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.beans.PropertyChangeEvent;
28 import java.beans.PropertyChangeListener;
30 import java.io.FileOutputStream;
31 import java.util.ArrayList;
32 import java.util.List;
33 import java.util.Locale;
35 import javax.swing.ButtonGroup;
36 import javax.swing.JMenuItem;
37 import javax.swing.JRadioButtonMenuItem;
38 import javax.swing.event.InternalFrameAdapter;
39 import javax.swing.event.InternalFrameEvent;
41 import org.jibble.epsgraphics.EpsGraphics2D;
43 import jalview.analysis.AlignmentSorter;
44 import jalview.analysis.AverageDistanceTree;
45 import jalview.analysis.NJTree;
46 import jalview.analysis.TreeBuilder;
47 import jalview.analysis.TreeModel;
48 import jalview.analysis.scoremodels.ScoreModels;
49 import jalview.api.analysis.ScoreModelI;
50 import jalview.api.analysis.SimilarityParamsI;
51 import jalview.bin.Cache;
52 import jalview.bin.Console;
53 import jalview.commands.CommandI;
54 import jalview.commands.OrderCommand;
55 import jalview.datamodel.Alignment;
56 import jalview.datamodel.AlignmentAnnotation;
57 import jalview.datamodel.AlignmentI;
58 import jalview.datamodel.AlignmentView;
59 import jalview.datamodel.BinaryNode;
60 import jalview.datamodel.DBRefEntry;
61 import jalview.datamodel.HiddenColumns;
62 import jalview.datamodel.NodeTransformI;
63 import jalview.datamodel.SequenceFeature;
64 import jalview.datamodel.SequenceI;
65 import jalview.datamodel.SequenceNode;
66 import jalview.gui.ImageExporter.ImageWriterI;
67 import jalview.io.JalviewFileChooser;
68 import jalview.io.JalviewFileView;
69 import jalview.io.NewickFile;
70 import jalview.jbgui.GTreePanel;
71 import jalview.util.ImageMaker.TYPE;
72 import jalview.util.MessageManager;
73 import jalview.viewmodel.AlignmentViewport;
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.setFrameIcon(null);
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.setFrameIcon(null);
123 this.treeTitle = theTitle;
124 initTreePanel(alignPanel, null, null, newtree, inputData);
128 * columnwise tree associated with positions in aa
135 public TreePanel(AlignmentPanel alignPanel, NewickFile fin,
136 AlignmentAnnotation aa, String title)
140 assocAnnotation = aa;
141 this.setFrameIcon(null);
142 this.treeTitle = title;
143 initTreePanel(alignPanel, null, null, fin, null);
146 boolean columnWise = false;
148 AlignmentAnnotation assocAnnotation = null;
150 public boolean isColumnWise()
155 public AlignmentAnnotation getAssocAnnotation()
157 return assocAnnotation;
160 public AlignmentI getAlignment()
162 return getTreeCanvas().getViewport().getAlignment();
165 public AlignmentViewport getViewPort()
167 // @Mungo - Why don't we return our own viewport ???
168 return getTreeCanvas().getViewport();
171 void initTreePanel(AlignmentPanel ap, String type, String modelName,
172 NewickFile newTree, AlignmentView inputData)
176 this.treeType = type;
177 this.scoreModelName = modelName;
181 bootstrapMenu.setVisible(false);
182 placeholdersMenu.setSelected(false);
183 placeholdersMenu.setVisible(false);
184 fitToWindow.setSelected(false);
185 sortAssocViews.setVisible(false);
188 treeCanvas = new TreeCanvas(this, ap, scrollPane);
189 scrollPane.setViewportView(treeCanvas);
191 PaintRefresher.Register(this, ap.av.getSequenceSetId());
193 buildAssociatedViewMenu();
195 final PropertyChangeListener listener = addAlignmentListener();
198 * remove listener when window is closed, so that this
199 * panel can be garbage collected
201 addInternalFrameListener(new InternalFrameAdapter()
204 public void internalFrameClosed(InternalFrameEvent evt)
208 av.removePropertyChangeListener(listener);
214 TreeLoader tl = new TreeLoader(newTree, inputData);
220 * Ensure any potentially large object references are nulled
222 public void releaseReferences()
225 this.treeCanvas.tree = null;
226 this.treeCanvas.nodeHash = null;
227 this.treeCanvas.nameHash = null;
233 protected PropertyChangeListener addAlignmentListener()
235 final PropertyChangeListener listener = new PropertyChangeListener()
238 public void propertyChange(PropertyChangeEvent evt)
240 if (evt.getPropertyName().equals("alignment"))
244 System.out.println("tree is null");
245 // TODO: deal with case when a change event is received whilst a
246 // tree is still being calculated - should save reference for
247 // processing message later.
