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 java.util.Locale;
25 import jalview.analysis.AlignmentSorter;
26 import jalview.analysis.TreeModel;
27 import jalview.bin.Cache;
28 import jalview.bin.Console;
29 import jalview.commands.CommandI;
30 import jalview.commands.OrderCommand;
31 import jalview.datamodel.Alignment;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.AlignmentView;
34 import jalview.datamodel.BinaryNode;
35 import jalview.datamodel.DBRefEntry;
36 import jalview.datamodel.HiddenColumns;
37 import jalview.datamodel.NodeTransformI;
38 import jalview.datamodel.SequenceFeature;
39 import jalview.datamodel.SequenceI;
40 import jalview.datamodel.SequenceNode;
41 import jalview.gui.ImageExporter.ImageWriterI;
42 import jalview.io.JalviewFileChooser;
43 import jalview.io.JalviewFileView;
44 import jalview.io.NewickFile;
45 import jalview.jbgui.GTreePanel;
46 import jalview.util.ImageMaker.TYPE;
47 import jalview.util.MessageManager;
48 import jalview.viewmodel.AlignmentViewport;
51 import java.awt.Graphics;
52 import java.awt.event.ActionEvent;
53 import java.awt.event.ActionListener;
54 import java.beans.PropertyChangeEvent;
55 import java.beans.PropertyChangeListener;
57 import java.io.FileOutputStream;
58 import java.util.ArrayList;
59 import java.util.List;
61 import javax.swing.ButtonGroup;
62 import javax.swing.JMenuItem;
63 import javax.swing.JRadioButtonMenuItem;
65 import org.jibble.epsgraphics.EpsGraphics2D;
73 public class TreePanel extends GTreePanel
75 String substitutionMatrix;
79 String treeTitle; // if tree loaded
81 SimilarityParamsI similarityParams;
83 TreeCanvas treeCanvas;
87 private AlignViewport av;
90 * Creates a new TreePanel object.
95 * @param substitutionMatrix
97 public TreePanel(AlignmentPanel ap, TreeModel tree, String treeType,
98 String substitutionMatrix)
101 this.treeType = treeType;
102 this.substitutionMatrix = substitutionMatrix;
104 initTreePanel(ap, tree);
106 // We know this tree has distances. JBPNote TODO: prolly should add this as
107 // a userdefined default
108 // showDistances(true);
112 * Creates a new TreePanel object.
119 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
120 String theTitle, AlignmentView inputData)
123 this.treeTitle = theTitle;
124 initTreePanel(alignPanel, newtree, inputData);
127 public AlignmentI getAlignment()
129 return getTreeCanvas().getViewport().getAlignment();
132 public AlignmentViewport getViewPort()
134 // @Mungo - Why don't we return our own viewport ???
135 return getTreeCanvas().getViewport();
139 * Initialize a tree panel based on a calculated tree
144 void initTreePanel(AlignmentPanel ap, TreeModel tree)
148 TreeLoader tl = new TreeLoader(null, null);
154 * Initialize a tree panel based on a loaded in tree file.
160 void initTreePanel(AlignmentPanel ap,
161 NewickFile loadedTree, AlignmentView inputData)
165 TreeLoader tl = new TreeLoader(loadedTree, inputData);
169 public void buildTreeCanvas(AlignmentPanel ap) {
172 treeCanvas = new TreeCanvas(this, ap, scrollPane);
173 scrollPane.setViewportView(treeCanvas);
176 PaintRefresher.Register(this, ap.av.getSequenceSetId());
178 buildAssociatedViewMenu();
180 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
183 public void propertyChange(PropertyChangeEvent evt)
185 if (evt.getPropertyName().equals("alignment"))
189 System.out.println("tree is null");
190 // TODO: deal with case when a change event is received whilst a
191 // tree is still being calculated - should save reference for
192 // processing message later.
