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 TreeCanvas treeCanvas;
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 treeCanvas.av.getAlignment();
127 public AlignmentViewport getViewPort()
129 return treeCanvas.av;
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)
158 av.removePropertyChangeListener(listener);
162 TreeLoader tl = new TreeLoader(newTree, inputData);
170 protected PropertyChangeListener addAlignmentListener()
172 final PropertyChangeListener listener = new PropertyChangeListener()
175 public void propertyChange(PropertyChangeEvent evt)
177 if (evt.getPropertyName().equals("alignment"))
181 System.out.println("tree is null");
182 // TODO: deal with case when a change event is received whilst a
183 // tree is still being calculated - should save reference for
184 // processing message later.
187 if (evt.getNewValue() == null)
190 "new alignment sequences vector value is null");
193 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
194 treeCanvas.nameHash.clear(); // reset the mapping between canvas
195 // rectangles and leafnodes
200 av.addPropertyChangeListener(listener);
205 public void viewMenu_menuSelected()
207 buildAssociatedViewMenu();
210 void buildAssociatedViewMenu()
212 AlignmentPanel[] aps = PaintRefresher
213 .getAssociatedPanels(av.getSequenceSetId());
214 if (aps.length == 1 && treeCanvas.ap == aps[0])
216 associateLeavesMenu.setVisible(false);
220 associateLeavesMenu.setVisible(true);
223 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
225 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
228 associateLeavesMenu.removeAll();
230 JRadioButtonMenuItem item;
231 ButtonGroup buttonGroup = new ButtonGroup();
232 int i, iSize = aps.length;
233 final TreePanel thisTreePanel = this;
234 for (i = 0; i < iSize; i++)
236 final AlignmentPanel ap = aps[i];
237 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
238 buttonGroup.add(item);
239 item.addActionListener(new ActionListener()
242 public void actionPerformed(ActionEvent evt)
244 treeCanvas.applyToAllViews = false;
246 treeCanvas.av = ap.av;
247 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
251 associateLeavesMenu.add(item);
254 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
255 MessageManager.getString("label.all_views"));
256 buttonGroup.add(itemf);
257 itemf.setSelected(treeCanvas.applyToAllViews);
258 itemf.addActionListener(new ActionListener()
261 public void actionPerformed(ActionEvent evt)
263 treeCanvas.applyToAllViews = itemf.isSelected();
266 associateLeavesMenu.add(itemf);
270 class TreeLoader extends Thread
272 private NewickFile newtree;
274 private AlignmentView odata = null;
276 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
278 this.newtree = newickFile;
279 this.odata = inputData;
281 if (newickFile != null)
283 // Must be outside run(), as Jalview2XML tries to
284 // update distance/bootstrap visibility at the same time
285 showBootstrap(newickFile.HasBootstrap());
286 showDistances(newickFile.HasDistances());
296 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
298 if (tree.getOriginalData() == null)
300 originalSeqData.setVisible(false);
305 ScoreModelI sm = ScoreModels.getInstance()
306 .getScoreModel(scoreModelName, treeCanvas.ap);
307 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
308 ? new NJTree(av, sm, similarityParams)
309 : new AverageDistanceTree(av, sm, similarityParams);
310 tree = new TreeModel(njtree);
314 tree.reCount(tree.getTopNode());
315 tree.findHeight(tree.getTopNode());
316 treeCanvas.setTree(tree);
317 treeCanvas.repaint();
318 av.setCurrentTree(tree);
319 if (av.getSortByTree())
321 sortByTree_actionPerformed();
326 public void showDistances(boolean b)
328 treeCanvas.setShowDistances(b);
329 distanceMenu.setSelected(b);
332 public void showBootstrap(boolean b)
334 treeCanvas.setShowBootstrap(b);
335 bootstrapMenu.setSelected(b);
338 public void showPlaceholders(boolean b)
340 placeholdersMenu.setState(b);
341 treeCanvas.setMarkPlaceholders(b);
347 * @return DOCUMENT ME!
