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.ext.archaeopteryx.ArchaeopteryxInit;
45 import jalview.io.JalviewFileChooser;
46 import jalview.io.JalviewFileView;
47 import jalview.io.NewickFile;
48 import jalview.jbgui.GTreePanel;
49 import jalview.util.ImageMaker;
50 import jalview.util.MessageManager;
51 import jalview.viewmodel.AlignmentViewport;
54 import java.awt.Graphics;
55 import java.awt.event.ActionEvent;
56 import java.awt.event.ActionListener;
57 import java.awt.image.BufferedImage;
58 import java.beans.PropertyChangeEvent;
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;
68 import org.jibble.epsgraphics.EpsGraphics2D;
76 public class TreePanel extends GTreePanel
80 String scoreModelName; // if tree computed
82 String treeTitle; // if tree loaded
84 SimilarityParamsI similarityParams;
86 TreeCanvas treeCanvas;
93 * Creates a new TreePanel object.
100 public TreePanel(AlignmentPanel ap, String type, String modelName,
101 SimilarityParamsI options)
104 this.similarityParams = options;
105 initTreePanel(ap, type, modelName, null, null);
107 // We know this tree has distances. JBPNote TODO: prolly should add this as
108 // a userdefined default
109 // showDistances(true);
112 public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
113 String theTitle, AlignmentView inputData)
116 this.treeTitle = theTitle;
117 initTreePanel(alignPanel, null, null, newtree, inputData);
120 public AlignmentI getAlignment()
122 return treeCanvas.av.getAlignment();
125 public AlignmentViewport getViewPort()
127 return treeCanvas.av;
130 void initTreePanel(AlignmentPanel ap, String type, String modelName,
131 NewickFile newTree, AlignmentView inputData)
135 this.treeType = type;
136 this.scoreModelName = modelName;
138 treeCanvas = new TreeCanvas(this, ap, scrollPane);
139 scrollPane.setViewportView(treeCanvas);
141 PaintRefresher.Register(this, ap.av.getSequenceSetId());
143 buildAssociatedViewMenu();
145 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
148 public void propertyChange(PropertyChangeEvent evt)
150 if (evt.getPropertyName().equals("alignment"))
154 System.out.println("tree is null");
155 // TODO: deal with case when a change event is received whilst a
156 // tree is still being calculated - should save reference for
157 // processing message later.
160 if (evt.getNewValue() == null)
163 "new alignment sequences vector value is null");
166 tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
167 treeCanvas.nameHash.clear(); // reset the mapping between canvas
168 // rectangles and leafnodes
175 TreeLoader tl = new TreeLoader(newTree, inputData);
181 public void viewMenu_menuSelected()
183 buildAssociatedViewMenu();
186 void buildAssociatedViewMenu()
188 AlignmentPanel[] aps = PaintRefresher
189 .getAssociatedPanels(av.getSequenceSetId());
190 if (aps.length == 1 && treeCanvas.ap == aps[0])
192 associateLeavesMenu.setVisible(false);
196 associateLeavesMenu.setVisible(true);
199 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
201 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
204 associateLeavesMenu.removeAll();
206 JRadioButtonMenuItem item;
207 ButtonGroup buttonGroup = new ButtonGroup();
208 int i, iSize = aps.length;
209 final TreePanel thisTreePanel = this;
210 for (i = 0; i < iSize; i++)
212 final AlignmentPanel ap = aps[i];
213 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
214 buttonGroup.add(item);
215 item.addActionListener(new ActionListener()
218 public void actionPerformed(ActionEvent evt)
220 treeCanvas.applyToAllViews = false;
222 treeCanvas.av = ap.av;
223 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
227 associateLeavesMenu.add(item);
230 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
231 MessageManager.getString("label.all_views"));
232 buttonGroup.add(itemf);
233 itemf.setSelected(treeCanvas.applyToAllViews);
234 itemf.addActionListener(new ActionListener()
237 public void actionPerformed(ActionEvent evt)
239 treeCanvas.applyToAllViews = itemf.isSelected();
242 associateLeavesMenu.add(itemf);
246 class TreeLoader extends Thread
248 private NewickFile newtree;
250 private AlignmentView odata = null;
252 public TreeLoader(NewickFile newickFile, AlignmentView inputData)
254 this.newtree = newickFile;
255 this.odata = inputData;
257 if (newickFile != null)
259 // Must be outside run(), as Jalview2XML tries to
260 // update distance/bootstrap visibility at the same time
261 showBootstrap(newickFile.hasBootstrap());
262 showDistances(newickFile.hasDistances());
274 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
276 if (tree.getOriginalData() == null)
278 originalSeqData.setVisible(false);
281 ArchaeopteryxInit archae = new ArchaeopteryxInit(newtree);
282 archae.startArchaeopteryx();
287 ScoreModelI sm = ScoreModels.getInstance()
288 .getScoreModel(scoreModelName, treeCanvas.ap);
289 TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
290 ? new NJTree(av, sm, similarityParams)
291 : new AverageDistanceTree(av, sm, similarityParams);
292 tree = new TreeModel(njtree);
295 ArchaeopteryxInit archae = new ArchaeopteryxInit(tree);
296 archae.startArchaeopteryx();
300 tree.reCount(tree.getTopNode());
301 tree.findHeight(tree.getTopNode());
302 treeCanvas.setTree(tree);
303 treeCanvas.repaint();
305 av.setCurrentTree(tree);
306 if (av.getSortByTree())
308 sortByTree_actionPerformed();
313 public void showDistances(boolean b)
315 treeCanvas.setShowDistances(b);
316 distanceMenu.setSelected(b);
319 public void showBootstrap(boolean b)
321 treeCanvas.setShowBootstrap(b);
322 bootstrapMenu.setSelected(b);
325 public void showPlaceholders(boolean b)
327 placeholdersMenu.setState(b);
328 treeCanvas.setMarkPlaceholders(b);
334 * @return DOCUMENT ME!
