X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=202fc2537afd594fd974e4a4d86090b31b30a08d;hb=4cb58ab40ed4521e8ac732665098a6c57ad43896;hp=f35b886cac6a80aff32e8240df1febae4e51975c;hpb=eeb9907df14f1015db254a87bcc8db35e10ba02d;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index f35b886..202fc25 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -20,6 +20,9 @@
  */
 package jalview.schemes;
 
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.AlignViewportI;
+import jalview.api.analysis.PairwiseScoreModelI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -31,6 +34,7 @@ import java.util.Map;
 public class Blosum62ColourScheme extends ResidueColourScheme
 {
   private static final Color LIGHT_BLUE = new Color(204, 204, 255);
+
   private static final Color DARK_BLUE = new Color(154, 154, 255);
 
   public Blosum62ColourScheme()
@@ -43,7 +47,8 @@ public class Blosum62ColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new Blosum62ColourScheme();
@@ -53,6 +58,8 @@ public class Blosum62ColourScheme extends ResidueColourScheme
   public Color findColour(char res, int j, SequenceI seq,
           String consensusResidue, float pid)
   {
+    PairwiseScoreModelI sm = ScoreModels.getInstance().getBlosum62();
+
     /*
      * compare as upper case; note consensusResidue is 
      * always computed as uppercase
@@ -75,14 +82,14 @@ public class Blosum62ColourScheme extends ResidueColourScheme
     }
     else
     {
-      int c = 0;
+      float score = 0;
 
       for (char consensus : consensusResidue.toCharArray())
       {
-        c += ResidueProperties.getBLOSUM62(consensus, res);
+        score += sm.getPairwiseScore(consensus, res);
       }
 
-      if (c > 0)
+      if (score > 0)
       {
         colour = LIGHT_BLUE;
       }