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 buildAssociatedViewMenu();
122 treeCanvas = new TreeCanvas(ap, scrollPane);
123 scrollPane.setViewportView(treeCanvas);
125 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
127 public void propertyChange(PropertyChangeEvent evt)
129 if (evt.getPropertyName().equals("alignment"))
132 System.out.println("tree is null");
133 if(evt.getNewValue()==null)
134 System.out.println("new alignment sequences vector value is null");
136 tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
137 treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes
143 TreeLoader tl = new TreeLoader(newTree);
144 if (inputData!=null) {
151 void buildAssociatedViewMenu()
153 AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
156 associateLeavesMenu.setVisible(false);
159 associateLeavesMenu.addSeparator();
161 JRadioButtonMenuItem item;
162 ButtonGroup buttonGroup = new ButtonGroup();
163 int i, iSize = aps.length;
164 for(i=0; i<iSize; i++)
166 final AlignmentPanel ap = aps[i];
167 item = new JRadioButtonMenuItem(ap.av.viewName, ap.av==av );
168 buttonGroup.add(item);
169 item.addActionListener(new ActionListener()
171 public void actionPerformed(ActionEvent evt)
173 treeCanvas.applyToAllViews = false;
175 treeCanvas.av = ap.av;
176 PaintRefresher.RemoveComponent(treeCanvas);
177 PaintRefresher.Register(treeCanvas, ap.av.getSequenceSetId());
181 associateLeavesMenu.add(item);
184 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
185 buttonGroup.add(itemf);
186 itemf.addActionListener(new ActionListener()
188 public void actionPerformed(ActionEvent evt)
190 treeCanvas.applyToAllViews = itemf.isSelected();
193 associateLeavesMenu.add(itemf);
197 class TreeLoader extends Thread
200 jalview.datamodel.AlignmentView odata=null;
201 public TreeLoader(NewickFile newtree)
203 this.newtree = newtree;
206 // Must be outside run(), as Jalview2XML tries to
207 // update distance/bootstrap visibility at the same time
208 showBootstrap(newtree.HasBootstrap());
209 showDistances(newtree.HasDistances());
219 tree = new NJTree(av.alignment.getSequencesArray(),
222 tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
224 if (!tree.hasOriginalSequenceData())
225 allowOriginalSeqData(false);
231 AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
232 if(av.getSelectionGroup()==null)
235 end = av.alignment.getWidth();
236 seqs = av.alignment.getSequencesArray();
240 start = av.getSelectionGroup().getStartRes();
241 end = av.getSelectionGroup().getEndRes()+1;
242 seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
245 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
250 tree.reCount(tree.getTopNode());
251 tree.findHeight(tree.getTopNode());
252 treeCanvas.setTree(tree);
253 treeCanvas.repaint();
254 av.setCurrentTree(tree);
259 public void showDistances(boolean b)
261 treeCanvas.setShowDistances(b);
262 distanceMenu.setSelected(b);
265 public void showBootstrap(boolean b)
267 treeCanvas.setShowBootstrap(b);
268 bootstrapMenu.setSelected(b);
271 public void showPlaceholders(boolean b)
273 placeholdersMenu.setState(b);
274 treeCanvas.setMarkPlaceholders(b);
277 private void allowOriginalSeqData(boolean b) {
278 originalSeqData.setVisible(b);
286 * @return DOCUMENT ME!
288 public NJTree getTree()
297 * @param e DOCUMENT ME!
299 public void textbox_actionPerformed(ActionEvent e)
301 CutAndPasteTransfer cap = new CutAndPasteTransfer();
303 StringBuffer buffer = new StringBuffer();
305 if (type.equals("AV"))
307 buffer.append("Average distance tree using ");
311 buffer.append("Neighbour joining tree using ");
314 if (pwtype.equals("BL"))
316 buffer.append("BLOSUM62");
320 buffer.append("PID");
323 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
325 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
326 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
332 * @param e DOCUMENT ME!
334 public void saveAsNewick_actionPerformed(ActionEvent e)
336 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
338 chooser.setFileView(new JalviewFileView());
339 chooser.setDialogTitle("Save tree as newick file");
340 chooser.setToolTipText("Save");
342 int value = chooser.showSaveDialog(null);
344 if (value == JalviewFileChooser.APPROVE_OPTION)
346 String choice = chooser.getSelectedFile().getPath();
347 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
348 chooser.getSelectedFile().getParent());
352 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
353 String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
354 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
361 ex.printStackTrace();
369 * @param e DOCUMENT ME!
