put bioinformatics into message

[jalview.git] / src / jalview / schemes / ClustalxColourScheme.java

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index b28ac76..2e4678e 100755 (executable)
--- 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())\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
-          res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) + "")).intValue();\r
+          if(seq.length()-1<i)\r
+            res = 23;\r
+          else\r
+            res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) + "")).intValue();\r
           cons2[i][res]++;\r
         }\r
         j++;\r
@@ -227,7 +231,7 @@ public class ClustalxColourScheme implements ColourSchemeI
 \r
      Color c = Color.white;\r
 \r
-     if(i>20)\r
+     if(i>19)\r
        return c;\r
 \r
      for (int k=0; k < ResidueColour[i].conses.length ; k++)\r