2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 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
24 import javax.imageio.*;
27 import java.awt.event.*;
28 import java.awt.image.*;
31 import org.jibble.epsgraphics.*;
32 import jalview.analysis.*;
33 import jalview.datamodel.*;
35 import jalview.jbgui.*;
43 public class TreePanel extends GTreePanel
49 TreeCanvas treeCanvas;
56 * Creates a new TreePanel object.
71 public TreePanel(AlignmentPanel ap, String type, String pwtype)
74 initTreePanel(ap, type, pwtype, null, null);
76 // We know this tree has distances. JBPNote TODO: prolly should add this as
77 // a userdefined default
78 // showDistances(true);
82 * Creates a new TreePanel object.
95 public TreePanel(AlignmentPanel ap, String type, String pwtype,
99 initTreePanel(ap, type, pwtype, newtree, null);
102 public TreePanel(AlignmentPanel av, String type, String pwtype,
103 NewickFile newtree, AlignmentView inputData)
106 initTreePanel(av, type, pwtype, newtree, inputData);
109 public AlignmentI getAlignment()
111 return treeCanvas.av.getAlignment();
114 public AlignViewport getViewPort()
116 return treeCanvas.av;
119 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
120 NewickFile newTree, AlignmentView inputData)
125 this.pwtype = pwtype;
127 treeCanvas = new TreeCanvas(this, ap, scrollPane);
128 scrollPane.setViewportView(treeCanvas);
130 PaintRefresher.Register(this, ap.av.getSequenceSetId());
132 buildAssociatedViewMenu();
134 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
136 public void propertyChange(PropertyChangeEvent evt)
138 if (evt.getPropertyName().equals("alignment"))
142 System.out.println("tree is null");
144 if (evt.getNewValue() == null)
147 .println("new alignment sequences vector value is null");
150 tree.UpdatePlaceHolders((Vector) evt.getNewValue());
151 treeCanvas.nameHash.clear(); // reset the mapping between canvas
152 // rectangles and leafnodes
158 TreeLoader tl = new TreeLoader(newTree);
159 if (inputData != null)
161 tl.odata = inputData;
167 public void viewMenu_menuSelected()
169 buildAssociatedViewMenu();
172 void buildAssociatedViewMenu()
174 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
175 .getSequenceSetId());
176 if (aps.length == 1 && treeCanvas.ap == aps[0])
178 associateLeavesMenu.setVisible(false);
182 associateLeavesMenu.setVisible(true);
184 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
186 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
189 associateLeavesMenu.removeAll();
191 JRadioButtonMenuItem item;
192 ButtonGroup buttonGroup = new ButtonGroup();
193 int i, iSize = aps.length;
194 final TreePanel thisTreePanel = this;
195 for (i = 0; i < iSize; i++)
197 final AlignmentPanel ap = aps[i];
198 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
199 buttonGroup.add(item);
200 item.addActionListener(new ActionListener()
202 public void actionPerformed(ActionEvent evt)
204 treeCanvas.applyToAllViews = false;
206 treeCanvas.av = ap.av;
207 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
211 associateLeavesMenu.add(item);
214 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
215 buttonGroup.add(itemf);
216 itemf.setSelected(treeCanvas.applyToAllViews);
217 itemf.addActionListener(new ActionListener()
219 public void actionPerformed(ActionEvent evt)
221 treeCanvas.applyToAllViews = itemf.isSelected();
224 associateLeavesMenu.add(itemf);
228 class TreeLoader extends Thread
232 jalview.datamodel.AlignmentView odata = null;
234 public TreeLoader(NewickFile newtree)
236 this.newtree = newtree;
239 // Must be outside run(), as Jalview2XML tries to
240 // update distance/bootstrap visibility at the same time
241 showBootstrap(newtree.HasBootstrap());
242 showDistances(newtree.HasDistances());
253 tree = new NJTree(av.alignment.getSequencesArray(), newtree);
257 tree = new NJTree(av.alignment.getSequencesArray(), odata,
260 if (!tree.hasOriginalSequenceData())
262 allowOriginalSeqData(false);
269 AlignmentView seqStrings = av.getAlignmentView(av
270 .getSelectionGroup() != null);
271 if (av.getSelectionGroup() == null)
274 end = av.alignment.getWidth();
275 seqs = av.alignment.getSequencesArray();
279 start = av.getSelectionGroup().getStartRes();
280 end = av.getSelectionGroup().getEndRes() + 1;
281 seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
284 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
288 tree.reCount(tree.getTopNode());
289 tree.findHeight(tree.getTopNode());
290 treeCanvas.setTree(tree);
291 treeCanvas.repaint();
292 av.setCurrentTree(tree);
297 public void showDistances(boolean b)
299 treeCanvas.setShowDistances(b);
300 distanceMenu.setSelected(b);
303 public void showBootstrap(boolean b)
305 treeCanvas.setShowBootstrap(b);
306 bootstrapMenu.setSelected(b);
309 public void showPlaceholders(boolean b)
311 placeholdersMenu.setState(b);
312 treeCanvas.setMarkPlaceholders(b);
315 private void allowOriginalSeqData(boolean b)
317 originalSeqData.setVisible(b);
323 * @return DOCUMENT ME!
