X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=0db55c03c8b0946692a5709acc6fa28744358476;hb=1698842ec6755d1995dae7c1a590efbfc8f6e4d5;hp=ec5d4f1517aa4f3e120097d4a268f8ddc7761c92;hpb=c3c305755d392741176209a0274a47897ac4d8a8;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index ec5d4f1..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) 2006 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 +18,9 @@
  */
 package jalview.schemes;
 
-
 import java.awt.*;
-import jalview.analysis.AAFrequency;
+
+import jalview.analysis.*;
 
 public class Blosum62ColourScheme
     extends ResidueColourScheme
@@ -30,28 +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 (consensus == null ||
         j >= consensus.length ||
         consensus[j] == null ||
-        (threshold != 0 && !aboveThreshold(s, j)))
+        (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(AAFrequency.MAXRESIDUE);
 
-      if (max.indexOf(s) > -1)
+      if (max.indexOf(res) > -1)
       {
         currentColour = new Color(154, 154, 255);
       }
@@ -63,8 +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);
 
@@ -78,8 +79,10 @@ public class Blosum62ColourScheme
         }
       }
 
-      if(conservationColouring)
-         applyConservation(j);
+      if (conservationColouring)
+      {
+        currentColour = applyConservation(currentColour, j);
+      }
     }
     else
     {