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.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.DBRefEntry;
39 import jalview.datamodel.HiddenColumns;
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.beans.PropertyChangeListener;
59 import java.io.FileOutputStream;
60 import java.util.ArrayList;
61 import java.util.List;
63 import javax.imageio.ImageIO;
64 import javax.swing.ButtonGroup;
65 import javax.swing.JMenuItem;
66 import javax.swing.JRadioButtonMenuItem;
67 import javax.swing.event.InternalFrameAdapter;
68 import javax.swing.event.InternalFrameEvent;
70 import org.jibble.epsgraphics.EpsGraphics2D;
78 public class TreePanel extends GTreePanel
82 String scoreModelName; // if tree computed
84 String treeTitle; // if tree loaded
86 SimilarityParamsI similarityParams;
88 private TreeCanvas treeCanvas;
92 private AlignViewport av;
95 * Creates a new TreePanel object.
102 public TreePanel(AlignmentPanel ap, String type, String modelName,
103 SimilarityParamsI options)
106 this.similarityParams = options;
107 initTreePanel(ap, type, modelName, null, null);
109 // We know this tree has distances. JBPNote TODO: prolly should add this as
110 // a userdefined default
111 // showDistances(true);
114 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
115 String theTitle, AlignmentView inputData)
118 this.treeTitle = theTitle;
119 initTreePanel(alignPanel, null, null, newtree, inputData);
122 public AlignmentI getAlignment()
124 return getTreeCanvas().getViewport().getAlignment();
127 public AlignmentViewport getViewPort()
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(getTreeCanvas());
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)
158 if (getViewport() != null)
160 getViewport().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 getTreeCanvas().nameHash.clear(); // reset the mapping between canvas
210 // rectangles and leafnodes
215 getViewport().addPropertyChangeListener(listener);
220 public void viewMenu_menuSelected()
222 buildAssociatedViewMenu();
225 void buildAssociatedViewMenu()
227 AlignmentPanel[] aps = PaintRefresher
228 .getAssociatedPanels(getViewport().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(), ap == getTreeCanvas().getAssociatedPanel());
253 buttonGroup.add(item);
254 item.addActionListener(new ActionListener()
257 public void actionPerformed(ActionEvent evt)
259 getTreeCanvas().applyToAllViews = false;
260 getTreeCanvas().setAssociatedPanel(ap);
261 getTreeCanvas().setViewport(ap.av);
262 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
266 associateLeavesMenu.add(item);
269 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
270 MessageManager.getString("label.all_views"));
271 buttonGroup.add(itemf);
272 itemf.setSelected(getTreeCanvas().applyToAllViews);
273 itemf.addActionListener(new ActionListener()
276 public void actionPerformed(ActionEvent evt)
278 getTreeCanvas().applyToAllViews = itemf.isSelected();
281 associateLeavesMenu.add(itemf);
285 class TreeLoader extends Thread
287 private NewickFile newtree;
289 private AlignmentView odata = null;
291 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
293 this.newtree = newickFile;
294 this.odata = inputData;
296 if (newickFile != null)
298 // Must be outside run(), as Jalview2XML tries to
299 // update distance/bootstrap visibility at the same time
300 showBootstrap(newickFile.HasBootstrap());
301 showDistances(newickFile.HasDistances());
311 tree = new TreeModel(getViewport().getAlignment().getSequencesArray(), odata,
313 if (tree.getOriginalData() == null)
315 originalSeqData.setVisible(false);
320 ScoreModelI sm = ScoreModels.getInstance()
321 .getScoreModel(scoreModelName, getTreeCanvas().getAssociatedPanel());
322 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
323 ? new NJTree(getViewport(), sm, similarityParams)
324 : new AverageDistanceTree(getViewport(), sm, similarityParams);
325 tree = new TreeModel(njtree);
329 tree.reCount(tree.getTopNode());
330 tree.findHeight(tree.getTopNode());
331 getTreeCanvas().setTree(tree);
332 getTreeCanvas().repaint();
333 getViewport().setCurrentTree(tree);
334 if (getViewport().getSortByTree())
336 sortByTree_actionPerformed();
341 public void showDistances(boolean b)
343 getTreeCanvas().setShowDistances(b);
344 distanceMenu.setSelected(b);
347 public void showBootstrap(boolean b)
349 getTreeCanvas().setShowBootstrap(b);
350 bootstrapMenu.setSelected(b);
353 public void showPlaceholders(boolean b)
355 placeholdersMenu.setState(b);
356 getTreeCanvas().setMarkPlaceholders(b);
362 * @return DOCUMENT ME!
