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.jbgui.GTreePanel;
73 import jalview.util.ImageMaker.TYPE;
74 import jalview.util.MessageManager;
75 import jalview.viewmodel.AlignmentViewport;
83 public class TreePanel extends GTreePanel
87 String scoreModelName; // if tree computed
89 String treeTitle; // if tree loaded
91 SimilarityParamsI similarityParams;
93 private TreeCanvas treeCanvas;
97 private AlignViewport av;
100 * Creates a new TreePanel object.
107 public TreePanel(AlignmentPanel ap, String type, String modelName,
108 SimilarityParamsI options)
111 this.setFrameIcon(null);
112 this.similarityParams = options;
113 initTreePanel(ap, type, modelName, null, null);
115 // We know this tree has distances. JBPNote TODO: prolly should add this as
116 // a userdefined default
117 // showDistances(true);
120 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
121 String theTitle, AlignmentView inputData)
124 this.setFrameIcon(null);
125 this.treeTitle = theTitle;
126 initTreePanel(alignPanel, null, null, newtree, inputData);
130 * columnwise tree associated with positions in aa
137 public TreePanel(AlignmentPanel alignPanel, NewickFile fin,
138 AlignmentAnnotation aa, String title)
142 assocAnnotation = aa;
143 this.setFrameIcon(null);
144 this.treeTitle = title;
145 initTreePanel(alignPanel, null, null, fin, null);
148 boolean columnWise = false;
150 AlignmentAnnotation assocAnnotation = null;
152 public boolean isColumnWise()
157 public AlignmentAnnotation getAssocAnnotation()
159 return assocAnnotation;
162 public AlignmentI getAlignment()
164 return getTreeCanvas().getViewport().getAlignment();
167 public AlignmentViewport getViewPort()
169 // @Mungo - Why don't we return our own viewport ???
170 return getTreeCanvas().getViewport();
173 void initTreePanel(AlignmentPanel ap, String type, String modelName,
174 NewickFile newTree, AlignmentView inputData)
178 this.treeType = type;
179 this.scoreModelName = modelName;
183 bootstrapMenu.setVisible(false);
184 placeholdersMenu.setSelected(false);
185 placeholdersMenu.setVisible(false);
186 fitToWindow.setSelected(false);
187 sortAssocViews.setVisible(false);
190 treeCanvas = new TreeCanvas(this, ap, scrollPane);
191 scrollPane.setViewportView(treeCanvas);
193 addKeyListener(new KeyAdapter()
196 public void keyPressed(KeyEvent e)
198 switch (e.getKeyCode())
201 treeCanvas.clearSelectedLeaves();
209 PaintRefresher.Register(this, ap.av.getSequenceSetId());
211 buildAssociatedViewMenu();
213 final PropertyChangeListener listener = addAlignmentListener();
216 * remove listener when window is closed, so that this
217 * panel can be garbage collected
219 addInternalFrameListener(new InternalFrameAdapter()
222 public void internalFrameClosed(InternalFrameEvent evt)
226 av.removePropertyChangeListener(listener);
232 TreeLoader tl = new TreeLoader(newTree, inputData);
238 * Ensure any potentially large object references are nulled
240 public void releaseReferences()
243 this.treeCanvas.tree = null;
244 this.treeCanvas.nodeHash = null;
245 this.treeCanvas.nameHash = null;
251 protected PropertyChangeListener addAlignmentListener()
253 final PropertyChangeListener listener = new PropertyChangeListener()
256 public void propertyChange(PropertyChangeEvent evt)
258 if (evt.getPropertyName().equals("alignment"))
262 System.out.println("tree is null");
263 // TODO: deal with case when a change event is received whilst a
264 // tree is still being calculated - should save reference for
265 // processing message later.