195 if (evt.getNewValue() == null)
198 "new alignment sequences vector value is null");
201 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
202 treeCanvas.nameHash.clear(); // reset the mapping between canvas
203 // rectangles and leafnodes
215 public void viewMenu_menuSelected()
217 buildAssociatedViewMenu();
220 void buildAssociatedViewMenu()
222 AlignmentPanel[] aps = PaintRefresher
223 .getAssociatedPanels(av.getSequenceSetId());
224 if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
226 associateLeavesMenu.setVisible(false);
230 associateLeavesMenu.setVisible(true);
233 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
235 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
238 associateLeavesMenu.removeAll();
240 JRadioButtonMenuItem item;
241 ButtonGroup buttonGroup = new ButtonGroup();
242 int i, iSize = aps.length;
243 final TreePanel thisTreePanel = this;
244 for (i = 0; i < iSize; i++)
246 final AlignmentPanel ap = aps[i];
247 item = new JRadioButtonMenuItem(ap.av.getViewName(),
248 ap == treeCanvas.getAssociatedPanel());
249 buttonGroup.add(item);
250 item.addActionListener(new ActionListener()
253 public void actionPerformed(ActionEvent evt)
255 treeCanvas.applyToAllViews = false;
256 treeCanvas.setAssociatedPanel(ap);
257 treeCanvas.setViewport(ap.av);
258 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
262 associateLeavesMenu.add(item);
265 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
266 MessageManager.getString("label.all_views"));
267 buttonGroup.add(itemf);
268 itemf.setSelected(treeCanvas.applyToAllViews);
269 itemf.addActionListener(new ActionListener()
272 public void actionPerformed(ActionEvent evt)
274 treeCanvas.applyToAllViews = itemf.isSelected();
277 associateLeavesMenu.add(itemf);
281 class TreeLoader extends Thread
283 private NewickFile newTree;
285 private AlignmentView odata = null;
287 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
289 this.newTree = newickFile;
290 this.odata = inputData;
294 // Must be outside run(), as Jalview2XML tries to
295 // update distance/bootstrap visibility at the same time
296 showBootstrap(newTree.hasBootstrap());
297 showDistances(newTree.hasDistances());
309 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
311 if (tree.getOriginalData() == null)
313 originalSeqData.setVisible(false);
320 public void showTree(TreeModel tree)
322 tree.reCount(tree.getTopNode());
323 tree.findHeight(tree.getTopNode());
324 treeCanvas.setTree(tree);
325 treeCanvas.repaint();
327 av.setCurrentTree(tree);
328 if (av.getSortByTree())
330 sortByTree_actionPerformed();
336 public void showDistances(boolean b)
338 treeCanvas.setShowDistances(b);
339 distanceMenu.setSelected(b);
342 public void showBootstrap(boolean b)
344 treeCanvas.setShowBootstrap(b);
345 bootstrapMenu.setSelected(b);
348 public void showPlaceholders(boolean b)
350 placeholdersMenu.setState(b);
351 treeCanvas.setMarkPlaceholders(b);
357 * @return DOCUMENT ME!
359 public TreeModel getTree()
371 public void textbox_actionPerformed(ActionEvent e)
373 CutAndPasteTransfer cap = new CutAndPasteTransfer();
375 String newTitle = getPanelTitle();
377 NewickFile fout = new NewickFile(tree.getTopNode());
380 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
381 tree.hasRootDistance()));
382 Desktop.addInternalFrame(cap, newTitle, 500, 100);
383 } catch (OutOfMemoryError oom)
385 new OOMWarning("generating newick tree file", oom);
398 public void saveAsNewick_actionPerformed(ActionEvent e)
400 // TODO: JAL-3048 save newick file for Jalview-JS
401 JalviewFileChooser chooser = new JalviewFileChooser(
402 Cache.getProperty("LAST_DIRECTORY"));
403 chooser.setFileView(new JalviewFileView());
404 chooser.setDialogTitle(
405 MessageManager.getString("label.save_tree_as_newick"));
406 chooser.setToolTipText(MessageManager.getString("action.save"));
408 int value = chooser.showSaveDialog(null);
410 if (value == JalviewFileChooser.APPROVE_OPTION)
412 String choice = chooser.getSelectedFile().getPath();
413 Cache.setProperty("LAST_DIRECTORY",
414 chooser.getSelectedFile().getParent());
418 jalview.io.NewickFile fout = new jalview.io.NewickFile(
420 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
421 tree.hasRootDistance());
422 java.io.PrintWriter out = new java.io.PrintWriter(
423 new java.io.FileWriter(choice));
426 } catch (Exception ex)
428 ex.printStackTrace();
440 public void printMenu_actionPerformed(ActionEvent e)
442 // Putting in a thread avoids Swing painting problems
443 treeCanvas.startPrinting();
447 public void originalSeqData_actionPerformed(ActionEvent e)
449 AlignmentView originalData = tree.getOriginalData();
450 if (originalData == null)
453 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
456 // decide if av alignment is sufficiently different to original data to
457 // warrant a new window to be created
458 // create new alignmnt window with hidden regions (unhiding hidden regions
459 // yields unaligned seqs)
460 // or create a selection box around columns in alignment view
461 // test Alignment(SeqCigar[])
465 // we try to get the associated view's gap character
466 // but this may fail if the view was closed...
467 gc = av.getGapCharacter();
469 } catch (Exception ex)
473 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
475 if (alAndColsel != null && alAndColsel[0] != null)
477 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
479 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
480 AlignmentI dataset = (av != null && av.getAlignment() != null)
481 ? av.getAlignment().getDataset()
485 al.setDataset(dataset);
491 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
492 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
494 // >>>This is a fix for the moment, until a better solution is
496 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
498 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
501 Desktop.addInternalFrame(af, MessageManager.formatMessage(
502 "label.original_data_for_params", new Object[]
503 { this.title }), AlignFrame.DEFAULT_WIDTH,
504 AlignFrame.DEFAULT_HEIGHT);
516 public void fitToWindow_actionPerformed(ActionEvent e)
518 treeCanvas.fitToWindow = fitToWindow.isSelected();
523 * sort the associated alignment view by the current tree.
