From 74aa9aa23dce90e649abce71577e56be2c9ac00e Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Dec 2004 13:19:57 +0000
Subject: [PATCH] ilen and jlen no longer +1

---
 src/jalview/util/Comparison.java |    4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index d8e599b..e6aae96 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -13,8 +13,8 @@ public class Comparison {
      String si   = ii.getSequence();
      String sj   = jj.getSequence();
 
-     int ilen = end-start+1;
-     int jlen = end-start+1;
+     int ilen = end-start;
+     int jlen = end-start;
 
      if ( jalview.util.Comparison.isGap( si.charAt(start+ilen)) )
       {
-- 
1.7.10.2