JAL-3675 release notes for JAL-3750 JAL-3751

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

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index a88f74f..8188f4d 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -20,19 +20,19 @@
  */
 package jalview.schemes;
 
-import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
 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;
 import jalview.util.Comparison;
 
 import java.awt.Color;
-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()
@@ -45,8 +45,8 @@ public class Blosum62ColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll)
   {
     return new Blosum62ColourScheme();
   }
@@ -55,8 +55,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme
   public Color findColour(char res, int j, SequenceI seq,
           String consensusResidue, float pid)
   {
-    PairwiseSeqScoreModel sm = (PairwiseSeqScoreModel) ScoreModels
-            .getInstance().forName(ScoreModels.BLOSUM62);
+    PairwiseScoreModelI sm = ScoreModels.getInstance().getBlosum62();
 
     /*
      * compare as upper case; note consensusResidue is 
@@ -85,7 +84,6 @@ public class Blosum62ColourScheme extends ResidueColourScheme
       for (char consensus : consensusResidue.toCharArray())
       {
         score += sm.getPairwiseScore(consensus, res);
-        // score += ResidueProperties.getBLOSUM62(consensus, res);
       }
 
       if (score > 0)