Important bug fix in the insertGap() move of MC

lafita · lafita · commit 6be8893b4cdf · 2015-06-26T16:46:51.000+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)
@@ -44,7 +44,7 @@ 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, POSA, Gerstein&Levitt 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)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleAlignmentOptimizerMC.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleAlignmentOptimizerMC.java
@@ -193,15 +193,15 @@ private void optimizeMC(int maxIter) throws StructureException {
 				//Randomly select one of the steps to modify the alignment. 
 				//Because two moves are biased, the probabilities are not the same
 				double move = rnd.nextDouble();
-				if (move < 0.5){
+				if (move < 0.4){
 						moved = shiftRow();
 						if (debug) System.out.println("did shift");
 				}
-				else if (move < 0.8){
+				else if (move < 0.7){
 						moved = expandBlock();
 						if (debug) System.out.println("did expand");
 				}
-				else if (move < 0.9){
+				else if (move < 0.85){
 						moved = shrinkBlock();
 						if (debug) System.out.println("did shrink");
 				}
@@ -319,7 +319,8 @@ private boolean insertGap() {
 							if (rnd.nextDouble() > 0.5) {   //Introduce some randomness in the choice
 								structure = str;
 								block = b;
-								position = col; 
+								position = col;
+								maxDist = residueDistances.get(str, column);
 							}
 						}
 					}

Original file line number	Diff line number	Diff line change
`@@ -193,15 +193,15 @@ private void optimizeMC(int maxIter) throws StructureException {`
`193`	`193`	`//Randomly select one of the steps to modify the alignment.`
`194`	`194`	`//Because two moves are biased, the probabilities are not the same`
`195`	`195`	`double move = rnd.nextDouble();`
`196`		`- if (move < 0.5){`
	`196`	`+ if (move < 0.4){`
`197`	`197`	`moved = shiftRow();`
`198`	`198`	`if (debug) System.out.println("did shift");`
`199`	`199`	`}`
`200`		`- else if (move < 0.8){`
	`200`	`+ else if (move < 0.7){`
`201`	`201`	`moved = expandBlock();`
`202`	`202`	`if (debug) System.out.println("did expand");`
`203`	`203`	`}`
`204`		`- else if (move < 0.9){`
	`204`	`+ else if (move < 0.85){`
`205`	`205`	`moved = shrinkBlock();`
`206`	`206`	`if (debug) System.out.println("did shrink");`
`207`	`207`	`}`
`@@ -319,7 +319,8 @@ private boolean insertGap() {`
`319`	`319`	`if (rnd.nextDouble() > 0.5) { //Introduce some randomness in the choice`
`320`	`320`	`structure = str;`
`321`	`321`	`block = b;`
`322`		`- position = col;`
	`322`	`+ position = col;`
	`323`	`+ maxDist = residueDistances.get(str, column);`
`323`	`324`	`}`
`324`	`325`	`}`
`325`	`326`	`}`