2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 import java.awt.Graphics;
25 import java.awt.event.ActionEvent;
26 import java.awt.event.ActionListener;
27 import java.beans.PropertyChangeEvent;
28 import java.beans.PropertyChangeListener;
30 import java.io.FileOutputStream;
31 import java.util.ArrayList;
32 import java.util.List;
33 import java.util.Locale;
35 import javax.swing.ButtonGroup;
36 import javax.swing.JMenuItem;
37 import javax.swing.JRadioButtonMenuItem;
38 import javax.swing.event.InternalFrameAdapter;
39 import javax.swing.event.InternalFrameEvent;
41 import org.jibble.epsgraphics.EpsGraphics2D;
43 import jalview.analysis.AlignmentSorter;
44 import jalview.analysis.AverageDistanceTree;
45 import jalview.analysis.NJTree;
46 import jalview.analysis.TreeBuilder;
47 import jalview.analysis.TreeModel;
48 import jalview.analysis.scoremodels.ScoreModels;
49 import jalview.api.analysis.ScoreModelI;
50 import jalview.api.analysis.SimilarityParamsI;
51 import jalview.bin.Cache;
52 import jalview.bin.Console;
53 import jalview.commands.CommandI;
54 import jalview.commands.OrderCommand;
55 import jalview.datamodel.Alignment;
56 import jalview.datamodel.AlignmentI;
57 import jalview.datamodel.AlignmentView;
58 import jalview.datamodel.BinaryNode;
59 import jalview.datamodel.DBRefEntry;
60 import jalview.datamodel.HiddenColumns;
61 import jalview.datamodel.NodeTransformI;
62 import jalview.datamodel.SequenceFeature;
63 import jalview.datamodel.SequenceI;
64 import jalview.datamodel.SequenceNode;
65 import jalview.gui.ImageExporter.ImageWriterI;
66 import jalview.io.JalviewFileChooser;
67 import jalview.io.JalviewFileView;
68 import jalview.io.NewickFile;
69 import jalview.jbgui.GTreePanel;
70 import jalview.util.ImageMaker.TYPE;
71 import jalview.util.MessageManager;
72 import jalview.viewmodel.AlignmentViewport;
80 public class TreePanel extends GTreePanel
84 String scoreModelName; // if tree computed
86 String treeTitle; // if tree loaded
88 SimilarityParamsI similarityParams;
90 private TreeCanvas treeCanvas;
94 private AlignViewport av;
97 * Creates a new TreePanel object.
104 public TreePanel(AlignmentPanel ap, String type, String modelName,
105 SimilarityParamsI options)
108 this.setFrameIcon(null);
109 this.similarityParams = options;
110 initTreePanel(ap, type, modelName, null, null);
112 // We know this tree has distances. JBPNote TODO: prolly should add this as
113 // a userdefined default
114 // showDistances(true);
117 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
118 String theTitle, AlignmentView inputData)
121 this.setFrameIcon(null);
122 this.treeTitle = theTitle;
123 initTreePanel(alignPanel, null, null, newtree, inputData);
126 public AlignmentI getAlignment()
128 return getTreeCanvas().getViewport().getAlignment();
131 public AlignmentViewport getViewPort()
133 // @Mungo - Why don't we return our own viewport ???
134 return getTreeCanvas().getViewport();
137 void initTreePanel(AlignmentPanel ap, String type, String modelName,
138 NewickFile newTree, AlignmentView inputData)
142 this.treeType = type;
143 this.scoreModelName = modelName;
145 treeCanvas = new TreeCanvas(this, ap, scrollPane);
146 scrollPane.setViewportView(treeCanvas);
148 PaintRefresher.Register(this, ap.av.getSequenceSetId());
150 buildAssociatedViewMenu();
152 final PropertyChangeListener listener = addAlignmentListener();
155 * remove listener when window is closed, so that this
156 * panel can be garbage collected
158 addInternalFrameListener(new InternalFrameAdapter()
161 public void internalFrameClosed(InternalFrameEvent evt)
165 av.removePropertyChangeListener(listener);
171 TreeLoader tl = new TreeLoader(newTree, inputData);
177 * Ensure any potentially large object references are nulled
179 public void releaseReferences()
182 this.treeCanvas.tree = null;
183 this.treeCanvas.nodeHash = null;
184 this.treeCanvas.nameHash = null;
190 protected PropertyChangeListener addAlignmentListener()
192 final PropertyChangeListener listener = new PropertyChangeListener()
195 public void propertyChange(PropertyChangeEvent evt)
197 if (evt.getPropertyName().equals("alignment"))
201 System.out.println("tree is null");
202 // TODO: deal with case when a change event is received whilst a
203 // tree is still being calculated - should save reference for
204 // processing message later.
