2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 The Jalview Authors
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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 import java.util.List;
26 import javax.imageio.*;
29 import java.awt.event.*;
30 import java.awt.image.*;
33 import org.jibble.epsgraphics.*;
34 import jalview.analysis.*;
35 import jalview.commands.CommandI;
36 import jalview.commands.OrderCommand;
37 import jalview.datamodel.*;
39 import jalview.jbgui.*;
40 import jalview.util.MessageManager;
48 public class TreePanel extends GTreePanel
54 TreeCanvas treeCanvas;
61 * Creates a new TreePanel object.
76 public TreePanel(AlignmentPanel ap, String type, String pwtype)
79 initTreePanel(ap, type, pwtype, null, null);
81 // We know this tree has distances. JBPNote TODO: prolly should add this as
82 // a userdefined default
83 // showDistances(true);
87 * Creates a new TreePanel object.
100 public TreePanel(AlignmentPanel ap, String type, String pwtype,
104 initTreePanel(ap, type, pwtype, newtree, null);
107 public TreePanel(AlignmentPanel av, String type, String pwtype,
108 NewickFile newtree, AlignmentView inputData)
111 initTreePanel(av, type, pwtype, newtree, inputData);
114 public AlignmentI getAlignment()
116 return treeCanvas.av.getAlignment();
119 public AlignViewport getViewPort()
121 return treeCanvas.av;
124 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
125 NewickFile newTree, AlignmentView inputData)
130 this.pwtype = pwtype;
132 treeCanvas = new TreeCanvas(this, ap, scrollPane);
133 scrollPane.setViewportView(treeCanvas);
135 PaintRefresher.Register(this, ap.av.getSequenceSetId());
137 buildAssociatedViewMenu();
139 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
141 public void propertyChange(PropertyChangeEvent evt)
143 if (evt.getPropertyName().equals("alignment"))
147 System.out.println("tree is null");
148 // TODO: deal with case when a change event is received whilst a
149 // tree is still being calculated - should save reference for
150 // processing message later.
153 if (evt.getNewValue() == null)
156 .println("new alignment sequences vector value is null");
159 tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
160 treeCanvas.nameHash.clear(); // reset the mapping between canvas
161 // rectangles and leafnodes
167 TreeLoader tl = new TreeLoader(newTree);
168 if (inputData != null)
170 tl.odata = inputData;
176 public void viewMenu_menuSelected()
178 buildAssociatedViewMenu();
181 void buildAssociatedViewMenu()
183 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
184 .getSequenceSetId());
185 if (aps.length == 1 && treeCanvas.ap == aps[0])
187 associateLeavesMenu.setVisible(false);
191 associateLeavesMenu.setVisible(true);
193 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
195 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
198 associateLeavesMenu.removeAll();
200 JRadioButtonMenuItem item;
201 ButtonGroup buttonGroup = new ButtonGroup();
202 int i, iSize = aps.length;
203 final TreePanel thisTreePanel = this;
204 for (i = 0; i < iSize; i++)
206 final AlignmentPanel ap = aps[i];
207 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
208 buttonGroup.add(item);
209 item.addActionListener(new ActionListener()
211 public void actionPerformed(ActionEvent evt)
213 treeCanvas.applyToAllViews = false;
215 treeCanvas.av = ap.av;
216 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
220 associateLeavesMenu.add(item);
223 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
224 buttonGroup.add(itemf);
225 itemf.setSelected(treeCanvas.applyToAllViews);
226 itemf.addActionListener(new ActionListener()
228 public void actionPerformed(ActionEvent evt)
230 treeCanvas.applyToAllViews = itemf.isSelected();
233 associateLeavesMenu.add(itemf);
237 class TreeLoader extends Thread
241 jalview.datamodel.AlignmentView odata = null;
243 public TreeLoader(NewickFile newtree)
245 this.newtree = newtree;
248 // Must be outside run(), as Jalview2XML tries to
249 // update distance/bootstrap visibility at the same time
250 showBootstrap(newtree.HasBootstrap());
251 showDistances(newtree.HasDistances());
262 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
266 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
269 if (!tree.hasOriginalSequenceData())
271 allowOriginalSeqData(false);
278 boolean selview = av.getSelectionGroup() != null
279 && av.getSelectionGroup().getSize() > 1;
280 AlignmentView seqStrings = av.getAlignmentView(selview);
284 end = av.getAlignment().getWidth();
285 seqs = av.getAlignment().getSequencesArray();
289 start = av.getSelectionGroup().getStartRes();
290 end = av.getSelectionGroup().getEndRes() + 1;
291 seqs = av.getSelectionGroup().getSequencesInOrder(
295 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
299 tree.reCount(tree.getTopNode());
300 tree.findHeight(tree.getTopNode());
301 treeCanvas.setTree(tree);
302 treeCanvas.repaint();
303 av.setCurrentTree(tree);
304 if (av.getSortByTree())
306 sortByTree_actionPerformed(null);
311 public void showDistances(boolean b)
313 treeCanvas.setShowDistances(b);
314 distanceMenu.setSelected(b);
317 public void showBootstrap(boolean b)
319 treeCanvas.setShowBootstrap(b);
320 bootstrapMenu.setSelected(b);
323 public void showPlaceholders(boolean b)
325 placeholdersMenu.setState(b);
326 treeCanvas.setMarkPlaceholders(b);
329 private void allowOriginalSeqData(boolean b)
331 originalSeqData.setVisible(b);
337 * @return DOCUMENT ME!
