X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=5b12fa6e45f4079ad16f319a2601a1954583d79e;hb=7f5ab7d1f58d870622968e0e6a430f33403b8e4f;hp=b4b8ec2b1d50af04210b35a0e01b014f11214b15;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index b4b8ec2..5b12fa6 100644
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -21,6 +21,7 @@
 package jalview.appletgui;
 
 import jalview.analysis.NJTree;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.ViewBasedAnalysisI;
 import jalview.datamodel.Alignment;
@@ -28,7 +29,6 @@ import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
 import jalview.io.NewickFile;
-import jalview.schemes.ResidueProperties;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -69,6 +69,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     return tree;
   }
 
+  @Override
   public void finalize() throws Throwable
   {
     ap = null;
@@ -200,6 +201,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       this.newtree = newtree;
     }
 
+    @Override
     public void run()
     {
       if (newtree != null)
@@ -235,7 +237,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
           seqs = av.getSelectionGroup().getSequencesInOrder(
                   av.getAlignment());
         }
-        ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+        ScoreModelI sm = ScoreModels.getInstance().forName(pwtype);
         if (sm instanceof ViewBasedAnalysisI)
         {
           try
@@ -249,13 +251,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
                     + sm.getName());
             q.printStackTrace();
           }
-          tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
-        }
-        else
-        {
-          tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
-                  end);
         }
+        tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
       }
 
       tree.reCount(tree.getTopNode());
@@ -286,6 +283,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     }
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == newickOutput)
@@ -302,6 +300,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     }
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == fitToWindow)