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 initTreePanel(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 initTreePanel(alignPanel, newtree, inputData);
121 public AlignmentI getAlignment()
123 return treeCanvas.av.getAlignment();
126 public AlignmentViewport getViewPort()
128 return treeCanvas.av;
132 * Initialize a tree panel based on a calculated tree
137 void initTreePanel(AlignmentPanel ap, TreeModel tree)
141 TreeLoader tl = new TreeLoader(null, null);
147 * Initialize a tree panel based on a loaded in tree file.
153 void initTreePanel(AlignmentPanel ap,
154 NewickFile loadedTree, AlignmentView inputData)
158 TreeLoader tl = new TreeLoader(loadedTree, inputData);
162 public void buildTreeCanvas(AlignmentPanel ap) {
165 treeCanvas = new TreeCanvas(this, ap, scrollPane);
166 scrollPane.setViewportView(treeCanvas);
169 PaintRefresher.Register(this, ap.av.getSequenceSetId());
171 buildAssociatedViewMenu();
173 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
176 public void propertyChange(PropertyChangeEvent evt)
178 if (evt.getPropertyName().equals("alignment"))
182 System.out.println("tree is null");
183 // TODO: deal with case when a change event is received whilst a
184 // tree is still being calculated - should save reference for
185 // processing message later.
188 if (evt.getNewValue() == null)
191 "new alignment sequences vector value is null");
194 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
195 treeCanvas.nameHash.clear(); // reset the mapping between canvas
196 // rectangles and leafnodes
208 public void viewMenu_menuSelected()
210 buildAssociatedViewMenu();
213 void buildAssociatedViewMenu()
215 AlignmentPanel[] aps = PaintRefresher
216 .getAssociatedPanels(av.getSequenceSetId());
217 if (aps.length == 1 && treeCanvas.ap == aps[0])
219 associateLeavesMenu.setVisible(false);
223 associateLeavesMenu.setVisible(true);
226 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
228 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
231 associateLeavesMenu.removeAll();
233 JRadioButtonMenuItem item;
234 ButtonGroup buttonGroup = new ButtonGroup();
235 int i, iSize = aps.length;
236 final TreePanel thisTreePanel = this;
237 for (i = 0; i < iSize; i++)
239 final AlignmentPanel ap = aps[i];
240 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
241 buttonGroup.add(item);
242 item.addActionListener(new ActionListener()
245 public void actionPerformed(ActionEvent evt)
247 treeCanvas.applyToAllViews = false;
249 treeCanvas.av = ap.av;
250 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
254 associateLeavesMenu.add(item);
257 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
258 MessageManager.getString("label.all_views"));
259 buttonGroup.add(itemf);
260 itemf.setSelected(treeCanvas.applyToAllViews);
261 itemf.addActionListener(new ActionListener()
264 public void actionPerformed(ActionEvent evt)
266 treeCanvas.applyToAllViews = itemf.isSelected();
269 associateLeavesMenu.add(itemf);
273 class TreeLoader extends Thread
275 private NewickFile newTree;
277 private AlignmentView odata = null;
279 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
281 this.newTree = newickFile;
282 this.odata = inputData;
286 // Must be outside run(), as Jalview2XML tries to
287 // update distance/bootstrap visibility at the same time
288 showBootstrap(newTree.hasBootstrap());
289 showDistances(newTree.hasDistances());
301 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
303 if (tree.getOriginalData() == null)
305 originalSeqData.setVisible(false);
315 public void showTree(TreeModel tree)
317 tree.reCount(tree.getTopNode());
318 tree.findHeight(tree.getTopNode());
319 treeCanvas.setTree(tree);
320 treeCanvas.repaint();
322 av.setCurrentTree(tree);
323 if (av.getSortByTree())
325 sortByTree_actionPerformed();
331 public void showDistances(boolean b)
333 treeCanvas.setShowDistances(b);
334 distanceMenu.setSelected(b);
337 public void showBootstrap(boolean b)
339 treeCanvas.setShowBootstrap(b);
340 bootstrapMenu.setSelected(b);
343 public void showPlaceholders(boolean b)
345 placeholdersMenu.setState(b);
346 treeCanvas.setMarkPlaceholders(b);
352 * @return DOCUMENT ME!