339 public NJTree getTree()
350 public void textbox_actionPerformed(ActionEvent e)
352 CutAndPasteTransfer cap = new CutAndPasteTransfer();
354 StringBuffer buffer = new StringBuffer();
356 if (type.equals("AV"))
358 buffer.append("Average distance tree using ");
362 buffer.append("Neighbour joining tree using ");
365 if (pwtype.equals("BL"))
367 buffer.append("BLOSUM62");
371 buffer.append("PID");
374 jalview.io.NewickFile fout = new jalview.io.NewickFile(
378 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
379 tree.isHasRootDistance()));
380 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
381 } catch (OutOfMemoryError oom)
383 new OOMWarning("generating newick tree file", oom);
395 public void saveAsNewick_actionPerformed(ActionEvent e)
397 JalviewFileChooser chooser = new JalviewFileChooser(
398 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
399 chooser.setFileView(new JalviewFileView());
400 chooser.setDialogTitle("Save tree as newick file");
401 chooser.setToolTipText(MessageManager.getString("action.save"));
403 int value = chooser.showSaveDialog(null);
405 if (value == JalviewFileChooser.APPROVE_OPTION)
407 String choice = chooser.getSelectedFile().getPath();
408 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
409 .getSelectedFile().getParent());
413 jalview.io.NewickFile fout = new jalview.io.NewickFile(
415 String output = fout.print(tree.isHasBootstrap(),
416 tree.isHasDistances(), tree.isHasRootDistance());
417 java.io.PrintWriter out = new java.io.PrintWriter(
418 new java.io.FileWriter(choice));
421 } catch (Exception ex)
423 ex.printStackTrace();
434 public void printMenu_actionPerformed(ActionEvent e)
436 // Putting in a thread avoids Swing painting problems
437 treeCanvas.startPrinting();
440 public void originalSeqData_actionPerformed(ActionEvent e)
442 if (!tree.hasOriginalSequenceData())
444 jalview.bin.Cache.log
445 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
448 // decide if av alignment is sufficiently different to original data to
449 // warrant a new window to be created
450 // create new alignmnt window with hidden regions (unhiding hidden regions
451 // yields unaligned seqs)
452 // or create a selection box around columns in alignment view
453 // test Alignment(SeqCigar[])
457 // we try to get the associated view's gap character
458 // but this may fail if the view was closed...
459 gc = av.getGapCharacter();
461 } catch (Exception ex)
465 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
467 if (alAndColsel != null && alAndColsel[0] != null)
469 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
471 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
472 Alignment dataset = (av != null && av.getAlignment() != null) ? av
473 .getAlignment().getDataset() : null;
476 al.setDataset(dataset);
482 AlignFrame af = new AlignFrame(al,
483 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
484 AlignFrame.DEFAULT_HEIGHT);
486 // >>>This is a fix for the moment, until a better solution is
488 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
490 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
493 Desktop.addInternalFrame(af, MessageManager.formatMessage("label.original_data_for_params", new String[]{this.title}),
494 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
505 public void fitToWindow_actionPerformed(ActionEvent e)
507 treeCanvas.fitToWindow = fitToWindow.isSelected();
512 * sort the associated alignment view by the current tree.
