X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=fcf208c84a226e3b21f808e2cf53a4b64ef0592f;hb=c6e8e8ccd10f21698226ae37196cd9680e6804a0;hp=e0e50fbf505b18d63dfd8bf9c9942483a3346b20;hpb=1750b2f1dcdb6e7de41d0ef7beda88dc3400afba;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index e0e50fb..fcf208c 100644
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -20,6 +20,7 @@
  */
 package jalview.analysis;
 
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.analysis.ScoreModelI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.BinaryNode;
@@ -30,7 +31,6 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
 import jalview.io.NewickFile;
-import jalview.schemes.ResidueProperties;
 
 import java.util.Enumeration;
 import java.util.List;
@@ -244,7 +244,7 @@ public class NJTree
 
     if (sm == null && !(pwtype.equals("PID")))
     {
-      if (ResidueProperties.getScoreMatrix(pwtype) == null)
+      if (ScoreModels.getInstance().forName(pwtype) == null)
       {
         pwtype = "BLOSUM62";
       }
@@ -734,10 +734,10 @@ public class NJTree
     if (_pwmatrix == null)
     {
       // Resolve substitution model
-      _pwmatrix = ResidueProperties.getScoreModel(pwtype);
+      _pwmatrix = ScoreModels.getInstance().forName(pwtype);
       if (_pwmatrix == null)
       {
-        _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
+        _pwmatrix = ScoreModels.getInstance().forName("BLOSUM62");
       }
     }
     dist = _pwmatrix.findDistances(seqData);