From d56c9edd1c42755347d4bea66b2feb95809f848f Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 24 Jan 2005 17:27:36 +0000
Subject: [PATCH] bug in compare fixed

---
 src/jalview/util/Comparison.java |   20 +++++---------------
 1 file changed, 5 insertions(+), 15 deletions(-)

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index e6aae96..becfe08 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -13,27 +13,17 @@ public class Comparison {
      String si   = ii.getSequence();
      String sj   = jj.getSequence();
 
-     int ilen = end-start;
-     int jlen = end-start;
+     int ilen = si.length()-1;
+     int jlen = sj.length()-1;
 
-     if ( jalview.util.Comparison.isGap( si.charAt(start+ilen)) )
-      {
+     while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
+     {
        ilen--;
-
-       while (jalview.util.Comparison.isGap( si.charAt(start+ilen)))
-       {
-         ilen--;
-       }
      }
 
-     if ( jalview.util.Comparison.isGap( sj.charAt(start+jlen)) )
+     while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
      {
        jlen--;
-
-       while (jalview.util.Comparison.isGap( sj.charAt(start+jlen)))
-       {
-         jlen--;
-       }
      }
 
      int   count = 0;
-- 
1.7.10.2