354 public TreeModel getTree()
366 public void textbox_actionPerformed(ActionEvent e)
368 CutAndPasteTransfer cap = new CutAndPasteTransfer();
370 String newTitle = getPanelTitle();
372 NewickFile fout = new NewickFile(tree.getTopNode());
375 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
376 tree.hasRootDistance()));
377 Desktop.addInternalFrame(cap, newTitle, 500, 100);
378 } catch (OutOfMemoryError oom)
380 new OOMWarning("generating newick tree file", oom);
393 public void saveAsNewick_actionPerformed(ActionEvent e)
395 JalviewFileChooser chooser = new JalviewFileChooser(
396 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
397 chooser.setFileView(new JalviewFileView());
398 chooser.setDialogTitle(
399 MessageManager.getString("label.save_tree_as_newick"));
400 chooser.setToolTipText(MessageManager.getString("action.save"));
402 int value = chooser.showSaveDialog(null);
404 if (value == JalviewFileChooser.APPROVE_OPTION)
406 String choice = chooser.getSelectedFile().getPath();
407 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
408 chooser.getSelectedFile().getParent());
412 jalview.io.NewickFile fout = new jalview.io.NewickFile(
414 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
415 tree.hasRootDistance());
416 java.io.PrintWriter out = new java.io.PrintWriter(
417 new java.io.FileWriter(choice));
420 } catch (Exception ex)
422 ex.printStackTrace();
434 public void printMenu_actionPerformed(ActionEvent e)
436 // Putting in a thread avoids Swing painting problems
437 treeCanvas.startPrinting();
441 public void originalSeqData_actionPerformed(ActionEvent e)
443 AlignmentView originalData = tree.getOriginalData();
444 if (originalData == null)
446 jalview.bin.Cache.log.info(
447 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
450 // decide if av alignment is sufficiently different to original data to
451 // warrant a new window to be created
452 // create new alignmnt window with hidden regions (unhiding hidden regions
453 // yields unaligned seqs)
454 // or create a selection box around columns in alignment view
455 // test Alignment(SeqCigar[])
459 // we try to get the associated view's gap character
460 // but this may fail if the view was closed...
461 gc = av.getGapCharacter();
463 } catch (Exception ex)
467 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
469 if (alAndColsel != null && alAndColsel[0] != null)
471 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
473 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
474 AlignmentI dataset = (av != null && av.getAlignment() != null)
475 ? av.getAlignment().getDataset()
479 al.setDataset(dataset);
485 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
486 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
488 // >>>This is a fix for the moment, until a better solution is
490 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
492 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
495 Desktop.addInternalFrame(af, MessageManager.formatMessage(
496 "label.original_data_for_params", new Object[]
497 { this.title }), AlignFrame.DEFAULT_WIDTH,
498 AlignFrame.DEFAULT_HEIGHT);
510 public void fitToWindow_actionPerformed(ActionEvent e)
512 treeCanvas.fitToWindow = fitToWindow.isSelected();
517 * sort the associated alignment view by the current tree.
522 public void sortByTree_actionPerformed()
525 if (treeCanvas.applyToAllViews)
527 final ArrayList<CommandI> commands = new ArrayList<>();
528 for (AlignmentPanel ap : PaintRefresher
529 .getAssociatedPanels(av.getSequenceSetId()))
531 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
533 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
537 public void undoCommand(AlignmentI[] views)
539 for (CommandI tsort : commands)
541 tsort.undoCommand(views);
548 return commands.size();
552 public String getDescription()
554 return "Tree Sort (many views)";
558 public void doCommand(AlignmentI[] views)
561 for (CommandI tsort : commands)
563 tsort.doCommand(views);
567 for (AlignmentPanel ap : PaintRefresher
568 .getAssociatedPanels(av.getSequenceSetId()))
570 // ensure all the alignFrames refresh their GI after adding an undo item
571 ap.alignFrame.updateEditMenuBar();
576 treeCanvas.ap.alignFrame
577 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
582 public CommandI sortAlignmentIn(AlignmentPanel ap)
584 // TODO: move to alignment view controller
585 AlignmentViewport viewport = ap.av;
586 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
587 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
589 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
591 ap.paintAlignment(true, false);
602 public void font_actionPerformed(ActionEvent e)
604 if (treeCanvas == null)
609 new FontChooser(this);
612 public Font getTreeFont()
614 return treeCanvas.font;
617 public void setTreeFont(Font f)
619 if (treeCanvas != null)
