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 java.util.Locale;
25 import jalview.analysis.AlignmentSorter;
26 import jalview.analysis.AverageDistanceTree;
27 import jalview.analysis.NJTree;
28 import jalview.analysis.TreeBuilder;
29 import jalview.analysis.TreeModel;
30 import jalview.analysis.scoremodels.ScoreModels;
31 import jalview.api.analysis.ScoreModelI;
32 import jalview.api.analysis.SimilarityParamsI;
33 import jalview.commands.CommandI;
34 import jalview.commands.OrderCommand;
35 import jalview.datamodel.Alignment;
36 import jalview.datamodel.AlignmentI;
37 import jalview.datamodel.AlignmentView;
38 import jalview.datamodel.BinaryNode;
39 import jalview.datamodel.DBRefEntry;
40 import jalview.datamodel.HiddenColumns;
41 import jalview.datamodel.NodeTransformI;
42 import jalview.datamodel.SequenceFeature;
43 import jalview.datamodel.SequenceI;
44 import jalview.datamodel.SequenceNode;
45 import jalview.gui.ImageExporter.ImageWriterI;
46 import jalview.io.JalviewFileChooser;
47 import jalview.io.JalviewFileView;
48 import jalview.io.NewickFile;
49 import jalview.jbgui.GTreePanel;
50 import jalview.util.ImageMaker.TYPE;
51 import jalview.util.MessageManager;
52 import jalview.viewmodel.AlignmentViewport;
55 import java.awt.Graphics;
56 import java.awt.event.ActionEvent;
57 import java.awt.event.ActionListener;
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;
65 import javax.swing.ButtonGroup;
66 import javax.swing.JMenuItem;
67 import javax.swing.JRadioButtonMenuItem;
68 import javax.swing.event.InternalFrameAdapter;
69 import javax.swing.event.InternalFrameEvent;
71 import org.jibble.epsgraphics.EpsGraphics2D;
79 public class TreePanel extends GTreePanel
83 String scoreModelName; // if tree computed
85 String treeTitle; // if tree loaded
87 SimilarityParamsI similarityParams;
89 private TreeCanvas treeCanvas;
93 private AlignViewport av;
96 * Creates a new TreePanel object.
103 public TreePanel(AlignmentPanel ap, String type, String modelName,
104 SimilarityParamsI options)
107 this.similarityParams = options;
108 initTreePanel(ap, type, modelName, null, null);
110 // We know this tree has distances. JBPNote TODO: prolly should add this as
111 // a userdefined default
112 // showDistances(true);
115 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
116 String theTitle, AlignmentView inputData)
119 this.treeTitle = theTitle;
120 initTreePanel(alignPanel, null, null, newtree, inputData);
123 public AlignmentI getAlignment()
125 return getTreeCanvas().getViewport().getAlignment();
128 public AlignmentViewport getViewPort()
130 // @Mungo - Why don't we return our own viewport ???
131 return getTreeCanvas().getViewport();
134 void initTreePanel(AlignmentPanel ap, String type, String modelName,
135 NewickFile newTree, AlignmentView inputData)
139 this.treeType = type;
140 this.scoreModelName = modelName;
142 treeCanvas = new TreeCanvas(this, ap, scrollPane);
143 scrollPane.setViewportView(treeCanvas);
145 PaintRefresher.Register(this, ap.av.getSequenceSetId());
147 buildAssociatedViewMenu();
149 final PropertyChangeListener listener = addAlignmentListener();
152 * remove listener when window is closed, so that this
153 * panel can be garbage collected
155 addInternalFrameListener(new InternalFrameAdapter()
158 public void internalFrameClosed(InternalFrameEvent evt)
162 av.removePropertyChangeListener(listener);
168 TreeLoader tl = new TreeLoader(newTree, inputData);
174 * Ensure any potentially large object references are nulled
176 public void releaseReferences()
179 this.treeCanvas.tree = null;
180 this.treeCanvas.nodeHash = null;
181 this.treeCanvas.nameHash = null;
187 protected PropertyChangeListener addAlignmentListener()
189 final PropertyChangeListener listener = new PropertyChangeListener()
192 public void propertyChange(PropertyChangeEvent evt)
194 if (evt.getPropertyName().equals("alignment"))
198 System.out.println("tree is null");
199 // TODO: deal with case when a change event is received whilst a
200 // tree is still being calculated - should save reference for
201 // processing message later.
