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.TreeModel;
25 import jalview.bin.Cache;
26 import jalview.commands.CommandI;
27 import jalview.commands.OrderCommand;
28 import jalview.datamodel.Alignment;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.AlignmentView;
31 import jalview.datamodel.BinaryNode;
32 import jalview.datamodel.DBRefEntry;
33 import jalview.datamodel.HiddenColumns;
34 import jalview.datamodel.NodeTransformI;
35 import jalview.datamodel.SequenceFeature;
36 import jalview.datamodel.SequenceI;
37 import jalview.datamodel.SequenceNode;
38 import jalview.io.JalviewFileChooser;
39 import jalview.io.JalviewFileView;
40 import jalview.io.NewickFile;
41 import jalview.jbgui.GTreePanel;
42 import jalview.util.ImageMaker;
43 import jalview.util.MessageManager;
44 import jalview.viewmodel.AlignmentViewport;
47 import java.awt.Graphics;
48 import java.awt.event.ActionEvent;
49 import java.awt.event.ActionListener;
50 import java.awt.image.BufferedImage;
51 import java.beans.PropertyChangeEvent;
52 import java.io.FileOutputStream;
53 import java.util.ArrayList;
54 import java.util.List;
56 import javax.imageio.ImageIO;
57 import javax.swing.ButtonGroup;
58 import javax.swing.JMenuItem;
59 import javax.swing.JRadioButtonMenuItem;
61 import org.jibble.epsgraphics.EpsGraphics2D;
69 public class TreePanel extends GTreePanel
71 String substitutionMatrix;
75 String treeTitle; // if tree loaded
77 TreeCanvas treeCanvas;
84 * Creates a new TreePanel object.
89 * @param substitutionMatrix
91 public TreePanel(AlignmentPanel ap, TreeModel tree, String treeType,
92 String substitutionMatrix)
95 this.treeType = treeType;
96 this.substitutionMatrix = substitutionMatrix;
98 initNewTreePanel(ap, tree);
100 // We know this tree has distances. JBPNote TODO: prolly should add this as
101 // a userdefined default
102 // showDistances(true);
106 * Creates a new TreePanel object.
113 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
114 String theTitle, AlignmentView inputData)
117 this.treeTitle = theTitle;
118 initLoadedTreePanel(alignPanel, newtree, inputData);
121 public AlignmentI getAlignment()
123 return treeCanvas.av.getAlignment();
126 public AlignmentViewport getViewPort()
128 return treeCanvas.av;
131 void initNewTreePanel(AlignmentPanel ap, TreeModel tree)
135 TreeLoader tl = new TreeLoader(null, null);
139 void initLoadedTreePanel(AlignmentPanel ap,
140 NewickFile newTree, AlignmentView inputData)
144 TreeLoader tl = new TreeLoader(newTree, inputData);
148 public void buildTreeCanvas(AlignmentPanel ap) {
151 treeCanvas = new TreeCanvas(this, ap, scrollPane);
152 scrollPane.setViewportView(treeCanvas);
155 PaintRefresher.Register(this, ap.av.getSequenceSetId());
157 buildAssociatedViewMenu();
159 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
162 public void propertyChange(PropertyChangeEvent evt)
164 if (evt.getPropertyName().equals("alignment"))
168 System.out.println("tree is null");
169 // TODO: deal with case when a change event is received whilst a
170 // tree is still being calculated - should save reference for
171 // processing message later.
