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)
138 this(alignPanel, fin, title, null);
140 assocAnnotation = aa;
144 boolean columnWise=false;
145 AlignmentAnnotation assocAnnotation=null;
146 public boolean getColumnWise()
151 public AlignmentI getAlignment()
153 return getTreeCanvas().getViewport().getAlignment();
156 public AlignmentViewport getViewPort()
158 // @Mungo - Why don't we return our own viewport ???
159 return getTreeCanvas().getViewport();
162 void initTreePanel(AlignmentPanel ap, String type, String modelName,
163 NewickFile newTree, AlignmentView inputData)
167 this.treeType = type;
168 this.scoreModelName = modelName;
170 treeCanvas = new TreeCanvas(this, ap, scrollPane);
171 scrollPane.setViewportView(treeCanvas);
173 PaintRefresher.Register(this, ap.av.getSequenceSetId());
175 buildAssociatedViewMenu();
177 final PropertyChangeListener listener = addAlignmentListener();
180 * remove listener when window is closed, so that this
181 * panel can be garbage collected
183 addInternalFrameListener(new InternalFrameAdapter()
186 public void internalFrameClosed(InternalFrameEvent evt)
190 av.removePropertyChangeListener(listener);
196 TreeLoader tl = new TreeLoader(newTree, inputData);
202 * Ensure any potentially large object references are nulled
204 public void releaseReferences()
207 this.treeCanvas.tree = null;
208 this.treeCanvas.nodeHash = null;
209 this.treeCanvas.nameHash = null;
215 protected PropertyChangeListener addAlignmentListener()
217 final PropertyChangeListener listener = new PropertyChangeListener()
220 public void propertyChange(PropertyChangeEvent evt)
222 if (evt.getPropertyName().equals("alignment"))
226 System.out.println("tree is null");
227 // TODO: deal with case when a change event is received whilst a
228 // tree is still being calculated - should save reference for
229 // processing message later.
232 if (evt.getNewValue() == null)
235 "new alignment sequences vector value is null");
238 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
239 treeCanvas.nameHash.clear(); // reset the mapping between canvas
240 // rectangles and leafnodes
245 av.addPropertyChangeListener(listener);
250 public void viewMenu_menuSelected()
252 buildAssociatedViewMenu();
255 void buildAssociatedViewMenu()
257 AlignmentPanel[] aps = PaintRefresher
258 .getAssociatedPanels(av.getSequenceSetId());
259 if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
261 associateLeavesMenu.setVisible(false);
265 associateLeavesMenu.setVisible(true);
268 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
270 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
273 associateLeavesMenu.removeAll();
275 JRadioButtonMenuItem item;
276 ButtonGroup buttonGroup = new ButtonGroup();
277 int i, iSize = aps.length;
278 final TreePanel thisTreePanel = this;
279 for (i = 0; i < iSize; i++)
281 final AlignmentPanel ap = aps[i];
282 item = new JRadioButtonMenuItem(ap.av.getViewName(),
283 ap == treeCanvas.getAssociatedPanel());
284 buttonGroup.add(item);
285 item.addActionListener(new ActionListener()
288 public void actionPerformed(ActionEvent evt)
290 treeCanvas.applyToAllViews = false;
291 treeCanvas.setAssociatedPanel(ap);
292 treeCanvas.setViewport(ap.av);
293 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
297 associateLeavesMenu.add(item);
300 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
301 MessageManager.getString("label.all_views"));
302 buttonGroup.add(itemf);
303 itemf.setSelected(treeCanvas.applyToAllViews);
304 itemf.addActionListener(new ActionListener()
307 public void actionPerformed(ActionEvent evt)
309 treeCanvas.applyToAllViews = itemf.isSelected();
312 associateLeavesMenu.add(itemf);
316 class TreeLoader extends Thread
318 private NewickFile newtree;
320 private AlignmentView odata = null;
322 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
324 this.newtree = newickFile;
325 this.odata = inputData;
327 if (newickFile != null)
329 // Must be outside run(), as Jalview2XML tries to
330 // update distance/bootstrap visibility at the same time
331 showBootstrap(newickFile.HasBootstrap());
332 showDistances(newickFile.HasDistances());
342 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
344 if (tree.getOriginalData() == null)
346 originalSeqData.setVisible(false);
351 ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
352 scoreModelName, treeCanvas.getAssociatedPanel());
353 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
354 ? new NJTree(av, sm, similarityParams)
355 : new AverageDistanceTree(av, sm, similarityParams);
356 tree = new TreeModel(njtree);
360 tree.reCount(tree.getTopNode());
361 tree.findHeight(tree.getTopNode());
362 treeCanvas.setTree(tree);
363 treeCanvas.repaint();
364 av.setCurrentTree(tree);
365 if (av.getSortByTree())
367 sortByTree_actionPerformed();
372 public void showDistances(boolean b)
374 treeCanvas.setShowDistances(b);
375 distanceMenu.setSelected(b);
378 public void showBootstrap(boolean b)
380 treeCanvas.setShowBootstrap(b);
381 bootstrapMenu.setSelected(b);
384 public void showPlaceholders(boolean b)
386 placeholdersMenu.setState(b);
387 treeCanvas.setMarkPlaceholders(b);
393 * @return DOCUMENT ME!