250 if (evt.getNewValue() == null)
253 "new alignment sequences vector value is null");
256 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
257 treeCanvas.nameHash.clear(); // reset the mapping between canvas
258 // rectangles and leafnodes
263 av.addPropertyChangeListener(listener);
268 public void viewMenu_menuSelected()
270 buildAssociatedViewMenu();
273 void buildAssociatedViewMenu()
275 AlignmentPanel[] aps = PaintRefresher
276 .getAssociatedPanels(av.getSequenceSetId());
277 if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
279 associateLeavesMenu.setVisible(false);
283 associateLeavesMenu.setVisible(true);
286 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
288 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
291 associateLeavesMenu.removeAll();
293 JRadioButtonMenuItem item;
294 ButtonGroup buttonGroup = new ButtonGroup();
295 int i, iSize = aps.length;
296 final TreePanel thisTreePanel = this;
297 for (i = 0; i < iSize; i++)
299 final AlignmentPanel ap = aps[i];
300 item = new JRadioButtonMenuItem(ap.av.getViewName(),
301 ap == treeCanvas.getAssociatedPanel());
302 buttonGroup.add(item);
303 item.addActionListener(new ActionListener()
306 public void actionPerformed(ActionEvent evt)
308 treeCanvas.applyToAllViews = false;
309 treeCanvas.setAssociatedPanel(ap);
310 treeCanvas.setViewport(ap.av);
311 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
315 associateLeavesMenu.add(item);
318 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
319 MessageManager.getString("label.all_views"));
320 buttonGroup.add(itemf);
321 itemf.setSelected(treeCanvas.applyToAllViews);
322 itemf.addActionListener(new ActionListener()
325 public void actionPerformed(ActionEvent evt)
327 treeCanvas.applyToAllViews = itemf.isSelected();
330 associateLeavesMenu.add(itemf);
334 class TreeLoader extends Thread
336 private NewickFile newtree;
338 private AlignmentView odata = null;
340 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
342 this.newtree = newickFile;
343 this.odata = inputData;
345 if (newickFile != null)
347 // Must be outside run(), as Jalview2XML tries to
348 // update distance/bootstrap visibility at the same time
349 showBootstrap(newickFile.HasBootstrap());
350 showDistances(newickFile.HasDistances());
360 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
362 if (tree.getOriginalData() == null)
364 originalSeqData.setVisible(false);
369 ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
370 scoreModelName, treeCanvas.getAssociatedPanel());
371 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
372 ? new NJTree(av, sm, similarityParams)
373 : new AverageDistanceTree(av, sm, similarityParams);
374 tree = new TreeModel(njtree);
378 tree.reCount(tree.getTopNode());
379 tree.findHeight(tree.getTopNode());
380 treeCanvas.setTree(tree);
381 treeCanvas.repaint();
382 av.setCurrentTree(tree);
383 if (av.getSortByTree())
385 sortByTree_actionPerformed();
390 public void showDistances(boolean b)
392 treeCanvas.setShowDistances(b);
393 distanceMenu.setSelected(b);
396 public void showBootstrap(boolean b)
398 treeCanvas.setShowBootstrap(b);
399 bootstrapMenu.setSelected(b);
402 public void showPlaceholders(boolean b)
404 placeholdersMenu.setState(b);
405 treeCanvas.setMarkPlaceholders(b);
411 * @return DOCUMENT ME!
