X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=1bf8567861579edd333dcd8bd658f1a8bfa26f84;hb=58ba1562a8a739699ce47a338803b2641f6d7913;hp=b28ac7679efe7e260671db6bdb1a6544f9cbe42c;hpb=0f530039f8c0ac9c6613063a576c3a13c8644fcd;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index b28ac76..1bf8567 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -60,10 +60,14 @@ public class ClustalxColourScheme implements ColourSchemeI
       String seq;
       while(j < seqs.size())
       {
-        seq = ( (SequenceI) seqs.get(j)).getSequence();
-        for (i = start; i <= end; i++)
+        seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
+        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++;
@@ -221,13 +225,13 @@ public class ClustalxColourScheme implements ColourSchemeI
    size = i;
  }
 
-  public Color findColour(String s, int j, Vector seqs)
+  public Color findColour(String s, int j)
    {
      int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();
 
      Color c = Color.white;
 
-     if(i>20)
+     if(i>19)
        return c;
 
      for (int k=0; k < ResidueColour[i].conses.length ; k++)
@@ -245,6 +249,10 @@ public class ClustalxColourScheme implements ColourSchemeI
 
    }
 
+  public void setConsensus(Vector consensus)
+  {
+    // Clustal colouring cannot be coloured by PID
+  }
 
   public boolean canThreshold()
   {