From ef3acde250d7d83304fb328a428b4d834fe3ac05 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 27 Feb 2007 13:38:40 +0000
Subject: [PATCH] check conservation length

---
 src/jalview/schemes/ResidueColourScheme.java |    8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 67828ce..f43aa02 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -47,6 +47,7 @@ public class ResidueColourScheme
 
   /** Conservation string as a char array */
   char[] conservation;
+  int conservationLength=0;
 
   /** DOCUMENT ME!! */
   int inc = 30;
@@ -144,7 +145,7 @@ public class ResidueColourScheme
       c -= ('a' - 'A');
     }
 
-    if (consensus == null || consensus[j] == null)
+    if (consensus == null || consensus.length<j || consensus[j] == null)
     {
       return false;
     }
@@ -207,6 +208,7 @@ public class ResidueColourScheme
       {
         conservation[i] = cons.getConsSequence().getCharAt(i);
       }
+      conservationLength = conservation.length;
     }
 
   }
@@ -223,9 +225,9 @@ public class ResidueColourScheme
   Color applyConservation(Color currentColour, int i)
   {
 
-    if ( (conservation[i] != '*') && (conservation[i] != '+'))
+    if ((conservationLength>i) && (conservation[i] != '*') && (conservation[i] != '+'))
     {
-      if (jalview.util.Comparison.isGap(conservation[i]))
+      if ( jalview.util.Comparison.isGap(conservation[i]))
       {
         currentColour = Color.white;
       }
-- 
1.7.10.2