Bug Fix

deblasiolab · Mar 2, 2016 · dc21f26 · dc21f26
1 parent 16c778e
commit dc21f26
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/opal/realignment/realignmentDriver.java b/opal/realignment/realignmentDriver.java
@@ -148,7 +148,11 @@ private char[][] realignWindow(int startIndex, int endIndex){
 				originalWindowSequences[i][j-startIndex] = Character.toUpperCase(sequence[i][j]);;
 			}
 			if(numberOfNonGaps[i] > 0) numberOfNonBlankSequences++;
-			realignmentIndexes += "("+stringStartChar+","+stringEndChar+");";
+			if(stringStartChar<stringEndChar){
+				realignmentIndexes += "("+stringStartChar+","+(stringEndChar-1)+");";
+			}else{
+				realignmentIndexes += "(--,--);";
+			}
 		}
 
 		char[][] windowSequences = new char[numberOfNonBlankSequences][];