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.NJTree;
25 import jalview.api.analysis.ScoreModelI;
26 import jalview.api.analysis.SimilarityParamsI;
27 import jalview.api.analysis.ViewBasedAnalysisI;
28 import jalview.bin.Cache;
29 import jalview.commands.CommandI;
30 import jalview.commands.OrderCommand;
31 import jalview.datamodel.Alignment;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.AlignmentView;
34 import jalview.datamodel.BinaryNode;
35 import jalview.datamodel.ColumnSelection;
36 import jalview.datamodel.DBRefEntry;
37 import jalview.datamodel.NodeTransformI;
38 import jalview.datamodel.SequenceFeature;
39 import jalview.datamodel.SequenceI;
40 import jalview.datamodel.SequenceNode;
41 import jalview.io.JalviewFileChooser;
42 import jalview.io.JalviewFileView;
43 import jalview.io.NewickFile;
44 import jalview.jbgui.GTreePanel;
45 import jalview.util.ImageMaker;
46 import jalview.util.MessageManager;
47 import jalview.viewmodel.AlignmentViewport;
50 import java.awt.Graphics;
51 import java.awt.event.ActionEvent;
52 import java.awt.event.ActionListener;
53 import java.awt.image.BufferedImage;
54 import java.beans.PropertyChangeEvent;
55 import java.io.FileOutputStream;
56 import java.util.ArrayList;
57 import java.util.List;
59 import javax.imageio.ImageIO;
60 import javax.swing.ButtonGroup;
61 import javax.swing.JMenuItem;
62 import javax.swing.JRadioButtonMenuItem;
64 import org.jibble.epsgraphics.EpsGraphics2D;
72 public class TreePanel extends GTreePanel
76 ScoreModelI scoreModel; // if tree computed
78 String treeTitle; // if tree loaded
80 SimilarityParamsI similarityParams;
82 TreeCanvas treeCanvas;
89 * Creates a new TreePanel object.
96 public TreePanel(AlignmentPanel ap, String type, ScoreModelI sm,
97 SimilarityParamsI options)
100 this.similarityParams = options;
101 initTreePanel(ap, type, sm, null, null);
103 // We know this tree has distances. JBPNote TODO: prolly should add this as
104 // a userdefined default
105 // showDistances(true);
108 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
109 String theTitle, AlignmentView inputData)
112 this.treeTitle = theTitle;
113 initTreePanel(alignPanel, null, null, newtree, inputData);
116 public AlignmentI getAlignment()
118 return treeCanvas.av.getAlignment();
121 public AlignmentViewport getViewPort()
123 return treeCanvas.av;
126 void initTreePanel(AlignmentPanel ap, String type, ScoreModelI sm,
127 NewickFile newTree, AlignmentView inputData)
131 this.treeType = type;
132 this.scoreModel = sm;
134 treeCanvas = new TreeCanvas(this, ap, scrollPane);
135 scrollPane.setViewportView(treeCanvas);
137 PaintRefresher.Register(this, ap.av.getSequenceSetId());
139 buildAssociatedViewMenu();
141 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
144 public void propertyChange(PropertyChangeEvent evt)
146 if (evt.getPropertyName().equals("alignment"))
150 System.out.println("tree is null");
151 // TODO: deal with case when a change event is received whilst a
152 // tree is still being calculated - should save reference for
153 // processing message later.
