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);
166 TreeLoader tl = new TreeLoader(newTree, inputData);
172 * Ensure any potentially large object references are nulled
174 public void releaseReferences()
177 this.treeCanvas.tree = null;
178 this.treeCanvas.nodeHash = null;
179 this.treeCanvas.nameHash = null;
185 protected PropertyChangeListener addAlignmentListener()
187 final PropertyChangeListener listener = new PropertyChangeListener()
190 public void propertyChange(PropertyChangeEvent evt)
192 if (evt.getPropertyName().equals("alignment"))
196 System.out.println("tree is null");
197 // TODO: deal with case when a change event is received whilst a
198 // tree is still being calculated - should save reference for
199 // processing message later.
202 if (evt.getNewValue() == null)
205 "new alignment sequences vector value is null");
208 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
209 treeCanvas.nameHash.clear(); // reset the mapping between canvas
210 // rectangles and leafnodes
215 av.addPropertyChangeListener(listener);
220 public void viewMenu_menuSelected()
222 buildAssociatedViewMenu();
225 void buildAssociatedViewMenu()
227 AlignmentPanel[] aps = PaintRefresher
228 .getAssociatedPanels(av.getSequenceSetId());
229 if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
231 associateLeavesMenu.setVisible(false);
235 associateLeavesMenu.setVisible(true);
238 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
240 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
243 associateLeavesMenu.removeAll();
245 JRadioButtonMenuItem item;
246 ButtonGroup buttonGroup = new ButtonGroup();
247 int i, iSize = aps.length;
248 final TreePanel thisTreePanel = this;
249 for (i = 0; i < iSize; i++)
251 final AlignmentPanel ap = aps[i];
252 item = new JRadioButtonMenuItem(ap.av.getViewName(),
253 ap == treeCanvas.getAssociatedPanel());
254 buttonGroup.add(item);
255 item.addActionListener(new ActionListener()
258 public void actionPerformed(ActionEvent evt)
260 treeCanvas.applyToAllViews = false;
261 treeCanvas.setAssociatedPanel(ap);
262 treeCanvas.setViewport(ap.av);
263 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
267 associateLeavesMenu.add(item);
270 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
271 MessageManager.getString("label.all_views"));
272 buttonGroup.add(itemf);
273 itemf.setSelected(treeCanvas.applyToAllViews);
274 itemf.addActionListener(new ActionListener()
277 public void actionPerformed(ActionEvent evt)
279 treeCanvas.applyToAllViews = itemf.isSelected();
282 associateLeavesMenu.add(itemf);
286 class TreeLoader extends Thread
288 private NewickFile newtree;
290 private AlignmentView odata = null;
292 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
294 this.newtree = newickFile;
295 this.odata = inputData;
297 if (newickFile != null)
299 // Must be outside run(), as Jalview2XML tries to
300 // update distance/bootstrap visibility at the same time
301 showBootstrap(newickFile.HasBootstrap());
302 showDistances(newickFile.HasDistances());
312 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
314 if (tree.getOriginalData() == null)
316 originalSeqData.setVisible(false);
321 ScoreModelI sm = ScoreModels.getInstance()
322 .getScoreModel(scoreModelName,
323 treeCanvas.getAssociatedPanel());
324 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
325 ? new NJTree(av, sm, similarityParams)
326 : new AverageDistanceTree(av, sm, similarityParams);
327 tree = new TreeModel(njtree);
331 tree.reCount(tree.getTopNode());
332 tree.findHeight(tree.getTopNode());
333 treeCanvas.setTree(tree);
334 treeCanvas.repaint();
335 av.setCurrentTree(tree);
336 if (av.getSortByTree())
338 sortByTree_actionPerformed();
343 public void showDistances(boolean b)
345 treeCanvas.setShowDistances(b);
346 distanceMenu.setSelected(b);
349 public void showBootstrap(boolean b)
351 treeCanvas.setShowBootstrap(b);
352 bootstrapMenu.setSelected(b);
355 public void showPlaceholders(boolean b)
357 placeholdersMenu.setState(b);
358 treeCanvas.setMarkPlaceholders(b);
364 * @return DOCUMENT ME!
