MultiThreadedDBSearch.java          |   5 +-
 .../nbio/structure/align/ce/CECalculator.java |  12 +-
 .../nbio/structure/align/ce/CeMain.java       |   2 +-
 .../nbio/structure/align/ce/CeParameters.java |   6 +-
 .../structure/align/client/JFatCatClient.java | 477 +++++++++---------
 .../util/MultipleAlignmentScorer.java         |   4 +-
 .../align/pairwise/FragmentJoiner.java        |   2 +-
 .../nbio/structure/align/util/AtomCache.java  |   6 +-
 .../align/util/URLConnectionTools.java        |  45 +-
 .../align/util/UserConfiguration.java         |   4 +-
 .../structure/contact/InterfaceFinder.java    |   8 +-
 .../structure/domain/PDBDomainProvider.java   |   4 +-
 .../domain/RemoteDomainProvider.java          |   6 +-
 .../structure/domain/RemotePDPProvider.java   |   8 +-
 .../nbio/structure/io/LocalPDBDirectory.java  |   3 +-
 .../nbio/structure/io/MMCIFFileReader.java    |  12 +-
 .../io/mmcif/DownloadChemCompProvider.java    |  13 +-
 .../scop/CachedRemoteScopInstallation.java    |  22 +-
 .../scop/RemoteScopInstallation.java          |  75 ++-
 .../structure/scop/server/ScopDomains.java    |  11 +-
 .../biojava/nbio/structure/TestCloning.java   |   2 +-
 .../structure/contact/TestContactCalc.java    |  26 +-
 .../contact/TestInterfaceFinder.java          |  16 +-
 .../io/FastaAFPChainConverterTest.java        |  10 +-
 .../io/TestQuaternaryStructureProviders.java  |   4 +-
 .../biojava/nbio/ws/hmmer/HmmerResult.java    | 343 +++++++------
 .../nbio/ws/hmmer/RemoteHmmerScan.java        |   4 +-
 49 files changed, 890 insertions(+), 947 deletions(-)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
index 4cd9aa52d1..bdcc7bf05c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
@@ -44,7 +44,6 @@
 import org.biojava.nbio.core.sequence.io.template.SequenceParserInterface;
 import org.biojava.nbio.core.sequence.location.InsdcParser;
 import org.biojava.nbio.core.sequence.location.template.AbstractLocation;
-import org.biojava.nbio.core.sequence.location.template.Location;
 import org.biojava.nbio.core.sequence.reference.GenbankReference;
 import org.biojava.nbio.core.sequence.template.AbstractSequence;
 import org.biojava.nbio.core.sequence.template.Compound;
@@ -54,7 +53,6 @@
 
 import java.io.BufferedReader;
 import java.io.IOException;
-import java.io.Reader;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
@@ -148,7 +146,7 @@ private String parse(BufferedReader bufferedReader) {
 			sectionKey = s0[0];
 			if (sectionKey == null) {
 				//if we reach the end of the file, section contains empty strings
-				if(s0[1]==null || s0[1].equals("") ||
+				if(s0[1]==null || s0[1].isEmpty() ||
 						s0[1].length()==0) {
 					throw new ParserException(Messages.ENDOFFILE);
 				}
@@ -287,10 +285,8 @@ private String parse(BufferedReader bufferedReader) {
 								if (key.equalsIgnoreCase("translation")) {
 									// strip spaces from sequence
 									val = val.replaceAll("\\s+", "");
-									gbFeature.addQualifier(key, new Qualifier(key, val));
-								} else {
-									gbFeature.addQualifier(key, new Qualifier(key, val));
 								}
+								gbFeature.addQualifier(key, new Qualifier(key, val));
 							}
 						} else {
 							// new feature!
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
index bcdf19b550..af982f4846 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
@@ -24,7 +24,6 @@
 
 import java.io.BufferedReader;
 import java.io.IOException;
-import java.io.Reader;
 
 /**
  *
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
index d9cfa03982..9cfa6e3e61 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
@@ -42,7 +42,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
@@ -76,7 +79,7 @@ public GenbankProxySequenceReader(String accessionID, CompoundSet<C> compoundSet
 
 		String db = compoundSet instanceof AminoAcidCompoundSet ? "protein" : "nuccore";
 
-		BufferedInputStream inStream1;
+//		BufferedInputStream inStream1;
 //		if (genbankDirectoryCache != null && genbankDirectoryCache.length() > 0) {
 //			File f = new File(genbankDirectoryCache + File.separatorChar + accessionID + ".gb");
 //			if (f.exists()) {
@@ -93,41 +96,40 @@ public GenbankProxySequenceReader(String accessionID, CompoundSet<C> compoundSet
 //		URL genbank = new URL(genbankURL);
 //		inStream1 = new BufferedInputStream(genbank.openConnection().getInputStream());
 //		}
-		InputStream inStream = Download.stream(new URL(genbankURL));
 		genbankParser = new GenbankSequenceParser<>();
 
-		String s = genbankParser.getSequence(new BufferedReader(new InputStreamReader(inStream)), 0);
-		setContents(s);
-		headerParser = genbankParser.getSequenceHeaderParser();
-		header = genbankParser.getHeader();
-		features = genbankParser.getFeatures();
-
-		if (compoundSet.getClass().equals(AminoAcidCompoundSet.class)) {
-			if (!genbankParser.getCompoundType().equals(compoundSet)) {
-				logger.error("Declared compount type {} does not mach the real: {}", genbankParser.getCompoundType().toString(), compoundSet.toString());
-				throw new IOException("Wrong declared compound type for: " + accessionID);
+		try (InputStream inStream = Download.stream(new URL(genbankURL))) {
+			String s = genbankParser.getSequence(new BufferedReader(new InputStreamReader(inStream)), 0);
+			setContents(s);
+			headerParser = genbankParser.getSequenceHeaderParser();
+			header = genbankParser.getHeader();
+			features = genbankParser.getFeatures();
+
+			if (compoundSet.getClass().equals(AminoAcidCompoundSet.class)) {
+				if (!genbankParser.getCompoundType().equals(compoundSet)) {
+					logger.error("Declared compount type {} does not mach the real: {}", genbankParser.getCompoundType().toString(), compoundSet.toString());
+					throw new IOException("Wrong declared compound type for: " + accessionID);
+				}
 			}
 		}
-
-		inStream.close();
 	}
 
-	private void copyInputStreamToFile(InputStream in, File f) throws IOException, InterruptedException {
-		FileOutputStream out = new FileOutputStream(f);
-		byte[] buffer = new byte[1024];
-		int len = in.read(buffer);
-		while (len != -1) {
-			out.write(buffer, 0, len);
-			len = in.read(buffer);
-			if (Thread.interrupted()) {
-				in.close();
-				out.close();
-				throw new InterruptedException();
-			}
-		}
-		in.close();
-		out.close();
-	}
+//	private void copyInputStreamToFile(InputStream in, File f) throws IOException, InterruptedException {
+//		FileOutputStream out = new FileOutputStream(f);
+//		byte[] buffer = new byte[1024];
+//		int len = in.read(buffer);
+//		while (len != -1) {
+//			out.write(buffer, 0, len);
+//			len = in.read(buffer);
+//			if (Thread.interrupted()) {
+//				in.close();
+//				out.close();
+//				throw new InterruptedException();
+//			}
+//		}
+//		in.close();
+//		out.close();
+//	}
 
 	//	/**
 //	 * Local directory cache of Genbank that can be downloaded
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
index 2585d1ae5e..61b605c1fb 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
@@ -97,7 +97,7 @@ public void setCompoundSet(CompoundSet<C> compoundSet) {
 	 *  Load the sequence
 	 * @return
 	 */
-	private boolean init() throws IOException, CompoundNotFoundException {
+	private boolean init() throws IOException {
 
 		BufferedReader br = new BufferedReader(new FileReader(file));
 		br.skip(sequenceStartIndex);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
index cd54b5823d..f643c0335d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
@@ -32,7 +32,6 @@
 import org.biojava.nbio.core.sequence.template.*;
 import org.biojava.nbio.core.util.Equals;
 
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/Download.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/Download.java
index 6465cd3e2b..7b49e8b356 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/Download.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/Download.java
@@ -22,11 +22,11 @@
 package org.biojava.nbio.core.util;
 
 import okhttp3.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import java.io.*;
-import java.net.*;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.net.URLConnection;
 import java.nio.channels.FileChannel;
 import java.nio.file.*;
 import java.nio.file.attribute.BasicFileAttributes;
@@ -35,7 +35,7 @@
 
 public class Download {
 
-	private static final Logger logger = LoggerFactory.getLogger(Download.class);
+	//private static final Logger logger = LoggerFactory.getLogger(Download.class);
 	private static final int DOWNLOAD_TIMEOUT_MS_DEFAULT = 60000;
 
 	/**
@@ -77,7 +77,7 @@ public static String getFilePrefix(File f) {
 		OkHttpClient.Builder bb = new OkHttpClient.Builder();
 		bb.followRedirects(true);
 		bb.followSslRedirects(true);
-
+		bb.retryOnConnectionFailure(true);
 
 //		try {
 			File cacheDir = Paths.get(System.getProperty("java.io.tmpdir"), "biojava").toFile();
@@ -247,24 +247,21 @@ public static InputStream stream(URL url, int timeoutMS) throws IOException {
 				.build());
 
 		c.timeout().deadline(timeoutMS, TimeUnit.MILLISECONDS);
+
 		try (Response r = c.execute()) {
+			InputStream inStream;
+			ResponseBody b = r.body();
 			if (!r.isSuccessful()) {
 				//throw new IOException("Unexpected code " + r);
-				return new ByteArrayInputStream(new byte[] { } ); //HACK
+				inStream = new ByteArrayInputStream(new byte[] { } ); //HACK
+			} else {
+				inStream =
+						//b.byteStream();
+						new ByteArrayInputStream(b.bytes()); //b.byteStream();
 			}
 
-			ResponseBody b = r.body();
-//			if (b.contentLength()==0) {
-//				return new ByteArrayInputStream(new byte[] { } ); //HACK
-//			}
-
-			InputStream inStream =
-					//b.byteStream();
-					new ByteArrayInputStream(b.bytes()); //b.byteStream();
-
-			if (b.contentType().toString().contains("-gzip")) {
+			if (b.contentType().toString().contains("-gzip"))
 				return new GZIPInputStream(inStream);
-			}
 
 			return inStream;
 		}
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
index 7544a84247..5650ad4822 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
@@ -152,7 +152,7 @@ public void testProcess() throws Exception {
 	 * The underlying {@link InputStream} should remain open until the last call.
 	 */
 	@Test
-	public void testPartialProcess() throws IOException, CompoundNotFoundException {
+	public void testPartialProcess() throws IOException {
 		CheckableInputStream inStream = new CheckableInputStream(this.getClass().getResourceAsStream("/two-dnaseqs.gb"));
 
 		GenbankReader<DNASequence, NucleotideCompound> genbankDNA
@@ -217,7 +217,7 @@ public void CDStest() throws Exception {
 
 	}
 
-	private DNASequence readGenbankResource(final String resource) throws IOException, CompoundNotFoundException {
+	private DNASequence readGenbankResource(final String resource) throws IOException {
 		InputStream inputStream = getClass().getResourceAsStream(resource);
 		GenbankReader<DNASequence, NucleotideCompound> genbankDNA
 		= new GenbankReader<>(
@@ -229,7 +229,7 @@ private DNASequence readGenbankResource(final String resource) throws IOExceptio
 		return dnaSequences.values().iterator().next();
 	}
 	
-	private RNASequence readGenbankRNAResource(final String resource) throws IOException, CompoundNotFoundException {
+	private RNASequence readGenbankRNAResource(final String resource) throws IOException {
 		InputStream inputStream = getClass().getResourceAsStream(resource);
 		GenbankReader<RNASequence, NucleotideCompound> genbankRNA
 		= new GenbankReader<>(
@@ -241,7 +241,7 @@ private RNASequence readGenbankRNAResource(final String resource) throws IOExcep
 		return rnaSequences.values().iterator().next();	
 	}
 	
-	private ProteinSequence readGenbankProteinResource(final String resource) throws IOException, CompoundNotFoundException {
+	private ProteinSequence readGenbankProteinResource(final String resource) throws IOException {
 		InputStream inputStream = getClass().getResourceAsStream(resource);
         GenbankReader<ProteinSequence, AminoAcidCompound> genbankProtein
 		= new GenbankReader<>(
@@ -253,7 +253,7 @@ private ProteinSequence readGenbankProteinResource(final String resource) throws
 		return proteinSequences.values().iterator().next();	
 	}
 	
-	private AbstractSequence<?> readUnknownGenbankResource(final String resource) throws IOException, CompoundNotFoundException {
+	private AbstractSequence<?> readUnknownGenbankResource(final String resource) throws IOException {
 		InputStream inputStream = getClass().getResourceAsStream(resource);
 		GenbankSequenceParser genbankParser = new GenbankSequenceParser();
 		BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(inputStream));
@@ -270,7 +270,7 @@ private AbstractSequence<?> readUnknownGenbankResource(final String resource) th
 	}
 
 	@Test
-	public void testNcbiExpandedAccessionFormats() throws IOException, CompoundNotFoundException {
+	public void testNcbiExpandedAccessionFormats() throws IOException {
 		DNASequence header0 = readGenbankResource("/empty_header0.gb");
 		assertEquals("CP032762             5868661 bp    DNA     circular BCT 15-OCT-2018", header0.getOriginalHeader());
 
@@ -282,7 +282,7 @@ public void testNcbiExpandedAccessionFormats() throws IOException, CompoundNotFo
 	}
 	
 	@Test
-	public void testLegacyLocusCompatable() throws IOException, CompoundNotFoundException {
+	public void testLegacyLocusCompatable() throws IOException {
 		
 		// Testing opening a genbank file with uppercase units, strand and topology
 		AbstractSequence header0 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io/uppercase_locus0.gb");
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
index 57cb736ee0..90900e0a58 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
@@ -82,14 +82,13 @@ public static Collection<String[]> getExamples() {
 	 * In {@link GenbankProxySequenceReader} there is a check to see if the requested files are already in the temp
 	 * directory before attempting to retrieve them from the remote server. so simply copying the test files to the temp
 	 * directory avoids calling out to the server and hitting a 429 status code from the server which fails the build.
-	 * @throws IOException
 	 */
 	@Before
-	public void copyTestFiles() throws IOException {
-		Collection<String[]> accessorIds = getExamples();
-		for (String[] arr: accessorIds) {
-			copyTestFileToWorkingDirectory(arr[0]+".gb");
-		}
+	public void copyTestFiles() {
+//		Collection<String[]> accessorIds = getExamples();
+//		for (String[] arr: accessorIds) {
+//			copyTestFileToWorkingDirectory(arr[0]+".gb");
+//		}
 	}
 
 	/**
@@ -122,7 +121,7 @@ private void copyTestFileToWorkingDirectory(String filename) throws IOException
 
 
 	@Test
-	public void testFeatures() throws IOException, InterruptedException, CompoundNotFoundException {
+	public void testFeatures() throws IOException, InterruptedException {
 		logger.info("run test for protein: {}", gi);
 		GenbankProxySequenceReader<AminoAcidCompound> genbankReader
 				= new GenbankProxySequenceReader<>(
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
index 43463b92fb..6a4b1baeea 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
@@ -293,22 +293,22 @@ public Location intersection(Location other) {
 		}
 	}
 
-	private Location intersect(int a1, int a2, int b1, int b2) {
+	private static Location intersect(int a1, int a2, int b1, int b2) {
 		if (a1 > b1) {
 			return intersect(b1, b2, a1, a2);
 		}
 		// Safe to assume a1 <= b1
-		if (b1 >= a2) {
+		else if (b1 >= a2) {
 			// b starts after a ends
 			return null;
-		} else if (b1 < a2 && b2 <= a2) {
+		} else if (b2 <= a2) {
 			// b starts after a starts and ends before or at where a ends
 			return new Location(b1, b2);
-		} else if (b1 >= a1 && a2 <= b2) {
+		} else if (a2 <= b2) {
 			// b starts after a but extends after the end of a
 			return new Location(b1, a2);
-		}
-		return null;
+		} else
+			return null;
 	}
 
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/contact/TestInterfaceFinder.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/contact/TestInterfaceFinder.java
index 7eb07e95f6..b71f4d63d1 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/contact/TestInterfaceFinder.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/contact/TestInterfaceFinder.java
@@ -3,11 +3,7 @@
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.contact.AtomContactSet;
-import org.biojava.nbio.structure.contact.InterfaceFinder;
-import org.biojava.nbio.structure.contact.Pair;
-import org.biojava.nbio.structure.contact.StructureInterface;
-import org.biojava.nbio.structure.contact.StructureInterfaceList;
+import org.biojava.nbio.structure.contact.*;
 import org.junit.Test;
 
 import java.io.IOException;
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java
index b8370dbd02..b311b10917 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java
@@ -39,10 +39,9 @@ public class TestBioassemblies {
 	/**
 	 * A test for an NMR structure
 	 * @throws StructureException
-	 * @throws IOException
-	 */
+     */
 	@Test
-	public void test1E17() throws IOException, StructureException {
+	public void test1E17() throws StructureException {
 
 		AtomCache prevAtomCache = StructureIO.getAtomCache();
 
@@ -72,10 +71,9 @@ public void test1E17() throws IOException, StructureException {
 	/**
 	 * A test for an entry with a biounit that is a subset of the AU
 	 * @throws StructureException
-	 * @throws IOException
-	 */
+     */
 	@Test
-	public void test4TTX() throws IOException, StructureException {
+	public void test4TTX() throws StructureException {
 
 		AtomCache prevAtomCache = StructureIO.getAtomCache();
 		AtomCache cache = new AtomCache();
@@ -145,11 +143,10 @@ public void test1M4X() throws IOException, StructureException {
 
 	/**
 	 * A difficult case: see http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg25927.html
-	 * @throws IOException
 	 * @throws StructureException
 	 */
 	@Test
-	public void test4OPJ() throws IOException, StructureException {
+	public void test4OPJ() throws StructureException {
 
 		AtomCache prevAtomCache = StructureIO.getAtomCache();
 		AtomCache cache = new AtomCache();
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java
index c63f9aad23..d3ebca831e 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java
@@ -562,8 +562,7 @@ private void addTriple(Triple t) {
 		}
 
 		private void pushTriple(Map<Term,Set<Triple>> m, Term key, Triple t) {
-			Set<Triple> s = m.computeIfAbsent(key, k -> new HashSet<>());
-			s.add(t);
+			m.computeIfAbsent(key, k -> new HashSet<>(1)).add(t);
 		}
 
 		private void removeTriple(Triple t) {
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java
index 0f6dfca151..98a027ddf7 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ORonnModel.java
@@ -76,7 +76,7 @@ final float[] detect() {
         int sResidue;
         int dIndex;
         int r;
-        float est, fOrder, pDisor, fDisor;
+        double est, fOrder, pDisor, fDisor;
         final float[][] Z = new float[seqAA.length][ORonnModel.maxR];
         final int[] Q = new int[seqAA.length];
         final Threshold thold = new ModelLoader.Threshold(model.modelNum);
@@ -87,7 +87,7 @@ final float[] detect() {
          * such condition
          */
         for (sResidue = 0; sResidue <= query.length - ORonnModel.AA_ALPHABET; sResidue++) {
-            est = 0.0f;
+            est = 0.0;
 
             for (dIndex = 0; dIndex < model.numOfDBAAseq; dIndex++) {
                 final float[] rho = align(sResidue, dIndex);// search for the
@@ -105,7 +105,7 @@ final float[] detect() {
             pDisor = (float) (disorder_weight * fDisor / ((1.0 - disorder_weight)
                     * fOrder + disorder_weight * fDisor));
             for (r = sResidue; r < sResidue + ORonnModel.AA_ALPHABET; r++) {
-                Z[r][Q[r]] = pDisor;
+                Z[r][Q[r]] = (float) pDisor;
                 Q[r]++;
             }
         }
@@ -114,10 +114,10 @@ final float[] detect() {
             est = 0.0f;
             float[] zRow = Z[sResidue];
             int numOfIterations = Q[sResidue];
-            for (r = 0; r < numOfIterations; r++) {
+            for (r = 0; r < numOfIterations; r++)
                 est += zRow[r];
-            }
-            scores[sResidue] = est / numOfIterations;
+
+            scores[sResidue] = (float) (est / numOfIterations);
         }
         return scores;
     }
@@ -140,19 +140,17 @@ public void getScores(final File outfile) throws FileNotFoundException {
     // sResidue query sequence index and dIndex database sequence index
     private float[] align(final int sResidue, final int dIndex) {
         int dResidue, r;
-        float maxScore = Float.NEGATIVE_INFINITY;
-        float rho1;
+        double maxScore = Double.NEGATIVE_INFINITY;
         int maxIdx = 0;
         float rho0 = 0;
         short[] dbAARow = model.dbAA[dIndex];
         int numOfIterations = model.Length[dIndex] - ORonnModel.AA_ALPHABET;
         for (dResidue = 0; dResidue <= numOfIterations; dResidue++) {
             // go though the database sequence for maximised alignment
-            rho1 = 0.0f;
+            double rho1 = 0.0f;
             for (r = 0; r < ORonnModel.AA_ALPHABET; r++) {
                 // go through the query sequence for one alignment
-                rho1 += RonnConstraint.Blosum62[seqAA[sResidue + r]][dbAARow[dResidue
-                        + r]];
+                rho1 += RonnConstraint.Blosum62[seqAA[sResidue + r]][dbAARow[dResidue + r]];
             }
             if (rho1 > maxScore) {
                 maxScore = rho1;
@@ -162,25 +160,26 @@ private float[] align(final int sResidue, final int dIndex) {
         for (r = 0; r < ORonnModel.AA_ALPHABET; r++) {
             rho0 += RonnConstraint.Blosum62[dbAARow[maxIdx + r]][dbAARow[maxIdx + r]];
         }
-        return new float[]{rho0, maxScore};
+        return new float[]{rho0, (float)maxScore};
     }
 
     public ORonnModel(final String sequence, final Model model,
                       final float disorder) throws NumberFormatException {
-        this.disorder_weight = disorder;
-        this.model = model;
-        query = sequence.toCharArray();
-        seqAA = new short[query.length];
+
         assert model != null;
         assert model.numOfDBAAseq > 0;
+
+        this.disorder_weight = disorder;
+        this.model = model;
+        this.query = sequence.toCharArray();
+        this.seqAA = new short[query.length];
+
         int sLen = sequence.length();
         for (int sResidue = 0; sResidue < sLen; sResidue++) {
             short r = RonnConstraint.INDEX[query[sResidue] - 'A'];
-            if ((r < 0) || (r > 19)) {
-                logger.error("seqAA[sResidue]={}({})", r, query[sResidue]);
-                System.exit(1);
-            }
-            seqAA[sResidue] = r;
+            if ((r < 0) || (r > 19))
+                throw new RuntimeException("seqAA[sResidue]=" + r + "(" + query[sResidue] + ")");//System.exit(1);
+            this.seqAA[sResidue] = r;
         }
     }
 }
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/RonnConstraint.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/RonnConstraint.java
index 995ecbda6b..4329a8e521 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/RonnConstraint.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/RonnConstraint.java
@@ -37,197 +37,202 @@
  */
 public final class RonnConstraint {
 
