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.awt.event.KeyAdapter;
28 import java.awt.event.KeyEvent;
29 import java.beans.PropertyChangeEvent;
30 import java.beans.PropertyChangeListener;
32 import java.io.FileOutputStream;
33 import java.util.ArrayList;
34 import java.util.List;
35 import java.util.Locale;
37 import javax.swing.ButtonGroup;
38 import javax.swing.JMenuItem;
39 import javax.swing.JRadioButtonMenuItem;
40 import javax.swing.event.InternalFrameAdapter;
41 import javax.swing.event.InternalFrameEvent;
43 import org.jibble.epsgraphics.EpsGraphics2D;
45 import jalview.analysis.AlignmentSorter;
46 import jalview.analysis.AverageDistanceTree;
47 import jalview.analysis.NJTree;
48 import jalview.analysis.TreeBuilder;
49 import jalview.analysis.TreeModel;
50 import jalview.analysis.scoremodels.ScoreModels;
51 import jalview.api.analysis.ScoreModelI;
52 import jalview.api.analysis.SimilarityParamsI;
53 import jalview.bin.Cache;
54 import jalview.bin.Console;
55 import jalview.commands.CommandI;
56 import jalview.commands.OrderCommand;
57 import jalview.datamodel.Alignment;
58 import jalview.datamodel.AlignmentAnnotation;
59 import jalview.datamodel.AlignmentI;
60 import jalview.datamodel.AlignmentView;
61 import jalview.datamodel.BinaryNode;
62 import jalview.datamodel.DBRefEntry;
63 import jalview.datamodel.HiddenColumns;
64 import jalview.datamodel.NodeTransformI;
65 import jalview.datamodel.SequenceFeature;
66 import jalview.datamodel.SequenceI;
67 import jalview.datamodel.SequenceNode;
68 import jalview.gui.ImageExporter.ImageWriterI;
69 import jalview.io.JalviewFileChooser;
70 import jalview.io.JalviewFileView;
71 import jalview.io.NewickFile;
72 import jalview.io.exceptions.ImageOutputException;
73 import jalview.jbgui.GTreePanel;
74 import jalview.util.ImageMaker.TYPE;
75 import jalview.util.MessageManager;
76 import jalview.viewmodel.AlignmentViewport;
84 public class TreePanel extends GTreePanel
88 String scoreModelName; // if tree computed
90 String treeTitle; // if tree loaded
92 SimilarityParamsI similarityParams;
94 private TreeCanvas treeCanvas;
98 private AlignViewport av;
101 * Creates a new TreePanel object.
108 public TreePanel(AlignmentPanel ap, String type, String modelName,
109 SimilarityParamsI options)
112 this.setFrameIcon(null);
113 this.similarityParams = options;
114 initTreePanel(ap, type, modelName, null, null);
116 // We know this tree has distances. JBPNote TODO: prolly should add this as
117 // a userdefined default
118 // showDistances(true);
121 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
122 String theTitle, AlignmentView inputData)
125 this.setFrameIcon(null);
126 this.treeTitle = theTitle;
127 initTreePanel(alignPanel, null, null, newtree, inputData);
131 * columnwise tree associated with positions in aa
138 public TreePanel(AlignmentPanel alignPanel, NewickFile fin,
139 AlignmentAnnotation aa, String title)
143 assocAnnotation = aa;
144 this.setFrameIcon(null);
145 this.treeTitle = title;
146 initTreePanel(alignPanel, null, null, fin, null);
149 boolean columnWise = false;
151 AlignmentAnnotation assocAnnotation = null;
153 public boolean isColumnWise()
158 public AlignmentAnnotation getAssocAnnotation()
160 return assocAnnotation;
163 public AlignmentI getAlignment()
165 return getTreeCanvas().getViewport().getAlignment();
168 public AlignmentViewport getViewPort()
170 // @Mungo - Why don't we return our own viewport ???
