bug in compare fixed

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index e6aae96..becfe08 100755 (executable)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -13,27 +13,17 @@ public class Comparison {
      String si   = ii.getSequence();\r
      String sj   = jj.getSequence();\r
 \r
-     int ilen = end-start;\r
-     int jlen = end-start;\r
+     int ilen = si.length()-1;\r
+     int jlen = sj.length()-1;\r
 \r
-     if ( jalview.util.Comparison.isGap( si.charAt(start+ilen)) )\r
-      {\r
+     while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))\r
+     {\r
        ilen--;\r
-\r
-       while (jalview.util.Comparison.isGap( si.charAt(start+ilen)))\r
-       {\r
-         ilen--;\r
-       }\r
      }\r
 \r
-     if ( jalview.util.Comparison.isGap( sj.charAt(start+jlen)) )\r
+     while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))\r
      {\r
        jlen--;\r
-\r
-       while (jalview.util.Comparison.isGap( sj.charAt(start+jlen)))\r
-       {\r
-         jlen--;\r
-       }\r
      }\r
 \r
      int   count = 0;\r