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.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AverageDistanceTree;
25 import jalview.analysis.NJTree;
26 import jalview.analysis.TreeBuilder;
27 import jalview.analysis.TreeModel;
28 import jalview.analysis.scoremodels.ScoreModels;
29 import jalview.api.analysis.ScoreModelI;
30 import jalview.api.analysis.SimilarityParamsI;
31 import jalview.commands.CommandI;
32 import jalview.commands.OrderCommand;
33 import jalview.datamodel.Alignment;
34 import jalview.datamodel.AlignmentI;
35 import jalview.datamodel.AlignmentView;
36 import jalview.datamodel.BinaryNode;
37 import jalview.datamodel.DBRefEntry;
38 import jalview.datamodel.HiddenColumns;
39 import jalview.datamodel.NodeTransformI;
40 import jalview.datamodel.SequenceFeature;
41 import jalview.datamodel.SequenceI;
42 import jalview.datamodel.SequenceNode;
43 import jalview.gui.ImageExporter.ImageWriterI;
44 import jalview.io.JalviewFileChooser;
45 import jalview.io.JalviewFileView;
46 import jalview.io.NewickFile;
47 import jalview.jbgui.GTreePanel;
48 import jalview.util.ImageMaker.TYPE;
49 import jalview.util.MessageManager;
50 import jalview.viewmodel.AlignmentViewport;
53 import java.awt.Graphics;
54 import java.awt.event.ActionEvent;
55 import java.awt.event.ActionListener;
56 import java.beans.PropertyChangeEvent;
57 import java.beans.PropertyChangeListener;
59 import java.io.FileOutputStream;
60 import java.util.ArrayList;
61 import java.util.List;
63 import javax.swing.ButtonGroup;
64 import javax.swing.JMenuItem;
65 import javax.swing.JRadioButtonMenuItem;
66 import javax.swing.event.InternalFrameAdapter;
67 import javax.swing.event.InternalFrameEvent;
69 import org.jibble.epsgraphics.EpsGraphics2D;
77 public class TreePanel extends GTreePanel
81 String scoreModelName; // if tree computed
83 String treeTitle; // if tree loaded
85 SimilarityParamsI similarityParams;
87 private TreeCanvas treeCanvas;
91 private AlignViewport av;
94 * Creates a new TreePanel object.
101 public TreePanel(AlignmentPanel ap, String type, String modelName,
102 SimilarityParamsI options)
105 this.similarityParams = options;
106 initTreePanel(ap, type, modelName, null, null);
108 // We know this tree has distances. JBPNote TODO: prolly should add this as
109 // a userdefined default
110 // showDistances(true);
113 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
114 String theTitle, AlignmentView inputData)
117 this.treeTitle = theTitle;
118 initTreePanel(alignPanel, null, null, newtree, inputData);
121 public AlignmentI getAlignment()
123 return getTreeCanvas().getViewport().getAlignment();
126 public AlignmentViewport getViewPort()
128 // @Mungo - Why don't we return our own viewport ???
129 return getTreeCanvas().getViewport();
132 void initTreePanel(AlignmentPanel ap, String type, String modelName,
133 NewickFile newTree, AlignmentView inputData)
137 this.treeType = type;
138 this.scoreModelName = modelName;
140 treeCanvas = new TreeCanvas(this, ap, scrollPane);
141 scrollPane.setViewportView(treeCanvas);
143 PaintRefresher.Register(this, ap.av.getSequenceSetId());
145 buildAssociatedViewMenu();
147 final PropertyChangeListener listener = addAlignmentListener();
150 * remove listener when window is closed, so that this
151 * panel can be garbage collected
153 addInternalFrameListener(new InternalFrameAdapter()
156 public void internalFrameClosed(InternalFrameEvent evt)
160 av.removePropertyChangeListener(listener);
165 TreeLoader tl = new TreeLoader(newTree, inputData);
173 protected PropertyChangeListener addAlignmentListener()
175 final PropertyChangeListener listener = new PropertyChangeListener()
177 @SuppressWarnings("unchecked")
179 public void propertyChange(PropertyChangeEvent evt)
181 switch (evt.getPropertyName()) {
182 case AlignmentViewport.PROPERTY_ALIGNMENT:
185 System.out.println("tree is null");
186 // TODO: deal with case when a change event is received whilst a
187 // tree is still being calculated - should save reference for
188 // processing message later.