349 public TreeModel getTree()
361 public void textbox_actionPerformed(ActionEvent e)
363 CutAndPasteTransfer cap = new CutAndPasteTransfer();
365 String newTitle = getPanelTitle();
367 NewickFile fout = new NewickFile(tree.getTopNode());
370 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
371 tree.hasRootDistance()));
372 Desktop.addInternalFrame(cap, newTitle, 500, 100);
373 } catch (OutOfMemoryError oom)
375 new OOMWarning("generating newick tree file", oom);
388 public void saveAsNewick_actionPerformed(ActionEvent e)
390 JalviewFileChooser chooser = new JalviewFileChooser(
391 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
392 chooser.setFileView(new JalviewFileView());
393 chooser.setDialogTitle(
394 MessageManager.getString("label.save_tree_as_newick"));
395 chooser.setToolTipText(MessageManager.getString("action.save"));
397 int value = chooser.showSaveDialog(null);
399 if (value == JalviewFileChooser.APPROVE_OPTION)
401 String choice = chooser.getSelectedFile().getPath();
402 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
403 chooser.getSelectedFile().getParent());
407 jalview.io.NewickFile fout = new jalview.io.NewickFile(
409 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
410 tree.hasRootDistance());
411 java.io.PrintWriter out = new java.io.PrintWriter(
412 new java.io.FileWriter(choice));
415 } catch (Exception ex)
417 ex.printStackTrace();
429 public void printMenu_actionPerformed(ActionEvent e)
431 // Putting in a thread avoids Swing painting problems
432 treeCanvas.startPrinting();
436 public void originalSeqData_actionPerformed(ActionEvent e)
438 AlignmentView originalData = tree.getOriginalData();
439 if (originalData == null)
441 jalview.bin.Cache.log.info(
442 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
445 // decide if av alignment is sufficiently different to original data to
446 // warrant a new window to be created
447 // create new alignmnt window with hidden regions (unhiding hidden regions
448 // yields unaligned seqs)
449 // or create a selection box around columns in alignment view
450 // test Alignment(SeqCigar[])
454 // we try to get the associated view's gap character
455 // but this may fail if the view was closed...
456 gc = av.getGapCharacter();
458 } catch (Exception ex)
462 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
464 if (alAndColsel != null && alAndColsel[0] != null)
466 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
468 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
469 AlignmentI dataset = (av != null && av.getAlignment() != null)
470 ? av.getAlignment().getDataset()
474 al.setDataset(dataset);
480 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
481 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
483 // >>>This is a fix for the moment, until a better solution is
485 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
487 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
490 Desktop.addInternalFrame(af, MessageManager.formatMessage(
491 "label.original_data_for_params", new Object[]
492 { this.title }), AlignFrame.DEFAULT_WIDTH,
493 AlignFrame.DEFAULT_HEIGHT);
505 public void fitToWindow_actionPerformed(ActionEvent e)
507 treeCanvas.fitToWindow = fitToWindow.isSelected();
512 * sort the associated alignment view by the current tree.
517 public void sortByTree_actionPerformed()
520 if (treeCanvas.applyToAllViews)
522 final ArrayList<CommandI> commands = new ArrayList<>();
523 for (AlignmentPanel ap : PaintRefresher
524 .getAssociatedPanels(av.getSequenceSetId()))
526 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
528 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
532 public void undoCommand(AlignmentI[] views)
534 for (CommandI tsort : commands)
536 tsort.undoCommand(views);
543 return commands.size();
547 public String getDescription()
549 return "Tree Sort (many views)";
553 public void doCommand(AlignmentI[] views)
556 for (CommandI tsort : commands)
558 tsort.doCommand(views);
562 for (AlignmentPanel ap : PaintRefresher
563 .getAssociatedPanels(av.getSequenceSetId()))
565 // ensure all the alignFrames refresh their GI after adding an undo item
566 ap.alignFrame.updateEditMenuBar();
571 treeCanvas.ap.alignFrame
572 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
577 public CommandI sortAlignmentIn(AlignmentPanel ap)
579 // TODO: move to alignment view controller
580 AlignmentViewport viewport = ap.av;
581 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
582 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
584 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
586 ap.paintAlignment(true, false);
597 public void font_actionPerformed(ActionEvent e)
599 if (treeCanvas == null)
604 new FontChooser(this);
607 public Font getTreeFont()
609 return treeCanvas.font;
612 public void setTreeFont(Font f)
