JAL-2416 BLOSUM62 removed from ResidueProperties

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

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 8f7e57b..436be5b 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -20,6 +20,8 @@
  */
 package jalview.analysis;
 
+import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ResidueCount;
@@ -602,7 +604,8 @@ public class Conservation
     quality = new Vector<Double>();
 
     double max = -10000;
-    float[][] BLOSUM62 = ResidueProperties.getBLOSUM62();
+    float[][] BLOSUM62 = ((PairwiseSeqScoreModel) ScoreModels.getInstance()
+            .forName(ScoreModels.BLOSUM62)).getMatrix();
 
     // Loop over columns // JBPNote Profiling info
     // long ts = System.currentTimeMillis();