X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=f2d2c982033f4297fa29d0b8912ac5a06af161ca;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=356e3fe64dc4b5cac7eb8295b24fef3c89e7c91b;hpb=45845d73e614baf0e568c8bb384c5680d46e0e2e;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 356e3fe..f2d2c98 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
@@ -31,19 +32,31 @@ public class Blosum62ColourScheme
 
   public Color findColour(String s, int j)
   {
-    if ( (threshold != 0) && !aboveThreshold(s, j))
+
+    char res = s.charAt(0);
+    if ('a' <= res && res <= 'z' )
+    {
+       // TO UPPERCASE !!!
+       s = String.valueOf( res -= ('a' - 'A') );
+    }
+
+    if (consensus == null ||
+        j >= consensus.length ||
+        consensus[j] == null ||
+        (threshold != 0 && !aboveThreshold(s, j)))
     {
       return Color.white;
     }
 
+    Color currentColour;
 
-    if (!jalview.util.Comparison.isGap( (s.charAt(0))))
+    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
       {
@@ -60,17 +73,22 @@ 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)
+       currentColour =  applyConservation(currentColour, j);
     }
     else
     {
       return Color.white;
     }
+
+    return currentColour;
   }
 }