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;
147 AlignmentAnnotation assocAnnotation=null;
148 public boolean isColumnWise()
152 public AlignmentAnnotation getAssocAnnotation() {
153 return assocAnnotation;
156 public AlignmentI getAlignment()
158 return getTreeCanvas().getViewport().getAlignment();
161 public AlignmentViewport getViewPort()
163 // @Mungo - Why don't we return our own viewport ???
164 return getTreeCanvas().getViewport();
167 void initTreePanel(AlignmentPanel ap, String type, String modelName,
168 NewickFile newTree, AlignmentView inputData)
172 this.treeType = type;
173 this.scoreModelName = modelName;
177 bootstrapMenu.setVisible(false);
178 placeholdersMenu.setSelected(false);
179 placeholdersMenu.setVisible(false);
180 fitToWindow.setSelected(false);
181 sortAssocViews.setVisible(false);
184 treeCanvas = new TreeCanvas(this, ap, scrollPane);
185 scrollPane.setViewportView(treeCanvas);
187 PaintRefresher.Register(this, ap.av.getSequenceSetId());
189 buildAssociatedViewMenu();
191 final PropertyChangeListener listener = addAlignmentListener();
194 * remove listener when window is closed, so that this
195 * panel can be garbage collected
197 addInternalFrameListener(new InternalFrameAdapter()
200 public void internalFrameClosed(InternalFrameEvent evt)
204 av.removePropertyChangeListener(listener);
210 TreeLoader tl = new TreeLoader(newTree, inputData);
216 * Ensure any potentially large object references are nulled
218 public void releaseReferences()
221 this.treeCanvas.tree = null;
222 this.treeCanvas.nodeHash = null;
223 this.treeCanvas.nameHash = null;
229 protected PropertyChangeListener addAlignmentListener()
231 final PropertyChangeListener listener = new PropertyChangeListener()
234 public void propertyChange(PropertyChangeEvent evt)
236 if (evt.getPropertyName().equals("alignment"))
240 System.out.println("tree is null");
241 // TODO: deal with case when a change event is received whilst a
242 // tree is still being calculated - should save reference for
243 // processing message later.
246 if (evt.getNewValue() == null)
249 "new alignment sequences vector value is null");
252 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
253 treeCanvas.nameHash.clear(); // reset the mapping between canvas
254 // rectangles and leafnodes
259 av.addPropertyChangeListener(listener);
264 public void viewMenu_menuSelected()
266 buildAssociatedViewMenu();
269 void buildAssociatedViewMenu()
271 AlignmentPanel[] aps = PaintRefresher
272 .getAssociatedPanels(av.getSequenceSetId());
273 if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
275 associateLeavesMenu.setVisible(false);
279 associateLeavesMenu.setVisible(true);
282 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
284 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
287 associateLeavesMenu.removeAll();
289 JRadioButtonMenuItem item;
290 ButtonGroup buttonGroup = new ButtonGroup();
291 int i, iSize = aps.length;
292 final TreePanel thisTreePanel = this;
293 for (i = 0; i < iSize; i++)
295 final AlignmentPanel ap = aps[i];
296 item = new JRadioButtonMenuItem(ap.av.getViewName(),
297 ap == treeCanvas.getAssociatedPanel());
298 buttonGroup.add(item);
299 item.addActionListener(new ActionListener()
302 public void actionPerformed(ActionEvent evt)
304 treeCanvas.applyToAllViews = false;
305 treeCanvas.setAssociatedPanel(ap);
306 treeCanvas.setViewport(ap.av);
307 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
311 associateLeavesMenu.add(item);
314 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
315 MessageManager.getString("label.all_views"));
316 buttonGroup.add(itemf);
317 itemf.setSelected(treeCanvas.applyToAllViews);
318 itemf.addActionListener(new ActionListener()
321 public void actionPerformed(ActionEvent evt)
323 treeCanvas.applyToAllViews = itemf.isSelected();
326 associateLeavesMenu.add(itemf);
330 class TreeLoader extends Thread
332 private NewickFile newtree;
334 private AlignmentView odata = null;
336 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
338 this.newtree = newickFile;
339 this.odata = inputData;
341 if (newickFile != null)
343 // Must be outside run(), as Jalview2XML tries to
344 // update distance/bootstrap visibility at the same time
345 showBootstrap(newickFile.HasBootstrap());
346 showDistances(newickFile.HasDistances());
356 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
358 if (tree.getOriginalData() == null)
360 originalSeqData.setVisible(false);
365 ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
366 scoreModelName, treeCanvas.getAssociatedPanel());
367 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
368 ? new NJTree(av, sm, similarityParams)
369 : new AverageDistanceTree(av, sm, similarityParams);
370 tree = new TreeModel(njtree);
374 tree.reCount(tree.getTopNode());
375 tree.findHeight(tree.getTopNode());
376 treeCanvas.setTree(tree);
377 treeCanvas.repaint();
378 av.setCurrentTree(tree);
379 if (av.getSortByTree())
381 sortByTree_actionPerformed();
386 public void showDistances(boolean b)
388 treeCanvas.setShowDistances(b);
389 distanceMenu.setSelected(b);
392 public void showBootstrap(boolean b)
394 treeCanvas.setShowBootstrap(b);
395 bootstrapMenu.setSelected(b);
398 public void showPlaceholders(boolean b)
400 placeholdersMenu.setState(b);
401 treeCanvas.setMarkPlaceholders(b);
407 * @return DOCUMENT ME!