156 if (evt.getNewValue() == null)
159 .println("new alignment sequences vector value is null");
162 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
163 treeCanvas.nameHash.clear(); // reset the mapping between canvas
164 // rectangles and leafnodes
170 TreeLoader tl = new TreeLoader(newTree);
171 if (inputData != null)
173 tl.odata = inputData;
180 public void viewMenu_menuSelected()
182 buildAssociatedViewMenu();
185 void buildAssociatedViewMenu()
187 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
188 .getSequenceSetId());
189 if (aps.length == 1 && treeCanvas.ap == aps[0])
191 associateLeavesMenu.setVisible(false);
195 associateLeavesMenu.setVisible(true);
197 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
199 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
202 associateLeavesMenu.removeAll();
204 JRadioButtonMenuItem item;
205 ButtonGroup buttonGroup = new ButtonGroup();
206 int i, iSize = aps.length;
207 final TreePanel thisTreePanel = this;
208 for (i = 0; i < iSize; i++)
210 final AlignmentPanel ap = aps[i];
211 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
212 buttonGroup.add(item);
213 item.addActionListener(new ActionListener()
216 public void actionPerformed(ActionEvent evt)
218 treeCanvas.applyToAllViews = false;
220 treeCanvas.av = ap.av;
221 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
225 associateLeavesMenu.add(item);
228 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
229 MessageManager.getString("label.all_views"));
230 buttonGroup.add(itemf);
231 itemf.setSelected(treeCanvas.applyToAllViews);
232 itemf.addActionListener(new ActionListener()
235 public void actionPerformed(ActionEvent evt)
237 treeCanvas.applyToAllViews = itemf.isSelected();
240 associateLeavesMenu.add(itemf);
244 class TreeLoader extends Thread
248 AlignmentView odata = null;
250 public TreeLoader(NewickFile newickFile)
252 this.newtree = newickFile;
253 if (newickFile != null)
255 // Must be outside run(), as Jalview2XML tries to
256 // update distance/bootstrap visibility at the same time
257 showBootstrap(newickFile.HasBootstrap());
258 showDistances(newickFile.HasDistances());
270 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
274 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
277 if (!tree.hasOriginalSequenceData())
279 allowOriginalSeqData(false);
284 ScoreModelI sm = configureScoreModel();
285 tree = new NJTree(av, treeType, sm, similarityParams);
289 tree.reCount(tree.getTopNode());
290 tree.findHeight(tree.getTopNode());
291 treeCanvas.setTree(tree);
292 treeCanvas.repaint();
293 av.setCurrentTree(tree);
294 if (av.getSortByTree())
296 sortByTree_actionPerformed();
301 public void showDistances(boolean b)
303 treeCanvas.setShowDistances(b);
304 distanceMenu.setSelected(b);
307 public void showBootstrap(boolean b)
309 treeCanvas.setShowBootstrap(b);
310 bootstrapMenu.setSelected(b);
313 public void showPlaceholders(boolean b)
315 placeholdersMenu.setState(b);
316 treeCanvas.setMarkPlaceholders(b);
319 private void allowOriginalSeqData(boolean b)
321 originalSeqData.setVisible(b);
327 * @return DOCUMENT ME!
329 public NJTree getTree()
341 public void textbox_actionPerformed(ActionEvent e)
343 CutAndPasteTransfer cap = new CutAndPasteTransfer();
345 String newTitle = getPanelTitle();
347 NewickFile fout = new NewickFile(tree.getTopNode());
350 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
351 tree.hasRootDistance()));
352 Desktop.addInternalFrame(cap, newTitle, 500, 100);
353 } catch (OutOfMemoryError oom)
355 new OOMWarning("generating newick tree file", oom);
368 public void saveAsNewick_actionPerformed(ActionEvent e)
370 JalviewFileChooser chooser = new JalviewFileChooser(
371 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
372 chooser.setFileView(new JalviewFileView());
373 chooser.setDialogTitle(MessageManager
374 .getString("label.save_tree_as_newick"));
375 chooser.setToolTipText(MessageManager.getString("action.save"));
377 int value = chooser.showSaveDialog(null);
379 if (value == JalviewFileChooser.APPROVE_OPTION)
381 String choice = chooser.getSelectedFile().getPath();
382 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
383 .getSelectedFile().getParent());
387 jalview.io.NewickFile fout = new jalview.io.NewickFile(
389 String output = fout.print(tree.hasBootstrap(),
390 tree.hasDistances(), tree.hasRootDistance());
391 java.io.PrintWriter out = new java.io.PrintWriter(
392 new java.io.FileWriter(choice));
395 } catch (Exception ex)
397 ex.printStackTrace();
409 public void printMenu_actionPerformed(ActionEvent e)
411 // Putting in a thread avoids Swing painting problems
412 treeCanvas.startPrinting();
416 public void originalSeqData_actionPerformed(ActionEvent e)
418 if (!tree.hasOriginalSequenceData())
420 jalview.bin.Cache.log
421 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
424 // decide if av alignment is sufficiently different to original data to
425 // warrant a new window to be created
426 // create new alignmnt window with hidden regions (unhiding hidden regions
427 // yields unaligned seqs)
428 // or create a selection box around columns in alignment view
429 // test Alignment(SeqCigar[])
433 // we try to get the associated view's gap character
434 // but this may fail if the view was closed...
