From a6bb3b86034b01bafb3db8f7be826012cf58de6f Mon Sep 17 00:00:00 2001
From: dyrpsf <dyrpsf@gmail.com>
Date: Tue, 6 Jan 2026 19:45:06 +0530
Subject: [PATCH] Fix NPE in AbstractTreeNode clone when userObjects is null

---
 core/src/org/sbml/jsbml/AbstractTreeNode.java | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/core/src/org/sbml/jsbml/AbstractTreeNode.java b/core/src/org/sbml/jsbml/AbstractTreeNode.java
index 63bc6c716..c049c8cc4 100644
--- a/core/src/org/sbml/jsbml/AbstractTreeNode.java
+++ b/core/src/org/sbml/jsbml/AbstractTreeNode.java
@@ -167,9 +167,10 @@ public AbstractTreeNode(TreeNode node) {
       AbstractTreeNode anode = (AbstractTreeNode) node;
       // Do not clone listeners!
       //   this.listOfListeners.addAll(anode.listOfListeners);
-      if (anode.isSetUserObjects()) {
-        userObjects = new HashMap<Object, Object>();
-        userObjects.putAll(anode.userObjects);
+      // Copy userObjects if present. We must not rely on isSetUserObjects(),
+      // because subclasses may override it with different semantics.
+      if (anode.userObjects != null && !anode.userObjects.isEmpty()) {
+        userObjects = new HashMap<Object, Object>(anode.userObjects);
       }
       
       // TODO - add this for all objects when we start using the checkAttribute method for other classes than Compartment.