336 public TreeModel getTree()
348 public void textbox_actionPerformed(ActionEvent e)
350 CutAndPasteTransfer cap = new CutAndPasteTransfer();
352 String newTitle = getPanelTitle();
354 NewickFile fout = new NewickFile(tree.getTopNode());
357 cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
358 tree.hasRootDistance()));
359 Desktop.addInternalFrame(cap, newTitle, 500, 100);
360 } catch (OutOfMemoryError oom)
362 new OOMWarning("generating newick tree file", oom);
375 public void saveAsNewick_actionPerformed(ActionEvent e)
377 JalviewFileChooser chooser = new JalviewFileChooser(
378 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
379 chooser.setFileView(new JalviewFileView());
380 chooser.setDialogTitle(
381 MessageManager.getString("label.save_tree_as_newick"));
382 chooser.setToolTipText(MessageManager.getString("action.save"));
384 int value = chooser.showSaveDialog(null);
386 if (value == JalviewFileChooser.APPROVE_OPTION)
388 String choice = chooser.getSelectedFile().getPath();
389 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
390 chooser.getSelectedFile().getParent());
394 jalview.io.NewickFile fout = new jalview.io.NewickFile(
396 String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
397 tree.hasRootDistance());
398 java.io.PrintWriter out = new java.io.PrintWriter(
399 new java.io.FileWriter(choice));
402 } catch (Exception ex)
404 ex.printStackTrace();
416 public void printMenu_actionPerformed(ActionEvent e)
418 // Putting in a thread avoids Swing painting problems
419 treeCanvas.startPrinting();
423 public void originalSeqData_actionPerformed(ActionEvent e)
425 AlignmentView originalData = tree.getOriginalData();
426 if (originalData == null)
428 jalview.bin.Cache.log.info(
429 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
432 // decide if av alignment is sufficiently different to original data to
433 // warrant a new window to be created
434 // create new alignmnt window with hidden regions (unhiding hidden regions
435 // yields unaligned seqs)
436 // or create a selection box around columns in alignment view
437 // test Alignment(SeqCigar[])
441 // we try to get the associated view's gap character
442 // but this may fail if the view was closed...
443 gc = av.getGapCharacter();
445 } catch (Exception ex)
449 Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
451 if (alAndColsel != null && alAndColsel[0] != null)
453 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
455 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
456 AlignmentI dataset = (av != null && av.getAlignment() != null)
457 ? av.getAlignment().getDataset()
461 al.setDataset(dataset);
467 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
468 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
470 // >>>This is a fix for the moment, until a better solution is
472 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
474 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
477 Desktop.addInternalFrame(af, MessageManager.formatMessage(
478 "label.original_data_for_params", new Object[]
479 { this.title }), AlignFrame.DEFAULT_WIDTH,
480 AlignFrame.DEFAULT_HEIGHT);
492 public void fitToWindow_actionPerformed(ActionEvent e)
494 treeCanvas.fitToWindow = fitToWindow.isSelected();
499 * sort the associated alignment view by the current tree.
