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.*;
40 import javax.imageio.*;
42 import java.beans.PropertyChangeEvent;
51 public class TreePanel extends GTreePanel
55 TreeCanvas treeCanvas;
60 * Creates a new TreePanel object.
62 * @param av DOCUMENT ME!
63 * @param seqVector DOCUMENT ME!
64 * @param type DOCUMENT ME!
65 * @param pwtype DOCUMENT ME!
66 * @param s DOCUMENT ME!
67 * @param e DOCUMENT ME!
69 public TreePanel(AlignmentPanel ap, String type, String pwtype)
72 initTreePanel(ap, type, pwtype, null, null);
74 // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
75 // showDistances(true);
79 * Creates a new TreePanel object.
81 * @param av DOCUMENT ME!
82 * @param seqVector DOCUMENT ME!
83 * @param newtree DOCUMENT ME!
84 * @param type DOCUMENT ME!
85 * @param pwtype DOCUMENT ME!
87 public TreePanel(AlignmentPanel ap,
93 initTreePanel(ap, type, pwtype, newtree, null);
96 public TreePanel(AlignmentPanel av,
99 NewickFile newtree, AlignmentView inputData) {
101 initTreePanel(av,type,pwtype,newtree,inputData);
104 public AlignmentI getAlignment()
106 return treeCanvas.av.getAlignment();
108 public AlignViewport getViewPort() {
109 return treeCanvas.av;
112 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
113 NewickFile newTree, AlignmentView inputData)
118 this.pwtype = pwtype;
120 treeCanvas = new TreeCanvas(this, ap, scrollPane);
121 scrollPane.setViewportView(treeCanvas);
123 PaintRefresher.Register(this, ap.av.getSequenceSetId());
125 buildAssociatedViewMenu();
127 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
129 public void propertyChange(PropertyChangeEvent evt)
131 if (evt.getPropertyName().equals("alignment"))
134 System.out.println("tree is null");
135 if(evt.getNewValue()==null)
136 System.out.println("new alignment sequences vector value is null");
138 tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
139 treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes
145 TreeLoader tl = new TreeLoader(newTree);
146 if (inputData!=null) {
153 public void viewMenu_menuSelected()
155 buildAssociatedViewMenu();
159 void buildAssociatedViewMenu()
161 AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
162 if(aps.length==1 && treeCanvas.ap==aps[0])
164 associateLeavesMenu.setVisible(false);
168 associateLeavesMenu.setVisible(true);
170 if( (viewMenu.getItem(viewMenu.getItemCount()-2) instanceof JMenuItem))
172 viewMenu.insertSeparator(viewMenu.getItemCount()-1);
175 associateLeavesMenu.removeAll();
178 JRadioButtonMenuItem item;
179 ButtonGroup buttonGroup = new ButtonGroup();
180 int i, iSize = aps.length;
181 final TreePanel thisTreePanel = this;
182 for(i=0; i<iSize; i++)
184 final AlignmentPanel ap = aps[i];
185 item = new JRadioButtonMenuItem(ap.av.viewName, ap==treeCanvas.ap );
186 buttonGroup.add(item);
187 item.addActionListener(new ActionListener()
189 public void actionPerformed(ActionEvent evt)
191 treeCanvas.applyToAllViews = false;
193 treeCanvas.av = ap.av;
194 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
198 associateLeavesMenu.add(item);
201 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
202 buttonGroup.add(itemf);
203 itemf.setSelected(treeCanvas.applyToAllViews);
204 itemf.addActionListener(new ActionListener()
206 public void actionPerformed(ActionEvent evt)
208 treeCanvas.applyToAllViews = itemf.isSelected();
211 associateLeavesMenu.add(itemf);
215 class TreeLoader extends Thread
218 jalview.datamodel.AlignmentView odata=null;
219 public TreeLoader(NewickFile newtree)
221 this.newtree = newtree;
224 // Must be outside run(), as Jalview2XML tries to
225 // update distance/bootstrap visibility at the same time
226 showBootstrap(newtree.HasBootstrap());
227 showDistances(newtree.HasDistances());
237 tree = new NJTree(av.alignment.getSequencesArray(),
240 tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
242 if (!tree.hasOriginalSequenceData())
243 allowOriginalSeqData(false);
249 AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
250 if(av.getSelectionGroup()==null)
253 end = av.alignment.getWidth();
254 seqs = av.alignment.getSequencesArray();
258 start = av.getSelectionGroup().getStartRes();
259 end = av.getSelectionGroup().getEndRes()+1;
260 seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
263 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
268 tree.reCount(tree.getTopNode());
269 tree.findHeight(tree.getTopNode());
270 treeCanvas.setTree(tree);
271 treeCanvas.repaint();
272 av.setCurrentTree(tree);
277 public void showDistances(boolean b)
279 treeCanvas.setShowDistances(b);
280 distanceMenu.setSelected(b);
283 public void showBootstrap(boolean b)
285 treeCanvas.setShowBootstrap(b);
286 bootstrapMenu.setSelected(b);
289 public void showPlaceholders(boolean b)
291 placeholdersMenu.setState(b);
292 treeCanvas.setMarkPlaceholders(b);
295 private void allowOriginalSeqData(boolean b) {
296 originalSeqData.setVisible(b);
304 * @return DOCUMENT ME!
306 public NJTree getTree()
315 * @param e DOCUMENT ME!
