2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 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.commands.OrderCommand;
34 import jalview.datamodel.*;
36 import jalview.jbgui.*;
44 public class TreePanel extends GTreePanel
50 TreeCanvas treeCanvas;
57 * Creates a new TreePanel object.
72 public TreePanel(AlignmentPanel ap, String type, String pwtype)
75 initTreePanel(ap, type, pwtype, null, null);
77 // We know this tree has distances. JBPNote TODO: prolly should add this as
78 // a userdefined default
79 // showDistances(true);
83 * Creates a new TreePanel object.
96 public TreePanel(AlignmentPanel ap, String type, String pwtype,
100 initTreePanel(ap, type, pwtype, newtree, null);
103 public TreePanel(AlignmentPanel av, String type, String pwtype,
104 NewickFile newtree, AlignmentView inputData)
107 initTreePanel(av, type, pwtype, newtree, inputData);
110 public AlignmentI getAlignment()
112 return treeCanvas.av.getAlignment();
115 public AlignViewport getViewPort()
117 return treeCanvas.av;
120 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
121 NewickFile newTree, AlignmentView inputData)
126 this.pwtype = pwtype;
128 treeCanvas = new TreeCanvas(this, ap, scrollPane);
129 scrollPane.setViewportView(treeCanvas);
131 PaintRefresher.Register(this, ap.av.getSequenceSetId());
133 buildAssociatedViewMenu();
135 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
137 public void propertyChange(PropertyChangeEvent evt)
139 if (evt.getPropertyName().equals("alignment"))
143 System.out.println("tree is null");
145 if (evt.getNewValue() == null)
148 .println("new alignment sequences vector value is null");
151 tree.UpdatePlaceHolders((Vector) evt.getNewValue());
152 treeCanvas.nameHash.clear(); // reset the mapping between canvas
153 // rectangles and leafnodes
159 TreeLoader tl = new TreeLoader(newTree);
160 if (inputData != null)
162 tl.odata = inputData;
168 public void viewMenu_menuSelected()
170 buildAssociatedViewMenu();
173 void buildAssociatedViewMenu()
175 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
176 .getSequenceSetId());
177 if (aps.length == 1 && treeCanvas.ap == aps[0])
179 associateLeavesMenu.setVisible(false);
183 associateLeavesMenu.setVisible(true);
185 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
187 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
190 associateLeavesMenu.removeAll();
192 JRadioButtonMenuItem item;
193 ButtonGroup buttonGroup = new ButtonGroup();
194 int i, iSize = aps.length;
195 final TreePanel thisTreePanel = this;
196 for (i = 0; i < iSize; i++)
198 final AlignmentPanel ap = aps[i];
199 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
200 buttonGroup.add(item);
201 item.addActionListener(new ActionListener()
203 public void actionPerformed(ActionEvent evt)
205 treeCanvas.applyToAllViews = false;
207 treeCanvas.av = ap.av;
208 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
212 associateLeavesMenu.add(item);
215 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
216 buttonGroup.add(itemf);
217 itemf.setSelected(treeCanvas.applyToAllViews);
218 itemf.addActionListener(new ActionListener()
220 public void actionPerformed(ActionEvent evt)
222 treeCanvas.applyToAllViews = itemf.isSelected();
225 associateLeavesMenu.add(itemf);
229 class TreeLoader extends Thread
233 jalview.datamodel.AlignmentView odata = null;
235 public TreeLoader(NewickFile newtree)
237 this.newtree = newtree;
240 // Must be outside run(), as Jalview2XML tries to
241 // update distance/bootstrap visibility at the same time
242 showBootstrap(newtree.HasBootstrap());
243 showDistances(newtree.HasDistances());
254 tree = new NJTree(av.alignment.getSequencesArray(), newtree);
258 tree = new NJTree(av.alignment.getSequencesArray(), odata,
261 if (!tree.hasOriginalSequenceData())
263 allowOriginalSeqData(false);
270 AlignmentView seqStrings = av.getAlignmentView(av
271 .getSelectionGroup() != null);
272 if (av.getSelectionGroup() == null)
275 end = av.alignment.getWidth();
276 seqs = av.alignment.getSequencesArray();
280 start = av.getSelectionGroup().getStartRes();
281 end = av.getSelectionGroup().getEndRes() + 1;
282 seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
285 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
289 tree.reCount(tree.getTopNode());
290 tree.findHeight(tree.getTopNode());
291 treeCanvas.setTree(tree);
292 treeCanvas.repaint();
293 av.setCurrentTree(tree);
294 if (av.getSortByTree())
296 sortByTree_actionPerformed(null);
301 public void showDistances(boolean b)
303 treeCanvas.setShowDistances(b);
304 distanceMenu.setSelected(b);
307 public void showBootstrap(boolean b)
309 treeCanvas.setShowBootstrap(b);
310 bootstrapMenu.setSelected(b);
313 public void showPlaceholders(boolean b)
315 placeholdersMenu.setState(b);
316 treeCanvas.setMarkPlaceholders(b);
319 private void allowOriginalSeqData(boolean b)
321 originalSeqData.setVisible(b);
327 * @return DOCUMENT ME!