413 public TreeModel getTree()
425 public void textbox_actionPerformed(ActionEvent e)
427 CutAndPasteTransfer cap = new CutAndPasteTransfer();
429 String newTitle = getPanelTitle();
431 NewickFile fout = new NewickFile(tree.getTopNode());
434 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
435 tree.hasRootDistance()));
436 Desktop.addInternalFrame(cap, newTitle, 500, 100);
437 } catch (OutOfMemoryError oom)
439 new OOMWarning("generating newick tree file", oom);
452 public void saveAsNewick_actionPerformed(ActionEvent e)
454 // TODO: JAL-3048 save newick file for Jalview-JS
455 JalviewFileChooser chooser = new JalviewFileChooser(
456 Cache.getProperty("LAST_DIRECTORY"));
457 chooser.setFileView(new JalviewFileView());
458 chooser.setDialogTitle(
459 MessageManager.getString("label.save_tree_as_newick"));
460 chooser.setToolTipText(MessageManager.getString("action.save"));
462 int value = chooser.showSaveDialog(null);
464 if (value == JalviewFileChooser.APPROVE_OPTION)
466 String choice = chooser.getSelectedFile().getPath();
467 Cache.setProperty("LAST_DIRECTORY",
468 chooser.getSelectedFile().getParent());
472 jalview.io.NewickFile fout = new jalview.io.NewickFile(
474 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
475 tree.hasRootDistance());
476 java.io.PrintWriter out = new java.io.PrintWriter(
477 new java.io.FileWriter(choice));
480 } catch (Exception ex)
482 ex.printStackTrace();
494 public void printMenu_actionPerformed(ActionEvent e)
496 // Putting in a thread avoids Swing painting problems
497 treeCanvas.startPrinting();
501 public void originalSeqData_actionPerformed(ActionEvent e)
503 AlignmentView originalData = tree.getOriginalData();
504 if (originalData == null)
507 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
510 // decide if av alignment is sufficiently different to original data to
511 // warrant a new window to be created
512 // create new alignmnt window with hidden regions (unhiding hidden regions
513 // yields unaligned seqs)
514 // or create a selection box around columns in alignment view
515 // test Alignment(SeqCigar[])
519 // we try to get the associated view's gap character
520 // but this may fail if the view was closed...
521 gc = av.getGapCharacter();
523 } catch (Exception ex)
527 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
529 if (alAndColsel != null && alAndColsel[0] != null)
531 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
533 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
534 AlignmentI dataset = (av != null && av.getAlignment() != null)
535 ? av.getAlignment().getDataset()
539 al.setDataset(dataset);
545 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
546 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
548 // >>>This is a fix for the moment, until a better solution is
550 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
552 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
555 Desktop.addInternalFrame(af, MessageManager.formatMessage(
556 "label.original_data_for_params", new Object[]
557 { this.title }), AlignFrame.DEFAULT_WIDTH,
558 AlignFrame.DEFAULT_HEIGHT);
570 public void fitToWindow_actionPerformed(ActionEvent e)
572 treeCanvas.fitToWindow = fitToWindow.isSelected();
577 * sort the associated alignment view by the current tree.
582 public void sortByTree_actionPerformed()
585 if (treeCanvas.applyToAllViews)
587 final ArrayList<CommandI> commands = new ArrayList<>();
588 for (AlignmentPanel ap : PaintRefresher
589 .getAssociatedPanels(av.getSequenceSetId()))
591 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
593 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
597 public void undoCommand(AlignmentI[] views)
599 for (CommandI tsort : commands)
601 tsort.undoCommand(views);
608 return commands.size();
612 public String getDescription()
614 return "Tree Sort (many views)";
618 public void doCommand(AlignmentI[] views)
621 for (CommandI tsort : commands)
623 tsort.doCommand(views);
627 for (AlignmentPanel ap : PaintRefresher
628 .getAssociatedPanels(av.getSequenceSetId()))
630 // ensure all the alignFrames refresh their GI after adding an undo item
631 ap.alignFrame.updateEditMenuBar();
636 treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
637 sortAlignmentIn(treeCanvas.getAssociatedPanel()));
642 public CommandI sortAlignmentIn(AlignmentPanel ap)
644 // TODO: move to alignment view controller
645 AlignmentViewport viewport = ap.av;
646 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
647 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
649 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
651 ap.paintAlignment(true, false);
662 public void font_actionPerformed(ActionEvent e)
664 if (treeCanvas == null)
669 new FontChooser(this);
672 public Font getTreeFont()
674 return treeCanvas.font;
677 public void setTreeFont(Font f)
679 if (treeCanvas != null)
681 treeCanvas.setFont(f);
692 public void distanceMenu_actionPerformed(ActionEvent e)
694 treeCanvas.setShowDistances(distanceMenu.isSelected());
704 public void bootstrapMenu_actionPerformed(ActionEvent e)
706 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
716 public void placeholdersMenu_actionPerformed(ActionEvent e)
718 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
722 * Outputs the Tree in image format (currently EPS or PNG). The user is
723 * prompted for the file to save to, and for EPS (unless a preference is
724 * already set) for the choice of Text or Lineart for character rendering.