317 public void textbox_actionPerformed(ActionEvent e)
319 CutAndPasteTransfer cap = new CutAndPasteTransfer();
321 StringBuffer buffer = new StringBuffer();
323 if (type.equals("AV"))
325 buffer.append("Average distance tree using ");
329 buffer.append("Neighbour joining tree using ");
332 if (pwtype.equals("BL"))
334 buffer.append("BLOSUM62");
338 buffer.append("PID");
341 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
343 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
344 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
350 * @param e DOCUMENT ME!
352 public void saveAsNewick_actionPerformed(ActionEvent e)
354 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
356 chooser.setFileView(new JalviewFileView());
357 chooser.setDialogTitle("Save tree as newick file");
358 chooser.setToolTipText("Save");
360 int value = chooser.showSaveDialog(null);
362 if (value == JalviewFileChooser.APPROVE_OPTION)
364 String choice = chooser.getSelectedFile().getPath();
365 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
366 chooser.getSelectedFile().getParent());
370 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
371 String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
372 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
379 ex.printStackTrace();
387 * @param e DOCUMENT ME!
389 public void printMenu_actionPerformed(ActionEvent e)
391 //Putting in a thread avoids Swing painting problems
392 treeCanvas.startPrinting();
396 public void originalSeqData_actionPerformed(ActionEvent e)
398 if (!tree.hasOriginalSequenceData())
400 jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
403 // decide if av alignment is sufficiently different to original data to warrant a new window to be created
404 // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
405 // or create a selection box around columns in alignment view
406 // test Alignment(SeqCigar[])
407 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
411 if (alAndColsel != null && alAndColsel[0]!=null)
413 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
415 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
416 Alignment dataset = av.getAlignment().getDataset();
419 al.setDataset(dataset);
425 AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
426 AlignFrame.DEFAULT_WIDTH,
427 AlignFrame.DEFAULT_HEIGHT
430 //>>>This is a fix for the moment, until a better solution is found!!<<<
431 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
433 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
436 Desktop.addInternalFrame(af, "Original Data for " + this.title,
437 AlignFrame.DEFAULT_WIDTH,
438 AlignFrame.DEFAULT_HEIGHT);
447 * @param e DOCUMENT ME!
449 public void fitToWindow_actionPerformed(ActionEvent e)
451 treeCanvas.fitToWindow = fitToWindow.isSelected();
458 * @param e DOCUMENT ME!
460 public void font_actionPerformed(ActionEvent e)
462 if (treeCanvas == null)
467 new FontChooser(this);
470 public Font getTreeFont()
472 return treeCanvas.font;
475 public void setTreeFont(Font font)
478 treeCanvas.setFont(font);
484 * @param e DOCUMENT ME!
486 public void distanceMenu_actionPerformed(ActionEvent e)
488 treeCanvas.setShowDistances(distanceMenu.isSelected());
494 * @param e DOCUMENT ME!
496 public void bootstrapMenu_actionPerformed(ActionEvent e)
498 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
504 * @param e DOCUMENT ME!
506 public void placeholdersMenu_actionPerformed(ActionEvent e)
508 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
514 * @param e DOCUMENT ME!
516 public void epsTree_actionPerformed(ActionEvent e)
518 boolean accurateText = true;
520 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
523 // If we need to prompt, and if the GUI is visible then
524 // Prompt for EPS rendering style
525 if (renderStyle.equalsIgnoreCase("Prompt each time")
527 (System.getProperty("java.awt.headless") != null
528 && System.getProperty("java.awt.headless").equals("true")))
530 EPSOptions eps = new EPSOptions();
531 renderStyle = eps.getValue();
533 if (renderStyle==null || eps.cancelled)
539 if (renderStyle.equalsIgnoreCase("text"))
541 accurateText = false;
544 int width = treeCanvas.getWidth();
545 int height = treeCanvas.getHeight();
549 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
550 "LAST_DIRECTORY"), new String[] { "eps" },
551 new String[] { "Encapsulated Postscript" },
552 "Encapsulated Postscript");
553 chooser.setFileView(new jalview.io.JalviewFileView());
554 chooser.setDialogTitle("Create EPS file from tree");
555 chooser.setToolTipText("Save");
557 int value = chooser.showSaveDialog(this);
559 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
564 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
565 chooser.getSelectedFile().getParent());
567 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
568 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
571 pg.setAccurateTextMode(accurateText);
573 treeCanvas.draw(pg, width, height);
580 ex.printStackTrace();
587 * @param e DOCUMENT ME!
589 public void pngTree_actionPerformed(ActionEvent e)
591 int width = treeCanvas.getWidth();
592 int height = treeCanvas.getHeight();
596 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
597 "LAST_DIRECTORY"), new String[] { "png" },
598 new String[] { "Portable network graphics" },
599 "Portable network graphics");
601 chooser.setFileView(new jalview.io.JalviewFileView());
602 chooser.setDialogTitle("Create PNG image from tree");
603 chooser.setToolTipText("Save");
605 int value = chooser.showSaveDialog(this);
607 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
612 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
613 chooser.getSelectedFile().getParent());
615 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
617 BufferedImage bi = new BufferedImage(width, height,
618 BufferedImage.TYPE_INT_RGB);
619 Graphics png = bi.getGraphics();
621 treeCanvas.draw(png, width, height);
623 ImageIO.write(bi, "png", out);
628 ex.printStackTrace();