325 public NJTree getTree()
336 public void textbox_actionPerformed(ActionEvent e)
338 CutAndPasteTransfer cap = new CutAndPasteTransfer();
340 StringBuffer buffer = new StringBuffer();
342 if (type.equals("AV"))
344 buffer.append("Average distance tree using ");
348 buffer.append("Neighbour joining tree using ");
351 if (pwtype.equals("BL"))
353 buffer.append("BLOSUM62");
357 buffer.append("PID");
360 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
362 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
364 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
365 tree.isHasRootDistance()));
374 public void saveAsNewick_actionPerformed(ActionEvent e)
376 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
377 .getProperty("LAST_DIRECTORY"));
378 chooser.setFileView(new JalviewFileView());
379 chooser.setDialogTitle("Save tree as newick file");
380 chooser.setToolTipText("Save");
382 int value = chooser.showSaveDialog(null);
384 if (value == JalviewFileChooser.APPROVE_OPTION)
386 String choice = chooser.getSelectedFile().getPath();
387 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
388 .getSelectedFile().getParent());
392 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
394 String output = fout.print(tree.isHasBootstrap(), tree
395 .isHasDistances(), tree.isHasRootDistance());
396 java.io.PrintWriter out = new java.io.PrintWriter(
397 new java.io.FileWriter(choice));
400 } catch (Exception ex)
402 ex.printStackTrace();
413 public void printMenu_actionPerformed(ActionEvent e)
415 // Putting in a thread avoids Swing painting problems
416 treeCanvas.startPrinting();
419 public void originalSeqData_actionPerformed(ActionEvent e)
421 if (!tree.hasOriginalSequenceData())
423 jalview.bin.Cache.log
424 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
427 // decide if av alignment is sufficiently different to original data to
428 // warrant a new window to be created
429 // create new alignmnt window with hidden regions (unhiding hidden regions
430 // yields unaligned seqs)
431 // or create a selection box around columns in alignment view
432 // test Alignment(SeqCigar[])
436 // we try to get the associated view's gap character
437 // but this may fail if the view was closed...
438 gc = av.getGapCharacter();
440 } catch (Exception ex)
444 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
446 if (alAndColsel != null && alAndColsel[0] != null)
448 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
450 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
451 Alignment dataset = (av != null && av.getAlignment() != null) ? av
452 .getAlignment().getDataset() : null;
455 al.setDataset(dataset);
461 AlignFrame af = new AlignFrame(al,
462 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
463 AlignFrame.DEFAULT_HEIGHT);
465 // >>>This is a fix for the moment, until a better solution is
467 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
469 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
472 Desktop.addInternalFrame(af, "Original Data for " + this.title,
473 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
484 public void fitToWindow_actionPerformed(ActionEvent e)
486 treeCanvas.fitToWindow = fitToWindow.isSelected();
496 public void font_actionPerformed(ActionEvent e)
498 if (treeCanvas == null)
503 new FontChooser(this);
506 public Font getTreeFont()
508 return treeCanvas.font;
511 public void setTreeFont(Font font)
513 if (treeCanvas != null)
515 treeCanvas.setFont(font);
525 public void distanceMenu_actionPerformed(ActionEvent e)
527 treeCanvas.setShowDistances(distanceMenu.isSelected());
536 public void bootstrapMenu_actionPerformed(ActionEvent e)
538 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
547 public void placeholdersMenu_actionPerformed(ActionEvent e)
549 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
558 public void epsTree_actionPerformed(ActionEvent e)
560 boolean accurateText = true;
562 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
565 // If we need to prompt, and if the GUI is visible then
566 // Prompt for EPS rendering style
567 if (renderStyle.equalsIgnoreCase("Prompt each time")
568 && !(System.getProperty("java.awt.headless") != null && System
569 .getProperty("java.awt.headless").equals("true")))
571 EPSOptions eps = new EPSOptions();
572 renderStyle = eps.getValue();
574 if (renderStyle == null || eps.cancelled)
581 if (renderStyle.equalsIgnoreCase("text"))
583 accurateText = false;
586 int width = treeCanvas.getWidth();
587 int height = treeCanvas.getHeight();
591 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
592 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
593 { "eps" }, new String[]
594 { "Encapsulated Postscript" }, "Encapsulated Postscript");
595 chooser.setFileView(new jalview.io.JalviewFileView());
596 chooser.setDialogTitle("Create EPS file from tree");
597 chooser.setToolTipText("Save");
599 int value = chooser.showSaveDialog(this);
601 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
606 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
607 .getSelectedFile().getParent());
609 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
610 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
612 pg.setAccurateTextMode(accurateText);
614 treeCanvas.draw(pg, width, height);
618 } catch (Exception ex)
620 ex.printStackTrace();
630 public void pngTree_actionPerformed(ActionEvent e)
632 int width = treeCanvas.getWidth();
633 int height = treeCanvas.getHeight();
637 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
638 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
639 { "png" }, new String[]
640 { "Portable network graphics" }, "Portable network graphics");
642 chooser.setFileView(new jalview.io.JalviewFileView());
643 chooser.setDialogTitle("Create PNG image from tree");
644 chooser.setToolTipText("Save");
646 int value = chooser.showSaveDialog(this);
648 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
653 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
654 .getSelectedFile().getParent());
656 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
658 BufferedImage bi = new BufferedImage(width, height,
659 BufferedImage.TYPE_INT_RGB);
660 Graphics png = bi.getGraphics();
662 treeCanvas.draw(png, width, height);
664 ImageIO.write(bi, "png", out);
666 } catch (Exception ex)
668 ex.printStackTrace();