528 public void sortByTree_actionPerformed()// modify for Aptx
531 if (treeCanvas.applyToAllViews)
533 final ArrayList<CommandI> commands = new ArrayList<>();
534 for (AlignmentPanel ap : PaintRefresher
535 .getAssociatedPanels(av.getSequenceSetId()))
537 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
539 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
543 public void undoCommand(AlignmentI[] views)
545 for (CommandI tsort : commands)
547 tsort.undoCommand(views);
554 return commands.size();
558 public String getDescription()
560 return "Tree Sort (many views)";
564 public void doCommand(AlignmentI[] views)
567 for (CommandI tsort : commands)
569 tsort.doCommand(views);
573 for (AlignmentPanel ap : PaintRefresher
574 .getAssociatedPanels(av.getSequenceSetId()))
576 // ensure all the alignFrames refresh their GI after adding an undo item
577 ap.alignFrame.updateEditMenuBar();
582 treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
583 sortAlignmentIn(treeCanvas.getAssociatedPanel()));
588 public CommandI sortAlignmentIn(AlignmentPanel ap)
590 // TODO: move to alignment view controller
591 AlignmentViewport viewport = ap.av;
592 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
593 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
595 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
597 ap.paintAlignment(true, false);
608 public void font_actionPerformed(ActionEvent e)
610 if (treeCanvas == null)
615 new FontChooser(this);
618 public Font getTreeFont()
620 return treeCanvas.font;
623 public void setTreeFont(Font f)
625 if (treeCanvas != null)
627 treeCanvas.setFont(f);
638 public void distanceMenu_actionPerformed(ActionEvent e)
640 treeCanvas.setShowDistances(distanceMenu.isSelected());
650 public void bootstrapMenu_actionPerformed(ActionEvent e)
652 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
662 public void placeholdersMenu_actionPerformed(ActionEvent e)
664 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
668 * Outputs the Tree in image format (currently EPS or PNG). The user is
669 * prompted for the file to save to, and for EPS (unless a preference is
670 * already set) for the choice of Text or Lineart for character rendering.
673 public void writeTreeImage(TYPE imageFormat)
675 int width = treeCanvas.getWidth();
676 int height = treeCanvas.getHeight();
677 ImageWriterI writer = new ImageWriterI()
680 public void exportImage(Graphics g) throws Exception
682 treeCanvas.draw(g, width, height);
685 String tree = MessageManager.getString("label.tree");
686 ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
688 exporter.doExport(null, this, width, height,
689 tree.toLowerCase(Locale.ROOT));
693 * change node labels to the annotation referred to by labelClass TODO:
694 * promote to a datamodel modification that can be undone TODO: make argument
695 * one case of a generic transformation function ie { undoStep = apply(Tree,
696 * TransformFunction)};
700 public void changeNames(final String labelClass)
702 tree.applyToNodes(new NodeTransformI()
706 public void transform(BinaryNode node)
708 if (node instanceof SequenceNode
709 && !((SequenceNode) node).isPlaceholder()
710 && !((SequenceNode) node).isDummy())
712 String newname = null;
713 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
716 // search dbrefs, features and annotation
717 List<DBRefEntry> refs = jalview.util.DBRefUtils
718 .selectRefs(sq.getDBRefs(), new String[]
719 { labelClass.toUpperCase(Locale.ROOT) });
722 for (int i = 0, ni = refs.size(); i < ni; i++)
726 newname = new String(refs.get(i).getAccessionId());
730 newname += "; " + refs.get(i).getAccessionId();
736 List<SequenceFeature> features = sq.getFeatures()
737 .getPositionalFeatures(labelClass);
738 for (SequenceFeature feature : features)
742 newname = feature.getDescription();
746 newname = newname + "; " + feature.getDescription();
753 // String oldname = ((SequenceNode) node).getName();
754 // TODO : save oldname in the undo object for this modification.
755 ((SequenceNode) node).setName(newname);
763 * Formats a localised title for the tree panel, like
765 * Neighbour Joining Using BLOSUM62
767 * For a tree loaded from file, just uses the file name
771 public String getPanelTitle() // to be moved/fixed
773 if (treeTitle != null)
780 * i18n description of Neighbour Joining or Average Distance method
782 String treecalcnm = MessageManager
783 .getString("label.tree_calc_" + treeType.toLowerCase());
786 * i18n description of Neighbour Joining or Average Distance method
788 String treecalcnm = MessageManager.getString(
789 "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
792 * short score model name (long description can be too long)
794 String smn = scoreModelName;
797 * put them together as <method> Using <model>
799 final String ttl = MessageManager.formatMessage("label.calc_title",
806 * Builds an EPS image and writes it to the specified file.
810 * true for Text character rendering, false for Lineart
812 protected void writeEpsFile(File outFile, boolean textOption)
816 int width = treeCanvas.getWidth();
817 int height = treeCanvas.getHeight();
819 FileOutputStream out = new FileOutputStream(outFile);
820 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
822 pg.setAccurateTextMode(!textOption);
823 treeCanvas.draw(pg, width, height);
827 } catch (Exception ex)
829 System.err.println("Error writing tree as EPS");
830 ex.printStackTrace();
834 public AlignViewport getViewport()
839 public void setViewport(AlignViewport av)
844 public TreeCanvas getTreeCanvas()