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.bin.Cache;
32 import jalview.commands.CommandI;
33 import jalview.commands.OrderCommand;
34 import jalview.datamodel.Alignment;
35 import jalview.datamodel.AlignmentI;
36 import jalview.datamodel.AlignmentView;
37 import jalview.datamodel.BinaryNode;
38 import jalview.datamodel.DBRefEntry;
39 import jalview.datamodel.HiddenColumns;
40 import jalview.datamodel.NodeTransformI;
41 import jalview.datamodel.SequenceFeature;
42 import jalview.datamodel.SequenceI;
43 import jalview.datamodel.SequenceNode;
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;
49 import jalview.util.MessageManager;
50 import jalview.util.dialogrunner.RunResponse;
51 import jalview.viewmodel.AlignmentViewport;
54 import java.awt.Graphics;
55 import java.awt.event.ActionEvent;
56 import java.awt.event.ActionListener;
57 import java.awt.image.BufferedImage;
58 import java.beans.PropertyChangeEvent;
59 import java.beans.PropertyChangeListener;
61 import java.io.FileOutputStream;
62 import java.util.ArrayList;
63 import java.util.List;
64 import java.util.concurrent.atomic.AtomicBoolean;
66 import javax.imageio.ImageIO;
67 import javax.swing.ButtonGroup;
68 import javax.swing.JMenuItem;
69 import javax.swing.JOptionPane;
70 import javax.swing.JRadioButtonMenuItem;
71 import javax.swing.event.InternalFrameAdapter;
72 import javax.swing.event.InternalFrameEvent;
74 import org.jibble.epsgraphics.EpsGraphics2D;
82 public class TreePanel extends GTreePanel
86 String scoreModelName; // if tree computed
88 String treeTitle; // if tree loaded
90 SimilarityParamsI similarityParams;
92 TreeCanvas treeCanvas;
99 * Creates a new TreePanel object.
106 public TreePanel(AlignmentPanel ap, String type, String modelName,
107 SimilarityParamsI options)
110 this.similarityParams = options;
111 initTreePanel(ap, type, modelName, null, null);
113 // We know this tree has distances. JBPNote TODO: prolly should add this as
114 // a userdefined default
115 // showDistances(true);
118 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
119 String theTitle, AlignmentView inputData)
122 this.treeTitle = theTitle;
123 initTreePanel(alignPanel, null, null, newtree, inputData);
126 public AlignmentI getAlignment()
128 return treeCanvas.av.getAlignment();
131 public AlignmentViewport getViewPort()
133 return treeCanvas.av;
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);
169 TreeLoader tl = new TreeLoader(newTree, inputData);
177 protected PropertyChangeListener addAlignmentListener()
179 final PropertyChangeListener listener = new PropertyChangeListener()
182 public void propertyChange(PropertyChangeEvent evt)
184 if (evt.getPropertyName().equals("alignment"))
188 System.out.println("tree is null");
189 // TODO: deal with case when a change event is received whilst a
190 // tree is still being calculated - should save reference for
191 // processing message later.
194 if (evt.getNewValue() == null)
197 "new alignment sequences vector value is null");
200 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
201 treeCanvas.nameHash.clear(); // reset the mapping between canvas
202 // rectangles and leafnodes
207 av.addPropertyChangeListener(listener);
212 public void viewMenu_menuSelected()
214 buildAssociatedViewMenu();
217 void buildAssociatedViewMenu()
219 AlignmentPanel[] aps = PaintRefresher
220 .getAssociatedPanels(av.getSequenceSetId());
221 if (aps.length == 1 && treeCanvas.ap == aps[0])
223 associateLeavesMenu.setVisible(false);
227 associateLeavesMenu.setVisible(true);
230 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
232 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
235 associateLeavesMenu.removeAll();
237 JRadioButtonMenuItem item;
238 ButtonGroup buttonGroup = new ButtonGroup();
239 int i, iSize = aps.length;
240 final TreePanel thisTreePanel = this;
241 for (i = 0; i < iSize; i++)
243 final AlignmentPanel ap = aps[i];
244 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
245 buttonGroup.add(item);
246 item.addActionListener(new ActionListener()
249 public void actionPerformed(ActionEvent evt)
251 treeCanvas.applyToAllViews = false;
253 treeCanvas.av = 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, treeCanvas.ap);
314 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
315 ? new NJTree(av, sm, similarityParams)
316 : new AverageDistanceTree(av, sm, similarityParams);
317 tree = new TreeModel(njtree);
321 tree.reCount(tree.getTopNode());
322 tree.findHeight(tree.getTopNode());
323 treeCanvas.setTree(tree);
324 treeCanvas.repaint();
325 av.setCurrentTree(tree);
326 if (av.getSortByTree())
328 sortByTree_actionPerformed();
333 public void showDistances(boolean b)
335 treeCanvas.setShowDistances(b);
336 distanceMenu.setSelected(b);
339 public void showBootstrap(boolean b)
341 treeCanvas.setShowBootstrap(b);
342 bootstrapMenu.setSelected(b);
345 public void showPlaceholders(boolean b)
347 placeholdersMenu.setState(b);
348 treeCanvas.setMarkPlaceholders(b);
354 * @return DOCUMENT ME!