-	public final static float DEFAULT_DISORDER = 0.53f;
-	public final static float DEFAULT_ORDER = 0.47f;
-
-	public final static float DEFAULT_RANGE_PROBABILITY_THRESHOLD = 0.50f;
-
-	// A b C D E F G H I j K L M N o P Q R S T u V W x Y
-	//
-	// 0 0 1 2 3 4 5 6 7 0 8 9 10 11 0 12 13 14 15 16 0 17 18 0 19
-
-	public static final short[] INDEX = new short[] { 0, 0, 1, 2, 3, 4, 5, 6,
-		7, 0, 8, 9, 10, 11, 0, 12, 13, 14, 15, 16, 0, 17, 18, 0, 19 };
-
-	public static final short[][] Blosum62 = new short[][] {
-		{ 4, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -1, -1, -1, -1, 1, -1,
-			-2, -3, -2 },
-		{ 0, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1,
-			-1, -2, -2 },
-		{ -2, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -1, 0, -2, 0, 1, -3,
-			-4, -3 },
-		{ -1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -1, 2, 0, 0, 0, -3,
-			-3, -2 },
-		{ -2, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -3, -3, -2, -2,
-			-1, 1, 3 },
-		{ 0, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, -2, -2, -2, -2, 0, 1,
-			0, -2, -3 },
-		{ -2, -3, 1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -2, 0, 0, -1, 0, -2,
-			-2, 2 },
-		{ -1, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -3, -3, -3, -2, -2,
-			1, -3, -1 },
-		{ -1, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -1, 1, 2, 0, 0, -3,
-			-3, -2 },
-		{ -1, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -3, -2, -2, -2, -2,
-			3, -2, -1 },
-		{ -1, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -2, 0, -1, -1, -1,
-			-2, -1, -1 },
-		{ -2, -3, 1, 0, -3, 0, -1, -3, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3,
-			-4, -2 },
-		{ -1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -1, 7, -1, -2, -1, 1,
-			-2, -4, -3 },
-		{ -1, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, 1, 0, 0, -2, -2,
-			-1 },
-		{ -1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, -1, -1, -3,
-			-3, -2 },
-		{ 1, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, 1, -2,
-			-3, -2 },
-		{ -1, -1, 1, 0, -2, 1, 0, -2, 0, -2, -1, 0, 1, 0, -1, 1, 4, -2, -3,
-			-2 },
-		{ 0, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, -2,
-			4, -3, -1 },
-		{ -3, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3,
-			-3, -3, 11, 2 },
-		{ -2, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2,
-			-1, 2, 7 } };
-
-	public enum Threshold {
-	T0(0, RonnConstraint.THRESHOLD0), T1(1, RonnConstraint.THRESHOLD1), T2(
-		2, RonnConstraint.THRESHOLD2), T3(3, RonnConstraint.THRESHOLD3), T4(
-		4, RonnConstraint.THRESHOLD4), T5(5, RonnConstraint.THRESHOLD5), T6(
-		6, RonnConstraint.THRESHOLD6), T7(7, RonnConstraint.THRESHOLD7), T8(
-		8, RonnConstraint.THRESHOLD8), T9(9, RonnConstraint.THRESHOLD9);
-
-	private final int tnum;
-	private final float[] values;
-
-	Threshold(final int tnum, final float[] values) {
-		this.tnum = tnum;
-		this.values = values;
-	}
-
-	public float[] getValues() {
-		return values;
-	}
-
-	public static float[] getTreshold(final int number) {
-		assert (number >= 0) && (number < 10) : number;
-		for (final Threshold t : Threshold.values()) {
-		if (t.tnum == number) {
-			return t.values;
-		}
-		}
-		return null;
-	}
-
-	}
-
-	static final float[] THRESHOLD0 = { 0.09847548204866169f,
-		0.5537946867723033f, 0.052493213903229766f, 0.07714031903493762f };
-
-	static final float[] THRESHOLD1 = { 0.09032956077766974f,
-		0.5167594539472075f, 0.04596823441915963f, 0.06455503987769765f };
-
-	static final float[] THRESHOLD2 = { 0.09266796710382286f,
-		0.5127732233896729f, 0.04963484289158484f, 0.061048745226114226f };
-
-	static final float[] THRESHOLD3 = { 0.10562230953899814f,
-		0.4488757690530404f, 0.04922765471815812f, 0.0824807293665649f };
-
-	static final float[] THRESHOLD4 = { 0.1163716006651586f,
-		0.5315238539228951f, 0.0556565226094971f, 0.0714892726762588f };
-
-	static final float[] THRESHOLD5 = { 0.09358976618303182f,
-		0.49296410198137725f, 0.054219917228374236f, 0.06593535778132877f };
-
-	static final float[] THRESHOLD6 = { 0.10526844980518248f,
-		0.4842710501752991f, 0.05215080306266067f, 0.06518758643119664f };
-
-	static final float[] THRESHOLD7 = { 0.08434396215650031f,
-		0.6007148113473553f, 0.05107636795876212f, 0.10341362611675203f };
-
-	static final float[] THRESHOLD8 = { 0.1309148603226209f,
-		0.5122245658772394f, 0.06436561753520677f, 0.06639259175313134f };
-
-	static final float[] THRESHOLD9 = { 0.18610705811017647f,
-		0.5279244438321989f, 0.0721466513318003f, 0.07983168408322228f };
-
-	static final byte MIN_SEQUENCE_LENGTH = 19;
-
-	static final String HELP_MESSAGE = " \r\n" +
-			"JRONN version 3.1b usage 1 August 2011:\r\n" +
-			"java -jar JRONN_JAR_NAME -i=inputfile <OPTIONS>\r\n" +
-			"\r\n" +
-			"Where -i=input file \r\n" +
-			"	Input file can contain one or more FASTA formatted sequences.\r\n" +
-			"\r\n" +
-			"All OPTIONS are optional\r\n" +
-			"Supported OPTIONS are: \r\n" +
-			"	-o=output file\r\n" +
-			"	-d=disorder value\r\n" +
-			"	-f=V or H \r\n" +
-			"	-s=statistics file\r\n" +
-			"	-n=number of threads to use\r\n" +
-			"OPTION DETAILED DESCRIPTION:\r\n" +
-			"	-o full path to the output file, if not specified \r\n" +
-			"	standard out is used\r\n" +
-			"\r\n" +
-			"	-d the value of disorder, defaults to 0.5\r\n" +
-			"\r\n" +
-			"	-f output format, V for vertical, where the letters \r\n" +
-			"	of the sequence and corresponding disorder values are \r\n" +
-			"	output in two column layout. H for horizontal, where the\r\n" +
-			"	disorder values are provided under the letters of the \r\n" +
-			"	sequence. Letters and values separated by tabulation in\r\n" +
-			"	this case. Defaults to V.\r\n" +
-			"\r\n" +
-			"	-s the file name to write execution statistics to.\r\n" +
-			"\r\n" +
-			"	-n the number of threads to use. Defaults to the number of \r\n" +
-			"	cores available on the computer. n=1 mean sequential \r\n" +
-			"	processing. Valid values are 1 < n < (2 x num_of_cores)\r\n" +
-			"	Default value will give the best performance.\r\n" +
-			"	\r\n" +
-			"EXAMPLES: \r\n" +
-			"\r\n" +
-			"	Predict disorder values for sequences from input file /home/input.fasta\r\n" +
-			"	output the results to the standard out. Use default disorder value\r\n" +
-			"	and utilise all cpus available on the computer.\r\n" +
-			"\r\n" +
-			"	java -jar JRONN.JAR -i=/home/input.fasta\r\n" +
-			"	\r\n" +
-			"	Predict disorder values for sequences from input file /home/input.fasta\r\n" +
-			"	output the results in horizontal layout to the /home/jronn.out, collect \r\n" +
-			"	execution statistics to /home/jronn.stat.txt file and limit the number \r\n" +
-			"	of threads to two. \r\n" +
-			"	\r\n" +
-			"	java -jar JRONN.JAR -i=/home/input.fasta -o=/home/jronn.out -d=0.6 -n=2 -f=H\r\n" +
-			"	 \r\n" +
-			"	The arguments can be provided in any order.\r\n" +
-			"\r\n" +
-			"ABOUT THE PROGRAM: 	\r\n" +
-			"	\r\n" +
-			"	JRONN is a Java implementation of RONN. JRONN is based on RONN and uses the \r\n" +
-			"	same model data, therefore gives the same predictions. Main motivation \r\n" +
-			"	behind JRONN development was providing an implementation of RONN more \r\n" +
-			"	suitable to use by the automated analysis pipelines and web services.  \r\n" +
-			"	\r\n" +
-			"	Original version of RONN is described in Yang,Z.R., Thomson,R., \r\n" +
-			"	McMeil,P. and Esnouf,R.M. (2005) RONN: the bio-basis function neural network\r\n" +
-			"	technique applied to the detection of natively disordered regions in proteins  \r\n" +
-			"	Bioinformatics 21: 3369-3376\r\n" +
-			"	See also http://www.strubi.ox.ac.uk/RONN\r\n" +
-			"	\r\n" +
-			"	Author: Peter Troshin \r\n" +
-			"	email: to.petr AT gmail DOT com\r\n" +
-			"	\r\n" +
-			"	This is a free software which comes with no guarantees.\r\n" +
-			"	JRONN is distributed under Apache Licence version 2. The full version of \r\n" +
-			"	licence	can be obtained from http://www.apache.org/licenses/LICENSE-2.0\r\n" +
-			"	";
-	/**
-	 * 700 - maximum number of lines (with sequence values) in the single model
-	 * file.
-	 */
-	static final int maxD = 700;
+    public final static float DEFAULT_DISORDER = 0.53f;
+    public final static float DEFAULT_ORDER = 0.47f;
+
+    public final static float DEFAULT_RANGE_PROBABILITY_THRESHOLD = 0.50f;
+
+    // A b C D E F G H I j K L M N o P Q R S T u V W x Y
+    //
+    // 0 0 1 2 3 4 5 6 7 0 8 9 10 11 0 12 13 14 15 16 0 17 18 0 19
+
+    /**
+     * TODO signed byte?
+     */
+    public static final short[] INDEX = new short[]{0, 0, 1, 2, 3, 4, 5, 6,
+            7, 0, 8, 9, 10, 11, 0, 12, 13, 14, 15, 16, 0, 17, 18, 0, 19};
+
+    /**
+     * TODO signed byte?
+     */
+    public static final short[][] Blosum62 = new short[][]{
+            {4, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -1, -1, -1, -1, 1, -1,
+                    -2, -3, -2},
+            {0, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1,
+                    -1, -2, -2},
+            {-2, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -1, 0, -2, 0, 1, -3,
+                    -4, -3},
+            {-1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -1, 2, 0, 0, 0, -3,
+                    -3, -2},
+            {-2, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -3, -3, -2, -2,
+                    -1, 1, 3},
+            {0, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, -2, -2, -2, -2, 0, 1,
+                    0, -2, -3},
+            {-2, -3, 1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -2, 0, 0, -1, 0, -2,
+                    -2, 2},
+            {-1, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -3, -3, -3, -2, -2,
+                    1, -3, -1},
+            {-1, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -1, 1, 2, 0, 0, -3,
+                    -3, -2},
+            {-1, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -3, -2, -2, -2, -2,
+                    3, -2, -1},
+            {-1, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -2, 0, -1, -1, -1,
+                    -2, -1, -1},
+            {-2, -3, 1, 0, -3, 0, -1, -3, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3,
+                    -4, -2},
+            {-1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -1, 7, -1, -2, -1, 1,
+                    -2, -4, -3},
+            {-1, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, 1, 0, 0, -2, -2,
+                    -1},
+            {-1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, -1, -1, -3,
+                    -3, -2},
+            {1, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, 1, -2,
+                    -3, -2},
+            {-1, -1, 1, 0, -2, 1, 0, -2, 0, -2, -1, 0, 1, 0, -1, 1, 4, -2, -3,
+                    -2},
+            {0, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, -2,
+                    4, -3, -1},
+            {-3, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3,
+                    -3, -3, 11, 2},
+            {-2, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2,
+                    -1, 2, 7}};
+
+    public enum Threshold {
+        T0(0, RonnConstraint.THRESHOLD0), T1(1, RonnConstraint.THRESHOLD1), T2(
+                2, RonnConstraint.THRESHOLD2), T3(3, RonnConstraint.THRESHOLD3), T4(
+                4, RonnConstraint.THRESHOLD4), T5(5, RonnConstraint.THRESHOLD5), T6(
+                6, RonnConstraint.THRESHOLD6), T7(7, RonnConstraint.THRESHOLD7), T8(
+                8, RonnConstraint.THRESHOLD8), T9(9, RonnConstraint.THRESHOLD9);
+
+        private final int tnum;
+        private final float[] values;
+
+        Threshold(final int tnum, final float[] values) {
+            this.tnum = tnum;
+            this.values = values;
+        }
+
+//	public float[] getValues() {
+//		return values;
+//	}
+
+        public static float[] getTreshold(final int number) {
+            assert (number >= 0) && (number < 10) : number;
+            for (final Threshold t : Threshold.values()) { //TODO use a Map
+                if (t.tnum == number)
+                    return t.values;
+            }
+            return null;
+        }
+
+    }
+
+    static final float[] THRESHOLD0 = {0.09847548204866169f,
+            0.5537946867723033f, 0.052493213903229766f, 0.07714031903493762f};
+
+    static final float[] THRESHOLD1 = {0.09032956077766974f,
+            0.5167594539472075f, 0.04596823441915963f, 0.06455503987769765f};
+
+    static final float[] THRESHOLD2 = {0.09266796710382286f,
+            0.5127732233896729f, 0.04963484289158484f, 0.061048745226114226f};
+
+    static final float[] THRESHOLD3 = {0.10562230953899814f,
+            0.4488757690530404f, 0.04922765471815812f, 0.0824807293665649f};
+
+    static final float[] THRESHOLD4 = {0.1163716006651586f,
+            0.5315238539228951f, 0.0556565226094971f, 0.0714892726762588f};
+
+    static final float[] THRESHOLD5 = {0.09358976618303182f,
+            0.49296410198137725f, 0.054219917228374236f, 0.06593535778132877f};
+
+    static final float[] THRESHOLD6 = {0.10526844980518248f,
+            0.4842710501752991f, 0.05215080306266067f, 0.06518758643119664f};
+
+    static final float[] THRESHOLD7 = {0.08434396215650031f,
+            0.6007148113473553f, 0.05107636795876212f, 0.10341362611675203f};
+
+    static final float[] THRESHOLD8 = {0.1309148603226209f,
+            0.5122245658772394f, 0.06436561753520677f, 0.06639259175313134f};
+
+    static final float[] THRESHOLD9 = {0.18610705811017647f,
+            0.5279244438321989f, 0.0721466513318003f, 0.07983168408322228f};
+
+    static final byte MIN_SEQUENCE_LENGTH = 19;
+
+    static final String HELP_MESSAGE = " \r\n" +
+            "JRONN version 3.1b usage 1 August 2011:\r\n" +
+            "java -jar JRONN_JAR_NAME -i=inputfile <OPTIONS>\r\n" +
+            "\r\n" +
+            "Where -i=input file \r\n" +
+            "	Input file can contain one or more FASTA formatted sequences.\r\n" +
+            "\r\n" +
+            "All OPTIONS are optional\r\n" +
+            "Supported OPTIONS are: \r\n" +
+            "	-o=output file\r\n" +
+            "	-d=disorder value\r\n" +
+            "	-f=V or H \r\n" +
+            "	-s=statistics file\r\n" +
+            "	-n=number of threads to use\r\n" +
+            "OPTION DETAILED DESCRIPTION:\r\n" +
+            "	-o full path to the output file, if not specified \r\n" +
+            "	standard out is used\r\n" +
+            "\r\n" +
+            "	-d the value of disorder, defaults to 0.5\r\n" +
+            "\r\n" +
+            "	-f output format, V for vertical, where the letters \r\n" +
+            "	of the sequence and corresponding disorder values are \r\n" +
+            "	output in two column layout. H for horizontal, where the\r\n" +
+            "	disorder values are provided under the letters of the \r\n" +
+            "	sequence. Letters and values separated by tabulation in\r\n" +
+            "	this case. Defaults to V.\r\n" +
+            "\r\n" +
+            "	-s the file name to write execution statistics to.\r\n" +
+            "\r\n" +
+            "	-n the number of threads to use. Defaults to the number of \r\n" +
+            "	cores available on the computer. n=1 mean sequential \r\n" +
+            "	processing. Valid values are 1 < n < (2 x num_of_cores)\r\n" +
+            "	Default value will give the best performance.\r\n" +
+            "	\r\n" +
+            "EXAMPLES: \r\n" +
+            "\r\n" +
+            "	Predict disorder values for sequences from input file /home/input.fasta\r\n" +
+            "	output the results to the standard out. Use default disorder value\r\n" +
+            "	and utilise all cpus available on the computer.\r\n" +
+            "\r\n" +
+            "	java -jar JRONN.JAR -i=/home/input.fasta\r\n" +
+            "	\r\n" +
+            "	Predict disorder values for sequences from input file /home/input.fasta\r\n" +
+            "	output the results in horizontal layout to the /home/jronn.out, collect \r\n" +
+            "	execution statistics to /home/jronn.stat.txt file and limit the number \r\n" +
+            "	of threads to two. \r\n" +
+            "	\r\n" +
+            "	java -jar JRONN.JAR -i=/home/input.fasta -o=/home/jronn.out -d=0.6 -n=2 -f=H\r\n" +
+            "	 \r\n" +
+            "	The arguments can be provided in any order.\r\n" +
+            "\r\n" +
+            "ABOUT THE PROGRAM: 	\r\n" +
+            "	\r\n" +
+            "	JRONN is a Java implementation of RONN. JRONN is based on RONN and uses the \r\n" +
+            "	same model data, therefore gives the same predictions. Main motivation \r\n" +
+            "	behind JRONN development was providing an implementation of RONN more \r\n" +
+            "	suitable to use by the automated analysis pipelines and web services.  \r\n" +
+            "	\r\n" +
+            "	Original version of RONN is described in Yang,Z.R., Thomson,R., \r\n" +
+            "	McMeil,P. and Esnouf,R.M. (2005) RONN: the bio-basis function neural network\r\n" +
+            "	technique applied to the detection of natively disordered regions in proteins  \r\n" +
+            "	Bioinformatics 21: 3369-3376\r\n" +
+            "	See also http://www.strubi.ox.ac.uk/RONN\r\n" +
+            "	\r\n" +
+            "	Author: Peter Troshin \r\n" +
+            "	email: to.petr AT gmail DOT com\r\n" +
+            "	\r\n" +
+            "	This is a free software which comes with no guarantees.\r\n" +
+            "	JRONN is distributed under Apache Licence version 2. The full version of \r\n" +
+            "	licence	can be obtained from http://www.apache.org/licenses/LICENSE-2.0\r\n" +
+            "	";
+    /**
+     * 700 - maximum number of lines (with sequence values) in the single model
+     * file.
+     */
+    static final int maxD = 700;
 }
diff --git a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
index e71e4351b5..864e74ee1f 100644
--- a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
+++ b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
@@ -55,7 +55,7 @@ public void test() throws IOException, InterruptedException {
 			try {
 				testUniprot(id);
 				// throttle load on uniprot server
-				Thread.sleep(1000);
+				Thread.sleep(200);
 
 			} catch (CompoundNotFoundException e){
 
@@ -65,7 +65,7 @@ public void test() throws IOException, InterruptedException {
 		}
 	}
 
-	private void testUniprot(String uniprotID) throws CompoundNotFoundException, IOException {
+	private void testUniprot(String uniprotID) throws IOException {
 
 		ProteinSequence seq = getUniprot(uniprotID);
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
index 6d49cd3b18..ac1360b238 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
@@ -217,14 +217,19 @@ public void windowClosing(WindowEvent e) {
 			evalString("save selection; select *; color grey; "
 					+ "select ligand; color CPK;");
 
-			if (value.equals("Set1")) {
-				colorPalette = ColorBrewer.Set1;
-			} else if (value.equals("Set2")) {
-				colorPalette = ColorBrewer.Set2;
-			} else if (value.equals("Spectral")) {
-				colorPalette = ColorBrewer.Spectral;
-			} else if (value.equals("Pastel")) {
-				colorPalette = ColorBrewer.Pastel1;
+			switch (value) {
+				case "Set1":
+					colorPalette = ColorBrewer.Set1;
+					break;
+				case "Set2":
+					colorPalette = ColorBrewer.Set2;
+					break;
+				case "Spectral":
+					colorPalette = ColorBrewer.Spectral;
+					break;
+				case "Pastel":
+					colorPalette = ColorBrewer.Pastel1;
+					break;
 			}
 			String script = getJmolString(multAln, transformedAtoms,
 					colorPalette, colorByBlocks.isSelected());
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
index ff5fb8589b..2570348365 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -86,7 +86,7 @@ public static double getDistance(Atom a, Atom b) {
 	 *            an Atom object
 	 * @return a double
 	 */
-	public static double getDistanceFast(Atom a, Atom b) {
+	public static double getDistanceSqr(Atom a, Atom b) {
 		double x = a.getX() - b.getX();
 		double y = a.getY() - b.getY();
 		double z = a.getZ() - b.getZ();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java
index e99f1ef523..e826ee7eb8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java
@@ -406,8 +406,10 @@ private ResidueNumber findResNumInOtherChains(int i, Chain chain) {
 			Group seqResGroup = c.getSeqResGroup(i);
 
 			if (seqResGroup==null) {
-				logger.warn("The SEQRES group is null for index {} in chain with asym_id {}, whilst it wasn't null in chain with asym_id {}",
-						 i, c.getId(), chain.getId());
+				if (logger.isWarnEnabled()) {
+					logger.warn("The SEQRES group is null for index {} in chain with asym_id {}, whilst it wasn't null in chain with asym_id {}",
+							i, c.getId(), chain.getId());
+				}
 				continue;
 			}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
index 2e5d5724e4..0a357f6bf1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
@@ -222,7 +222,7 @@ private void printAuthors(StringBuffer buf){
 
 	}
 
-	private void printMultiLine(StringBuffer buf, String lineStart, String data, char breakChar){
+	private static void printMultiLine(StringBuffer buf, String lineStart, String data, char breakChar){
 		if ( lineStart.length() !=  9)
 			logger.info("lineStart != 9, there will be problems :" + lineStart);
 
@@ -306,7 +306,7 @@ private void printMultiLine(StringBuffer buf, String lineStart, String data, cha
 
 	}
 
-	private void fillLine(StringBuffer buf, int currentPos){
+	private static void fillLine(StringBuffer buf, int currentPos){
 		int l = currentPos;
 		while (l < 67){
 			l++;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java
index 5a12b5b026..990fd0bab1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java
@@ -447,7 +447,7 @@ private static void mergeReversed(List<String> merged, final List<String> other)
      * 		newPdbId, or <tt>null</tt> if an error occurred.
      */
     public static List<String> getReplaces(String newPdbId, boolean recurse) {
-        List<Map<String, String>> attrList = getStatusIdRecords(new String[]{newPdbId});
+        List<Map<String, String>> attrList = getStatusIdRecords(newPdbId);
         //Expect a single record
         if (attrList == null || attrList.size() != 1) {
             //TODO Is it possible to have multiple record per ID?
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
index 6ba01d7e48..95fb0dc929 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
@@ -189,9 +189,8 @@ public static Structure getBiologicalAssembly(String pdbId, int biolAssemblyNr,
 	 * @param biolAssemblyNr - the ith biological assembly that is available for a PDB ID (we start counting at 1, 0 represents the asym unit).
 	 * @return a Structure object or null if that assembly is not available
 	 * @throws StructureException if there is no bioassembly available for given biolAssemblyNr or some other problems encountered while loading it
-	 * @throws IOException
-	 */
-	public static Structure getBiologicalAssembly(String pdbId, int biolAssemblyNr) throws IOException, StructureException {
+     */
+	public static Structure getBiologicalAssembly(String pdbId, int biolAssemblyNr) throws StructureException {
 		return getBiologicalAssembly(pdbId, biolAssemblyNr, AtomCache.DEFAULT_BIOASSEMBLY_STYLE);
 	}
 
@@ -230,11 +229,10 @@ public static List<Structure> getBiologicalAssemblies(String pdbId, boolean mult
 	 * If only one biological assembly is required use {@link #getBiologicalAssembly(String)} or {@link #getBiologicalAssembly(String, int)} instead.
 	 * @param pdbId
 	 * @return
-	 * @throws IOException
 	 * @throws StructureException
 	 * @since 5.0
 	 */
-	public static List<Structure> getBiologicalAssemblies(String pdbId) throws IOException, StructureException {
+	public static List<Structure> getBiologicalAssemblies(String pdbId) throws StructureException {
 		return getBiologicalAssemblies(pdbId, AtomCache.DEFAULT_BIOASSEMBLY_STYLE);
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
index 1dabf61ddb..224519064c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -35,7 +35,6 @@
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
-import java.io.InputStream;
 import java.util.*;
 
 /**
@@ -1511,7 +1510,7 @@ public static Map<Group, Double> getGroupDistancesWithinShell(
         // we only need this if we're averaging distances
         // note that we can't use group.getAtoms().size() because some the
         // group's atoms be outside the shell
-        Map<Group, Integer> atomCounts = new HashMap<>();
+        Map<Group, Integer> atomCounts = useAverageDistance ? new HashMap<>() : null;
 
         for (Chain chain : structure.getChains()) {
             groupLoop:
@@ -1521,40 +1520,36 @@ public static Map<Group, Double> getGroupDistancesWithinShell(
                 if (!includeWater && chainGroup.isWater())
                     continue;
 
+                ResidueNumber residue = chainGroup.getResidueNumber();
+
                 // check blacklist of residue numbers
                 for (ResidueNumber rn : excludeResidues) {
-                    if (rn.equals(chainGroup.getResidueNumber()))
+                    if (rn.equals(residue))
                         continue groupLoop;
                 }
 
                 for (Atom testAtom : chainGroup.getAtoms()) {
 
                     // use getDistanceFast as we are doing a lot of comparisons
-                    double dist = Calc.getDistanceFast(centroid, testAtom);
+                    double dist = Calc.getDistanceSqr(centroid, testAtom);
 
                     // if we're the shell
                     if (dist <= radius) {
-                        if (!distances.containsKey(chainGroup))
-                            distances.put(chainGroup, Double.POSITIVE_INFINITY);
+
+
                         if (useAverageDistance) {
                             // sum the distance; we'll divide by the total
                             // number later
                             // here, we CANNOT use fastDistance (distance
                             // squared) because we want the arithmetic mean
-                            distances.put(chainGroup, distances.get(chainGroup)
-                                    + Math.sqrt(dist));
-                            if (!atomCounts.containsKey(chainGroup))
-                                atomCounts.put(chainGroup, 0);
-                            atomCounts.put(chainGroup,
-                                    atomCounts.get(chainGroup) + 1);
+                            distances.put(chainGroup, distances.get(chainGroup) + Math.sqrt(dist));
+                            atomCounts.compute(chainGroup, (Group g, Integer y) -> y + 1);
                         } else {
                             // take the minimum distance among all atoms of
                             // chainGroup
                             // note that we can't break here because we might
                             // find a smaller distance
-                            if (dist < distances.get(chainGroup)) {
-                                distances.put(chainGroup, dist);
-                            }
+                            distances.merge(chainGroup, dist, Math::min);
                         }
                     }
 
@@ -1563,10 +1558,7 @@ public static Map<Group, Double> getGroupDistancesWithinShell(
         }
 
         if (useAverageDistance) {
-            for (Map.Entry<Group, Double> entry : distances.entrySet()) {
-                int count = atomCounts.get(entry.getKey());
-                distances.put(entry.getKey(), entry.getValue() / count);
-            }
+            distances.replaceAll((k, v) -> v / (int) atomCounts.get(k));
         } else {
             // in this case we used getDistanceFast
             distances.replaceAll((k, v) -> Math.sqrt(v));
@@ -1584,21 +1576,25 @@ public static Set<Group> getGroupsWithinShell(Structure structure,
         // which returns the square of a distance.
         distance = distance * distance;
 
-        Set<Group> returnSet = new LinkedHashSet<>();
+        Set<Group> returnSet = null;
         for (Chain chain : structure.getChains()) {
             groupLoop:
             for (Group chainGroup : chain.getAtomGroups()) {
                 if (!includeWater && chainGroup.isWater())
                     continue;
+
+                ResidueNumber residue = chainGroup.getResidueNumber();
                 for (ResidueNumber rn : excludeResidues) {
-                    if (rn.equals(chainGroup.getResidueNumber()))
+                    if (rn.equals(residue))
                         continue groupLoop;
                 }
+
                 for (Atom atomB : chainGroup.getAtoms()) {
 
                     // use getDistanceFast as we are doing a lot of comparisons
-                    double dist = Calc.getDistanceFast(atom, atomB);
+                    double dist = Calc.getDistanceSqr(atom, atomB);
                     if (dist <= distance) {
+                        if (returnSet==null) returnSet = new LinkedHashSet<>();
                         returnSet.add(chainGroup);
                         break;
                     }
@@ -1606,7 +1602,7 @@ public static Set<Group> getGroupsWithinShell(Structure structure,
                 }
             }
         }
-        return returnSet;
+        return returnSet == null ? Collections.EMPTY_SET : returnSet;
     }
 
     /**
@@ -1633,9 +1629,7 @@ public static Set<Group> getGroupsWithinShell(Structure structure,
         Set<ResidueNumber> excludeGroups = new HashSet<>();
         excludeGroups.add(group.getResidueNumber());
         for (Atom atom : group.getAtoms()) {
-            Set<Group> set = getGroupsWithinShell(structure, atom,
-                    excludeGroups, distance, includeWater);
-            returnList.addAll(set);
+            returnList.addAll(getGroupsWithinShell(structure, atom, excludeGroups, distance, includeWater));
         }
 
         return returnList;
@@ -1677,18 +1671,15 @@ public static Structure removeModels(Structure s) {
      */
     public static List<Group> filterLigands(List<Group> allGroups) {
 
-        List<Group> groups = new ArrayList<>();
+        List<Group> groups = null;
         for (Group g : allGroups) {
-
-            if (g.isPolymeric())
-                continue;
-
-            if (!g.isWater()) {
+            if (!g.isPolymeric() && !g.isWater()) {
+                if (groups == null) groups = new ArrayList(1);
                 groups.add(g);
             }
         }
 
-        return groups;
+        return groups!=null ? groups : Collections.EMPTY_LIST;
     }
 
     /**
@@ -1735,8 +1726,7 @@ public static Structure getStructure(String name, PDBFileParser parser,
             if (parser == null) {
                 parser = new PDBFileParser();
             }
-            InputStream inStream = new FileInputStream(f);
-            return parser.parsePDBFile(inStream);
+            return parser.parsePDBFile(new FileInputStream(f));
         } else {
             if (cache == null) {
                 cache = new AtomCache();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java
index 6dcf3165c3..6ddc78e86d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java
@@ -33,15 +33,12 @@
 import org.biojava.nbio.structure.align.client.FarmJobParameters;
 import org.biojava.nbio.structure.align.client.JFatCatClient;
 import org.biojava.nbio.structure.align.client.PdbPair;
-import org.biojava.nbio.structure.align.client.StructureName;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.align.util.SynchronizedOutFile;
 import org.biojava.nbio.structure.domain.DomainProvider;
 import org.biojava.nbio.structure.domain.DomainProviderFactory;
 import org.biojava.nbio.structure.domain.RemoteDomainProvider;
-import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
-import org.biojava.nbio.structure.io.PDBFileReader;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -396,7 +393,7 @@ private void checkLocalFiles() throws IOException, StructureException {
 	}
 
 
-	@Deprecated private void checkFile(String repre) throws IOException, StructureException {
+	@Deprecated private void checkFile(String repre) {
 
 //		StructureName name = new StructureName(repre);
 //
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
index a9bb046229..6fac17efc5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
@@ -97,7 +97,7 @@ public class CECalculator {
 	private Atom t;
 	protected int nTraces;
 
-	private double z;
+//	private double z;
 	private int[] traceIndexContainer;
 
 	protected final CeParameters params;
@@ -926,7 +926,7 @@ public void nextStep( AFPChain afpChain,
 	private void checkBestTraces( AFPChain afpChain,
 			Atom[] ca1, Atom[] ca2) {
 
-		z=0.0;
+		double z = 0.0;
 
 
 		int nGaps;
@@ -946,7 +946,6 @@ private void checkBestTraces( AFPChain afpChain,
 		Atom[] strBuf1 = new Atom[traceMaxSize];
 		Atom[] strBuf2 = new Atom[traceMaxSize];
 
-		double rmsdNew;
 
 
 
@@ -963,7 +962,7 @@ private void checkBestTraces( AFPChain afpChain,
 		for(int ir=0; ir<nBestTraces; ir++) {
 			if(bestTracesN[ir]!=nBestTrace) continue;
 
-			rmsdNew = getRMSDForBestTrace(ir, strBuf1, strBuf2, bestTracesN,bestTraces1, bestTrace2,winSize,ca1,ca2);
+			double rmsdNew = getRMSDForBestTrace(ir, strBuf1, strBuf2, bestTracesN,bestTraces1, bestTrace2,winSize,ca1,ca2);
 			if ( isPrint)
 				System.out.println(String.format("%d %d %d %.2f", ir, bestTracesN[ir], nBestTrace, rmsdNew));
 
@@ -1087,7 +1086,7 @@ private void checkBestTraces( AFPChain afpChain,
 								}
 								// Check new RMSD
 								//sup_str(strBuf1, strBuf2, strLen, d_);
-								rmsdNew=calc_rmsd(strBuf1, strBuf2, strLen, true);
+								double rmsdNew=calc_rmsd(strBuf1, strBuf2, strLen, true);
 								//System.out.println(String.format("step %d %d %d %.2f old: %.2f", it, idir, idep, rmsdNew, rmsd));
 
 								// Update best trace if RMSD improved
@@ -1109,7 +1108,8 @@ private void checkBestTraces( AFPChain afpChain,
 							}
 					}
 			}
-		rmsdNew=calc_rmsd(strBuf1, strBuf2, strLen,true);
+			
+		double rmsdNew=calc_rmsd(strBuf1, strBuf2, strLen,true);
 		if ( isPrint)
 			System.out.println("rmsdNew: " + rmsdNew + " rmsd " + rmsd);
 		afpChain.setTotalRmsdIni(rmsdNew);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
index e9bb7fd501..16802329be 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
@@ -95,7 +95,7 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureExce
 
 		int pos = 0;
 		for (Atom a : ca2){
-			Group g = (Group)a.getGroup().clone(); // works because each group has only a CA atom
+			Group g = a.getGroup();//.clone(); // works because each group has only a CA atom
 
 			ca2clone[pos] = g.getAtom(a.getName());
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
index 6ed2601fa8..ee7dc561d5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
@@ -161,9 +161,9 @@ public void setRmsdThr(Double rmsdThr) {
 	public Double getRmsdThrJoin() {
 		return rmsdThrJoin;
 	}
-	public void setRmsdThrJoin(Double rmsdThrJoin) {
-		this.rmsdThrJoin = rmsdThrJoin;
-	}
+//	public void setRmsdThrJoin(Double rmsdThrJoin) {
+//		this.rmsdThrJoin = rmsdThrJoin;
+//	}
 
 	public ScoringStrategy getScoringStrategy()
 	{
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
index 5e5217d569..b8097e14a2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
@@ -20,6 +20,7 @@
  */
 package org.biojava.nbio.structure.align.client;
 
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.align.fatcat.FatCatRigid;
 import org.biojava.nbio.structure.align.model.AFPChain;
@@ -41,363 +42,353 @@
 import java.util.TreeSet;
 
 public class JFatCatClient {
-	private final static Logger logger = LoggerFactory.getLogger(JFatCatClient.class);
+    private final static Logger logger = LoggerFactory.getLogger(JFatCatClient.class);
 
-	private static final ResourceManager resourceManager = ResourceManager.getResourceManager("jfatcat");
+    private static final ResourceManager resourceManager = ResourceManager.getResourceManager("jfatcat");
 
-	private static final String serverAPPEND    = "show?name1=%s&name2=%s";
+    private static final String serverAPPEND = "show?name1=%s&name2=%s";
 
-	private static final String sendAPPEND      = "submit?name1=%s&name2=%s&version=%s";
+    private static final String sendAPPEND = "submit?name1=%s&name2=%s&version=%s";
 
-	private static final String multiSendAPPEND = "jobSubmit?username=%s&version=%s";
+    private static final String multiSendAPPEND = "jobSubmit?username=%s&version=%s";
 
-	private static final String representAPPEND = "representatives?cluster=%s";
+    private static final String representAPPEND = "representatives?cluster=%s";
 
-	private static final String serverHasResult = "hasResult?method=%s&name1=%s&name2=%s";
+    private static final String serverHasResult = "hasResult?method=%s&name1=%s&name2=%s";
 
-	private static final int DEFAULT_TIMEOUT = 5000;
+    private static final int DEFAULT_TIMEOUT = 5000;
 
-	private static final String serverPositionInQueue =  "queuePosition?method=%s&name1=%s&name2=%s";
+    private static final String serverPositionInQueue = "queuePosition?method=%s&name1=%s&name2=%s";
 
-	private static final Random generator;
+    private static final Random generator;
 
-	private static final String newline = System.getProperty("line.separator");
+    private static final String newline = System.getProperty("line.separator");
 
-	private static final String KILL_JOB = "KILL_JOB";
+    private static final String KILL_JOB = "KILL_JOB";
 
-	private static final String COME_BACK_LATER = "COME_BACK_LATER";
+    private static final String COME_BACK_LATER = "COME_BACK_LATER";
 
-	static {
+    static {
 
-		generator = new Random();
+        generator = new Random();
 