621 treeCanvas.setFont(f);
632 public void distanceMenu_actionPerformed(ActionEvent e)
634 treeCanvas.setShowDistances(distanceMenu.isSelected());
644 public void bootstrapMenu_actionPerformed(ActionEvent e)
646 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
656 public void placeholdersMenu_actionPerformed(ActionEvent e)
658 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
668 public void epsTree_actionPerformed(ActionEvent e)
670 boolean accurateText = true;
672 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
675 // If we need to prompt, and if the GUI is visible then
676 // Prompt for EPS rendering style
677 if (renderStyle.equalsIgnoreCase("Prompt each time")
678 && !(System.getProperty("java.awt.headless") != null && System
679 .getProperty("java.awt.headless").equals("true")))
681 EPSOptions eps = new EPSOptions();
682 renderStyle = eps.getValue();
684 if (renderStyle == null || eps.cancelled)
691 if (renderStyle.equalsIgnoreCase("text"))
693 accurateText = false;
696 int width = treeCanvas.getWidth();
697 int height = treeCanvas.getHeight();
701 JalviewFileChooser chooser = new JalviewFileChooser(
702 ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
703 chooser.setFileView(new JalviewFileView());
704 chooser.setDialogTitle(
705 MessageManager.getString("label.create_eps_from_tree"));
706 chooser.setToolTipText(MessageManager.getString("action.save"));
708 int value = chooser.showSaveDialog(this);
710 if (value != JalviewFileChooser.APPROVE_OPTION)
715 Cache.setProperty("LAST_DIRECTORY",
716 chooser.getSelectedFile().getParent());
718 FileOutputStream out = new FileOutputStream(
719 chooser.getSelectedFile());
720 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
723 pg.setAccurateTextMode(accurateText);
725 treeCanvas.draw(pg, width, height);
729 } catch (Exception ex)
731 ex.printStackTrace();
742 public void pngTree_actionPerformed(ActionEvent e)
744 int width = treeCanvas.getWidth();
745 int height = treeCanvas.getHeight();
749 JalviewFileChooser chooser = new JalviewFileChooser(
750 ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
752 chooser.setFileView(new jalview.io.JalviewFileView());
753 chooser.setDialogTitle(
754 MessageManager.getString("label.create_png_from_tree"));
755 chooser.setToolTipText(MessageManager.getString("action.save"));
757 int value = chooser.showSaveDialog(this);
759 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
764 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
765 chooser.getSelectedFile().getParent());
767 FileOutputStream out = new FileOutputStream(
768 chooser.getSelectedFile());
770 BufferedImage bi = new BufferedImage(width, height,
771 BufferedImage.TYPE_INT_RGB);
772 Graphics png = bi.getGraphics();
774 treeCanvas.draw(png, width, height);
776 ImageIO.write(bi, "png", out);
778 } catch (Exception ex)
780 ex.printStackTrace();
785 * change node labels to the annotation referred to by labelClass TODO:
786 * promote to a datamodel modification that can be undone TODO: make argument
787 * one case of a generic transformation function ie { undoStep = apply(Tree,
788 * TransformFunction)};
792 public void changeNames(final String labelClass)
794 tree.applyToNodes(new NodeTransformI()
798 public void transform(BinaryNode node)
800 if (node instanceof SequenceNode
801 && !((SequenceNode) node).isPlaceholder()
802 && !((SequenceNode) node).isDummy())
804 String newname = null;
805 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
808 // search dbrefs, features and annotation
809 DBRefEntry[] refs = jalview.util.DBRefUtils
810 .selectRefs(sq.getDBRefs(), new String[]
811 { labelClass.toUpperCase() });
814 for (int i = 0; i < refs.length; i++)
818 newname = new String(refs[i].getAccessionId());
822 newname = newname + "; " + refs[i].getAccessionId();
828 List<SequenceFeature> features = sq.getFeatures()
829 .getPositionalFeatures(labelClass);
830 for (SequenceFeature feature : features)
834 newname = feature.getDescription();
838 newname = newname + "; " + feature.getDescription();
845 // String oldname = ((SequenceNode) node).getName();
846 // TODO : save oldname in the undo object for this modification.
847 ((SequenceNode) node).setName(newname);
855 * Formats a localised title for the tree panel, like
857 * Neighbour Joining Using BLOSUM62
859 * For a tree loaded from file, just uses the file name
863 public String getPanelTitle() // to be moved/fixed
865 if (treeTitle != null)
872 * i18n description of Neighbour Joining or Average Distance method
874 String treecalcnm = MessageManager
875 .getString("label.tree_calc_" + treeType.toLowerCase());
878 * short score model name (long description can be too long)
880 String smn = substitutionMatrix;
883 * put them together as <method> Using <model>
885 final String ttl = MessageManager
886 .formatMessage("label.treecalc_title", treecalcnm, smn);