364 public TreeModel getTree()
376 public void textbox_actionPerformed(ActionEvent e)
378 CutAndPasteTransfer cap = new CutAndPasteTransfer();
380 String newTitle = getPanelTitle();
382 NewickFile fout = new NewickFile(tree.getTopNode());
385 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
386 tree.hasRootDistance()));
387 Desktop.addInternalFrame(cap, newTitle, 500, 100);
388 } catch (OutOfMemoryError oom)
390 new OOMWarning("generating newick tree file", oom);
403 public void saveAsNewick_actionPerformed(ActionEvent e)
405 JalviewFileChooser chooser = new JalviewFileChooser(
406 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
407 chooser.setFileView(new JalviewFileView());
408 chooser.setDialogTitle(
409 MessageManager.getString("label.save_tree_as_newick"));
410 chooser.setToolTipText(MessageManager.getString("action.save"));
412 int value = chooser.showSaveDialog(null);
414 if (value == JalviewFileChooser.APPROVE_OPTION)
416 String choice = chooser.getSelectedFile().getPath();
417 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
418 chooser.getSelectedFile().getParent());
422 jalview.io.NewickFile fout = new jalview.io.NewickFile(
424 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
425 tree.hasRootDistance());
426 java.io.PrintWriter out = new java.io.PrintWriter(
427 new java.io.FileWriter(choice));
430 } catch (Exception ex)
432 ex.printStackTrace();
444 public void printMenu_actionPerformed(ActionEvent e)
446 // Putting in a thread avoids Swing painting problems
447 getTreeCanvas().startPrinting();
451 public void originalSeqData_actionPerformed(ActionEvent e)
453 AlignmentView originalData = tree.getOriginalData();
454 if (originalData == null)
456 jalview.bin.Cache.log.info(
457 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
460 // decide if av alignment is sufficiently different to original data to
461 // warrant a new window to be created
462 // create new alignmnt window with hidden regions (unhiding hidden regions
463 // yields unaligned seqs)
464 // or create a selection box around columns in alignment view
465 // test Alignment(SeqCigar[])
469 // we try to get the associated view's gap character
470 // but this may fail if the view was closed...
471 gc = getViewport().getGapCharacter();
473 } catch (Exception ex)
477 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
479 if (alAndColsel != null && alAndColsel[0] != null)
481 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
483 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
484 AlignmentI dataset = (getViewport() != null && getViewport().getAlignment() != null)
485 ? getViewport().getAlignment().getDataset()
489 al.setDataset(dataset);
495 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
496 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
498 // >>>This is a fix for the moment, until a better solution is
500 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
502 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
505 Desktop.addInternalFrame(af, MessageManager.formatMessage(
506 "label.original_data_for_params", new Object[]
507 { this.title }), AlignFrame.DEFAULT_WIDTH,
508 AlignFrame.DEFAULT_HEIGHT);
520 public void fitToWindow_actionPerformed(ActionEvent e)
522 getTreeCanvas().fitToWindow = fitToWindow.isSelected();
527 * sort the associated alignment view by the current tree.
532 public void sortByTree_actionPerformed()
535 if (getTreeCanvas().applyToAllViews)
537 final ArrayList<CommandI> commands = new ArrayList<>();
538 for (AlignmentPanel ap : PaintRefresher
539 .getAssociatedPanels(getViewport().getSequenceSetId()))
541 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
543 getViewport().getAlignPanel().alignFrame.addHistoryItem(new CommandI()
547 public void undoCommand(AlignmentI[] views)
549 for (CommandI tsort : commands)
551 tsort.undoCommand(views);
558 return commands.size();
562 public String getDescription()
564 return "Tree Sort (many views)";
568 public void doCommand(AlignmentI[] views)
571 for (CommandI tsort : commands)
573 tsort.doCommand(views);
577 for (AlignmentPanel ap : PaintRefresher
578 .getAssociatedPanels(getViewport().getSequenceSetId()))
580 // ensure all the alignFrames refresh their GI after adding an undo item
581 ap.alignFrame.updateEditMenuBar();
586 getTreeCanvas().getAssociatedPanel().alignFrame
587 .addHistoryItem(sortAlignmentIn(getTreeCanvas().getAssociatedPanel()));
592 public CommandI sortAlignmentIn(AlignmentPanel ap)
594 // TODO: move to alignment view controller
595 AlignmentViewport viewport = ap.av;
596 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
597 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
599 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
601 ap.paintAlignment(true, false);
612 public void font_actionPerformed(ActionEvent e)
614 if (getTreeCanvas() == null)
619 new FontChooser(this);
622 public Font getTreeFont()
624 return getTreeCanvas().font;
627 public void setTreeFont(Font f)
629 if (getTreeCanvas() != null)
