tidy imports

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

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
old mode 100755 (executable)
new mode 100644 (file)
index 92dcde4..65f3d91
--- 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.*;
@@ -42,6 +41,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
 
   NJTree tree;
 
+  AlignmentPanel ap;
+
   AlignViewport av;
 
   public NJTree getTree()
@@ -49,6 +50,13 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     return tree;
   }
 
+  public void finalize() throws Throwable
+  {
+    ap = null;
+    av = null;
+    super.finalize();
+  }
+
   /**
    * Creates a new TreePanel object.
    * 
@@ -65,7 +73,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
    * @param e
    *          DOCUMENT ME!
    */
-  public TreePanel(AlignViewport av, String type, String pwtype)
+  public TreePanel(AlignmentPanel ap, String type, String pwtype)
   {
     try
     {
@@ -76,7 +84,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       ex.printStackTrace();
     }
 
-    initTreePanel(av, type, pwtype, null);
+    initTreePanel(ap, type, pwtype, null);
   }
 
   /**
@@ -93,7 +101,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
    * @param pwtype
    *          DOCUMENT ME!
    */
-  public TreePanel(AlignViewport av, String type, String pwtype,
+  public TreePanel(AlignmentPanel ap, String type, String pwtype,
           NewickFile newtree)
   {
     try
@@ -105,18 +113,19 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       e.printStackTrace();
     }
 
-    initTreePanel(av, type, pwtype, newtree);
+    initTreePanel(ap, type, pwtype, newtree);
   }
 
-  void initTreePanel(AlignViewport av, String type, String pwtype,
+  void initTreePanel(AlignmentPanel ap, String type, String pwtype,
           NewickFile newTree)
   {
 
-    this.av = av;
+    this.ap = ap;
+    this.av = ap.av;
     this.type = type;
     this.pwtype = pwtype;
 
-    treeCanvas = new TreeCanvas(av, scrollPane);
+    treeCanvas = new TreeCanvas(ap, scrollPane);
     TreeLoader tl = new TreeLoader(newTree);
     tl.start();
     embedMenuIfNeeded(treeCanvas);
@@ -178,11 +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);
         }
 
@@ -191,19 +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);
@@ -280,8 +291,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
 
   public void newickOutput_actionPerformed()
   {
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
-            .getTopNode());
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(
+            tree.getTopNode());
     String output = fout.print(false, true);
     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
     cap.setText(output);