From b0c3862ae342f88419e5e685de2b56f060358c05 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 7 Apr 2006 08:23:34 +0000
Subject: [PATCH] Must check consensus length if autocalculate off

---
 src/jalview/schemes/Blosum62ColourScheme.java |    2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 6e91e0b..2c0836d 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -39,7 +39,7 @@ public class Blosum62ColourScheme
     }
 
 
-    if ( (threshold != 0) && !aboveThreshold(s, j))
+    if ( j>=consensus.length || (threshold != 0 && !aboveThreshold(s, j) ))
     {
       return Color.white;
     }
-- 
1.7.10.2