X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=b7c766a07310c179498059dd2704b242b6410e33;hb=cf82c19425ee457a01c3f1a04aabfb0d9817af6f;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..b7c766a
--- 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 2.8.2)
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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);