204 if (evt.getNewValue() == null)
207 "new alignment sequences vector value is null");
210 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
211 treeCanvas.nameHash.clear(); // reset the mapping between canvas
212 // rectangles and leafnodes
217 av.addPropertyChangeListener(listener);
222 public void viewMenu_menuSelected()
224 buildAssociatedViewMenu();
227 void buildAssociatedViewMenu()
229 AlignmentPanel[] aps = PaintRefresher
230 .getAssociatedPanels(av.getSequenceSetId());
231 if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
233 associateLeavesMenu.setVisible(false);
237 associateLeavesMenu.setVisible(true);
240 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
242 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
245 associateLeavesMenu.removeAll();
247 JRadioButtonMenuItem item;
248 ButtonGroup buttonGroup = new ButtonGroup();
249 int i, iSize = aps.length;
250 final TreePanel thisTreePanel = this;
251 for (i = 0; i < iSize; i++)
253 final AlignmentPanel ap = aps[i];
254 item = new JRadioButtonMenuItem(ap.av.getViewName(),
255 ap == treeCanvas.getAssociatedPanel());
256 buttonGroup.add(item);
257 item.addActionListener(new ActionListener()
260 public void actionPerformed(ActionEvent evt)
262 treeCanvas.applyToAllViews = false;
263 treeCanvas.setAssociatedPanel(ap);
264 treeCanvas.setViewport(ap.av);
265 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
269 associateLeavesMenu.add(item);
272 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
273 MessageManager.getString("label.all_views"));
274 buttonGroup.add(itemf);
275 itemf.setSelected(treeCanvas.applyToAllViews);
276 itemf.addActionListener(new ActionListener()
279 public void actionPerformed(ActionEvent evt)
281 treeCanvas.applyToAllViews = itemf.isSelected();
284 associateLeavesMenu.add(itemf);
288 class TreeLoader extends Thread
290 private NewickFile newtree;
292 private AlignmentView odata = null;
294 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
296 this.newtree = newickFile;
297 this.odata = inputData;
299 if (newickFile != null)
301 // Must be outside run(), as Jalview2XML tries to
302 // update distance/bootstrap visibility at the same time
303 showBootstrap(newickFile.HasBootstrap());
304 showDistances(newickFile.HasDistances());
314 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
316 if (tree.getOriginalData() == null)
318 originalSeqData.setVisible(false);
323 ScoreModelI sm = ScoreModels.getInstance()
324 .getScoreModel(scoreModelName,
325 treeCanvas.getAssociatedPanel());
326 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
327 ? new NJTree(av, sm, similarityParams)
328 : new AverageDistanceTree(av, sm, similarityParams);
329 tree = new TreeModel(njtree);
333 tree.reCount(tree.getTopNode());
334 tree.findHeight(tree.getTopNode());
335 treeCanvas.setTree(tree);
336 treeCanvas.repaint();
337 av.setCurrentTree(tree);
338 if (av.getSortByTree())
340 sortByTree_actionPerformed();
345 public void showDistances(boolean b)
347 treeCanvas.setShowDistances(b);
348 distanceMenu.setSelected(b);
351 public void showBootstrap(boolean b)
353 treeCanvas.setShowBootstrap(b);
354 bootstrapMenu.setSelected(b);
357 public void showPlaceholders(boolean b)
359 placeholdersMenu.setState(b);
360 treeCanvas.setMarkPlaceholders(b);
366 * @return DOCUMENT ME!
