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.io.FileOutputStream;
59 import java.util.ArrayList;
60 import java.util.List;
62 import javax.imageio.ImageIO;
63 import javax.swing.ButtonGroup;
64 import javax.swing.JMenuItem;
65 import javax.swing.JRadioButtonMenuItem;
67 import org.jibble.epsgraphics.EpsGraphics2D;
75 public class TreePanel extends GTreePanel
79 String scoreModelName; // if tree computed
81 String treeTitle; // if tree loaded
83 SimilarityParamsI similarityParams;
85 TreeCanvas treeCanvas;
92 * Creates a new TreePanel object.
99 public TreePanel(AlignmentPanel ap, String type, String modelName,
100 SimilarityParamsI options)
103 this.similarityParams = options;
104 initTreePanel(ap, type, modelName, null, null);
106 // We know this tree has distances. JBPNote TODO: prolly should add this as
107 // a userdefined default
108 // showDistances(true);
111 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
112 String theTitle, AlignmentView inputData)
115 this.treeTitle = theTitle;
116 initTreePanel(alignPanel, null, null, newtree, inputData);
119 public AlignmentI getAlignment()
121 return treeCanvas.av.getAlignment();
124 public AlignmentViewport getViewPort()
126 return treeCanvas.av;
129 void initTreePanel(AlignmentPanel ap, String type, String modelName,
130 NewickFile newTree, AlignmentView inputData)
134 this.treeType = type;
135 this.scoreModelName = modelName;
137 treeCanvas = new TreeCanvas(this, ap, scrollPane);
138 scrollPane.setViewportView(treeCanvas);
140 PaintRefresher.Register(this, ap.av.getSequenceSetId());
142 buildAssociatedViewMenu();
144 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
147 public void propertyChange(PropertyChangeEvent evt)
149 if (evt.getPropertyName().equals("alignment"))
153 System.out.println("tree is null");
154 // TODO: deal with case when a change event is received whilst a
155 // tree is still being calculated - should save reference for
156 // processing message later.
159 if (evt.getNewValue() == null)
162 "new alignment sequences vector value is null");
165 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
166 treeCanvas.nameHash.clear(); // reset the mapping between canvas
167 // rectangles and leafnodes
173 TreeLoader tl = new TreeLoader(newTree, inputData);
179 public void viewMenu_menuSelected()
181 buildAssociatedViewMenu();
184 void buildAssociatedViewMenu()
186 AlignmentPanel[] aps = PaintRefresher
187 .getAssociatedPanels(av.getSequenceSetId());
188 if (aps.length == 1 && treeCanvas.ap == aps[0])
190 associateLeavesMenu.setVisible(false);
194 associateLeavesMenu.setVisible(true);
197 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
199 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
202 associateLeavesMenu.removeAll();
204 JRadioButtonMenuItem item;
205 ButtonGroup buttonGroup = new ButtonGroup();
206 int i, iSize = aps.length;
207 final TreePanel thisTreePanel = this;
208 for (i = 0; i < iSize; i++)
210 final AlignmentPanel ap = aps[i];
211 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
212 buttonGroup.add(item);
213 item.addActionListener(new ActionListener()
216 public void actionPerformed(ActionEvent evt)
218 treeCanvas.applyToAllViews = false;
220 treeCanvas.av = ap.av;
221 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
225 associateLeavesMenu.add(item);
228 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
229 MessageManager.getString("label.all_views"));
230 buttonGroup.add(itemf);
231 itemf.setSelected(treeCanvas.applyToAllViews);
232 itemf.addActionListener(new ActionListener()
235 public void actionPerformed(ActionEvent evt)
237 treeCanvas.applyToAllViews = itemf.isSelected();
240 associateLeavesMenu.add(itemf);
244 class TreeLoader extends Thread
246 private NewickFile newtree;
248 private AlignmentView odata = null;
250 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
252 this.newtree = newickFile;
253 this.odata = inputData;
255 if (newickFile != null)
257 // Must be outside run(), as Jalview2XML tries to
258 // update distance/bootstrap visibility at the same time
259 showBootstrap(newickFile.HasBootstrap());
260 showDistances(newickFile.HasDistances());
270 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
272 if (tree.getOriginalData() == null)
274 originalSeqData.setVisible(false);
279 ScoreModelI sm = ScoreModels.getInstance()
280 .getScoreModel(scoreModelName, treeCanvas.ap);
281 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
282 ? new NJTree(av, sm, similarityParams)
283 : new AverageDistanceTree(av, sm, similarityParams);
284 tree = new TreeModel(njtree);
288 tree.reCount(tree.getTopNode());
289 tree.findHeight(tree.getTopNode());
290 treeCanvas.setTree(tree);
291 treeCanvas.repaint();
292 av.setCurrentTree(tree);
293 if (av.getSortByTree())
295 sortByTree_actionPerformed();
300 public void showDistances(boolean b)
302 treeCanvas.setShowDistances(b);
303 distanceMenu.setSelected(b);
306 public void showBootstrap(boolean b)
308 treeCanvas.setShowBootstrap(b);
309 bootstrapMenu.setSelected(b);
312 public void showPlaceholders(boolean b)
314 placeholdersMenu.setState(b);
315 treeCanvas.setMarkPlaceholders(b);
321 * @return DOCUMENT ME!