-	}
+    }
 
-	public static void main(String[] args) throws Exception {
-		//System.out.println(hasPrecalculatedResult("http://source.rcsb.org/jfatcatserver/align/", "jCE Circular Permutation", "1CDG.A", "1TIM.A"));
-		AtomCache cache = new AtomCache();
-		String name1= "2W72.A";
-		String name2= "1D2Z.D";
+    public static void main(String[] args) throws Exception {
+        //System.out.println(hasPrecalculatedResult("http://source.rcsb.org/jfatcatserver/align/", "jCE Circular Permutation", "1CDG.A", "1TIM.A"));
+        AtomCache cache = new AtomCache();
+        String name1 = "2W72.A";
+        String name2 = "1D2Z.D";
 
-		Atom[] ca1 = cache.getAtoms(name1);
-		Atom[] ca2 = cache.getAtoms(name2);
+        Atom[] ca1 = cache.getAtoms(name1);
+        Atom[] ca2 = cache.getAtoms(name2);
 
-		int timeout = 10000;
+        int timeout = 10000;
 
-		String testServer = "http://source.rcsb.org/jfatcatserver/align/";
+        String testServer = "http://source.rcsb.org/jfatcatserver/align/";
 
-		System.out.println(getAFPChainFromServer(testServer, FatCatRigid.algorithmName, name1, name2, ca1, ca2, timeout));
+        System.out.println(getAFPChainFromServer(testServer, FatCatRigid.algorithmName, name1, name2, ca1, ca2, timeout));
 
-		PdbPairsMessage msg = getPdbPairs(testServer, 1, "test");
+        PdbPairsMessage msg = getPdbPairs(testServer, 1, "test");
 
-		System.out.println(msg);
+        System.out.println(msg);
 
-		System.out.println(getRepresentatives(FarmJobParameters.DEFAULT_SERVER_URL, 40));
-	}
+        System.out.println(getRepresentatives(FarmJobParameters.DEFAULT_SERVER_URL, 40));
+    }
 
-	public static boolean hasPrecalculatedResult(String serverLocation, String method, String name1, String name2 ){
-		return hasPrecalculatedResult(serverLocation, method, name1, name2, DEFAULT_TIMEOUT );
-	}
+    public static boolean hasPrecalculatedResult(String serverLocation, String method, String name1, String name2) {
+        return hasPrecalculatedResult(serverLocation, method, name1, name2, DEFAULT_TIMEOUT);
+    }
 
-	public static boolean hasPrecalculatedResult(String serverLocation, String method, String name1, String name2, int timeout){
+    public static boolean hasPrecalculatedResult(String serverLocation, String method, String name1, String name2, int timeout) {
 
-		String serverURL = serverLocation + serverHasResult;
+        String serverURL = serverLocation + serverHasResult;
 
 
-		boolean hasResults = false;
-		try {
-			String u = String.format(serverURL,URLEncoder.encode(method,"UTF-8"),name1,name2) ;
-			URL url = new URL(u);
-			//System.out.println("has result ? ..."  + url);
+        boolean hasResults = false;
+        try {
+            String u = String.format(serverURL, URLEncoder.encode(method, "UTF-8"), name1, name2);
+            URL url = new URL(u);
+            //System.out.println("has result ? ..."  + url);
 
-			InputStream stream = URLConnectionTools.getInputStream(url,timeout);
+            InputStream stream = URLConnectionTools.getInputStream(url, timeout);
 
-			String xml;
+            String xml;
 
-			if ( stream != null) {
+            if (stream != null) {
 
-				xml = convertStreamToString(stream);
-				logger.info(" has PrecalcResults got XML from server: " + xml);
-				HasResultXMLConverter conv = new HasResultXMLConverter();
-				hasResults = conv.fromXML(xml);
-			}
+                xml = convertStreamToString(stream);
+                logger.info(" has PrecalcResults got XML from server: " + xml);
+                HasResultXMLConverter conv = new HasResultXMLConverter();
+                hasResults = conv.fromXML(xml);
+            }
 
-		} catch (IOException e){
-			// log error and return false
-			logger.error("error in JFatCatClient: getAFPChainFromServer",e);
-		}
-		return hasResults;
-	}
+        } catch (IOException e) {
+            // log error and return false
+            logger.error("error in JFatCatClient: getAFPChainFromServer", e);
+        }
+        return hasResults;
+    }
 
 
-	public int getPositionInQueue(String serverLocation, String method, String name1, String name2){
-		return getPositionInQueue(serverLocation, method, name1, name2, DEFAULT_TIMEOUT);
-	}
+    public int getPositionInQueue(String serverLocation, String method, String name1, String name2) {
+        return getPositionInQueue(serverLocation, method, name1, name2, DEFAULT_TIMEOUT);
+    }
 
-	public int getPositionInQueue(String serverLocation, String method, String name1, String name2, int timeout){
-		String serverURL = serverLocation + serverPositionInQueue;
+    public int getPositionInQueue(String serverLocation, String method, String name1, String name2, int timeout) {
+        String serverURL = serverLocation + serverPositionInQueue;
 
 
-		int position = Integer.MIN_VALUE;
-		try {
-			String u = String.format(serverURL,URLEncoder.encode(method,"UTF-8"),name1,name2) ;
-			URL url = new URL(u);
+        int position = Integer.MIN_VALUE;
+        try {
+            String u = String.format(serverURL, URLEncoder.encode(method, "UTF-8"), name1, name2);
+            URL url = new URL(u);
 
-			InputStream stream = URLConnectionTools.getInputStream(url,timeout);
+            InputStream stream = URLConnectionTools.getInputStream(url, timeout);
 
-			String xml;
+            String xml;
 
-			if ( stream != null) {
+            if (stream != null) {
 
-				xml = convertStreamToString(stream);
-				//System.out.println("got XML from server: " + xml);
-				PositionInQueueXMLConverter conv = new PositionInQueueXMLConverter();
-				position = conv.fromXML(xml);
-			}
+                xml = convertStreamToString(stream);
+                //System.out.println("got XML from server: " + xml);
+                PositionInQueueXMLConverter conv = new PositionInQueueXMLConverter();
+                position = conv.fromXML(xml);
+            }
 
-		} catch (IOException e){
-			logger.error("error in JFatCatClient: getAFPChainFromServer",e); // TODO dmyersturnbull: method should throw; we shouldn't catch here
-		}
-		return position;
+        } catch (IOException e) {
+            logger.error("error in JFatCatClient: getAFPChainFromServer", e); // TODO dmyersturnbull: method should throw; we shouldn't catch here
+        }
+        return position;
 
-	}
-	public static AFPChain getAFPChainFromServer(String serverLocation ,  String name1, String name2, Atom[] ca1, Atom[] ca2) {
-		String method = FatCatRigid.algorithmName;
-		return getAFPChainFromServer(serverLocation, method, name1, name2, ca1, ca2,DEFAULT_TIMEOUT);
-	}
+    }
 
-	public static AFPChain getAFPChainFromServer(String serverLocation , String method, String name1, String name2, Atom[] ca1, Atom[] ca2, int timeout)
-	{
+    public static AFPChain getAFPChainFromServer(String serverLocation, String name1, String name2, Atom[] ca1, Atom[] ca2) {
+        String method = FatCatRigid.algorithmName;
+        return getAFPChainFromServer(serverLocation, method, name1, name2, ca1, ca2, DEFAULT_TIMEOUT);
+    }
 
-		String serverURL = serverLocation + serverAPPEND;
+    public static AFPChain getAFPChainFromServer(String serverLocation, String method, String name1, String name2, Atom[] ca1, Atom[] ca2, int timeout) {
 
-		try {
-			String u = String.format(serverURL,name1,name2) ;
+        String serverURL = serverLocation + serverAPPEND;
 
-			if ( method != null)
-				u+= "&method=" + URLEncoder.encode(method,"UTF-8");
+        try {
+            String u = String.format(serverURL, name1, name2);
 
-			URL url = new URL(u);
-			logger.info("requesting alignment from server..."  + url);
-			// have a short timeout for this...
-			// 5 sec
-			InputStream stream = URLConnectionTools.getInputStream(url,timeout);
+            if (method != null)
+                u += "&method=" + URLEncoder.encode(method, "UTF-8");
 
+            URL url = new URL(u);
+            logger.info("requesting alignment from server..." + url);
+            // have a short timeout for this...
+            // 5 sec
+            InputStream stream = URLConnectionTools.getInputStream(url, timeout);
 
 
-			if ( stream != null) {
-				String xml = convertStreamToString(stream);
-				return AFPChainXMLParser.fromXML(xml, name1, name2, ca1, ca2);
-			}
+            if (stream != null) {
+                String xml = convertStreamToString(stream);
+                return AFPChainXMLParser.fromXML(xml, name1, name2, ca1, ca2);
+            }
 
 
-			return null;
-
-			// TODO dmyersturnbull: method should throw; we shouldn't catch here
-		} catch (IOException e){
-			logger.error("error in JFatCatClient: getAFPChainFromServer",e);
-		}
-		return null;
-	}
+            return null;
 
+            // TODO dmyersturnbull: method should throw; we shouldn't catch here
+        } catch (IOException e) {
+            logger.error("error in JFatCatClient: getAFPChainFromServer", e);
+        }
+        return null;
+    }
 
-	public static String convertStreamToString(InputStream stream){
-		BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
-		StringBuilder sb = new StringBuilder();
 
-		String line;
-		try {
-			while ((line = reader.readLine()) != null) {
-				sb.append(line).append(newline);
-			}
-		} catch (IOException e) {
-			logger.error("Couldn't convert stream to string", e); // TODO dmyersturnbull: method should throw; we shouldn't catch here
-		} finally {
-			try {
-				stream.close();
-			} catch (IOException e) {
-				logger.warn("Can't close stream", e);
-			}
-		}
+    public static String convertStreamToString(InputStream stream) {
 
-		return sb.toString();
-	}
+        BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
 
-	public static String sendMultiAFPChainToServer(String serverLocation, String multiXML, String username) throws JobKillException{
-		String version = resourceManager.getString("jfatcat.version");
-		return sendMultiAFPChainToServer(serverLocation, multiXML, username, version);
-	}
+        try {
+            String line;
+            StringBuilder sb = new StringBuilder(stream.available());
+            while ((line = reader.readLine()) != null) {
+                sb.append(line).append(newline);
+            }
+            return sb.toString();
+        } catch (IOException e) {
+            logger.error("Couldn't convert stream to string", e); // TODO dmyersturnbull: method should throw; we shouldn't catch here
+			return null;
+        } finally {
+            try {
+                stream.close();
+            } catch (IOException e) {
+                logger.warn("Can't close stream", e);
+            }
+        }
 
-	public static String sendMultiAFPChainToServer(String serverLocation, String multiXML, String username, String version) throws JobKillException{
-		String multiSendURL = serverLocation + multiSendAPPEND;
+    }
 
-		String responseS = "";
+    public static String sendMultiAFPChainToServer(String serverLocation, String multiXML, String username) throws JobKillException {
+        String version = resourceManager.getString("jfatcat.version");
+        return sendMultiAFPChainToServer(serverLocation, multiXML, username, version);
+    }
 
-		String u = String.format(multiSendURL,username,version);
+    public static String sendMultiAFPChainToServer(String serverLocation, String multiXML, String username, String version) throws JobKillException {
+        String multiSendURL = serverLocation + multiSendAPPEND;
 
-		int timeout = getTimeout();
+        String responseS = "";
 
-		boolean submitted = false;
+        String u = String.format(multiSendURL, username, version);
 
-		while (! submitted ){
-			try {
-				URL url = new URL(u);
-				InputStream response = URLConnectionTools.doPOST(url, multiXML,timeout);
-				responseS = convertStreamToString(response);
-				submitted = true;
-				if (! responseS.contains("OK"))
-					logger.error("server returned " + responseS);
+        int timeout = getTimeout();
 
-				// server is busy... wait a bit and try again
-				if ( responseS.startsWith(COME_BACK_LATER)){
-					submitted = false;
-				}
+        boolean submitted = false;
 
-			} catch (Exception e){
-				logger.error("Error in JFatCatClient: while sending results back to server",e);
+        while (!submitted) {
+            try {
+                URL url = new URL(u);
+                InputStream response = URLConnectionTools.doPOST(url, multiXML, timeout);
+                responseS = convertStreamToString(response);
+                submitted = true;
+                if (!responseS.contains("OK"))
+                    logger.error("server returned " + responseS);
 
-				try {
-					int randomSleep = getRandomSleepTime();
-					logger.warn("sleeping " + (randomSleep/1000) + " sec.");
-					Thread.sleep(randomSleep);
-				} catch (InterruptedException ex){
-					logger.warn("Interrupted while sleeping", ex);
-				}
-			}
-		}
+                // server is busy... wait a bit and try again
+                if (responseS.startsWith(COME_BACK_LATER)) {
+                    submitted = false;
+                }
 
-		if ( responseS.startsWith(KILL_JOB)){
-			throw new JobKillException("Server responded with KILL message.");
+            } catch (Exception e) {
+                logger.error("Error in JFatCatClient: while sending results back to server", e);
 
-		}
+                try {
+                    int randomSleep = getRandomSleepTime();
+                    logger.warn("sleeping " + (randomSleep / 1000) + " sec.");
+                    Thread.sleep(randomSleep);
+                } catch (InterruptedException ex) {
+                    logger.warn("Interrupted while sleeping", ex);
+                }
+            }
+        }
 
+        if (responseS.startsWith(KILL_JOB)) {
+            throw new JobKillException("Server responded with KILL message.");
 
-		return responseS;
-	}
+        }
 
-	public static int getRandomSleepTime() {
 
-		// now wait between 7 and 13 min.
+        return responseS;
+    }
 
-		int minTime = 560000;
+    public static int getRandomSleepTime() {
 
-		int maxTime = 7800000 - minTime;
+        // now wait between 7 and 13 min.
 
-		int nextId = generator.nextInt(maxTime);
-		return minTime + nextId;
+        int minTime = 560000;
 
-	}
+        int maxTime = 7800000 - minTime;
 
+        int nextId = generator.nextInt(maxTime);
+        return minTime + nextId;
 
-	public static void sendAFPChainToServer(String serverLocation, AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws JobKillException
-	{
+    }
 
-		String sendURL = serverLocation + sendAPPEND;
 
-		String version = resourceManager.getString("jfatcat.version");
+    public static void sendAFPChainToServer(String serverLocation, AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws JobKillException {
 
-		int timeout = getTimeout();
+        String sendURL = serverLocation + sendAPPEND;
 
-		try {
+        String version = resourceManager.getString("jfatcat.version");
 
-			// just to make sure that similarity has been calculated!
-			afpChain.getSimilarity();
+        int timeout = getTimeout();
 
-			String xml = AFPChainXMLConverter.toXML(afpChain, ca1, ca2);
+        try {
 
-			String u = String.format(sendURL,afpChain.getName1() , afpChain.getName2(),version);
+            // just to make sure that similarity has been calculated!
+            afpChain.getSimilarity();
 
-			URL url = new URL(u);
+            String xml = AFPChainXMLConverter.toXML(afpChain, ca1, ca2);
 
-			InputStream response = URLConnectionTools.doPOST(url, xml,timeout);
+            String u = String.format(sendURL, afpChain.getName1(), afpChain.getName2(), version);
 
-			logger.debug("got response: {}", convertStreamToString(response));
+            URL url = new URL(u);
 
-			if ( xml.startsWith("KILL_JOB")){
-				throw new JobKillException("Server responded with KILL message.");
-			}
+            InputStream response = URLConnectionTools.doPOST(url, xml, timeout);
 
-		} catch (IOException e){
-			logger.error("error in JFatCatClient: sendAFPChainToServer",e);
-		}
+            logger.debug("got response: {}", convertStreamToString(response));
 
-	}
+            if (xml.startsWith("KILL_JOB")) {
+                throw new JobKillException("Server responded with KILL message.");
+            }
 
-	public static int getTimeout(){
-		String timeoutS = resourceManager.getString("connection.timeout");
-		int timeout = 60000;
+        } catch (IOException e) {
+            logger.error("error in JFatCatClient: sendAFPChainToServer", e);
+        }
 
-		try {
-			timeout = Integer.parseInt(timeoutS);
-		} catch (NumberFormatException ex ){
-			logger.error("Bad connection.timeout parameter",ex);
-		}
-		return timeout;
-	}
+    }
 
+    public static int getTimeout() {
+        String timeoutS = resourceManager.getString("connection.timeout");
+        int timeout = 60000;
 
-	public static PdbPairsMessage getPdbPairs(String url, int nrPair, String username) throws IOException, JobKillException {
+        try {
+            timeout = Integer.parseInt(timeoutS);
+        } catch (NumberFormatException ex) {
+            logger.error("Bad connection.timeout parameter", ex);
+        }
+        return timeout;
+    }
 
 
-		String urlS= url + "getPairs?" + "nrPairs=" + nrPair + "&username=" + URLEncoder.encode(username, "UTF-8");
-		int timeout = getTimeout();
+    public static PdbPairsMessage getPdbPairs(String url, int nrPair, String username) throws IOException, JobKillException {
 
-		PdbPairsMessage msg = null;
-		logger.info("requesting {}", urlS);
-		URL serverUrl = new URL(urlS);
-		// we are very tolerant with requesting a set of pairs, since we probably depend on getting it to get work started...
-		// 1 min...
-		InputStream stream = URLConnectionTools.getInputStream(serverUrl,timeout);
-		String xml;
 
-		if ( stream != null) {
+        String urlS = url + "getPairs?" + "nrPairs=" + nrPair + "&username=" + URLEncoder.encode(username, "UTF-8");
+        int timeout = getTimeout();
 
-			xml = convertStreamToString(stream);
-			if (xml != null) {
-				if ( xml.startsWith("KILL_JOB")){
-					// we got the KILL signal from the server...
-					throw new JobKillException("Server responded with KILL message.");
-				}
-				msg = PdbPairXMLConverter.convertXMLtoPairs(xml);
+        logger.info("requesting {}", urlS);
+        URL serverUrl = new URL(urlS);
+        // we are very tolerant with requesting a set of pairs, since we probably depend on getting it to get work started...
+        // 1 min...
+        InputStream stream = Download.stream(serverUrl, timeout); //URLConnectionTools.getInputStream(serverUrl,timeout);
+        String xml;
 
-			}
-		}
+        xml = convertStreamToString(stream);
 
-		return msg;
-	}
+        if (xml.startsWith("KILL_JOB"))
+            throw new JobKillException("Server responded with KILL message."); // we got the KILL signal from the server...
 
+        return PdbPairXMLConverter.convertXMLtoPairs(xml);
+    }
 
-	public static SortedSet<String> getRepresentatives(String serverLocation, int cutoff){
-		SortedSet<String> representatives = new TreeSet<>();
 
-		String representURL = serverLocation + representAPPEND;
+    public static SortedSet<String> getRepresentatives(String serverLocation, int cutoff) {
+        SortedSet<String> representatives = new TreeSet<>();
 
-		if ( cutoff < 20)
-			cutoff = 40;
-		int timeout = getTimeout();
-		String u = String.format(representURL,cutoff);
+        String representURL = serverLocation + representAPPEND;
 
-		logger.info("Fetching representatives from "+u);
-		try {
-			URL url = new URL(u);
+        if (cutoff < 20)
+            cutoff = 40;
+        int timeout = getTimeout();
+        String u = String.format(representURL, cutoff);
 
-			InputStream stream = URLConnectionTools.getInputStream(url,timeout);
+        logger.info("Fetching representatives from " + u);
+        try {
+            URL url = new URL(u);
 
-			String xml = null;
+            InputStream stream = URLConnectionTools.getInputStream(url, timeout);
 
-			if ( stream != null) {
+            String xml = null;
 
-				xml = convertStreamToString(stream);
-			}
-			if (xml != null) {
-				representatives = RepresentativeXMLConverter.fromXML(xml);
-			}
-		} catch (IOException e){ // TODO dmyersturnbull: method should throw; we shouldn't catch here
-			logger.error("Error fetching representatives",e);
-		}
-		return representatives;
-	}
+            if (stream != null) {
 
+                xml = convertStreamToString(stream);
+            }
+            if (xml != null) {
+                representatives = RepresentativeXMLConverter.fromXML(xml);
+            }
+        } catch (IOException e) { // TODO dmyersturnbull: method should throw; we shouldn't catch here
+            logger.error("Error fetching representatives", e);
+        }
+        return representatives;
+    }
 
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
index 3f0827edd3..45851e90a6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
@@ -121,7 +121,7 @@ public static double getRMSD(List<Atom[]> transformed) {
 				for (int r2 = r1 + 1; r2 < transformed.size(); r2++) {
 					Atom atom = transformed.get(r2)[c];
 					if (atom != null) {
-						nonNullSqDist += Calc.getDistanceFast(refAtom, atom);
+						nonNullSqDist += Calc.getDistanceSqr(refAtom, atom);
 						nonNullLength++;
 					}
 				}
@@ -208,7 +208,7 @@ public static double getRefRMSD(List<Atom[]> transformed, int reference) {
 					continue;
 				Atom atom = transformed.get(r)[c];
 				if (atom != null) {
-					nonNullSqDist += Calc.getDistanceFast(refAtom, atom);
+					nonNullSqDist += Calc.getDistanceSqr(refAtom, atom);
 					nonNullLength++;
 				}
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
index 520e73d169..4e14c85912 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
@@ -453,7 +453,7 @@ public static JointFragments[] frag_pairwise_compat(FragmentPair[] fraglst, int
 	}
 
 
-	public void extendFragments(Atom[] ca1, Atom[] ca2 ,JointFragments[] fragments, StrucAligParameters params) throws StructureException {
+	public void extendFragments(Atom[] ca1, Atom[] ca2 ,JointFragments[] fragments, StrucAligParameters params) {
 
 		for(JointFragments p : fragments){
 			extendFragments(ca1, ca2, p, params);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index 071b4d74cd..d5591981bf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -490,10 +490,9 @@ public Structure getStructure(StructureIdentifier strucId) throws IOException, S
 	 * @param domain
 	 *            a SCOP domain
 	 * @return a Structure object
-	 * @throws IOException
 	 * @throws StructureException
 	 */
-	public Structure getStructureForDomain(ScopDomain domain) throws IOException, StructureException {
+	public Structure getStructureForDomain(ScopDomain domain) throws StructureException {
 		return getStructureForDomain(domain, ScopFactory.getSCOP());
 	}
 
@@ -619,10 +618,9 @@ public Structure getStructureForDomain(String scopId) throws IOException, Struct
 	 * @param scopDatabase
 	 *            A {@link ScopDatabase} to use
 	 * @return a Structure object
-	 * @throws IOException
 	 * @throws StructureException
 	 */
-	public Structure getStructureForDomain(String scopId, ScopDatabase scopDatabase) throws IOException,
+	public Structure getStructureForDomain(String scopId, ScopDatabase scopDatabase) throws
 			StructureException {
 		return getStructureForDomain(scopDatabase.getDomainByScopID(scopId), scopDatabase);
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java
index 12e461e01f..75f7b681ca 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java
@@ -93,36 +93,21 @@ public static InputStream getInputStream(URL url, int timeout) throws IOExceptio
 		return Download.stream(url, timeout);
 	}
 
-
-	/**
-	 * Connect to a URL and return result as an InputStream.
-	 * always asks for response to be in GZIP encoded
-	 * <p>
-	 * The caller is responsible to close the returned InputStream not to cause
-	 * resource leaks.
-	 * @param url the input URL to be read
-	 * @return an {@link InputStream} of response
-	 * @throws IOException due to an error opening the URL
-	 */
-	public static InputStream getInputStream(URL url) throws IOException
-	{
-		return Download.stream(url, DEFAULT_CONNECTION_TIMEOUT);
-	}
-
-	/**
-	 * Do a POST to a URL and return the response stream for further processing elsewhere.
-	 * <p>
-	 * The caller is responsible to close the returned InputStream not to cause
-	 * resource leaks.
-	 * @param url  the input URL to be read
-	 * @param data the post data
-	 * @return an {@link InputStream} of response
-	 * @throws IOException due to an error opening the URL
-	 */
-	public static InputStream doPOST(URL url, String data) throws IOException
-	{
-		return doPOST(url,data,DEFAULT_CONNECTION_TIMEOUT);
-	}
+//
+//	/**
+//	 * Do a POST to a URL and return the response stream for further processing elsewhere.
+//	 * <p>
+//	 * The caller is responsible to close the returned InputStream not to cause
+//	 * resource leaks.
+//	 * @param url  the input URL to be read
+//	 * @param data the post data
+//	 * @return an {@link InputStream} of response
+//	 * @throws IOException due to an error opening the URL
+//	 */
+//	public static InputStream doPOST(URL url, String data) throws IOException
+//	{
+//		return doPOST(url,data,DEFAULT_CONNECTION_TIMEOUT);
+//	}
 
 	/**
 	 * Do a POST to a URL and return the response stream for further processing elsewhere.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
index b1e1635937..da03a26a6a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
@@ -55,8 +55,8 @@ public class UserConfiguration
 
 	public static final String lineSplit = System.getProperty("file.separator");
 
-	private String pdbFilePath;
-	private String cacheFilePath;
+	@Deprecated private String pdbFilePath;
+	@Deprecated private String cacheFilePath;
 
 	private FetchBehavior fetchBehavior;
 	private ObsoleteBehavior obsoleteBehavior;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/InterfaceFinder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/InterfaceFinder.java
index a7b01400f2..fbe6c34223 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/InterfaceFinder.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/InterfaceFinder.java
@@ -1,10 +1,6 @@
 package org.biojava.nbio.structure.contact;
 
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.xtal.CrystalTransform;
 import org.biojava.nbio.structure.xtal.SpaceGroup;
 
@@ -23,7 +19,7 @@ public class InterfaceFinder {
     private static final CrystalTransform IDENTITY_TRANSFORM = new CrystalTransform((SpaceGroup) null);
     private static final boolean INCLUDE_HETATOMS = true;
 
-    private Structure structure;
+    private final Structure structure;
     private double cutoff;
 
     private BoundingBox[] boundingBoxes;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java
index d20ca5c2e6..ecc455ef20 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java
@@ -20,7 +20,7 @@
  */
 package org.biojava.nbio.structure.domain;
 
-import org.biojava.nbio.structure.align.util.URLConnectionTools;
+import org.biojava.nbio.core.util.Download;
 import org.xml.sax.Attributes;
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
@@ -127,7 +127,7 @@ public void startElement(String uri, String localName,String qName,
 	private static void handleRestRequest(String url, DefaultHandler handler) throws SAXException, IOException, ParserConfigurationException {
 		// Fetch XML stream
 		URL u = new URL(url);
-		InputStream response = URLConnectionTools.getInputStream(u);
+        InputStream response = Download.stream(u);
 		InputSource xml = new InputSource(response);
 
 		// Parse XML
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java
index c997360ce5..c588f0a377 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemoteDomainProvider.java
@@ -20,10 +20,10 @@
  */
 package org.biojava.nbio.structure.domain;
 
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.client.JFatCatClient;
 import org.biojava.nbio.structure.align.client.StructureName;
-import org.biojava.nbio.structure.align.util.URLConnectionTools;
 import org.biojava.nbio.structure.scop.ScopDatabase;
 import org.biojava.nbio.structure.scop.ScopDomain;
 import org.biojava.nbio.structure.scop.ScopFactory;
@@ -96,7 +96,7 @@ private void loadRepresentativeDomainAssignments() throws IOException {
 		try {
 			URL u = new URL(url + "getRepresentativeDomains");
 			logger.info("Fetching {}",u);
-			InputStream response = URLConnectionTools.getInputStream(u);
+            InputStream response = Download.stream(u);
 			String xml = JFatCatClient.convertStreamToString(response);
 			results  = AssignmentXMLSerializer.fromXML(xml);
 
@@ -210,7 +210,7 @@ public SortedSet<String> getRepresentativeDomains() throws IOException {
 		try {
 			URL u = new URL(url);
 			logger.info("Fetching {}",url);
-			InputStream response = URLConnectionTools.getInputStream(u);
+            InputStream response = Download.stream(u);
 			String xml = JFatCatClient.convertStreamToString(response);
 			//System.out.println(xml);
 			domainRanges = XMLUtil.getDomainRangesFromXML(xml);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
index 05824c3483..06ef1bc3b2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
@@ -24,13 +24,13 @@
  */
 package org.biojava.nbio.structure.domain;
 
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.structure.ResidueRange;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.SubstructureIdentifier;
 import org.biojava.nbio.structure.align.client.JFatCatClient;
 import org.biojava.nbio.structure.align.util.AtomCache;
-import org.biojava.nbio.structure.align.util.URLConnectionTools;
 import org.biojava.nbio.structure.scop.server.XMLUtil;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -111,7 +111,7 @@ private void loadRepresentativeDomains() throws IOException {
 		try {
 			URL u = new URL(server + "getRepresentativePDPDomains");
 			logger.info("Fetching {}",u);
-			InputStream response = URLConnectionTools.getInputStream(u);
+            InputStream response = Download.stream(u);
 			String xml = JFatCatClient.convertStreamToString(response);
 			results  = AssignmentXMLSerializer.fromXML(xml);
 
@@ -180,7 +180,7 @@ public PDPDomain getPDPDomain(String pdpDomainName) throws IOException{
 			if (shouldRequestDomainRanges){
 				URL u = new URL(server + "getPDPDomain?pdpId="+pdpDomainName);
 				logger.info("Fetching {}",u);
-				InputStream response = URLConnectionTools.getInputStream(u);
+                InputStream response = Download.stream(u);
 				String xml = JFatCatClient.convertStreamToString(response);
 				domainRanges = XMLUtil.getDomainRangesFromXML(xml);
 				if ( domainRanges != null)
@@ -240,7 +240,7 @@ public SortedSet<String> getPDPDomainNamesForPDB(String pdbId) throws IOExceptio
 		try {
 			URL u = new URL(server + "getPDPDomainNamesForPDB?pdbId="+pdbId);
 			logger.info("Fetching {}",u);
-			InputStream response = URLConnectionTools.getInputStream(u);
+            InputStream response = Download.stream(u);
 			String xml = JFatCatClient.convertStreamToString(response);
 			results  = XMLUtil.getDomainRangesFromXML(xml);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
index 83238fc0bb..058fd0d8d9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
@@ -493,7 +493,7 @@ private InputStream structureInputStream(String pdbId, String pathOnServer) thro
 			ftp = String.format("%s%s/%s/%s", serverName, pathOnServer, pdbId.substring(1,3).toLowerCase(), getFilename(pdbId));
 		}
 
-		URL url = new URL(ftp);
+		return Download.stream(new URL(ftp));
 
 //		Date serverFileDate;
 //		if (existingFile!=null) {
@@ -516,7 +516,6 @@ private InputStream structureInputStream(String pdbId, String pathOnServer) thro
 //		logger.info("Fetching " + ftp);
 //		logger.info("Writing to "+ realFile);
 
-		return Download.stream(url);
 
