2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
21 import jalview.analysis.*;
23 import jalview.datamodel.*;
27 import jalview.jbgui.*;
29 import org.jibble.epsgraphics.*;
32 import java.awt.event.*;
33 import java.awt.image.*;
39 import javax.imageio.*;
41 import java.beans.PropertyChangeEvent;
50 public class TreePanel extends GTreePanel
54 TreeCanvas treeCanvas;
59 * Creates a new TreePanel object.
61 * @param av DOCUMENT ME!
62 * @param seqVector DOCUMENT ME!
63 * @param type DOCUMENT ME!
64 * @param pwtype DOCUMENT ME!
65 * @param s DOCUMENT ME!
66 * @param e DOCUMENT ME!
68 public TreePanel(AlignViewport av, String type, String pwtype)
71 initTreePanel(av, type, pwtype, null);
73 // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
74 // showDistances(true);
78 * Creates a new TreePanel object.
80 * @param av DOCUMENT ME!
81 * @param seqVector DOCUMENT ME!
82 * @param newtree DOCUMENT ME!
83 * @param type DOCUMENT ME!
84 * @param pwtype DOCUMENT ME!
86 public TreePanel(AlignViewport av,
92 initTreePanel(av, type, pwtype, newtree);
95 public AlignmentI getAlignment()
97 return treeCanvas.av.getAlignment();
101 void initTreePanel(AlignViewport av, String type, String pwtype,
106 this.pwtype = pwtype;
108 treeCanvas = new TreeCanvas(av, scrollPane);
109 scrollPane.setViewportView(treeCanvas);
111 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
113 public void propertyChange(PropertyChangeEvent evt)
115 if (evt.getPropertyName().equals("alignment"))
118 System.out.println("tree is null");
119 if(evt.getNewValue()==null)
120 System.out.println("new value is null");
122 tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
132 TreeLoader tl = new TreeLoader(newTree);
137 class TreeLoader extends Thread
140 jalview.datamodel.AlignmentView odata=null;
141 public TreeLoader(NewickFile newtree)
143 this.newtree = newtree;
146 // Must be outside run(), as Jalview2XML tries to
147 // update distance/bootstrap visibility at the same time
148 showBootstrap(newtree.HasBootstrap());
149 showDistances(newtree.HasDistances());
159 tree = new NJTree(av.alignment.getSequencesArray(),
162 tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
164 if (!tree.hasOriginalSequenceData())
165 allowOriginalSeqData(false);
171 AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
172 if(av.getSelectionGroup()==null)
175 end = av.alignment.getWidth();
176 seqs = av.alignment.getSequencesArray();
180 start = av.getSelectionGroup().getStartRes();
181 end = av.getSelectionGroup().getEndRes()+1;
182 seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
185 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
190 tree.reCount(tree.getTopNode());
191 tree.findHeight(tree.getTopNode());
192 treeCanvas.setTree(tree);
193 treeCanvas.repaint();
194 av.setCurrentTree(tree);
199 public void showDistances(boolean b)
201 treeCanvas.setShowDistances(b);
202 distanceMenu.setSelected(b);
205 public void showBootstrap(boolean b)
207 treeCanvas.setShowBootstrap(b);
208 bootstrapMenu.setSelected(b);
211 public void showPlaceholders(boolean b)
213 placeholdersMenu.setState(b);
214 treeCanvas.setMarkPlaceholders(b);
217 private void allowOriginalSeqData(boolean b) {
218 originalSeqData.setVisible(b);
226 * @return DOCUMENT ME!
228 public NJTree getTree()
237 * @param e DOCUMENT ME!
239 public void textbox_actionPerformed(ActionEvent e)
241 CutAndPasteTransfer cap = new CutAndPasteTransfer();
243 StringBuffer buffer = new StringBuffer();
245 if (type.equals("AV"))
247 buffer.append("Average distance tree using ");
251 buffer.append("Neighbour joining tree using ");
254 if (pwtype.equals("BL"))
256 buffer.append("BLOSUM62");
260 buffer.append("PID");
263 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
265 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
266 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
272 * @param e DOCUMENT ME!
274 public void saveAsNewick_actionPerformed(ActionEvent e)
276 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
278 chooser.setFileView(new JalviewFileView());
279 chooser.setDialogTitle("Save tree as newick file");
280 chooser.setToolTipText("Save");
282 int value = chooser.showSaveDialog(null);
284 if (value == JalviewFileChooser.APPROVE_OPTION)
286 String choice = chooser.getSelectedFile().getPath();
287 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
288 chooser.getSelectedFile().getParent());
292 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
293 String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
294 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
301 ex.printStackTrace();
309 * @param e DOCUMENT ME!