174 if (evt.getNewValue() == null)
177 "new alignment sequences vector value is null");
180 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
181 treeCanvas.nameHash.clear(); // reset the mapping between canvas
182 // rectangles and leafnodes
194 public void viewMenu_menuSelected()
196 buildAssociatedViewMenu();
199 void buildAssociatedViewMenu()
201 AlignmentPanel[] aps = PaintRefresher
202 .getAssociatedPanels(av.getSequenceSetId());
203 if (aps.length == 1 && treeCanvas.ap == aps[0])
205 associateLeavesMenu.setVisible(false);
209 associateLeavesMenu.setVisible(true);
212 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
214 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
217 associateLeavesMenu.removeAll();
219 JRadioButtonMenuItem item;
220 ButtonGroup buttonGroup = new ButtonGroup();
221 int i, iSize = aps.length;
222 final TreePanel thisTreePanel = this;
223 for (i = 0; i < iSize; i++)
225 final AlignmentPanel ap = aps[i];
226 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
227 buttonGroup.add(item);
228 item.addActionListener(new ActionListener()
231 public void actionPerformed(ActionEvent evt)
233 treeCanvas.applyToAllViews = false;
235 treeCanvas.av = ap.av;
236 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
240 associateLeavesMenu.add(item);
243 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
244 MessageManager.getString("label.all_views"));
245 buttonGroup.add(itemf);
246 itemf.setSelected(treeCanvas.applyToAllViews);
247 itemf.addActionListener(new ActionListener()
250 public void actionPerformed(ActionEvent evt)
252 treeCanvas.applyToAllViews = itemf.isSelected();
255 associateLeavesMenu.add(itemf);
259 class TreeLoader extends Thread
261 private NewickFile newTree;
263 private AlignmentView odata = null;
265 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
267 this.newTree = newickFile;
268 this.odata = inputData;
272 // Must be outside run(), as Jalview2XML tries to
273 // update distance/bootstrap visibility at the same time
274 showBootstrap(newTree.hasBootstrap());
275 showDistances(newTree.hasDistances());
287 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
289 if (tree.getOriginalData() == null)
291 originalSeqData.setVisible(false);
301 public void showTree(TreeModel tree)
303 tree.reCount(tree.getTopNode());
304 tree.findHeight(tree.getTopNode());
305 treeCanvas.setTree(tree);
306 treeCanvas.repaint();
308 av.setCurrentTree(tree);
309 if (av.getSortByTree())
311 sortByTree_actionPerformed();
317 public void showDistances(boolean b)
319 treeCanvas.setShowDistances(b);
320 distanceMenu.setSelected(b);
323 public void showBootstrap(boolean b)
325 treeCanvas.setShowBootstrap(b);
326 bootstrapMenu.setSelected(b);
329 public void showPlaceholders(boolean b)
331 placeholdersMenu.setState(b);
332 treeCanvas.setMarkPlaceholders(b);
338 * @return DOCUMENT ME!
340 public TreeModel getTree()
352 public void textbox_actionPerformed(ActionEvent e)
354 CutAndPasteTransfer cap = new CutAndPasteTransfer();
356 String newTitle = getPanelTitle();
358 NewickFile fout = new NewickFile(tree.getTopNode());
361 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
362 tree.hasRootDistance()));
363 Desktop.addInternalFrame(cap, newTitle, 500, 100);
364 } catch (OutOfMemoryError oom)
366 new OOMWarning("generating newick tree file", oom);
379 public void saveAsNewick_actionPerformed(ActionEvent e)
381 JalviewFileChooser chooser = new JalviewFileChooser(
382 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
383 chooser.setFileView(new JalviewFileView());
384 chooser.setDialogTitle(
385 MessageManager.getString("label.save_tree_as_newick"));
386 chooser.setToolTipText(MessageManager.getString("action.save"));
388 int value = chooser.showSaveDialog(null);
390 if (value == JalviewFileChooser.APPROVE_OPTION)
392 String choice = chooser.getSelectedFile().getPath();
393 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
394 chooser.getSelectedFile().getParent());
398 jalview.io.NewickFile fout = new jalview.io.NewickFile(
400 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
401 tree.hasRootDistance());
402 java.io.PrintWriter out = new java.io.PrintWriter(
403 new java.io.FileWriter(choice));
406 } catch (Exception ex)
408 ex.printStackTrace();
420 public void printMenu_actionPerformed(ActionEvent e)
422 // Putting in a thread avoids Swing painting problems
423 treeCanvas.startPrinting();
427 public void originalSeqData_actionPerformed(ActionEvent e)
429 AlignmentView originalData = tree.getOriginalData();
430 if (originalData == null)
432 jalview.bin.Cache.log.info(
433 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
436 // decide if av alignment is sufficiently different to original data to
437 // warrant a new window to be created
438 // create new alignmnt window with hidden regions (unhiding hidden regions
439 // yields unaligned seqs)
440 // or create a selection box around columns in alignment view
441 // test Alignment(SeqCigar[])
445 // we try to get the associated view's gap character
446 // but this may fail if the view was closed...