631 getTreeCanvas().setFont(f);
642 public void distanceMenu_actionPerformed(ActionEvent e)
644 getTreeCanvas().setShowDistances(distanceMenu.isSelected());
654 public void bootstrapMenu_actionPerformed(ActionEvent e)
656 getTreeCanvas().setShowBootstrap(bootstrapMenu.isSelected());
666 public void placeholdersMenu_actionPerformed(ActionEvent e)
668 getTreeCanvas().setMarkPlaceholders(placeholdersMenu.isSelected());
678 public void epsTree_actionPerformed(ActionEvent e)
680 boolean accurateText = true;
682 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
685 // If we need to prompt, and if the GUI is visible then
686 // Prompt for EPS rendering style
687 if (renderStyle.equalsIgnoreCase("Prompt each time")
688 && !(System.getProperty("java.awt.headless") != null && System
689 .getProperty("java.awt.headless").equals("true")))
691 EPSOptions eps = new EPSOptions();
692 renderStyle = eps.getValue();
694 if (renderStyle == null || eps.cancelled)
701 if (renderStyle.equalsIgnoreCase("text"))
703 accurateText = false;
706 int width = getTreeCanvas().getWidth();
707 int height = getTreeCanvas().getHeight();
711 JalviewFileChooser chooser = new JalviewFileChooser(
712 ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
713 chooser.setFileView(new JalviewFileView());
714 chooser.setDialogTitle(
715 MessageManager.getString("label.create_eps_from_tree"));
716 chooser.setToolTipText(MessageManager.getString("action.save"));
718 int value = chooser.showSaveDialog(this);
720 if (value != JalviewFileChooser.APPROVE_OPTION)
725 Cache.setProperty("LAST_DIRECTORY",
726 chooser.getSelectedFile().getParent());
728 FileOutputStream out = new FileOutputStream(
729 chooser.getSelectedFile());
730 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
733 pg.setAccurateTextMode(accurateText);
735 getTreeCanvas().draw(pg, width, height);
739 } catch (Exception ex)
741 ex.printStackTrace();
752 public void pngTree_actionPerformed(ActionEvent e)
754 int width = getTreeCanvas().getWidth();
755 int height = getTreeCanvas().getHeight();
759 JalviewFileChooser chooser = new JalviewFileChooser(
760 ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
762 chooser.setFileView(new jalview.io.JalviewFileView());
763 chooser.setDialogTitle(
764 MessageManager.getString("label.create_png_from_tree"));
765 chooser.setToolTipText(MessageManager.getString("action.save"));
767 int value = chooser.showSaveDialog(this);
769 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
774 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
775 chooser.getSelectedFile().getParent());
777 FileOutputStream out = new FileOutputStream(
778 chooser.getSelectedFile());
780 BufferedImage bi = new BufferedImage(width, height,
781 BufferedImage.TYPE_INT_RGB);
782 Graphics png = bi.getGraphics();
784 getTreeCanvas().draw(png, width, height);
786 ImageIO.write(bi, "png", out);
788 } catch (Exception ex)
790 ex.printStackTrace();
795 * change node labels to the annotation referred to by labelClass TODO:
796 * promote to a datamodel modification that can be undone TODO: make argument
797 * one case of a generic transformation function ie { undoStep = apply(Tree,
798 * TransformFunction)};
802 public void changeNames(final String labelClass)
804 tree.applyToNodes(new NodeTransformI()
808 public void transform(BinaryNode node)
810 if (node instanceof SequenceNode
811 && !((SequenceNode) node).isPlaceholder()
812 && !((SequenceNode) node).isDummy())
814 String newname = null;
815 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
818 // search dbrefs, features and annotation
819 DBRefEntry[] refs = jalview.util.DBRefUtils
820 .selectRefs(sq.getDBRefs(), new String[]
821 { labelClass.toUpperCase() });
824 for (int i = 0; i < refs.length; i++)
828 newname = new String(refs[i].getAccessionId());
832 newname = newname + "; " + refs[i].getAccessionId();
838 List<SequenceFeature> features = sq.getFeatures()
839 .getPositionalFeatures(labelClass);
840 for (SequenceFeature feature : features)
844 newname = feature.getDescription();
848 newname = newname + "; " + feature.getDescription();
855 // String oldname = ((SequenceNode) node).getName();
856 // TODO : save oldname in the undo object for this modification.
857 ((SequenceNode) node).setName(newname);
865 * Formats a localised title for the tree panel, like
867 * Neighbour Joining Using BLOSUM62
869 * For a tree loaded from file, just uses the file name
873 public String getPanelTitle()
875 if (treeTitle != null)
881 * i18n description of Neighbour Joining or Average Distance method
883 String treecalcnm = MessageManager
884 .getString("label.tree_calc_" + treeType.toLowerCase());
887 * short score model name (long description can be too long)
889 String smn = scoreModelName;
892 * put them together as <method> Using <model>
894 final String ttl = MessageManager.formatMessage("label.calc_title",
899 public AlignViewport getViewport()
904 public void setViewport(AlignViewport av)
909 public TreeCanvas getTreeCanvas()