X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=0db55c03c8b0946692a5709acc6fa28744358476;hb=bcb00c5d25c6c0783a5057ab23a267d81cc1e353;hp=4b1bf153473cafc2f45ab0bc9c8d7180b5f48d6e;hpb=503ebba0021fa583fa7af58f9406f9234274fd7c;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 4b1bf15..0db55c0 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) 2007 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
@@ -18,9 +18,10 @@
  */
 package jalview.schemes;
 
-
 import java.awt.*;
 
+import jalview.analysis.*;
+
 public class Blosum62ColourScheme
     extends ResidueColourScheme
 {
@@ -29,27 +30,31 @@ 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' )
+    if ('a' <= res && res <= 'z')
     {
-       s = Character.toString( res -= ('a' - 'A') );
+      // TO UPPERCASE !!!
+      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;
     }
 
-    if (!jalview.util.Comparison.isGap( res ))
+    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)
       {
-        return new Color(154, 154, 255);
+        currentColour = new Color(154, 154, 255);
       }
       else
       {
@@ -59,24 +64,31 @@ 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);
 
         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;
   }
 }