From 5f7d80cd8b01e051a6175b0ce8db0ad94d73df2f Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 10 Feb 2005 13:26:25 +0000
Subject: [PATCH] check that we're not off the end of a sequence

---
 src/jalview/schemes/ClustalxColourScheme.java |    5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index b28ac76..d4789e6 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -63,7 +63,10 @@ public class ClustalxColourScheme implements ColourSchemeI
         seq = ( (SequenceI) seqs.get(j)).getSequence();
         for (i = start; i <= end; i++)
         {
-          res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) + "")).intValue();
+          if(seq.length()-1<i)
+            res = 23;
+          else
+            res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) + "")).intValue();
           cons2[i][res]++;
         }
         j++;
-- 
1.7.10.2