191 if (evt.getNewValue() == null)
194 "new alignment sequences vector value is null");
198 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
199 treeCanvas.nameHash.clear(); // reset the mapping between canvas
200 // rectangles and leafnodes
206 av.addPropertyChangeListener(listener);
211 public void viewMenu_menuSelected()
213 buildAssociatedViewMenu();
216 void buildAssociatedViewMenu()
218 AlignmentPanel[] aps = PaintRefresher
219 .getAssociatedPanels(av.getSequenceSetId());
220 if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
222 associateLeavesMenu.setVisible(false);
226 associateLeavesMenu.setVisible(true);
229 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
231 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
234 associateLeavesMenu.removeAll();
236 JRadioButtonMenuItem item;
237 ButtonGroup buttonGroup = new ButtonGroup();
238 int i, iSize = aps.length;
239 final TreePanel thisTreePanel = this;
240 for (i = 0; i < iSize; i++)
242 final AlignmentPanel ap = aps[i];
243 item = new JRadioButtonMenuItem(ap.av.getViewName(),
244 ap == treeCanvas.getAssociatedPanel());
245 buttonGroup.add(item);
246 item.addActionListener(new ActionListener()
249 public void actionPerformed(ActionEvent evt)
251 treeCanvas.applyToAllViews = false;
252 treeCanvas.setAssociatedPanel(ap);
253 treeCanvas.setViewport(ap.av);
254 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
258 associateLeavesMenu.add(item);
261 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
262 MessageManager.getString("label.all_views"));
263 buttonGroup.add(itemf);
264 itemf.setSelected(treeCanvas.applyToAllViews);
265 itemf.addActionListener(new ActionListener()
268 public void actionPerformed(ActionEvent evt)
270 treeCanvas.applyToAllViews = itemf.isSelected();
273 associateLeavesMenu.add(itemf);
277 class TreeLoader extends Thread
279 private NewickFile newtree;
281 private AlignmentView odata = null;
283 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
285 this.newtree = newickFile;
286 this.odata = inputData;
288 if (newickFile != null)
290 // Must be outside run(), as Jalview2XML tries to
291 // update distance/bootstrap visibility at the same time
292 showBootstrap(newickFile.HasBootstrap());
293 showDistances(newickFile.HasDistances());
303 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
305 if (tree.getOriginalData() == null)
307 originalSeqData.setVisible(false);
312 ScoreModelI sm = ScoreModels.getInstance()
313 .getScoreModel(scoreModelName,
314 treeCanvas.getAssociatedPanel());
315 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
316 ? new NJTree(av, sm, similarityParams)
317 : new AverageDistanceTree(av, sm, similarityParams);
318 tree = new TreeModel(njtree);
322 tree.reCount(tree.getTopNode());
323 tree.findHeight(tree.getTopNode());
324 treeCanvas.setTree(tree);
325 treeCanvas.repaint();
326 av.setCurrentTree(tree);
327 if (av.getSortByTree())
329 sortByTree_actionPerformed();
334 public void showDistances(boolean b)
336 treeCanvas.setShowDistances(b);
337 distanceMenu.setSelected(b);
340 public void showBootstrap(boolean b)
342 treeCanvas.setShowBootstrap(b);
343 bootstrapMenu.setSelected(b);
346 public void showPlaceholders(boolean b)
348 placeholdersMenu.setState(b);
349 treeCanvas.setMarkPlaceholders(b);
355 * @return DOCUMENT ME!
