consensus held in residueColour

[jalview.git] / src / jalview / schemes / Blosum62ColourScheme.java

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index d91d49f..2e18c6a 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -27,37 +27,44 @@ import jalview.datamodel.*;
 public class Blosum62ColourScheme extends ResidueColourScheme\r
 {\r
 \r
-  // need to keep an eye on the changing visible consensus sequence\r
-  AlignViewport av;\r
-\r
-  public Blosum62ColourScheme(AlignViewport av)\r
+  public Blosum62ColourScheme()\r
   {\r
     super();\r
-    this.av = av;\r
   }\r
 \r
-  public Color findColour(SequenceI seq, String s, int j, Vector aa)\r
+  public Color findColour(String s, int j)\r
   {\r
-      if (!s.equals("-") && !s.equals(".") && !s.equals(" "))\r
-      {\r
-        String max = av.getVisibleConsensus().charAt(j) + "";\r
+    Hashtable hash = (Hashtable)consensus.elementAt(j);\r
+\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
-        if (s.equals(max))\r
-          return new Color(154, 154, 255);\r
-        else if (ResidueProperties.getBLOSUM62(max, s) > 0)\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
 \r
   public boolean canThreshold()\r
   {\r
-    return false;\r
+    return true;\r
   }\r
 \r
 }\r