MultipleAlignmentJmol modifies state, causing NullPointerException

[sbliven]

I get a NullPointerException when running the following code:

String pdb = "4i4q";
Structure s = StructureTools.getStructure(pdb);
assertNotNull(s);

Atom[] atoms = StructureTools.getRepresentativeAtomArray(s);
assertNotNull(atoms);
assertEquals(146, atoms.length);

CeSymmResult result = CeSymm.analyze(atoms);

MultipleAlignment msa = result.getMultipleAlignment();
List<Atom[]> msaAtoms = msa.getAtomArrays();

// Commenting our this line fixes the error below
new MultipleAlignmentJmol(msa, msaAtoms);

// Throws NPE
SymmetryTools.divideStructure(result);

Stack trace:

Exception in thread "main" java.lang.NullPointerException
	at org.biojava.nbio.structure.StructureTools.addGroupToStructure(StructureTools.java:547)
	at org.biojava.nbio.structure.symmetry.utils.SymmetryTools.divideStructure(SymmetryTools.java:538)
	at main.TestSymmetryDisplay.main(TestSymmetryDisplay.java:53)

The weird thing is that the error goes away if I don't create the MultipleAlignmentJmol instance. We must be modifying the CESymmResult state in a way that breaks divideStructure.

Note that this blocks moving CE-Symm to BioJava 5

[josemduarte]

A bug in cloning perhaps?

[sbliven]

I've fixed the NPE, but I'm still a bit concerned about MultipleAlignmentJmol modifying stuff. I'm not sure if I have time to track this bug down though.

[sbliven]

Reopening for potential cloning bug

[sbliven]

I have a test for this issue in my fix817 branch (83f2b38). Basically, creating MultipleAlignmentJmol results in all atoms having null EntityInfo.