357 public TreeModel getTree()
369 public void textbox_actionPerformed(ActionEvent e)
371 CutAndPasteTransfer cap = new CutAndPasteTransfer();
373 String newTitle = getPanelTitle();
375 NewickFile fout = new NewickFile(tree.getTopNode());
378 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
379 tree.hasRootDistance()));
380 Desktop.addInternalFrame(cap, newTitle, 500, 100);
381 } catch (OutOfMemoryError oom)
383 new OOMWarning("generating newick tree file", oom);
396 public void saveAsNewick_actionPerformed(ActionEvent e)
398 // TODO: JAL-3048 save newick file for Jalview-JS
399 JalviewFileChooser chooser = new JalviewFileChooser(
400 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
401 chooser.setFileView(new JalviewFileView());
402 chooser.setDialogTitle(
403 MessageManager.getString("label.save_tree_as_newick"));
404 chooser.setToolTipText(MessageManager.getString("action.save"));
406 int value = chooser.showSaveDialog(null);
408 if (value == JalviewFileChooser.APPROVE_OPTION)
410 String choice = chooser.getSelectedFile().getPath();
411 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
412 chooser.getSelectedFile().getParent());
416 jalview.io.NewickFile fout = new jalview.io.NewickFile(
418 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
419 tree.hasRootDistance());
420 java.io.PrintWriter out = new java.io.PrintWriter(
421 new java.io.FileWriter(choice));
424 } catch (Exception ex)
426 ex.printStackTrace();
438 public void printMenu_actionPerformed(ActionEvent e)
440 // Putting in a thread avoids Swing painting problems
441 treeCanvas.startPrinting();
445 public void originalSeqData_actionPerformed(ActionEvent e)
447 AlignmentView originalData = tree.getOriginalData();
448 if (originalData == null)
450 jalview.bin.Cache.log.info(
451 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
454 // decide if av alignment is sufficiently different to original data to
455 // warrant a new window to be created
456 // create new alignmnt window with hidden regions (unhiding hidden regions
457 // yields unaligned seqs)
458 // or create a selection box around columns in alignment view
459 // test Alignment(SeqCigar[])
463 // we try to get the associated view's gap character
464 // but this may fail if the view was closed...
465 gc = av.getGapCharacter();
467 } catch (Exception ex)
471 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
473 if (alAndColsel != null && alAndColsel[0] != null)
475 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
477 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
478 AlignmentI dataset = (av != null && av.getAlignment() != null)
479 ? av.getAlignment().getDataset()
483 al.setDataset(dataset);
489 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
490 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
492 // >>>This is a fix for the moment, until a better solution is
494 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
496 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
499 Desktop.addInternalFrame(af, MessageManager.formatMessage(
500 "label.original_data_for_params", new Object[]
501 { this.title }), AlignFrame.DEFAULT_WIDTH,
502 AlignFrame.DEFAULT_HEIGHT);
514 public void fitToWindow_actionPerformed(ActionEvent e)
516 treeCanvas.fitToWindow = fitToWindow.isSelected();
521 * sort the associated alignment view by the current tree.
526 public void sortByTree_actionPerformed()
529 if (treeCanvas.applyToAllViews)
531 final ArrayList<CommandI> commands = new ArrayList<>();
532 for (AlignmentPanel ap : PaintRefresher
533 .getAssociatedPanels(av.getSequenceSetId()))
535 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
537 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
541 public void undoCommand(AlignmentI[] views)
543 for (CommandI tsort : commands)
545 tsort.undoCommand(views);
552 return commands.size();
556 public String getDescription()
558 return "Tree Sort (many views)";
562 public void doCommand(AlignmentI[] views)
565 for (CommandI tsort : commands)
567 tsort.doCommand(views);
571 for (AlignmentPanel ap : PaintRefresher
572 .getAssociatedPanels(av.getSequenceSetId()))
574 // ensure all the alignFrames refresh their GI after adding an undo item
575 ap.alignFrame.updateEditMenuBar();
580 treeCanvas.getAssociatedPanel().alignFrame
582 sortAlignmentIn(treeCanvas.getAssociatedPanel()));
587 public CommandI sortAlignmentIn(AlignmentPanel ap)
589 // TODO: move to alignment view controller
590 AlignmentViewport viewport = ap.av;
591 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
592 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
594 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
596 ap.paintAlignment(true, false);
607 public void font_actionPerformed(ActionEvent e)
609 if (treeCanvas == null)
614 new FontChooser(this);
617 public Font getTreeFont()
619 return treeCanvas.font;
622 public void setTreeFont(Font f)
624 if (treeCanvas != null)
626 treeCanvas.setFont(f);
637 public void distanceMenu_actionPerformed(ActionEvent e)
639 treeCanvas.setShowDistances(distanceMenu.isSelected());
649 public void bootstrapMenu_actionPerformed(ActionEvent e)
651 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
661 public void placeholdersMenu_actionPerformed(ActionEvent e)
663 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
667 * Outputs the Tree in image format (currently EPS or PNG). The user is
668 * prompted for the file to save to, and for EPS (unless a preference is
669 * already set) for the choice of Text or Lineart for character rendering.
