From d18ec5d6a72d262bbd6a8233010b92737b3840b7 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 13 Apr 2005 16:40:53 +0000
Subject: [PATCH] Fixed so that all alternate residues are used to calculate
 blosum62 conservation.

---
 src/jalview/schemes/Blosum62ColourScheme.java |   31 ++++++++++++++++++-------
 1 file changed, 23 insertions(+), 8 deletions(-)

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index d0546dc..6c83920 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -38,20 +38,35 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 
   public Color findColour(String s, int j, Vector aa)
   {
+    Hashtable hash;
 
-      if (!jalview.util.Comparison.isGap((s.charAt(0))))
-      {
-        String max = av.getVisibleConsensus().charAt(j) + "";
+    if (aa != null)
+      hash = (Hashtable)aa.elementAt(j);
+    else
+      return Color.white;
 
-        if (s.equals(max))
-          return new Color(154, 154, 255);
-        else if (ResidueProperties.getBLOSUM62(max, s) > 0)
+    if (!jalview.util.Comparison.isGap((s.charAt(0))))
+    {
+      String    max  = (String)hash.get("maxResidue");
+
+      if (max.indexOf(s)>-1)
+        return new Color(154, 154, 255);
+      else {
+
+        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;
 
   }
-- 
1.7.10.2