368 public TreeModel getTree()
380 public void textbox_actionPerformed(ActionEvent e)
382 CutAndPasteTransfer cap = new CutAndPasteTransfer();
384 String newTitle = getPanelTitle();
386 NewickFile fout = new NewickFile(tree.getTopNode());
389 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
390 tree.hasRootDistance()));
391 Desktop.addInternalFrame(cap, newTitle, 500, 100);
392 } catch (OutOfMemoryError oom)
394 new OOMWarning("generating newick tree file", oom);
407 public void saveAsNewick_actionPerformed(ActionEvent e)
409 // TODO: JAL-3048 save newick file for Jalview-JS
410 JalviewFileChooser chooser = new JalviewFileChooser(
411 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
412 chooser.setFileView(new JalviewFileView());
413 chooser.setDialogTitle(
414 MessageManager.getString("label.save_tree_as_newick"));
415 chooser.setToolTipText(MessageManager.getString("action.save"));
417 int value = chooser.showSaveDialog(null);
419 if (value == JalviewFileChooser.APPROVE_OPTION)
421 String choice = chooser.getSelectedFile().getPath();
422 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
423 chooser.getSelectedFile().getParent());
427 jalview.io.NewickFile fout = new jalview.io.NewickFile(
429 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
430 tree.hasRootDistance());
431 java.io.PrintWriter out = new java.io.PrintWriter(
432 new java.io.FileWriter(choice));
435 } catch (Exception ex)
437 ex.printStackTrace();
449 public void printMenu_actionPerformed(ActionEvent e)
451 // Putting in a thread avoids Swing painting problems
452 treeCanvas.startPrinting();
456 public void originalSeqData_actionPerformed(ActionEvent e)
458 AlignmentView originalData = tree.getOriginalData();
459 if (originalData == null)
461 jalview.bin.Cache.log.info(
462 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
465 // decide if av alignment is sufficiently different to original data to
466 // warrant a new window to be created
467 // create new alignmnt window with hidden regions (unhiding hidden regions
468 // yields unaligned seqs)
469 // or create a selection box around columns in alignment view
470 // test Alignment(SeqCigar[])
474 // we try to get the associated view's gap character
475 // but this may fail if the view was closed...
476 gc = av.getGapCharacter();
478 } catch (Exception ex)
482 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
484 if (alAndColsel != null && alAndColsel[0] != null)
486 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
488 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
489 AlignmentI dataset = (av != null && av.getAlignment() != null)
490 ? av.getAlignment().getDataset()
494 al.setDataset(dataset);
500 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
501 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
503 // >>>This is a fix for the moment, until a better solution is
505 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
507 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
510 Desktop.addInternalFrame(af, MessageManager.formatMessage(
511 "label.original_data_for_params", new Object[]
512 { this.title }), AlignFrame.DEFAULT_WIDTH,
513 AlignFrame.DEFAULT_HEIGHT);
525 public void fitToWindow_actionPerformed(ActionEvent e)
527 treeCanvas.fitToWindow = fitToWindow.isSelected();
532 * sort the associated alignment view by the current tree.
537 public void sortByTree_actionPerformed()
540 if (treeCanvas.applyToAllViews)
542 final ArrayList<CommandI> commands = new ArrayList<>();
543 for (AlignmentPanel ap : PaintRefresher
544 .getAssociatedPanels(av.getSequenceSetId()))
546 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
548 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
552 public void undoCommand(AlignmentI[] views)
554 for (CommandI tsort : commands)
556 tsort.undoCommand(views);
563 return commands.size();
567 public String getDescription()
569 return "Tree Sort (many views)";
573 public void doCommand(AlignmentI[] views)
576 for (CommandI tsort : commands)
578 tsort.doCommand(views);
582 for (AlignmentPanel ap : PaintRefresher
583 .getAssociatedPanels(av.getSequenceSetId()))
585 // ensure all the alignFrames refresh their GI after adding an undo item
586 ap.alignFrame.updateEditMenuBar();
591 treeCanvas.getAssociatedPanel().alignFrame
593 sortAlignmentIn(treeCanvas.getAssociatedPanel()));
598 public CommandI sortAlignmentIn(AlignmentPanel ap)
600 // TODO: move to alignment view controller
601 AlignmentViewport viewport = ap.av;
602 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
603 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
605 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
607 ap.paintAlignment(true, false);
618 public void font_actionPerformed(ActionEvent e)
620 if (treeCanvas == null)
625 new FontChooser(this);
628 public Font getTreeFont()
630 return treeCanvas.font;
633 public void setTreeFont(Font f)
635 if (treeCanvas != null)
637 treeCanvas.setFont(f);
648 public void distanceMenu_actionPerformed(ActionEvent e)
650 treeCanvas.setShowDistances(distanceMenu.isSelected());
660 public void bootstrapMenu_actionPerformed(ActionEvent e)
662 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
672 public void placeholdersMenu_actionPerformed(ActionEvent e)
674 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
678 * Outputs the Tree in image format (currently EPS or PNG). The user is
679 * prompted for the file to save to, and for EPS (unless a preference is
680 * already set) for the choice of Text or Lineart for character rendering.
