2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
23 import javax.imageio.*;
26 import java.awt.event.*;
27 import java.awt.image.*;
30 import org.jibble.epsgraphics.*;
31 import jalview.analysis.*;
32 import jalview.commands.OrderCommand;
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");
143 // TODO: deal with case when a change event is received whilst a
144 // tree is still being calculated - should save reference for
145 // processing message later.
148 if (evt.getNewValue() == null)
151 .println("new alignment sequences vector value is null");
154 tree.UpdatePlaceHolders((Vector) evt.getNewValue());
155 treeCanvas.nameHash.clear(); // reset the mapping between canvas
156 // rectangles and leafnodes
162 TreeLoader tl = new TreeLoader(newTree);
163 if (inputData != null)
165 tl.odata = inputData;
171 public void viewMenu_menuSelected()
173 buildAssociatedViewMenu();
176 void buildAssociatedViewMenu()
178 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
179 .getSequenceSetId());
180 if (aps.length == 1 && treeCanvas.ap == aps[0])
182 associateLeavesMenu.setVisible(false);
186 associateLeavesMenu.setVisible(true);
188 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
190 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
193 associateLeavesMenu.removeAll();
195 JRadioButtonMenuItem item;
196 ButtonGroup buttonGroup = new ButtonGroup();
197 int i, iSize = aps.length;
198 final TreePanel thisTreePanel = this;
199 for (i = 0; i < iSize; i++)
201 final AlignmentPanel ap = aps[i];
202 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
203 buttonGroup.add(item);
204 item.addActionListener(new ActionListener()
206 public void actionPerformed(ActionEvent evt)
208 treeCanvas.applyToAllViews = false;
210 treeCanvas.av = ap.av;
211 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
215 associateLeavesMenu.add(item);
218 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
219 buttonGroup.add(itemf);
220 itemf.setSelected(treeCanvas.applyToAllViews);
221 itemf.addActionListener(new ActionListener()
223 public void actionPerformed(ActionEvent evt)
225 treeCanvas.applyToAllViews = itemf.isSelected();
228 associateLeavesMenu.add(itemf);
232 class TreeLoader extends Thread
236 jalview.datamodel.AlignmentView odata = null;
238 public TreeLoader(NewickFile newtree)
240 this.newtree = newtree;
243 // Must be outside run(), as Jalview2XML tries to
244 // update distance/bootstrap visibility at the same time
245 showBootstrap(newtree.HasBootstrap());
246 showDistances(newtree.HasDistances());
257 tree = new NJTree(av.alignment.getSequencesArray(), newtree);
261 tree = new NJTree(av.alignment.getSequencesArray(), odata,
264 if (!tree.hasOriginalSequenceData())
266 allowOriginalSeqData(false);
273 AlignmentView seqStrings = av.getAlignmentView(av
274 .getSelectionGroup() != null);
275 if (av.getSelectionGroup() == null)
278 end = av.alignment.getWidth();
279 seqs = av.alignment.getSequencesArray();
283 start = av.getSelectionGroup().getStartRes();
284 end = av.getSelectionGroup().getEndRes() + 1;
285 seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
288 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
292 tree.reCount(tree.getTopNode());
293 tree.findHeight(tree.getTopNode());
294 treeCanvas.setTree(tree);
295 treeCanvas.repaint();
296 av.setCurrentTree(tree);
297 if (av.getSortByTree())
299 sortByTree_actionPerformed(null);
304 public void showDistances(boolean b)
306 treeCanvas.setShowDistances(b);
307 distanceMenu.setSelected(b);
310 public void showBootstrap(boolean b)
312 treeCanvas.setShowBootstrap(b);
313 bootstrapMenu.setSelected(b);
316 public void showPlaceholders(boolean b)
318 placeholdersMenu.setState(b);
319 treeCanvas.setMarkPlaceholders(b);
322 private void allowOriginalSeqData(boolean b)
324 originalSeqData.setVisible(b);
330 * @return DOCUMENT ME!
332 public NJTree getTree()
343 public void textbox_actionPerformed(ActionEvent e)
345 CutAndPasteTransfer cap = new CutAndPasteTransfer();
347 StringBuffer buffer = new StringBuffer();
349 if (type.equals("AV"))
351 buffer.append("Average distance tree using ");
355 buffer.append("Neighbour joining tree using ");
358 if (pwtype.equals("BL"))
360 buffer.append("BLOSUM62");
364 buffer.append("PID");
367 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
369 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
371 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
372 tree.isHasRootDistance()));
381 public void saveAsNewick_actionPerformed(ActionEvent e)
383 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
384 .getProperty("LAST_DIRECTORY"));
385 chooser.setFileView(new JalviewFileView());
386 chooser.setDialogTitle("Save tree as newick file");
387 chooser.setToolTipText("Save");
389 int value = chooser.showSaveDialog(null);
391 if (value == JalviewFileChooser.APPROVE_OPTION)
393 String choice = chooser.getSelectedFile().getPath();
394 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
395 .getSelectedFile().getParent());
399 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
401 String output = fout.print(tree.isHasBootstrap(), tree
402 .isHasDistances(), tree.isHasRootDistance());
403 java.io.PrintWriter out = new java.io.PrintWriter(
404 new java.io.FileWriter(choice));
407 } catch (Exception ex)
409 ex.printStackTrace();
420 public void printMenu_actionPerformed(ActionEvent e)
422 // Putting in a thread avoids Swing painting problems
423 treeCanvas.startPrinting();
426 public void originalSeqData_actionPerformed(ActionEvent e)
428 if (!tree.hasOriginalSequenceData())
430 jalview.bin.Cache.log
431 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
434 // decide if av alignment is sufficiently different to original data to
435 // warrant a new window to be created
436 // create new alignmnt window with hidden regions (unhiding hidden regions
437 // yields unaligned seqs)
438 // or create a selection box around columns in alignment view
439 // test Alignment(SeqCigar[])
443 // we try to get the associated view's gap character
444 // but this may fail if the view was closed...
