JAL-1503 update version in GPL header

[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 d424367..ee070a9
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,29 +1,30 @@
 /*
- * 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 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.util.Hashtable;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.io.*;
+import jalview.util.MessageManager;
 
 public class TreePanel extends EmbmenuFrame implements ActionListener,
         ItemListener
@@ -41,6 +42,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
   TreeCanvas treeCanvas;
 
   NJTree tree;
+
   AlignmentPanel ap;
 
   AlignViewport av;
@@ -50,6 +52,13 @@ 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.
    * 
@@ -180,11 +189,11 @@ 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);
         }
 
@@ -193,19 +202,21 @@ 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);
@@ -342,22 +353,22 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     setLayout(borderLayout1);
     this.setBackground(Color.white);
     this.setFont(new java.awt.Font("Verdana", 0, 12));
-    jMenu2.setLabel("View");
-    fontSize.setLabel("Font...");
+    jMenu2.setLabel(MessageManager.getString("action.view"));
+    fontSize.setLabel(MessageManager.getString("action.font"));
     fontSize.addActionListener(this);
-    bootstrapMenu.setLabel("Show Bootstrap Values");
+    bootstrapMenu.setLabel(MessageManager.getString("label.show_bootstrap_values"));
     bootstrapMenu.addItemListener(this);
-    distanceMenu.setLabel("Show Distances");
+    distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
     distanceMenu.addItemListener(this);
-    placeholdersMenu.setLabel("Mark Unassociated Leaves");
+    placeholdersMenu.setLabel(MessageManager.getString("label.mark_unassociated_leaves"));
     placeholdersMenu.addItemListener(this);
     fitToWindow.setState(true);
-    fitToWindow.setLabel("Fit To Window");
+    fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
     fitToWindow.addItemListener(this);
-    fileMenu.setLabel("File");
-    newickOutput.setLabel("Newick Format");
+    fileMenu.setLabel(MessageManager.getString("action.file"));
+    newickOutput.setLabel(MessageManager.getString("label.newick_format"));
     newickOutput.addActionListener(this);
-    inputData.setLabel("Input Data...");
+    inputData.setLabel(MessageManager.getString("label.input_data"));
 
     add(scrollPane, BorderLayout.CENTER);
     jMenuBar1.add(fileMenu);