207 if (evt.getNewValue() == null)
210 "new alignment sequences vector value is null");
213 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
214 treeCanvas.nameHash.clear(); // reset the mapping between canvas
215 // rectangles and leafnodes
220 av.addPropertyChangeListener(listener);
225 public void viewMenu_menuSelected()
227 buildAssociatedViewMenu();
230 void buildAssociatedViewMenu()
232 AlignmentPanel[] aps = PaintRefresher
233 .getAssociatedPanels(av.getSequenceSetId());
234 if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
236 associateLeavesMenu.setVisible(false);
240 associateLeavesMenu.setVisible(true);
243 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
245 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
248 associateLeavesMenu.removeAll();
250 JRadioButtonMenuItem item;
251 ButtonGroup buttonGroup = new ButtonGroup();
252 int i, iSize = aps.length;
253 final TreePanel thisTreePanel = this;
254 for (i = 0; i < iSize; i++)
256 final AlignmentPanel ap = aps[i];
257 item = new JRadioButtonMenuItem(ap.av.getViewName(),
258 ap == treeCanvas.getAssociatedPanel());
259 buttonGroup.add(item);
260 item.addActionListener(new ActionListener()
263 public void actionPerformed(ActionEvent evt)
265 treeCanvas.applyToAllViews = false;
266 treeCanvas.setAssociatedPanel(ap);
267 treeCanvas.setViewport(ap.av);
268 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
272 associateLeavesMenu.add(item);
275 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
276 MessageManager.getString("label.all_views"));
277 buttonGroup.add(itemf);
278 itemf.setSelected(treeCanvas.applyToAllViews);
279 itemf.addActionListener(new ActionListener()
282 public void actionPerformed(ActionEvent evt)
284 treeCanvas.applyToAllViews = itemf.isSelected();
287 associateLeavesMenu.add(itemf);
291 class TreeLoader extends Thread
293 private NewickFile newtree;
295 private AlignmentView odata = null;
297 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
299 this.newtree = newickFile;
300 this.odata = inputData;
302 if (newickFile != null)
304 // Must be outside run(), as Jalview2XML tries to
305 // update distance/bootstrap visibility at the same time
306 showBootstrap(newickFile.HasBootstrap());
307 showDistances(newickFile.HasDistances());
317 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
319 if (tree.getOriginalData() == null)
321 originalSeqData.setVisible(false);
326 ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
327 scoreModelName, treeCanvas.getAssociatedPanel());
328 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
329 ? new NJTree(av, sm, similarityParams)
330 : new AverageDistanceTree(av, sm, similarityParams);
331 tree = new TreeModel(njtree);
335 tree.reCount(tree.getTopNode());
336 tree.findHeight(tree.getTopNode());
337 treeCanvas.setTree(tree);
338 treeCanvas.repaint();
339 av.setCurrentTree(tree);
340 if (av.getSortByTree())
342 sortByTree_actionPerformed();
347 public void showDistances(boolean b)
349 treeCanvas.setShowDistances(b);
350 distanceMenu.setSelected(b);
353 public void showBootstrap(boolean b)
355 treeCanvas.setShowBootstrap(b);
356 bootstrapMenu.setSelected(b);
359 public void showPlaceholders(boolean b)
361 placeholdersMenu.setState(b);
362 treeCanvas.setMarkPlaceholders(b);
368 * @return DOCUMENT ME!