 		// Commented out following code used for setting the modified date to the downloaded file - JD 2015-01-15
 		// The only reason to have it was in order to get an rsync-like behavior, respecting the timestamps
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/MMCIFFileReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/MMCIFFileReader.java
index ca91f8d70d..d3c5ed4ea8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/MMCIFFileReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/MMCIFFileReader.java
@@ -97,13 +97,14 @@ public MMCIFFileReader(String path){
 	@Override
 	public Structure getStructure(InputStream inStream) throws IOException{
 
-		MMcifParser parser = new SimpleMMcifParser();
 
 		consumer = new SimpleMMcifConsumer();
 
 		consumer.setFileParsingParameters(getFileParsingParameters());
 
 
+		MMcifParser parser = new SimpleMMcifParser();
+
 		// The Consumer builds up the BioJava - structure object.
 		// you could also hook in your own and build up you own data model.
 		parser.addMMcifConsumer(consumer);
@@ -112,14 +113,13 @@ public Structure getStructure(InputStream inStream) throws IOException{
 
 
 		// now get the protein structure.
-		Structure cifStructure = consumer.getStructure();
 
-		return cifStructure;
+		return consumer.getStructure();
 	}
 
-	public SimpleMMcifConsumer getMMcifConsumer(){
-		return consumer;
-	}
+//	public SimpleMMcifConsumer getMMcifConsumer(){
+//		return consumer;
+//	}
 
 //	public void setMMCifConsumer(SimpleMMcifConsumer consumer){
 //		this.consumer = consumer;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
index c4a1228aea..03864ef7b5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
@@ -35,6 +35,7 @@
 import java.nio.file.Paths;
 import java.nio.file.StandardCopyOption;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.zip.GZIPOutputStream;
@@ -79,12 +80,14 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 	// flags to make sure there is only one thread running that is loading the dictionary
 	static final AtomicBoolean loading = new AtomicBoolean(false);
 
-	static final List<String> protectedIDs = new ArrayList<>();
+	static final List<String> protectedIDs;
 	static {
-		protectedIDs.add("CON");
-		protectedIDs.add("PRN");
-		protectedIDs.add("AUX");
-		protectedIDs.add("NUL");
+		ArrayList<String> p = new ArrayList<>(4);
+		p.add("CON");
+		p.add("PRN");
+		p.add("AUX");
+		p.add("NUL");
+		protectedIDs = Collections.unmodifiableList(p);
 	}
 
 	private static ChemCompProvider fallback = null; // Fallback provider if the download fails
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/CachedRemoteScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/CachedRemoteScopInstallation.java
index aec7572600..74d81c3a18 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/CachedRemoteScopInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/CachedRemoteScopInstallation.java
@@ -24,8 +24,8 @@
  */
 package org.biojava.nbio.structure.scop;
 
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.structure.align.client.JFatCatClient;
-import org.biojava.nbio.structure.align.util.URLConnectionTools;
 import org.biojava.nbio.structure.domain.SerializableCache;
 import org.biojava.nbio.structure.scop.server.ScopDomains;
 import org.slf4j.Logger;
@@ -91,17 +91,17 @@ private void loadRepresentativeDomains() throws IOException {
 		} catch (MalformedURLException e) {
 			throw new IOException("URL " + RemoteScopInstallation.DEFAULT_SERVER + "getRepresentativeScopDomains" + " is wrong", e);
 		}
-		logger.info("Using " + u + " to download representative domains");
-		InputStream response = URLConnectionTools.getInputStream(u);
-		String xml = JFatCatClient.convertStreamToString(response);
-		ScopDomains results  = ScopDomains.fromXML(xml);
-
-		logger.info("got " + results.getScopDomain().size() + " domain ranges for Scop domains from server.");
-		for (ScopDomain dom : results.getScopDomain()){
-			String scopId = dom.getScopId();
-			serializedCache.put(scopId, dom);
-		}
 
+		logger.info("Using {} to download representative domains", u);
+
+		InputStream response = Download.stream(u);
+
+		ScopDomains results  = ScopDomains.fromXML(JFatCatClient.convertStreamToString(response));
+
+		logger.info("got {} domain ranges for Scop domains from server.", results.getScopDomain().size());
+
+		for (ScopDomain dom : results.getScopDomain())
+			serializedCache.put(dom.getScopId(), dom);
 	}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/RemoteScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/RemoteScopInstallation.java
index a1534f0071..6f8305ad96 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/RemoteScopInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/RemoteScopInstallation.java
@@ -24,8 +24,8 @@
  */
 package org.biojava.nbio.structure.scop;
 
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.structure.align.client.JFatCatClient;
-import org.biojava.nbio.structure.align.util.URLConnectionTools;
 import org.biojava.nbio.structure.scop.server.ScopDescriptions;
 import org.biojava.nbio.structure.scop.server.ScopDomains;
 import org.biojava.nbio.structure.scop.server.ScopNodes;
@@ -74,7 +74,7 @@ public List<ScopDescription> getByCategory(ScopCategory category) {
 		List<ScopDescription> results = null;
 		try {
 			URL u = new URL(server + "getByCategory?category="+category+"&version="+getScopVersion());
-			InputStream response = URLConnectionTools.getInputStream(u);
+			InputStream response = Download.stream(u);
 			String xml = JFatCatClient.convertStreamToString(response);
 
 			if(! xml.trim().isEmpty()) {
@@ -92,7 +92,7 @@ public List<ScopDescription> filterByClassificationId(String query) {
 		List<ScopDescription> results = null;
 		try {
 			URL u = new URL(server + "filterByClassificationId?query="+query+"&version="+getScopVersion());
-			InputStream response = URLConnectionTools.getInputStream(u);
+			InputStream response = Download.stream(u);
 			String xml = JFatCatClient.convertStreamToString(response);
 
 			if(! xml.trim().isEmpty()) {
@@ -110,7 +110,7 @@ public List<ScopNode> getTree(ScopDomain domain) {
 		List<ScopNode> results = null;
 		try {
 			URL u = new URL(server + "getTree?scopId="+domain.getScopId()+"&version="+getScopVersion());
-			InputStream response = URLConnectionTools.getInputStream(u);
+			InputStream response = Download.stream(u);
 			String xml = JFatCatClient.convertStreamToString(response);
 
 			if(! xml.trim().isEmpty()) {
@@ -130,7 +130,7 @@ public List<ScopDomain> filterByDomainName(String query) {
 		try {
 			URL u = new URL(server + "filterByDomainName?query="+query+"&version="+getScopVersion());
 			//System.out.println(u);
-			InputStream response = URLConnectionTools.getInputStream(u);
+			InputStream response = Download.stream(u);
 			String xml = JFatCatClient.convertStreamToString(response);
 
 			if(! xml.trim().isEmpty()) {
@@ -148,7 +148,7 @@ public List<ScopDescription> filterByDescription(String query) {
 		List<ScopDescription> results = null;
 		try {
 			URL u = new URL(server + "filterByDescription?query="+query+"&version="+getScopVersion());
-			InputStream response = URLConnectionTools.getInputStream(u);
+			InputStream response = Download.stream(u);
 			String xml = JFatCatClient.convertStreamToString(response);
 
 			if(! xml.trim().isEmpty()) {
@@ -170,7 +170,7 @@ public ScopDescription getScopDescriptionBySunid(int sunid) {
 		try {
 
 			URL u = new URL(server + "getScopDescriptionBySunid?sunid="+sunid+"&version="+getScopVersion());
-			InputStream response = URLConnectionTools.getInputStream(u);
+			InputStream response = Download.stream(u);
 			String xml = JFatCatClient.convertStreamToString(response);
 
 			if(! xml.trim().isEmpty()) {
@@ -185,39 +185,32 @@ public ScopDescription getScopDescriptionBySunid(int sunid) {
 
 	@Override
 	public List<ScopDomain> getDomainsForPDB(String pdbId) {
-		List<ScopDomain> results = null;
+		String urlString = server + "getDomainsForPDB?pdbId=" + pdbId + "&version=" + getScopVersion();
+
 		try {
-			URL u = new URL(server + "getDomainsForPDB?pdbId="+pdbId+"&version="+getScopVersion());
-			InputStream response = URLConnectionTools.getInputStream(u);
+			InputStream response = Download.stream(new URL(urlString));
 			String xml = JFatCatClient.convertStreamToString(response);
 
-			if( !xml.trim().isEmpty()) {
-				ScopDomains container = ScopDomains.fromXML(xml);
-				results = container.getScopDomain();
-			}
+			if( !xml.trim().isEmpty())
+				return ScopDomains.fromXML(xml).getScopDomain();
+
 		} catch (Exception e){
-			throw new RuntimeException("Unable to reach "+ server + "getDomainsForPDB?pdbId="+pdbId+"&version="+getScopVersion(), e);
+			throw new RuntimeException("Unable to reach "+ urlString); //server + "getDomainsForPDB?pdbId="+pdbId+"&version="+getScopVersion(), e);
 		}
-		return results;
-	}
 
-	private ScopDomain requestRemoteDomainByScopID(String scopId)
-			throws IOException{
-		scopId = scopId.trim();
-		URL u = new URL(server + "getDomainByScopID?scopId="+scopId+"&version="+getScopVersion());
-		InputStream response = URLConnectionTools.getInputStream(u);
-		String xml = JFatCatClient.convertStreamToString(response);
-
-		if( !xml.trim().isEmpty()) {
-			return XMLUtil.getScopDomainFromXML(xml);
-		}
 		return null;
 	}
 
 	@Override
 	public ScopDomain getDomainByScopID(String scopId) {
 		try {
-			return requestRemoteDomainByScopID(scopId);
+			String scopId1 = scopId;
+			scopId1 = scopId1.trim();
+			URL u = new URL(server + "getDomainByScopID?scopId="+ scopId1 +"&version="+getScopVersion());
+			InputStream response = Download.stream(u);
+			String xml = JFatCatClient.convertStreamToString(response);
+
+			return !xml.trim().isEmpty() ? XMLUtil.getScopDomainFromXML(xml) : null;
 		} catch (Exception e){
 			throw new RuntimeException("Unable to reach "+ server + "getDomainByScopID?scopId="+scopId+"&version="+getScopVersion(), e);
 		}
@@ -225,19 +218,20 @@ public ScopDomain getDomainByScopID(String scopId) {
 
 	@Override
 	public ScopNode getScopNode(int sunid) {
-		ScopNode desc = null;
+
+		String uu = server + "getScopNode?sunid=" + sunid + "&version=" + getScopVersion();
 		try {
-			URL u = new URL(server + "getScopNode?sunid="+sunid+"&version="+getScopVersion());
-			InputStream response = URLConnectionTools.getInputStream(u);
+			InputStream response = Download.stream(new URL(uu));
 			String xml = JFatCatClient.convertStreamToString(response);
 
-			if( !xml.trim().isEmpty()) {
-				desc = XMLUtil.getScopNodeFromXML(xml);
-			}
+			if( !xml.trim().isEmpty())
+				return XMLUtil.getScopNodeFromXML(xml);
+
 		} catch (Exception e){
-			throw new RuntimeException("Unable to reach "+ server + "getScopNode?sunid="+sunid+"&version="+getScopVersion(), e);
+			throw new RuntimeException("Unable to reach "+ uu);
 		}
-		return desc;
+
+		return null;
 	}
 
 	@Override
@@ -246,7 +240,7 @@ public String getScopVersion() {
 		if( version == null) {
 			try {
 				URL u = new URL(server + "getScopVersion");
-				InputStream response = URLConnectionTools.getInputStream(u);
+				InputStream response = Download.stream(u);
 				version = JFatCatClient.convertStreamToString(response);
 				if( version != null)
 					version = version.trim();
@@ -268,12 +262,11 @@ public List<ScopDomain> getScopDomainsBySunid(Integer sunid) {
 		List<ScopDomain> results = null;
 		try {
 			URL u = new URL(server + "getScopDomainsBySunid?sunid="+sunid+"&version="+getScopVersion());
-			InputStream response = URLConnectionTools.getInputStream(u);
+			InputStream response = Download.stream(u);
 			String xml = JFatCatClient.convertStreamToString(response);
 
 			if( !xml.trim().isEmpty()) {
-				ScopDomains container = ScopDomains.fromXML(xml);
-				results = container.getScopDomain();
+				results = ScopDomains.fromXML(xml).getScopDomain();
 			}
 		} catch (Exception e){
 			throw new RuntimeException("Unable to reach "+ server + "getScopDomainsBySunid?sunid="+sunid+"&version="+getScopVersion(), e);
@@ -287,7 +280,7 @@ public List<String> getComments(int sunid) {
 		List<String> results = null;
 		try {
 			URL u = new URL(server + "getComments?sunid="+sunid+"&version="+getScopVersion());
-			InputStream response = URLConnectionTools.getInputStream(u);
+			InputStream response = Download.stream(u);
 			String xml = JFatCatClient.convertStreamToString(response);
 
 			if( !xml.trim().isEmpty()) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDomains.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDomains.java
index 3c42467b5b..5360b6808d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDomains.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/ScopDomains.java
@@ -28,14 +28,13 @@
 
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.Marshaller;
-import javax.xml.bind.Unmarshaller;
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlRootElement;
-import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.PrintStream;
 import java.io.Serializable;
+import java.io.StringReader;
 import java.util.List;
 
 @XmlRootElement(name = "ScopDomains", namespace ="http://source.rcsb.org")
@@ -93,21 +92,15 @@ public  String toXML(){
 
 	public static ScopDomains fromXML(String xml){
 
-		ScopDomains job;
 
 		try {
 
-			Unmarshaller un = jaxbContext.createUnmarshaller();
-
-			ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
-
-			job = (ScopDomains) un.unmarshal(bais);
+			return (ScopDomains) jaxbContext.createUnmarshaller().unmarshal(new StringReader(xml));
 
 		} catch (Exception e){
 			throw new RuntimeException("Could not parse " + ScopDomains.class + " from XML", e);
 		}
 
-		return job;
 	}
 
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java
index fb314939cc..d77a84e9ac 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java
@@ -107,7 +107,7 @@ public void testBiounitEntitiesFlatChains() throws StructureException, IOExcepti
 	}
 
 	@Test
-	public void testBiounitEntitiesMultimodel() throws StructureException, IOException {
+	public void testBiounitEntitiesMultimodel() throws StructureException {
 		Structure s;
 		s = StructureIO.getBiologicalAssembly("1stp", 1, true);
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java
index 1f697aabe2..f1c5a0fa8d 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java
@@ -275,24 +275,28 @@ public void testInterChainContactsVsDistMatrix2TRX() throws IOException, Structu
 
 	private double[][] calcDistanceMatrix(Atom[] atoms) {
 
-		double[][] distMatrix = new double[atoms.length][atoms.length];
-
-		for (int i=0;i<atoms.length;i++) {
-			for (int j=i+1;j<atoms.length;j++) {
-				distMatrix[i][j] = Calc.getDistance(atoms[i], atoms[j]);
-			}
+		int n = atoms.length;
+		double[][] distMatrix = new double[n][n];
+
+		for (int i = 0; i< n; i++) {
+			double[] di = distMatrix[i];
+			Atom ai = atoms[i];
+			for (int j = i+1; j< n; j++)
+				di[j] = Calc.getDistance(ai, atoms[j]);
 		}
 		return distMatrix;
 	}
 
 	private double[][] calcDistanceMatrix(Atom[] atoms1, Atom[] atoms2) {
 
-		double[][] distMatrix = new double[atoms1.length][atoms2.length];
+		int h = atoms1.length;
+		int w = atoms2.length;
+		double[][] distMatrix = new double[h][w];
 
-		for (int i=0;i<atoms1.length;i++) {
-			for (int j=0;j<atoms2.length;j++) {
-				distMatrix[i][j] = Calc.getDistance(atoms1[i], atoms2[j]);
-			}
+		for (int i = 0; i< h; i++) {
+			double[] di = distMatrix[i];
+			for (int j = 0; j< w; j++)
+				di[j] = Calc.getDistance(atoms1[i], atoms2[j]);
 		}
 		return distMatrix;
 	}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestInterfaceFinder.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestInterfaceFinder.java
index 0ad1d6544e..71f4dacea4 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestInterfaceFinder.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestInterfaceFinder.java
@@ -1,28 +1,18 @@
 package org.biojava.nbio.structure.contact;
 
-import org.biojava.nbio.structure.AminoAcidImpl;
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.AtomImpl;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.ChainImpl;
-import org.biojava.nbio.structure.EntityInfo;
-import org.biojava.nbio.structure.Group;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureImpl;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.junit.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import static org.junit.Assert.*;
-
 import javax.vecmath.Point3d;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
+import static org.junit.Assert.assertEquals;
+
 public class TestInterfaceFinder {
 
     private static final Logger logger = LoggerFactory.getLogger(TestInterfaceFinder.class);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java
index 75e1d9c31a..35f325e7d7 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java
@@ -100,7 +100,7 @@ public void setUp() {
 	}
 
 	@Test
-	public void testCpAsymmetric() throws IOException, StructureException, CompoundNotFoundException {
+	public void testCpAsymmetric() throws IOException, StructureException {
 		Structure structure = cache.getStructure("1w0p");
 		String first = ("alfdynatgdtefdspakqgwmqdntnngsgvltnadgmpawlvqgiggraqwtyslstnqhaqassfgwrmttemkvlsggmitnyyangtqrvlpiisldssgnlvvefegqtgrtvlatgtaateyhkfelvflpgsnpsasfyfdgklirdniqptaskQNMIVWGNGSSntdgvaayrdikfei------------------------------------------------------------------------------------------------------------------QGDVIf------------RGPDRIPSIVASsvTPGVVTAFAEKRVGGgdpgalsntNDIITRTSRDGGITWDTELNLTEQinvsdeFDFSDPRPIYDPs---SNTVLVSYARWPtdaaqngdrikpwmpNGIFYSVYDVASgnWQAPIDVTdqvkersfqiagwggselyrrntslnsqqdwqsnakirivdgaanqiqvadgsrkyvvtlsidesgglvanlngvsapiilqsehakvhsfhdyelqysalnhtttlfvdgqqittwagevsqenniqfgnadaqidgrlhvqkivltqqghnlvefdafylaqqtpevekdleklgwtkiktgntmslygNASVNPGpgHGITLtrqqnisgsqNGRLIYPAIVLdrfFLNVMSIYSDDGgsnwq-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGSTLpipfrwksssileTLEPSEADMVELQN--GDLLLTARLDFNQivngvny--SPRQQFLSKDGGITWSLLEANNANvfsnistgTVDASITRFEqsdgSHFLLFTNPQGnpagTNgr------------QNLGLWFSFDEG--VTWKGPIQ--LVNGasaysdiyqldsenaivivetdnsnmrilrmpitllkqklt");
 		String second =   ("--------------------------------------------------------------------------------------------kirivdgaanqiqvadgsrkyvvtlsidesgglvanlngvsapiilqsehakvhsfhdyelqysalnhtttLFVDGQQITTWagevsqenniqfgnadaqidgrlhvqkivltqqghnlvefdafylaqqtpevekdleklgwtkiktgntmslygnasvnpgpghgitltrqqnisgsqngrliypaivldrfflnvmsiysddggsnwqTGSTLpipfrwksssileTLEPSEADMVEL--QNGDLLLTARLDFNQivngvny--SPRQQFLSKDGGITWSLLEANNANvfsnisTGTVDASITRFEqsdgSHFLLFTNPQGNpagtngr--------QNLGLWFSFDEG--VTWKGPIQlv---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NGASAYS--DIYQLd---------SENAIVIVETD---NSNMRILRMPITllkqkltalfdynatgdtefdspakqgwmqdntnngsgvltnadgmpawlvqgiggraqwtyslstnqhaqassfgwrmttemkvlsggmitnyyangtqrvlpiisldssgnlvvefegqtgrtvlatgtaateyhkfelvflpgsnpsasfyfdgklirdniqptaskqnmivwgngssntdgvaayrdikfeiQGDVIf------------RGPDRIPSIVASSVtpGVVTAFAEKRVGGgdpgalsntNDIITRTSRDGGITWDTELNLTEQinvsdefdFSDPRPIYDPs---SNTVLVSYARW----PTdaaqngdrikpwmpNGIFYSVYDVASgnWQAPIDVTdqVKERsfqiagwggselyrrntslnsqqdwqsna------------");
@@ -110,7 +110,7 @@ public void testCpAsymmetric() throws IOException, StructureException, CompoundN
 	}
 
 	@Test
-	public void testCpSymmetric2() throws IOException,StructureException, CompoundNotFoundException {
+	public void testCpSymmetric2() throws IOException,StructureException {
 		String a = "--vRSLNCTLRDSQQ-KSLVMSG---PYELKALHLQgqdmeq-----QVVFSMSFVQGeesndkiPVALGLKEK-NLYLSSVLKdDKPTLQLESVdpknypkkkmekRFVFNKIEInn--KLEFESAQFpnWYISTSqAENmPVFLGGT----KGgqDITDFTMQFV---";
 		String b = "esnDKIPVALGLKEKnLYLSSVLkddKPTLQLESVDpknypkkkmekRFVFNKIEINN-------KLEFESAQFpNWYISTSQA-ENMPVFLGGTkggqd-------ITDFTMQFVvrslNCTLRDSQQ--KSLVMS-GPY-ELKALHLqgqdME--QQVVFSMSFVqge";
 		Structure structure = StructureTools.getStructure("31BI");
@@ -120,7 +120,7 @@ public void testCpSymmetric2() throws IOException,StructureException, CompoundNo
 	}
 
 	@Test
-	public void testBug1() throws IOException, StructureException, CompoundNotFoundException {
+	public void testBug1() throws IOException, StructureException {
 		/*
 		 * From CriteriaDifference:
 		 * [d3er9b_: TM-score=0.6984812617301941, Tmpr=0.14740000665187836]
@@ -139,7 +139,7 @@ public void testBug1() throws IOException, StructureException, CompoundNotFoundE
 	}
 
 	@Test
-	public void testCpSymmetric1() throws IOException,StructureException, CompoundNotFoundException {
+	public void testCpSymmetric1() throws IOException,StructureException {
 		//cat 2GG6-best.fasta |tr -d \\n|pbcopy
 		String a = "-SSRPATAR-KSSGLSGTVRIPGDKSISHRSFMFGGLA-SGETRITGLLEG-EDvINTGKAMQAMGARIRKEGd---------TWIIDGVgngglLAPEAPLD---FGNAATGCRLTMGLVGvydFDSTFIGDASLtkrp---MGRVLNPLREMGVQVKSEDgdrLPVTLRGPK---TPT---PITYRVpMASAQVKSAVLLAGLNTPGITTVIEpi---MTRDHTEKMLQGFGANLTVEtdadGVRTIRLEgRGKLTGQVIDVPGDPSSTAFPLVAALLVpGSDVTILNVLMNpTR-TGLILTLQEMGADIEVINprlaggedvaDLRVRSS-----TLKGVTVPedrAPSMIDEYPILAVAAAFAEGATVMNGLEELrvkesdrLSAVANGLKLNGVDCDEGE---TSLVVRGRPdgkGLGNasgAAVAT-HLDHRIAMSFLVMGLVSENPVTVDDatmIATSFPEFMDLMAGLGAKIELS---";
 		String b = "dGVRTIRLEgRGKLTGQVIDVPGDPSSTAFPLVAALLVpGSDVTILNVLMNpTR-TGLILTLQEMGADIEVINprlaggedvaDLRVRSS-----TLKGVTVPedrAPSMIDEYPILAVAAAfaeGATVMNGLEELrvkesdrLSAVANGLKLNGVDCDEGE---TSLVVRGRPdgkGLGnasGAAVAT-HLDHRIAMSFLVMGLVSENPVTVDDatmiaTSFPEFMDLMAGLGAKIELS----SSRPATAR-KSSGLSGTVRIPGDKSISHRSFMFGGLA-SGETRITGLLEG-EDvINTGKAMQAMGARIRKEGd---------TWIIDGVgngglLAPEAPLD---FGNAATGCRLTMGLVGVYDFDSTFIGDASLtkrp---MGRVLNPLREMGVQVKSEDgdrLPVTLRGPK---TPTP---ITYRVpMASAQVKSAVLLAGLNTPGITTVIE---PIMTRDHTEKMLQGFGANLTVEtda";
@@ -150,7 +150,7 @@ public void testCpSymmetric1() throws IOException,StructureException, CompoundNo
 	}
 
 	@Test
-	public void testFromFasta() throws IOException, StructureException, CompoundNotFoundException {
+	public void testFromFasta() throws IOException, StructureException {
 		Structure s1 = cache.getStructure("1w0p");
 		Structure s2 = cache.getStructure("1qdm");
 		ProteinSequence seq1 = new ProteinSequence("GWGG----SEL--YRRNTSLNS--QQDW-------QSNAKIRIVDGAA-----NQIQ");
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestQuaternaryStructureProviders.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestQuaternaryStructureProviders.java
index 9b619d2e5a..664237b100 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestQuaternaryStructureProviders.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestQuaternaryStructureProviders.java
@@ -195,7 +195,7 @@ private void comparePdbVsMmcif(String pdbId, int bioMolecule, int mmSize) throws
 
 	}
 
-	private Structure getPdbBioAssembly(String pdbId, int bioMolecule, boolean multiModel) throws IOException, StructureException {
+	private Structure getPdbBioAssembly(String pdbId, int bioMolecule, boolean multiModel) throws StructureException {
 		// get bio assembly from PDB file
 		AtomCache cache = new AtomCache();
 		cache.setUseMmCif(false);
@@ -204,7 +204,7 @@ private Structure getPdbBioAssembly(String pdbId, int bioMolecule, boolean multi
 		return pdbS;
 	}
 
-	private Structure getMmcifBioAssembly(String pdbId, int bioMolecule, boolean multiModel) throws IOException, StructureException {
+	private Structure getMmcifBioAssembly(String pdbId, int bioMolecule, boolean multiModel) throws StructureException {
 		// get bio assembly from mmcif file
 		AtomCache cache = new AtomCache();
 		cache.setUseMmCif(true);
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
index 6fd2918780..0e9be75a82 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
@@ -23,174 +23,187 @@
 import java.io.Serializable;
 import java.util.SortedSet;
 
-/** The results of a Hmmer search for a single sequence
+/**
+ * The results of a Hmmer search for a single sequence
  *
  * @author Andreas Prlic
  * @since 3.0.3
  */
-public class HmmerResult implements Comparable<HmmerResult>, Serializable{
-
-	/**
-	 *
-	 */
-	private static final long serialVersionUID = -6016026193090737943L;
-
-	String desc ;
-	Float score;
-	Float evalue;
-	Double pvalue;
-	String acc;
-	Integer dcl;
-	String name;
-	Integer ndom;
-	Integer nreported;
-
-	SortedSet<HmmerDomain>domains;
-
-	public SortedSet<HmmerDomain> getDomains() {
-		return domains;
-	}
-	public void setDomains(SortedSet<HmmerDomain> domains) {
-		this.domains = domains;
-	}
-	public String getDesc() {
-		return desc;
-	}
-	public void setDesc(String desc) {
-		this.desc = desc;
-	}
-	public Float getScore() {
-		return score;
-	}
-	public void setScore(Float score) {
-		this.score = score;
-	}
-	public Float getEvalue() {
-		return evalue;
-	}
-	public void setEvalue(Float evalue) {
-		this.evalue = evalue;
-	}
-	public Double getPvalue() {
-		return pvalue;
-	}
-	public void setPvalue(Double pvalue) {
-		this.pvalue = pvalue;
-	}
-	public String getAcc() {
-		return acc;
-	}
-	public void setAcc(String acc) {
-		this.acc = acc;
-	}
-	public Integer getDcl() {
-		return dcl;
-	}
-	public void setDcl(Integer dcl) {
-		this.dcl = dcl;
-	}
-	public String getName() {
-		return name;
-	}
-	public void setName(String name) {
-		this.name = name;
-	}
-	public Integer getNdom() {
-		return ndom;
-	}
-	public void setNdom(Integer ndom) {
-		this.ndom = ndom;
-	}
-	public Integer getNreported() {
-		return nreported;
-	}
-	public void setNreported(Integer nreported) {
-		this.nreported = nreported;
-	}
-	@Override
-	public String toString() {
-		return "HmmerResult [acc=" + acc + ", desc=" + desc + ", score=" + score + ", evalue="
-				+ evalue + ", pvalue=" + pvalue + ", dcl="
-				+ dcl + ", name=" + name + ", ndom=" + ndom + ", nreported="
-				+ nreported + ", domains=" + domains + "]";
-	}
-
-
-	@Override
-	public int compareTo(HmmerResult o) {
-		// 	sort  by the start position of the first domain
-
-		if ( emptyDomains(this) && emptyDomains(o)){
-			return 0;
-		}
-
-		if ( ! emptyDomains(this) && emptyDomains(o))
-			return -1;
-
-		if ( emptyDomains(this) && (! emptyDomains(o)))
-			return 1;
-
-		// ok when we are here, both domains are not empty
-
-		HmmerDomain me = this.getDomains().first();
-		HmmerDomain other = o.getDomains().first();
-
-		//System.out.println(" domains: " + me.getHmmAcc() + " " + other.getHmmAcc()+ " " + me.getSqFrom().compareTo(other.getSqFrom()));
-
-		return(me.getSqFrom().compareTo(other.getSqFrom()));
-	}
-	private boolean emptyDomains(HmmerResult o) {
-		SortedSet<HmmerDomain> d = o.getDomains();
-		return d == null || d.size() == 0;
-	}
-
-
-	/** Get the overlap between two HmmerResult objects
-	 *
-	 * @param other
-	 * @return 0 if no overlap, otherwise the length of the overlap
-	 */
-	public int getOverlapLength(HmmerResult other){
-
-		int overlap = 0;
-		for ( HmmerDomain d1 : getDomains()){
-			for (HmmerDomain d2 : other.getDomains()){
-				overlap += getOverlap(d1, d2);
-			}
-		}
-		return overlap;
-
-	}
-
-	private int getOverlap(HmmerDomain one, HmmerDomain other){
-		int xs = one.getSqFrom();
-		int ys = one.getSqTo();
-		int as = other.getSqFrom();
-		int bs = other.getSqTo();
-
-		int overlap = 0;
-		//1:
-
-		if ((( xs< as)  && ( as<ys)) || ((xs < bs) && ( bs <= ys)) || (as<xs && ys<bs)) {
-
-			//2:
-
-			if ( xs < as) {
-				if ( ys < bs)
-					overlap = ys-as;
-				else
-					overlap = bs-as;
-			} else {
-				if  ( ys < bs)
-					overlap = ys -xs;
-				else
-					overlap = bs - xs;
-
-			}
-
-		}
-
-		return overlap;
-	}
+public class HmmerResult implements Comparable<HmmerResult>, Serializable {
+
+    /**
+     *
+     */
+    private static final long serialVersionUID = -6016026193090737943L;
+
+    String desc;
+    Float score;
+    Float evalue;
+    Double pvalue;
+    String acc;
+    Integer dcl;
+    String name;
+    Integer ndom;
+    Integer nreported;
+
+    SortedSet<HmmerDomain> domains;
+
+    public SortedSet<HmmerDomain> getDomains() {
+        return domains;
+    }
+
+    public void setDomains(SortedSet<HmmerDomain> domains) {
+        this.domains = domains;
+    }
+
+    public String getDesc() {
+        return desc;
+    }
+
+    public void setDesc(String desc) {
+        this.desc = desc;
+    }
+
+    public Float getScore() {
+        return score;
+    }
+
+    public void setScore(Float score) {
+        this.score = score;
+    }
+
+    public Float getEvalue() {
+        return evalue;
+    }
+
+    public void setEvalue(Float evalue) {
+        this.evalue = evalue;
+    }
+
+    public Double getPvalue() {
+        return pvalue;
+    }
+
+    public void setPvalue(Double pvalue) {
+        this.pvalue = pvalue;
+    }
+
+    public String getAcc() {
+        return acc;
+    }
+
+    public void setAcc(String acc) {
+        this.acc = acc;
+    }
+
+    public Integer getDcl() {
+        return dcl;
+    }
+
+    public void setDcl(Integer dcl) {
+        this.dcl = dcl;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public Integer getNdom() {
+        return ndom;
+    }
+
+    public void setNdom(Integer ndom) {
+        this.ndom = ndom;
+    }
+
+    public Integer getNreported() {
+        return nreported;
+    }
+
+    public void setNreported(Integer nreported) {
+        this.nreported = nreported;
+    }
+
+    @Override
+    public String toString() {
+        return "HmmerResult [acc=" + acc + ", desc=" + desc + ", score=" + score + ", evalue="
+                + evalue + ", pvalue=" + pvalue + ", dcl="
+                + dcl + ", name=" + name + ", ndom=" + ndom + ", nreported="
+                + nreported + ", domains=" + domains + "]";
+    }
+
+
+    @Override
+    public int compareTo(HmmerResult o) {
+
+        if (this == o) return 0;
+        // 	sort  by the start position of the first domain
+
+        boolean eThis = emptyDomains(this);
+        boolean eThat = emptyDomains(o);
+        if (eThis && eThat)
+            return 0;
+
+        if (!eThis && eThat)
+            return -1;
+
+        if (eThis && !eThat)
+            return 1;
+
+        // ok when we are here, both domains are not empty
+
+        //System.out.println(" domains: " + me.getHmmAcc() + " " + other.getHmmAcc()+ " " + me.getSqFrom().compareTo(other.getSqFrom()));
+
+        return this.getDomains().first().getSqFrom().compareTo(o.getDomains().first().getSqFrom());
+    }
+
+    private boolean emptyDomains(HmmerResult o) {
+        SortedSet<HmmerDomain> d = o.getDomains();
+        return d == null || d.size() == 0;
+    }
+
+
+    /**
+     * Get the overlap between two HmmerResult objects
+     *
+     * @param other
+     * @return 0 if no overlap, otherwise the length of the overlap
+     */
+    public int getOverlapLength(HmmerResult other) {
+
+        int overlap = 0;
+        for (HmmerDomain d1 : getDomains()) {
+            for (HmmerDomain d2 : other.getDomains()) {
+                overlap += getOverlap(d1, d2);
+            }
+        }
+        return overlap;
+
+    }
+
+    private int getOverlap(HmmerDomain one, HmmerDomain other) {
+        int xs = one.getSqFrom();
+        int ys = one.getSqTo();
+        int as = other.getSqFrom();
+        int bs = other.getSqTo();
+
+        if (((xs < as) && (as < ys)) || ((xs < bs) && (bs <= ys)) || (as < xs && ys < bs)) {
+
+            //2:
+
+            if (xs < as) {
+                return ys < bs ? ys - as : bs - as;
+            } else {
+                return ys < bs ? ys - xs : bs - xs;
+            }
+
+        }
+
+        return 0;
+    }
 
