Fix broken CE-Symm Test

lafita · lafita · commit 285f1a77c25a · 2015-11-30T18:18:55.000+01:00
diff --git a/biojava-structure-gui/src/main/java/demo/DemoCeSymm.java b/biojava-structure-gui/src/main/java/demo/DemoCeSymm.java
@@ -61,8 +61,8 @@ public static void main(String[] args)
 		CeSymm ceSymm = new CeSymm();
 
 		//Choose some parameters
-		CESymmParameters params = (CESymmParameters) ceSymm.getParameters();
-		params.setRefineMethod(RefineMethod.SINGLE);
+		CESymmParameters params = ceSymm.getParameters();
+		params.setRefineMethod(RefineMethod.NOT_REFINED);
 		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
@@ -427,7 +427,7 @@ public MultipleAlignment analyze(Atom[] atoms, CESymmParameters param)
 	 * @return
 	 * @throws StructureException
 	 */
-	MultipleAlignment analyzeLevel(Atom[] atoms) throws StructureException {
+	public MultipleAlignment analyzeLevel(Atom[] atoms) throws StructureException {
 
 		// Reset all the variables from previous calls
 		reset();
@@ -436,10 +436,10 @@ MultipleAlignment analyzeLevel(Atom[] atoms) throws StructureException {
 			throw new IllegalArgumentException("Empty Atom array given.");
 		}
 
-		AFPChain selfAFP = align(atoms);
+		selfAlignments.add(align(atoms));
 
 		if (refined) {
-			msa = SymmetryTools.fromAFP(selfAFP, atoms);
+			msa = SymmetryTools.fromAFP(selfAlignments.get(0), atoms);
 			CoreSuperimposer imposer = new CoreSuperimposer();
 			imposer.superimpose(msa);
 			MultipleAlignmentScorer.calculateScores(msa);
@@ -458,7 +458,7 @@ MultipleAlignment analyzeLevel(Atom[] atoms) throws StructureException {
 		} else {
 			// Convert the optimal pairwise alignment to MSA
 			MultipleAlignmentEnsemble e = new MultipleAlignmentEnsembleImpl(
-					selfAFP, atoms, atoms, false);
+					selfAlignments.get(0), atoms, atoms, false);
 			msa = e.getMultipleAlignment(0);
 			logger.debug("Returning optimal self-alignment");
 			msa.putScore("isRefined", 0.0);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
@@ -133,7 +133,6 @@ private boolean iterate(Atom[] atoms) throws StructureException {
 		}
 
 		// Perform one level CeSymm alignment
-		CeSymm aligner = new CeSymm();
 		msa = aligner.analyzeLevel(atoms);
 
 		// End iterations if asymmetric (not refined, or lower thresholds)
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSequenceFunctionOrderDetector.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSequenceFunctionOrderDetector.java
@@ -40,7 +40,7 @@ public void testGetSymmetryOrder()
 			ce.getParameters().setRefineMethod(RefineMethod.NOT_REFINED);
 			Atom[] ca1 = cache.getAtoms(name);
 			
-			ce.analyze(ca1);
+			ce.analyzeLevel(ca1);
 			AFPChain afpChain = ce.getSelfAlignments().get(0);
 			
 			int order = new SequenceFunctionOrderDetector().calculateOrder(afpChain, ca1);

Original file line number	Diff line number	Diff line change
`@@ -133,7 +133,6 @@ private boolean iterate(Atom[] atoms) throws StructureException {`
`133`	`133`	`}`
`134`	`134`
`135`	`135`	`// Perform one level CeSymm alignment`
`136`		`- CeSymm aligner = new CeSymm();`
`137`	`136`	`msa = aligner.analyzeLevel(atoms);`
`138`	`137`
`139`	`138`	`// End iterations if asymmetric (not refined, or lower thresholds)`