370 public TreeModel getTree()
382 public void textbox_actionPerformed(ActionEvent e)
384 CutAndPasteTransfer cap = new CutAndPasteTransfer();
386 String newTitle = getPanelTitle();
388 NewickFile fout = new NewickFile(tree.getTopNode());
391 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
392 tree.hasRootDistance()));
393 Desktop.addInternalFrame(cap, newTitle, 500, 100);
394 } catch (OutOfMemoryError oom)
396 new OOMWarning("generating newick tree file", oom);
409 public void saveAsNewick_actionPerformed(ActionEvent e)
411 // TODO: JAL-3048 save newick file for Jalview-JS
412 JalviewFileChooser chooser = new JalviewFileChooser(
413 Cache.getProperty("LAST_DIRECTORY"));
414 chooser.setFileView(new JalviewFileView());
415 chooser.setDialogTitle(
416 MessageManager.getString("label.save_tree_as_newick"));
417 chooser.setToolTipText(MessageManager.getString("action.save"));
419 int value = chooser.showSaveDialog(null);
421 if (value == JalviewFileChooser.APPROVE_OPTION)
423 String choice = chooser.getSelectedFile().getPath();
424 Cache.setProperty("LAST_DIRECTORY",
425 chooser.getSelectedFile().getParent());
429 jalview.io.NewickFile fout = new jalview.io.NewickFile(
431 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
432 tree.hasRootDistance());
433 java.io.PrintWriter out = new java.io.PrintWriter(
434 new java.io.FileWriter(choice));
437 } catch (Exception ex)
439 ex.printStackTrace();
451 public void printMenu_actionPerformed(ActionEvent e)
453 // Putting in a thread avoids Swing painting problems
454 treeCanvas.startPrinting();
458 public void originalSeqData_actionPerformed(ActionEvent e)
460 AlignmentView originalData = tree.getOriginalData();
461 if (originalData == null)
464 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
467 // decide if av alignment is sufficiently different to original data to
468 // warrant a new window to be created
469 // create new alignmnt window with hidden regions (unhiding hidden regions
470 // yields unaligned seqs)
471 // or create a selection box around columns in alignment view
472 // test Alignment(SeqCigar[])
476 // we try to get the associated view's gap character
477 // but this may fail if the view was closed...
478 gc = av.getGapCharacter();
480 } catch (Exception ex)
484 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
486 if (alAndColsel != null && alAndColsel[0] != null)
488 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
490 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
491 AlignmentI dataset = (av != null && av.getAlignment() != null)
492 ? av.getAlignment().getDataset()
496 al.setDataset(dataset);
502 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
503 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
505 // >>>This is a fix for the moment, until a better solution is
507 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
509 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
512 Desktop.addInternalFrame(af, MessageManager.formatMessage(
513 "label.original_data_for_params", new Object[]
514 { this.title }), AlignFrame.DEFAULT_WIDTH,
515 AlignFrame.DEFAULT_HEIGHT);
527 public void fitToWindow_actionPerformed(ActionEvent e)
529 treeCanvas.fitToWindow = fitToWindow.isSelected();
534 * sort the associated alignment view by the current tree.