371 public void printMenu_actionPerformed(ActionEvent e)
373 //Putting in a thread avoids Swing painting problems
374 treeCanvas.startPrinting();
378 public void originalSeqData_actionPerformed(ActionEvent e)
380 if (!tree.hasOriginalSequenceData())
382 jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
385 // decide if av alignment is sufficiently different to original data to warrant a new window to be created
386 // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
387 // or create a selection box around columns in alignment view
388 // test Alignment(SeqCigar[])
389 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
393 if (alAndColsel != null && alAndColsel[0]!=null)
395 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
397 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
398 Alignment dataset = av.getAlignment().getDataset();
401 al.setDataset(dataset);
407 AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
408 AlignFrame.DEFAULT_WIDTH,
409 AlignFrame.DEFAULT_HEIGHT
412 //>>>This is a fix for the moment, until a better solution is found!!<<<
413 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
415 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
418 Desktop.addInternalFrame(af, "Original Data for " + this.title,
419 AlignFrame.DEFAULT_WIDTH,
420 AlignFrame.DEFAULT_HEIGHT);
429 * @param e DOCUMENT ME!
431 public void fitToWindow_actionPerformed(ActionEvent e)
433 treeCanvas.fitToWindow = fitToWindow.isSelected();
440 * @param e DOCUMENT ME!
442 public void font_actionPerformed(ActionEvent e)
444 if (treeCanvas == null)
449 new FontChooser(this);
452 public Font getTreeFont()
454 return treeCanvas.font;
457 public void setTreeFont(Font font)
460 treeCanvas.setFont(font);
466 * @param e DOCUMENT ME!
468 public void distanceMenu_actionPerformed(ActionEvent e)
470 treeCanvas.setShowDistances(distanceMenu.isSelected());
476 * @param e DOCUMENT ME!
478 public void bootstrapMenu_actionPerformed(ActionEvent e)
480 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
486 * @param e DOCUMENT ME!
488 public void placeholdersMenu_actionPerformed(ActionEvent e)
490 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
496 * @param e DOCUMENT ME!
498 public void epsTree_actionPerformed(ActionEvent e)
500 boolean accurateText = true;
502 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
505 // If we need to prompt, and if the GUI is visible then
506 // Prompt for EPS rendering style
507 if (renderStyle.equalsIgnoreCase("Prompt each time")
509 (System.getProperty("java.awt.headless") != null
510 && System.getProperty("java.awt.headless").equals("true")))
512 EPSOptions eps = new EPSOptions();
513 renderStyle = eps.getValue();
515 if (renderStyle==null || eps.cancelled)
521 if (renderStyle.equalsIgnoreCase("text"))
523 accurateText = false;
526 int width = treeCanvas.getWidth();
527 int height = treeCanvas.getHeight();
531 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
532 "LAST_DIRECTORY"), new String[] { "eps" },
533 new String[] { "Encapsulated Postscript" },
534 "Encapsulated Postscript");
535 chooser.setFileView(new jalview.io.JalviewFileView());
536 chooser.setDialogTitle("Create EPS file from tree");
537 chooser.setToolTipText("Save");
539 int value = chooser.showSaveDialog(this);
541 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
546 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
547 chooser.getSelectedFile().getParent());
549 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
550 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
553 pg.setAccurateTextMode(accurateText);
555 treeCanvas.draw(pg, width, height);
562 ex.printStackTrace();
569 * @param e DOCUMENT ME!
571 public void pngTree_actionPerformed(ActionEvent e)
573 int width = treeCanvas.getWidth();
574 int height = treeCanvas.getHeight();
578 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
579 "LAST_DIRECTORY"), new String[] { "png" },
580 new String[] { "Portable network graphics" },
581 "Portable network graphics");
583 chooser.setFileView(new jalview.io.JalviewFileView());
584 chooser.setDialogTitle("Create PNG image from tree");
585 chooser.setToolTipText("Save");
587 int value = chooser.showSaveDialog(this);
589 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
594 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
595 chooser.getSelectedFile().getParent());
597 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
599 BufferedImage bi = new BufferedImage(width, height,
600 BufferedImage.TYPE_INT_RGB);
601 Graphics png = bi.getGraphics();
603 treeCanvas.draw(png, width, height);
605 ImageIO.write(bi, "png", out);
610 ex.printStackTrace();