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 jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AverageDistanceTree;
25 import jalview.analysis.NJTree;
26 import jalview.analysis.TreeBuilder;
27 import jalview.analysis.TreeModel;
28 import jalview.analysis.scoremodels.ScoreModels;
29 import jalview.api.analysis.ScoreModelI;
30 import jalview.api.analysis.SimilarityParamsI;
31 import jalview.commands.CommandI;
32 import jalview.commands.OrderCommand;
33 import jalview.datamodel.Alignment;
34 import jalview.datamodel.AlignmentI;
35 import jalview.datamodel.AlignmentView;
36 import jalview.datamodel.BinaryNode;
37 import jalview.datamodel.DBRefEntry;
38 import jalview.datamodel.HiddenColumns;
39 import jalview.datamodel.NodeTransformI;
40 import jalview.datamodel.SequenceFeature;
41 import jalview.datamodel.SequenceI;
42 import jalview.datamodel.SequenceNode;
43 import jalview.gui.ImageExporter.ImageWriterI;
44 import jalview.io.JalviewFileChooser;
45 import jalview.io.JalviewFileView;
46 import jalview.io.NewickFile;
47 import jalview.jbgui.GTreePanel;
48 import jalview.util.ImageMaker.TYPE;
49 import jalview.util.MessageManager;
50 import jalview.viewmodel.AlignmentViewport;
53 import java.awt.Graphics;
54 import java.awt.event.ActionEvent;
55 import java.awt.event.ActionListener;
56 import java.beans.PropertyChangeEvent;
57 import java.beans.PropertyChangeListener;
59 import java.io.FileOutputStream;
60 import java.util.ArrayList;
61 import java.util.List;
63 import javax.swing.ButtonGroup;
64 import javax.swing.JMenuItem;
65 import javax.swing.JRadioButtonMenuItem;
66 import javax.swing.event.InternalFrameAdapter;
67 import javax.swing.event.InternalFrameEvent;
69 import org.jibble.epsgraphics.EpsGraphics2D;
77 public class TreePanel extends GTreePanel
81 String scoreModelName; // if tree computed
83 String treeTitle; // if tree loaded
85 SimilarityParamsI similarityParams;
87 private TreeCanvas treeCanvas;
91 private AlignViewport av;
94 * Creates a new TreePanel object.
101 public TreePanel(AlignmentPanel ap, String type, String modelName,
102 SimilarityParamsI options)
105 this.similarityParams = options;
106 initTreePanel(ap, type, modelName, null, null);
108 // We know this tree has distances. JBPNote TODO: prolly should add this as
109 // a userdefined default
110 // showDistances(true);
113 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
114 String theTitle, AlignmentView inputData)
117 this.treeTitle = theTitle;
118 initTreePanel(alignPanel, null, null, newtree, inputData);
121 public AlignmentI getAlignment()
123 return getTreeCanvas().getViewport().getAlignment();
126 public AlignmentViewport getViewPort()
128 // @Mungo - Why don't we return our own viewport ???
129 return getTreeCanvas().getViewport();
132 void initTreePanel(AlignmentPanel ap, String type, String modelName,
133 NewickFile newTree, AlignmentView inputData)
137 this.treeType = type;
138 this.scoreModelName = modelName;
140 treeCanvas = new TreeCanvas(this, ap, scrollPane);
141 scrollPane.setViewportView(treeCanvas);
143 PaintRefresher.Register(this, ap.av.getSequenceSetId());
145 buildAssociatedViewMenu();
147 final PropertyChangeListener listener = addAlignmentListener();
150 * remove listener when window is closed, so that this
151 * panel can be garbage collected
153 addInternalFrameListener(new InternalFrameAdapter()
156 public void internalFrameClosed(InternalFrameEvent evt)
160 av.removePropertyChangeListener(listener);
165 TreeLoader tl = new TreeLoader(newTree, inputData);
173 protected PropertyChangeListener addAlignmentListener()
175 final PropertyChangeListener listener = new PropertyChangeListener()
178 public void propertyChange(PropertyChangeEvent evt)
180 if (evt.getPropertyName().equals("alignment"))
184 System.out.println("tree is null");
185 // TODO: deal with case when a change event is received whilst a
186 // tree is still being calculated - should save reference for
187 // processing message later.