614 if (treeCanvas != null)
616 treeCanvas.setFont(f);
627 public void distanceMenu_actionPerformed(ActionEvent e)
629 treeCanvas.setShowDistances(distanceMenu.isSelected());
639 public void bootstrapMenu_actionPerformed(ActionEvent e)
641 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
651 public void placeholdersMenu_actionPerformed(ActionEvent e)
653 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
663 public void epsTree_actionPerformed(ActionEvent e)
665 boolean accurateText = true;
667 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
670 // If we need to prompt, and if the GUI is visible then
671 // Prompt for EPS rendering style
672 if (renderStyle.equalsIgnoreCase("Prompt each time")
673 && !(System.getProperty("java.awt.headless") != null && System
674 .getProperty("java.awt.headless").equals("true")))
676 EPSOptions eps = new EPSOptions();
677 renderStyle = eps.getValue();
679 if (renderStyle == null || eps.cancelled)
686 if (renderStyle.equalsIgnoreCase("text"))
688 accurateText = false;
691 int width = treeCanvas.getWidth();
692 int height = treeCanvas.getHeight();
696 JalviewFileChooser chooser = new JalviewFileChooser(
697 ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
698 chooser.setFileView(new JalviewFileView());
699 chooser.setDialogTitle(
700 MessageManager.getString("label.create_eps_from_tree"));
701 chooser.setToolTipText(MessageManager.getString("action.save"));
703 int value = chooser.showSaveDialog(this);
705 if (value != JalviewFileChooser.APPROVE_OPTION)
710 Cache.setProperty("LAST_DIRECTORY",
711 chooser.getSelectedFile().getParent());
713 FileOutputStream out = new FileOutputStream(
714 chooser.getSelectedFile());
715 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
718 pg.setAccurateTextMode(accurateText);
720 treeCanvas.draw(pg, width, height);
724 } catch (Exception ex)
726 ex.printStackTrace();
737 public void pngTree_actionPerformed(ActionEvent e)
739 int width = treeCanvas.getWidth();
740 int height = treeCanvas.getHeight();
744 JalviewFileChooser chooser = new JalviewFileChooser(
745 ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
747 chooser.setFileView(new jalview.io.JalviewFileView());
748 chooser.setDialogTitle(
749 MessageManager.getString("label.create_png_from_tree"));
750 chooser.setToolTipText(MessageManager.getString("action.save"));
752 int value = chooser.showSaveDialog(this);
754 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
759 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
760 chooser.getSelectedFile().getParent());
762 FileOutputStream out = new FileOutputStream(
763 chooser.getSelectedFile());
765 BufferedImage bi = new BufferedImage(width, height,
766 BufferedImage.TYPE_INT_RGB);
767 Graphics png = bi.getGraphics();
769 treeCanvas.draw(png, width, height);
771 ImageIO.write(bi, "png", out);
773 } catch (Exception ex)
775 ex.printStackTrace();
780 * change node labels to the annotation referred to by labelClass TODO:
781 * promote to a datamodel modification that can be undone TODO: make argument
782 * one case of a generic transformation function ie { undoStep = apply(Tree,
783 * TransformFunction)};
787 public void changeNames(final String labelClass)
789 tree.applyToNodes(new NodeTransformI()
793 public void transform(BinaryNode node)
795 if (node instanceof SequenceNode
796 && !((SequenceNode) node).isPlaceholder()
797 && !((SequenceNode) node).isDummy())
799 String newname = null;
800 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
803 // search dbrefs, features and annotation
804 DBRefEntry[] refs = jalview.util.DBRefUtils
805 .selectRefs(sq.getDBRefs(), new String[]
806 { labelClass.toUpperCase() });
809 for (int i = 0; i < refs.length; i++)
813 newname = new String(refs[i].getAccessionId());
817 newname = newname + "; " + refs[i].getAccessionId();
823 List<SequenceFeature> features = sq.getFeatures()
824 .getPositionalFeatures(labelClass);
825 for (SequenceFeature feature : features)
829 newname = feature.getDescription();
833 newname = newname + "; " + feature.getDescription();
840 // String oldname = ((SequenceNode) node).getName();
841 // TODO : save oldname in the undo object for this modification.
842 ((SequenceNode) node).setName(newname);
850 * Formats a localised title for the tree panel, like
852 * Neighbour Joining Using BLOSUM62
854 * For a tree loaded from file, just uses the file name
858 public String getPanelTitle()
860 if (treeTitle != null)
866 * i18n description of Neighbour Joining or Average Distance method
868 String treecalcnm = MessageManager
869 .getString("label.tree_calc_" + treeType.toLowerCase());
872 * short score model name (long description can be too long)
874 String smn = scoreModelName;
877 * put them together as <method> Using <model>
879 final String ttl = MessageManager.formatMessage("label.treecalc_title",