Fixed so that all alternate residues are used to calculate blosum62

conservation.

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index d0546dc..6c83920 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -38,20 +38,35 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 \r
   public Color findColour(String s, int j, Vector aa)\r
   {\r
+    Hashtable hash;\r
 \r
-      if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
-      {\r
-        String max = av.getVisibleConsensus().charAt(j) + "";\r
+    if (aa != null)\r
+      hash = (Hashtable)aa.elementAt(j);\r
+    else\r
+      return Color.white;\r
 \r
-        if (s.equals(max))\r
-          return new Color(154, 154, 255);\r
-        else if (ResidueProperties.getBLOSUM62(max, s) > 0)\r
+    if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
+    {\r
+      String    max  = (String)hash.get("maxResidue");\r
+\r
+      if (max.indexOf(s)>-1)\r
+        return new Color(154, 154, 255);\r
+      else {\r
+\r
+        int c = 0,\r
+            max_aa=0,\r
+            n=max.length();\r
+        do {\r
+          c+=ResidueProperties.getBLOSUM62(max.substring(max_aa, max_aa+1), s);\r
+        } while (++max_aa<n);\r
+\r
+        if (c>0)\r
           return new Color(204, 204, 255);\r
         else\r
           return Color.white;\r
-\r
       }\r
-      else\r
+    }\r
+    else\r
         return Color.white;\r
 \r
   }\r