2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.gui;
\r
21 import jalview.analysis.*;
\r
23 import jalview.datamodel.*;
\r
25 import jalview.io.*;
\r
27 import jalview.jbgui.*;
\r
31 import java.awt.event.*;
\r
37 import java.beans.PropertyChangeEvent;
\r
44 * @version $Revision$
\r
46 public class TreePanel extends GTreePanel
\r
53 TreeCanvas treeCanvas;
\r
57 * Creates a new TreePanel object.
\r
59 * @param av DOCUMENT ME!
\r
60 * @param seqVector DOCUMENT ME!
\r
61 * @param type DOCUMENT ME!
\r
62 * @param pwtype DOCUMENT ME!
\r
63 * @param s DOCUMENT ME!
\r
64 * @param e DOCUMENT ME!
\r
66 public TreePanel(AlignViewport av, Vector seqVector, String type,
\r
67 String pwtype, int s, int e)
\r
70 initTreePanel(av, seqVector, type, pwtype, s, e, null);
\r
72 // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
\r
73 showDistances(true);
\r
77 * Creates a new TreePanel object.
\r
79 * @param av DOCUMENT ME!
\r
80 * @param seqVector DOCUMENT ME!
\r
81 * @param newtree DOCUMENT ME!
\r
82 * @param type DOCUMENT ME!
\r
83 * @param pwtype DOCUMENT ME!
\r
85 public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
\r
86 String type, String pwtype)
\r
89 initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
\r
92 public AlignmentI getAlignment()
\r
94 return treeCanvas.av.getAlignment();
\r
98 void initTreePanel(AlignViewport av, Vector seqVector, String type,
\r
99 String pwtype, int s, int e, NewickFile newTree)
\r
103 this.pwtype = pwtype;
\r
108 seq = new Sequence[seqVector.size()];
\r
109 seqVector.toArray(seq);
\r
112 treeCanvas = new TreeCanvas(av, scrollPane);
\r
113 scrollPane.setViewportView(treeCanvas);
\r
115 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
117 public void propertyChange(PropertyChangeEvent evt)
\r
119 if (evt.getPropertyName().equals("alignment"))
\r
122 System.out.println("tree is null");
\r
123 if(evt.getNewValue()==null)
\r
124 System.out.println("new value is null");
\r
126 tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
\r
134 TreeLoader tl = new TreeLoader(newTree);
\r
139 class TreeLoader extends Thread
\r
141 NewickFile newtree;
\r
143 public TreeLoader(NewickFile newtree)
\r
145 this.newtree = newtree;
\r
146 if (newtree != null)
\r
148 // Must be outside run(), as Jalview2XML tries to
\r
149 // update distance/bootstrap visibility at the same time
\r
150 showBootstrap(newtree.HasBootstrap());
\r
151 showDistances(newtree.HasDistances());
\r
152 showPlaceholders(true);
\r
159 tree = new NJTree(seq, newtree);
\r
161 tree = new NJTree(seq, type, pwtype, start, end);
\r
163 tree.reCount(tree.getTopNode());
\r
164 tree.findHeight(tree.getTopNode());
\r
165 treeCanvas.setTree(tree);
\r
167 treeCanvas.repaint();
\r
170 fullid.setState(treeCanvas.av.showDBPrefix);
\r
171 if(!treeCanvas.av.showDBPrefix)
\r
173 fullid_actionPerformed(null);
\r
179 public void showDistances(boolean b)
\r
181 treeCanvas.setShowDistances(b);
\r
182 distanceMenu.setSelected(b);
\r
185 public void showBootstrap(boolean b)
\r
187 treeCanvas.setShowBootstrap(b);
\r
188 bootstrapMenu.setSelected(b);
\r
191 public void showPlaceholders(boolean b)
\r
193 placeholdersMenu.setState(b);
\r
194 treeCanvas.setMarkPlaceholders(b);
\r
203 * @return DOCUMENT ME!
\r
205 public NJTree getTree()
\r
214 * @param e DOCUMENT ME!
