JAL-1632 JAL-2416 load score matrices from file, as float[][]

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

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index e0e50fb..fcf208c 100644 (file)
--- 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);