Fix bug when an empty alignment is produced in CeSymm

lafita · lafita · commit d365f3f5763b · 2015-09-14T16:47:25.000+02:00
This was solved by throwing a RefinerException and allowing missing
information in the AFPChain to MultipleAlignment conversion method.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
@@ -149,7 +149,12 @@ public MultipleAlignmentEnsembleImpl(
 		if (flexible){
 			for (int bs=0; bs<afp.getBlockNum(); bs++){
 				BlockSet blockSet = new BlockSetImpl(msa);
-				Matrix4d blockTr = Calc.getTransformation(rot[bs], shift[bs]);
+				Matrix4d blockTr = null;
+				try {
+					blockTr = Calc.getTransformation(rot[bs], shift[bs]);
+				} catch (IndexOutOfBoundsException e){
+					blockTr = ident;
+				}
 				blockSet.setTransformations(Arrays.asList(ident, blockTr));
 				Block block = new BlockImpl(blockSet);
 				block.setAlignRes(new ArrayList<List<Integer>>());
@@ -171,7 +176,12 @@ public MultipleAlignmentEnsembleImpl(
 		} //Create a Block for every block in AFPChain if not flexible
 		else {
 			BlockSet blockSet = new BlockSetImpl(msa);
-			Matrix4d blockTr = Calc.getTransformation(rot[0], shift[0]);
+			Matrix4d blockTr = null;
+			try {
+				blockTr = Calc.getTransformation(rot[0], shift[0]);
+			} catch (IndexOutOfBoundsException e){
+				blockTr = ident;
+			}
 			blockSet.setTransformations(Arrays.asList(ident, blockTr));
 			for (int bs=0; bs<afp.getBlockNum(); bs++){
 				Block block = new BlockImpl(blockSet);
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
@@ -371,8 +371,7 @@ public boolean isSignificant() throws StructureException {
 
 	/**
 	 * If available, get the list of subalignments.<p>
-	 * Should be length one unless {@link CESymmParameters#getMaxSymmOrder()}
-	 * was set.
+	 * Should be length one unless using the MULTIPLE refiner.
 	 * @return List of AFP alignments
 	 */
 	public List<AFPChain> getAfpAlignments() {
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
@@ -38,7 +38,8 @@
  */
 public class CeSymmIterative {
 	
-	private static Logger logger = LoggerFactory.getLogger(CeSymmIterative.class);
+	private static Logger logger = 
+			LoggerFactory.getLogger(CeSymmIterative.class);
 
 	private CESymmParameters params;
 	private MultipleAlignment msa;
@@ -109,17 +110,23 @@ public MultipleAlignment execute(Atom[] atoms)
 	 * @throws StructureException
 	 */
 	private void iterate(Atom[] atoms) throws StructureException {
-		if( atoms.length <= params.getWinSize() || atoms.length <= params.getMinSubunitLength()) {
-			logger.debug("Aborting iteration due to insufficient length: %d",atoms.length);
+		
+		logger.debug("Starting new iteration...");
+		
+		if( atoms.length <= params.getWinSize() || 
+				atoms.length <= params.getMinSubunitLength()) {
+			logger.debug("Aborting iteration due to insufficient Atom "
+					+ "array length: %d", atoms.length);
 			return;
 		}
+		
 		//Perform the CeSymm alignment
 		CeSymm aligner = new CeSymm();
 		MultipleAlignment align = aligner.analyze(atoms, params);
 		if (name == null) 
 			name = align.getEnsemble().getStructureNames().get(0);
 
-		//End iterations if non symmetric
+		//End iterations if asymmetric
 		if (!SymmetryTools.isRefined(align)) return;
 		else if (align.getScore(MultipleAlignmentScorer.AVGTM_SCORE) < 
 				params.getSymmetryThreshold() || 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/OpenRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/OpenRefiner.java
@@ -134,6 +134,10 @@ else if (neigh.size() > 0) {
 				if (group.size()==order) subunits.add(group);
 			}
 		}
+		
+		if (subunits.size() == 0){
+			throw new RefinerFailedException("Empty alignment");
+		}
 
 		int[][][] optAln = new int[order][2][subunits.size()];
 		for (int bk=0; bk<order; bk++){
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
@@ -443,7 +443,7 @@ public static Structure getQuaternaryStructure(MultipleAlignment symmetry) {
 		}
 
 		Atom[] atoms = symmetry.getAtomArrays().get(0);
-		Structure cloned = atoms[0].getGroup().getChain().getParent().clone();
+		Structure cloned = atoms[0].getGroup().getChain().getStructure().clone();
 		atoms = StructureTools.getRepresentativeAtomArray(cloned);
 
 		Structure symm = new StructureImpl();

Original file line number	Diff line number	Diff line change
`@@ -134,6 +134,10 @@ else if (neigh.size() > 0) {`
`134`	`134`	`if (group.size()==order) subunits.add(group);`
`135`	`135`	`}`
`136`	`136`	`}`
	`137`	`+`
	`138`	`+ if (subunits.size() == 0){`
	`139`	`+ throw new RefinerFailedException("Empty alignment");`
	`140`	`+ }`
`137`	`141`
`138`	`142`	`int[][][] optAln = new int[order][2][subunits.size()];`
`139`	`143`	`for (int bk=0; bk<order; bk++){`
Original file line number	Diff line number	Diff line change
`@@ -443,7 +443,7 @@ public static Structure getQuaternaryStructure(MultipleAlignment symmetry) {`
`443`	`443`	`}`
`444`	`444`
`445`	`445`	`Atom[] atoms = symmetry.getAtomArrays().get(0);`
`446`		`- Structure cloned = atoms[0].getGroup().getChain().getParent().clone();`
	`446`	`+ Structure cloned = atoms[0].getGroup().getChain().getStructure().clone();`
`447`	`447`	`atoms = StructureTools.getRepresentativeAtomArray(cloned);`
`448`	`448`
`449`	`449`	`Structure symm = new StructureImpl();`