Fix NullPointerException in AbstractTreeNode used by ASTNode clone

[dyrpsf]

This PR fixes a NullPointerException that could occur when cloning AbstractTreeNode (and thus ASTNode) when userObjects is null.

Previously, the copy constructor in AbstractTreeNode did:

if (anode.isSetUserObjects()) {
userObjects = new HashMap<Object, Object>();
userObjects.putAll(anode.userObjects);
}

If a subclass overrides isSetUserObjects() (e.g. ASTNode) and returns true even when the underlying userObjects map is still null, putAll throws an NPE.

The constructor is now changed to check the field directly:

if (anode.userObjects != null && !anode.userObjects.isEmpty()) {
userObjects = new HashMap<Object, Object>(anode.userObjects);
}

This makes the clone logic robust to such overrides.
I verified the fix by:

Building JSBML and running its tests locally.
Building SBSCL 2.1.1 against this JSBML snapshot.
Running the SBMLTestSuite wrapper used in draeger-lab/SBSCL#74 without encountering the previous NPE in ASTNode.clone.
Related issues:

Fixes #258
Related to draeger-lab/SBSCL#74

[draeger]

I am wondering if this is actually a bug in JSBML? If so, shouldn't it be fixed there?

[luciansmith]

This is jsbml? Unless I'm missing something?

[draeger]

This is jsbml? Unless I'm missing something?

Yes, there were several edits on SBSCL. I'll check this PR here, of course.