329 public NJTree getTree()
340 public void textbox_actionPerformed(ActionEvent e)
342 CutAndPasteTransfer cap = new CutAndPasteTransfer();
344 StringBuffer buffer = new StringBuffer();
346 if (type.equals("AV"))
348 buffer.append("Average distance tree using ");
352 buffer.append("Neighbour joining tree using ");
355 if (pwtype.equals("BL"))
357 buffer.append("BLOSUM62");
361 buffer.append("PID");
364 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
366 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
368 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
369 tree.isHasRootDistance()));
378 public void saveAsNewick_actionPerformed(ActionEvent e)
380 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
381 .getProperty("LAST_DIRECTORY"));
382 chooser.setFileView(new JalviewFileView());
383 chooser.setDialogTitle("Save tree as newick file");
384 chooser.setToolTipText("Save");
386 int value = chooser.showSaveDialog(null);
388 if (value == JalviewFileChooser.APPROVE_OPTION)
390 String choice = chooser.getSelectedFile().getPath();
391 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
392 .getSelectedFile().getParent());
396 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
398 String output = fout.print(tree.isHasBootstrap(), tree
399 .isHasDistances(), tree.isHasRootDistance());
400 java.io.PrintWriter out = new java.io.PrintWriter(
401 new java.io.FileWriter(choice));
404 } catch (Exception ex)
406 ex.printStackTrace();
417 public void printMenu_actionPerformed(ActionEvent e)
419 // Putting in a thread avoids Swing painting problems
420 treeCanvas.startPrinting();
423 public void originalSeqData_actionPerformed(ActionEvent e)
425 if (!tree.hasOriginalSequenceData())
427 jalview.bin.Cache.log
428 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
431 // decide if av alignment is sufficiently different to original data to
432 // warrant a new window to be created
433 // create new alignmnt window with hidden regions (unhiding hidden regions
434 // yields unaligned seqs)
435 // or create a selection box around columns in alignment view
436 // test Alignment(SeqCigar[])
440 // we try to get the associated view's gap character
441 // but this may fail if the view was closed...
442 gc = av.getGapCharacter();
444 } catch (Exception ex)
448 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
450 if (alAndColsel != null && alAndColsel[0] != null)
452 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
454 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
455 Alignment dataset = (av != null && av.getAlignment() != null) ? av
456 .getAlignment().getDataset() : null;
459 al.setDataset(dataset);
465 AlignFrame af = new AlignFrame(al,
466 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
467 AlignFrame.DEFAULT_HEIGHT);
469 // >>>This is a fix for the moment, until a better solution is
471 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
473 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
476 Desktop.addInternalFrame(af, "Original Data for " + this.title,
477 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
488 public void fitToWindow_actionPerformed(ActionEvent e)
490 treeCanvas.fitToWindow = fitToWindow.isSelected();
495 * sort the associated alignment view by the current tree.
