X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=0db55c03c8b0946692a5709acc6fa28744358476;hb=990fd5f012601024aaeeb09e2901791d242636c4;hp=2c0836de99c6d7dec867547d7579e9c3cd4c30e2;hpb=b0c3862ae342f88419e5e685de2b56f060358c05;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 2c0836d..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
 {
@@ -29,26 +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' )
+    if ('a' <= res && res <= 'z')
     {
-       // TO UPPERCASE !!!
-       s = String.valueOf( res -= ('a' - 'A') );
+      // TO UPPERCASE !!!
+      res -= ('a' - 'A');
     }
 
-
-    if ( j>=consensus.length || (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)
       {
         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);
 
@@ -75,8 +79,10 @@ public class Blosum62ColourScheme
         }
       }
 
-      if(conservationColouring)
-         applyConservation(j);
+      if (conservationColouring)
+      {
+        currentColour = applyConservation(currentColour, j);
+      }
     }
     else
     {