672 public void writeTreeImage(TYPE imageFormat)
674 int width = treeCanvas.getWidth();
675 int height = treeCanvas.getHeight();
676 ImageWriterI writer = new ImageWriterI()
679 public void exportImage(Graphics g) throws Exception
681 treeCanvas.draw(g, width, height);
684 String tree = MessageManager.getString("label.tree");
685 ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
687 exporter.doExport(null, this, width, height, tree.toLowerCase());
691 * change node labels to the annotation referred to by labelClass TODO:
692 * promote to a datamodel modification that can be undone TODO: make argument
693 * one case of a generic transformation function ie { undoStep = apply(Tree,
694 * TransformFunction)};
698 public void changeNames(final String labelClass)
700 tree.applyToNodes(new NodeTransformI()
704 public void transform(BinaryNode node)
706 if (node instanceof SequenceNode
707 && !((SequenceNode) node).isPlaceholder()
708 && !((SequenceNode) node).isDummy())
710 String newname = null;
711 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
714 // search dbrefs, features and annotation
715 List<DBRefEntry> refs = jalview.util.DBRefUtils
716 .selectRefs(sq.getDBRefs(), new String[]
717 { labelClass.toUpperCase() });
720 for (int i = 0, ni = refs.size(); i < ni; i++)
724 newname = new String(refs.get(i).getAccessionId());
728 newname += "; " + refs.get(i).getAccessionId();
734 List<SequenceFeature> features = sq.getFeatures()
735 .getPositionalFeatures(labelClass);
736 for (SequenceFeature feature : features)
740 newname = feature.getDescription();
744 newname = newname + "; " + feature.getDescription();
751 // String oldname = ((SequenceNode) node).getName();
752 // TODO : save oldname in the undo object for this modification.
753 ((SequenceNode) node).setName(newname);
761 * Formats a localised title for the tree panel, like
763 * Neighbour Joining Using BLOSUM62
765 * For a tree loaded from file, just uses the file name
769 public String getPanelTitle()
771 if (treeTitle != null)
777 * i18n description of Neighbour Joining or Average Distance method
779 String treecalcnm = MessageManager
780 .getString("label.tree_calc_" + treeType.toLowerCase());
783 * short score model name (long description can be too long)
785 String smn = scoreModelName;
788 * put them together as <method> Using <model>
790 final String ttl = MessageManager.formatMessage("label.calc_title",
796 * Builds an EPS image and writes it to the specified file.
800 * true for Text character rendering, false for Lineart
802 protected void writeEpsFile(File outFile, boolean textOption)
806 int width = treeCanvas.getWidth();
807 int height = treeCanvas.getHeight();
809 FileOutputStream out = new FileOutputStream(
811 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
813 pg.setAccurateTextMode(!textOption);
814 treeCanvas.draw(pg, width, height);
818 } catch (Exception ex)
820 System.err.println("Error writing tree as EPS");
821 ex.printStackTrace();
825 public AlignViewport getViewport()
830 public void setViewport(AlignViewport av)
835 public TreeCanvas getTreeCanvas()