JAL-2416 better encapsulated 'constants' for BLOSUM62, PAM250

[jalview.git] / src / jalview / analysis / Conservation.java

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 436be5b..79fa3d6 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -20,7 +20,6 @@
  */
 package jalview.analysis;
 
-import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
@@ -604,8 +603,8 @@ public class Conservation
     quality = new Vector<Double>();
 
     double max = -10000;
-    float[][] BLOSUM62 = ((PairwiseSeqScoreModel) ScoreModels.getInstance()
-            .forName(ScoreModels.BLOSUM62)).getMatrix();
+    float[][] BLOSUM62 = ScoreModels.getInstance().getBlosum62()
+            .getMatrix();
 
     // Loop over columns // JBPNote Profiling info
     // long ts = System.currentTimeMillis();