323 public TreeModel getTree()
335 public void textbox_actionPerformed(ActionEvent e)
337 CutAndPasteTransfer cap = new CutAndPasteTransfer();
339 String newTitle = getPanelTitle();
341 NewickFile fout = new NewickFile(tree.getTopNode());
344 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
345 tree.hasRootDistance()));
346 Desktop.addInternalFrame(cap, newTitle, 500, 100);
347 } catch (OutOfMemoryError oom)
349 new OOMWarning("generating newick tree file", oom);
362 public void saveAsNewick_actionPerformed(ActionEvent e)
364 JalviewFileChooser chooser = new JalviewFileChooser(
365 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
366 chooser.setFileView(new JalviewFileView());
367 chooser.setDialogTitle(
368 MessageManager.getString("label.save_tree_as_newick"));
369 chooser.setToolTipText(MessageManager.getString("action.save"));
371 int value = chooser.showSaveDialog(null);
373 if (value == JalviewFileChooser.APPROVE_OPTION)
375 String choice = chooser.getSelectedFile().getPath();
376 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
377 chooser.getSelectedFile().getParent());
381 jalview.io.NewickFile fout = new jalview.io.NewickFile(
383 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
384 tree.hasRootDistance());
385 java.io.PrintWriter out = new java.io.PrintWriter(
386 new java.io.FileWriter(choice));
389 } catch (Exception ex)
391 ex.printStackTrace();
403 public void printMenu_actionPerformed(ActionEvent e)
405 // Putting in a thread avoids Swing painting problems
406 treeCanvas.startPrinting();
410 public void originalSeqData_actionPerformed(ActionEvent e)
412 AlignmentView originalData = tree.getOriginalData();
413 if (originalData == null)
415 jalview.bin.Cache.log.info(
416 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
419 // decide if av alignment is sufficiently different to original data to
420 // warrant a new window to be created
421 // create new alignmnt window with hidden regions (unhiding hidden regions
422 // yields unaligned seqs)
423 // or create a selection box around columns in alignment view
424 // test Alignment(SeqCigar[])
428 // we try to get the associated view's gap character
429 // but this may fail if the view was closed...
430 gc = av.getGapCharacter();
432 } catch (Exception ex)
436 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
438 if (alAndColsel != null && alAndColsel[0] != null)
440 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
442 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
443 AlignmentI dataset = (av != null && av.getAlignment() != null)
444 ? av.getAlignment().getDataset()
448 al.setDataset(dataset);
454 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
455 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
457 // >>>This is a fix for the moment, until a better solution is
459 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
461 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
464 Desktop.addInternalFrame(af, MessageManager.formatMessage(
465 "label.original_data_for_params", new Object[]
466 { this.title }), AlignFrame.DEFAULT_WIDTH,
467 AlignFrame.DEFAULT_HEIGHT);
479 public void fitToWindow_actionPerformed(ActionEvent e)
481 treeCanvas.fitToWindow = fitToWindow.isSelected();
486 * sort the associated alignment view by the current tree.
