X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=ec5d4f1517aa4f3e120097d4a268f8ddc7761c92;hb=bc39ee8df9694f820a8a8bd2430f527b87c07f31;hp=5e862635662f22345363260e016a8e049faae6c4;hpb=83b55697263efc7b0c660eba6ea7091f6904257d;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 5e86263..ec5d4f1 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -20,6 +20,7 @@ package jalview.schemes;
 
 
 import java.awt.*;
+import jalview.analysis.AAFrequency;
 
 public class Blosum62ColourScheme
     extends ResidueColourScheme
@@ -34,22 +35,25 @@ public class Blosum62ColourScheme
     char res = s.charAt(0);
     if ('a' <= res && res <= 'z' )
     {
+       // TO UPPERCASE !!!
        s = String.valueOf( res -= ('a' - 'A') );
     }
 
-
-    if ( (threshold != 0) && !aboveThreshold(s, j))
+    if (consensus == null ||
+        j >= consensus.length ||
+        consensus[j] == null ||
+        (threshold != 0 && !aboveThreshold(s, j)))
     {
       return Color.white;
     }
 
     if (!jalview.util.Comparison.isGap( res ))
     {
-      String max = (String) consensus[j].get("maxResidue");
+      String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
 
       if (max.indexOf(s) > -1)
       {
-        return new Color(154, 154, 255);
+        currentColour = new Color(154, 154, 255);
       }
       else
       {
@@ -66,17 +70,22 @@ public class Blosum62ColourScheme
 
         if (c > 0)
         {
-          return new Color(204, 204, 255);
+          currentColour = new Color(204, 204, 255);
         }
         else
         {
-          return Color.white;
+          currentColour = Color.white;
         }
       }
+
+      if(conservationColouring)
+         applyConservation(j);
     }
     else
     {
       return Color.white;
     }
+
+    return currentColour;
   }
 }