190 if (evt.getNewValue() == null)
193 "new alignment sequences vector value is null");
196 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
197 treeCanvas.nameHash.clear(); // reset the mapping between canvas
198 // rectangles and leafnodes
203 av.addPropertyChangeListener(listener);
208 public void viewMenu_menuSelected()
210 buildAssociatedViewMenu();
213 void buildAssociatedViewMenu()
215 AlignmentPanel[] aps = PaintRefresher
216 .getAssociatedPanels(av.getSequenceSetId());
217 if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
219 associateLeavesMenu.setVisible(false);
223 associateLeavesMenu.setVisible(true);
226 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
228 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
231 associateLeavesMenu.removeAll();
233 JRadioButtonMenuItem item;
234 ButtonGroup buttonGroup = new ButtonGroup();
235 int i, iSize = aps.length;
236 final TreePanel thisTreePanel = this;
237 for (i = 0; i < iSize; i++)
239 final AlignmentPanel ap = aps[i];
240 item = new JRadioButtonMenuItem(ap.av.getViewName(),
241 ap == treeCanvas.getAssociatedPanel());
242 buttonGroup.add(item);
243 item.addActionListener(new ActionListener()
246 public void actionPerformed(ActionEvent evt)
248 treeCanvas.applyToAllViews = false;
249 treeCanvas.setAssociatedPanel(ap);
250 treeCanvas.setViewport(ap.av);
251 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
255 associateLeavesMenu.add(item);
258 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
259 MessageManager.getString("label.all_views"));
260 buttonGroup.add(itemf);
261 itemf.setSelected(treeCanvas.applyToAllViews);
262 itemf.addActionListener(new ActionListener()
265 public void actionPerformed(ActionEvent evt)
267 treeCanvas.applyToAllViews = itemf.isSelected();
270 associateLeavesMenu.add(itemf);
274 class TreeLoader extends Thread
276 private NewickFile newtree;
278 private AlignmentView odata = null;
280 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
282 this.newtree = newickFile;
283 this.odata = inputData;
285 if (newickFile != null)
287 // Must be outside run(), as Jalview2XML tries to
288 // update distance/bootstrap visibility at the same time
289 showBootstrap(newickFile.HasBootstrap());
290 showDistances(newickFile.HasDistances());
300 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
302 if (tree.getOriginalData() == null)
304 originalSeqData.setVisible(false);
309 ScoreModelI sm = ScoreModels.getInstance()
310 .getScoreModel(scoreModelName,
311 treeCanvas.getAssociatedPanel());
312 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
313 ? new NJTree(av, sm, similarityParams)
314 : new AverageDistanceTree(av, sm, similarityParams);
315 tree = new TreeModel(njtree);
319 tree.reCount(tree.getTopNode());
320 tree.findHeight(tree.getTopNode());
321 treeCanvas.setTree(tree);
322 treeCanvas.repaint();
323 av.setCurrentTree(tree);
324 if (av.getSortByTree())
326 sortByTree_actionPerformed();
331 public void showDistances(boolean b)
333 treeCanvas.setShowDistances(b);
334 distanceMenu.setSelected(b);
337 public void showBootstrap(boolean b)
339 treeCanvas.setShowBootstrap(b);
340 bootstrapMenu.setSelected(b);
343 public void showPlaceholders(boolean b)
345 placeholdersMenu.setState(b);
346 treeCanvas.setMarkPlaceholders(b);
352 * @return DOCUMENT ME!
