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.api.analysis.ScoreModelI;
29 import jalview.api.analysis.SimilarityParamsI;
30 import jalview.api.analysis.ViewBasedAnalysisI;
31 import jalview.bin.Cache;
32 import jalview.commands.CommandI;
33 import jalview.commands.OrderCommand;
34 import jalview.datamodel.Alignment;
35 import jalview.datamodel.AlignmentI;
36 import jalview.datamodel.AlignmentView;
37 import jalview.datamodel.BinaryNode;
38 import jalview.datamodel.ColumnSelection;
39 import jalview.datamodel.DBRefEntry;
40 import jalview.datamodel.NodeTransformI;
41 import jalview.datamodel.SequenceFeature;
42 import jalview.datamodel.SequenceI;
43 import jalview.datamodel.SequenceNode;
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;
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.awt.image.BufferedImage;
57 import java.beans.PropertyChangeEvent;
58 import java.io.FileOutputStream;
59 import java.util.ArrayList;
60 import java.util.List;
62 import javax.imageio.ImageIO;
63 import javax.swing.ButtonGroup;
64 import javax.swing.JMenuItem;
65 import javax.swing.JRadioButtonMenuItem;
67 import org.jibble.epsgraphics.EpsGraphics2D;
75 public class TreePanel extends GTreePanel
79 ScoreModelI scoreModel; // if tree computed
81 String treeTitle; // if tree loaded
83 SimilarityParamsI similarityParams;
85 TreeCanvas treeCanvas;
92 * Creates a new TreePanel object.
99 public TreePanel(AlignmentPanel ap, String type, ScoreModelI sm,
100 SimilarityParamsI options)
103 this.similarityParams = options;
104 initTreePanel(ap, type, sm, null, null);
106 // We know this tree has distances. JBPNote TODO: prolly should add this as
107 // a userdefined default
108 // showDistances(true);
111 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
112 String theTitle, AlignmentView inputData)
115 this.treeTitle = theTitle;
116 initTreePanel(alignPanel, null, null, newtree, inputData);
119 public AlignmentI getAlignment()
121 return treeCanvas.av.getAlignment();
124 public AlignmentViewport getViewPort()
126 return treeCanvas.av;
129 void initTreePanel(AlignmentPanel ap, String type, ScoreModelI sm,
130 NewickFile newTree, AlignmentView inputData)
134 this.treeType = type;
135 this.scoreModel = sm;
137 treeCanvas = new TreeCanvas(this, ap, scrollPane);
138 scrollPane.setViewportView(treeCanvas);
140 PaintRefresher.Register(this, ap.av.getSequenceSetId());
142 buildAssociatedViewMenu();
144 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
147 public void propertyChange(PropertyChangeEvent evt)
149 if (evt.getPropertyName().equals("alignment"))
153 System.out.println("tree is null");
154 // TODO: deal with case when a change event is received whilst a
155 // tree is still being calculated - should save reference for
156 // processing message later.