 }
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
index b5d178e90c..5d4e1ab2c3 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
@@ -56,9 +56,7 @@ public RemoteHmmerScan(){
 	@Override
 	public  SortedSet<HmmerResult> scan(ProteinSequence sequence) throws IOException {
 
-		URL url = new URL(HMMER_SERVICE);
-
-		return scan(sequence, url);
+		return scan(sequence, new URL(HMMER_SERVICE));
 
 	}
 

From d5e2351ff31b318fa6f6e221fc2796554ad3ac1a Mon Sep 17 00:00:00 2001
From: me <me@internet.earth>
Date: Sun, 15 Mar 2020 15:55:56 -0400
Subject: [PATCH 18/18] updates

---
 .../template/AbstractMatrixAligner.java       |  30 +-
 .../matrices/SimpleSubstitutionMatrix.java    |  14 +-
 .../nbio/core/sequence/ProteinSequence.java   |   6 +-
 .../compound/AmbiguityDNACompoundSet.java     |   2 +-
 .../loader/GenbankProxySequenceReader.java    |  30 +-
 .../org/biojava/nbio/core/util/Download.java  |   6 +
 .../core/sequence/io/GenbankReaderTest.java   |   1 -
 .../GenbankProxySequenceReaderTest.java       |   1 -
 .../genename/GeneChromosomePosition.java      |   2 +
 .../GeneChromosomePositionParser.java         |   6 +-
 .../nbio/genome/TestGenomeMapping.java        |   5 +-
 .../align/seq/TestSmithWaterman3Daligner.java |   9 +-
 .../biojava/nbio/structure/HetatomImpl.java   |  22 +-
 .../align/BioJavaStructureAlignment.java      |  18 +-
 .../structure/align/StructurePairAligner.java |   4 +-
 .../nbio/structure/align/ce/CECalculator.java |  18 +-
 .../nbio/structure/align/ce/CeMain.java       |  16 +-
 .../structure/align/client/JFatCatClient.java |  27 +-
 .../structure/align/client/StructureName.java |   4 +-
 .../structure/align/helper/AligMatEl.java     |  23 +-
 .../structure/align/helper/IndexPair.java     |  77 ++--
 .../align/pairwise/AltAligComparator.java     |   5 +-
 .../align/pairwise/AlternativeAlignment.java  | 104 ++---
 .../align/pairwise/FragmentJoiner.java        |   1 -
 .../nbio/structure/align/pairwise/Gotoh.java  |  17 +-
 .../structure/align/quaternary/QsAlign.java   | 110 +++---
 .../nbio/structure/cath/CathInstallation.java |  45 ++-
 .../structure/cluster/SubunitCluster.java     |   7 +-
 .../nbio/structure/ecod/EcodFactory.java      |  10 +-
 .../nbio/structure/ecod/EcodInstallation.java | 210 +++++-----
 .../nbio/structure/geometry/CalcPoint.java    |   3 +
 .../structure/geometry/UnitQuaternions.java   |   6 +-
 .../nbio/structure/io/PDBFileParser.java      | 218 +++++------
 .../nbio/structure/io/PDBFileReader.java      |   3 +-
 .../structure/io/mmcif/SimpleMMcifParser.java | 362 ++++++++----------
 .../scop/RemoteScopInstallation.java          |   5 +-
 .../nbio/structure/scop/server/XMLUtil.java   |   7 +-
 .../symmetry/core/QuatSymmetryDetector.java   |   6 +-
 .../symmetry/core/QuatSymmetryResults.java    |   8 +-
 .../symmetry/core/RotationGroup.java          |  34 +-
 .../io/FastaAFPChainConverterTest.java        |   1 -
 .../nbio/structure/io/TestSiftsParsing.java   |   6 +-
 .../io/mmtf/TestMmtfPerformance.java          |  19 +-
 43 files changed, 730 insertions(+), 778 deletions(-)

diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
index c1831c24c1..4fbd047a58 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
@@ -314,6 +314,8 @@ protected void align() {
 		Last[][][] traceback = new Last[dim[0]][][];
 		List<Step> sx = new ArrayList<>(), sy = new ArrayList<>();
 
+		int extensionPenalty = gapPenalty.getExtensionPenalty();
+		int openPenalty = gapPenalty.getOpenPenalty();
 		if (!local) {
 			xyMax = new int[] { dim[0] - 1, dim[1] - 1 };
 			xyStart = new int[] { 0, 0 };
@@ -324,12 +326,11 @@ protected void align() {
 				Subproblem subproblem = problems.get(i);
 				for (int x = subproblem.getQueryStartIndex(); x <= subproblem.getQueryEndIndex(); x++) {
 
-					traceback[x] =
+					int[] scoreVector = getSubstitutionScoreVector(x, subproblem);
 
-					  linear ?
-						setScoreVector(x, subproblem, gapPenalty.getExtensionPenalty(), getSubstitutionScoreVector(x, subproblem), storingScoreMatrix, scores) :
-
-						setScoreVector(x, subproblem, gapPenalty.getOpenPenalty(), gapPenalty.getExtensionPenalty(), getSubstitutionScoreVector(x, subproblem), storingScoreMatrix, scores);
+					traceback[x] = linear ?
+						setScoreVector(x, subproblem, extensionPenalty, scoreVector, storingScoreMatrix, scores) :
+						setScoreVector(x, subproblem, openPenalty, extensionPenalty, scoreVector, storingScoreMatrix, scores);
 				}
 			}
 			setSteps(traceback, scores, sx, sy);
@@ -341,25 +342,20 @@ protected void align() {
 		} else {
 			for (int x = 0; x < dim[0]; x++) {
 
-				traceback[x] =
-
-				  linear ?
-					setScoreVector(x, gapPenalty.getExtensionPenalty(), getSubstitutionScoreVector(x), storingScoreMatrix, scores, xyMax, score) :
-
-					setScoreVector(x, gapPenalty.getOpenPenalty(), gapPenalty.getExtensionPenalty(), getSubstitutionScoreVector(x), storingScoreMatrix, scores, xyMax, score);
-
-				if (xyMax[0] == x) {
-					score = scores[x][xyMax[1]][0];
-				}
+				int[] score = getSubstitutionScoreVector(x);
+				traceback[x] = linear ?
+					setScoreVector(x, extensionPenalty, score, storingScoreMatrix, scores, xyMax, this.score) :
+					setScoreVector(x, openPenalty, extensionPenalty, score, storingScoreMatrix, scores, xyMax, this.score);
+				if (xyMax[0] == x)
+					this.score = scores[x][xyMax[1]][0];
 			}
 			xyStart = local ? setSteps(traceback, xyMax, sx, sy) : setSteps(traceback, scores, sx, sy);
 		}
 
 		setProfile(sx, sy);
 
-		if (!storingScoreMatrix) {
+		if (!storingScoreMatrix)
 			scores = null;
-		}
 
 		time = System.nanoTime() - timeStart;
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java
index cb8f23d8dd..9f56bc31e9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java
@@ -243,14 +243,16 @@ private static <C extends Compound> int getIndexOfCompound(List<C> list, C compo
 	}
 	@Override
 	public short getValue(C from, C to) {
-		int row = getIndexOfCompound(rows, from), col = getIndexOfCompound(cols, to);
-		if (row == -1 || col == -1) {
-			row = getIndexOfCompound(cols, from);
-			col = getIndexOfCompound(rows, to);
-			if (row == -1 || col == -1) {
+		int row, col;
+		if ((row=getIndexOfCompound(rows, from)) == -1 || (col = getIndexOfCompound(cols, to)) == -1) {
+
+			if ((row = getIndexOfCompound(cols, from)) == -1)
+				return min;
+
+			if ((col = getIndexOfCompound(rows, to)) == -1)
 				return min;
-			}
 		}
+
 		return matrix[row][col];
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
index c6ee24831d..f58cbf04b9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
@@ -161,11 +161,9 @@ private DNASequence getRawParentSequence(String accessId) throws IOException {
 
 		InputStream is = Download.stream(url); //url.openConnection().getInputStream();
 
-		FastaReader<DNASequence, NucleotideCompound> parentReader
-				= new FastaReader<>(is,
+		LinkedHashMap<String, DNASequence> seq = new FastaReader<DNASequence, NucleotideCompound>(is,
 				new PlainFastaHeaderParser<>(),
-				new DNASequenceCreator(AmbiguityDNACompoundSet.getDNACompoundSet()));
-		LinkedHashMap<String, DNASequence> seq = parentReader.process();
+				new DNASequenceCreator(AmbiguityDNACompoundSet.getDNACompoundSet())).process();
 
 		DNASequence parentSeq = null;
 		if (seq.size() == 1) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundSet.java
index d803c642cd..bc8a7ecc03 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundSet.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundSet.java
@@ -33,7 +33,7 @@ private static class InitaliseOnDemand {
 	}
 
 	public static AmbiguityDNACompoundSet getDNACompoundSet() {
-	return InitaliseOnDemand.INSTANCE;
+		return InitaliseOnDemand.INSTANCE;
 	}
 
 	public AmbiguityDNACompoundSet() {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
index 9cfa6e3e61..0e9b6b5ad1 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
@@ -44,8 +44,6 @@
 
 import java.io.BufferedReader;
 import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
@@ -60,8 +58,12 @@ public class GenbankProxySequenceReader<C extends Compound> extends StringProxyS
 	private static final Logger logger = LoggerFactory.getLogger(GenbankProxySequenceReader.class);
 
 	private static final String eutilBaseURL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"; //
-//	private String genbankDirectoryCache = null;
-	private final GenbankSequenceParser<AbstractSequence<C>, C> genbankParser;
+//		logger.trace("Loading: {}", genbankURL);
+//		URL genbank = new URL(genbankURL);
+//		inStream1 = new BufferedInputStream(genbank.openConnection().getInputStream());
+//		}
+	//	private String genbankDirectoryCache = null;
+	private final GenbankSequenceParser<AbstractSequence<C>, C> genbankParser = new GenbankSequenceParser<>();
 	private final GenericGenbankHeaderParser<AbstractSequence<C>, C> headerParser;
 	private final String header;
 	private final Map<String, ArrayList<AbstractFeature>> features;
@@ -92,24 +94,18 @@ public GenbankProxySequenceReader(String accessionID, CompoundSet<C> compoundSet
 //			}
 //		} else {
 		String genbankURL = eutilBaseURL + "efetch.fcgi?db=" + db + "&id=" + accessionID + "&rettype=gb&retmode=text";
-//		logger.trace("Loading: {}", genbankURL);
-//		URL genbank = new URL(genbankURL);
-//		inStream1 = new BufferedInputStream(genbank.openConnection().getInputStream());
-//		}
-		genbankParser = new GenbankSequenceParser<>();
 
-		try (InputStream inStream = Download.stream(new URL(genbankURL))) {
-			String s = genbankParser.getSequence(new BufferedReader(new InputStreamReader(inStream)), 0);
-			setContents(s);
+		try (BufferedReader r = Download.bufferedReader(new URL(genbankURL))) {
+			setContents(genbankParser.getSequence(r, 0));
 			headerParser = genbankParser.getSequenceHeaderParser();
 			header = genbankParser.getHeader();
 			features = genbankParser.getFeatures();
+		}
 
-			if (compoundSet.getClass().equals(AminoAcidCompoundSet.class)) {
-				if (!genbankParser.getCompoundType().equals(compoundSet)) {
-					logger.error("Declared compount type {} does not mach the real: {}", genbankParser.getCompoundType().toString(), compoundSet.toString());
-					throw new IOException("Wrong declared compound type for: " + accessionID);
-				}
+		if (compoundSet.getClass().equals(AminoAcidCompoundSet.class)) {
+			if (!genbankParser.getCompoundType().equals(compoundSet)) {
+				logger.error("Declared compount type {} does not mach the real: {}", genbankParser.getCompoundType().toString(), compoundSet.toString());
+				throw new IOException("Wrong declared compound type for: " + accessionID);
 			}
 		}
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/Download.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/Download.java
index 7b49e8b356..6f48381bec 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/Download.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/Download.java
@@ -341,6 +341,12 @@ public static void downloadFile(URL url, File destination) throws IOException {
 
 	}
 
+	public static BufferedReader bufferedReader(URL u) throws IOException {
+		return new BufferedReader(new InputStreamReader(stream(u)));
+	}
+
+
+
 //	/**
 //	 * Recursively delete a folder & contents
 //	 *
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
index 5650ad4822..899a5633b9 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.core.sequence.io;
 
-import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.DNASequence;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.RNASequence;
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
index 90900e0a58..046730c938 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.core.sequence.loader;
 
-import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePosition.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePosition.java
index 51e6657b5a..71a76e2a4e 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePosition.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePosition.java
@@ -38,7 +38,9 @@ public class GeneChromosomePosition implements Comparable<GeneChromosomePosition
 	private Integer cdsStart;
 	private Integer cdsEnd;
 	int exonCount;
+	/** TODO int[] */
 	private List<Integer> exonStarts;
+	/** TODO int[] */
 	private List<Integer> exonEnds;
 
 	public String getGeneName() {
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
index eb6d9682c6..f1416e5683 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java
@@ -116,11 +116,9 @@ private static GeneChromosomePosition getGeneChromosomePosition(String line) {
 
 	private static List<Integer> getIntegerList(String lst){
 		String[] spl = lst.split(",");
-		ArrayList<Integer> l = new ArrayList<>();
-		for (String s : spl){
+		ArrayList<Integer> l = new ArrayList<>(spl.length);
+		for (String s : spl)
 			l.add(Integer.parseInt(s));
-		}
-		l.trimToSize();
 		return l;
 	}
 }
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
index 395a66c401..b4859b722d 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
@@ -22,6 +22,7 @@
 
 import com.google.common.collect.Lists;
 import com.google.common.collect.Range;
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition;
 import org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser;
 import org.biojava.nbio.genome.util.ChromosomeMappingTools;
@@ -33,7 +34,6 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import java.util.zip.GZIPInputStream;
 
 /**
  * Created by andreas on 7/19/16.
@@ -47,8 +47,7 @@ public class TestGenomeMapping {
 	static {
 		List<GeneChromosomePosition> g;
 		try {
-			g = GeneChromosomePositionParser.getChromosomeMappings(
-					new GZIPInputStream(new URL(geneChromosomeFile).openStream()));
+			g = GeneChromosomePositionParser.getChromosomeMappings( Download.stream(new URL(geneChromosomeFile)) );
 		} catch (IOException e) {
 			e.printStackTrace();
 			g = null;
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/seq/TestSmithWaterman3Daligner.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/seq/TestSmithWaterman3Daligner.java
index 129717d1b2..253f4685be 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/seq/TestSmithWaterman3Daligner.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/seq/TestSmithWaterman3Daligner.java
@@ -21,7 +21,6 @@
 package org.biojava.nbio.structure.test.align.seq;
 
 import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.model.AFPChain;
@@ -51,11 +50,6 @@ public class TestSmithWaterman3Daligner {
 	@Test
 	public void testMaxRMSD() throws StructureException, IOException {
 
-		Structure s1 = StructureTools.getStructure("1A3N.A");
-		Structure s2 = StructureTools.getStructure("1A3N.B");
-
-		Atom[] ca1 = StructureTools.getRepresentativeAtomArray(s1);
-		Atom[] ca2 = StructureTools.getRepresentativeAtomArray(s2);
 
 		SmithWaterman3Daligner aligner = new SmithWaterman3Daligner();
 		SmithWaterman3DParameters params = new SmithWaterman3DParameters();
@@ -63,6 +57,9 @@ public void testMaxRMSD() throws StructureException, IOException {
 		// Use no restriction on the RMSD
 		params.setMaxRmsd(99.0);
 
+		Atom[] ca1 = StructureTools.getRepresentativeAtomArray(StructureTools.getStructure("1A3N.A"));
+		Atom[] ca2 = StructureTools.getRepresentativeAtomArray(StructureTools.getStructure("1A3N.B"));
+
 		AFPChain afpChain = aligner.align(ca1, ca2, params);
 
 		assertEquals("RMSD is wrong", 1.39, afpChain.getTotalRmsdOpt(), 0.005);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
index b52b9b7c23..ffd95ed824 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
@@ -595,34 +595,28 @@ public boolean isWater() {
 	public void trimToSize(){
 
 		if ( atoms instanceof ArrayList<?>) {
-			ArrayList<Atom> myatoms = (ArrayList<Atom>) atoms;
-			myatoms.trimToSize();
+			((ArrayList<Atom>) atoms).trimToSize();
 		}
 		if ( altLocs instanceof ArrayList<?>){
-			ArrayList<Group> myAltLocs = (ArrayList<Group>) altLocs;
-			myAltLocs.trimToSize();
+			((ArrayList<Group>) altLocs).trimToSize();
 		}
 
 		if ( hasAltLoc()) {
-			for (Group alt : getAltLocs()){
+			for (Group alt : getAltLocs())
 				alt.trimToSize();
-			}
 		}
 
-		// now let's fit the hashmaps to size
-		properties = new HashMap<>(properties);
-
-		if ( atomNameLookup != null)
-			atomNameLookup = new HashMap<>(atomNameLookup);
-
+//		// now let's fit the hashmaps to size
+//		properties = new HashMap<>(properties);
+//		if ( atomNameLookup != null)
+//			atomNameLookup = new HashMap<>(atomNameLookup);
 	}
 
 
 	@Override
 	public String toSDF() {
 		// Function to return the SDF of a given strucutre
-		GroupToSDF gts = new GroupToSDF();
-		return gts.getText(this);
+		return new GroupToSDF().getText(this);
 	}
 
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/BioJavaStructureAlignment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/BioJavaStructureAlignment.java
index 6b5b279f20..c94e85e307 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/BioJavaStructureAlignment.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/BioJavaStructureAlignment.java
@@ -161,13 +161,13 @@ private void copyResults(AFPChain afpChain, AlternativeAlignment altAlig, Atom[]
 
 			IndexPair align_se = path[ia];
 			// no gap
-			if(align_se.getRow() !=-1 && align_se.getCol()!=-1) {
+			if(align_se.row() !=-1 && align_se.col()!=-1) {
 
-				optAln[0][0][pos] = align_se.getRow();
-				optAln[0][1][pos] = align_se.getCol();
+				optAln[0][0][pos] = align_se.row();
+				optAln[0][1][pos] = align_se.col();
 
-				char l1 = getOneLetter(ca1[align_se.getRow()].getGroup());
-				char l2 = getOneLetter(ca2[align_se.getCol()].getGroup());
+				char l1 = getOneLetter(ca1[align_se.row()].getGroup());
+				char l2 = getOneLetter(ca2[align_se.col()].getGroup());
 
 				alnseq1[ia] = Character.toUpperCase(l1);
 				alnseq2[ia] = Character.toUpperCase(l2);
@@ -177,16 +177,16 @@ private void copyResults(AFPChain afpChain, AlternativeAlignment altAlig, Atom[]
 			} else {
 				// there is a gap on this position
 				alnsymb[ia] = ' ';
-				if (align_se.getRow() == -1 ) {
+				if (align_se.row() == -1 ) {
 					alnseq1[ia] = '-';
 				} else {
-					char l1 = getOneLetter(ca1[align_se.getRow()].getGroup());
+					char l1 = getOneLetter(ca1[align_se.row()].getGroup());
 					alnseq1[ia] = Character.toLowerCase(l1);
 				}
-				if ( align_se.getCol() == -1 ) {
+				if ( align_se.col() == -1 ) {
 					alnseq2[ia] = '-';
 				} else {
-					char l2 = getOneLetter(ca2[align_se.getCol()].getGroup());
+					char l2 = getOneLetter(ca2[align_se.col()].getGroup());
 					alnseq2[ia] = Character.toLowerCase(l2);
 				}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
index 7eeabb1d89..e9319546e0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
@@ -41,7 +41,6 @@
 import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.Comparator;
 import java.util.List;
 
 /**
@@ -555,8 +554,7 @@ public void align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)
 		}
 
 		// sort the alternative alignments
-		Comparator<AlternativeAlignment> comp = new AltAligComparator();
-		aas.sort(comp);
+		aas.sort(AltAligComparator.the);
 		Collections.reverse(aas);
 
 		alts = aas.toArray(new AlternativeAlignment[0]);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
index 6fac17efc5..fabe6df622 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
@@ -127,8 +127,7 @@ public CECalculator(CeParameters params){
 	 * @param ca2
 	 * @return afpChain
 	 */
-	public AFPChain extractFragments(AFPChain afpChain,
-			Atom[] ca1, Atom[] ca2) {
+	public AFPChain extractFragments(AFPChain afpChain, Atom[] ca1, Atom[] ca2) {
 
 		int nse1 = ca1.length;
 		int nse2 = ca2.length;
@@ -161,15 +160,12 @@ public AFPChain extractFragments(AFPChain afpChain,
 
 		// CE: unused code. distAll is always false and both loops do the same???
 		// CE v2.3 calls this Weight factors for trace extension
-		if(distAll ) {
+		if(distAll) {
 			for(int i=0; i<traceMaxSize; i++)
 				traceIndexContainer[i]=(i+1)*i*winSize*winSize/2+(i+1)*winSizeComb1;
 		} else {
-			for(int i=0; i<traceMaxSize; i++) {
+			for(int i=0; i<traceMaxSize; i++)
 				traceIndexContainer[i]=(i+1)*i*winSize/2+(i+1)*winSizeComb1;
-
-
-			}
 		}
 
 		// verified: a[] is set correctly.
@@ -1602,7 +1598,7 @@ private double dpAlign(int nSeq1, int nSeq2, double gapI, double gapE,
 
 		int i, j, is, js, iMax, jMax, k;
 		boolean ge=(gapE != 0.0);
-		double sum, sum_ret, sum_brk;
+		double sum_ret, sum_brk;
 
 		boolean[][] brk_flg=new boolean [nSeq1][nSeq2];
 		for(i=0; i<nSeq1; i++) brk_flg[i]=new boolean [nSeq2];
@@ -1627,6 +1623,7 @@ private double dpAlign(int nSeq1, int nSeq2, double gapI, double gapE,
 				for(j=nSeq2-1; j>=0; j--)
 				{
 					brk_flg[i][j]=false;
+					double sum;
 					if(j<nSeq2-1 && i<nSeq1-1)
 					{
 						sum=mat[i+1][j+1];
@@ -1665,6 +1662,7 @@ private double dpAlign(int nSeq1, int nSeq2, double gapI, double gapE,
 			for(i=nSeq1-1; i>=0; i--)
 				for(j=nSeq2-1; j>=0; j--)
 				{
+					double sum;
 					brk_flg[i][j]=false;
 					if(j<nSeq2-1 && i<nSeq1-1)
 					{
@@ -1747,7 +1745,7 @@ private double dpAlign(int nSeq1, int nSeq2, double gapI, double gapE,
 			for(j=0; j<nSeq2; j++)
 			{
 				if(i==0 && j==0) continue;
-				sum=mat[i][j];
+				double sum=mat[i][j];
 				if(isGlobal1) sum+=-gapI-gapE*i;
 				if(isGlobal2) sum+=-gapI-gapE*j;
 				if(sum>sum_ret)
@@ -1765,7 +1763,7 @@ private double dpAlign(int nSeq1, int nSeq2, double gapI, double gapE,
 		for(i=is, j=js; i<nSeq1 && j<nSeq2; i++, j++)
 		{
 			iMax=i; jMax=j;
-			sum=mat[i][j];
+			double sum=mat[i][j];
 			if(!ge)
 			{
 				for(k=i+1; k<nSeq1; k++)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
index 16802329be..4bc30741a4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
@@ -94,12 +94,8 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureExce
 		ca2clone = new Atom[ca2.length];
 
 		int pos = 0;
-		for (Atom a : ca2){
-			Group g = a.getGroup();//.clone(); // works because each group has only a CA atom
-
-			ca2clone[pos] = g.getAtom(a.getName());
-
-			pos++;
+		for (Atom a : ca2) {
+			ca2clone[pos++] = ((Group) a.getGroup().clone()).getAtom(a.getName());  // works because each group has only a CA atom
 		}
 
 		calculator = new CECalculator(params);
@@ -121,15 +117,17 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureExce
 		if (ca2.length!=0 && ca2[0].getGroup().getChain()!=null && ca2[0].getGroup().getChain().getStructure()!=null)
 			afpChain.setName2(ca2[0].getGroup().getChain().getStructure().getName());
 
-		if ( afpChain.getNrEQR() == 0)
+		if (afpChain.getNrEQR() == 0)
 		   return afpChain;
 
 		// Set the distance matrix
 
 		int winSize = params.getWinSize();
 		int winSizeComb1 = (winSize-1)*(winSize-2)/2;
-		double[][] m = calculator.initSumOfDistances(ca1.length, ca2.length, winSize, winSizeComb1, ca1, ca2clone);
-		afpChain.setDistanceMatrix(new Matrix(m));
+
+		afpChain.setDistanceMatrix(new Matrix(
+				calculator.initSumOfDistances(ca1.length, ca2.length, winSize, winSizeComb1, ca1, ca2clone)
+		));
 		afpChain.setSequentialAlignment(true);
 
 		return afpChain;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
index b8097e14a2..6773045baa 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/JFatCatClient.java
@@ -40,6 +40,7 @@
 import java.util.Random;
 import java.util.SortedSet;
 import java.util.TreeSet;
+import java.util.stream.Collectors;
 
 public class JFatCatClient {
     private final static Logger logger = LoggerFactory.getLogger(JFatCatClient.class);
@@ -203,18 +204,22 @@ public static AFPChain getAFPChainFromServer(String serverLocation, String metho
 
     public static String convertStreamToString(InputStream stream) {
 
-        BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
-
         try {
-            String line;
-            StringBuilder sb = new StringBuilder(stream.available());
-            while ((line = reader.readLine()) != null) {
-                sb.append(line).append(newline);
-            }
-            return sb.toString();
-        } catch (IOException e) {
-            logger.error("Couldn't convert stream to string", e); // TODO dmyersturnbull: method should throw; we shouldn't catch here
-			return null;
+
+//            int aa = stream.available();
+
+            return new BufferedReader(new InputStreamReader(stream))
+                    .lines()
+                    .collect(Collectors.joining("\n"));
+//            String line;
+//            StringBuilder sb = new StringBuilder(aa);
+//            while ((line = reader.readLine()) != null) {
+//                sb.append(line).append(newline);
+//            }
+//            return sb.toString();
+//        } catch (IOException e) {
+//            logger.error("Couldn't convert stream to string", e); // TODO dmyersturnbull: method should throw; we shouldn't catch here
+//			return null;
         } finally {
             try {
                 stream.close();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
index 267059d591..9962048059 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
@@ -620,9 +620,9 @@ public static ScopDomain guessScopDomain(String name, ScopDatabase scopDB) {
 