311 public void printMenu_actionPerformed(ActionEvent e)
313 //Putting in a thread avoids Swing painting problems
314 treeCanvas.startPrinting();
318 public void originalSeqData_actionPerformed(ActionEvent e)
320 if (!tree.hasOriginalSequenceData())
322 jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
325 // decide if av alignment is sufficiently different to original data to warrant a new window to be created
326 // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
327 // or create a selection box around columns in alignment view
328 // test Alignment(SeqCigar[])
329 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
333 if (alAndColsel != null && alAndColsel[0]!=null)
335 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
337 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
338 Alignment dataset = av.getAlignment().getDataset();
341 al.setDataset(dataset);
347 AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1]);
349 //>>>This is a fix for the moment, until a better solution is found!!<<<
350 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
352 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
355 Desktop.addInternalFrame(af, "Original Data for " + this.title,
356 AlignFrame.NEW_WINDOW_WIDTH,
357 AlignFrame.NEW_WINDOW_HEIGHT);
366 * @param e DOCUMENT ME!
368 public void fitToWindow_actionPerformed(ActionEvent e)
370 treeCanvas.fitToWindow = fitToWindow.isSelected();
377 * @param e DOCUMENT ME!
379 public void font_actionPerformed(ActionEvent e)
381 if (treeCanvas == null)
386 new FontChooser(this);
389 public Font getTreeFont()
391 return treeCanvas.font;
394 public void setTreeFont(Font font)
397 treeCanvas.setFont(font);
403 * @param e DOCUMENT ME!
405 public void distanceMenu_actionPerformed(ActionEvent e)
407 treeCanvas.setShowDistances(distanceMenu.isSelected());
413 * @param e DOCUMENT ME!
415 public void bootstrapMenu_actionPerformed(ActionEvent e)
417 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
423 * @param e DOCUMENT ME!
425 public void placeholdersMenu_actionPerformed(ActionEvent e)
427 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
433 * @param e DOCUMENT ME!
435 public void epsTree_actionPerformed(ActionEvent e)
437 boolean accurateText = true;
439 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
442 // If we need to prompt, and if the GUI is visible then
443 // Prompt for EPS rendering style
444 if (renderStyle.equalsIgnoreCase("Prompt each time")
446 (System.getProperty("java.awt.headless") != null
447 && System.getProperty("java.awt.headless").equals("true")))
449 EPSOptions eps = new EPSOptions();
450 renderStyle = eps.getValue();
452 if (renderStyle==null || eps.cancelled)
458 if (renderStyle.equalsIgnoreCase("text"))
460 accurateText = false;
463 int width = treeCanvas.getWidth();
464 int height = treeCanvas.getHeight();
468 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
469 "LAST_DIRECTORY"), new String[] { "eps" },
470 new String[] { "Encapsulated Postscript" },
471 "Encapsulated Postscript");
472 chooser.setFileView(new jalview.io.JalviewFileView());
473 chooser.setDialogTitle("Create EPS file from tree");
474 chooser.setToolTipText("Save");
476 int value = chooser.showSaveDialog(this);
478 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
483 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
484 chooser.getSelectedFile().getParent());
486 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
487 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
490 pg.setAccurateTextMode(accurateText);
492 treeCanvas.draw(pg, width, height);
499 ex.printStackTrace();
506 * @param e DOCUMENT ME!
508 public void pngTree_actionPerformed(ActionEvent e)
510 int width = treeCanvas.getWidth();
511 int height = treeCanvas.getHeight();
515 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
516 "LAST_DIRECTORY"), new String[] { "png" },
517 new String[] { "Portable network graphics" },
518 "Portable network graphics");
520 chooser.setFileView(new jalview.io.JalviewFileView());
521 chooser.setDialogTitle("Create PNG image from tree");
522 chooser.setToolTipText("Save");
524 int value = chooser.showSaveDialog(this);
526 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
531 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
532 chooser.getSelectedFile().getParent());
534 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
536 BufferedImage bi = new BufferedImage(width, height,
537 BufferedImage.TYPE_INT_RGB);
538 Graphics png = bi.getGraphics();
540 treeCanvas.draw(png, width, height);
542 ImageIO.write(bi, "png", out);
547 ex.printStackTrace();