Fix bug with 4D Transformation Calc

lafita · lafita · commit d6be0540c03e · 2015-06-09T17:39:41.000+02:00
Packing by columns is needed instead of by rows.
diff --git a/biojava-structure-gui/src/main/java/demo/DemoMultipleAlignmentJmol.java b/biojava-structure-gui/src/main/java/demo/DemoMultipleAlignmentJmol.java
@@ -43,7 +43,8 @@ public static void main(String[] args) throws IOException, StructureException, S
 		for (String name:names) atomArrays.add(cache.getAtoms(name));
 		
 		//Here the multiple structural alignment algorithm comes in place to generate the alignment object
-		MultipleAlignment fakeMultAln = fakeMultipleAlignment("globins",atomArrays);
+		MultipleAlignment fakeMultAln = fakeMultipleAlignment("globins", atomArrays);
+		fakeMultAln.getEnsemble().setStructureNames(names);
 		
 		//Generate a pairwise alignment and convert it to a MultipleAlignment
 		FatCat fatcat  = new FatCat();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -1057,7 +1057,7 @@ public static void shift(Atom[] ca, Atom b) {
 	 * @return 4x4 transformation matrix
 	 */
 	public static Matrix4d getTransformation(Matrix rot, Matrix trans) {
-		return new Matrix4d( new Matrix3d(rot.getRowPackedCopy()),
+		return new Matrix4d( new Matrix3d(rot.getColumnPackedCopy()),
 				new Vector3d(trans.getColumnPackedCopy()),
 				1.0);
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/cemc/CeMcMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/cemc/CeMcMain.java
@@ -62,7 +62,9 @@ public CeMcMain(){
 	 * of the structures. The alignments are generated in parallel using the Java API for concurrency management. 
 	 * The closest structure to all others is chosen as the reference and all the alignments to it are taken to generate 
 	 * an ungapped seed MultipleAlignment.
+	 * 
 	 * This method is static because can be used outside this alignment class.
+	 * 
 	 * @param atomArrays List of Atoms to align of the structures
 	 * @return MultipleAlignment seed alignment
 	 * @throws ExecutionException 
@@ -129,6 +131,7 @@ public MultipleAlignment generateSeed(List<Atom[]> atomArrays) throws Interrupte
 	 * This method takes a list of pairwise alignments to the reference structure and calculates the 
 	 * MultipleAlignment resulting from them. It ignores blocks in AFPChain (flexible parts) and builds 
 	 * the Blocks as the definition of MultipleAlignment dictates {@link Block}. Gaps are not included.
+	 * 
 	 * @param afpList the list of pairwise alignments to the reference
 	 * @param atomArrays List of Atoms of the structures
 	 * @param ref index of the reference structure
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/BlockSetImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/BlockSetImpl.java
@@ -22,7 +22,7 @@ public class BlockSetImpl extends AbstractScoresCache implements Serializable, B
 	private List<Block> blocks;				//aligned positions as a list of Blocks
 	
 	//Cache variables (can be updated)
-	private List<Matrix4d> pose;						//3D superimposition information Pose
+	private List<Matrix4d> pose;			//3D superimposition information pose
 	private int length;						//total number of aligned positions, including gaps = sum of blocks lengths (cache)
 	private int coreLength;					//number of aligned positions without gaps (cache)
 	
@@ -32,7 +32,7 @@ public class BlockSetImpl extends AbstractScoresCache implements Serializable, B
 	 * @return BlockSetImpl a BlockSetImpl instance linked to its parent MultipleAlignment.
 	 * @throws StructureAlignmentException 
 	 */
-	public BlockSetImpl(MultipleAlignment multipleAlignment) throws StructureAlignmentException{
+	public BlockSetImpl(MultipleAlignment multipleAlignment) {
 		
 		parent = multipleAlignment;
 		if (parent!=null) parent.getBlockSets().add(this);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/MultipleAlignmentEnsembleImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/MultipleAlignmentEnsembleImpl.java
@@ -305,8 +305,9 @@ public void addMultipleAlignment( MultipleAlignment alignment) {
 
 	@Override
 	public int size() throws StructureAlignmentException {
-		if (structureNames == null) throw new StructureAlignmentException("Empty MultipleAlignmentEnsemble: structureNames == null");
-		else return structureNames.size();
+		if (structureNames != null) return structureNames.size();
+		else if (atomArrays != null) return atomArrays.size();
+		else throw new StructureAlignmentException("Empty MultipleAlignmentEnsemble: structureNames == null");
 	}
 	
 	/**

Original file line number	Diff line number	Diff line change
`@@ -1057,7 +1057,7 @@ public static void shift(Atom[] ca, Atom b) {`
`1057`	`1057`	`* @return 4x4 transformation matrix`
`1058`	`1058`	`*/`
`1059`	`1059`	`public static Matrix4d getTransformation(Matrix rot, Matrix trans) {`
`1060`		`- return new Matrix4d( new Matrix3d(rot.getRowPackedCopy()),`
	`1060`	`+ return new Matrix4d( new Matrix3d(rot.getColumnPackedCopy()),`
`1061`	`1061`	`new Vector3d(trans.getColumnPackedCopy()),`
`1062`	`1062`	`1.0);`
`1063`	`1063`	`}`