447 gc = av.getGapCharacter();
449 } catch (Exception ex)
453 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
455 if (alAndColsel != null && alAndColsel[0] != null)
457 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
459 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
460 AlignmentI dataset = (av != null && av.getAlignment() != null)
461 ? av.getAlignment().getDataset()
465 al.setDataset(dataset);
471 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
472 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
474 // >>>This is a fix for the moment, until a better solution is
476 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
478 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
481 Desktop.addInternalFrame(af, MessageManager.formatMessage(
482 "label.original_data_for_params", new Object[]
483 { this.title }), AlignFrame.DEFAULT_WIDTH,
484 AlignFrame.DEFAULT_HEIGHT);
496 public void fitToWindow_actionPerformed(ActionEvent e)
498 treeCanvas.fitToWindow = fitToWindow.isSelected();
503 * sort the associated alignment view by the current tree.
508 public void sortByTree_actionPerformed()
511 if (treeCanvas.applyToAllViews)
513 final ArrayList<CommandI> commands = new ArrayList<>();
514 for (AlignmentPanel ap : PaintRefresher
515 .getAssociatedPanels(av.getSequenceSetId()))
517 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
519 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
523 public void undoCommand(AlignmentI[] views)
525 for (CommandI tsort : commands)
527 tsort.undoCommand(views);
534 return commands.size();
538 public String getDescription()
540 return "Tree Sort (many views)";
544 public void doCommand(AlignmentI[] views)
547 for (CommandI tsort : commands)
549 tsort.doCommand(views);
553 for (AlignmentPanel ap : PaintRefresher
554 .getAssociatedPanels(av.getSequenceSetId()))
556 // ensure all the alignFrames refresh their GI after adding an undo item
557 ap.alignFrame.updateEditMenuBar();
562 treeCanvas.ap.alignFrame
563 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
568 public CommandI sortAlignmentIn(AlignmentPanel ap)
570 AlignmentViewport viewport = ap.av;
571 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
572 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
574 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
576 ap.paintAlignment(true);
587 public void font_actionPerformed(ActionEvent e)
589 if (treeCanvas == null)
594 new FontChooser(this);
597 public Font getTreeFont()
599 return treeCanvas.font;
602 public void setTreeFont(Font f)
604 if (treeCanvas != null)
606 treeCanvas.setFont(f);
617 public void distanceMenu_actionPerformed(ActionEvent e)
619 treeCanvas.setShowDistances(distanceMenu.isSelected());
629 public void bootstrapMenu_actionPerformed(ActionEvent e)
631 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
641 public void placeholdersMenu_actionPerformed(ActionEvent e)
643 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
653 public void epsTree_actionPerformed(ActionEvent e)
655 boolean accurateText = true;
657 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
660 // If we need to prompt, and if the GUI is visible then
661 // Prompt for EPS rendering style
662 if (renderStyle.equalsIgnoreCase("Prompt each time")
663 && !(System.getProperty("java.awt.headless") != null && System
664 .getProperty("java.awt.headless").equals("true")))
666 EPSOptions eps = new EPSOptions();
667 renderStyle = eps.getValue();
669 if (renderStyle == null || eps.cancelled)
676 if (renderStyle.equalsIgnoreCase("text"))
678 accurateText = false;
681 int width = treeCanvas.getWidth();
682 int height = treeCanvas.getHeight();
686 JalviewFileChooser chooser = new JalviewFileChooser(