 		// Try exact match first
 		ScopDomain domain = scopDB.getDomainByScopID(name);
-		if (domain != null) {
+		if (domain != null)
 			return domain;
-		}
+
 
 		// Didn't work. Guess it!
 		logger.warn("Warning, could not find SCOP domain: " + name);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/AligMatEl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/AligMatEl.java
index 2f8215292c..db903447f4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/AligMatEl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/AligMatEl.java
@@ -22,6 +22,8 @@
  */
 package org.biojava.nbio.structure.align.helper;
 
+import java.util.Objects;
+
 public class AligMatEl
 extends IndexPair{
 
@@ -36,7 +38,7 @@ public class AligMatEl
 
 
 		public AligMatEl(){
-			super();
+			super((short)-1, (short)-1);
 			value  = -1;
 			contig = -1;
 		}
@@ -55,10 +57,25 @@ public void setValue(int value) {
 			this.value = value;
 		}
 
-		@Override
+	@Override
+	public boolean equals(Object o) {
+		if (this == o) return true;
+		if (!(o instanceof AligMatEl)) return false;
+		if (!super.equals(o)) return false;
+		AligMatEl aligMatEl = (AligMatEl) o;
+		return value == aligMatEl.value &&
+				contig == aligMatEl.contig;
+	}
+
+	@Override
+	public int hashCode() {
+		return Objects.hash(super.hashCode(), value, contig);
+	}
+
+	@Override
 		public String toString(){
 			String ret = "AligMatEl val:" + value + " contig:" + contig +
-			" trackrow:" + getRow() + " trackcol:" + getCol();
+			" trackrow:" + row() + " trackcol:" + col();
 			return ret;
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/IndexPair.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/IndexPair.java
index ce8fd47e5a..e85b0c5803 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/IndexPair.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/IndexPair.java
@@ -23,42 +23,61 @@
 package org.biojava.nbio.structure.align.helper;
 
 import java.io.Serializable;
+import java.util.Objects;
 
 public class IndexPair implements Serializable {
 
-	/**
-	 *
-	 */
-	private static final long serialVersionUID = 1832393751152650420L;
-	short row;
-	short col;
+    /**
+     *
+     */
+    private static final long serialVersionUID = 1832393751152650420L;
+    private short row;
+    private short col;
 
-	public IndexPair(){
-		row = -1;
-		col = -1;
+	public IndexPair(int row, int col) {
+    	this.row = (short)row;
+    	this.col = (short)col;
+    	if (this.row!=row || this.col!=col)
+    		throw new ArithmeticException();
 	}
 
-	public IndexPair(short row, short col){
-		this.row = row;
-		this.col=col;
+    public IndexPair(short row, short col) {
+        this.row = row;
+        this.col = col;
+    }
 
-	}
-	public short getCol() {
-		return col;
-	}
-	public void setCol(short col) {
-		this.col = col;
-	}
-	public short getRow() {
-		return row;
-	}
-	public void setRow(short row) {
-		this.row = row;
-	}
+    public short col() {
+        return col;
+    }
 
-	@Override
-public String toString(){
-		return "["+row + " " + col+"]";
-	}
+    public void setCol(short col) {
+        this.col = col;
+    }
+
+    public short row() {
+        return row;
+    }
+
+    public void setRow(short row) {
+        this.row = row;
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (!(o instanceof IndexPair)) return false;
+        IndexPair indexPair = (IndexPair) o;
+        return row == indexPair.row && col == indexPair.col;
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(row, col);
+    }
+
+    @Override
+    public String toString() {
+        return "[" + row + " " + col + "]";
+    }
 }
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AltAligComparator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AltAligComparator.java
index 2608ab4f87..f3ea6adcf4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AltAligComparator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AltAligComparator.java
@@ -33,9 +33,12 @@
  *
  */
 public class AltAligComparator implements Comparator<AlternativeAlignment>, Serializable {
+
+	public static final AltAligComparator the = new AltAligComparator();
+
 	private static final long serialVersionUID = 1;
 
-	public AltAligComparator() {
+	private AltAligComparator() {
 		super();
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
index 01a3ec22a7..c5bd2e8e0b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
@@ -238,7 +238,7 @@ public void  apairs_from_seed(int l,int i, int j){
 		for (int x = 0 ; x < l ; x++) {
 			idx1[x]=i+x;
 			idx2[x]=j+x;
-			aligpath[x] = new IndexPair((short)(i+x),(short)(j+x));
+			aligpath[x] = new IndexPair((i+x),(j+x));
 		}
 	}
 
@@ -250,16 +250,14 @@ public void apairs_from_idxlst(JointFragments jf) {
 		List<int[]> il = jf.getIdxlist();
 		//System.out.println("Alt Alig apairs_from_idxlst");
 
-		aligpath = new IndexPair[il.size()];
-		idx1 = new int[il.size()];
-		idx2 = new int[il.size()];
-		for (int i =0 ; i < il.size();i++) {
+		int ils = il.size();
+		aligpath = new IndexPair[ils];
+		idx1 = new int[ils];
+		idx2 = new int[ils];
+		for (int i = 0; i < ils; i++) {
 			int[] p = il.get(i);
 			//System.out.print(" idx1 " + p[0] + " idx2 " + p[1]);
-			idx1[i] = p[0];
-			idx2[i] = p[1];
-			aligpath[i] = new IndexPair((short)p[0],(short)p[1]);
-
+			aligpath[i] = new IndexPair(idx1[i] = p[0], idx2[i] = p[1]);
 		}
 		eqr0  = idx1.length;
 		//System.out.println("eqr " + eqr0);
@@ -285,16 +283,10 @@ public void setAltAligNumber(int fromia) {
 	 * @param ca
 	 */
 	private void rotateShiftAtoms(Atom[] ca){
-
-		for (int i  = 0 ; i < ca.length; i++){
-			Atom c = ca[i];
-
-			Calc.rotate(c,currentRotMatrix);
-			Calc.shift(c,currentTranMatrix);
-			//System.out.println("after " + c);
-			ca[i] = c;
+		for (Atom c : ca) {
+			Calc.rotate(c, currentRotMatrix);
+			Calc.shift(c, currentTranMatrix);
 		}
-		//System.out.println("after " + ca[0]);
 	}
 
 	public void finish(StrucAligParameters params,Atom[]ca1,Atom[]ca2) {
@@ -302,7 +294,6 @@ public void finish(StrucAligParameters params,Atom[]ca1,Atom[]ca2) {
 		Atom[] ca3 = new Atom[ca2.length];
 		for ( int i = 0 ; i < ca2.length;i++){
 			ca3[i] = (Atom) ca2[i].clone();
-
 		}
 		// do the inital superpos...
 
@@ -310,7 +301,7 @@ public void finish(StrucAligParameters params,Atom[]ca1,Atom[]ca2) {
 		rotateShiftAtoms(ca3);
 
 		calcScores(ca1,ca2);
-		logger.debug("eqr " + eqr0 + " " + gaps0 + " "  +idx1[0] + " " +idx1[1]);
+		//logger.debug("eqr " + eqr0 + " " + gaps0 + " "  +idx1[0] + " " +idx1[1]);
 
 		getPdbRegions(ca1,ca2);
 
@@ -503,10 +494,10 @@ public void refine(StrucAligParameters params,Atom[]ca1,Atom[]ca2) {
 
 			// now for a superimposable permutation. First we need to check the size and
 			// position of the quadrant left out by the optimal path
-			int firsta = path[0].getRow();
-			int firstb = path[0].getCol();
-			int lasta  = path[pathsize-1].getRow();
-			int lastb  = path[pathsize-1].getCol();
+			int firsta = path[0].row();
+			int firstb = path[0].col();
+			int lasta  = path[pathsize-1].row();
+			int lastb  = path[pathsize-1].col();
 
 			int quada_beg, quada_end, quadb_beg,quadb_end;
 
@@ -546,8 +537,7 @@ public void refine(StrucAligParameters params,Atom[]ca1,Atom[]ca2) {
 
 						//System.out.println(s+" " +t);
 						//double val = sim.get(s,t);
-						double val = aligmat[s][t].getValue();
-						submat.set(s-quada_beg,t-quadb_beg,val);
+						submat.set(s-quada_beg,t-quadb_beg, aligmat[s][t].getValue());
 					}
 				}
 				// and perform a dp alignment again. (Note, that we fix the superposition).
@@ -562,8 +552,8 @@ public void refine(StrucAligParameters params,Atom[]ca1,Atom[]ca2) {
 				int subpathsize = subali.getPathSize();
 				for ( int p=0;p<subpath.length;p++){
 					IndexPair sp = subpath[p];
-					sp.setRow((short)(sp.getRow()+quada_beg));
-					sp.setCol((short)(sp.getCol()+quadb_beg));
+					sp.setRow((short)(sp.row()+quada_beg));
+					sp.setCol((short)(sp.col()+quadb_beg));
 				}
 
 				// now we join the two solutions
@@ -583,16 +573,12 @@ public void refine(StrucAligParameters params,Atom[]ca1,Atom[]ca2) {
 			int j =0 ;
 			//System.out.println("pathsize,path " + pathsize + " " + path.length);
 
+			double cutoffSqr = params.getEvalCutoff(); cutoffSqr*=cutoffSqr;
+
 			for (int i=0; i < pathsize; i++){
-				int x = path[i].getRow();
-				int y = path[i].getCol();
-				//System.out.println(x+ " " + y);
-				double d = Calc.getDistance(ca1[x], ca3[y]);
-				//double d = dismat.get(x,y);
+				int x = path[i].row(), y = path[i].col();
 				// now we apply the evaluation distance cutoff
-				if ( d < params.getEvalCutoff()){
-					//System.out.println("j:"+j+ " " + x+" " + y + " " + d );
-
+				if (Calc.getDistanceSqr(ca1[x], ca3[y]) < cutoffSqr){
 					idx1[j] = x;
 					idx2[j] = y;
 					j+=1;
@@ -628,8 +614,6 @@ public void refine(StrucAligParameters params,Atom[]ca1,Atom[]ca2) {
 
 		}
 
-
-
 		idx1 = (int[]) FragmentJoiner.resizeArray(idx1,lenneu);
 		idx2 = (int[]) FragmentJoiner.resizeArray(idx2,lenneu);
 		//		new ... get rms...
@@ -647,30 +631,17 @@ private void getPdbRegions(Atom[] ca1, Atom[] ca2){
 		pdbresnum2 = new String[idx2.length];
 
 		for (int i =0 ; i < idx1.length;i++){
-			Atom a1 = ca1[idx1[i]];
-			Atom a2 = ca2[idx2[i]];
-			Group p1 = a1.getGroup();
-			Group p2 = a2.getGroup();
-			Chain c1 = p1.getChain();
-			Chain c2 = p2.getChain();
+			Group p1 = ca1[idx1[i]].getGroup();
+			Group p2 = ca2[idx2[i]].getGroup();
 
-			String cid1 = c1.getId();
-			String cid2 = c2.getId();
+			String cid1 = p1.getChain().getId();
+			String cid2 = p2.getChain().getId();
 
 			String pdb1 = p1.getResidueNumber().toString();
 			String pdb2 = p2.getResidueNumber().toString();
 
-
-			if ( ! cid1.equals(" "))
-				pdb1 += ":" + cid1;
-
-
-			if ( ! cid2.equals(" "))
-				pdb2 += ":" + cid2;
-
-
-			pdbresnum1[i] = pdb1;
-			pdbresnum2[i] = pdb2;
+			pdbresnum1[i] = !cid1.equals(" ") ? (pdb1 + ":" + cid1) : pdb1;
+			pdbresnum2[i] = !cid2.equals(" ") ? (pdb2 + ":" + cid2) : pdb2;
 		}
 	}
 
@@ -716,9 +687,9 @@ private static int count_gaps(int[] i1, int[] i2){
 		int j0 = i2[0];
 		int gaps = 0;
 		for (int i =1 ; i<i1.length;i++ ){
-			if (Math.abs(i1[i]-i0) != 1 || Math.abs(i2[i]-j0) != 1){
-				gaps +=1;
-			}
+			if (Math.abs(i1[i]-i0) != 1 || Math.abs(i2[i]-j0) != 1)
+				gaps++;
+
 			i0 = i1[i];
 			j0 = i2[i];
 		}
@@ -806,11 +777,8 @@ public void calcScores(Atom[] ca1, Atom[] ca2){
 		percId = 0;
 		// calc the % id
 		for (int i=0 ; i< idx1.length; i++){
-			Atom a1 = ca1[idx1[i]];
-			Atom a2 = ca2[idx2[i]];
-
-			Group g1 = a1.getGroup();
-			Group g2 = a2.getGroup();
+			Group g1 = ca1[idx1[i]].getGroup();
+			Group g2 = ca2[idx2[i]].getGroup();
 			if ( g1.getPDBName().equals(g2.getPDBName())){
 				percId++;
 			}
@@ -858,11 +826,7 @@ public Structure getAlignedStructure(Structure s1, Structure s2){
 	 * @return a PDB file as a String
 	 */
 	public String toPDB(Structure s1, Structure s2){
-
-
-		Structure newpdb = getAlignedStructure(s1, s2);
-
-		return newpdb.toPDB();
+		return getAlignedStructure(s1, s2).toPDB();
 	}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
index 4e14c85912..27fdc1fa0c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java
@@ -24,7 +24,6 @@
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.StrucAligParameters;
 import org.biojava.nbio.structure.align.helper.AlignUtils;
 import org.biojava.nbio.structure.align.helper.JointFragments;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java
index 5f0125acd6..8292b6e28c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java
@@ -211,7 +211,7 @@ private void setPath(){
 		IndexPair[] backId = new IndexPair[a.getRows()+1+a.getCols()+1];
 		List<IndexPair> path = new ArrayList<>();
 
-		backId[0] = new IndexPair((short)(a.getRows()),(short)(a.getCols()));
+		backId[0] = new IndexPair((a.getRows()),(a.getCols()));
 
 		// backtrace, get backId indices, the indices in diagonal store in path
 
@@ -222,13 +222,13 @@ private void setPath(){
 
 
 		n=1;
-		while ( (backId[n-1].getRow()>=1) &&
-				(backId[n-1].getCol()>=1)
+		while ( (backId[n-1].row()>=1) &&
+				(backId[n-1].col()>=1)
 				)
 		{
 			// get backtrace index
-			int x = backId[n-1].getRow();
-			int y = backId[n-1].getCol();
+			int x = backId[n-1].row();
+			int y = backId[n-1].col();
 
 			try {
 
@@ -256,8 +256,8 @@ private void setPath(){
 				System.exit(0);
 			}
 			// get diagonal indeces into path
-			if (((backId[n-1].getRow() - backId[n].getRow()) == 1)
-					&& (( backId[n-1].getCol() - backId[n].getCol()) == 1)) {
+			if (((backId[n-1].row() - backId[n].row()) == 1)
+					&& (( backId[n-1].col() - backId[n].col()) == 1)) {
 				path.add(backId[n-1]);
 				pathsize++;
 
@@ -270,8 +270,7 @@ private void setPath(){
 		IndexPair[] newpath = new IndexPair[pathsize];
 		for (int i = 0 ; i < pathsize; i++){
 			IndexPair o = path.get(pathsize-1-i);
-			IndexPair np = new IndexPair((short)(o.getRow()-1),(short)(o.getCol()-1));
-			newpath[i] = np;
+			newpath[i] = new IndexPair((o.row()-1), (o.col()-1));
 		}
 
 		a.setPath(newpath);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java
index 55fd3d3342..3b7e31951e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java
@@ -64,7 +64,7 @@ public static QsAlignResult align(Structure s1, Structure s2,
 	}
 
 	public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
-			SubunitClustererParameters cParams, QsAlignParameters aParams)
+			SubunitClustererParameters cParams, final QsAlignParameters aParams)
 			throws StructureException {
 
 		QsAlignResult result = new QsAlignResult(s1, s2);
@@ -74,26 +74,34 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 		List<SubunitCluster> c1 = SubunitClusterer.cluster(s1, cParams).getClusters();
 		List<SubunitCluster> c2 = SubunitClusterer.cluster(s2, cParams).getClusters();
 
+		int c1s = c1.size();
+		int c2s = c2.size();
+
 		// STEP 2: match each subunit cluster between groups O(N^2*L^2) - inter
 		Map<Integer, Integer> clusterMap = new HashMap<>();
-		for (int i = 0; i < c1.size(); i++) {
-			for (int j = 0; j < c2.size(); j++) {
 
-				if (clusterMap.containsKey(i))
-					break;
+		for (int i = 0; i < c1s; i++) {
+			if (clusterMap.containsKey(i))
+				continue;
+
+			SubunitCluster ci = c1.get(i);
+
+			for (int j = 0; j < c2s; j++) {
 				if (clusterMap.containsValue(j))
 					continue;
 
 				// Use structural alignment to match the subunit clusters
-				if (c1.get(i).mergeStructure(c2.get(j),cParams)) {
+				if (ci.mergeStructure(c2.get(j),cParams))
 					clusterMap.put(i, j);
-				}
 			}
 		}
 
-		logger.info("Cluster Map: " + clusterMap.toString());
+		logger.info("Cluster Map: {}", clusterMap);
 		result.setClusters(c1);
 
+		final double aParamsCutOff = aParams.getdCutoff();
+		final double maxOrientationAngle = aParams.getMaxOrientationAngle();
+
 		// STEP 3: Align the assemblies for each cluster match O(N^2*L)
 		for (Entry<Integer, Integer> e : clusterMap.entrySet()) {
 			int globalKey = e.getKey();
@@ -105,11 +113,11 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 			// Take a cluster match as reference
 			int index1 = 0;
 			int index2 = clust1.size() - clust2.size();
-			Map<Integer, Integer> subunitMap = new HashMap<>();
+			Map<Integer, Integer> subunitMap = new HashMap<>(1);
 			subunitMap.put(index1, index2);
 
 			// Map cluster id to their subunit matching
-			Map<Integer, Map<Integer, Integer>> clustSubunitMap = new HashMap<>();
+			Map<Integer, Map<Integer, Integer>> clustSubunitMap = new HashMap<>(1);
 			clustSubunitMap.put(globalKey, subunitMap);
 
 			// Change order of key set so that globalKey is first
@@ -121,10 +129,7 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 				int key = entry.getKey();
 
 				// Recover subunitMap if it is the reference, new one otherwise
-				if (key == globalKey)
-					subunitMap = clustSubunitMap.get(key);
-				else
-					subunitMap = new HashMap<>();
+				subunitMap = key == globalKey ? clustSubunitMap.get(key) : new HashMap<Integer, Integer>();
 
 				// Obtain the clusters of each subunit group
 				clust1 = c1.get(key);
@@ -135,16 +140,15 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 				index2 = clust1.size() - clust2.size();
 
 				for (int i = 0; i < index2; i++) {
-					for (int j = index2; j < clust1.size(); j++) {
+					if (subunitMap.containsKey(i))
+						continue;
 
-						if (subunitMap.containsKey(i))
-							break;
+					for (int j = index2; j < clust1.size(); j++) {
 						if (subunitMap.containsValue(j))
 							continue;
 
 						// Obtain cumulative transformation matrix
-						Matrix4d transform = getTransformForClusterSubunitMap(
-								c1, clustSubunitMap);
+						Matrix4d transform = getTransformForClusterSubunitMap(c1, clustSubunitMap);
 
 						// Obtain Atom arrays of the subunit pair to match
 						Atom[] atoms1 = clust1.getAlignedAtomsSubunit(i);
@@ -157,11 +161,13 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 
 						// 1- Check that the distance fulfills maximum
 						double dCentroid = Calc.getDistance(centr1, centr2);
-						if (dCentroid > aParams.getdCutoff()) {
-							logger.debug(String.format("Subunit matching %d "
-									+ "vs %d of cluster %d could not be "
-									+ "matched, because centroid distance is "
-									+ "%.2f", index1, index2, key, dCentroid));
+						if (dCentroid > aParamsCutOff) {
+							if (logger.isDebugEnabled()) {
+								logger.debug(String.format("Subunit matching %d "
+										+ "vs %d of cluster %d could not be "
+										+ "matched, because centroid distance is "
+										+ "%.2f", index1, index2, key, dCentroid));
+							}
 							continue;
 						}
 
@@ -174,28 +180,34 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 								Calc.atomsToPoints(atoms1),
 								Calc.atomsToPoints(atoms2c), false);
 						qOrient = Math.min(Math.abs(2*Math.PI - qOrient), qOrient);
-						if (qOrient > aParams.getMaxOrientationAngle()) {
-							logger.debug(String.format("Subunit matching %d "
-									+ "vs %d of cluster %d could not be "
-									+ "matched, because orientation metric is "
-									+ "%.2f", i, j, key, qOrient));
+						if (qOrient > maxOrientationAngle) {
+							if (logger.isDebugEnabled()) {
+								logger.debug(String.format("Subunit matching %d "
+										+ "vs %d of cluster %d could not be "
+										+ "matched, because orientation metric is "
+										+ "%.2f", i, j, key, qOrient));
+							}
 							continue;
 						}
 
 						// 3- Check the RMSD condition
 						double rmsd = Calc.rmsd(atoms1, atoms2c);
 						if (rmsd > aParams.getMaxRmsd()) {
-							logger.debug(String.format("Subunit matching %d "
-									+ "vs %d of cluster %d could not be "
-									+ "matched, because RMSD is %.2f", i,
-									j, key, rmsd));
+							if (logger.isDebugEnabled()) {
+								logger.debug(String.format("Subunit matching %d "
+												+ "vs %d of cluster %d could not be "
+												+ "matched, because RMSD is %.2f", i,
+										j, key, rmsd));
+							}
 							continue;
 						}
 
-						logger.info(String.format("Subunit matching %d vs %d"
-								+ " of cluster %d with centroid distance %.2f"
-								+ ", orientation metric %.2f and RMSD %.2f",
-								i, j, key, dCentroid, qOrient, rmsd));
+						if (logger.isDebugEnabled()) {
+							logger.debug(String.format("Subunit matching %d vs %d"
+											+ " of cluster %d with centroid distance %.2f"
+											+ ", orientation metric %.2f and RMSD %.2f",
+									i, j, key, dCentroid, qOrient, rmsd));
+						}
 
 						subunitMap.put(i, j);
 					}
@@ -204,7 +216,7 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 				clustSubunitMap.put(key, subunitMap);
 			}
 
-			logger.info("Cluster Subunit Map: " + clustSubunitMap.toString());
+			logger.info("Cluster Subunit Map: {}", clustSubunitMap);
 
 			// Unfold the nested map into subunit map and alignment
 			subunitMap = new HashMap<>();
@@ -247,11 +259,15 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 			}
 
 			// Evaluate the goodness of the match with an alignment object
+
+			MultipleAlignmentEnsembleImpl msai = new MultipleAlignmentEnsembleImpl();
+			msai.setAtomArrays(Arrays.asList(
+					atomArray1.toArray(Atom.EmptyAtomArray),
+					atomArray2.toArray(Atom.EmptyAtomArray))
+			);
+
 			MultipleAlignment msa = new MultipleAlignmentImpl();
-			msa.setEnsemble(new MultipleAlignmentEnsembleImpl());
-			msa.getEnsemble().setAtomArrays(
-					Arrays.asList(atomArray1.toArray(Atom.EmptyAtomArray),
-							atomArray2.toArray(Atom.EmptyAtomArray)));
+			msa.setEnsemble(msai);
 
 			// Fill in the alignment information
 			BlockSet bs = new BlockSetImpl(msa);
@@ -268,11 +284,13 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 			MultipleAlignmentScorer.calculateScores(msa);
 
 			// If it is the best match found so far store it
-			if (subunitMap.size() > result.getSubunitMap().size()) {
+			int resultSubUnitMapSize = result.getSubunitMap().size();
+			int subUnitMapSize = subunitMap.size();
+			if (subUnitMapSize > resultSubUnitMapSize) {
 				result.setSubunitMap(subunitMap);
 				result.setAlignment(msa);
-				logger.info("Better result found: " + result.toString());
-			} else if (subunitMap.size() == result.getSubunitMap().size()) {
+				logger.info("Better result found: {}", result);
+			} else if (subUnitMapSize == resultSubUnitMapSize) {
 				if (result.getAlignment() == null) {
 					result.setSubunitMap(subunitMap);
 					result.setAlignment(msa);
@@ -280,7 +298,7 @@ public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,
 						.getRmsd()) {
 					result.setSubunitMap(subunitMap);
 					result.setAlignment(msa);
-					logger.info("Better result found: " + result.toString());
+					logger.info("Better result found: {}", result);
 				}
 			}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
index 868948051b..5fa58a1cdb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
@@ -342,12 +342,12 @@ public List<CathFragment> getFragmentsByPdbId(String pdbId) {
 		return fragmentMap.get(pdbId);
 	}
 
-	private void parseCathDomainList() throws IOException {
-		File file = new File(getDomainListFileName());
-		InputStreamProvider ips = new InputStreamProvider();
-		BufferedReader buffer = new BufferedReader (new InputStreamReader(ips.getInputStream(file)));
-		parseCathDomainList(buffer);
-	}
+//	private void parseCathDomainList() throws IOException {
+//		File file = new File(getDomainListFileName());
+//		InputStreamProvider ips = new InputStreamProvider();
+//		BufferedReader buffer = new BufferedReader (new InputStreamReader(ips.getInputStream(file)));
+//		parseCathDomainList(buffer);
+//	}
 
 	private void parseCathDomainList(BufferedReader bufferedReader) throws IOException{
 		String line;
@@ -668,7 +668,7 @@ protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOEx
 		LOGGER.info("Downloaded {} in {} sec. to {}", String.format("%.1f",disp) + unit, (timeE - timeS)/1000, localFile);
 	}
 
-	private boolean domainDescriptionFileAvailable(){
+	@Deprecated private boolean domainDescriptionFileAvailable(){
 		String fileName = getDomainDescriptionFileName();
 		File f = new File(fileName);
 		return f.exists();
@@ -692,15 +692,13 @@ private boolean domallFileAvailable() {
 		return f.exists();
 	}
 
-	protected void downloadDomainListFile() throws IOException{
+	protected void downloadAndParseDomainListFile() throws IOException{
 		String remoteFilename = domainListFileName;
 		URL url = new URL(buildUrl(remoteFilename));
-		String localFileName = getDomainListFileName();
-		File localFile = new File(localFileName);
-		downloadFileFromRemote(url, localFile);
+		parseCathNames(Download.bufferedReader(url));
 	}
 
-	protected void downloadDomainDescriptionFile() throws IOException{
+	@Deprecated protected void downloadDomainDescriptionFile() throws IOException{
 		String remoteFilename = domainDescriptionFileName;
 		URL url = new URL(buildUrl(remoteFilename));
 		String localFileName = getDomainDescriptionFileName();
@@ -708,7 +706,7 @@ protected void downloadDomainDescriptionFile() throws IOException{
 		downloadFileFromRemote(url, localFile);
 	}
 
-	protected void downloadNodeListFile() throws IOException{
+	@Deprecated protected void downloadNodeListFile() throws IOException{
 		String remoteFilename = nodeListFileName;
 		URL url = new URL(buildUrl(remoteFilename));
 		String localFileName = getNodeListFileName();
@@ -727,18 +725,19 @@ protected void downloadDomallFile() throws IOException {
 	public void ensureDomainListInstalled(){
 		if ( installedDomainList.get() ) return;
 
-		if ( ! domainListFileAvailable() ){
-			try {
-				downloadDomainListFile();
-			} catch (Exception e){
-				LOGGER.error("Could not download CATH domain list file. Error: {}", e.getMessage());
-				installedDomainList.set(false);
-				return;
-			}
-		}
+//		if ( ! domainListFileAvailable() ){
+//			try {
+//				downloadDomainListFile();
+//			} catch (Exception e){
+//				LOGGER.error("Could not download CATH domain list file. Error: {}", e.getMessage());
+//				installedDomainList.set(false);
+//				return;
+//			}
+//		}
 
 		try {
-			parseCathDomainList();
+			downloadAndParseDomainListFile();
+			//parseCathDomainList();
 		} catch (Exception e){
 			LOGGER.error(e.getMessage(), e);
 			installedDomainList.set(false);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
index 428d1d62a2..27b3d1fce0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
@@ -384,12 +384,7 @@ public boolean mergeSequence(SubunitCluster other, SubunitClustererParameters pa
 				.getPairwiseAligner(thisSequence, otherSequence, alignerType,
 						gapPenalty, subsMatrix);
 
-		double sequenceIdentity;
-		if(params.isUseGlobalMetrics()) {
-			sequenceIdentity = aligner.getPair().getPercentageOfIdentity(true);
-		} else {
-			sequenceIdentity = aligner.getPair().getPercentageOfIdentity(false);
-		}
+		double sequenceIdentity = aligner.getPair().getPercentageOfIdentity(params.isUseGlobalMetrics());
 
 		if (sequenceIdentity < params.getSequenceIdentityThreshold())
 			return false;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
index f70fde2f6f..fad6f663b5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
@@ -84,14 +84,14 @@ public static EcodDatabase getEcodDatabase(String version) {
 				// If the parsed version differed from that requested, add that too
 				// Note that getVersion() may trigger file parsing
 				try {
-					if( ! versionedEcodDBs.containsKey(ecod.getVersion().toLowerCase()) ) {
-						versionedEcodDBs.put(ecod.getVersion().toLowerCase(), new SoftReference<>(ecod));
-					}
+
+					versionedEcodDBs.putIfAbsent(ecod.getVersion().toLowerCase(), new SoftReference<>(ecod));
+
 				} catch (IOException e) {
 					// For parsing errors, just use the requested version
 				}
 			}
-			logger.trace("Releasing EcodFactory lock after getting version "+version);
+			//logger.trace("Releasing EcodFactory lock after getting version "+version);
 
 			return ecod;
 		}
@@ -107,7 +107,7 @@ private static void releaseReferences() {
 				Entry<String, SoftReference<EcodDatabase>> entry = it.next();
 				SoftReference<EcodDatabase> ref = entry.getValue();
 				if(ref.get() == null) {
-					logger.debug("Removed version {} from EcodFactory to save memory.",entry.getKey());
+					//logger.debug("Removed version {} from EcodFactory to save memory.",entry.getKey());
 					it.remove();
 				}
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
index 05635e578e..92cd5ebdbb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
@@ -26,10 +26,8 @@
 import org.slf4j.LoggerFactory;
 
 import java.io.*;
-import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.*;
-import java.util.concurrent.locks.ReadWriteLock;
 import java.util.concurrent.locks.ReentrantReadWriteLock;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -69,7 +67,7 @@ public class EcodInstallation implements EcodDatabase {
 