268 if (evt.getNewValue() == null)
271 "new alignment sequences vector value is null");
274 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
275 treeCanvas.nameHash.clear(); // reset the mapping between canvas
276 // rectangles and leafnodes
281 av.addPropertyChangeListener(listener);
286 public void viewMenu_menuSelected()
288 buildAssociatedViewMenu();
291 void buildAssociatedViewMenu()
293 AlignmentPanel[] aps = PaintRefresher
294 .getAssociatedPanels(av.getSequenceSetId());
295 if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
297 associateLeavesMenu.setVisible(false);
301 associateLeavesMenu.setVisible(true);
304 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
306 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
309 associateLeavesMenu.removeAll();
311 JRadioButtonMenuItem item;
312 ButtonGroup buttonGroup = new ButtonGroup();
313 int i, iSize = aps.length;
314 final TreePanel thisTreePanel = this;
315 for (i = 0; i < iSize; i++)
317 final AlignmentPanel ap = aps[i];
318 item = new JRadioButtonMenuItem(ap.av.getViewName(),
319 ap == treeCanvas.getAssociatedPanel());
320 buttonGroup.add(item);
321 item.addActionListener(new ActionListener()
324 public void actionPerformed(ActionEvent evt)
326 treeCanvas.applyToAllViews = false;
327 treeCanvas.setAssociatedPanel(ap);
328 treeCanvas.setViewport(ap.av);
329 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
333 associateLeavesMenu.add(item);
336 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
337 MessageManager.getString("label.all_views"));
338 buttonGroup.add(itemf);
339 itemf.setSelected(treeCanvas.applyToAllViews);
340 itemf.addActionListener(new ActionListener()
343 public void actionPerformed(ActionEvent evt)
345 treeCanvas.applyToAllViews = itemf.isSelected();
348 associateLeavesMenu.add(itemf);
352 class TreeLoader extends Thread
354 private NewickFile newtree;
356 private AlignmentView odata = null;
358 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
360 this.newtree = newickFile;
361 this.odata = inputData;
363 if (newickFile != null)
365 // Must be outside run(), as Jalview2XML tries to
366 // update distance/bootstrap visibility at the same time
367 showBootstrap(newickFile.HasBootstrap());
368 showDistances(newickFile.HasDistances());
378 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
380 if (tree.getOriginalData() == null)
382 originalSeqData.setVisible(false);
387 ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
388 scoreModelName, treeCanvas.getAssociatedPanel());
389 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
390 ? new NJTree(av, sm, similarityParams)
391 : new AverageDistanceTree(av, sm, similarityParams);
392 tree = new TreeModel(njtree);
396 tree.reCount(tree.getTopNode());
397 tree.findHeight(tree.getTopNode());
398 treeCanvas.setTree(tree);
399 treeCanvas.repaint();
400 av.setCurrentTree(tree);
401 if (av.getSortByTree())
403 sortByTree_actionPerformed();
408 public void showDistances(boolean b)
410 treeCanvas.setShowDistances(b);
411 distanceMenu.setSelected(b);
414 public void showBootstrap(boolean b)
416 treeCanvas.setShowBootstrap(b);
417 bootstrapMenu.setSelected(b);
420 public void showPlaceholders(boolean b)
422 placeholdersMenu.setState(b);
423 treeCanvas.setMarkPlaceholders(b);
429 * @return DOCUMENT ME!
431 public TreeModel getTree()
443 public void textbox_actionPerformed(ActionEvent e)
445 CutAndPasteTransfer cap = new CutAndPasteTransfer();
447 String newTitle = getPanelTitle();
449 NewickFile fout = new NewickFile(tree.getTopNode());
452 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
453 tree.hasRootDistance()));
454 Desktop.addInternalFrame(cap, newTitle, 500, 100);
455 } catch (OutOfMemoryError oom)
457 new OOMWarning("generating newick tree file", oom);
470 public void saveAsNewick_actionPerformed(ActionEvent e)
472 // TODO: JAL-3048 save newick file for Jalview-JS
473 JalviewFileChooser chooser = new JalviewFileChooser(
474 Cache.getProperty("LAST_DIRECTORY"));
475 chooser.setFileView(new JalviewFileView());
476 chooser.setDialogTitle(
477 MessageManager.getString("label.save_tree_as_newick"));
478 chooser.setToolTipText(MessageManager.getString("action.save"));
480 int value = chooser.showSaveDialog(null);
482 if (value == JalviewFileChooser.APPROVE_OPTION)
484 String choice = chooser.getSelectedFile().getPath();
485 Cache.setProperty("LAST_DIRECTORY",
486 chooser.getSelectedFile().getParent());
490 jalview.io.NewickFile fout = new jalview.io.NewickFile(
492 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
493 tree.hasRootDistance());
494 java.io.PrintWriter out = new java.io.PrintWriter(
495 new java.io.FileWriter(choice));
498 } catch (Exception ex)
500 ex.printStackTrace();
512 public void printMenu_actionPerformed(ActionEvent e)
514 // Putting in a thread avoids Swing painting problems
515 treeCanvas.startPrinting();
519 public void originalSeqData_actionPerformed(ActionEvent e)
521 AlignmentView originalData = tree.getOriginalData();
522 if (originalData == null)
525 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
528 // decide if av alignment is sufficiently different to original data to
529 // warrant a new window to be created
530 // create new alignmnt window with hidden regions (unhiding hidden regions
531 // yields unaligned seqs)
532 // or create a selection box around columns in alignment view
533 // test Alignment(SeqCigar[])
537 // we try to get the associated view's gap character
538 // but this may fail if the view was closed...
539 gc = av.getGapCharacter();
541 } catch (Exception ex)
545 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
547 if (alAndColsel != null && alAndColsel[0] != null)
549 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
551 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
552 AlignmentI dataset = (av != null && av.getAlignment() != null)
553 ? av.getAlignment().getDataset()
557 al.setDataset(dataset);
563 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
564 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
566 // >>>This is a fix for the moment, until a better solution is
568 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
570 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
573 Desktop.addInternalFrame(af, MessageManager.formatMessage(
574 "label.original_data_for_params", new Object[]
575 { this.title }), AlignFrame.DEFAULT_WIDTH,
576 AlignFrame.DEFAULT_HEIGHT);
588 public void fitToWindow_actionPerformed(ActionEvent e)
590 treeCanvas.fitToWindow = fitToWindow.isSelected();
595 * sort the associated alignment view by the current tree.