687 ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
688 chooser.setFileView(new JalviewFileView());
689 chooser.setDialogTitle(
690 MessageManager.getString("label.create_eps_from_tree"));
691 chooser.setToolTipText(MessageManager.getString("action.save"));
693 int value = chooser.showSaveDialog(this);
695 if (value != JalviewFileChooser.APPROVE_OPTION)
700 Cache.setProperty("LAST_DIRECTORY",
701 chooser.getSelectedFile().getParent());
703 FileOutputStream out = new FileOutputStream(
704 chooser.getSelectedFile());
705 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
708 pg.setAccurateTextMode(accurateText);
710 treeCanvas.draw(pg, width, height);
714 } catch (Exception ex)
716 ex.printStackTrace();
727 public void pngTree_actionPerformed(ActionEvent e)
729 int width = treeCanvas.getWidth();
730 int height = treeCanvas.getHeight();
734 JalviewFileChooser chooser = new JalviewFileChooser(
735 ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
737 chooser.setFileView(new jalview.io.JalviewFileView());
738 chooser.setDialogTitle(
739 MessageManager.getString("label.create_png_from_tree"));
740 chooser.setToolTipText(MessageManager.getString("action.save"));
742 int value = chooser.showSaveDialog(this);
744 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
749 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
750 chooser.getSelectedFile().getParent());
752 FileOutputStream out = new FileOutputStream(
753 chooser.getSelectedFile());
755 BufferedImage bi = new BufferedImage(width, height,
756 BufferedImage.TYPE_INT_RGB);
757 Graphics png = bi.getGraphics();
759 treeCanvas.draw(png, width, height);
761 ImageIO.write(bi, "png", out);
763 } catch (Exception ex)
765 ex.printStackTrace();
770 * change node labels to the annotation referred to by labelClass TODO:
771 * promote to a datamodel modification that can be undone TODO: make argument
772 * one case of a generic transformation function ie { undoStep = apply(Tree,
773 * TransformFunction)};
777 public void changeNames(final String labelClass)
779 tree.applyToNodes(new NodeTransformI()
783 public void transform(BinaryNode node)
785 if (node instanceof SequenceNode
786 && !((SequenceNode) node).isPlaceholder()
787 && !((SequenceNode) node).isDummy())
789 String newname = null;
790 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
793 // search dbrefs, features and annotation
794 DBRefEntry[] refs = jalview.util.DBRefUtils
795 .selectRefs(sq.getDBRefs(), new String[]
796 { labelClass.toUpperCase() });
799 for (int i = 0; i < refs.length; i++)
803 newname = new String(refs[i].getAccessionId());
807 newname = newname + "; " + refs[i].getAccessionId();
813 List<SequenceFeature> features = sq.getFeatures()
814 .getPositionalFeatures(labelClass);
815 for (SequenceFeature feature : features)
819 newname = feature.getDescription();
823 newname = newname + "; " + feature.getDescription();
830 // String oldname = ((SequenceNode) node).getName();
831 // TODO : save oldname in the undo object for this modification.
832 ((SequenceNode) node).setName(newname);
840 * Formats a localised title for the tree panel, like
842 * Neighbour Joining Using BLOSUM62
844 * For a tree loaded from file, just uses the file name
848 public String getPanelTitle() // to be moved/fixed
850 if (treeTitle != null)
857 * i18n description of Neighbour Joining or Average Distance method
859 String treecalcnm = MessageManager
860 .getString("label.tree_calc_" + treeType.toLowerCase());
863 * short score model name (long description can be too long)
865 String smn = substitutionMatrix;
868 * put them together as <method> Using <model>
870 final String ttl = MessageManager
871 .formatMessage("label.treecalc_title", treecalcnm, smn);