Core length used as the the min block length

lafita · lafita · commit e5055516588f · 2015-07-20T09:58:34.000+02:00
diff --git a/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java b/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java
@@ -32,7 +32,7 @@ public static void main(String[] args) throws IOException, StructureException, I
 		//Protein Kinases (CEMC paper)
 		//List<String> names = Arrays.asList("1cdk.A", "1cja.A", "1csn", "1b6c.B", "1ir3.A", "1fgk.A", "1byg.A", "1hck", "1blx.A", "3erk", "1bmk.A", "1kob.A", "1tki.A", "1phk", "1a06");
 		//DHFR (Gerstein 1998 paper)
-		//List<String> names = Arrays.asList("d1dhfa_", "8dfr", "d4dfra_", "3dfr");
+		List<String> names = Arrays.asList("d1dhfa_", "8dfr", "d4dfra_", "3dfr");
 		//TIM barrels (MUSTA paper)
 		//List<String> names = Arrays.asList("1tim.A", "1vzw", "1nsj", "3tha.A", "4enl", "2mnr", "7tim.A", "1tml", "1btc", "a1piia1", "6xia", "5rub.A", "2taa.B");
 		//Calcium Binding (MUSTA paper)
@@ -54,11 +54,12 @@ public static void main(String[] args) throws IOException, StructureException, I
 		//Circular Permutations: SAND and MFPT domains
 		//List<String> names = Arrays.asList("d2bjqa1", "d1h5pa_", "d1ufna_");  //"d1oqja"
 		//Flexible domain family of proteins (FatCat paper?)
+		//List<String> names = Arrays.asList();
 		//Amonium Transporters (Aleix Bachelor's Thesis)
 		//List<String> names = Arrays.asList("1xqf.A","2b2f.A", "3b9w.A","3hd6.A");
 		//Cytochrome C Oxidases (Aleix Bachelor's Thesis)
 		//List<String> names = Arrays.asList("2dyr.A","2gsm.A","2yev.A","3hb3.A","3omn.A","1fft.A","1xme.A","3o0r.B","3ayf.A");
-		List<String> names = Arrays.asList("2dyr.A","2gsm.A","1fft.A","1xme.A","3o0r.B","3ayf.A");
+		//List<String> names = Arrays.asList("2dyr.A","2gsm.A","1fft.A","1xme.A","3o0r.B","3ayf.A");
 		//Cation Transporting ATPases (Aleix Bachelor's Thesis)
 		//List<String> names = Arrays.asList("3b8e.A","2zxe.A", "3tlm.A","1iwo.A");
 		//Ankyrin Repeats
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -45,7 +45,7 @@ public class MultipleMcOptimizer
 implements Callable<MultipleAlignment> {
 
 	//Print info and save evolution history
-	private static final boolean debug = true;
+	private static final boolean debug = false;
 
 	private Random rnd;
 	private MultipleSuperimposer imposer;
@@ -113,19 +113,26 @@ public MultipleMcOptimizer(MultipleAlignment seedAln,
 		C = 20*size;
 		Lmin = params.getMinBlockLen();
 
-		//Delete all shorter than Lmin blocks
+		//Delete all shorter than Lmin blocks, and empty blocksets
 		List<Block> toDelete = new ArrayList<Block>();
+		List<BlockSet> emptyBs = new ArrayList<BlockSet>();
+
 		for (Block b : msa.getBlocks()){
 			if (b.getCoreLength() < Lmin){
 				toDelete.add(b);
 				if (debug) System.err.println("Deleting Block: too short.");
 			}
 		}
 		for (Block b : toDelete){
-			for (BlockSet bs : msa.getBlockSets()){
+			for (BlockSet bs : msa.getBlockSets()) {
 				bs.getBlocks().remove(b);
+				if (bs.getBlocks().size() == 0) emptyBs.add(bs);
 			}
 		}
+		for (BlockSet bs : emptyBs){
+			msa.getBlockSets().remove(bs);
+		}
+
 		blockNr = msa.getBlocks().size();
 		if (blockNr < 1){
 			throw new IllegalArgumentException(
@@ -381,7 +388,7 @@ private boolean insertGap() {
 			}
 		}
 		Block bk = msa.getBlocks().get(block);
-		if (bk.length() <= Lmin) return false;
+		if (bk.getCoreLength() <= Lmin) return false;
 
 		//Insert the gap at the position
 		Integer residueL = bk.getAlignRes().get(structure).get(position);
@@ -411,6 +418,7 @@ private boolean shiftRow(){
 		int res = rnd.nextInt(msa.getBlocks().get(bk).length());
 
 		Block block = msa.getBlocks().get(bk);
+		if (block.getCoreLength() <= Lmin) return false;
 
 		//When the pivot residue is null try to add a residue from the freePool
 		if (block.getAlignRes().get(str).get(res) == null){
@@ -746,8 +754,8 @@ private boolean shrinkBlock(){
 				column++;
 			}
 		}
-		if (msa.getBlocks().get(block).length() <= Lmin) return false;
 		Block currentBlock = msa.getBlocks().get(block);
+		if (currentBlock.getCoreLength() <= Lmin) return false;
 
 		for (int str=0; str<size; str++){
 			Integer residue = 