 	// lock to prevent multiple threads from downloading simultaneously
 	// Should hold the lock when reading/writing allDomains or domainMap
-	private final ReadWriteLock domainsFileLock;
+	private final ReentrantReadWriteLock domainsFileLock;
 	private List<EcodDomain> allDomains;
 	private Map<String,List<EcodDomain>> domainMap;//PDB ID -> domains, lazily constructed from allDomains
 
@@ -86,7 +84,7 @@ public class EcodInstallation implements EcodDatabase {
 	 * @param requestedVersion ECOD requestedVersion to fetch
 	 */
 	public EcodInstallation(String cacheLocation, String version) {
-		domainsFileLock = new ReentrantReadWriteLock();
+		domainsFileLock = new ReentrantReadWriteLock(true);
 
 		this.cacheLocation = cacheLocation;
 
@@ -121,11 +119,11 @@ public List<EcodDomain> getDomainsForPdb(String pdbId) throws IOException {
 			logger.trace("LOCK readlock");
 			while( domainMap == null ) {
 				// unlock to allow ensureDomainsFileInstalled to get the write lock
-				logger.trace("UNLOCK readlock");
-				domainsFileLock.readLock().unlock();
+				//logger.trace("UNLOCK readlock");
+				//domainsFileLock.readLock().unlock();
 				indexDomains();
-				domainsFileLock.readLock().lock();
-				logger.trace("LOCK readlock");
+				//domainsFileLock.readLock().lock();
+				//logger.trace("LOCK readlock");
 			}
 
 			if(pdbId != null)
@@ -219,8 +217,8 @@ public EcodDomain getDomainsById(String ecodId) throws IOException {
 	 */
 	@Override
 	public List<EcodDomain> getAllDomains() throws IOException {
-		domainsFileLock.readLock().lock();
 		logger.trace("LOCK readlock");
+		domainsFileLock.readLock().lock();
 		try {
 			while( allDomains == null) {
 				// unlock to allow ensureDomainsFileInstalled to get the write lock
@@ -322,81 +320,80 @@ public void ensureDomainsFileInstalled() throws IOException{
 			if( allDomains != null ) {
 				return;
 			}
-		} finally {
-			logger.trace("UNLOCK readlock");
-			domainsFileLock.readLock().unlock();
-		}
 
-		// Download domains
-		domainsFileLock.writeLock().lock();
-		logger.trace("LOCK writelock");
-		try {
-			if( !domainsAvailable() ) {
-				downloadDomains();
+			domainsFileLock.writeLock().lock();
+			logger.trace("LOCK writelock");
+			try {
+				parseDomains(new URL( url + DOMAINS_PATH + getDomainFilename()));
+			} finally {
+				logger.trace("UNLOCK writelock");
+				domainsFileLock.writeLock().unlock();
 			}
-			parseDomains();
-		} finally {
-			logger.trace("UNLOCK writelock");
-			domainsFileLock.writeLock().unlock();
-		}
-	}
 
-	/**
-	 * Checks that the domains file has been downloaded
-	 * @return
-	 */
-	private boolean domainsAvailable() {
-		domainsFileLock.readLock().lock();
-		logger.trace("LOCK readlock");
-		try {
-			File f = getDomainFile();
-
-			if (!f.exists() || f.length() <= 0 )
-				return false;
-
-			// Re-download old copies of "latest"
-			if(updateFrequency != null && requestedVersion.equals(DEFAULT_VERSION)) {
-				long mod = f.lastModified();
-				// Time of last update
-				Date lastUpdate = new Date();
-				Calendar cal = Calendar.getInstance();
-				cal.setTime(lastUpdate);
-				cal.add(Calendar.DAY_OF_WEEK, -updateFrequency);
-				long updateTime = cal.getTimeInMillis();
-				// Check if file predates last update
-				if( mod < updateTime ) {
-					logger.info("{} is out of date.",f);
-					return false;
-				}
-			}
-			return true;
 		} finally {
 			logger.trace("UNLOCK readlock");
 			domainsFileLock.readLock().unlock();
 		}
-	}
 
-	/**
-	 * Downloads the domains file, overwriting any existing file
-	 * @throws IOException
-	 */
-	private void downloadDomains() throws IOException {
-		domainsFileLock.writeLock().lock();
-		logger.trace("LOCK writelock");
-		try {
-			URL domainsURL = new URL( url + DOMAINS_PATH + getDomainFilename());
-			File localFile = getDomainFile();
 
-			logger.info("Downloading {} to: {}",domainsURL, localFile);
-			Download.downloadFile(domainsURL, localFile);
-		} catch (MalformedURLException e) {
-			logger.error("Malformed url: "+ url + DOMAINS_PATH + getDomainFilename(),e);
-		} finally {
-			logger.trace("UNLOCK writelock");
-			domainsFileLock.writeLock().unlock();
-		}
 	}
 
+//	/**
+//	 * Checks that the domains file has been downloaded
+//	 * @return
+//	 */
+//	private boolean domainsAvailable() {
+//		domainsFileLock.readLock().lock();
+//		logger.trace("LOCK readlock");
+//		try {
+//			File f = getDomainFile();
+//
+//			if (!f.exists() || f.length() <= 0 )
+//				return false;
+//
+//			// Re-download old copies of "latest"
+//			if(updateFrequency != null && requestedVersion.equals(DEFAULT_VERSION)) {
+//				long mod = f.lastModified();
+//				// Time of last update
+//				Date lastUpdate = new Date();
+//				Calendar cal = Calendar.getInstance();
+//				cal.setTime(lastUpdate);
+//				cal.add(Calendar.DAY_OF_WEEK, -updateFrequency);
+//				long updateTime = cal.getTimeInMillis();
+//				// Check if file predates last update
+//				if( mod < updateTime ) {
+//					logger.info("{} is out of date.",f);
+//					return false;
+//				}
+//			}
+//			return true;
+//		} finally {
+//			logger.trace("UNLOCK readlock");
+//			domainsFileLock.readLock().unlock();
+//		}
+//	}
+
+//	/**
+//	 * Downloads the domains file, overwriting any existing file
+//	 * @throws IOException
+//	 */
+//	private void downloadDomains() throws IOException {
+//		domainsFileLock.writeLock().lock();
+//		logger.trace("LOCK writelock");
+//		try {
+//			URL domainsURL = new URL( url + DOMAINS_PATH + getDomainFilename());
+//			File localFile = getDomainFile();
+//
+//			logger.info("Downloading {} to: {}",domainsURL, localFile);
+//			Download.downloadFile(domainsURL, localFile);
+//		} catch (MalformedURLException e) {
+//			logger.error("Malformed url: "+ url + DOMAINS_PATH + getDomainFilename(),e);
+//		} finally {
+//			logger.trace("UNLOCK writelock");
+//			domainsFileLock.writeLock().unlock();
+//		}
+//	}
+
 	/**
 	 * Basename for the domains file with the current requestedVersion.
 	 * @return
@@ -413,42 +410,35 @@ private File getDomainFile() {
 		return new File(getCacheLocation(),getDomainFilename());
 	}
 
-	/**
-	 * The expected ECOD update frequency determines whether the version
-	 * "latest" should be re-downloaded
-	 * @return the expected ECOD update frequency, in days
-	 */
-	public Integer getUpdateFrequency() {
-		return updateFrequency;
-	}
-
-	/**
-	 * The "latest" version will be re-downloaded if it is older than
-	 * {@link #getUpdateFrequency()} days. Setting this to null disables
-	 * re-downloading (delete $PDB_CACHE_DIR/ecod.latest.domains.txt manually
-	 * to force updating). Setting to 0 will force downloading for every
-	 * program execution.
-	 * @param updateFrequency the updateFrequency to set
-	 */
-	public void setUpdateFrequency(Integer updateFrequency) {
-		this.updateFrequency = updateFrequency;
-	}
+//	/**
+//	 * The expected ECOD update frequency determines whether the version
+//	 * "latest" should be re-downloaded
+//	 * @return the expected ECOD update frequency, in days
+//	 */
+//	public Integer getUpdateFrequency() {
+//		return updateFrequency;
+//	}
+//
+//	/**
+//	 * The "latest" version will be re-downloaded if it is older than
+//	 * {@link #getUpdateFrequency()} days. Setting this to null disables
+//	 * re-downloading (delete $PDB_CACHE_DIR/ecod.latest.domains.txt manually
+//	 * to force updating). Setting to 0 will force downloading for every
+//	 * program execution.
+//	 * @param updateFrequency the updateFrequency to set
+//	 */
+//	public void setUpdateFrequency(Integer updateFrequency) {
+//		this.updateFrequency = updateFrequency;
+//	}
 
 	/**
 	 * Parses the domains from the local file
 	 * @throws IOException
 	 */
-	private void parseDomains() throws IOException {
-		domainsFileLock.writeLock().lock();
-		logger.trace("LOCK writelock");
-		try {
-			EcodParser parser = new EcodParser(getDomainFile());
-			allDomains = parser.getDomains();
-			parsedVersion = parser.getVersion();
-		} finally {
-			logger.trace("UNLOCK writelock");
-			domainsFileLock.writeLock().unlock();
-		}
+	private void parseDomains(URL u) throws IOException {
+		EcodParser parser = new EcodParser(Download.bufferedReader(u));
+		allDomains = parser.getDomains();
+		parsedVersion = parser.getVersion();
 	}
 
 	/**
@@ -473,20 +463,12 @@ private void indexDomains() throws IOException {
 				if( pdbId == null ) {
 					String ecodId = d.getDomainId();
 					if( ecodId != null && !ecodId.isEmpty() ) {
-						Matcher match = ECOD_RE.matcher(ecodId);
-						pdbId = match.group(1);
+						pdbId = ECOD_RE.matcher(ecodId).group(1);
 					}
 				}
 
 				// Add current domain to the map
-				List<EcodDomain> currDomains;
-				if( domainMap.containsKey(pdbId) ) {
-					currDomains = domainMap.get(pdbId);
-				} else {
-					currDomains = new LinkedList<>();
-					domainMap.put(pdbId,currDomains);
-				}
-				currDomains.add(d);
+				domainMap.computeIfAbsent(pdbId, k -> new LinkedList<>()).add(d);
 			}
 		} finally {
 			logger.trace("UNLOCK writelock");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java
index 894a6a9178..a114aac8be 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java
@@ -60,6 +60,9 @@ public static void center(Point3d[] x) {
 	 * @return centroid as Point3d
 	 */
 	public static Point3d centroid(Point3d[] x) {
+		if (x.length == 1)
+			return x[0];
+
 		Point3d center = new Point3d();
 		for (Point3d p : x) {
 			center.add(p);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/UnitQuaternions.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/UnitQuaternions.java
index 5ab2cb8788..81132dc6a7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/UnitQuaternions.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/UnitQuaternions.java
@@ -178,10 +178,8 @@ public static double orientationAngle(Point3d[] fixed, Point3d[] moved) {
 	public static double orientationAngle(Point3d[] fixed, Point3d[] moved,
 			boolean centered) {
 		if (!centered) {
-			fixed = CalcPoint.clonePoint3dArray(fixed);
-			moved = CalcPoint.clonePoint3dArray(moved);
-			CalcPoint.center(fixed);
-			CalcPoint.center(moved);
+			CalcPoint.center(fixed = CalcPoint.clonePoint3dArray(fixed));
+			CalcPoint.center(moved = CalcPoint.clonePoint3dArray(moved));
 		}
 		return orientationAngle(fixed, moved);
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
index f1ab415700..646f9d25e8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -334,7 +334,7 @@ private void pdb_HEADER_Handler(String line) {
 			pdbCode         = line.substring (62, min(len,66)).trim() ;
 			pdbId = pdbCode;
 
-			logger.debug("Parsing entry " + pdbId);
+			logger.debug("Parsing entry {}", pdbId);
 
 
 			structure.setPDBCode(pdbCode);
@@ -870,14 +870,16 @@ private void pdb_JRNL_Handler(String line) {
 	 */
 	private void pdb_COMPND_Handler(String line) {
 
-		logger.debug("previousContinuationField  is "
+		if (logger.isDebugEnabled()) {
+			logger.debug("previousContinuationField  is "
 					+ previousContinuationField);
-		logger.debug("current continuationField  is "
+			logger.debug("current continuationField  is "
 					+ continuationField);
-		logger.debug("current continuationString is "
+			logger.debug("current continuationString is "
 					+ continuationString);
-		logger.debug("current compound           is "
+			logger.debug("current compound           is "
 					+ current_compound);
+		}
 
 
 		// In legacy PDB files the line ends with the PDB code and a serial number, chop those off!
@@ -932,13 +934,12 @@ private void pdb_COMPND_Handler(String line) {
 			if (previousContinuationField.equals(continuationField)
 					&& compndFieldValues.contains(continuationField)) {
 
-				logger.debug("Still in field " + continuationField);
-				logger.debug("token = " + token);
+				logger.debug("Still in field {}", continuationField);
+				logger.debug("token = {}", token);
 
 				continuationString = continuationString.concat(token + " ");
 
-				logger.debug("continuationString = "
-							+ continuationString);
+				logger.debug("continuationString = {}", continuationString);
 
 			}
 			if (!continuationField.equals(previousContinuationField)) {
@@ -1101,16 +1102,18 @@ private void pdb_SOURCE_Handler(String line) {
 
 
 
-		logger.debug("current continuationNo     is "
-				+ continuationNr);
-		logger.debug("previousContinuationField  is "
-				+ previousContinuationField);
-		logger.debug("current continuationField  is "
-				+ continuationField);
-		logger.debug("current continuationString is "
-				+ continuationString);
-		logger.debug("current compound           is "
-				+ current_compound);
+		if (logger.isDebugEnabled()) {
+			logger.debug("current continuationNo     is "
+					+ continuationNr);
+			logger.debug("previousContinuationField  is "
+					+ previousContinuationField);
+			logger.debug("current continuationField  is "
+					+ continuationField);
+			logger.debug("current continuationString is "
+					+ continuationString);
+			logger.debug("current compound           is "
+					+ current_compound);
+		}
 
 
 		// following the docs, the last valid character should be 79, chop off the rest
@@ -1120,7 +1123,7 @@ private void pdb_SOURCE_Handler(String line) {
 
 		line = line.substring(10);
 
-		logger.debug("LINE: >" + line + "<");
+		logger.debug("LINE: >{}<", line);
 
 		String[] fieldList = line.split("\\s+");
 
@@ -1169,12 +1172,11 @@ private void pdb_SOURCE_Handler(String line) {
 			if (previousContinuationField.equals(continuationField)
 					&& sourceFieldValues.contains(continuationField)) {
 
-				logger.debug("Still in field " + continuationField);
+				//logger.debug("Still in field " + continuationField);
 
 				continuationString = continuationString.concat(token + " ");
 
-				logger.debug("continuationString = "
-							+ continuationString);
+				//logger.debug("continuationString = " + continuationString);
 			}
 			if (!continuationField.equals(previousContinuationField)) {
 
@@ -1739,7 +1741,8 @@ private void  pdb_ATOM_Handler(String line)	{
 
 			// test altLoc
 			if ( ! altLoc.equals(' ')) {
-				logger.debug("found altLoc! " + currentGroup + " " + altGroup);
+				logger.debug("found altLoc! {} {}", currentGroup, altGroup);
+
 				altGroup = getCorrectAltLocGroup( altLoc,recordName,aminoCode1,groupCode3);
 				if ( altGroup.getChain() == null) {
 					// need to set current chain
@@ -2151,7 +2154,7 @@ private void pdb_TER_Handler() {
 	 */
 	private void pdb_DBREF_Handler(String line){
 
-		logger.debug("Parsing DBREF " + line);
+		logger.debug("Parsing DBREF {}", line);
 
 		DBRef dbref = new DBRef();
 		String idCode      = line.substring(7,11);
@@ -2362,7 +2365,7 @@ private void pdb_SITE_Handler(String line){
 
 		//  make a map of: SiteId to List<ResidueNumber>
 
-		logger.debug("Site Line:"+line);
+		//logger.debug("Site Line: "+line);
 
 
 		String siteID = line.substring(11, 14);
@@ -2374,12 +2377,12 @@ private void pdb_SITE_Handler(String line){
 			siteResidues = new ArrayList<>();
 			siteToResidueMap.put(siteID.trim(), siteResidues);
 
-			logger.debug(String.format("New Site made: %s %s", siteID,  siteResidues));
-			logger.debug("Now made " + siteMap.size() + " sites");
+			//logger.debug(String.format("New Site made: %s %s", siteID,  siteResidues));
+			//logger.debug("Now made " + siteMap.size() + " sites");
 
 		}
 
-		logger.debug(String.format("SiteId: %s", siteID));
+		//logger.debug(String.format("SiteId: %s", siteID));
 
 
 		//line = 'SITE     1 AC1  6 ARG H 221A LYS H 224  HOH H 403  HOH H 460'
@@ -2391,7 +2394,7 @@ private void pdb_SITE_Handler(String line){
 		while (!(groupString = line.substring(0, 10)).equals("          ")) {
 			//groupstring: 'ARG H 221A'
 
-			logger.debug("groupString: '" + groupString + "'");
+			//logger.debug("groupString: '" + groupString + "'");
 
 			//set the residue name
 			//residueName = 'ARG'
@@ -2415,13 +2418,13 @@ private void pdb_SITE_Handler(String line){
 			//                        insCode = null;
 			//                    }
 
-			logger.debug(String.format("Site: %s: 'resName:%s resNum:%s insCode:%s'", siteID, residueName, resNum, insCode));
+			//logger.debug(String.format("Site: %s: 'resName:%s resNum:%s insCode:%s'", siteID, residueName, resNum, insCode));
 
 			//make a new resNum with the data - this will be linked up with a site later
 			ResidueNumber residueNumber = new ResidueNumber();
 
 
-			logger.debug("pdbCode: '" + resNum + insCode + "'");
+			//logger.debug("pdbCode: '" + resNum + insCode + "'");
 
 			residueNumber.setChainName(chainId);
 			residueNumber.setSeqNum(resNum);
@@ -2429,15 +2432,15 @@ private void pdb_SITE_Handler(String line){
 			//add the resNum to the groups
 			siteResidues.add(residueNumber);
 
-			logger.debug("Adding residueNumber " + residueNumber + " to site " + siteID);
+			//logger.debug("Adding residueNumber " + residueNumber + " to site " + siteID);
 
 			line = line.substring(11);
 		}
 
-		logger.debug("Current SiteMap (contains "+ siteToResidueMap.keySet().size() + " sites):");
-		for (Map.Entry<String, List<ResidueNumber>> entry : siteToResidueMap.entrySet()) {
-			logger.debug(entry.getKey() + " : " + entry.getValue());
-		}
+//		logger.debug("Current SiteMap (contains "+ siteToResidueMap.keySet().size() + " sites):");
+//		for (Map.Entry<String, List<ResidueNumber>> entry : siteToResidueMap.entrySet()) {
+//			logger.debug(entry.getKey() + " : " + entry.getValue());
+//		}
 
 	}
 
@@ -2456,7 +2459,7 @@ private void pdb_REMARK_800_Handler(String line){
 				//                    remark800Counter++;
 				String siteID = fields[1].trim();
 
-				logger.debug("siteID: '" + siteID +"'");
+				//logger.debug("siteID: '" + siteID +"'");
 
 				//fetch the siteResidues from the map
 				site = siteMap.get(siteID);
@@ -2466,8 +2469,8 @@ private void pdb_REMARK_800_Handler(String line){
 					site = new Site(siteID, new ArrayList<>());
 					siteMap.put(site.getSiteID(), site);
 
-					logger.debug("New Site made: " + site);
-					logger.debug("Now made " + siteMap.size() + " sites");
+					//logger.debug("New Site made: " + site);
+					//logger.debug("Now made " + siteMap.size() + " sites");
 
 				}
 			}
@@ -2475,7 +2478,7 @@ private void pdb_REMARK_800_Handler(String line){
 				//                    remark800Counter++;
 				String evCode = fields[1].trim();
 
-				logger.debug("evCode: '" + evCode +"'");
+				//logger.debug("evCode: '" + evCode +"'");
 
 				//fetch the siteResidues from the map
 				site.setEvCode(evCode);
@@ -2484,13 +2487,13 @@ private void pdb_REMARK_800_Handler(String line){
 				//                    remark800Counter++;
 				String desc = fields[1].trim();
 
-				logger.debug("desc: '" + desc +"'");
+				//logger.debug("desc: '" + desc +"'");
 
 				//fetch the siteResidues from the map
 				site.setDescription(desc);
 
-				logger.debug("Finished making REMARK 800 for site " + site.getSiteID());
-				logger.debug(site.remark800toPDB());
+				//logger.debug("Finished making REMARK 800 for site " + site.getSiteID());
+				//logger.debug(site.remark800toPDB());
 
 			}
 		}
@@ -2724,7 +2727,7 @@ else if (recordName.equals("LINK"))
 
 		return structure;
 
-			}
+	}
 
 
 	/**
@@ -2846,12 +2849,12 @@ private void triggerEndFileChecks(){
 		// Only align if requested (default) and not when headerOnly mode with no Atoms.
 		// Otherwise, we store the empty SeqRes Groups unchanged in the right chains.
 		if ( params.isAlignSeqRes() && !params.isHeaderOnly() && !seqResChains.isEmpty()){
-			logger.debug("Parsing mode align_seqres, will parse SEQRES and align to ATOM sequence");
+			//logger.debug("Parsing mode align_seqres, will parse SEQRES and align to ATOM sequence");
 			SeqRes2AtomAligner aligner = new SeqRes2AtomAligner();
 			aligner.align(structure,seqResChains);
 
 		} else {
-			logger.debug("Parsing mode unalign_seqres, will parse SEQRES but not align it to ATOM sequence");
+			//logger.debug("Parsing mode unalign_seqres, will parse SEQRES but not align it to ATOM sequence");
 			SeqRes2AtomAligner.storeUnAlignedSeqRes(structure, seqResChains, params.isHeaderOnly());
 		}
 
@@ -3266,48 +3269,50 @@ private void linkSitesToGroups() {
 		if (structure.getChains().isEmpty()) {
 			sites = new ArrayList<>(siteMap.values());
 			logger.info("No chains to link Site Groups with - Sites will not be present in the Structure");
-			return;
-		}
+		} else {
 
-		//check that the keys in the siteMap and SiteToResidueMap are equal
-		if (! siteMap.keySet().equals(siteToResidueMap.keySet())) {
-			logger.info("Not all sites have been properly described in the PDB " + pdbId + " header - some Sites will not be present in the Structure");
-			logger.debug(siteMap.keySet() + " | " + siteToResidueMap.keySet());
-			//return;
-		}
+			if (logger.isInfoEnabled()) {
+				if (!siteMap.keySet().equals(siteToResidueMap.keySet())) {
+					//check that the keys in the siteMap and SiteToResidueMap are equal
+					logger.info("Not all sites have been properly described in the PDB {} header - some Sites will not be present in the Structure", pdbId);
+					//logger.debug("{} | {}", siteMap, siteToResidueMap.keySet());
+					//return;
+				}
+			}
 
-		//so we have chains - associate the siteResidues-related groups with the ones
-		//already in in the chains
-		for (Map.Entry<String, Site> entry : siteMap.entrySet()) {
-			Site currentSite = entry.getValue();
-			List<ResidueNumber> linkedGroups = siteToResidueMap.get(entry.getKey());
-			if ( linkedGroups == null)
-				continue;
-			for (ResidueNumber residueNumber : linkedGroups) {
+			//so we have chains - associate the siteResidues-related groups with the ones
+			//already in in the chains
+			for (Map.Entry<String, Site> entry : siteMap.entrySet()) {
+				Site currentSite = entry.getValue();
+				List<ResidueNumber> linkedGroups = siteToResidueMap.get(entry.getKey());
+				if (linkedGroups == null)
+					continue;
+				for (ResidueNumber residueNumber : linkedGroups) {
 
-				String pdbCode = residueNumber.toString();
-				String chain = residueNumber.getChainName();
-				//                    System.out.println("chain: '" + chain + "'");
-				//                    String resNum = resNum.getSeqNum().toString();
-				//                    System.out.println("resNum: '" + resNum + "'");
+					String pdbCode = residueNumber.toString();
+					String chain = residueNumber.getChainName();
+					//                    System.out.println("chain: '" + chain + "'");
+					//                    String resNum = resNum.getSeqNum().toString();
+					//                    System.out.println("resNum: '" + resNum + "'");
 
-				Group linkedGroup;
-				try {
-					//TODO: implement findGroup(ResidueNumber resNum)
-					linkedGroup = structure.findGroup(chain, pdbCode);
-				} catch (StructureException ex) {
-					logger.info("Can't find group " + pdbCode + " in chain " + chain + " in order to link up SITE records (PDB ID " + pdbId +")");
-					continue;
-				}
 
-				//                    System.out.println("Adding group: " + linkedGroup.getSeqNum() + " to site " + site.getSiteID());
-				currentSite.getGroups().add(linkedGroup);
+					try {
+						//TODO: implement findGroup(ResidueNumber resNum)
+						Group linkedGroup = structure.findGroup(chain, pdbCode);
+						currentSite.getGroups().add(linkedGroup);
+					} catch (StructureException ex) {
+						logger.info("Can't find group {} in chain {} in order to link up SITE records (PDB ID {})", pdbCode, chain, pdbId);
+					}
+
+					//                    System.out.println("Adding group: " + linkedGroup.getSeqNum() + " to site " + site.getSiteID());
+				}
 			}
-		}
 
-		//System.out.println("SITEMAP: " + siteMap);
+			//System.out.println("SITEMAP: " + siteMap);
+
+			sites = new ArrayList<>(siteMap.values());
+		}
 
-		sites = new ArrayList<>(siteMap.values());
 		structure.setSites(sites);
 		//System.out.println("STRUCTURE SITES: " + structure.getSites().size());
 		//            for (Site site : structure.getSites()) {
@@ -3353,7 +3358,7 @@ private void buildjournalArticle() {
 			if (subField.equals("AUTH")) {
 				auth.append(line.substring(19).trim());
 
-				logger.debug("AUTH '" + auth + "'");
+				//logger.debug("AUTH '" + auth + "'");
 
 			}
 			if (subField.equals("TITL")) {
@@ -3361,26 +3366,26 @@ private void buildjournalArticle() {
 				//words on the join won't be concatenated
 				titl.append(line.substring(19).trim()).append(" ");
 
-				logger.debug("TITL '" + titl + "'");
+				//logger.debug("TITL '" + titl + "'");
 
 			}
 			if (subField.equals("EDIT")) {
 				edit.append(line.substring(19).trim());
 
-				logger.debug("EDIT '" + edit + "'");
+				//logger.debug("EDIT '" + edit + "'");
 
 			}
 			//        JRNL        REF    NAT.IMMUNOL.                  V.   8   430 2007
 			if (subField.equals("REF ")) {
 				ref.append(line.substring(19).trim()).append(" ");
 
-				logger.debug("REF '" + ref + "'");
+				//logger.debug("REF '" + ref + "'");
 
 			}
 			if (subField.equals("PUBL")) {
 				publ.append(line.substring(19).trim()).append(" ");
 
-				logger.debug("PUBL '" + publ + "'");
+				//logger.debug("PUBL '" + publ + "'");
 
 			}
 			//        JRNL        REFN                   ISSN 1529-2908
@@ -3391,21 +3396,21 @@ private void buildjournalArticle() {
 				}
 				refn.append(line.substring(35).trim());
 
-				logger.debug("REFN '" + refn + "'");
+				//logger.debug("REFN '" + refn + "'");
 
 			}
 			//        JRNL        PMID   17351618
 			if (subField.equals("PMID")) {
 				pmid.append(line.substring(19).trim());
 
-				logger.debug("PMID '" + pmid + "'");
+				//logger.debug("PMID '" + pmid + "'");
 
 			}
 			//        JRNL        DOI    10.1038/NI1450
 			if (subField.equals("DOI ")) {
 				doi.append(line.substring(19).trim());
 
-				logger.debug("DOI '" + doi + "'");
+				//logger.debug("DOI '" + doi + "'");
 
 			}
 		}
@@ -3429,9 +3434,7 @@ private void buildjournalArticle() {
 		journalArticle.setDoi(doi.toString().trim());
 
 
-		logger.debug("Made JournalArticle:");
-		logger.debug(journalArticle.toString());
-
+		logger.debug("Made JournalArticle: {}", journalArticle);
 	}
 
 	//inner class to deal with all the journal info
@@ -3445,13 +3448,13 @@ private static class JournalParser {
 
 		public JournalParser(String ref) {
 
-			logger.debug("JournalParser init '" + ref + "'");
+			logger.debug("JournalParser init '{}'", ref);
 
 
 			if (ref.equals("TO BE PUBLISHED ")) {
 				journalName = ref.trim();
 
-				logger.debug(String.format("JournalParser found journalString '%s'", journalName));
+				logger.debug("JournalParser found journalString '{}'", journalName);
 
 				return;
 			}
@@ -3486,7 +3489,7 @@ public JournalParser(String ref) {
 			//'NAT.STRUCT.MOL.BIOL.          V.  16   238 2009'
 			String volumeInformation = ref.substring(30, 48);
 
-			logger.debug(String.format("Parsing volumeInformation: '%s'", volumeInformation));
+			logger.debug("Parsing volumeInformation: '{}'", volumeInformation);
 
 			//volumeInformation: 'V. 293    53 1981 '
 			//                      String dateString = ref.substring(ref.length() - 5 , ref.length() - 1).trim();
@@ -3501,10 +3504,12 @@ public JournalParser(String ref) {
 			journalString = journalString.trim();
 			//                        System.out.println("journalString: " + journalString);
 
-			logger.debug(String.format("JournalParser found volumeString '%s'", volumeString));
-			logger.debug(String.format("JournalParser found startPageString '%s'", startPageString));
-			logger.debug(String.format("JournalParser found dateString '%s'", dateString));
-			logger.debug(String.format("JournalParser found journalString '%s'", journalString));
+			if (logger.isDebugEnabled()) {
+				logger.debug(String.format("JournalParser found volumeString '%s'", volumeString));
+				logger.debug(String.format("JournalParser found startPageString '%s'", startPageString));
+				logger.debug(String.format("JournalParser found dateString '%s'", dateString));
+				logger.debug(String.format("JournalParser found journalString '%s'", journalString));
+			}
 
 
 			if (!dateString.equals("    ")) {
@@ -3535,7 +3540,7 @@ public JournalParser(String ref) {
 			if (!journalString.equals("    ")) {
 				journalName = journalString;
 
-				logger.debug("JournalParser set journalName " + journalName);
+				logger.debug("JournalParser set journalName {}", journalName);
 
 			}
 		}
@@ -3585,14 +3590,14 @@ private List<Author> authorBuilder(String authorString) {
 			Author author = new Author();
 			author.setSurname(authors[0]);
 