491 public void sortByTree_actionPerformed()
494 if (treeCanvas.applyToAllViews)
496 final ArrayList<CommandI> commands = new ArrayList<CommandI>();
497 for (AlignmentPanel ap : PaintRefresher
498 .getAssociatedPanels(av.getSequenceSetId()))
500 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
502 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
506 public void undoCommand(AlignmentI[] views)
508 for (CommandI tsort : commands)
510 tsort.undoCommand(views);
517 return commands.size();
521 public String getDescription()
523 return "Tree Sort (many views)";
527 public void doCommand(AlignmentI[] views)
530 for (CommandI tsort : commands)
532 tsort.doCommand(views);
536 for (AlignmentPanel ap : PaintRefresher
537 .getAssociatedPanels(av.getSequenceSetId()))
539 // ensure all the alignFrames refresh their GI after adding an undo item
540 ap.alignFrame.updateEditMenuBar();
545 treeCanvas.ap.alignFrame
546 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
551 public CommandI sortAlignmentIn(AlignmentPanel ap)
553 AlignmentViewport viewport = ap.av;
554 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
555 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
557 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
559 ap.paintAlignment(true);
570 public void font_actionPerformed(ActionEvent e)
572 if (treeCanvas == null)
577 new FontChooser(this);
580 public Font getTreeFont()
582 return treeCanvas.font;
585 public void setTreeFont(Font f)
587 if (treeCanvas != null)
589 treeCanvas.setFont(f);
600 public void distanceMenu_actionPerformed(ActionEvent e)
602 treeCanvas.setShowDistances(distanceMenu.isSelected());
612 public void bootstrapMenu_actionPerformed(ActionEvent e)
614 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
624 public void placeholdersMenu_actionPerformed(ActionEvent e)
626 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
636 public void epsTree_actionPerformed(ActionEvent e)
638 boolean accurateText = true;
640 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
643 // If we need to prompt, and if the GUI is visible then
644 // Prompt for EPS rendering style
645 if (renderStyle.equalsIgnoreCase("Prompt each time")
646 && !(System.getProperty("java.awt.headless") != null && System
647 .getProperty("java.awt.headless").equals("true")))
649 EPSOptions eps = new EPSOptions();
650 renderStyle = eps.getValue();
652 if (renderStyle == null || eps.cancelled)
659 if (renderStyle.equalsIgnoreCase("text"))
661 accurateText = false;
664 int width = treeCanvas.getWidth();
665 int height = treeCanvas.getHeight();
669 JalviewFileChooser chooser = new JalviewFileChooser(
670 ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
671 chooser.setFileView(new JalviewFileView());
672 chooser.setDialogTitle(
673 MessageManager.getString("label.create_eps_from_tree"));
674 chooser.setToolTipText(MessageManager.getString("action.save"));
676 int value = chooser.showSaveDialog(this);
678 if (value != JalviewFileChooser.APPROVE_OPTION)
683 Cache.setProperty("LAST_DIRECTORY",
684 chooser.getSelectedFile().getParent());
686 FileOutputStream out = new FileOutputStream(
687 chooser.getSelectedFile());
688 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
691 pg.setAccurateTextMode(accurateText);
693 treeCanvas.draw(pg, width, height);
697 } catch (Exception ex)
699 ex.printStackTrace();
710 public void pngTree_actionPerformed(ActionEvent e)
712 int width = treeCanvas.getWidth();
713 int height = treeCanvas.getHeight();
717 JalviewFileChooser chooser = new JalviewFileChooser(
718 ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
720 chooser.setFileView(new jalview.io.JalviewFileView());
721 chooser.setDialogTitle(
722 MessageManager.getString("label.create_png_from_tree"));
723 chooser.setToolTipText(MessageManager.getString("action.save"));
725 int value = chooser.showSaveDialog(this);
727 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
732 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
733 chooser.getSelectedFile().getParent());
735 FileOutputStream out = new FileOutputStream(
736 chooser.getSelectedFile());
738 BufferedImage bi = new BufferedImage(width, height,
739 BufferedImage.TYPE_INT_RGB);
740 Graphics png = bi.getGraphics();
742 treeCanvas.draw(png, width, height);
744 ImageIO.write(bi, "png", out);
746 } catch (Exception ex)
748 ex.printStackTrace();
753 * change node labels to the annotation referred to by labelClass TODO:
754 * promote to a datamodel modification that can be undone TODO: make argument
755 * one case of a generic transformation function ie { undoStep = apply(Tree,
756 * TransformFunction)};
760 public void changeNames(final String labelClass)
762 tree.applyToNodes(new NodeTransformI()
766 public void transform(BinaryNode node)
768 if (node instanceof SequenceNode
769 && !((SequenceNode) node).isPlaceholder()
770 && !((SequenceNode) node).isDummy())
772 String newname = null;
773 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
776 // search dbrefs, features and annotation
777 DBRefEntry[] refs = jalview.util.DBRefUtils
778 .selectRefs(sq.getDBRefs(), new String[]
779 { labelClass.toUpperCase() });
782 for (int i = 0; i < refs.length; i++)
786 newname = new String(refs[i].getAccessionId());
790 newname = newname + "; " + refs[i].getAccessionId();
796 List<SequenceFeature> features = sq.getFeatures()
797 .getPositionalFeatures(labelClass);
798 for (SequenceFeature feature : features)
802 newname = feature.getDescription();
806 newname = newname + "; " + feature.getDescription();
813 // String oldname = ((SequenceNode) node).getName();
814 // TODO : save oldname in the undo object for this modification.
815 ((SequenceNode) node).setName(newname);
823 * Formats a localised title for the tree panel, like
825 * Neighbour Joining Using BLOSUM62
827 * For a tree loaded from file, just uses the file name
831 public String getPanelTitle()
833 if (treeTitle != null)
839 * i18n description of Neighbour Joining or Average Distance method
841 String treecalcnm = MessageManager
842 .getString("label.tree_calc_" + treeType.toLowerCase());
845 * short score model name (long description can be too long)
847 String smn = scoreModelName;
850 * put them together as <method> Using <model>
852 final String ttl = MessageManager.formatMessage("label.treecalc_title",