354 public TreeModel getTree()
366 public void textbox_actionPerformed(ActionEvent e)
368 CutAndPasteTransfer cap = new CutAndPasteTransfer();
370 String newTitle = getPanelTitle();
372 NewickFile fout = new NewickFile(tree.getTopNode());
375 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
376 tree.hasRootDistance()));
377 Desktop.addInternalFrame(cap, newTitle, 500, 100);
378 } catch (OutOfMemoryError oom)
380 new OOMWarning("generating newick tree file", oom);
393 public void saveAsNewick_actionPerformed(ActionEvent e)
395 // TODO: JAL-3048 save newick file for Jalview-JS
396 JalviewFileChooser chooser = new JalviewFileChooser(
397 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
398 chooser.setFileView(new JalviewFileView());
399 chooser.setDialogTitle(
400 MessageManager.getString("label.save_tree_as_newick"));
401 chooser.setToolTipText(MessageManager.getString("action.save"));
403 int value = chooser.showSaveDialog(null);
405 if (value == JalviewFileChooser.APPROVE_OPTION)
407 String choice = chooser.getSelectedFile().getPath();
408 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
409 chooser.getSelectedFile().getParent());
413 jalview.io.NewickFile fout = new jalview.io.NewickFile(
415 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
416 tree.hasRootDistance());
417 java.io.PrintWriter out = new java.io.PrintWriter(
418 new java.io.FileWriter(choice));
421 } catch (Exception ex)
423 ex.printStackTrace();
435 public void printMenu_actionPerformed(ActionEvent e)
437 // Putting in a thread avoids Swing painting problems
438 treeCanvas.startPrinting();
442 public void originalSeqData_actionPerformed(ActionEvent e)
444 AlignmentView originalData = tree.getOriginalData();
445 if (originalData == null)
447 jalview.bin.Cache.log.info(
448 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
451 // decide if av alignment is sufficiently different to original data to
452 // warrant a new window to be created
453 // create new alignmnt window with hidden regions (unhiding hidden regions
454 // yields unaligned seqs)
455 // or create a selection box around columns in alignment view
456 // test Alignment(SeqCigar[])
460 // we try to get the associated view's gap character
461 // but this may fail if the view was closed...
462 gc = av.getGapCharacter();
464 } catch (Exception ex)
468 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
470 if (alAndColsel != null && alAndColsel[0] != null)
472 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
474 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
475 AlignmentI dataset = (av != null && av.getAlignment() != null)
476 ? av.getAlignment().getDataset()
480 al.setDataset(dataset);
486 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
487 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
489 // >>>This is a fix for the moment, until a better solution is
491 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
493 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
496 Desktop.addInternalFrame(af, MessageManager.formatMessage(
497 "label.original_data_for_params", new Object[]
498 { this.title }), AlignFrame.DEFAULT_WIDTH,
499 AlignFrame.DEFAULT_HEIGHT);
511 public void fitToWindow_actionPerformed(ActionEvent e)
513 treeCanvas.fitToWindow = fitToWindow.isSelected();
518 * sort the associated alignment view by the current tree.
523 public void sortByTree_actionPerformed()
526 if (treeCanvas.applyToAllViews)
528 final ArrayList<CommandI> commands = new ArrayList<>();
529 for (AlignmentPanel ap : PaintRefresher
530 .getAssociatedPanels(av.getSequenceSetId()))
532 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
534 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
538 public void undoCommand(AlignmentI[] views)
540 for (CommandI tsort : commands)
542 tsort.undoCommand(views);
549 return commands.size();
553 public String getDescription()
555 return "Tree Sort (many views)";
559 public void doCommand(AlignmentI[] views)
562 for (CommandI tsort : commands)
564 tsort.doCommand(views);
568 for (AlignmentPanel ap : PaintRefresher
569 .getAssociatedPanels(av.getSequenceSetId()))
571 // ensure all the alignFrames refresh their GI after adding an undo item
572 ap.alignFrame.updateEditMenuBar();
577 treeCanvas.getAssociatedPanel().alignFrame
579 sortAlignmentIn(treeCanvas.getAssociatedPanel()));
584 public CommandI sortAlignmentIn(AlignmentPanel ap)
586 // TODO: move to alignment view controller
587 AlignmentViewport viewport = ap.av;
588 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
589 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
591 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
593 ap.paintAlignment(true, false);
604 public void font_actionPerformed(ActionEvent e)
606 if (treeCanvas == null)
611 new FontChooser(this);
614 public Font getTreeFont()
616 return treeCanvas.font;
619 public void setTreeFont(Font f)
621 if (treeCanvas != null)
623 treeCanvas.setFont(f);
634 public void distanceMenu_actionPerformed(ActionEvent e)
636 treeCanvas.setShowDistances(distanceMenu.isSelected());
646 public void bootstrapMenu_actionPerformed(ActionEvent e)
648 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
658 public void placeholdersMenu_actionPerformed(ActionEvent e)
660 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
664 * Outputs the Tree in image format (currently EPS or PNG). The user is
665 * prompted for the file to save to, and for EPS (unless a preference is
666 * already set) for the choice of Text or Lineart for character rendering.
