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 java.util.Locale;
25 import jalview.analysis.AlignmentSorter;
26 import jalview.analysis.AverageDistanceTree;
27 import jalview.analysis.NJTree;
28 import jalview.analysis.TreeBuilder;
29 import jalview.analysis.TreeModel;
30 import jalview.analysis.scoremodels.ScoreModels;
31 import jalview.api.analysis.ScoreModelI;
32 import jalview.api.analysis.SimilarityParamsI;
33 import jalview.bin.Cache;
34 import jalview.bin.Console;
35 import jalview.commands.CommandI;
36 import jalview.commands.OrderCommand;
37 import jalview.datamodel.Alignment;
38 import jalview.datamodel.AlignmentI;
39 import jalview.datamodel.AlignmentView;
40 import jalview.datamodel.BinaryNode;
41 import jalview.datamodel.DBRefEntry;
42 import jalview.datamodel.HiddenColumns;
43 import jalview.datamodel.NodeTransformI;
44 import jalview.datamodel.SequenceFeature;
45 import jalview.datamodel.SequenceI;
46 import jalview.datamodel.SequenceNode;
47 import jalview.gui.ImageExporter.ImageWriterI;
48 import jalview.io.JalviewFileChooser;
49 import jalview.io.JalviewFileView;
50 import jalview.io.NewickFile;
51 import jalview.jbgui.GTreePanel;
52 import jalview.util.ImageMaker.TYPE;
53 import jalview.util.MessageManager;
54 import jalview.viewmodel.AlignmentViewport;
57 import java.awt.Graphics;
58 import java.awt.event.ActionEvent;
59 import java.awt.event.ActionListener;
60 import java.beans.PropertyChangeEvent;
61 import java.beans.PropertyChangeListener;
63 import java.io.FileOutputStream;
64 import java.util.ArrayList;
65 import java.util.List;
67 import javax.swing.ButtonGroup;
68 import javax.swing.JMenuItem;
69 import javax.swing.JRadioButtonMenuItem;
70 import javax.swing.event.InternalFrameAdapter;
71 import javax.swing.event.InternalFrameEvent;
73 import org.jibble.epsgraphics.EpsGraphics2D;
81 public class TreePanel extends GTreePanel
85 String scoreModelName; // if tree computed
87 String treeTitle; // if tree loaded
89 SimilarityParamsI similarityParams;
91 private TreeCanvas treeCanvas;
95 private AlignViewport av;
98 * Creates a new TreePanel object.
105 public TreePanel(AlignmentPanel ap, String type, String modelName,
106 SimilarityParamsI options)
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.treeTitle = theTitle;
122 initTreePanel(alignPanel, null, null, newtree, inputData);
125 public AlignmentI getAlignment()
127 return getTreeCanvas().getViewport().getAlignment();
130 public AlignmentViewport getViewPort()
132 // @Mungo - Why don't we return our own viewport ???
133 return getTreeCanvas().getViewport();
136 void initTreePanel(AlignmentPanel ap, String type, String modelName,
137 NewickFile newTree, AlignmentView inputData)
141 this.treeType = type;
142 this.scoreModelName = modelName;
144 treeCanvas = new TreeCanvas(this, ap, scrollPane);
145 scrollPane.setViewportView(treeCanvas);
147 PaintRefresher.Register(this, ap.av.getSequenceSetId());
149 buildAssociatedViewMenu();
151 final PropertyChangeListener listener = addAlignmentListener();
154 * remove listener when window is closed, so that this
155 * panel can be garbage collected
157 addInternalFrameListener(new InternalFrameAdapter()
160 public void internalFrameClosed(InternalFrameEvent evt)
164 av.removePropertyChangeListener(listener);
170 TreeLoader tl = new TreeLoader(newTree, inputData);
176 * Ensure any potentially large object references are nulled
178 public void releaseReferences()
181 this.treeCanvas.tree = null;
182 this.treeCanvas.nodeHash = null;
183 this.treeCanvas.nameHash = null;
189 protected PropertyChangeListener addAlignmentListener()
191 final PropertyChangeListener listener = new PropertyChangeListener()
194 public void propertyChange(PropertyChangeEvent evt)
196 if (evt.getPropertyName().equals("alignment"))
200 System.out.println("tree is null");
201 // TODO: deal with case when a change event is received whilst a
202 // tree is still being calculated - should save reference for
203 // processing message later.
