JAL-2403 JAL-1483 changes to ScoreModelI hierarchy and signatures to

[jalview.git] / src / jalview / appletgui / TreePanel.java

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 655e182..5b12fa6 100644 (file)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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)