X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=90f4bd001b824678816b34181bfc60c2e1fee3db;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=92dcde4360bf693cbeadf506639a7ed993d00318;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
old mode 100755
new mode 100644
index 92dcde4..90f4bd0
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,29 +1,32 @@
 /*
- * 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 2.8.2b1)
+ * 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.
- * 
+ * 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/>.
+ * 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
@@ -42,6 +45,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
 
   NJTree tree;
 
+  AlignmentPanel ap;
+
   AlignViewport av;
 
   public NJTree getTree()
@@ -49,6 +54,13 @@ 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 +77,7 @@ 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 +88,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       ex.printStackTrace();
     }
 
-    initTreePanel(av, type, pwtype, null);
+    initTreePanel(ap, type, pwtype, null);
   }
 
   /**
@@ -93,7 +105,7 @@ 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 +117,19 @@ 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 +191,11 @@ 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 +204,21 @@ 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 +295,8 @@ 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);
@@ -340,22 +355,24 @@ 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);