Feature/silac workflow#1
Open
timosachsenberg wants to merge 184 commits intoNantiaL:feature/SILACWorkflowfrom
Open
Feature/silac workflow#1timosachsenberg wants to merge 184 commits intoNantiaL:feature/SILACWorkflowfrom
timosachsenberg wants to merge 184 commits intoNantiaL:feature/SILACWorkflowfrom
Conversation
underlying class. Signed-off-by: Julianus Pfeuffer <jpfeuffer@fu-berlin.de>
Cleaned up namespace usage. Signed-off-by: Julianus Pfeuffer <jpfeuffer@fu-berlin.de>
Signed-off-by: Julianus Pfeuffer <jpfeuffer@fu-berlin.de>
library in the contrib includes. Signed-off-by: Julianus Pfeuffer <jpfeuffer@fu-berlin.de>
Peptides and Proteins. Refactored so you have to give the graph a functor. Otherwise it is too dangerous that the ID structures are changed inbetween. Signed-off-by: Julianus Pfeuffer <jpfeuffer@fu-berlin.de>
… into feature/proteomic_lfq
added carbamidomethyl exception if not specified
* added flag for f_and_c:make_unique * intermediate commit: towards make unique * introduces "makeUnique" for f and c FeatureXML This commit introduces a new "f_and_c:make_unique" flag that keeps only features with highest intensity for their corresponding (charge, sequence) pair. This is an intermediate (but compiling) implementation that is likely going to require changes to work properly. * featureXML implementation ready. Tested manually on a large input file, will convert this manual test to a proper one next. * make makeUnique maintain unannotated features * committing test for f_and_c:make unique Open question: why is FileFilter so slow on src/tests/topp/FileFilter_47_input.featureXML? This is independent of `f_and_c:make_unique` as the slowness can also be observed when our new flag is not set. * documentation and help description To facilitate discussion, this commit provides detailed in-code documentation and a full description of the flag. * chg: test file size drastically reduced * moving to IDConflictResolver;fixed review comments * moved to IDConflictResolver implementation now resides in `IDConflictResolver`, accessible through new flag `make_unique`. We also generalized implementation to support both `FeatureMap` and `ConsensusMap` by templating. Test `IDConflictResolver_4` passes on a `featureXML` input and demonstrates our new interface. * changed interface from flag to string option Default behavior remains the old one. * [INTERNAL] remove ID annotations instead of complete features * [INTERNAL] move obsolete peptide IDs to unassigned list * [API] change user interface * [TEST] fix TOPP test * [INTERNAL] sort peptide hits first * [DOCU] clarify TOPP tool docu * [DOCU] fix TOPP tool docu * [INTERNAL] make peptide hits const * [DOCU] update code docu * [API] rename TOPP param * [API] replace flag by string option in TOPP user interface * [API] rename algorithm method makeUnique --> resolveBetweenFeatures * [TEST] fix TOPP test * [TEST] add class test * [TEST] class test extended * [API] introduce provate method resolveBetweenFeatures_() * [API] add python wrapper * Update IDConflictResolverAlgorithm.pxd * [TEST] remove unused TOPP test file
…de_motif Feature/sse peptide motif
* [FIX] bugfix in FuzzyDiff - Fixes the following bug: when a large ratio was found but does not lead to failure (due to small absolute difference) then smaller ratios than the original one that *should* lead to failure are ignored. * [NOP] whitespace / debug changes * nop * [TEST] add test for FuzzyDiff * fix * [FIX] small fix
* [FIX] const-correctness * [DOC] current Qt compilation docu * typo * [FEATURE] unique way to compute precursor id * [FEATURE] use unique way to compute precursor id * [FIX] move constructor out of the loop
…rely Hyperlink DOIs against preferred resolver
…into feature/SILACWorkflow
…ature/SILACWorkflow
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
8 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.