X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=65f3d9156a22cf76fb34df2f4fa5eb0b48648c92;hb=ad20cd92225f2ee8c251d39b00b90555d382a616;hp=7595a50cc71832fc0cb1625ce439577f52a99f7b;hpb=362f2db1b01f3562784864a1d6ac5f7b9be0a18a;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 7595a50..65f3d91 100644
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -19,7 +19,6 @@ package jalview.appletgui;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.util.Hashtable;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
@@ -41,6 +40,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
   TreeCanvas treeCanvas;
 
   NJTree tree;
+
   AlignmentPanel ap;
 
   AlignViewport av;
@@ -49,10 +49,11 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
   {
     return tree;
   }
-  
-  public void finalize() throws Throwable {
-    ap=null;
-    av=null;
+
+  public void finalize() throws Throwable
+  {
+    ap = null;
+    av = null;
     super.finalize();
   }
 
@@ -186,11 +187,11 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       {
         if (odata == null)
         {
-          tree = new NJTree(av.alignment.getSequencesArray(), newtree);
+          tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
         }
         else
         {
-          tree = new NJTree(av.alignment.getSequencesArray(), odata,
+          tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
                   newtree);
         }
 
@@ -199,19 +200,21 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       {
         int start, end;
         SequenceI[] seqs;
-        AlignmentView seqStrings = av.getAlignmentView(av
-                .getSelectionGroup() != null);
-        if (av.getSelectionGroup() == null)
+        boolean selview = (av.getSelectionGroup() != null)
+                && (av.getSelectionGroup().getSize() > 1);
+        AlignmentView seqStrings = av.getAlignmentView(selview);
+        if (!selview)
         {
           start = 0;
-          end = av.alignment.getWidth();
-          seqs = av.alignment.getSequencesArray();
+          end = av.getAlignment().getWidth();
+          seqs = av.getAlignment().getSequencesArray();
         }
         else
         {
           start = av.getSelectionGroup().getStartRes();
           end = av.getSelectionGroup().getEndRes() + 1;
-          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+          seqs = av.getSelectionGroup().getSequencesInOrder(
+                  av.getAlignment());
         }
 
         tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);