Fix TestCeSymm failing

lafita · lafita · commit fd606579c81e · 2015-11-30T21:52:41.000+01:00
It was an error introduced when trying to solve the other CeSymm test.
diff --git a/biojava-structure-gui/src/main/java/demo/DemoCeSymm.java b/biojava-structure-gui/src/main/java/demo/DemoCeSymm.java
@@ -62,7 +62,7 @@ public static void main(String[] args)
 
 		//Choose some parameters
 		CESymmParameters params = ceSymm.getParameters();
-		params.setRefineMethod(RefineMethod.NOT_REFINED);
+		params.setRefineMethod(RefineMethod.SINGLE);
 		params.setSymmType(SymmetryType.AUTO);
 		params.setOptimization(true);
 		params.setSymmLevels(0);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
@@ -436,10 +436,10 @@ public MultipleAlignment analyzeLevel(Atom[] atoms) throws StructureException {
 			throw new IllegalArgumentException("Empty Atom array given.");
 		}
 
-		selfAlignments.add(align(atoms));
+		AFPChain selfAFP = align(atoms);
 
 		if (refined) {
-			msa = SymmetryTools.fromAFP(selfAlignments.get(0), atoms);
+			msa = SymmetryTools.fromAFP(selfAFP, atoms);
 			CoreSuperimposer imposer = new CoreSuperimposer();
 			imposer.superimpose(msa);
 			MultipleAlignmentScorer.calculateScores(msa);
@@ -458,7 +458,7 @@ public MultipleAlignment analyzeLevel(Atom[] atoms) throws StructureException {
 		} else {
 			// Convert the optimal pairwise alignment to MSA
 			MultipleAlignmentEnsemble e = new MultipleAlignmentEnsembleImpl(
-					selfAlignments.get(0), atoms, atoms, false);
+					selfAFP, atoms, atoms, false);
 			msa = e.getMultipleAlignment(0);
 			logger.debug("Returning optimal self-alignment");
 			msa.putScore("isRefined", 0.0);