171 return getTreeCanvas().getViewport();
174 void initTreePanel(AlignmentPanel ap, String type, String modelName,
175 NewickFile newTree, AlignmentView inputData)
179 this.treeType = type;
180 this.scoreModelName = modelName;
182 treeCanvas = new TreeCanvas(this, ap, scrollPane);
183 scrollPane.setViewportView(treeCanvas);
187 bootstrapMenu.setVisible(false);
188 placeholdersMenu.setState(false);
189 placeholdersMenu.setVisible(false);
190 fitToWindow.setState(false);
191 sortAssocViews.setVisible(false);
195 addKeyListener(new KeyAdapter()
198 public void keyPressed(KeyEvent e)
200 switch (e.getKeyCode())
203 treeCanvas.clearSelectedLeaves();
211 PaintRefresher.Register(this, ap.av.getSequenceSetId());
213 buildAssociatedViewMenu();
215 final PropertyChangeListener listener = addAlignmentListener();
218 * remove listener when window is closed, so that this
219 * panel can be garbage collected
221 addInternalFrameListener(new InternalFrameAdapter()
224 public void internalFrameClosed(InternalFrameEvent evt)
228 av.removePropertyChangeListener(listener);
234 TreeLoader tl = new TreeLoader(newTree, inputData);
240 * Ensure any potentially large object references are nulled
242 public void releaseReferences()
245 this.treeCanvas.tree = null;
246 this.treeCanvas.nodeHash = null;
247 this.treeCanvas.nameHash = null;
253 protected PropertyChangeListener addAlignmentListener()
255 final PropertyChangeListener listener = new PropertyChangeListener()
258 public void propertyChange(PropertyChangeEvent evt)
260 if (evt.getPropertyName().equals("alignment"))
264 System.out.println("tree is null");
265 // TODO: deal with case when a change event is received whilst a
266 // tree is still being calculated - should save reference for
267 // processing message later.
270 if (evt.getNewValue() == null)
273 "new alignment sequences vector value is null");
276 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
277 treeCanvas.nameHash.clear(); // reset the mapping between canvas
278 // rectangles and leafnodes
283 av.addPropertyChangeListener(listener);
288 public void viewMenu_menuSelected()
290 buildAssociatedViewMenu();
293 void buildAssociatedViewMenu()
295 AlignmentPanel[] aps = PaintRefresher
296 .getAssociatedPanels(av.getSequenceSetId());
297 if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
299 associateLeavesMenu.setVisible(false);
303 associateLeavesMenu.setVisible(true);
306 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
308 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
311 associateLeavesMenu.removeAll();
313 JRadioButtonMenuItem item;
314 ButtonGroup buttonGroup = new ButtonGroup();
315 int i, iSize = aps.length;
316 final TreePanel thisTreePanel = this;
317 for (i = 0; i < iSize; i++)
319 final AlignmentPanel ap = aps[i];
320 item = new JRadioButtonMenuItem(ap.av.getViewName(),
321 ap == treeCanvas.getAssociatedPanel());
322 buttonGroup.add(item);
323 item.addActionListener(new ActionListener()
326 public void actionPerformed(ActionEvent evt)
328 treeCanvas.applyToAllViews = false;
329 treeCanvas.setAssociatedPanel(ap);
330 treeCanvas.setViewport(ap.av);
331 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
335 associateLeavesMenu.add(item);
338 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
339 MessageManager.getString("label.all_views"));
340 buttonGroup.add(itemf);
341 itemf.setSelected(treeCanvas.applyToAllViews);
342 itemf.addActionListener(new ActionListener()
345 public void actionPerformed(ActionEvent evt)
347 treeCanvas.applyToAllViews = itemf.isSelected();
350 associateLeavesMenu.add(itemf);
354 class TreeLoader extends Thread
356 private NewickFile newtree;
358 private AlignmentView odata = null;
360 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
362 this.newtree = newickFile;
363 this.odata = inputData;
365 if (newickFile != null)
367 // Must be outside run(), as Jalview2XML tries to
368 // update distance/bootstrap visibility at the same time
369 showBootstrap(newickFile.HasBootstrap());
370 showDistances(newickFile.HasDistances());
380 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
382 if (tree.getOriginalData() == null)
384 originalSeqData.setVisible(false);
389 ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
390 scoreModelName, treeCanvas.getAssociatedPanel());
391 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
392 ? new NJTree(av, sm, similarityParams)
393 : new AverageDistanceTree(av, sm, similarityParams);
394 tree = new TreeModel(njtree);
395 // don't display distances for columnwise trees
397 showDistances(!columnWise);
398 tree.reCount(tree.getTopNode());
399 tree.findHeight(tree.getTopNode());
400 treeCanvas.setTree(tree);
401 treeCanvas.repaint();
402 av.setCurrentTree(tree);
403 if (av.getSortByTree())
405 sortByTree_actionPerformed();
410 public void showDistances(boolean b)
412 treeCanvas.setShowDistances(b);
413 distanceMenu.setSelected(b);
416 public void showBootstrap(boolean b)
418 treeCanvas.setShowBootstrap(b);
419 bootstrapMenu.setSelected(b);
422 public void showPlaceholders(boolean b)
424 placeholdersMenu.setState(b);
425 treeCanvas.setMarkPlaceholders(b);
431 * @return DOCUMENT ME!
