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 javax.swing.*;
\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 treeCanvas.setShowDistances(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
97 void initTreePanel(AlignViewport av, Vector seqVector, String type,
\r
98 String pwtype, int s, int e, NewickFile newTree)
\r
102 this.pwtype = pwtype;
\r
107 seq = new Sequence[seqVector.size()];
\r
108 seqVector.toArray(seq);
\r
111 treeCanvas = new TreeCanvas(av, scrollPane);
\r
112 scrollPane.setViewportView(treeCanvas);
\r
114 TreeLoader tl = new TreeLoader(newTree);
\r
119 class TreeLoader extends Thread
\r
121 NewickFile newtree;
\r
123 public TreeLoader(NewickFile newtree)
\r
125 this.newtree = newtree;
\r
132 tree = new NJTree(seq, newtree);
\r
134 tree = new NJTree(seq, type, pwtype, start, end);
\r
136 tree.reCount(tree.getTopNode());
\r
137 tree.findHeight(tree.getTopNode());
\r
138 treeCanvas.setTree(tree);
\r
141 treeCanvas.setShowBootstrap(newtree.HasBootstrap());
\r
142 treeCanvas.setShowDistances(newtree.HasDistances());
\r
145 setViewStateFromTreeCanvas(treeCanvas);
\r
147 treeCanvas.repaint();
\r
156 * @return DOCUMENT ME!
\r
158 public NJTree getTree()
\r
166 * @param tree DOCUMENT ME!
\r
168 private void setViewStateFromTreeCanvas(TreeCanvas tree)
\r
170 // update view menu state from treeCanvas render state
\r
171 distanceMenu.setSelected(tree.showDistances);
\r
172 bootstrapMenu.setSelected(tree.showBootstrap);
\r
173 placeholdersMenu.setSelected(tree.markPlaceholders);
\r
179 * @param tree DOCUMENT ME!
\r
181 private void setTreeCanvasFromViewState(TreeCanvas tree)
\r
183 // update view menu state from treeCanvas render state
\r
184 tree.showDistances = distanceMenu.isSelected();
\r
185 tree.showBootstrap = bootstrapMenu.isSelected();
\r
186 tree.markPlaceholders = placeholdersMenu.isSelected();
\r
192 * @param e DOCUMENT ME!
\r
194 public void textbox_actionPerformed(ActionEvent e)
\r
196 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
198 StringBuffer buffer = new StringBuffer();
\r
200 if (type.equals("AV"))
\r
202 buffer.append("Average distance tree using ");
\r
206 buffer.append("Neighbour joining tree using ");
\r
209 if (pwtype.equals("BL"))
\r
211 buffer.append("BLOSUM62");
\r
215 buffer.append("PID");
\r
218 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
\r
220 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
\r
221 cap.setText(fout.print(false, true));
\r
227 * @param e DOCUMENT ME!
\r
229 public void saveAsNewick_actionPerformed(ActionEvent e)
\r
231 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
232 "LAST_DIRECTORY"));
\r
233 chooser.setFileView(new JalviewFileView());
\r
234 chooser.setDialogTitle("Save tree as newick file");
\r
235 chooser.setToolTipText("Save");
\r
237 int value = chooser.showSaveDialog(null);
\r
239 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
241 String choice = chooser.getSelectedFile().getPath();
\r
242 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
\r
243 chooser.getSelectedFile().getParent());
\r
247 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
\r
248 String output = fout.print(false, true); // distances only
\r
249 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
\r
251 out.println(output);
\r
254 catch (Exception ex)
\r
256 ex.printStackTrace();
\r
264 * @param e DOCUMENT ME!
\r
266 public void printMenu_actionPerformed(ActionEvent e)
\r
268 //Putting in a thread avoids Swing painting problems
\r
269 treeCanvas.startPrinting();
\r
275 * @param e DOCUMENT ME!
\r
277 public void fitToWindow_actionPerformed(ActionEvent e)
\r
279 treeCanvas.fitToWindow = fitToWindow.isSelected();
\r
286 * @param e DOCUMENT ME!
\r
288 public void fontSize_actionPerformed(ActionEvent e)
\r
290 if (treeCanvas == null)
\r
295 String size = fontSize.getText().substring(fontSize.getText().indexOf("-") +
\r
298 Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
299 "Select font size", "Font size", JOptionPane.QUESTION_MESSAGE,
\r
303 "1", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20"
\r
304 }, "Font Size - " + size);
\r
306 if (selection != null)
\r
308 fontSize.setText("Font Size - " + selection);
\r
310 int i = Integer.parseInt(selection.toString());
\r
311 treeCanvas.setFontSize(i);
\r
314 scrollPane.setViewportView(treeCanvas);
\r
320 * @param e DOCUMENT ME!
\r
322 public void distanceMenu_actionPerformed(ActionEvent e)
\r
324 treeCanvas.setShowDistances(distanceMenu.isSelected());
\r
330 * @param e DOCUMENT ME!
\r
332 public void bootstrapMenu_actionPerformed(ActionEvent e)
\r
334 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
\r
340 * @param e DOCUMENT ME!
\r
342 public void placeholdersMenu_actionPerformed(ActionEvent e)
\r
344 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
\r
350 * @param e DOCUMENT ME!
\r
352 public void epsTree_actionPerformed(ActionEvent e)
\r
354 int width = treeCanvas.getWidth();
\r
355 int height = treeCanvas.getHeight();
\r
359 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
360 "LAST_DIRECTORY"), new String[] { "eps" },
\r
361 new String[] { "Encapsulated Postscript" },
\r
362 "Encapsulated Postscript");
\r
363 chooser.setFileView(new jalview.io.JalviewFileView());
\r
364 chooser.setDialogTitle("Create EPS file from tree");
\r
365 chooser.setToolTipText("Save");
\r
367 int value = chooser.showSaveDialog(this);
\r
369 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
374 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
\r
375 chooser.getSelectedFile().getParent());
\r
377 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
\r
378 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
\r
381 treeCanvas.draw(pg, width, height);
\r
386 catch (Exception ex)
\r
388 ex.printStackTrace();
\r
395 * @param e DOCUMENT ME!
\r
397 public void pngTree_actionPerformed(ActionEvent e)
\r
399 int width = treeCanvas.getWidth();
\r
400 int height = treeCanvas.getHeight();
\r
404 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
405 "LAST_DIRECTORY"), new String[] { "png" },
\r
406 new String[] { "Portable network graphics" },
\r
407 "Portable network graphics");
\r
409 chooser.setFileView(new jalview.io.JalviewFileView());
\r
410 chooser.setDialogTitle("Create PNG image from tree");
\r
411 chooser.setToolTipText("Save");
\r
413 int value = chooser.showSaveDialog(this);
\r
415 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
420 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
\r
421 chooser.getSelectedFile().getParent());
\r
423 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
\r
425 BufferedImage bi = new BufferedImage(width, height,
\r
426 BufferedImage.TYPE_INT_RGB);
\r
427 Graphics png = bi.getGraphics();
\r
429 treeCanvas.draw(png, width, height);
\r
431 ImageIO.write(bi, "png", out);
\r
434 catch (Exception ex)
\r
436 ex.printStackTrace();
\r