539 public void sortByTree_actionPerformed()
542 if (treeCanvas.applyToAllViews)
544 final ArrayList<CommandI> commands = new ArrayList<>();
545 for (AlignmentPanel ap : PaintRefresher
546 .getAssociatedPanels(av.getSequenceSetId()))
548 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
550 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
554 public void undoCommand(AlignmentI[] views)
556 for (CommandI tsort : commands)
558 tsort.undoCommand(views);
565 return commands.size();
569 public String getDescription()
571 return "Tree Sort (many views)";
575 public void doCommand(AlignmentI[] views)
578 for (CommandI tsort : commands)
580 tsort.doCommand(views);
584 for (AlignmentPanel ap : PaintRefresher
585 .getAssociatedPanels(av.getSequenceSetId()))
587 // ensure all the alignFrames refresh their GI after adding an undo item
588 ap.alignFrame.updateEditMenuBar();
593 treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
594 sortAlignmentIn(treeCanvas.getAssociatedPanel()));
599 public CommandI sortAlignmentIn(AlignmentPanel ap)
601 // TODO: move to alignment view controller
602 AlignmentViewport viewport = ap.av;
603 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
604 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
606 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
608 ap.paintAlignment(true, false);
619 public void font_actionPerformed(ActionEvent e)
621 if (treeCanvas == null)
626 new FontChooser(this);
629 public Font getTreeFont()
631 return treeCanvas.font;
634 public void setTreeFont(Font f)
636 if (treeCanvas != null)
638 treeCanvas.setFont(f);
649 public void distanceMenu_actionPerformed(ActionEvent e)
651 treeCanvas.setShowDistances(distanceMenu.isSelected());
661 public void bootstrapMenu_actionPerformed(ActionEvent e)
663 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
673 public void placeholdersMenu_actionPerformed(ActionEvent e)
675 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
679 * Outputs the Tree in image format (currently EPS or PNG). The user is
680 * prompted for the file to save to, and for EPS (unless a preference is
681 * already set) for the choice of Text or Lineart for character rendering.
684 public void writeTreeImage(TYPE imageFormat)
686 int width = treeCanvas.getWidth();
687 int height = treeCanvas.getHeight();
688 ImageWriterI writer = new ImageWriterI()
691 public void exportImage(Graphics g) throws Exception
693 treeCanvas.draw(g, width, height);
696 String tree = MessageManager.getString("label.tree");
697 ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
699 exporter.doExport(null, this, width, height,
700 tree.toLowerCase(Locale.ROOT));
704 * change node labels to the annotation referred to by labelClass TODO:
705 * promote to a datamodel modification that can be undone TODO: make argument
706 * one case of a generic transformation function ie { undoStep = apply(Tree,
707 * TransformFunction)};
711 public void changeNames(final String labelClass)
713 tree.applyToNodes(new NodeTransformI()
717 public void transform(BinaryNode node)
719 if (node instanceof SequenceNode
720 && !((SequenceNode) node).isPlaceholder()
721 && !((SequenceNode) node).isDummy())
723 String newname = null;
724 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
727 // search dbrefs, features and annotation
728 List<DBRefEntry> refs = jalview.util.DBRefUtils
729 .selectRefs(sq.getDBRefs(), new String[]
730 { labelClass.toUpperCase(Locale.ROOT) });
733 for (int i = 0, ni = refs.size(); i < ni; i++)
737 newname = new String(refs.get(i).getAccessionId());
741 newname += "; " + refs.get(i).getAccessionId();
747 List<SequenceFeature> features = sq.getFeatures()
748 .getPositionalFeatures(labelClass);
749 for (SequenceFeature feature : features)
753 newname = feature.getDescription();
757 newname = newname + "; " + feature.getDescription();
764 // String oldname = ((SequenceNode) node).getName();
765 // TODO : save oldname in the undo object for this modification.
766 ((SequenceNode) node).setName(newname);
774 * Formats a localised title for the tree panel, like
776 * Neighbour Joining Using BLOSUM62
778 * For a tree loaded from file, just uses the file name
782 public String getPanelTitle()
784 if (treeTitle != null)
790 * i18n description of Neighbour Joining or Average Distance method
792 String treecalcnm = MessageManager.getString(
793 "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
796 * short score model name (long description can be too long)
798 String smn = scoreModelName;
801 * put them together as <method> Using <model>
803 final String ttl = MessageManager.formatMessage("label.calc_title",
809 * Builds an EPS image and writes it to the specified file.
813 * true for Text character rendering, false for Lineart
815 protected void writeEpsFile(File outFile, boolean textOption)
819 int width = treeCanvas.getWidth();
820 int height = treeCanvas.getHeight();
822 FileOutputStream out = new FileOutputStream(outFile);
823 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
825 pg.setAccurateTextMode(!textOption);
826 treeCanvas.draw(pg, width, height);
830 } catch (Exception ex)
832 System.err.println("Error writing tree as EPS");
833 ex.printStackTrace();
837 public AlignViewport getViewport()
842 public void setViewport(AlignViewport av)
847 public TreeCanvas getTreeCanvas()