366 public TreeModel getTree()
378 public void textbox_actionPerformed(ActionEvent e)
380 CutAndPasteTransfer cap = new CutAndPasteTransfer();
382 String newTitle = getPanelTitle();
384 NewickFile fout = new NewickFile(tree.getTopNode());
387 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
388 tree.hasRootDistance()));
389 Desktop.addInternalFrame(cap, newTitle, 500, 100);
390 } catch (OutOfMemoryError oom)
392 new OOMWarning("generating newick tree file", oom);
405 public void saveAsNewick_actionPerformed(ActionEvent e)
407 // TODO: JAL-3048 save newick file for Jalview-JS
408 JalviewFileChooser chooser = new JalviewFileChooser(
409 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
410 chooser.setFileView(new JalviewFileView());
411 chooser.setDialogTitle(
412 MessageManager.getString("label.save_tree_as_newick"));
413 chooser.setToolTipText(MessageManager.getString("action.save"));
415 int value = chooser.showSaveDialog(null);
417 if (value == JalviewFileChooser.APPROVE_OPTION)
419 String choice = chooser.getSelectedFile().getPath();
420 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
421 chooser.getSelectedFile().getParent());
425 jalview.io.NewickFile fout = new jalview.io.NewickFile(
427 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
428 tree.hasRootDistance());
429 java.io.PrintWriter out = new java.io.PrintWriter(
430 new java.io.FileWriter(choice));
433 } catch (Exception ex)
435 ex.printStackTrace();
447 public void printMenu_actionPerformed(ActionEvent e)
449 // Putting in a thread avoids Swing painting problems
450 treeCanvas.startPrinting();
454 public void originalSeqData_actionPerformed(ActionEvent e)
456 AlignmentView originalData = tree.getOriginalData();
457 if (originalData == null)
459 jalview.bin.Cache.log.info(
460 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
463 // decide if av alignment is sufficiently different to original data to
464 // warrant a new window to be created
465 // create new alignmnt window with hidden regions (unhiding hidden regions
466 // yields unaligned seqs)
467 // or create a selection box around columns in alignment view
468 // test Alignment(SeqCigar[])
472 // we try to get the associated view's gap character
473 // but this may fail if the view was closed...
474 gc = av.getGapCharacter();
476 } catch (Exception ex)
480 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
482 if (alAndColsel != null && alAndColsel[0] != null)
484 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
486 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
487 AlignmentI dataset = (av != null && av.getAlignment() != null)
488 ? av.getAlignment().getDataset()
492 al.setDataset(dataset);
498 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
499 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
501 // >>>This is a fix for the moment, until a better solution is
503 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
505 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
508 Desktop.addInternalFrame(af, MessageManager.formatMessage(
509 "label.original_data_for_params", new Object[]
510 { this.title }), AlignFrame.DEFAULT_WIDTH,
511 AlignFrame.DEFAULT_HEIGHT);
523 public void fitToWindow_actionPerformed(ActionEvent e)
525 treeCanvas.fitToWindow = fitToWindow.isSelected();
530 * sort the associated alignment view by the current tree.
