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
29 import org.jibble.epsgraphics.*;
\r
32 import java.awt.event.*;
\r
33 import java.awt.image.*;
\r
39 import javax.imageio.*;
\r
41 import java.beans.PropertyChangeEvent;
\r
48 * @version $Revision$
\r
50 public class TreePanel extends GTreePanel
\r
57 TreeCanvas treeCanvas;
\r
61 * Creates a new TreePanel object.
\r
63 * @param av DOCUMENT ME!
\r
64 * @param seqVector DOCUMENT ME!
\r
65 * @param type DOCUMENT ME!
\r
66 * @param pwtype DOCUMENT ME!
\r
67 * @param s DOCUMENT ME!
\r
68 * @param e DOCUMENT ME!
\r
70 public TreePanel(AlignViewport av, Vector seqVector, String type,
\r
71 String pwtype, int s, int e)
\r
74 initTreePanel(av, seqVector, type, pwtype, s, e, null);
\r
76 // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
\r
77 showDistances(true);
\r
81 * Creates a new TreePanel object.
\r
83 * @param av DOCUMENT ME!
\r
84 * @param seqVector DOCUMENT ME!
\r
85 * @param newtree DOCUMENT ME!
\r
86 * @param type DOCUMENT ME!
\r
87 * @param pwtype DOCUMENT ME!
\r
89 public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
\r
90 String type, String pwtype)
\r
93 initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
\r
96 public AlignmentI getAlignment()
\r
98 return treeCanvas.av.getAlignment();
\r
102 void initTreePanel(AlignViewport av, Vector seqVector, String type,
\r
103 String pwtype, int s, int e, NewickFile newTree)
\r
107 this.pwtype = pwtype;
\r
112 seq = new Sequence[seqVector.size()];
\r
113 seqVector.toArray(seq);
\r
116 treeCanvas = new TreeCanvas(av, scrollPane);
\r
117 scrollPane.setViewportView(treeCanvas);
\r
119 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
121 public void propertyChange(PropertyChangeEvent evt)
\r
123 if (evt.getPropertyName().equals("alignment"))
\r
126 System.out.println("tree is null");
\r
127 if(evt.getNewValue()==null)
\r
128 System.out.println("new value is null");
\r
130 tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
\r
138 TreeLoader tl = new TreeLoader(newTree);
\r
143 class TreeLoader extends Thread
\r
145 NewickFile newtree;
\r
147 public TreeLoader(NewickFile newtree)
\r
149 this.newtree = newtree;
\r
150 if (newtree != null)
\r
152 // Must be outside run(), as Jalview2XML tries to
\r
153 // update distance/bootstrap visibility at the same time
\r
154 showBootstrap(newtree.HasBootstrap());
\r
155 showDistances(newtree.HasDistances());
\r
162 tree = new NJTree(seq, newtree);
\r
164 tree = new NJTree(seq, type, pwtype, start, end);
\r
166 tree.reCount(tree.getTopNode());
\r
167 tree.findHeight(tree.getTopNode());
\r
168 treeCanvas.setTree(tree);
\r
170 treeCanvas.repaint();
\r
175 public void showDistances(boolean b)
\r
177 treeCanvas.setShowDistances(b);
\r
178 distanceMenu.setSelected(b);
\r
181 public void showBootstrap(boolean b)
\r
183 treeCanvas.setShowBootstrap(b);
\r
184 bootstrapMenu.setSelected(b);
\r
187 public void showPlaceholders(boolean b)
\r
189 placeholdersMenu.setState(b);
\r
190 treeCanvas.setMarkPlaceholders(b);
\r
199 * @return DOCUMENT ME!
\r
201 public NJTree getTree()
\r
210 * @param e DOCUMENT ME!
\r
212 public void textbox_actionPerformed(ActionEvent e)
\r
214 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
216 StringBuffer buffer = new StringBuffer();
\r
218 if (type.equals("AV"))
\r
220 buffer.append("Average distance tree using ");
\r
224 buffer.append("Neighbour joining tree using ");
\r
227 if (pwtype.equals("BL"))
\r
229 buffer.append("BLOSUM62");
\r
233 buffer.append("PID");
\r
236 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
\r
238 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
\r
239 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
\r
245 * @param e DOCUMENT ME!