206 if (evt.getNewValue() == null)
209 "new alignment sequences vector value is null");
212 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
213 treeCanvas.nameHash.clear(); // reset the mapping between canvas
214 // rectangles and leafnodes
219 av.addPropertyChangeListener(listener);
224 public void viewMenu_menuSelected()
226 buildAssociatedViewMenu();
229 void buildAssociatedViewMenu()
231 AlignmentPanel[] aps = PaintRefresher
232 .getAssociatedPanels(av.getSequenceSetId());
233 if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
235 associateLeavesMenu.setVisible(false);
239 associateLeavesMenu.setVisible(true);
242 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
244 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
247 associateLeavesMenu.removeAll();
249 JRadioButtonMenuItem item;
250 ButtonGroup buttonGroup = new ButtonGroup();
251 int i, iSize = aps.length;
252 final TreePanel thisTreePanel = this;
253 for (i = 0; i < iSize; i++)
255 final AlignmentPanel ap = aps[i];
256 item = new JRadioButtonMenuItem(ap.av.getViewName(),
257 ap == treeCanvas.getAssociatedPanel());
258 buttonGroup.add(item);
259 item.addActionListener(new ActionListener()
262 public void actionPerformed(ActionEvent evt)
264 treeCanvas.applyToAllViews = false;
265 treeCanvas.setAssociatedPanel(ap);
266 treeCanvas.setViewport(ap.av);
267 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
271 associateLeavesMenu.add(item);
274 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
275 MessageManager.getString("label.all_views"));
276 buttonGroup.add(itemf);
277 itemf.setSelected(treeCanvas.applyToAllViews);
278 itemf.addActionListener(new ActionListener()
281 public void actionPerformed(ActionEvent evt)
283 treeCanvas.applyToAllViews = itemf.isSelected();
286 associateLeavesMenu.add(itemf);
290 class TreeLoader extends Thread
292 private NewickFile newtree;
294 private AlignmentView odata = null;
296 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
298 this.newtree = newickFile;
299 this.odata = inputData;
301 if (newickFile != null)
303 // Must be outside run(), as Jalview2XML tries to
304 // update distance/bootstrap visibility at the same time
305 showBootstrap(newickFile.HasBootstrap());
306 showDistances(newickFile.HasDistances());
316 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
318 if (tree.getOriginalData() == null)
320 originalSeqData.setVisible(false);
325 ScoreModelI sm = ScoreModels.getInstance()
326 .getScoreModel(scoreModelName,
327 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
595 sortAlignmentIn(treeCanvas.getAssociatedPanel()));
600 public CommandI sortAlignmentIn(AlignmentPanel ap)
602 // TODO: move to alignment view controller
603 AlignmentViewport viewport = ap.av;
604 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
605 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
607 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
609 ap.paintAlignment(true, false);
620 public void font_actionPerformed(ActionEvent e)
622 if (treeCanvas == null)
627 new FontChooser(this);
630 public Font getTreeFont()
632 return treeCanvas.font;
635 public void setTreeFont(Font f)
637 if (treeCanvas != null)
639 treeCanvas.setFont(f);
650 public void distanceMenu_actionPerformed(ActionEvent e)
652 treeCanvas.setShowDistances(distanceMenu.isSelected());
662 public void bootstrapMenu_actionPerformed(ActionEvent e)
664 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
674 public void placeholdersMenu_actionPerformed(ActionEvent e)
676 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
680 * Outputs the Tree in image format (currently EPS or PNG). The user is
681 * prompted for the file to save to, and for EPS (unless a preference is
682 * already set) for the choice of Text or Lineart for character rendering.
685 public void writeTreeImage(TYPE imageFormat)
687 int width = treeCanvas.getWidth();
688 int height = treeCanvas.getHeight();
689 ImageWriterI writer = new ImageWriterI()
692 public void exportImage(Graphics g) throws Exception
694 treeCanvas.draw(g, width, height);
697 String tree = MessageManager.getString("label.tree");
698 ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
700 exporter.doExport(null, this, width, height, 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
793 .getString("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(
824 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
826 pg.setAccurateTextMode(!textOption);
827 treeCanvas.draw(pg, width, height);
831 } catch (Exception ex)
833 System.err.println("Error writing tree as EPS");
834 ex.printStackTrace();
838 public AlignViewport getViewport()
843 public void setViewport(AlignViewport av)
848 public TreeCanvas getTreeCanvas()