JAL-2418 source formatting

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

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 53670e3..02f9b3e 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -20,6 +20,8 @@
  */
 package jalview.schemes;
 
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.PairwiseScoreModelI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -31,6 +33,7 @@ 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()
@@ -53,11 +56,12 @@ 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 toUpperCase does nothing 
-     * if the string is already uppercase
+     * compare as upper case; note consensusResidue is 
+     * always computed as uppercase
      */
-    consensusResidue = consensusResidue.toUpperCase();
     if ('a' <= res && res <= 'z')
     {
       res -= ('a' - 'A');
@@ -76,14 +80,14 @@ 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;
       }