From 90b966eae5932e288c332bf4fa8fceeab909592c Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 23 Feb 2005 15:48:40 +0000
Subject: [PATCH] bug fix for unaligned sequence sets and clustal colours
 (obviated by 'aligned' test).

---
 src/jalview/schemes/ClustalxColourScheme.java |    3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index d4789e6..7faa9a3 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -61,7 +61,8 @@ public class ClustalxColourScheme implements ColourSchemeI
       while(j < seqs.size())
       {
         seq = ( (SequenceI) seqs.get(j)).getSequence();
-        for (i = start; i <= end; i++)
+        int end_j = seq.length()-1;
+        for (i = start; i <= end_j; i++)
         {
           if(seq.length()-1<i)
             res = 23;
-- 
1.7.10.2