409 public TreeModel getTree()
421 public void textbox_actionPerformed(ActionEvent e)
423 CutAndPasteTransfer cap = new CutAndPasteTransfer();
425 String newTitle = getPanelTitle();
427 NewickFile fout = new NewickFile(tree.getTopNode());
430 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
431 tree.hasRootDistance()));
432 Desktop.addInternalFrame(cap, newTitle, 500, 100);
433 } catch (OutOfMemoryError oom)
435 new OOMWarning("generating newick tree file", oom);
448 public void saveAsNewick_actionPerformed(ActionEvent e)
450 // TODO: JAL-3048 save newick file for Jalview-JS
451 JalviewFileChooser chooser = new JalviewFileChooser(
452 Cache.getProperty("LAST_DIRECTORY"));
453 chooser.setFileView(new JalviewFileView());
454 chooser.setDialogTitle(
455 MessageManager.getString("label.save_tree_as_newick"));
456 chooser.setToolTipText(MessageManager.getString("action.save"));
458 int value = chooser.showSaveDialog(null);
460 if (value == JalviewFileChooser.APPROVE_OPTION)
462 String choice = chooser.getSelectedFile().getPath();
463 Cache.setProperty("LAST_DIRECTORY",
464 chooser.getSelectedFile().getParent());
468 jalview.io.NewickFile fout = new jalview.io.NewickFile(
470 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
471 tree.hasRootDistance());
472 java.io.PrintWriter out = new java.io.PrintWriter(
473 new java.io.FileWriter(choice));
476 } catch (Exception ex)
478 ex.printStackTrace();
490 public void printMenu_actionPerformed(ActionEvent e)
492 // Putting in a thread avoids Swing painting problems
493 treeCanvas.startPrinting();
497 public void originalSeqData_actionPerformed(ActionEvent e)
499 AlignmentView originalData = tree.getOriginalData();
500 if (originalData == null)
503 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
506 // decide if av alignment is sufficiently different to original data to
507 // warrant a new window to be created
508 // create new alignmnt window with hidden regions (unhiding hidden regions
509 // yields unaligned seqs)
510 // or create a selection box around columns in alignment view
511 // test Alignment(SeqCigar[])
515 // we try to get the associated view's gap character
516 // but this may fail if the view was closed...
517 gc = av.getGapCharacter();
519 } catch (Exception ex)
523 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
525 if (alAndColsel != null && alAndColsel[0] != null)
527 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
529 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
530 AlignmentI dataset = (av != null && av.getAlignment() != null)
531 ? av.getAlignment().getDataset()
535 al.setDataset(dataset);
541 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
542 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
544 // >>>This is a fix for the moment, until a better solution is
546 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
548 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
551 Desktop.addInternalFrame(af, MessageManager.formatMessage(
552 "label.original_data_for_params", new Object[]
553 { this.title }), AlignFrame.DEFAULT_WIDTH,
554 AlignFrame.DEFAULT_HEIGHT);
566 public void fitToWindow_actionPerformed(ActionEvent e)
568 treeCanvas.fitToWindow = fitToWindow.isSelected();
573 * sort the associated alignment view by the current tree.