435 gc = av.getGapCharacter();
437 } catch (Exception ex)
441 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
443 if (alAndColsel != null && alAndColsel[0] != null)
445 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
447 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
448 AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
449 .getAlignment().getDataset() : null;
452 al.setDataset(dataset);
458 AlignFrame af = new AlignFrame(al,
459 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
460 AlignFrame.DEFAULT_HEIGHT);
462 // >>>This is a fix for the moment, until a better solution is
464 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
466 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
469 Desktop.addInternalFrame(af, MessageManager.formatMessage(
470 "label.original_data_for_params",
471 new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
472 AlignFrame.DEFAULT_HEIGHT);
484 public void fitToWindow_actionPerformed(ActionEvent e)
486 treeCanvas.fitToWindow = fitToWindow.isSelected();
491 * sort the associated alignment view by the current tree.
496 public void sortByTree_actionPerformed()
499 if (treeCanvas.applyToAllViews)
501 final ArrayList<CommandI> commands = new ArrayList<CommandI>();
502 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
503 .getSequenceSetId()))
505 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
507 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
511 public void undoCommand(AlignmentI[] views)
513 for (CommandI tsort : commands)
515 tsort.undoCommand(views);
522 return commands.size();
526 public String getDescription()
528 return "Tree Sort (many views)";
532 public void doCommand(AlignmentI[] views)
535 for (CommandI tsort : commands)
537 tsort.doCommand(views);
541 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
542 .getSequenceSetId()))
544 // ensure all the alignFrames refresh their GI after adding an undo item
545 ap.alignFrame.updateEditMenuBar();
550 treeCanvas.ap.alignFrame
551 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
556 public CommandI sortAlignmentIn(AlignmentPanel ap)
558 AlignmentViewport viewport = ap.av;
559 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
560 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
562 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
564 ap.paintAlignment(true);
575 public void font_actionPerformed(ActionEvent e)
577 if (treeCanvas == null)
582 new FontChooser(this);
585 public Font getTreeFont()
587 return treeCanvas.font;
590 public void setTreeFont(Font f)
592 if (treeCanvas != null)
594 treeCanvas.setFont(f);
605 public void distanceMenu_actionPerformed(ActionEvent e)
607 treeCanvas.setShowDistances(distanceMenu.isSelected());
617 public void bootstrapMenu_actionPerformed(ActionEvent e)
619 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
629 public void placeholdersMenu_actionPerformed(ActionEvent e)
631 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
641 public void epsTree_actionPerformed(ActionEvent e)
643 boolean accurateText = true;
645 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
648 // If we need to prompt, and if the GUI is visible then
649 // Prompt for EPS rendering style
650 if (renderStyle.equalsIgnoreCase("Prompt each time")
651 && !(System.getProperty("java.awt.headless") != null && System
652 .getProperty("java.awt.headless").equals("true")))
654 EPSOptions eps = new EPSOptions();
655 renderStyle = eps.getValue();
657 if (renderStyle == null || eps.cancelled)
664 if (renderStyle.equalsIgnoreCase("text"))
666 accurateText = false;
669 int width = treeCanvas.getWidth();
670 int height = treeCanvas.getHeight();
674 JalviewFileChooser chooser = new JalviewFileChooser(
675 ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
676 chooser.setFileView(new JalviewFileView());
677 chooser.setDialogTitle(MessageManager
678 .getString("label.create_eps_from_tree"));
