JAL-2416 scoreMatrices removed from ResidueProperties

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

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index fe04156..f623a96 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -21,6 +21,7 @@
 package jalview.analysis;
 
 import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Mapping;
@@ -423,11 +424,11 @@ public class AlignSeq
 
     if (type.equals(AlignSeq.PEP))
     {
-      lookup = ResidueProperties.getDefaultPeptideMatrix();
+      lookup = ScoreModels.getInstance().getDefaultModel(true).getMatrix();
     }
     else if (type.equals(AlignSeq.DNA))
     {
-      lookup = ResidueProperties.getDefaultDnaMatrix();
+      lookup = ScoreModels.getInstance().getDefaultModel(false).getMatrix();
     }
   }