Fix Bugs in MultipleAlignment DS

lafita · lafita · commit dc365d75098f · 2015-06-18T12:22:06.000+02:00
A bug when the reference in the ReferenceSuperimposer was not the first
structure and a bug when trying to get the scores and they were null.
diff --git a/biojava-structure-gui/src/main/java/demo/DemoCEMC.java b/biojava-structure-gui/src/main/java/demo/DemoCEMC.java
@@ -14,7 +14,8 @@
 import org.biojava.nbio.structure.align.util.AtomCache;
 
 /**
- * Demo for running a CEMC Multiple Structure Alignment and visualizing the results.
+ * Demo for running the CEMC Algorithm on a protein family and visualizing the results.
+ * Choose the family by commenting out the protein family names.
  * 
  * @author Aleix Lafita
  * 
@@ -43,11 +44,15 @@ public static void main(String[] args) throws IOException, StructureException, I
 		//GPCRs
 		//List<String> names = Arrays.asList("2z73.A", "1u19.A", "4ug2.A", "4xt3", "4or2.A", "3odu.A");
 		//Immunoglobulins (MAMMOTH paper)
-		List<String> names = Arrays.asList("2hla.B", "3hla.B", "1cd8", "2rhe", "1tlk", "1ten", "1ttf");
+		//List<String> names = Arrays.asList("2hla.B", "3hla.B", "1cd8", "2rhe", "1tlk", "1ten", "1ttf");
 		//Globins (MAMMOTH and MUSTA papers)
 		//List<String> names = Arrays.asList("1mbc", "1hlb", "1thb.A", "1ith.A", "1idr.A", "1dlw", "1kr7.A", "1ew6.A", "1it2.A", "1eco", "3sdh.A", "1cg5.B", "1fhj.B", "1ird.A", "1mba", "2gdm", "1b0b", "1h97.A", "1ash.A", "1jl7.A");
 		//Rossman-Fold (POSA paper)
 		//List<String> names = Arrays.asList("d1heta2", "d1ek6a_", "d1obfo1", "2cmd", "d1np3a2", "d1bgva1", "d1id1a_", "d1id1a_", "d1oi7a1");
+		//Circular Permutations (Bliven CECP paper) - dynamin GTP-ase with CP G-domain
+		//List<String> names = Arrays.asList("d1u0la2", "d1jwyb_");
+		//Circular Permutations: SAND and MFPT domains
+		List<String> names = Arrays.asList("d2bjqa1", "d1h5pa_", "d1ufna_");  //"d1oqja"
 		
 		//Load the CA atoms of the structures
 		AtomCache cache = new AtomCache();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/AbstractScoresCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/AbstractScoresCache.java
@@ -48,6 +48,7 @@ public Double getScore(String property) {
 	 */
 	@Override
 	public Set<String> getScores() {
+		if(scores == null) return Collections.emptySet();
 		return Collections.unmodifiableSet(scores.keySet());
 	}
 	
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
@@ -44,8 +44,6 @@ public interface Block extends ScoresCache {
 	/**
 	 * Returns the double List containing the aligned residues for each structure.
 	 * alignRes.get(structure).get(residue) = alignRes.get(size).get(length).
-	 * <p>
-	 * Initializes the variable if it is null.
 	 * @return List a double List of aligned residues for each structure.
 	 * @see #setAlignRes()
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
@@ -85,7 +85,6 @@ public BlockSet getBlockSet() {
 
 	@Override
 	public List<List<Integer>> getAlignRes() {
-		if (alignRes == null) alignRes = new ArrayList<List<Integer>>();
 		return alignRes;
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java
@@ -131,8 +131,8 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	public void setMultipleAlignments(List<MultipleAlignment> multipleAlignments);
 
 	/**
-	 * Add a new multiple alignment to the end of the ensemble and set its
-	 * ensemble to this.
+	 * Add a new MultipleAlignment to the end of the ensemble and set its
+	 * parent ensemble to this.
 	 * @param alignment
 	 */
 	public void addMultipleAlignment( MultipleAlignment alignment);
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
@@ -251,7 +251,6 @@ public int getAlignmentNum() {
 
 	@Override
 	public List<Matrix> getDistanceMatrix() {
-		if (distanceMatrix == null) updateDistanceMatrix();
 		return distanceMatrix;
 	}
 
@@ -289,28 +288,20 @@ public void setMultipleAlignments(List<MultipleAlignment> multipleAlignments) {
 		this.multipleAlignments = multipleAlignments;
 	}
 	
-	/**
-	 * Add a new multiple alignment to the end of the ensemble and set its
-	 * ensemble to this.
-	 * @param alignment
-	 */
 	@Override
 	public void addMultipleAlignment( MultipleAlignment alignment) {
+		if (multipleAlignments == null) multipleAlignments = new ArrayList<MultipleAlignment>();
 		multipleAlignments.add(alignment);
 		alignment.setEnsemble(this);
 	}
 
-
 	@Override
 	public int size() {
 		if (structureNames != null) return structureNames.size();
 		else if (atomArrays != null) return atomArrays.size();
 		else throw new IndexOutOfBoundsException("Empty MultipleAlignmentEnsemble: structureNames == null && atomArrays == null");
 	}
 	
-	/**
-	 * Clear scores and distance matrix. Recursively clears member alignments.
-	 */
 	@Override
 	public void clear() {
 		super.clear();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/ReferenceSuperimposer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/ReferenceSuperimposer.java
@@ -104,7 +104,7 @@ public void superimpose(MultipleAlignment alignment) throws StructureException {
 					}
 					//Loop through all the columns of each Block (aligned residues)
 					for (int j=0; j<blk.length(); j++){
-						Integer pos1 = blk.getAlignRes().get(0).get(j);
+						Integer pos1 = blk.getAlignRes().get(reference).get(j);
 						Integer pos2 = blk.getAlignRes().get(i).get(j);
 	
 						if (pos1==null || pos2==null) continue;

Original file line number	Diff line number	Diff line change
`@@ -48,6 +48,7 @@ public Double getScore(String property) {`
`48`	`48`	`*/`
`49`	`49`	`@Override`
`50`	`50`	`public Set<String> getScores() {`
	`51`	`+ if(scores == null) return Collections.emptySet();`
`51`	`52`	`return Collections.unmodifiableSet(scores.keySet());`
`52`	`53`	`}`
`53`	`54`
Original file line number	Diff line number	Diff line change
`@@ -85,7 +85,6 @@ public BlockSet getBlockSet() {`
`85`	`85`
`86`	`86`	`@Override`
`87`	`87`	`public List<List<Integer>> getAlignRes() {`
`88`		`- if (alignRes == null) alignRes = new ArrayList<List<Integer>>();`
`89`	`88`	`return alignRes;`
`90`	`89`	`}`
`91`	`90`
Original file line number	Diff line number	Diff line change
`@@ -104,7 +104,7 @@ public void superimpose(MultipleAlignment alignment) throws StructureException {`
`104`	`104`	`}`
`105`	`105`	`//Loop through all the columns of each Block (aligned residues)`
`106`	`106`	`for (int j=0; j<blk.length(); j++){`
`107`		`- Integer pos1 = blk.getAlignRes().get(0).get(j);`
	`107`	`+ Integer pos1 = blk.getAlignRes().get(reference).get(j);`
`108`	`108`	`Integer pos2 = blk.getAlignRes().get(i).get(j);`
`109`	`109`
`110`	`110`	`if (pos1==null \|\| pos2==null) continue;`