bug fix for unaligned sequence sets and clustal colours (obviated by

'aligned' test).

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index d4789e6..7faa9a3 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -61,7 +61,8 @@ public class ClustalxColourScheme implements ColourSchemeI
       while(j < seqs.size())\r
       {\r
         seq = ( (SequenceI) seqs.get(j)).getSequence();\r
-        for (i = start; i <= end; i++)\r
+        int end_j = seq.length()-1;\r
+        for (i = start; i <= end_j; i++)\r
         {\r
           if(seq.length()-1<i)\r
             res = 23;\r