395 public TreeModel getTree()
407 public void textbox_actionPerformed(ActionEvent e)
409 CutAndPasteTransfer cap = new CutAndPasteTransfer();
411 String newTitle = getPanelTitle();
413 NewickFile fout = new NewickFile(tree.getTopNode());
416 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
417 tree.hasRootDistance()));
418 Desktop.addInternalFrame(cap, newTitle, 500, 100);
419 } catch (OutOfMemoryError oom)
421 new OOMWarning("generating newick tree file", oom);
434 public void saveAsNewick_actionPerformed(ActionEvent e)
436 // TODO: JAL-3048 save newick file for Jalview-JS
437 JalviewFileChooser chooser = new JalviewFileChooser(
438 Cache.getProperty("LAST_DIRECTORY"));
439 chooser.setFileView(new JalviewFileView());
440 chooser.setDialogTitle(
441 MessageManager.getString("label.save_tree_as_newick"));
442 chooser.setToolTipText(MessageManager.getString("action.save"));
444 int value = chooser.showSaveDialog(null);
446 if (value == JalviewFileChooser.APPROVE_OPTION)
448 String choice = chooser.getSelectedFile().getPath();
449 Cache.setProperty("LAST_DIRECTORY",
450 chooser.getSelectedFile().getParent());
454 jalview.io.NewickFile fout = new jalview.io.NewickFile(
456 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
457 tree.hasRootDistance());
458 java.io.PrintWriter out = new java.io.PrintWriter(
459 new java.io.FileWriter(choice));
462 } catch (Exception ex)
464 ex.printStackTrace();
476 public void printMenu_actionPerformed(ActionEvent e)
478 // Putting in a thread avoids Swing painting problems
479 treeCanvas.startPrinting();
483 public void originalSeqData_actionPerformed(ActionEvent e)
485 AlignmentView originalData = tree.getOriginalData();
486 if (originalData == null)
489 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
492 // decide if av alignment is sufficiently different to original data to
493 // warrant a new window to be created
494 // create new alignmnt window with hidden regions (unhiding hidden regions
495 // yields unaligned seqs)
496 // or create a selection box around columns in alignment view
497 // test Alignment(SeqCigar[])
501 // we try to get the associated view's gap character
502 // but this may fail if the view was closed...
503 gc = av.getGapCharacter();
505 } catch (Exception ex)
509 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
511 if (alAndColsel != null && alAndColsel[0] != null)
513 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
515 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
516 AlignmentI dataset = (av != null && av.getAlignment() != null)
517 ? av.getAlignment().getDataset()
521 al.setDataset(dataset);
527 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
528 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
530 // >>>This is a fix for the moment, until a better solution is
532 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
534 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
537 Desktop.addInternalFrame(af, MessageManager.formatMessage(
538 "label.original_data_for_params", new Object[]
539 { this.title }), AlignFrame.DEFAULT_WIDTH,
540 AlignFrame.DEFAULT_HEIGHT);
552 public void fitToWindow_actionPerformed(ActionEvent e)
554 treeCanvas.fitToWindow = fitToWindow.isSelected();
559 * sort the associated alignment view by the current tree.