433 public TreeModel getTree()
445 public void textbox_actionPerformed(ActionEvent e)
447 CutAndPasteTransfer cap = new CutAndPasteTransfer();
449 String newTitle = getPanelTitle();
451 NewickFile fout = new NewickFile(tree.getTopNode());
454 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
455 tree.hasRootDistance()));
456 Desktop.addInternalFrame(cap, newTitle, 500, 100);
457 } catch (OutOfMemoryError oom)
459 new OOMWarning("generating newick tree file", oom);
472 public void saveAsNewick_actionPerformed(ActionEvent e)
474 // TODO: JAL-3048 save newick file for Jalview-JS
475 JalviewFileChooser chooser = new JalviewFileChooser(
476 Cache.getProperty("LAST_DIRECTORY"));
477 chooser.setFileView(new JalviewFileView());
478 chooser.setDialogTitle(
479 MessageManager.getString("label.save_tree_as_newick"));
480 chooser.setToolTipText(MessageManager.getString("action.save"));
482 int value = chooser.showSaveDialog(null);
484 if (value == JalviewFileChooser.APPROVE_OPTION)
486 String choice = chooser.getSelectedFile().getPath();
487 Cache.setProperty("LAST_DIRECTORY",
488 chooser.getSelectedFile().getParent());
492 jalview.io.NewickFile fout = new jalview.io.NewickFile(
494 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
495 tree.hasRootDistance());
496 java.io.PrintWriter out = new java.io.PrintWriter(
497 new java.io.FileWriter(choice));
500 } catch (Exception ex)
502 ex.printStackTrace();
514 public void printMenu_actionPerformed(ActionEvent e)
516 // Putting in a thread avoids Swing painting problems
517 treeCanvas.startPrinting();
521 public void originalSeqData_actionPerformed(ActionEvent e)
523 AlignmentView originalData = tree.getOriginalData();
524 if (originalData == null)
527 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
530 // decide if av alignment is sufficiently different to original data to
531 // warrant a new window to be created
532 // create new alignmnt window with hidden regions (unhiding hidden regions
533 // yields unaligned seqs)
534 // or create a selection box around columns in alignment view
535 // test Alignment(SeqCigar[])
539 // we try to get the associated view's gap character
540 // but this may fail if the view was closed...
541 gc = av.getGapCharacter();
543 } catch (Exception ex)
547 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
549 if (alAndColsel != null && alAndColsel[0] != null)
551 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
553 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
554 AlignmentI dataset = (av != null && av.getAlignment() != null)
555 ? av.getAlignment().getDataset()
559 al.setDataset(dataset);
565 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
566 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
568 // >>>This is a fix for the moment, until a better solution is
570 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
572 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
575 Desktop.addInternalFrame(af, MessageManager.formatMessage(
576 "label.original_data_for_params", new Object[]
577 { this.title }), AlignFrame.DEFAULT_WIDTH,
578 AlignFrame.DEFAULT_HEIGHT);
590 public void fitToWindow_actionPerformed(ActionEvent e)
592 treeCanvas.fitToWindow = fitToWindow.isSelected();
597 * sort the associated alignment view by the current tree.