498 public void sortByTree_actionPerformed(ActionEvent e)
500 AlignmentPanel ap = av.getAlignPanel();
501 SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
502 AlignmentSorter.sortByTree(av.getAlignment(), tree);
505 .addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
508 ap.paintAlignment(true);
518 public void font_actionPerformed(ActionEvent e)
520 if (treeCanvas == null)
525 new FontChooser(this);
528 public Font getTreeFont()
530 return treeCanvas.font;
533 public void setTreeFont(Font font)
535 if (treeCanvas != null)
537 treeCanvas.setFont(font);
547 public void distanceMenu_actionPerformed(ActionEvent e)
549 treeCanvas.setShowDistances(distanceMenu.isSelected());
558 public void bootstrapMenu_actionPerformed(ActionEvent e)
560 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
569 public void placeholdersMenu_actionPerformed(ActionEvent e)
571 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
580 public void epsTree_actionPerformed(ActionEvent e)
582 boolean accurateText = true;
584 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
587 // If we need to prompt, and if the GUI is visible then
588 // Prompt for EPS rendering style
589 if (renderStyle.equalsIgnoreCase("Prompt each time")
590 && !(System.getProperty("java.awt.headless") != null && System
591 .getProperty("java.awt.headless").equals("true")))
593 EPSOptions eps = new EPSOptions();
594 renderStyle = eps.getValue();
596 if (renderStyle == null || eps.cancelled)
603 if (renderStyle.equalsIgnoreCase("text"))
605 accurateText = false;
608 int width = treeCanvas.getWidth();
609 int height = treeCanvas.getHeight();
613 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
614 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
615 { "eps" }, new String[]
616 { "Encapsulated Postscript" }, "Encapsulated Postscript");
617 chooser.setFileView(new jalview.io.JalviewFileView());
618 chooser.setDialogTitle("Create EPS file from tree");
619 chooser.setToolTipText("Save");
621 int value = chooser.showSaveDialog(this);
623 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
628 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
629 .getSelectedFile().getParent());
631 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
632 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
634 pg.setAccurateTextMode(accurateText);
636 treeCanvas.draw(pg, width, height);
640 } catch (Exception ex)
642 ex.printStackTrace();
652 public void pngTree_actionPerformed(ActionEvent e)
654 int width = treeCanvas.getWidth();
655 int height = treeCanvas.getHeight();
659 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
660 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
661 { "png" }, new String[]
662 { "Portable network graphics" }, "Portable network graphics");
664 chooser.setFileView(new jalview.io.JalviewFileView());
665 chooser.setDialogTitle("Create PNG image from tree");
666 chooser.setToolTipText("Save");
668 int value = chooser.showSaveDialog(this);
670 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
675 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
676 .getSelectedFile().getParent());
678 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
680 BufferedImage bi = new BufferedImage(width, height,
681 BufferedImage.TYPE_INT_RGB);
682 Graphics png = bi.getGraphics();
684 treeCanvas.draw(png, width, height);
686 ImageIO.write(bi, "png", out);
688 } catch (Exception ex)
690 ex.printStackTrace();
694 * change node labels to the annotation referred to by labelClass
695 * TODO: promote to a datamodel modification that can be undone
696 * TODO: make argument one case of a generic transformation function ie { undoStep = apply(Tree, TransformFunction)};
699 public void changeNames(final String labelClass)
701 tree.applyToNodes(new NodeTransformI() {
703 public void transform(BinaryNode node)
705 if (node instanceof SequenceNode && !((SequenceNode) node).isPlaceholder() && !((SequenceNode) node).isDummy())
708 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
711 // search dbrefs, features and annotation
712 DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(sq.getDBRef(), new String[] {labelClass.toUpperCase()});
715 for (int i=0; i<refs.length;i++)
717 if (newname == null) {
718 newname = new String(refs[i].getAccessionId());
720 newname = newname +"; "+refs[i].getAccessionId();
726 SequenceFeature sf[] = sq.getSequenceFeatures();
727 for (int i=0;sf!=null && i<sf.length; i++)
729 if (sf[i].getType().equals(labelClass))
733 newname = new String(sf[i].getDescription());
735 newname = newname + "; "+sf[i].getDescription();
743 String oldname = ((SequenceNode) node).getName();
744 // TODO : save in the undo object for this modification.
745 ((SequenceNode) node).setName(newname);