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 96b45c1..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);
@@ -878,8 +878,7 @@ public class NJTree
 
     if ((nd.left() == null) && (nd.right() == null))
     {
-      System.out
-              .println("Leaf = " + ((SequenceI) nd.element()).getName());
+      System.out.println("Leaf = " + ((SequenceI) nd.element()).getName());
       System.out.println("Dist " + nd.dist);
       System.out.println("Boot " + nd.getBootstrap());
     }
@@ -1108,8 +1107,7 @@ public class NJTree
     }
     else
     {
-      System.out.println(" name = "
-              + ((SequenceI) nd.element()).getName());
+      System.out.println(" name = " + ((SequenceI) nd.element()).getName());
     }
 
     System.out.println(" dist = " + nd.dist + " " + nd.count + " "
@@ -1303,8 +1301,8 @@ public class NJTree
   public void applyToNodes(NodeTransformI nodeTransformI)
   {
     for (Enumeration<SequenceNode> nodes = node.elements(); nodes
-            .hasMoreElements(); nodeTransformI
-            .transform(nodes.nextElement()))
+            .hasMoreElements(); nodeTransformI.transform(nodes
+            .nextElement()))
     {
       ;
     }