669 public void writeTreeImage(TYPE imageFormat)
671 int width = treeCanvas.getWidth();
672 int height = treeCanvas.getHeight();
673 ImageWriterI writer = new ImageWriterI()
676 public void exportImage(Graphics g) throws Exception
678 treeCanvas.draw(g, width, height);
681 String tree = MessageManager.getString("label.tree");
682 ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
684 exporter.doExport(null, this, width, height, tree.toLowerCase());
688 * change node labels to the annotation referred to by labelClass TODO:
689 * promote to a datamodel modification that can be undone TODO: make argument
690 * one case of a generic transformation function ie { undoStep = apply(Tree,
691 * TransformFunction)};
695 public void changeNames(final String labelClass)
697 tree.applyToNodes(new NodeTransformI()
701 public void transform(BinaryNode node)
703 if (node instanceof SequenceNode
704 && !((SequenceNode) node).isPlaceholder()
705 && !((SequenceNode) node).isDummy())
707 String newname = null;
708 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
711 // search dbrefs, features and annotation
712 List<DBRefEntry> refs = jalview.util.DBRefUtils
713 .selectRefs(sq.getDBRefs(), new String[]
714 { labelClass.toUpperCase() });
717 for (int i = 0, ni = refs.size(); i < ni; i++)
721 newname = new String(refs.get(i).getAccessionId());
725 newname += "; " + refs.get(i).getAccessionId();
731 List<SequenceFeature> features = sq.getFeatures()
732 .getPositionalFeatures(labelClass);
733 for (SequenceFeature feature : features)
737 newname = feature.getDescription();
741 newname = newname + "; " + feature.getDescription();
748 // String oldname = ((SequenceNode) node).getName();
749 // TODO : save oldname in the undo object for this modification.
750 ((SequenceNode) node).setName(newname);
758 * Formats a localised title for the tree panel, like
760 * Neighbour Joining Using BLOSUM62
762 * For a tree loaded from file, just uses the file name
766 public String getPanelTitle()
768 if (treeTitle != null)
774 * i18n description of Neighbour Joining or Average Distance method
776 String treecalcnm = MessageManager
777 .getString("label.tree_calc_" + treeType.toLowerCase());
780 * short score model name (long description can be too long)
782 String smn = scoreModelName;
785 * put them together as <method> Using <model>
787 final String ttl = MessageManager.formatMessage("label.treecalc_title",
793 * Builds an EPS image and writes it to the specified file.
797 * true for Text character rendering, false for Lineart
799 protected void writeEpsFile(File outFile, boolean textOption)
803 int width = treeCanvas.getWidth();
804 int height = treeCanvas.getHeight();
806 FileOutputStream out = new FileOutputStream(
808 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
810 pg.setAccurateTextMode(!textOption);
811 treeCanvas.draw(pg, width, height);
815 } catch (Exception ex)
817 System.err.println("Error writing tree as EPS");
818 ex.printStackTrace();
822 public AlignViewport getViewport()
827 public void setViewport(AlignViewport av)
832 public TreeCanvas getTreeCanvas()