602 public void sortByTree_actionPerformed()
605 if (treeCanvas.applyToAllViews)
607 final ArrayList<CommandI> commands = new ArrayList<>();
608 for (AlignmentPanel ap : PaintRefresher
609 .getAssociatedPanels(av.getSequenceSetId()))
611 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
613 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
617 public void undoCommand(AlignmentI[] views)
619 for (CommandI tsort : commands)
621 tsort.undoCommand(views);
628 return commands.size();
632 public String getDescription()
634 return "Tree Sort (many views)";
638 public void doCommand(AlignmentI[] views)
641 for (CommandI tsort : commands)
643 tsort.doCommand(views);
647 for (AlignmentPanel ap : PaintRefresher
648 .getAssociatedPanels(av.getSequenceSetId()))
650 // ensure all the alignFrames refresh their GI after adding an undo item
651 ap.alignFrame.updateEditMenuBar();
656 treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
657 sortAlignmentIn(treeCanvas.getAssociatedPanel()));
662 public CommandI sortAlignmentIn(AlignmentPanel ap)
664 // TODO: move to alignment view controller
665 AlignmentViewport viewport = ap.av;
666 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
667 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
669 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
671 ap.paintAlignment(true, false);
682 public void font_actionPerformed(ActionEvent e)
684 if (treeCanvas == null)
689 new FontChooser(this);
692 public Font getTreeFont()
694 return treeCanvas.font;
697 public void setTreeFont(Font f)
699 if (treeCanvas != null)
701 treeCanvas.setFont(f);
712 public void distanceMenu_actionPerformed(ActionEvent e)
714 treeCanvas.setShowDistances(distanceMenu.isSelected());
724 public void bootstrapMenu_actionPerformed(ActionEvent e)
726 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
736 public void placeholdersMenu_actionPerformed(ActionEvent e)
738 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
742 * Outputs the Tree in image format (currently EPS or PNG). The user is
743 * prompted for the file to save to, and for EPS (unless a preference is
744 * already set) for the choice of Text or Lineart for character rendering.
747 public void writeTreeImage(TYPE imageFormat)
749 int width = treeCanvas.getWidth();
750 int height = treeCanvas.getHeight();
751 ImageWriterI writer = new ImageWriterI()
754 public void exportImage(Graphics g) throws Exception
756 treeCanvas.draw(g, width, height);
759 String tree = MessageManager.getString("label.tree");
760 ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
763 exporter.doExport(null, this, width, height,
764 tree.toLowerCase(Locale.ROOT));
765 } catch (ImageOutputException ioex) {
766 Console.error("Unexpected error whilst writing "+imageFormat.toString(),ioex);
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()
784 public void transform(BinaryNode node)
786 if (node instanceof SequenceNode
787 && !((SequenceNode) node).isPlaceholder()
788 && !((SequenceNode) node).isDummy())
790 String newname = null;
791 SequenceI sq = (SequenceI) ((BinaryNode) node).element();
794 // search dbrefs, features and annotation
795 List<DBRefEntry> refs = jalview.util.DBRefUtils
796 .selectRefs(sq.getDBRefs(), new String[]
797 { labelClass.toUpperCase(Locale.ROOT) });
800 for (int i = 0, ni = refs.size(); i < ni; i++)
804 newname = new String(refs.get(i).getAccessionId());
808 newname += "; " + refs.get(i).getAccessionId();
814 List<SequenceFeature> features = sq.getFeatures()
815 .getPositionalFeatures(labelClass);
816 for (SequenceFeature feature : features)
820 newname = feature.getDescription();
824 newname = newname + "; " + feature.getDescription();
831 // String oldname = ((SequenceNode) node).getName();
832 // TODO : save oldname in the undo object for this modification.
833 ((BinaryNode) node).setName(newname);
841 * Formats a localised title for the tree panel, like
843 * Neighbour Joining Using BLOSUM62
845 * For a tree loaded from file, just uses the file name
849 public String getPanelTitle()
851 if (treeTitle != null)
857 * i18n description of Neighbour Joining or Average Distance method
859 String treecalcnm = MessageManager.getString(
860 "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
863 * short score model name (long description can be too long)
865 String smn = scoreModelName;
868 * put them together as <method> Using <model>
870 final String ttl = MessageManager.formatMessage("label.calc_title",
876 * Builds an EPS image and writes it to the specified file.
880 * true for Text character rendering, false for Lineart
882 protected void writeEpsFile(File outFile, boolean textOption)
886 int width = treeCanvas.getWidth();
887 int height = treeCanvas.getHeight();
889 FileOutputStream out = new FileOutputStream(outFile);
890 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
892 pg.setAccurateTextMode(!textOption);
893 treeCanvas.draw(pg, width, height);
897 } catch (Exception ex)
899 System.err.println("Error writing tree as EPS");
900 ex.printStackTrace();
904 public AlignViewport getViewport()
909 public void setViewport(AlignViewport av)
914 public TreeCanvas getTreeCanvas()