X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=77986720432060b8d5391e5318f8510040105c35;hb=5d2e589a842cf831e4fdeff6b8ed7e7ce6729fd5;hp=d0546dccc266acf4ffd169d0b0f89c6814afcc60;hpb=b78278b3ee2cb653c439fa207b78a469d53ce697;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index d0546dc..7798672 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -21,44 +21,48 @@ package jalview.schemes;
 
 import java.util.*;
 import java.awt.*;
-import jalview.gui.*;
-import jalview.datamodel.*;
 
 public class Blosum62ColourScheme extends ResidueColourScheme
 {
 
-  // need to keep an eye on the changing visible consensus sequence
-  AlignViewport av;
-
-  public Blosum62ColourScheme(AlignViewport av)
+  public Blosum62ColourScheme()
   {
     super();
-    this.av = av;
   }
 
-  public Color findColour(String s, int j, Vector aa)
+  public Color findColour(String s, int j)
   {
+    Hashtable hash = (Hashtable)consensus.elementAt(j);
+
+    if (!jalview.util.Comparison.isGap((s.charAt(0))))
+    {
+      String    max  = (String)hash.get("maxResidue");
 
-      if (!jalview.util.Comparison.isGap((s.charAt(0))))
-      {
-        String max = av.getVisibleConsensus().charAt(j) + "";
+      if (max.indexOf(s)>-1)
+        return new Color(154, 154, 255);
+      else {
 
-        if (s.equals(max))
-          return new Color(154, 154, 255);
-        else if (ResidueProperties.getBLOSUM62(max, s) > 0)
+        int c = 0,
+            max_aa=0,
+            n=max.length();
+        do {
+          c+=ResidueProperties.getBLOSUM62(max.substring(max_aa, max_aa+1), s);
+        } while (++max_aa<n);
+
+        if (c>0)
           return new Color(204, 204, 255);
         else
           return Color.white;
-
       }
-      else
+    }
+    else
         return Color.white;
 
   }
 
   public boolean canThreshold()
   {
-    return false;
+    return true;
   }
 
 }