Add failing test for #817

biojava-structure-gui/src/test/java/org/biojava/nbio/structure/gui/TestMultipleAlignmentJmol.java

@@ -0,0 +1,69 @@
+package org.biojava.nbio.structure.gui;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.io.IOException;
+import java.util.List;
+
+import org.biojava.nbio.structure.Atom;
+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.StructureTools;
+import org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
+import org.biojava.nbio.structure.symmetry.internal.CeSymm;
+import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
+import org.biojava.nbio.structure.symmetry.utils.SymmetryTools;
+import org.junit.Ignore;
+import org.junit.Test;
+
+public class TestMultipleAlignmentJmol {
+
+	/**
+	 * Test for biojava#817
+	 * 
+	 * Originally failed with a NPE if the MultipleAlignmentJmol was created.
+	 * This was fixed by biojava#817, but the underlying problem remains that
+	 * creating a MultipleAlignmentJmol modifies the CeSymmResult.
+	 * 
+	 * @throws StructureException
+	 * @throws IOException
+	 */
+	@Test
+	public void testJmolModification() throws StructureException, IOException {
+		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();
+
+		// Used to throw NPE before biojava#818
+		List<Structure> divided = SymmetryTools.divideStructure(result);
+		assertEquals(3, divided.size());
+
+		Atom[] atms = result.getAtoms();
+		Atom atm1 = atms[0];
+		Chain chain = atm1.getGroup().getChain();
+		EntityInfo info = chain.getEntityInfo();
+		assertNotNull(info);
+
+		// Creating Jmol loses EntityInfo
+		new MultipleAlignmentJmol(msa, msaAtoms);
+
+		atms = result.getAtoms();
+		atm1 = atoms[0];
+		chain = atm1.getGroup().getChain();
+		info = chain.getEntityInfo();
+		assertNotNull(info);
+	}
+}