159 if (evt.getNewValue() == null)
162 .println("new alignment sequences vector value is null");
165 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
166 treeCanvas.nameHash.clear(); // reset the mapping between canvas
167 // rectangles and leafnodes
173 TreeLoader tl = new TreeLoader(newTree);
174 if (inputData != null)
176 tl.odata = inputData;
183 public void viewMenu_menuSelected()
185 buildAssociatedViewMenu();
188 void buildAssociatedViewMenu()
190 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
191 .getSequenceSetId());
192 if (aps.length == 1 && treeCanvas.ap == aps[0])
194 associateLeavesMenu.setVisible(false);
198 associateLeavesMenu.setVisible(true);
200 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
202 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
205 associateLeavesMenu.removeAll();
207 JRadioButtonMenuItem item;
208 ButtonGroup buttonGroup = new ButtonGroup();
209 int i, iSize = aps.length;
210 final TreePanel thisTreePanel = this;
211 for (i = 0; i < iSize; i++)
213 final AlignmentPanel ap = aps[i];
214 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
215 buttonGroup.add(item);
216 item.addActionListener(new ActionListener()
219 public void actionPerformed(ActionEvent evt)
221 treeCanvas.applyToAllViews = false;
223 treeCanvas.av = ap.av;
224 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
228 associateLeavesMenu.add(item);
231 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
232 MessageManager.getString("label.all_views"));
233 buttonGroup.add(itemf);
234 itemf.setSelected(treeCanvas.applyToAllViews);
235 itemf.addActionListener(new ActionListener()
238 public void actionPerformed(ActionEvent evt)
240 treeCanvas.applyToAllViews = itemf.isSelected();
243 associateLeavesMenu.add(itemf);
247 class TreeLoader extends Thread
251 AlignmentView odata = null;
253 public TreeLoader(NewickFile newickFile)
255 this.newtree = newickFile;
256 if (newickFile != null)
258 // Must be outside run(), as Jalview2XML tries to
259 // update distance/bootstrap visibility at the same time
260 showBootstrap(newickFile.HasBootstrap());
261 showDistances(newickFile.HasDistances());
273 tree = new TreeModel(av.getAlignment().getSequencesArray(),
278 tree = new TreeModel(av.getAlignment().getSequencesArray(),
281 if (!tree.hasOriginalSequenceData())
283 allowOriginalSeqData(false);
288 ScoreModelI sm = configureScoreModel();
289 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
290 av, sm, similarityParams) : new AverageDistanceTree(av, sm,
292 tree = new TreeModel(njtree);
296 tree.reCount(tree.getTopNode());
297 tree.findHeight(tree.getTopNode());
298 treeCanvas.setTree(tree);
299 treeCanvas.repaint();
300 av.setCurrentTree(tree);
301 if (av.getSortByTree())
303 sortByTree_actionPerformed();
308 public void showDistances(boolean b)
310 treeCanvas.setShowDistances(b);
311 distanceMenu.setSelected(b);
314 public void showBootstrap(boolean b)
316 treeCanvas.setShowBootstrap(b);
317 bootstrapMenu.setSelected(b);
320 public void showPlaceholders(boolean b)
322 placeholdersMenu.setState(b);
323 treeCanvas.setMarkPlaceholders(b);
326 private void allowOriginalSeqData(boolean b)
328 originalSeqData.setVisible(b);
334 * @return DOCUMENT ME!
336 public TreeModel getTree()
348 public void textbox_actionPerformed(ActionEvent e)
350 CutAndPasteTransfer cap = new CutAndPasteTransfer();
352 String newTitle = getPanelTitle();
354 NewickFile fout = new NewickFile(tree.getTopNode());
357 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
358 tree.hasRootDistance()));
359 Desktop.addInternalFrame(cap, newTitle, 500, 100);
360 } catch (OutOfMemoryError oom)
362 new OOMWarning("generating newick tree file", oom);
375 public void saveAsNewick_actionPerformed(ActionEvent e)
377 JalviewFileChooser chooser = new JalviewFileChooser(
378 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
379 chooser.setFileView(new JalviewFileView());
380 chooser.setDialogTitle(MessageManager
381 .getString("label.save_tree_as_newick"));
382 chooser.setToolTipText(MessageManager.getString("action.save"));
384 int value = chooser.showSaveDialog(null);
386 if (value == JalviewFileChooser.APPROVE_OPTION)
388 String choice = chooser.getSelectedFile().getPath();
389 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
390 .getSelectedFile().getParent());
394 jalview.io.NewickFile fout = new jalview.io.NewickFile(
396 String output = fout.print(tree.hasBootstrap(),
397 tree.hasDistances(), tree.hasRootDistance());
398 java.io.PrintWriter out = new java.io.PrintWriter(
399 new java.io.FileWriter(choice));
402 } catch (Exception ex)
404 ex.printStackTrace();
416 public void printMenu_actionPerformed(ActionEvent e)
418 // Putting in a thread avoids Swing painting problems
419 treeCanvas.startPrinting();
423 public void originalSeqData_actionPerformed(ActionEvent e)
425 if (!tree.hasOriginalSequenceData())
427 jalview.bin.Cache.log
428 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
431 // decide if av alignment is sufficiently different to original data to
432 // warrant a new window to be created
433 // create new alignmnt window with hidden regions (unhiding hidden regions
434 // yields unaligned seqs)
435 // or create a selection box around columns in alignment view
436 // test Alignment(SeqCigar[])
440 // we try to get the associated view's gap character
441 // but this may fail if the view was closed...
