X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=9df7ab83fd182961c379ff12b052aab6c8e562b4;hb=e6798fd04b1d7a35836a2e84deae5a94a35b88b9;hp=f13a90cfa84961c1103314ecb6ea341040a6c0a9;hpb=b5579849960a79b7fc111bdc8f84c8b933632ef0;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index f13a90c..9df7ab8 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -106,19 +106,18 @@ public class ClustalxColourScheme extends ResidueColourScheme
 
     for (SequenceI sq : seqs)
     {
-      char[] seq = sq.getSequence();
-
-      int end_j = seq.length - 1;
+      int end_j = sq.getLength() - 1;
+      int length = sq.getLength();
 
       for (int i = 0; i <= end_j; i++)
       {
-        if ((seq.length - 1) < i)
+        if (length - 1 < i)
         {
           res = 23;
         }
         else
         {
-          res = ResidueProperties.aaIndex[seq[i]];
+          res = ResidueProperties.aaIndex[sq.getCharAt(i)];
         }
         cons2[i][res]++;
       }