683 public void writeTreeImage(TYPE imageFormat)
685 int width = treeCanvas.getWidth();
686 int height = treeCanvas.getHeight();
687 ImageWriterI writer = new ImageWriterI()
690 public void exportImage(Graphics g) throws Exception
692 treeCanvas.draw(g, width, height);
695 String tree = MessageManager.getString("label.tree");
696 ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
698 exporter.doExport(null, this, width, height, tree.toLowerCase(Locale.ROOT));
702 * change node labels to the annotation referred to by labelClass TODO:
703 * promote to a datamodel modification that can be undone TODO: make argument
704 * one case of a generic transformation function ie { undoStep = apply(Tree,
705 * TransformFunction)};
709 public void changeNames(final String labelClass)
711 tree.applyToNodes(new NodeTransformI()
715 public void transform(BinaryNode node)
717 if (node instanceof SequenceNode
718 && !((SequenceNode) node).isPlaceholder()
719 && !((SequenceNode) node).isDummy())
721 String newname = null;
722 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
725 // search dbrefs, features and annotation
726 List<DBRefEntry> refs = jalview.util.DBRefUtils
727 .selectRefs(sq.getDBRefs(), new String[]
728 { labelClass.toUpperCase(Locale.ROOT) });
731 for (int i = 0, ni = refs.size(); i < ni; i++)
735 newname = new String(refs.get(i).getAccessionId());
739 newname += "; " + refs.get(i).getAccessionId();
745 List<SequenceFeature> features = sq.getFeatures()
746 .getPositionalFeatures(labelClass);
747 for (SequenceFeature feature : features)
751 newname = feature.getDescription();
755 newname = newname + "; " + feature.getDescription();
762 // String oldname = ((SequenceNode) node).getName();
763 // TODO : save oldname in the undo object for this modification.
764 ((SequenceNode) node).setName(newname);
772 * Formats a localised title for the tree panel, like
774 * Neighbour Joining Using BLOSUM62
776 * For a tree loaded from file, just uses the file name
780 public String getPanelTitle()
782 if (treeTitle != null)
788 * i18n description of Neighbour Joining or Average Distance method
790 String treecalcnm = MessageManager
791 .getString("label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
794 * short score model name (long description can be too long)
796 String smn = scoreModelName;
799 * put them together as <method> Using <model>
801 final String ttl = MessageManager.formatMessage("label.calc_title",
807 * Builds an EPS image and writes it to the specified file.
811 * true for Text character rendering, false for Lineart
813 protected void writeEpsFile(File outFile, boolean textOption)
817 int width = treeCanvas.getWidth();
818 int height = treeCanvas.getHeight();
820 FileOutputStream out = new FileOutputStream(
822 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
824 pg.setAccurateTextMode(!textOption);
825 treeCanvas.draw(pg, width, height);
829 } catch (Exception ex)
831 System.err.println("Error writing tree as EPS");
832 ex.printStackTrace();
836 public AlignViewport getViewport()
841 public void setViewport(AlignViewport av)
846 public TreeCanvas getTreeCanvas()