Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java
===================================================================
--- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java	(revision 1580)
+++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java	(revision 1581)
@@ -227,4 +227,8 @@
 			if(count != 0)
 			{
+				if (length1+length2+2 == count) {	
+					Console.traceln(Level.WARNING, "Traceback longer than both sequences summed up!");
+					break;
+				}
 				aligned1[count] = tmp.getXvalue();
 				aligned2[count] = tmp.getYvalue();
@@ -233,9 +237,5 @@
 			tmp = tmp.getPrevious();
 			count++;
-		if (length1+length2+2 == count) {	
-			Console.traceln(Level.WARNING, "Traceback longer than both sequences summed up!");
-			break;
-		}
-			
+		
 		} while(tmp != null);
 		count--;