564 public void sortByTree_actionPerformed()
567 if (treeCanvas.applyToAllViews)
569 final ArrayList<CommandI> commands = new ArrayList<>();
570 for (AlignmentPanel ap : PaintRefresher
571 .getAssociatedPanels(av.getSequenceSetId()))
573 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
575 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
579 public void undoCommand(AlignmentI[] views)
581 for (CommandI tsort : commands)
583 tsort.undoCommand(views);
590 return commands.size();
594 public String getDescription()
596 return "Tree Sort (many views)";
600 public void doCommand(AlignmentI[] views)
603 for (CommandI tsort : commands)
605 tsort.doCommand(views);
609 for (AlignmentPanel ap : PaintRefresher
610 .getAssociatedPanels(av.getSequenceSetId()))
612 // ensure all the alignFrames refresh their GI after adding an undo item
613 ap.alignFrame.updateEditMenuBar();
618 treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
619 sortAlignmentIn(treeCanvas.getAssociatedPanel()));
624 public CommandI sortAlignmentIn(AlignmentPanel ap)
626 // TODO: move to alignment view controller
627 AlignmentViewport viewport = ap.av;
628 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
629 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
631 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
633 ap.paintAlignment(true, false);
644 public void font_actionPerformed(ActionEvent e)
646 if (treeCanvas == null)
651 new FontChooser(this);
654 public Font getTreeFont()
656 return treeCanvas.font;
659 public void setTreeFont(Font f)
661 if (treeCanvas != null)
663 treeCanvas.setFont(f);
674 public void distanceMenu_actionPerformed(ActionEvent e)
676 treeCanvas.setShowDistances(distanceMenu.isSelected());
686 public void bootstrapMenu_actionPerformed(ActionEvent e)
688 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
698 public void placeholdersMenu_actionPerformed(ActionEvent e)
700 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
704 * Outputs the Tree in image format (currently EPS or PNG). The user is
705 * prompted for the file to save to, and for EPS (unless a preference is
706 * already set) for the choice of Text or Lineart for character rendering.
709 public void writeTreeImage(TYPE imageFormat)
711 int width = treeCanvas.getWidth();
712 int height = treeCanvas.getHeight();
713 ImageWriterI writer = new ImageWriterI()
716 public void exportImage(Graphics g) throws Exception
718 treeCanvas.draw(g, width, height);
721 String tree = MessageManager.getString("label.tree");
722 ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
724 exporter.doExport(null, this, width, height,
725 tree.toLowerCase(Locale.ROOT));
729 * change node labels to the annotation referred to by labelClass TODO:
730 * promote to a datamodel modification that can be undone TODO: make argument
731 * one case of a generic transformation function ie { undoStep = apply(Tree,
732 * TransformFunction)};
736 public void changeNames(final String labelClass)
738 tree.applyToNodes(new NodeTransformI()
742 public void transform(BinaryNode node)
744 if (node instanceof SequenceNode
745 && !((SequenceNode) node).isPlaceholder()
746 && !((SequenceNode) node).isDummy())
748 String newname = null;
749 SequenceI sq = (SequenceI) ((BinaryNode) node).element();
752 // search dbrefs, features and annotation
753 List<DBRefEntry> refs = jalview.util.DBRefUtils
754 .selectRefs(sq.getDBRefs(), new String[]
755 { labelClass.toUpperCase(Locale.ROOT) });
758 for (int i = 0, ni = refs.size(); i < ni; i++)
762 newname = new String(refs.get(i).getAccessionId());
766 newname += "; " + refs.get(i).getAccessionId();
772 List<SequenceFeature> features = sq.getFeatures()
773 .getPositionalFeatures(labelClass);
774 for (SequenceFeature feature : features)
778 newname = feature.getDescription();
782 newname = newname + "; " + feature.getDescription();
789 // String oldname = ((SequenceNode) node).getName();
790 // TODO : save oldname in the undo object for this modification.
791 ((BinaryNode) node).setName(newname);
799 * Formats a localised title for the tree panel, like
801 * Neighbour Joining Using BLOSUM62
803 * For a tree loaded from file, just uses the file name
807 public String getPanelTitle()
809 if (treeTitle != null)
815 * i18n description of Neighbour Joining or Average Distance method
817 String treecalcnm = MessageManager.getString(
818 "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
821 * short score model name (long description can be too long)
823 String smn = scoreModelName;
826 * put them together as <method> Using <model>
828 final String ttl = MessageManager.formatMessage("label.calc_title",
834 * Builds an EPS image and writes it to the specified file.
838 * true for Text character rendering, false for Lineart
840 protected void writeEpsFile(File outFile, boolean textOption)
844 int width = treeCanvas.getWidth();
845 int height = treeCanvas.getHeight();
847 FileOutputStream out = new FileOutputStream(outFile);
848 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
850 pg.setAccurateTextMode(!textOption);
851 treeCanvas.draw(pg, width, height);
855 } catch (Exception ex)
857 System.err.println("Error writing tree as EPS");
858 ex.printStackTrace();
862 public AlignViewport getViewport()
867 public void setViewport(AlignViewport av)
872 public TreeCanvas getTreeCanvas()