504 public void sortByTree_actionPerformed()
507 if (treeCanvas.applyToAllViews)
509 final ArrayList<CommandI> commands = new ArrayList<>();
510 for (AlignmentPanel ap : PaintRefresher
511 .getAssociatedPanels(av.getSequenceSetId()))
513 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
515 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
519 public void undoCommand(AlignmentI[] views)
521 for (CommandI tsort : commands)
523 tsort.undoCommand(views);
530 return commands.size();
534 public String getDescription()
536 return "Tree Sort (many views)";
540 public void doCommand(AlignmentI[] views)
543 for (CommandI tsort : commands)
545 tsort.doCommand(views);
549 for (AlignmentPanel ap : PaintRefresher
550 .getAssociatedPanels(av.getSequenceSetId()))
552 // ensure all the alignFrames refresh their GI after adding an undo item
553 ap.alignFrame.updateEditMenuBar();
558 treeCanvas.ap.alignFrame
559 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
564 public CommandI sortAlignmentIn(AlignmentPanel ap)
566 AlignmentViewport viewport = ap.av;
567 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
568 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
570 undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
572 ap.paintAlignment(true);
583 public void font_actionPerformed(ActionEvent e)
585 if (treeCanvas == null)
590 new FontChooser(this);
593 public Font getTreeFont()
595 return treeCanvas.font;
598 public void setTreeFont(Font f)
600 if (treeCanvas != null)
602 treeCanvas.setFont(f);
613 public void distanceMenu_actionPerformed(ActionEvent e)
615 treeCanvas.setShowDistances(distanceMenu.isSelected());
625 public void bootstrapMenu_actionPerformed(ActionEvent e)
627 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
637 public void placeholdersMenu_actionPerformed(ActionEvent e)
639 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
649 public void epsTree_actionPerformed(ActionEvent e)
651 boolean accurateText = true;
653 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
656 // If we need to prompt, and if the GUI is visible then
657 // Prompt for EPS rendering style
658 if (renderStyle.equalsIgnoreCase("Prompt each time")
659 && !(System.getProperty("java.awt.headless") != null && System
660 .getProperty("java.awt.headless").equals("true")))
662 EPSOptions eps = new EPSOptions();
663 renderStyle = eps.getValue();
665 if (renderStyle == null || eps.cancelled)
672 if (renderStyle.equalsIgnoreCase("text"))
674 accurateText = false;
677 int width = treeCanvas.getWidth();
678 int height = treeCanvas.getHeight();
682 JalviewFileChooser chooser = new JalviewFileChooser(
683 ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
684 chooser.setFileView(new JalviewFileView());
685 chooser.setDialogTitle(
686 MessageManager.getString("label.create_eps_from_tree"));
687 chooser.setToolTipText(MessageManager.getString("action.save"));
689 int value = chooser.showSaveDialog(this);
691 if (value != JalviewFileChooser.APPROVE_OPTION)
696 Cache.setProperty("LAST_DIRECTORY",
697 chooser.getSelectedFile().getParent());
699 FileOutputStream out = new FileOutputStream(
700 chooser.getSelectedFile());
701 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
704 pg.setAccurateTextMode(accurateText);
706 treeCanvas.draw(pg, width, height);
710 } catch (Exception ex)
712 ex.printStackTrace();
723 public void pngTree_actionPerformed(ActionEvent e)
725 int width = treeCanvas.getWidth();
726 int height = treeCanvas.getHeight();
730 JalviewFileChooser chooser = new JalviewFileChooser(
731 ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
733 chooser.setFileView(new jalview.io.JalviewFileView());
734 chooser.setDialogTitle(
735 MessageManager.getString("label.create_png_from_tree"));
736 chooser.setToolTipText(MessageManager.getString("action.save"));
738 int value = chooser.showSaveDialog(this);
740 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
745 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
746 chooser.getSelectedFile().getParent());
748 FileOutputStream out = new FileOutputStream(
749 chooser.getSelectedFile());
751 BufferedImage bi = new BufferedImage(width, height,
752 BufferedImage.TYPE_INT_RGB);
753 Graphics png = bi.getGraphics();
755 treeCanvas.draw(png, width, height);
757 ImageIO.write(bi, "png", out);
759 } catch (Exception ex)
761 ex.printStackTrace();
766 * change node labels to the annotation referred to by labelClass TODO:
767 * promote to a datamodel modification that can be undone TODO: make argument
768 * one case of a generic transformation function ie { undoStep = apply(Tree,
769 * TransformFunction)};
773 public void changeNames(final String labelClass)
775 tree.applyToNodes(new NodeTransformI()
779 public void transform(BinaryNode node)
781 if (node instanceof SequenceNode
782 && !((SequenceNode) node).isPlaceholder()
783 && !((SequenceNode) node).isDummy())
785 String newname = null;
786 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
789 // search dbrefs, features and annotation
790 DBRefEntry[] refs = jalview.util.DBRefUtils
791 .selectRefs(sq.getDBRefs(), new String[]
792 { labelClass.toUpperCase() });
795 for (int i = 0; i < refs.length; i++)
799 newname = new String(refs[i].getAccessionId());
803 newname = newname + "; " + refs[i].getAccessionId();
809 List<SequenceFeature> features = sq.getFeatures()
810 .getPositionalFeatures(labelClass);
811 for (SequenceFeature feature : features)
815 newname = feature.getDescription();
819 newname = newname + "; " + feature.getDescription();
826 // String oldname = ((SequenceNode) node).getName();
827 // TODO : save oldname in the undo object for this modification.
828 ((SequenceNode) node).setName(newname);
836 * Formats a localised title for the tree panel, like
838 * Neighbour Joining Using BLOSUM62
840 * For a tree loaded from file, just uses the file name
844 public String getPanelTitle()
846 if (treeTitle != null)
852 * i18n description of Neighbour Joining or Average Distance method
854 String treecalcnm = MessageManager
855 .getString("label.tree_calc_" + treeType.toLowerCase());
858 * short score model name (long description can be too long)
860 String smn = scoreModelName;
863 * put them together as <method> Using <model>
865 final String ttl = MessageManager.formatMessage("label.treecalc_title",