X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=5b12fa6e45f4079ad16f319a2601a1954583d79e;hb=7f5ab7d1f58d870622968e0e6a430f33403b8e4f;hp=2fb34b0547b2431f2b04a6465cd2ff7ae7e663c4;hpb=7a2f4e9ee4119f0369743e7996bcebbb6ab46f9e;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 2fb34b0..5b12fa6 100644
--- 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 +21,9 @@
 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;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
@@ -66,6 +69,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     return tree;
   }
 
+  @Override
   public void finalize() throws Throwable
   {
     ap = null;
@@ -197,6 +201,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       this.newtree = newtree;
     }
 
+    @Override
     public void run()
     {
       if (newtree != null)
@@ -216,8 +221,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       {
         int start, end;
         SequenceI[] seqs;
-        boolean selview = (av.getSelectionGroup() != null)
-                && (av.getSelectionGroup().getSize() > 1);
+        boolean selview = av.getSelectionGroup() != null
+                && av.getSelectionGroup().getSize() > 1;
         AlignmentView seqStrings = av.getAlignmentView(selview);
         if (!selview)
         {
@@ -232,8 +237,22 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
           seqs = av.getSelectionGroup().getSequencesInOrder(
                   av.getAlignment());
         }
-
-        tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+        ScoreModelI sm = ScoreModels.getInstance().forName(pwtype);
+        if (sm instanceof ViewBasedAnalysisI)
+        {
+          try
+          {
+            sm = sm.getClass().newInstance();
+            ((ViewBasedAnalysisI) sm)
+                    .configureFromAlignmentView(treeCanvas.ap);
+          } catch (Exception q)
+          {
+            System.err.println("Couldn't create a scoremodel instance for "
+                    + sm.getName());
+            q.printStackTrace();
+          }
+        }
+        tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
       }
 
       tree.reCount(tree.getTopNode());
@@ -264,6 +283,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     }
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == newickOutput)
@@ -280,6 +300,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     }
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == fitToWindow)