-			logger.debug("Set consortium author name " + author.getSurname());
+			logger.debug("Set consortium author name {}", author.getSurname());
 
 			authorList.add(author);
 		} else {
 			for (int i = 0; i < authors.length; i++) {
 				String authorFullName = authors[i];
 
-				logger.debug("Building author " + authorFullName);
+				logger.debug("Building author {}", authorFullName);
 
 				Author author = new Author();
 				String regex = "\\.";
@@ -3608,15 +3613,14 @@ private List<Author> authorBuilder(String authorString) {
 				if (authorNames.length == 0) {
 					author.setSurname(authorFullName);
 
-					logger.debug("Unable to split using '" + regex + "' Setting whole name " + author.getSurname());
+					logger.debug("Unable to split using '{}' Setting whole name {}", regex, author.getSurname());
 
 				}
 				//again there might be a consortium name so there may be no elements
 				else if (authorNames.length == 1) {
 					author.setSurname(authorNames[0]);
 
-					logger.debug("Set consortium author name in multiple author block " + author.getSurname
-								());
+					logger.debug("Set consortium author name in multiple author block {}", author.getSurname());
 
 				} else {
 					String initials = "";
@@ -3629,14 +3633,14 @@ else if (authorNames.length == 1) {
 						initials += initial + ".";
 					}
 
-					logger.debug("built initials '" + initials + "'");
+					logger.debug("built initials '{}'", initials);
 
 					author.setInitials(initials);
 					//surname is always last
 					int lastName = authorNames.length - 1;
 					String surname = authorNames[lastName];
 
-					logger.debug("built author surname " + surname);
+					logger.debug("built author surname {}", surname);
 
 					author.setSurname(surname);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
index ae04756d9d..fa1dcecd14 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
@@ -138,8 +138,7 @@ public Structure getStructure(InputStream inStream) throws IOException {
 		PDBFileParser pdbpars = new PDBFileParser();
 		pdbpars.setFileParsingParameters(getFileParsingParameters());
 
-		Structure struc = pdbpars.parsePDBFile(inStream) ;
-		return struc ;
+		return pdbpars.parsePDBFile(inStream);
 	}
 
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
index 981e265f2c..2cb7ae6258 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
@@ -358,13 +358,13 @@ public void parse(BufferedReader buf)
 
 	}
 
-	private void resetBuffers(List<String> loopFields, List<String> lineData, Set<String> loopWarnings) {
+	private static void resetBuffers(List<String> loopFields, List<String> lineData, Set<String> loopWarnings) {
 		loopFields.clear();
 		lineData.clear();
 		loopWarnings.clear();
 	}
 
-	private List<String> processSingleLine(String line){
+	private static List<String> processSingleLine(String line){
 
 		List<String> data = new ArrayList<>();
 
@@ -379,7 +379,7 @@ private List<String> processSingleLine(String line){
 		boolean inString = false; // semicolon (;) quoting
 		boolean inS1     = false; // single quote (') quoting
 		boolean inS2     = false; // double quote (") quoting
-		String word 	 = "";
+		StringBuilder word 	 = new StringBuilder();
 
 		for (int i=0; i< line.length(); i++ ){
 
@@ -396,12 +396,12 @@ private List<String> processSingleLine(String line){
 			if  (c == ' ') {
 
 				if ( ! inString){
-					if (!word.isEmpty())
-						data.add(word.trim());
-					word = "";
+					if (word.length() > 0)
+						data.add(word.toString().trim());
+					word = new StringBuilder();
 				} else {
 					// we are in a string, add the space
-					word += c;
+					word.append(c);
 				}
 
 			} else if (c == S1 )  {
@@ -420,13 +420,13 @@ private List<String> processSingleLine(String line){
 					if ( wordEnd ) {
 
 						// at end of string
-						if (!word.isEmpty())
-							data.add(word.trim());
-						word     = "";
+						if (word.length() > 0)
+							data.add(word.toString().trim());
+						word = new StringBuilder();
 						inString = false;
 						inS1     = false;
 					} else {
-						word += c;
+						word.append(c);
 					}
 
 				} else if (prevC==null || prevC==' ') {
@@ -434,7 +434,7 @@ private List<String> processSingleLine(String line){
 					inString = true;
 					inS1     = true;
 				} else {
-					word += c;
+					word.append(c);
 				}
 			} else if ( c == S2 ){
 				if ( inString){
@@ -450,28 +450,28 @@ private List<String> processSingleLine(String line){
 					if ( wordEnd ) {
 
 						// at end of string
-						if (!word.isEmpty())
-							data.add(word.trim());
-						word     = "";
+						if (word.length() > 0)
+							data.add(word.toString().trim());
+						word = new StringBuilder();
 						inString = false;
 						inS2     = false;
 					} else {
-						word += c;
+						word.append(c);
 					}
 				}  else if (prevC==null || prevC==' ') {
 					// the beginning of a new string
 					inString = true;
 					inS2     = true;
 				} else {
-					word += c;
+					word.append(c);
 				}
 			} else {
-				word += c;
+				word.append(c);
 			}
 
 		}
-		if (!word.trim().isEmpty())
-			data.add(word);
+		if (!word.toString().trim().isEmpty())
+			data.add(word.toString());
 
 
 		return data;
@@ -485,9 +485,9 @@ private List<String> processSingleLine(String line){
 	 * @param buf
 	 * @return
 	 */
-	private List<String> processLine(String line,
-			BufferedReader buf,
-			int fieldLength)
+	private static List<String> processLine(String line,
+											BufferedReader buf,
+											int fieldLength)
 					throws IOException{
 
 		//System.out.println("XX processLine " + fieldLength + " " + line);
@@ -570,296 +570,257 @@ private void endLineChecks(String category,List<String> loopFields, List<String>
 		switch (category) {
 			case "_entity":
 
-				Entity e = (Entity) buildObject(
-						Entity.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewEntity(e);
+				triggerNewEntity(buildObject(
+						Entity.class,
+						loopFields, lineData, loopWarnings));
 
 				break;
 			case "_entity_poly":
-				EntityPoly ep = (EntityPoly) buildObject(EntityPoly.class.getName(), loopFields, lineData, loopWarnings);
-				triggerNewEntityPoly(ep);
+				triggerNewEntityPoly(buildObject(EntityPoly.class, loopFields, lineData, loopWarnings));
 
 				break;
 			case "_struct":
 
-				struct = (Struct) buildObject(
-						Struct.class.getName(),
-						loopFields, lineData, loopWarnings);
+				struct = buildObject(Struct.class, loopFields, lineData, loopWarnings);
 
 				break;
 			case "_atom_site":
 
-				AtomSite a = (AtomSite) buildObject(
-						AtomSite.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewAtomSite(a);
+				triggerNewAtomSite(buildObject(
+						AtomSite.class,
+						loopFields, lineData, loopWarnings));
 
 				break;
 			case "_database_PDB_rev": {
-				DatabasePDBrev dbrev = (DatabasePDBrev) buildObject(
-						DatabasePDBrev.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewDatabasePDBrev(dbrev);
+				triggerNewDatabasePDBrev(buildObject(
+						DatabasePDBrev.class,
+						loopFields, lineData, loopWarnings));
 
 				break;
 			}
 			case "_database_PDB_rev_record": {
-				DatabasePdbrevRecord dbrev = (DatabasePdbrevRecord) buildObject(
-						DatabasePdbrevRecord.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewDatabasePDBrevRecord(dbrev);
+				triggerNewDatabasePDBrevRecord(buildObject(
+						DatabasePdbrevRecord.class,
+						loopFields, lineData, loopWarnings));
 
 				// MMCIF version 5 dates
 				break;
 			}
 			case "_pdbx_audit_revision_history":
-				PdbxAuditRevisionHistory history = (PdbxAuditRevisionHistory) buildObject(
-						PdbxAuditRevisionHistory.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewPdbxAuditRevisionHistory(history);
+				triggerNewPdbxAuditRevisionHistory(buildObject(
+						PdbxAuditRevisionHistory.class,
+						loopFields, lineData, loopWarnings));
 
 				// MMCIF version 5 dates
 				break;
 			case "_pdbx_database_status":
-				PdbxDatabaseStatus status = (PdbxDatabaseStatus) buildObject(
-						PdbxDatabaseStatus.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewPdbxDatabaseStatus(status);
+				triggerNewPdbxDatabaseStatus(buildObject(
+						PdbxDatabaseStatus.class,
+						loopFields, lineData, loopWarnings));
 
 				break;
 			case "_database_PDB_remark":
-				DatabasePDBremark remark = (DatabasePDBremark) buildObject(
-						DatabasePDBremark.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewDatabasePDBremark(remark);
+				triggerNewDatabasePDBremark(buildObject(
+						DatabasePDBremark.class,
+						loopFields, lineData, loopWarnings));
 
 				break;
 			case "_exptl": {
-				Exptl exptl = (Exptl) buildObject(
-						Exptl.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerExptl(exptl);
+				triggerExptl(buildObject(
+						Exptl.class,
+						loopFields, lineData, loopWarnings));
 
 				break;
 			}
 			case "_cell":
-				Cell cell = (Cell) buildObject(
-						Cell.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewCell(cell);
+				triggerNewCell(buildObject(
+						Cell.class,
+						loopFields, lineData, loopWarnings));
 
 				break;
 			case "_symmetry":
-				Symmetry symmetry = (Symmetry) buildObject(
-						Symmetry.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewSymmetry(symmetry);
+				triggerNewSymmetry(buildObject(
+						Symmetry.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			case "_struct_ncs_oper":
 
-				StructNcsOper sNcsOper = (StructNcsOper) buildObject(
-						StructNcsOper.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewStructNcsOper(sNcsOper);
+				triggerNewStructNcsOper(buildObject(
+						StructNcsOper.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			case "_atom_sites":
 
-				AtomSites atomSites = (AtomSites) buildObject(
-						AtomSites.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewAtomSites(atomSites);
+				triggerNewAtomSites(buildObject(
+						AtomSites.class,
+						loopFields, lineData, loopWarnings));
 
 				break;
 			case "_struct_ref": {
-				StructRef sref = (StructRef) buildObject(
-						StructRef.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewStrucRef(sref);
+				triggerNewStrucRef(buildObject(
+						StructRef.class,
+						loopFields, lineData, loopWarnings));
 
 				break;
 			}
 			case "_struct_ref_seq": {
-				StructRefSeq sref = (StructRefSeq) buildObject(
-						StructRefSeq.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewStrucRefSeq(sref);
+				triggerNewStrucRefSeq(buildObject(
+						StructRefSeq.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			}
 			case "_struct_ref_seq_dif": {
-				StructRefSeqDif sref = (StructRefSeqDif) buildObject(
-						StructRefSeqDif.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewStrucRefSeqDif(sref);
+				triggerNewStrucRefSeqDif(buildObject(
+						StructRefSeqDif.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			}
 			case "_struct_site_gen": {
-				StructSiteGen sref = (StructSiteGen) buildObject(
-						StructSiteGen.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewStructSiteGen(sref);
+				triggerNewStructSiteGen(buildObject(
+						StructSiteGen.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			}
 			case "_struct_site": {
-				StructSite sref = (StructSite) buildObject(
-						StructSite.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewStructSite(sref);
+				triggerNewStructSite(buildObject(
+						StructSite.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			}
 			case "_entity_poly_seq": {
-				EntityPolySeq exptl = (EntityPolySeq) buildObject(
-						EntityPolySeq.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewEntityPolySeq(exptl);
+				triggerNewEntityPolySeq(buildObject(
+						EntityPolySeq.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			}
 			case "_entity_src_gen":
-				EntitySrcGen entitySrcGen = (EntitySrcGen) buildObject(
-						EntitySrcGen.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewEntitySrcGen(entitySrcGen);
+				triggerNewEntitySrcGen(buildObject(
+						EntitySrcGen.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			case "_entity_src_nat":
-				EntitySrcNat entitySrcNat = (EntitySrcNat) buildObject(
-						EntitySrcNat.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewEntitySrcNat(entitySrcNat);
+				triggerNewEntitySrcNat(buildObject(
+						EntitySrcNat.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			case "_pdbx_entity_src_syn":
-				EntitySrcSyn entitySrcSyn = (EntitySrcSyn) buildObject(
-						EntitySrcSyn.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewEntitySrcSyn(entitySrcSyn);
+				triggerNewEntitySrcSyn(buildObject(
+						EntitySrcSyn.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			case "_struct_asym":
-				StructAsym sasym = (StructAsym) buildObject(
-						StructAsym.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewStructAsym(sasym);
+				triggerNewStructAsym(buildObject(
+						StructAsym.class,
+						loopFields, lineData, loopWarnings));
 
 				break;
 			case "_pdbx_poly_seq_scheme": {
-				PdbxPolySeqScheme ppss = (PdbxPolySeqScheme) buildObject(
-						PdbxPolySeqScheme.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewPdbxPolySeqScheme(ppss);
+				triggerNewPdbxPolySeqScheme(buildObject(
+						PdbxPolySeqScheme.class,
+						loopFields, lineData, loopWarnings));
 
 				break;
 			}
 			case "_pdbx_nonpoly_scheme": {
-				PdbxNonPolyScheme ppss = (PdbxNonPolyScheme) buildObject(
-						PdbxNonPolyScheme.class.getName(),
-						loopFields, lineData, loopWarnings);
 
-				triggerNewPdbxNonPolyScheme(ppss);
+				triggerNewPdbxNonPolyScheme(buildObject(
+						PdbxNonPolyScheme.class,
+						loopFields, lineData, loopWarnings));
 
 				break;
 			}
 			case "_pdbx_entity_nonpoly":
-				PdbxEntityNonPoly pen = (PdbxEntityNonPoly) buildObject(
-						PdbxEntityNonPoly.class.getName(),
+				triggerNewPdbxEntityNonPoly(buildObject(
+						PdbxEntityNonPoly.class,
 						loopFields, lineData, loopWarnings
-				);
-				triggerNewPdbxEntityNonPoly(pen);
+				));
 				break;
 			case "_struct_keywords":
-				StructKeywords kw = (StructKeywords) buildObject(
-						StructKeywords.class.getName(),
+				triggerNewStructKeywords(buildObject(
+						StructKeywords.class,
 						loopFields, lineData, loopWarnings
-				);
-				triggerNewStructKeywords(kw);
+				));
 				break;
 			case "_refine":
-				Refine r = (Refine) buildObject(
-						Refine.class.getName(),
+				triggerNewRefine(buildObject(
+						Refine.class,
 						loopFields, lineData, loopWarnings
-				);
-				triggerNewRefine(r);
+				));
 				break;
 			case "_chem_comp":
-				ChemComp c = (ChemComp) buildObject(
-						ChemComp.class.getName(),
+				triggerNewChemComp(buildObject(
+						ChemComp.class,
 						loopFields, lineData, loopWarnings
-				);
-				triggerNewChemComp(c);
+				));
 				break;
 			case "_audit_author":
-				AuditAuthor aa = (AuditAuthor) buildObject(
-						AuditAuthor.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewAuditAuthor(aa);
+				triggerNewAuditAuthor(buildObject(
+						AuditAuthor.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			case "_pdbx_chem_comp_descriptor":
-				ChemCompDescriptor ccd = (ChemCompDescriptor) buildObject(
-						ChemCompDescriptor.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewChemCompDescriptor(ccd);
+				triggerNewChemCompDescriptor(buildObject(
+						ChemCompDescriptor.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			case "_pdbx_struct_oper_list":
 
-				PdbxStructOperList structOper = (PdbxStructOperList) buildObject(
-						PdbxStructOperList.class.getName(),
+				triggerNewPdbxStructOper(buildObject(
+						PdbxStructOperList.class,
 						loopFields, lineData, loopWarnings
-				);
-				triggerNewPdbxStructOper(structOper);
+				));
 
 				break;
 			case "_pdbx_struct_assembly": {
-				PdbxStructAssembly sa = (PdbxStructAssembly) buildObject(
-						PdbxStructAssembly.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewPdbxStructAssembly(sa);
+				triggerNewPdbxStructAssembly(buildObject(
+						PdbxStructAssembly.class,
+						loopFields, lineData, loopWarnings));
 
 				break;
 			}
 			case "_pdbx_struct_assembly_gen": {
-				PdbxStructAssemblyGen sa = (PdbxStructAssemblyGen) buildObject(
-						PdbxStructAssemblyGen.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewPdbxStructAssemblyGen(sa);
+				triggerNewPdbxStructAssemblyGen(buildObject(
+						PdbxStructAssemblyGen.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			}
 			case "_chem_comp_atom":
-				ChemCompAtom atom = (ChemCompAtom) buildObject(
-						ChemCompAtom.class.getName(),
+				ChemCompAtom atom = buildObject(
+						ChemCompAtom.class,
 						loopFields, lineData, loopWarnings);
 				triggerNewChemCompAtom(atom);
 
 				break;
 			case "_chem_comp_bond":
-				ChemCompBond bond = (ChemCompBond) buildObject(
-						ChemCompBond.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewChemCompBond(bond);
+				triggerNewChemCompBond(buildObject(
+						ChemCompBond.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			case "_pdbx_chem_comp_identifier": {
-				PdbxChemCompIdentifier id = (PdbxChemCompIdentifier) buildObject(
-						PdbxChemCompIdentifier.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewPdbxChemCompIdentifier(id);
+				triggerNewPdbxChemCompIdentifier(buildObject(
+						PdbxChemCompIdentifier.class,
+						loopFields, lineData, loopWarnings));
 				break;
 			}
 			case "_struct_conn": {
-				StructConn id = (StructConn) buildObject(
-						StructConn.class.getName(),
-						loopFields, lineData, loopWarnings);
-				triggerNewStructConn(id);
+				triggerNewStructConn(buildObject(
+						StructConn.class,
+						loopFields, lineData, loopWarnings));
 
 				break;
 			}
@@ -952,39 +913,49 @@ public void triggerNewAtomSites(AtomSites atomSites) {
 	 * @param warnings
 	 * @return
 	 */
-	private Object buildObject(String className, List<String> loopFields, List<String> lineData, Set<String> warnings) {
+	@Deprecated private Object buildObject(String className, List<String> loopFields, List<String> lineData, Set<String> warnings) {
 
-		Object o;
 		Class<?> c;
 
 		try {
 			// build up the Entity object from the line data...
 			c = Class.forName(className);
 
-			o = c.newInstance();
+		} catch (ClassNotFoundException e){
+			logger.error( "{} {}", className, e);
+			return null;
+		}
+
+		return buildObject(c, loopFields, lineData, warnings);
+	}
+
+	private static <X> X buildObject(Class<X> c, List<String> loopFields, List<String> lineData, Set<String> warnings) {
 
-		} catch (InstantiationException|ClassNotFoundException|IllegalAccessException e){
-			logger.error( "Error while constructing {}: {}", className, e.getMessage());
+		Object o;
+
+		try {
+			o = c.newInstance();
+		} catch (InstantiationException | IllegalAccessException e) {
+			logger.error( "{} {}", c, e);
 			return null;
 		}
 
 		// these methods get the fields but also looking at the IgnoreField and CIFLabel annotations
-		Field[] fields = MMCIFFileTools.getFields(c);
-		String[] names = MMCIFFileTools.getFieldNames(fields);
 
 		// let's build a map of all methods so that we can look up the setter methods later
 		Method[] methods = c.getMethods();
 
-		Map<String,Method> methodMap = new HashMap<>();
-		for (Method m : methods) {
+		Map<String,Method> methodMap = new HashMap<>(methods.length);
+		for (Method m : methods)
 			methodMap.put(m.getName(),m);
-		}
+
+		Field[] fields = MMCIFFileTools.getFields(c);
+		String[] names = MMCIFFileTools.getFieldNames(fields);
 
 		// and a map of all the fields so that we can lookup them up later
-		Map<String, Field> names2fields = new HashMap<>();
-		for (int i=0;i<fields.length;i++) {
+		Map<String, Field> names2fields = new HashMap<>(fields.length);
+		for (int i=0;i<fields.length;i++)
 			names2fields.put(names[i], fields[i]);
-		}
 
 		int pos = -1 ;
 		for (String key: loopFields){
@@ -1014,35 +985,28 @@ private Object buildObject(String className, List<String> loopFields, List<Strin
 				continue;
 			}
 
-
-
 			// now we populate the object with the values by invoking the corresponding setter method,
 			// note that all of the mmCif container classes have only one argument (they are beans)
 			Class<?>[] pType  = setter.getParameterTypes();
-
-
 			try {
 				if ( pType[0].getName().equals(Integer.class.getName())) {
 					if ( val != null && ! val.equals("?") && !val.equals(".")) {
-
-						Integer intVal = Integer.parseInt(val);
-						setter.invoke(o, intVal);
-
+						setter.invoke(o, Integer.parseInt(val));
 					}
 				} else {
 					// default val is a String
 					setter.invoke(o, val);
 				}
-			} catch (IllegalAccessException|InvocationTargetException e) {
-				logger.error("Could not invoke setter {} with value {} for class {}", setterMethodName, val, className);
+			} catch (IllegalAccessException| InvocationTargetException e) {
+				logger.error("Could not invoke setter {} with value {} for class {}", setterMethodName, val, c);
 			}
 
 		}
 
-		return o;
+		return (X) o;
 	}
 
-	private void produceWarning(String key, String val, Class<?> c, Set<String> warnings) {
+	private static void produceWarning(String key, String val, Class<?> c, Set<String> warnings) {
 
 		String warning = "Trying to set field " + key + " in "+ c.getName() +" found in file, but no corresponding field could be found in model class (value:" + val + ")";
 		String warnkey = key+"-"+c.getName();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/RemoteScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/RemoteScopInstallation.java
index 6f8305ad96..2c044b2055 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/RemoteScopInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/RemoteScopInstallation.java
@@ -207,10 +207,9 @@ public ScopDomain getDomainByScopID(String scopId) {
 			String scopId1 = scopId;
 			scopId1 = scopId1.trim();
 			URL u = new URL(server + "getDomainByScopID?scopId="+ scopId1 +"&version="+getScopVersion());
-			InputStream response = Download.stream(u);
-			String xml = JFatCatClient.convertStreamToString(response);
+//			String xml = JFatCatClient.convertStreamToString(Download.stream(u));
 
-			return !xml.trim().isEmpty() ? XMLUtil.getScopDomainFromXML(xml) : null;
+			return XMLUtil.getScopDomainFromXML(Download.stream(u));
 		} catch (Exception e){
 			throw new RuntimeException("Unable to reach "+ server + "getDomainByScopID?scopId="+scopId+"&version="+getScopVersion(), e);
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/XMLUtil.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/XMLUtil.java
index df5d7bca02..39acb9982a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/XMLUtil.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/server/XMLUtil.java
@@ -35,6 +35,7 @@
 import javax.xml.bind.Unmarshaller;
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
+import java.io.InputStream;
 import java.io.PrintStream;
 import java.util.List;
 import java.util.SortedSet;
@@ -272,16 +273,16 @@ public static String getScopDomainXML(ScopDomain domain){
 		return baos.toString();
 	}
 
-	public static ScopDomain getScopDomainFromXML(String xml){
+	public static ScopDomain getScopDomainFromXML(InputStream xml){
 		ScopDomain job;
 
 		try {
 
 			Unmarshaller un = jaxbContextScopDomain.createUnmarshaller();
 
-			ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
+			//ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
 
-			job = (ScopDomain) un.unmarshal(bais);
+			job = (ScopDomain) un.unmarshal(xml);
 
 		} catch (JAXBException e){
 			throw new RuntimeException("Could not serialize to XML", e);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
index 56b1576aba..7f6c183700 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
@@ -524,7 +524,7 @@ private static QuatSymmetryResults calcQuatSymmetry(Stoichiometry composition, Q
 		String symmetry = results.getSymmetry();
 
 		// Check structures with Cn symmetry (n = 1, ...) for helical symmetry
-		if (symmetry.startsWith("C")) {
+ 		if (symmetry.startsWith("C")) {
 			HelixSolver hc = new HelixSolver(subunits,
 					rotationGroup.getOrder(), parameters);
 			HelixLayers helixLayers = hc.getSymmetryOperations();
@@ -542,9 +542,7 @@ private static QuatSymmetryResults calcQuatSymmetry(Stoichiometry composition, Q
 				double hRmsd = helixLayers.getScores().getRmsd();
 				// System.out.println("cRMSD: " + cRmsd + " hRMSD: " + hRmsd);
 				double deltaRmsd = hRmsd - cRmsd;
-				if (symmetry.equals("C1")
-						|| (!symmetry.equals("C1") && deltaRmsd <= parameters
-								.getHelixRmsdThreshold())) {
+				if (symmetry.equals("C1") || deltaRmsd <= parameters.getHelixRmsdThreshold()) {
 					method = SymmetryPerceptionMethod.ROTO_TRANSLATION;
 					results = new QuatSymmetryResults(composition, helixLayers,
 							method);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java
index ba6b711643..9e9bc9f571 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java
@@ -200,12 +200,12 @@ public SymmetryPerceptionMethod getMethod() {
 	 *         group symbol and for helical symmetry returns "H".
 	 */
 	public String getSymmetry() {
-		if (helixLayers != null && helixLayers.size() > 0) {
+		if (helixLayers != null && helixLayers.size() > 0)
 			return "H";
-		} else if (rotationGroup != null && rotationGroup.getOrder() > 0) {
+		else if (rotationGroup != null && rotationGroup.getOrder() > 0)
 			return rotationGroup.getPointGroup();
-		}
-		return "";
+		else
+			return "";
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
index dbc1759c16..552a55f3f2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
@@ -28,6 +28,8 @@
 import java.util.Iterator;
 import java.util.List;
 
+import static java.lang.System.identityHashCode;
+
 /**
  * @see http://en.wikipedia.org/wiki/Rotation_group_SO(3)
  * @author Peter
@@ -88,7 +90,7 @@ public void complete() {
 				findHigherOrderAxes();
 				findTwoFoldsPerpendicular();
 				calcPointGroup();
-				sortByFoldDecending();
+				sortByFoldDescending();
 			}
 			modified = false;
 		}
@@ -350,20 +352,24 @@ private void calcPointGroup() {
 		}
 	}
 
-	public void sortByFoldDecending() {
-		rotations.sort((o1, o2) -> {
-			int delta = o1.getDirection() - o2.getDirection();
-			if (delta != 0) {
-				return delta;
-			}
-			delta = Math.round(Math.signum(o2.getFold() - o1.getFold()));
-			if (delta != 0) {
-				return delta;
-			}
+	public void sortByFoldDescending() {
+		if (rotations.size() > 1) {
+			rotations.sort((o1, o2) -> {
+
+				if (o1 == o2) return 0;
 
-			delta = (int) (Math.signum(o1.getAxisAngle().angle - o2.getAxisAngle().angle));
-			return delta;
-		});
+				int delta = Integer.compare(o1.getDirection(), o2.getDirection());
+				if (delta != 0) return delta;
+
+				delta = Integer.compare(o1.getFold(), o2.getFold());
+				if (delta != 0) return delta;
+
+				delta = Double.compare(o1.getAxisAngle().angle, o2.getAxisAngle().angle);
+				if (delta != 0) return delta;
+
+				return Integer.compare(identityHashCode(o1), identityHashCode(o2));
+			});
+		}
 	}
 
 	@Override
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java
index 35f325e7d7..90aa73f6c4 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java
@@ -24,7 +24,6 @@
  */
 package org.biojava.nbio.structure.io;
 
-import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java
index f34cca7454..6fffc52d61 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java
@@ -84,8 +84,10 @@ public void test4jn3() throws Exception {
 			//System.out.println(e.getEntityId() + " " +e.getType());
 
 
-			Assert.assertTrue(e.getSegments().size() > 0);
-			for (SiftsSegment seg : e.getSegments()) {
+			List<SiftsSegment> segments = e.getSegments();
+
+			Assert.assertTrue(segments.size() > 0);
+			for (SiftsSegment seg : segments) {
 				Assert.assertTrue(seg.getResidues().size() > 0);
 				//System.out.println(seg.getResidues().size());
 				//System.out.println(" Segment: " + seg.getSegId() + " " + seg.getStart() + " " + seg.getEnd()) ;
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java
index 26d9cbf202..4b27f09b3f 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java
@@ -20,17 +20,16 @@
  */
 package org.biojava.nbio.structure.io.mmtf;
 
+import org.biojava.nbio.core.util.Download;
 import org.biojava.nbio.structure.io.PDBFileParser;
 import org.junit.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URL;
-import java.util.zip.GZIPInputStream;
 
 import static org.junit.Assert.assertTrue;
 
@@ -75,34 +74,34 @@ public void test3HBX() throws Exception{
 
 		pdbId = pdbId.toUpperCase();
 
-		URL url = new URL("https://files.rcsb.org/download/"+pdbId+".pdb.gz");
+		URL pdbURL = new URL("https://files.rcsb.org/download/"+pdbId+".pdb.gz");
 
-		String pdbFile = convertStreamToString(new GZIPInputStream(url.openStream()));
+//		String pdbFile = convertStreamToString(new GZIPInputStream(pdbURL.openStream()));
 
 		long totalTimePDB = 0;
 		long totalTimeMMTF = 0;
 
-		byte[] pdbBytes = pdbFile.getBytes();
+//		byte[] pdbBytes = pdbFile.getBytes();
 
 		PDBFileParser parser = new PDBFileParser();
 
 		URL mmtfURL = new URL("https://mmtf.rcsb.org/v1.0/full/" + pdbId + ".mmtf.gz");
 
-		byte[] mmtfdata = getByteArrayFromInputStream(new GZIPInputStream((mmtfURL.openStream())));
+
 
 		// first make sure chemcomp cache is warmed up (chemcomp files are parsed). Like that we count the parsing time without the influence of chemcomp parsing
-		MmtfActions.readFromInputStream(new ByteArrayInputStream(mmtfdata));
+		MmtfActions.readFromInputStream(Download.stream(mmtfURL));
 		
-		parser.parsePDBFile(new ByteArrayInputStream(pdbBytes));
+		parser.parsePDBFile(Download.stream(pdbURL));
 
 		for ( int i =0 ; i< NUMBER_OF_REPEATS ; i++) {
 
 			long mmtfStart = System.nanoTime();
-			MmtfActions.readFromInputStream(new ByteArrayInputStream(mmtfdata));
+			MmtfActions.readFromInputStream(Download.stream(mmtfURL));
 			long mmtfEnd = System.nanoTime();
 
 			long pdbStart = System.nanoTime();
-			parser.parsePDBFile(new ByteArrayInputStream(pdbBytes));
+			parser.parsePDBFile(Download.stream(pdbURL));
 			long pdbEnd = System.nanoTime();
 
 			totalTimePDB += (pdbEnd - pdbStart);