X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=2e4678e118fdf2c384bee711cdf8609f39f258d7;hb=09b64bea954c283bde1d21c0a230f51f1ae89373;hp=b28ac7679efe7e260671db6bdb1a6544f9cbe42c;hpb=0f530039f8c0ac9c6613063a576c3a13c8644fcd;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index b28ac76..2e4678e 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -61,9 +61,13 @@ 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++)
         {
-          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++;
@@ -227,7 +231,7 @@ public class ClustalxColourScheme implements ColourSchemeI
 
      Color c = Color.white;
 
-     if(i>20)
+     if(i>19)
        return c;
 
      for (int k=0; k < ResidueColour[i].conses.length ; k++)