535 public void sortByTree_actionPerformed()
538 if (treeCanvas.applyToAllViews)
540 final ArrayList<CommandI> commands = new ArrayList<>();
541 for (AlignmentPanel ap : PaintRefresher
542 .getAssociatedPanels(av.getSequenceSetId()))
544 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
546 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
550 public void undoCommand(AlignmentI[] views)
552 for (CommandI tsort : commands)
554 tsort.undoCommand(views);
561 return commands.size();
565 public String getDescription()
567 return "Tree Sort (many views)";
571 public void doCommand(AlignmentI[] views)
574 for (CommandI tsort : commands)
576 tsort.doCommand(views);
580 for (AlignmentPanel ap : PaintRefresher
581 .getAssociatedPanels(av.getSequenceSetId()))
583 // ensure all the alignFrames refresh their GI after adding an undo item
584 ap.alignFrame.updateEditMenuBar();
589 treeCanvas.getAssociatedPanel().alignFrame
591 sortAlignmentIn(treeCanvas.getAssociatedPanel()));
596 public CommandI sortAlignmentIn(AlignmentPanel ap)
598 // TODO: move to alignment view controller
599 AlignmentViewport viewport = ap.av;
600 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
601 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
603 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
605 ap.paintAlignment(true, false);
616 public void font_actionPerformed(ActionEvent e)
618 if (treeCanvas == null)
623 new FontChooser(this);
626 public Font getTreeFont()
628 return treeCanvas.font;
631 public void setTreeFont(Font f)
633 if (treeCanvas != null)
635 treeCanvas.setFont(f);
646 public void distanceMenu_actionPerformed(ActionEvent e)
648 treeCanvas.setShowDistances(distanceMenu.isSelected());
658 public void bootstrapMenu_actionPerformed(ActionEvent e)
660 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
670 public void placeholdersMenu_actionPerformed(ActionEvent e)
672 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
676 * Outputs the Tree in image format (currently EPS or PNG). The user is
677 * prompted for the file to save to, and for EPS (unless a preference is
678 * already set) for the choice of Text or Lineart for character rendering.
681 public void writeTreeImage(TYPE imageFormat)
683 int width = treeCanvas.getWidth();
684 int height = treeCanvas.getHeight();
685 ImageWriterI writer = new ImageWriterI()
688 public void exportImage(Graphics g) throws Exception
690 treeCanvas.draw(g, width, height);
693 String tree = MessageManager.getString("label.tree");
694 ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
696 exporter.doExport(null, this, width, height, tree.toLowerCase());
700 * change node labels to the annotation referred to by labelClass TODO:
701 * promote to a datamodel modification that can be undone TODO: make argument
702 * one case of a generic transformation function ie { undoStep = apply(Tree,
703 * TransformFunction)};
707 public void changeNames(final String labelClass)
709 tree.applyToNodes(new NodeTransformI()
713 public void transform(BinaryNode node)
715 if (node instanceof SequenceNode
716 && !((SequenceNode) node).isPlaceholder()
717 && !((SequenceNode) node).isDummy())
719 String newname = null;
720 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
723 // search dbrefs, features and annotation
724 List<DBRefEntry> refs = jalview.util.DBRefUtils
725 .selectRefs(sq.getDBRefs(), new String[]
726 { labelClass.toUpperCase() });
729 for (int i = 0, ni = refs.size(); i < ni; i++)
733 newname = new String(refs.get(i).getAccessionId());
737 newname += "; " + refs.get(i).getAccessionId();
743 List<SequenceFeature> features = sq.getFeatures()
744 .getPositionalFeatures(labelClass);
745 for (SequenceFeature feature : features)
749 newname = feature.getDescription();
753 newname = newname + "; " + feature.getDescription();
760 // String oldname = ((SequenceNode) node).getName();
761 // TODO : save oldname in the undo object for this modification.
762 ((SequenceNode) node).setName(newname);
770 * Formats a localised title for the tree panel, like
772 * Neighbour Joining Using BLOSUM62
774 * For a tree loaded from file, just uses the file name
778 public String getPanelTitle()
780 if (treeTitle != null)
786 * i18n description of Neighbour Joining or Average Distance method
788 String treecalcnm = MessageManager
789 .getString("label.tree_calc_" + treeType.toLowerCase());
792 * short score model name (long description can be too long)
794 String smn = scoreModelName;
797 * put them together as <method> Using <model>
799 final String ttl = MessageManager.formatMessage("label.calc_title",
805 * Builds an EPS image and writes it to the specified file.
809 * true for Text character rendering, false for Lineart
811 protected void writeEpsFile(File outFile, boolean textOption)
815 int width = treeCanvas.getWidth();
816 int height = treeCanvas.getHeight();
818 FileOutputStream out = new FileOutputStream(
820 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
822 pg.setAccurateTextMode(!textOption);
823 treeCanvas.draw(pg, width, height);
827 } catch (Exception ex)
829 System.err.println("Error writing tree as EPS");
830 ex.printStackTrace();
834 public AlignViewport getViewport()
839 public void setViewport(AlignViewport av)
844 public TreeCanvas getTreeCanvas()