\r
216 public void textbox_actionPerformed(ActionEvent e)
\r
218 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
220 StringBuffer buffer = new StringBuffer();
\r
222 if (type.equals("AV"))
\r
224 buffer.append("Average distance tree using ");
\r
228 buffer.append("Neighbour joining tree using ");
\r
231 if (pwtype.equals("BL"))
\r
233 buffer.append("BLOSUM62");
\r
237 buffer.append("PID");
\r
240 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
\r
242 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
\r
243 cap.setText(fout.print(false, true));
\r
249 * @param e DOCUMENT ME!
\r
251 public void saveAsNewick_actionPerformed(ActionEvent e)
\r
253 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
254 "LAST_DIRECTORY"));
\r
255 chooser.setFileView(new JalviewFileView());
\r
256 chooser.setDialogTitle("Save tree as newick file");
\r
257 chooser.setToolTipText("Save");
\r
259 int value = chooser.showSaveDialog(null);
\r
261 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
263 String choice = chooser.getSelectedFile().getPath();
\r
264 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
\r
265 chooser.getSelectedFile().getParent());
\r
269 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
\r
270 String output = fout.print(false, true); // distances only
\r
271 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
\r
273 out.println(output);
\r
276 catch (Exception ex)
\r
278 ex.printStackTrace();
\r
286 * @param e DOCUMENT ME!
\r
288 public void printMenu_actionPerformed(ActionEvent e)
\r
290 //Putting in a thread avoids Swing painting problems
\r
291 treeCanvas.startPrinting();
\r
297 * @param e DOCUMENT ME!
\r
299 public void fitToWindow_actionPerformed(ActionEvent e)
\r
301 treeCanvas.fitToWindow = fitToWindow.isSelected();
\r
308 * @param e DOCUMENT ME!
\r
310 public void font_actionPerformed(ActionEvent e)
\r
312 if (treeCanvas == null)
\r
317 new FontChooser(this);
\r
320 public Font getTreeFont()
\r
322 return treeCanvas.font;
\r
325 public void setTreeFont(Font font)
\r
327 if(treeCanvas!=null)
\r
328 treeCanvas.setFont(font);
\r
334 * @param e DOCUMENT ME!
\r
336 public void distanceMenu_actionPerformed(ActionEvent e)
\r
338 treeCanvas.setShowDistances(distanceMenu.isSelected());
\r
344 * @param e DOCUMENT ME!
\r
346 public void bootstrapMenu_actionPerformed(ActionEvent e)
\r
348 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
\r
354 * @param e DOCUMENT ME!
\r
356 public void placeholdersMenu_actionPerformed(ActionEvent e)
\r
358 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
\r
362 public void fullid_actionPerformed(ActionEvent e)
\r
364 tree.findHeight(tree.getTopNode());
\r
366 // Now have to calculate longest name based on the leaves
\r
367 Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
\r
369 treeCanvas.longestName="";
\r
370 for (int i = 0; i < leaves.size(); i++)
\r
372 SequenceNode lf = (SequenceNode) leaves.elementAt(i);
\r
373 Sequence seq = (Sequence) lf.element();
\r
374 lf.setName(seq.getDisplayId(fullid.getState(), false));
\r
375 if(lf.getName().length() > treeCanvas.longestName.length())
\r
376 treeCanvas.longestName = lf.getName();
\r
379 treeCanvas.repaint();
\r
386 * @param e DOCUMENT ME!
\r
388 public void epsTree_actionPerformed(ActionEvent e)
\r
390 makeTreeImage(jalview.util.ImageMaker.EPS);
\r
396 * @param e DOCUMENT ME!
\r
398 public void pngTree_actionPerformed(ActionEvent e)
\r
400 makeTreeImage(jalview.util.ImageMaker.PNG);
\r
403 void makeTreeImage(int type)
\r
405 int width = treeCanvas.getWidth();
\r
406 int height = treeCanvas.getHeight();
\r
408 jalview.util.ImageMaker im;
\r
410 if(type == jalview.util.ImageMaker.PNG)
\r
411 im = new jalview.util.ImageMaker(this,
\r
412 jalview.util.ImageMaker.PNG,
\r
413 "Make PNG image from tree",
\r
417 im = new jalview.util.ImageMaker(this,
\r
418 jalview.util.ImageMaker.EPS,
\r
419 "Make EPS file from tree",
\r
421 null, this.getTitle());
\r
423 if(im.getGraphics()!=null)
\r
425 treeCanvas.draw(im.getGraphics(), width, height);
\r