Fix chain ID duplication bug in repeats alignment

lafita · lafita · commit 66d8ecbdaf92 · 2016-06-07T17:56:24.000+02:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
@@ -508,7 +508,7 @@ public static Structure getQuaternaryStructure(CeSymmResult symmetry) {
 			throw new IllegalArgumentException("The symmetry result "
 					+ "is not refined, repeats cannot be defined");
 
-		Atom[] atoms = symmetry.getAtoms();
+		Atom[] atoms = StructureTools.cloneAtomArray(symmetry.getAtoms());
 
 		Structure symm = new StructureImpl();
 		symm.setStructureIdentifier(symmetry.getStructureId());
@@ -593,8 +593,7 @@ public static MultipleAlignment toRepeatsAlignment(CeSymmResult result)
 
 		MultipleAlignment msa = result.getMultipleAlignment();
 		MultipleAlignmentEnsemble newEnsemble = msa.getEnsemble().clone();
-		newEnsemble.setStructureIdentifiers(result.getRepeatsID());
-
+		
 		// Modify atom arrays to include the repeat atoms only
 		List<Atom[]> atomArrays = new ArrayList<Atom[]>();
 		Structure divided = SymmetryTools.getQuaternaryStructure(result);
@@ -992,7 +991,7 @@ public static Atom[] getRepresentativeAtoms(Structure structure) {
 
 		else {
 
-			// Get Atoms of all models and rename chains (in case BIO)
+			// Get Atoms of all models
 			List<Atom> atomList = new ArrayList<Atom>();
 			for (int m = 0; m < structure.nrModels(); m++) {
 				for (Chain c : structure.getModel(m))