600 public void sortByTree_actionPerformed()
603 if (treeCanvas.applyToAllViews)
605 final ArrayList<CommandI> commands = new ArrayList<>();
606 for (AlignmentPanel ap : PaintRefresher
607 .getAssociatedPanels(av.getSequenceSetId()))
609 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
611 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
615 public void undoCommand(AlignmentI[] views)
617 for (CommandI tsort : commands)
619 tsort.undoCommand(views);
626 return commands.size();
630 public String getDescription()
632 return "Tree Sort (many views)";
636 public void doCommand(AlignmentI[] views)
639 for (CommandI tsort : commands)
641 tsort.doCommand(views);
645 for (AlignmentPanel ap : PaintRefresher
646 .getAssociatedPanels(av.getSequenceSetId()))
648 // ensure all the alignFrames refresh their GI after adding an undo item
649 ap.alignFrame.updateEditMenuBar();
654 treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
655 sortAlignmentIn(treeCanvas.getAssociatedPanel()));
660 public CommandI sortAlignmentIn(AlignmentPanel ap)
662 // TODO: move to alignment view controller
663 AlignmentViewport viewport = ap.av;
664 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
665 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
667 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
669 ap.paintAlignment(true, false);
680 public void font_actionPerformed(ActionEvent e)
682 if (treeCanvas == null)
687 new FontChooser(this);
690 public Font getTreeFont()
692 return treeCanvas.font;
695 public void setTreeFont(Font f)
697 if (treeCanvas != null)
699 treeCanvas.setFont(f);
710 public void distanceMenu_actionPerformed(ActionEvent e)
712 treeCanvas.setShowDistances(distanceMenu.isSelected());
722 public void bootstrapMenu_actionPerformed(ActionEvent e)
724 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
734 public void placeholdersMenu_actionPerformed(ActionEvent e)
736 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
740 * Outputs the Tree in image format (currently EPS or PNG). The user is
741 * prompted for the file to save to, and for EPS (unless a preference is
742 * already set) for the choice of Text or Lineart for character rendering.
745 public void writeTreeImage(TYPE imageFormat)
747 int width = treeCanvas.getWidth();
748 int height = treeCanvas.getHeight();
749 ImageWriterI writer = new ImageWriterI()
752 public void exportImage(Graphics g) throws Exception
754 treeCanvas.draw(g, width, height);
757 String tree = MessageManager.getString("label.tree");
758 ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
760 exporter.doExport(null, this, width, height,
761 tree.toLowerCase(Locale.ROOT));
765 * change node labels to the annotation referred to by labelClass TODO:
766 * promote to a datamodel modification that can be undone TODO: make argument
767 * one case of a generic transformation function ie { undoStep = apply(Tree,
768 * TransformFunction)};
772 public void changeNames(final String labelClass)
774 tree.applyToNodes(new NodeTransformI()
778 public void transform(BinaryNode node)
780 if (node instanceof SequenceNode
781 && !((SequenceNode) node).isPlaceholder()
782 && !((SequenceNode) node).isDummy())
784 String newname = null;
785 SequenceI sq = (SequenceI) ((BinaryNode) node).element();
788 // search dbrefs, features and annotation
789 List<DBRefEntry> refs = jalview.util.DBRefUtils
790 .selectRefs(sq.getDBRefs(), new String[]
791 { labelClass.toUpperCase(Locale.ROOT) });
794 for (int i = 0, ni = refs.size(); i < ni; i++)
798 newname = new String(refs.get(i).getAccessionId());
802 newname += "; " + refs.get(i).getAccessionId();
808 List<SequenceFeature> features = sq.getFeatures()
809 .getPositionalFeatures(labelClass);
810 for (SequenceFeature feature : features)
814 newname = feature.getDescription();
818 newname = newname + "; " + feature.getDescription();
825 // String oldname = ((SequenceNode) node).getName();
826 // TODO : save oldname in the undo object for this modification.
827 ((BinaryNode) node).setName(newname);
835 * Formats a localised title for the tree panel, like
837 * Neighbour Joining Using BLOSUM62
839 * For a tree loaded from file, just uses the file name
843 public String getPanelTitle()
845 if (treeTitle != null)
851 * i18n description of Neighbour Joining or Average Distance method
853 String treecalcnm = MessageManager.getString(
854 "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
857 * short score model name (long description can be too long)
859 String smn = scoreModelName;
862 * put them together as <method> Using <model>
864 final String ttl = MessageManager.formatMessage("label.calc_title",
870 * Builds an EPS image and writes it to the specified file.
874 * true for Text character rendering, false for Lineart
876 protected void writeEpsFile(File outFile, boolean textOption)
880 int width = treeCanvas.getWidth();
881 int height = treeCanvas.getHeight();
883 FileOutputStream out = new FileOutputStream(outFile);
884 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
886 pg.setAccurateTextMode(!textOption);
887 treeCanvas.draw(pg, width, height);
891 } catch (Exception ex)
893 System.err.println("Error writing tree as EPS");
894 ex.printStackTrace();
898 public AlignViewport getViewport()
903 public void setViewport(AlignViewport av)
908 public TreeCanvas getTreeCanvas()