442 gc = av.getGapCharacter();
444 } catch (Exception ex)
448 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
450 if (alAndColsel != null && alAndColsel[0] != null)
452 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
454 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
455 AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
456 .getAlignment().getDataset() : null;
459 al.setDataset(dataset);
465 AlignFrame af = new AlignFrame(al,
466 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
467 AlignFrame.DEFAULT_HEIGHT);
469 // >>>This is a fix for the moment, until a better solution is
471 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
473 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
476 Desktop.addInternalFrame(af, MessageManager.formatMessage(
477 "label.original_data_for_params",
478 new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
479 AlignFrame.DEFAULT_HEIGHT);
491 public void fitToWindow_actionPerformed(ActionEvent e)
493 treeCanvas.fitToWindow = fitToWindow.isSelected();
498 * sort the associated alignment view by the current tree.
503 public void sortByTree_actionPerformed()
506 if (treeCanvas.applyToAllViews)
508 final ArrayList<CommandI> commands = new ArrayList<CommandI>();
509 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
510 .getSequenceSetId()))
512 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
514 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
518 public void undoCommand(AlignmentI[] views)
520 for (CommandI tsort : commands)
522 tsort.undoCommand(views);
529 return commands.size();
533 public String getDescription()
535 return "Tree Sort (many views)";
539 public void doCommand(AlignmentI[] views)
542 for (CommandI tsort : commands)
544 tsort.doCommand(views);
548 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
549 .getSequenceSetId()))
551 // ensure all the alignFrames refresh their GI after adding an undo item
552 ap.alignFrame.updateEditMenuBar();
557 treeCanvas.ap.alignFrame
558 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
563 public CommandI sortAlignmentIn(AlignmentPanel ap)
565 AlignmentViewport viewport = ap.av;
566 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
567 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
569 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
571 ap.paintAlignment(true);
582 public void font_actionPerformed(ActionEvent e)
584 if (treeCanvas == null)
589 new FontChooser(this);
592 public Font getTreeFont()
594 return treeCanvas.font;
597 public void setTreeFont(Font f)
599 if (treeCanvas != null)
601 treeCanvas.setFont(f);
612 public void distanceMenu_actionPerformed(ActionEvent e)
614 treeCanvas.setShowDistances(distanceMenu.isSelected());
624 public void bootstrapMenu_actionPerformed(ActionEvent e)
626 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
636 public void placeholdersMenu_actionPerformed(ActionEvent e)
638 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
648 public void epsTree_actionPerformed(ActionEvent e)
650 boolean accurateText = true;
652 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
655 // If we need to prompt, and if the GUI is visible then
656 // Prompt for EPS rendering style
657 if (renderStyle.equalsIgnoreCase("Prompt each time")
658 && !(System.getProperty("java.awt.headless") != null && System
659 .getProperty("java.awt.headless").equals("true")))
661 EPSOptions eps = new EPSOptions();
662 renderStyle = eps.getValue();
664 if (renderStyle == null || eps.cancelled)
671 if (renderStyle.equalsIgnoreCase("text"))
673 accurateText = false;
676 int width = treeCanvas.getWidth();
677 int height = treeCanvas.getHeight();
681 JalviewFileChooser chooser = new JalviewFileChooser(
682 ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
683 chooser.setFileView(new JalviewFileView());
684 chooser.setDialogTitle(MessageManager
685 .getString("label.create_eps_from_tree"));