679 chooser.setToolTipText(MessageManager.getString("action.save"));
681 int value = chooser.showSaveDialog(this);
683 if (value != JalviewFileChooser.APPROVE_OPTION)
688 Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile()
691 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
692 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
694 pg.setAccurateTextMode(accurateText);
696 treeCanvas.draw(pg, width, height);
700 } catch (Exception ex)
702 ex.printStackTrace();
713 public void pngTree_actionPerformed(ActionEvent e)
715 int width = treeCanvas.getWidth();
716 int height = treeCanvas.getHeight();
720 JalviewFileChooser chooser = new JalviewFileChooser(
721 ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
723 chooser.setFileView(new jalview.io.JalviewFileView());
724 chooser.setDialogTitle(MessageManager
725 .getString("label.create_png_from_tree"));
726 chooser.setToolTipText(MessageManager.getString("action.save"));
728 int value = chooser.showSaveDialog(this);
730 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
735 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
736 .getSelectedFile().getParent());
738 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
740 BufferedImage bi = new BufferedImage(width, height,
741 BufferedImage.TYPE_INT_RGB);
742 Graphics png = bi.getGraphics();
744 treeCanvas.draw(png, width, height);
746 ImageIO.write(bi, "png", out);
748 } catch (Exception ex)
750 ex.printStackTrace();
755 * change node labels to the annotation referred to by labelClass TODO:
756 * promote to a datamodel modification that can be undone TODO: make argument
757 * one case of a generic transformation function ie { undoStep = apply(Tree,
758 * TransformFunction)};
762 public void changeNames(final String labelClass)
764 tree.applyToNodes(new NodeTransformI()
768 public void transform(BinaryNode node)
770 if (node instanceof SequenceNode
771 && !((SequenceNode) node).isPlaceholder()
772 && !((SequenceNode) node).isDummy())
774 String newname = null;
775 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
778 // search dbrefs, features and annotation
779 DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
781 new String[] { labelClass.toUpperCase() });
784 for (int i = 0; i < refs.length; i++)
788 newname = new String(refs[i].getAccessionId());
792 newname = newname + "; " + refs[i].getAccessionId();
798 SequenceFeature sf[] = sq.getSequenceFeatures();
799 for (int i = 0; sf != null && i < sf.length; i++)
801 if (sf[i].getType().equals(labelClass))
805 newname = new String(sf[i].getDescription());
809 newname = newname + "; " + sf[i].getDescription();
817 // String oldname = ((SequenceNode) node).getName();
818 // TODO : save oldname in the undo object for this modification.
819 ((SequenceNode) node).setName(newname);
827 * Formats a localised title for the tree panel, like
829 * Neighbour Joining Using BLOSUM62
831 * For a tree loaded from file, just uses the file name
834 public String getPanelTitle()
836 if (treeTitle != null)
842 * i18n description of Neighbour Joining or Average Distance method
844 String treecalcnm = MessageManager.getString("label.tree_calc_"
845 + treeType.toLowerCase());
848 * i18n description (if available) of score model used
850 String smn = MessageManager.getStringOrReturn("label.score_model_",
851 scoreModel.getName());
854 * put them together as <method> Using <model>
856 final String ttl = MessageManager.formatMessage("label.treecalc_title",
862 * If the score model is one that requires to get state data from the current
863 * view, create and configure a new instance of it
867 protected ScoreModelI configureScoreModel()
869 if (scoreModel instanceof ViewBasedAnalysisI)
873 scoreModel = scoreModel.getClass().newInstance();
874 ((ViewBasedAnalysisI) scoreModel)
875 .configureFromAlignmentView(treeCanvas.ap);
876 } catch (Exception q)
878 Cache.log.error("Couldn't create a scoremodel instance for "
879 + scoreModel.getName());