356 public TreeModel getTree()
368 public void textbox_actionPerformed(ActionEvent e)
370 CutAndPasteTransfer cap = new CutAndPasteTransfer();
372 String newTitle = getPanelTitle();
374 NewickFile fout = new NewickFile(tree.getTopNode());
377 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
378 tree.hasRootDistance()));
379 Desktop.addInternalFrame(cap, newTitle, 500, 100);
380 } catch (OutOfMemoryError oom)
382 new OOMWarning("generating newick tree file", oom);
395 public void saveAsNewick_actionPerformed(ActionEvent e)
397 // TODO: JAL-3048 save newick file for Jalview-JS
398 JalviewFileChooser chooser = new JalviewFileChooser(
399 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
400 chooser.setFileView(new JalviewFileView());
401 chooser.setDialogTitle(
402 MessageManager.getString("label.save_tree_as_newick"));
403 chooser.setToolTipText(MessageManager.getString("action.save"));
405 int value = chooser.showSaveDialog(null);
407 if (value == JalviewFileChooser.APPROVE_OPTION)
409 String choice = chooser.getSelectedFile().getPath();
410 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
411 chooser.getSelectedFile().getParent());
415 jalview.io.NewickFile fout = new jalview.io.NewickFile(
417 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
418 tree.hasRootDistance());
419 java.io.PrintWriter out = new java.io.PrintWriter(
420 new java.io.FileWriter(choice));
423 } catch (Exception ex)
425 ex.printStackTrace();
437 public void printMenu_actionPerformed(ActionEvent e)
439 // Putting in a thread avoids Swing painting problems
440 treeCanvas.startPrinting();
444 public void originalSeqData_actionPerformed(ActionEvent e)
446 AlignmentView originalData = tree.getOriginalData();
447 if (originalData == null)
449 jalview.bin.Cache.log.info(
450 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
453 // decide if av alignment is sufficiently different to original data to
454 // warrant a new window to be created
455 // create new alignmnt window with hidden regions (unhiding hidden regions
456 // yields unaligned seqs)
457 // or create a selection box around columns in alignment view
458 // test Alignment(SeqCigar[])
462 // we try to get the associated view's gap character
463 // but this may fail if the view was closed...
464 gc = av.getGapCharacter();
466 } catch (Exception ex)
470 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
472 if (alAndColsel != null && alAndColsel[0] != null)
474 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
476 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
477 AlignmentI dataset = (av != null && av.getAlignment() != null)
478 ? av.getAlignment().getDataset()
482 al.setDataset(dataset);
488 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
489 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
491 // >>>This is a fix for the moment, until a better solution is
493 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
495 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
498 Desktop.addInternalFrame(af, MessageManager.formatMessage(
499 "label.original_data_for_params", new Object[]
500 { this.title }), AlignFrame.DEFAULT_WIDTH,
501 AlignFrame.DEFAULT_HEIGHT);
513 public void fitToWindow_actionPerformed(ActionEvent e)
515 treeCanvas.fitToWindow = fitToWindow.isSelected();
520 * sort the associated alignment view by the current tree.
525 public void sortByTree_actionPerformed()
528 if (treeCanvas.applyToAllViews)
530 final ArrayList<CommandI> commands = new ArrayList<>();
531 for (AlignmentPanel ap : PaintRefresher
532 .getAssociatedPanels(av.getSequenceSetId()))
534 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
536 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
540 public void undoCommand(AlignmentI[] views)
542 for (CommandI tsort : commands)
544 tsort.undoCommand(views);
551 return commands.size();
555 public String getDescription()
557 return "Tree Sort (many views)";
561 public void doCommand(AlignmentI[] views)
564 for (CommandI tsort : commands)
566 tsort.doCommand(views);
570 for (AlignmentPanel ap : PaintRefresher
571 .getAssociatedPanels(av.getSequenceSetId()))
573 // ensure all the alignFrames refresh their GI after adding an undo item
574 ap.alignFrame.updateEditMenuBar();
579 treeCanvas.ap.alignFrame
580 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
585 public CommandI sortAlignmentIn(AlignmentPanel ap)
587 // TODO: move to alignment view controller
588 AlignmentViewport viewport = ap.av;
589 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
590 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
592 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
594 ap.paintAlignment(true, false);
605 public void font_actionPerformed(ActionEvent e)
607 if (treeCanvas == null)
612 new FontChooser(this);
615 public Font getTreeFont()
617 return treeCanvas.font;
620 public void setTreeFont(Font f)
622 if (treeCanvas != null)
624 treeCanvas.setFont(f);
635 public void distanceMenu_actionPerformed(ActionEvent e)
637 treeCanvas.setShowDistances(distanceMenu.isSelected());
647 public void bootstrapMenu_actionPerformed(ActionEvent e)
649 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
659 public void placeholdersMenu_actionPerformed(ActionEvent e)
661 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
665 * Outputs the Tree in EPS format. The user is prompted for the file to save
666 * to, and (unless a preference is already set) for the choice of Text or
667 * Lineart for character rendering.