686 chooser.setToolTipText(MessageManager.getString("action.save"));
688 int value = chooser.showSaveDialog(this);
690 if (value != JalviewFileChooser.APPROVE_OPTION)
695 Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile()
698 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
699 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
701 pg.setAccurateTextMode(accurateText);
703 treeCanvas.draw(pg, width, height);
707 } catch (Exception ex)
709 ex.printStackTrace();
720 public void pngTree_actionPerformed(ActionEvent e)
722 int width = treeCanvas.getWidth();
723 int height = treeCanvas.getHeight();
727 JalviewFileChooser chooser = new JalviewFileChooser(
728 ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
730 chooser.setFileView(new jalview.io.JalviewFileView());
731 chooser.setDialogTitle(MessageManager
732 .getString("label.create_png_from_tree"));
733 chooser.setToolTipText(MessageManager.getString("action.save"));
735 int value = chooser.showSaveDialog(this);
737 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
742 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
743 .getSelectedFile().getParent());
745 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
747 BufferedImage bi = new BufferedImage(width, height,
748 BufferedImage.TYPE_INT_RGB);
749 Graphics png = bi.getGraphics();
751 treeCanvas.draw(png, width, height);
753 ImageIO.write(bi, "png", out);
755 } catch (Exception ex)
757 ex.printStackTrace();
762 * change node labels to the annotation referred to by labelClass TODO:
763 * promote to a datamodel modification that can be undone TODO: make argument
764 * one case of a generic transformation function ie { undoStep = apply(Tree,
765 * TransformFunction)};
769 public void changeNames(final String labelClass)
771 tree.applyToNodes(new NodeTransformI()
775 public void transform(BinaryNode node)
777 if (node instanceof SequenceNode
778 && !((SequenceNode) node).isPlaceholder()
779 && !((SequenceNode) node).isDummy())
781 String newname = null;
782 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
785 // search dbrefs, features and annotation
786 DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
788 new String[] { labelClass.toUpperCase() });
791 for (int i = 0; i < refs.length; i++)
795 newname = new String(refs[i].getAccessionId());
799 newname = newname + "; " + refs[i].getAccessionId();
805 SequenceFeature sf[] = sq.getSequenceFeatures();
806 for (int i = 0; sf != null && i < sf.length; i++)
808 if (sf[i].getType().equals(labelClass))
812 newname = new String(sf[i].getDescription());
816 newname = newname + "; " + sf[i].getDescription();
824 // String oldname = ((SequenceNode) node).getName();
825 // TODO : save oldname in the undo object for this modification.
826 ((SequenceNode) node).setName(newname);
834 * Formats a localised title for the tree panel, like
836 * Neighbour Joining Using BLOSUM62
838 * For a tree loaded from file, just uses the file name
841 public String getPanelTitle()
843 if (treeTitle != null)
849 * i18n description of Neighbour Joining or Average Distance method
851 String treecalcnm = MessageManager.getString("label.tree_calc_"
852 + treeType.toLowerCase());
855 * i18n description (if available) of score model used
857 String smn = MessageManager.getStringOrReturn("label.score_model_",
858 scoreModel.getName());
861 * put them together as <method> Using <model>
863 final String ttl = MessageManager.formatMessage("label.treecalc_title",
869 * If the score model is one that requires to get state data from the current
870 * view, create and configure a new instance of it
874 protected ScoreModelI configureScoreModel()
876 if (scoreModel instanceof ViewBasedAnalysisI)
880 scoreModel = scoreModel.getClass().newInstance();
881 ((ViewBasedAnalysisI) scoreModel)
882 .configureFromAlignmentView(treeCanvas.ap);
883 } catch (Exception q)
885 Cache.log.error("Couldn't create a scoremodel instance for "
886 + scoreModel.getName());