X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=02545a3272fad1dfeb5973aa7f3f5fe1dfeff24f;hb=2e699d341f8e64868e3c279f9c02af617c4e9b44;hp=6e91e0b2256677455e368362efb51ae48ca60cb3;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 6e91e0b..02545a3 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
@@ -29,26 +30,29 @@ public class Blosum62ColourScheme
     super();
   }
 
-  public Color findColour(String s, int j)
+  public Color findColour(char res, int j)
   {
-    char res = s.charAt(0);
     if ('a' <= res && res <= 'z' )
     {
        // TO UPPERCASE !!!
-       s = String.valueOf( res -= ('a' - 'A') );
+       res -= ('a' - 'A');
     }
 
-
-    if ( (threshold != 0) && !aboveThreshold(s, j))
+    if (consensus == null ||
+        j >= consensus.length ||
+        consensus[j] == null ||
+        (threshold != 0 && !aboveThreshold(res, j)))
     {
       return Color.white;
     }
 
+    Color currentColour;
+
     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)
+      if (max.indexOf(res) > -1)
       {
         currentColour = new Color(154, 154, 255);
       }
@@ -60,8 +64,8 @@ public class Blosum62ColourScheme
 
         do
         {
-          c += ResidueProperties.getBLOSUM62(max.substring(max_aa,
-              max_aa + 1), s);
+          c += ResidueProperties.getBLOSUM62(
+              max.charAt(max_aa), res);
         }
         while (++max_aa < n);
 
@@ -76,7 +80,7 @@ public class Blosum62ColourScheme
       }
 
       if(conservationColouring)
-         applyConservation(j);
+       currentColour =  applyConservation(currentColour, j);
     }
     else
     {