727 public void writeTreeImage(TYPE imageFormat)
729 int width = treeCanvas.getWidth();
730 int height = treeCanvas.getHeight();
731 ImageWriterI writer = new ImageWriterI()
734 public void exportImage(Graphics g) throws Exception
736 treeCanvas.draw(g, width, height);
739 String tree = MessageManager.getString("label.tree");
740 ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
742 exporter.doExport(null, this, width, height,
743 tree.toLowerCase(Locale.ROOT));
747 * change node labels to the annotation referred to by labelClass TODO:
748 * promote to a datamodel modification that can be undone TODO: make argument
749 * one case of a generic transformation function ie { undoStep = apply(Tree,
750 * TransformFunction)};
754 public void changeNames(final String labelClass)
756 tree.applyToNodes(new NodeTransformI()
760 public void transform(BinaryNode node)
762 if (node instanceof SequenceNode
763 && !((SequenceNode) node).isPlaceholder()
764 && !((SequenceNode) node).isDummy())
766 String newname = null;
767 SequenceI sq = (SequenceI) ((BinaryNode) node).element();
770 // search dbrefs, features and annotation
771 List<DBRefEntry> refs = jalview.util.DBRefUtils
772 .selectRefs(sq.getDBRefs(), new String[]
773 { labelClass.toUpperCase(Locale.ROOT) });
776 for (int i = 0, ni = refs.size(); i < ni; i++)
780 newname = new String(refs.get(i).getAccessionId());
784 newname += "; " + refs.get(i).getAccessionId();
790 List<SequenceFeature> features = sq.getFeatures()
791 .getPositionalFeatures(labelClass);
792 for (SequenceFeature feature : features)
796 newname = feature.getDescription();
800 newname = newname + "; " + feature.getDescription();
807 // String oldname = ((SequenceNode) node).getName();
808 // TODO : save oldname in the undo object for this modification.
809 ((BinaryNode) node).setName(newname);
817 * Formats a localised title for the tree panel, like
819 * Neighbour Joining Using BLOSUM62
821 * For a tree loaded from file, just uses the file name
825 public String getPanelTitle()
827 if (treeTitle != null)
833 * i18n description of Neighbour Joining or Average Distance method
835 String treecalcnm = MessageManager.getString(
836 "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
839 * short score model name (long description can be too long)
841 String smn = scoreModelName;
844 * put them together as <method> Using <model>
846 final String ttl = MessageManager.formatMessage("label.calc_title",
852 * Builds an EPS image and writes it to the specified file.
856 * true for Text character rendering, false for Lineart
858 protected void writeEpsFile(File outFile, boolean textOption)
862 int width = treeCanvas.getWidth();
863 int height = treeCanvas.getHeight();
865 FileOutputStream out = new FileOutputStream(outFile);
866 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
868 pg.setAccurateTextMode(!textOption);
869 treeCanvas.draw(pg, width, height);
873 } catch (Exception ex)
875 System.err.println("Error writing tree as EPS");
876 ex.printStackTrace();
880 public AlignViewport getViewport()
885 public void setViewport(AlignViewport av)
890 public TreeCanvas getTreeCanvas()