445 gc = av.getGapCharacter();
447 } catch (Exception ex)
451 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
453 if (alAndColsel != null && alAndColsel[0] != null)
455 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
457 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
458 Alignment dataset = (av != null && av.getAlignment() != null) ? av
459 .getAlignment().getDataset() : null;
462 al.setDataset(dataset);
468 AlignFrame af = new AlignFrame(al,
469 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
470 AlignFrame.DEFAULT_HEIGHT);
472 // >>>This is a fix for the moment, until a better solution is
474 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
476 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
479 Desktop.addInternalFrame(af, "Original Data for " + this.title,
480 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
491 public void fitToWindow_actionPerformed(ActionEvent e)
493 treeCanvas.fitToWindow = fitToWindow.isSelected();
498 * sort the associated alignment view by the current tree.
502 public void sortByTree_actionPerformed(ActionEvent e)
504 AlignmentPanel ap = av.getAlignPanel();
505 SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
506 AlignmentSorter.sortByTree(av.getAlignment(), tree);
508 ap.alignFrame.addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
511 ap.paintAlignment(true);
521 public void font_actionPerformed(ActionEvent e)
523 if (treeCanvas == null)
528 new FontChooser(this);
531 public Font getTreeFont()
533 return treeCanvas.font;
536 public void setTreeFont(Font font)
538 if (treeCanvas != null)
540 treeCanvas.setFont(font);
550 public void distanceMenu_actionPerformed(ActionEvent e)
552 treeCanvas.setShowDistances(distanceMenu.isSelected());
561 public void bootstrapMenu_actionPerformed(ActionEvent e)
563 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
572 public void placeholdersMenu_actionPerformed(ActionEvent e)
574 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
583 public void epsTree_actionPerformed(ActionEvent e)
585 boolean accurateText = true;
587 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
590 // If we need to prompt, and if the GUI is visible then
591 // Prompt for EPS rendering style
592 if (renderStyle.equalsIgnoreCase("Prompt each time")
593 && !(System.getProperty("java.awt.headless") != null && System
594 .getProperty("java.awt.headless").equals("true")))
596 EPSOptions eps = new EPSOptions();
597 renderStyle = eps.getValue();
599 if (renderStyle == null || eps.cancelled)
606 if (renderStyle.equalsIgnoreCase("text"))
608 accurateText = false;
611 int width = treeCanvas.getWidth();
612 int height = treeCanvas.getHeight();
616 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
617 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
618 { "eps" }, new String[]
619 { "Encapsulated Postscript" }, "Encapsulated Postscript");
620 chooser.setFileView(new jalview.io.JalviewFileView());
621 chooser.setDialogTitle("Create EPS file from tree");
622 chooser.setToolTipText("Save");
624 int value = chooser.showSaveDialog(this);
626 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
631 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
632 .getSelectedFile().getParent());
634 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
635 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
637 pg.setAccurateTextMode(accurateText);
639 treeCanvas.draw(pg, width, height);
643 } catch (Exception ex)
645 ex.printStackTrace();
655 public void pngTree_actionPerformed(ActionEvent e)
657 int width = treeCanvas.getWidth();
658 int height = treeCanvas.getHeight();
662 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
663 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
664 { "png" }, new String[]
665 { "Portable network graphics" }, "Portable network graphics");
667 chooser.setFileView(new jalview.io.JalviewFileView());
668 chooser.setDialogTitle("Create PNG image from tree");
669 chooser.setToolTipText("Save");
671 int value = chooser.showSaveDialog(this);
673 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
678 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
679 .getSelectedFile().getParent());
681 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
683 BufferedImage bi = new BufferedImage(width, height,
684 BufferedImage.TYPE_INT_RGB);
685 Graphics png = bi.getGraphics();
687 treeCanvas.draw(png, width, height);
689 ImageIO.write(bi, "png", out);
691 } catch (Exception ex)
693 ex.printStackTrace();
698 * change node labels to the annotation referred to by labelClass TODO:
699 * promote to a datamodel modification that can be undone TODO: make argument
700 * one case of a generic transformation function ie { undoStep = apply(Tree,
701 * TransformFunction)};
705 public void changeNames(final String labelClass)
707 tree.applyToNodes(new NodeTransformI()
710 public void transform(BinaryNode node)
712 if (node instanceof SequenceNode
713 && !((SequenceNode) node).isPlaceholder()
714 && !((SequenceNode) node).isDummy())
716 String newname = null;
717 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
720 // search dbrefs, features and annotation
721 DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(sq
722 .getDBRef(), new String[]
723 { labelClass.toUpperCase() });
726 for (int i = 0; i < refs.length; i++)
730 newname = new String(refs[i].getAccessionId());
734 newname = newname + "; " + refs[i].getAccessionId();
740 SequenceFeature sf[] = sq.getSequenceFeatures();
741 for (int i = 0; sf != null && i < sf.length; i++)
743 if (sf[i].getType().equals(labelClass))
747 newname = new String(sf[i].getDescription());
751 newname = newname + "; " + sf[i].getDescription();
759 String oldname = ((SequenceNode) node).getName();
760 // TODO : save in the undo object for this modification.
761 ((SequenceNode) node).setName(newname);