Handle symmetry refinement Exceptions

lafita · lafita · commit d66cc12a16bc · 2016-02-03T16:22:13.000+01:00
diff --git a/biojava-phylo/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java b/biojava-phylo/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java
@@ -307,12 +307,13 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix dissimi
 							.get(j).getCompoundAt(k + 1));
 				}
 
-				if (i != j)
+				if (i != j){
+					score = Math.max(score, 0.0);
 					DM.setValue(i, j, score);
+				}
 
-				if (score > maxscore) {
+				if (score > maxscore)
 					maxscore = score;
-				}
 			}
 		}
 
@@ -324,7 +325,7 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix dissimi
 				if (i == j)
 					DM.setValue(i, j, 0.0);
 				else {
-					double dS = maxscore - DM.getValue(i, j);
+					double dS = Math.max(maxscore - DM.getValue(i, j), 0);
 					DM.setValue(i, j, dS);
 					DM.setValue(j, i, dS);
 				}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
@@ -86,6 +86,8 @@ public static AFPChain refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
 		try {
 			AFPChain refinedAFP = AlignmentTools.replaceOptAln(afpChain, ca1, ca2, refined);
 			refinedAFP = partitionAFPchain(refinedAFP, ca1, ca2, k);
+			if (refinedAFP.getOptLength() < 1)
+				throw new IndexOutOfBoundsException("Refined alignment is empty.");
 			return refinedAFP;
 		} catch (IndexOutOfBoundsException e){
 			// This Exception is thrown when the refined alignment is not consistent

Original file line number	Diff line number	Diff line change
`@@ -307,12 +307,13 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix dissimi`
`307`	`307`	`.get(j).getCompoundAt(k + 1));`
`308`	`308`	`}`
`309`	`309`
`310`		`- if (i != j)`
	`310`	`+ if (i != j){`
	`311`	`+ score = Math.max(score, 0.0);`
`311`	`312`	`DM.setValue(i, j, score);`
	`313`	`+ }`
`312`	`314`
`313`		`- if (score > maxscore) {`
	`315`	`+ if (score > maxscore)`
`314`	`316`	`maxscore = score;`
`315`		`- }`
`316`	`317`	`}`
`317`	`318`	`}`
`318`	`319`
`@@ -324,7 +325,7 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix dissimi`
`324`	`325`	`if (i == j)`
`325`	`326`	`DM.setValue(i, j, 0.0);`
`326`	`327`	`else {`
`327`		`- double dS = maxscore - DM.getValue(i, j);`
	`328`	`+ double dS = Math.max(maxscore - DM.getValue(i, j), 0);`
`328`	`329`	`DM.setValue(i, j, dS);`
`329`	`330`	`DM.setValue(j, i, dS);`
`330`	`331`	`}`