578 public void sortByTree_actionPerformed()
581 if (treeCanvas.applyToAllViews)
583 final ArrayList<CommandI> commands = new ArrayList<>();
584 for (AlignmentPanel ap : PaintRefresher
585 .getAssociatedPanels(av.getSequenceSetId()))
587 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
589 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
593 public void undoCommand(AlignmentI[] views)
595 for (CommandI tsort : commands)
597 tsort.undoCommand(views);
604 return commands.size();
608 public String getDescription()
610 return "Tree Sort (many views)";
614 public void doCommand(AlignmentI[] views)
617 for (CommandI tsort : commands)
619 tsort.doCommand(views);
623 for (AlignmentPanel ap : PaintRefresher
624 .getAssociatedPanels(av.getSequenceSetId()))
626 // ensure all the alignFrames refresh their GI after adding an undo item
627 ap.alignFrame.updateEditMenuBar();
632 treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
633 sortAlignmentIn(treeCanvas.getAssociatedPanel()));
638 public CommandI sortAlignmentIn(AlignmentPanel ap)
640 // TODO: move to alignment view controller
641 AlignmentViewport viewport = ap.av;
642 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
643 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
645 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
647 ap.paintAlignment(true, false);
658 public void font_actionPerformed(ActionEvent e)
660 if (treeCanvas == null)
665 new FontChooser(this);
668 public Font getTreeFont()
670 return treeCanvas.font;
673 public void setTreeFont(Font f)
675 if (treeCanvas != null)
677 treeCanvas.setFont(f);
688 public void distanceMenu_actionPerformed(ActionEvent e)
690 treeCanvas.setShowDistances(distanceMenu.isSelected());
700 public void bootstrapMenu_actionPerformed(ActionEvent e)
702 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
712 public void placeholdersMenu_actionPerformed(ActionEvent e)
714 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
718 * Outputs the Tree in image format (currently EPS or PNG). The user is
719 * prompted for the file to save to, and for EPS (unless a preference is
720 * already set) for the choice of Text or Lineart for character rendering.
723 public void writeTreeImage(TYPE imageFormat)
725 int width = treeCanvas.getWidth();
726 int height = treeCanvas.getHeight();
727 ImageWriterI writer = new ImageWriterI()
730 public void exportImage(Graphics g) throws Exception
732 treeCanvas.draw(g, width, height);
735 String tree = MessageManager.getString("label.tree");
736 ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
738 exporter.doExport(null, this, width, height,
739 tree.toLowerCase(Locale.ROOT));
743 * change node labels to the annotation referred to by labelClass TODO:
744 * promote to a datamodel modification that can be undone TODO: make argument
745 * one case of a generic transformation function ie { undoStep = apply(Tree,
746 * TransformFunction)};
750 public void changeNames(final String labelClass)
752 tree.applyToNodes(new NodeTransformI()
756 public void transform(BinaryNode node)
758 if (node instanceof SequenceNode
759 && !((SequenceNode) node).isPlaceholder()
760 && !((SequenceNode) node).isDummy())
762 String newname = null;
763 SequenceI sq = (SequenceI) ((BinaryNode) node).element();
766 // search dbrefs, features and annotation
767 List<DBRefEntry> refs = jalview.util.DBRefUtils
768 .selectRefs(sq.getDBRefs(), new String[]
769 { labelClass.toUpperCase(Locale.ROOT) });
772 for (int i = 0, ni = refs.size(); i < ni; i++)
776 newname = new String(refs.get(i).getAccessionId());
780 newname += "; " + refs.get(i).getAccessionId();
786 List<SequenceFeature> features = sq.getFeatures()
787 .getPositionalFeatures(labelClass);
788 for (SequenceFeature feature : features)
792 newname = feature.getDescription();
796 newname = newname + "; " + feature.getDescription();
803 // String oldname = ((SequenceNode) node).getName();
804 // TODO : save oldname in the undo object for this modification.
805 ((BinaryNode) node).setName(newname);
813 * Formats a localised title for the tree panel, like
815 * Neighbour Joining Using BLOSUM62
817 * For a tree loaded from file, just uses the file name
821 public String getPanelTitle()
823 if (treeTitle != null)
829 * i18n description of Neighbour Joining or Average Distance method
831 String treecalcnm = MessageManager.getString(
832 "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
835 * short score model name (long description can be too long)
837 String smn = scoreModelName;
840 * put them together as <method> Using <model>
842 final String ttl = MessageManager.formatMessage("label.calc_title",
848 * Builds an EPS image and writes it to the specified file.
852 * true for Text character rendering, false for Lineart
854 protected void writeEpsFile(File outFile, boolean textOption)
858 int width = treeCanvas.getWidth();
859 int height = treeCanvas.getHeight();
861 FileOutputStream out = new FileOutputStream(outFile);
862 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
864 pg.setAccurateTextMode(!textOption);
865 treeCanvas.draw(pg, width, height);
869 } catch (Exception ex)
871 System.err.println("Error writing tree as EPS");
872 ex.printStackTrace();
876 public AlignViewport getViewport()
881 public void setViewport(AlignViewport av)
886 public TreeCanvas getTreeCanvas()