X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=2e4678e118fdf2c384bee711cdf8609f39f258d7;hb=24efbd38f2c3dceaf6d3e305eef41ba0b0c9ebdc;hp=d4789e650654263c767e7685bcb2cc532bd68fe1;hpb=5f7d80cd8b01e051a6175b0ce8db0ad94d73df2f;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index d4789e6..2e4678e 100755
--- 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())
       {
         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++)
         {
           if(seq.length()-1<i)
             res = 23;
@@ -230,7 +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++)