670 public void epsTree_actionPerformed()
672 JalviewFileChooser chooser = new JalviewFileChooser(
673 ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
674 chooser.setFileView(new JalviewFileView());
675 chooser.setDialogTitle(
676 MessageManager.getString("label.create_eps_from_tree"));
677 chooser.setToolTipText(MessageManager.getString("action.save"));
679 int value = chooser.showSaveDialog(this);
681 if (value != JalviewFileChooser.APPROVE_OPTION)
685 File outFile = chooser.getSelectedFile();
686 Cache.setProperty("LAST_DIRECTORY", outFile.getParent());
688 String renderStyle = Cache.getDefault("EPS_RENDERING",
690 AtomicBoolean textOption = new AtomicBoolean(
691 !"Lineart".equals(renderStyle));
694 * configure the export action to run on OK in the dialog
696 RunResponse okAction = new RunResponse(JOptionPane.OK_OPTION)
701 writeEpsFile(outFile, textOption.get());
706 * Prompt for character rendering style if preference is not set
708 if (renderStyle.equalsIgnoreCase("Prompt each time")
709 && !(System.getProperty("java.awt.headless") != null && System
710 .getProperty("java.awt.headless").equals("true")))
712 LineartOptions eps = new LineartOptions("EPS_RENDERING", "EPS",
714 eps.setResponseAction(okAction);
716 /* no code here - JalviewJS won't execute it */
721 * if preference set, just run the export action
723 writeEpsFile(outFile, textOption.get());
734 public void pngTree_actionPerformed(ActionEvent e)
736 int width = treeCanvas.getWidth();
737 int height = treeCanvas.getHeight();
741 JalviewFileChooser chooser = new JalviewFileChooser(
742 ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
744 chooser.setFileView(new jalview.io.JalviewFileView());
745 chooser.setDialogTitle(
746 MessageManager.getString("label.create_png_from_tree"));
747 chooser.setToolTipText(MessageManager.getString("action.save"));
749 int value = chooser.showSaveDialog(this);
751 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
756 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
757 chooser.getSelectedFile().getParent());
759 FileOutputStream out = new FileOutputStream(
760 chooser.getSelectedFile());
762 BufferedImage bi = new BufferedImage(width, height,
763 BufferedImage.TYPE_INT_RGB);
764 Graphics png = bi.getGraphics();
766 treeCanvas.draw(png, width, height);
768 ImageIO.write(bi, "png", out);
770 } catch (Exception ex)
772 ex.printStackTrace();
777 * change node labels to the annotation referred to by labelClass TODO:
778 * promote to a datamodel modification that can be undone TODO: make argument
779 * one case of a generic transformation function ie { undoStep = apply(Tree,
780 * TransformFunction)};
784 public void changeNames(final String labelClass)
786 tree.applyToNodes(new NodeTransformI()
790 public void transform(BinaryNode node)
792 if (node instanceof SequenceNode
793 && !((SequenceNode) node).isPlaceholder()
794 && !((SequenceNode) node).isDummy())
796 String newname = null;
797 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
800 // search dbrefs, features and annotation
801 DBRefEntry[] refs = jalview.util.DBRefUtils
802 .selectRefs(sq.getDBRefs(), new String[]
803 { labelClass.toUpperCase() });
806 for (int i = 0; i < refs.length; i++)
810 newname = new String(refs[i].getAccessionId());
814 newname = newname + "; " + refs[i].getAccessionId();
820 List<SequenceFeature> features = sq.getFeatures()
821 .getPositionalFeatures(labelClass);
822 for (SequenceFeature feature : features)
826 newname = feature.getDescription();
830 newname = newname + "; " + feature.getDescription();
837 // String oldname = ((SequenceNode) node).getName();
838 // TODO : save oldname in the undo object for this modification.
839 ((SequenceNode) node).setName(newname);
847 * Formats a localised title for the tree panel, like
849 * Neighbour Joining Using BLOSUM62
851 * For a tree loaded from file, just uses the file name
855 public String getPanelTitle()
857 if (treeTitle != null)
863 * i18n description of Neighbour Joining or Average Distance method
865 String treecalcnm = MessageManager
866 .getString("label.tree_calc_" + treeType.toLowerCase());
869 * short score model name (long description can be too long)
871 String smn = scoreModelName;
874 * put them together as <method> Using <model>
876 final String ttl = MessageManager.formatMessage("label.treecalc_title",
882 * Builds an EPS image and writes it to the specified file.
886 * true for Text character rendering, false for Lineart
888 protected void writeEpsFile(File outFile, boolean textOption)
892 int width = treeCanvas.getWidth();
893 int height = treeCanvas.getHeight();
895 FileOutputStream out = new FileOutputStream(
897 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
899 pg.setAccurateTextMode(!textOption);
900 treeCanvas.draw(pg, width, height);
904 } catch (Exception ex)
906 System.err.println("Error writing tree as EPS");
907 ex.printStackTrace();