516 public void sortByTree_actionPerformed(ActionEvent e)
519 if (treeCanvas.applyToAllViews)
521 final ArrayList<CommandI> commands = new ArrayList<CommandI>();
522 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
523 .getSequenceSetId()))
525 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
527 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
531 public void undoCommand(AlignmentI[] views)
533 for (CommandI tsort : commands)
535 tsort.undoCommand(views);
542 return commands.size();
546 public String getDescription()
548 return "Tree Sort (many views)";
552 public void doCommand(AlignmentI[] views)
555 for (CommandI tsort : commands)
557 tsort.doCommand(views);
561 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
562 .getSequenceSetId()))
564 // ensure all the alignFrames refresh their GI after adding an undo item
565 ap.alignFrame.updateEditMenuBar();
570 treeCanvas.ap.alignFrame
571 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
576 public CommandI sortAlignmentIn(AlignmentPanel ap)
578 AlignViewport av = ap.av;
579 SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
580 AlignmentSorter.sortByTree(av.getAlignment(), tree);
582 undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
584 ap.paintAlignment(true);
594 public void font_actionPerformed(ActionEvent e)
596 if (treeCanvas == null)
601 new FontChooser(this);
604 public Font getTreeFont()
606 return treeCanvas.font;
609 public void setTreeFont(Font font)
611 if (treeCanvas != null)
613 treeCanvas.setFont(font);
623 public void distanceMenu_actionPerformed(ActionEvent e)
625 treeCanvas.setShowDistances(distanceMenu.isSelected());
634 public void bootstrapMenu_actionPerformed(ActionEvent e)
636 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
645 public void placeholdersMenu_actionPerformed(ActionEvent e)
647 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
656 public void epsTree_actionPerformed(ActionEvent e)
658 boolean accurateText = true;
660 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
663 // If we need to prompt, and if the GUI is visible then
664 // Prompt for EPS rendering style
665 if (renderStyle.equalsIgnoreCase("Prompt each time")
666 && !(System.getProperty("java.awt.headless") != null && System
667 .getProperty("java.awt.headless").equals("true")))
669 EPSOptions eps = new EPSOptions();
670 renderStyle = eps.getValue();
672 if (renderStyle == null || eps.cancelled)
679 if (renderStyle.equalsIgnoreCase("text"))
681 accurateText = false;
684 int width = treeCanvas.getWidth();
685 int height = treeCanvas.getHeight();
689 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
690 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
691 { "eps" }, new String[]
692 { "Encapsulated Postscript" }, "Encapsulated Postscript");
693 chooser.setFileView(new jalview.io.JalviewFileView());
694 chooser.setDialogTitle("Create EPS file from tree");
695 chooser.setToolTipText(MessageManager.getString("action.save"));
697 int value = chooser.showSaveDialog(this);
699 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
704 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
705 .getSelectedFile().getParent());
707 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
708 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
710 pg.setAccurateTextMode(accurateText);
712 treeCanvas.draw(pg, width, height);
716 } catch (Exception ex)
718 ex.printStackTrace();
728 public void pngTree_actionPerformed(ActionEvent e)
730 int width = treeCanvas.getWidth();
731 int height = treeCanvas.getHeight();
735 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
736 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
737 { "png" }, new String[]
738 { "Portable network graphics" }, "Portable network graphics");
740 chooser.setFileView(new jalview.io.JalviewFileView());
741 chooser.setDialogTitle("Create PNG image from tree");
742 chooser.setToolTipText(MessageManager.getString("action.save"));
744 int value = chooser.showSaveDialog(this);
746 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
751 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
752 .getSelectedFile().getParent());
754 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
756 BufferedImage bi = new BufferedImage(width, height,
757 BufferedImage.TYPE_INT_RGB);
758 Graphics png = bi.getGraphics();
760 treeCanvas.draw(png, width, height);
762 ImageIO.write(bi, "png", out);
764 } catch (Exception ex)
766 ex.printStackTrace();
771 * change node labels to the annotation referred to by labelClass TODO:
772 * promote to a datamodel modification that can be undone TODO: make argument
773 * one case of a generic transformation function ie { undoStep = apply(Tree,
774 * TransformFunction)};
778 public void changeNames(final String labelClass)
780 tree.applyToNodes(new NodeTransformI()
783 public void transform(BinaryNode node)
785 if (node instanceof SequenceNode
786 && !((SequenceNode) node).isPlaceholder()
787 && !((SequenceNode) node).isDummy())
789 String newname = null;
790 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
793 // search dbrefs, features and annotation
794 DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
795 sq.getDBRef(), new String[]
796 { labelClass.toUpperCase() });
799 for (int i = 0; i < refs.length; i++)
803 newname = new String(refs[i].getAccessionId());
807 newname = newname + "; " + refs[i].getAccessionId();
813 SequenceFeature sf[] = sq.getSequenceFeatures();
814 for (int i = 0; sf != null && i < sf.length; i++)
816 if (sf[i].getType().equals(labelClass))
820 newname = new String(sf[i].getDescription());
824 newname = newname + "; " + sf[i].getDescription();
832 String oldname = ((SequenceNode) node).getName();
833 // TODO : save in the undo object for this modification.
834 ((SequenceNode) node).setName(newname);