\r
247 public void saveAsNewick_actionPerformed(ActionEvent e)
\r
249 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
250 "LAST_DIRECTORY"));
\r
251 chooser.setFileView(new JalviewFileView());
\r
252 chooser.setDialogTitle("Save tree as newick file");
\r
253 chooser.setToolTipText("Save");
\r
255 int value = chooser.showSaveDialog(null);
\r
257 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
259 String choice = chooser.getSelectedFile().getPath();
\r
260 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
\r
261 chooser.getSelectedFile().getParent());
\r
265 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
\r
266 String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
\r
267 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
\r
269 out.println(output);
\r
272 catch (Exception ex)
\r
274 ex.printStackTrace();
\r
282 * @param e DOCUMENT ME!
\r
284 public void printMenu_actionPerformed(ActionEvent e)
\r
286 //Putting in a thread avoids Swing painting problems
\r
287 treeCanvas.startPrinting();
\r
293 * @param e DOCUMENT ME!
\r
295 public void fitToWindow_actionPerformed(ActionEvent e)
\r
297 treeCanvas.fitToWindow = fitToWindow.isSelected();
\r
304 * @param e DOCUMENT ME!
\r
306 public void font_actionPerformed(ActionEvent e)
\r
308 if (treeCanvas == null)
\r
313 new FontChooser(this);
\r
316 public Font getTreeFont()
\r
318 return treeCanvas.font;
\r
321 public void setTreeFont(Font font)
\r
323 if(treeCanvas!=null)
\r
324 treeCanvas.setFont(font);
\r
330 * @param e DOCUMENT ME!
\r
332 public void distanceMenu_actionPerformed(ActionEvent e)
\r
334 treeCanvas.setShowDistances(distanceMenu.isSelected());
\r
340 * @param e DOCUMENT ME!
\r
342 public void bootstrapMenu_actionPerformed(ActionEvent e)
\r
344 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
\r
350 * @param e DOCUMENT ME!
\r
352 public void placeholdersMenu_actionPerformed(ActionEvent e)
\r
354 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
\r
360 * @param e DOCUMENT ME!
\r
362 public void epsTree_actionPerformed(ActionEvent e)
\r
364 boolean accurateText = true;
\r
366 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
\r
367 "Prompt each time");
\r
369 // If we need to prompt, and if the GUI is visible then
\r
370 // Prompt for EPS rendering style
\r
371 if (renderStyle.equalsIgnoreCase("Prompt each time")
\r
373 (System.getProperty("java.awt.headless") != null
\r
374 && System.getProperty("java.awt.headless").equals("true")))
\r
376 EPSOptions eps = new EPSOptions();
\r
377 renderStyle = eps.getValue();
\r
379 if (renderStyle==null || eps.cancelled)
\r
385 if (renderStyle.equalsIgnoreCase("text"))
\r
387 accurateText = false;
\r
390 int width = treeCanvas.getWidth();
\r
391 int height = treeCanvas.getHeight();
\r
395 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
396 "LAST_DIRECTORY"), new String[] { "eps" },
\r
397 new String[] { "Encapsulated Postscript" },
\r
398 "Encapsulated Postscript");
\r
399 chooser.setFileView(new jalview.io.JalviewFileView());
\r
400 chooser.setDialogTitle("Create EPS file from tree");
\r
401 chooser.setToolTipText("Save");
\r
403 int value = chooser.showSaveDialog(this);
\r
405 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
410 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
\r
411 chooser.getSelectedFile().getParent());
\r
413 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
\r
414 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
\r
417 pg.setAccurateTextMode(accurateText);
\r
419 treeCanvas.draw(pg, width, height);
\r
424 catch (Exception ex)
\r
426 ex.printStackTrace();
\r
433 * @param e DOCUMENT ME!
\r
435 public void pngTree_actionPerformed(ActionEvent e)
\r
437 int width = treeCanvas.getWidth();
\r
438 int height = treeCanvas.getHeight();
\r
442 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
443 "LAST_DIRECTORY"), new String[] { "png" },
\r
444 new String[] { "Portable network graphics" },
\r
445 "Portable network graphics");
\r
447 chooser.setFileView(new jalview.io.JalviewFileView());
\r
448 chooser.setDialogTitle("Create PNG image from tree");
\r
449 chooser.setToolTipText("Save");
\r
451 int value = chooser.showSaveDialog(this);
\r
453 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
458 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
\r
459 chooser.getSelectedFile().getParent());
\r
461 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
\r
463 BufferedImage bi = new BufferedImage(width, height,
\r
464 BufferedImage.TYPE_INT_RGB);
\r
465 Graphics png = bi.getGraphics();
\r
467 treeCanvas.draw(png, width, height);
\r
469 ImageIO.write(bi, "png", out);
\r
472 catch (Exception ex)
\r
474 ex.printStackTrace();
\r