2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
3 * Copyright (C) 2015 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.NJTree;
25 import jalview.api.analysis.ScoreModelI;
26 import jalview.api.analysis.ViewBasedAnalysisI;
27 import jalview.bin.Cache;
28 import jalview.commands.CommandI;
29 import jalview.commands.OrderCommand;
30 import jalview.datamodel.Alignment;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.AlignmentView;
33 import jalview.datamodel.BinaryNode;
34 import jalview.datamodel.ColumnSelection;
35 import jalview.datamodel.DBRefEntry;
36 import jalview.datamodel.NodeTransformI;
37 import jalview.datamodel.SequenceFeature;
38 import jalview.datamodel.SequenceI;
39 import jalview.datamodel.SequenceNode;
40 import jalview.io.JalviewFileChooser;
41 import jalview.io.JalviewFileView;
42 import jalview.io.NewickFile;
43 import jalview.jbgui.GTreePanel;
44 import jalview.schemes.ResidueProperties;
45 import jalview.util.MessageManager;
46 import jalview.viewmodel.AlignmentViewport;
49 import java.awt.Graphics;
50 import java.awt.event.ActionEvent;
51 import java.awt.event.ActionListener;
52 import java.awt.image.BufferedImage;
53 import java.beans.PropertyChangeEvent;
54 import java.io.FileOutputStream;
55 import java.util.ArrayList;
56 import java.util.List;
58 import javax.imageio.ImageIO;
59 import javax.swing.ButtonGroup;
60 import javax.swing.JMenuItem;
61 import javax.swing.JRadioButtonMenuItem;
63 import org.jibble.epsgraphics.EpsGraphics2D;
71 public class TreePanel extends GTreePanel
77 TreeCanvas treeCanvas;
84 * Creates a new TreePanel object.
99 public TreePanel(AlignmentPanel ap, String type, String pwtype)
102 initTreePanel(ap, type, pwtype, null, null);
104 // We know this tree has distances. JBPNote TODO: prolly should add this as
105 // a userdefined default
106 // showDistances(true);
110 * Creates a new TreePanel object.
123 public TreePanel(AlignmentPanel ap, String type, String pwtype,
127 initTreePanel(ap, type, pwtype, newtree, null);
130 public TreePanel(AlignmentPanel av, String type, String pwtype,
131 NewickFile newtree, AlignmentView inputData)
134 initTreePanel(av, type, pwtype, newtree, inputData);
137 public AlignmentI getAlignment()
139 return treeCanvas.av.getAlignment();
142 public AlignmentViewport getViewPort()
144 return treeCanvas.av;
147 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
148 NewickFile newTree, AlignmentView inputData)
153 this.pwtype = pwtype;
155 treeCanvas = new TreeCanvas(this, ap, scrollPane);
156 scrollPane.setViewportView(treeCanvas);
158 PaintRefresher.Register(this, ap.av.getSequenceSetId());
160 buildAssociatedViewMenu();
162 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
164 public void propertyChange(PropertyChangeEvent evt)
166 if (evt.getPropertyName().equals("alignment"))
170 System.out.println("tree is null");
171 // TODO: deal with case when a change event is received whilst a
172 // tree is still being calculated - should save reference for
173 // processing message later.
176 if (evt.getNewValue() == null)
179 .println("new alignment sequences vector value is null");
182 tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
183 treeCanvas.nameHash.clear(); // reset the mapping between canvas
184 // rectangles and leafnodes
190 TreeLoader tl = new TreeLoader(newTree);
191 if (inputData != null)
193 tl.odata = inputData;
199 public void viewMenu_menuSelected()
201 buildAssociatedViewMenu();
204 void buildAssociatedViewMenu()
206 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
207 .getSequenceSetId());
208 if (aps.length == 1 && treeCanvas.ap == aps[0])
210 associateLeavesMenu.setVisible(false);
214 associateLeavesMenu.setVisible(true);
216 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
218 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
221 associateLeavesMenu.removeAll();
223 JRadioButtonMenuItem item;
224 ButtonGroup buttonGroup = new ButtonGroup();
225 int i, iSize = aps.length;
226 final TreePanel thisTreePanel = this;
227 for (i = 0; i < iSize; i++)
229 final AlignmentPanel ap = aps[i];
230 item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
231 buttonGroup.add(item);
232 item.addActionListener(new ActionListener()
234 public void actionPerformed(ActionEvent evt)
236 treeCanvas.applyToAllViews = false;
238 treeCanvas.av = ap.av;
239 PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
243 associateLeavesMenu.add(item);
246 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
247 MessageManager.getString("label.all_views"));
248 buttonGroup.add(itemf);
249 itemf.setSelected(treeCanvas.applyToAllViews);
250 itemf.addActionListener(new ActionListener()
252 public void actionPerformed(ActionEvent evt)
254 treeCanvas.applyToAllViews = itemf.isSelected();
257 associateLeavesMenu.add(itemf);
261 class TreeLoader extends Thread
265 jalview.datamodel.AlignmentView odata = null;
267 public TreeLoader(NewickFile newtree)
269 this.newtree = newtree;
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());
286 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
290 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
293 if (!tree.hasOriginalSequenceData())
295 allowOriginalSeqData(false);
302 boolean selview = av.getSelectionGroup() != null
303 && av.getSelectionGroup().getSize() > 1;
304 AlignmentView seqStrings = av.getAlignmentView(selview);
308 end = av.getAlignment().getWidth();
309 seqs = av.getAlignment().getSequencesArray();
313 start = av.getSelectionGroup().getStartRes();
314 end = av.getSelectionGroup().getEndRes() + 1;
315 seqs = av.getSelectionGroup().getSequencesInOrder(
318 ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
319 if (sm instanceof ViewBasedAnalysisI)
323 sm = sm.getClass().newInstance();
324 ((ViewBasedAnalysisI) sm)
325 .configureFromAlignmentView(treeCanvas.ap);
326 } catch (Exception q)
328 Cache.log.error("Couldn't create a scoremodel instance for "
331 tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
335 tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
341 tree.reCount(tree.getTopNode());
342 tree.findHeight(tree.getTopNode());
343 treeCanvas.setTree(tree);
344 treeCanvas.repaint();
345 av.setCurrentTree(tree);
346 if (av.getSortByTree())
348 sortByTree_actionPerformed();
353 public void showDistances(boolean b)
355 treeCanvas.setShowDistances(b);
356 distanceMenu.setSelected(b);
359 public void showBootstrap(boolean b)
361 treeCanvas.setShowBootstrap(b);
362 bootstrapMenu.setSelected(b);
365 public void showPlaceholders(boolean b)
367 placeholdersMenu.setState(b);
368 treeCanvas.setMarkPlaceholders(b);
371 private void allowOriginalSeqData(boolean b)
373 originalSeqData.setVisible(b);
379 * @return DOCUMENT ME!
381 public NJTree getTree()
392 public void textbox_actionPerformed(ActionEvent e)
394 CutAndPasteTransfer cap = new CutAndPasteTransfer();
396 StringBuffer buffer = new StringBuffer();
398 if (type.equals("AV"))
400 buffer.append("Average distance tree using ");
404 buffer.append("Neighbour joining tree using ");
407 if (pwtype.equals("BL"))
409 buffer.append("BLOSUM62");
413 buffer.append("PID");
416 jalview.io.NewickFile fout = new jalview.io.NewickFile(
420 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
421 tree.isHasRootDistance()));
422 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
423 } catch (OutOfMemoryError oom)
425 new OOMWarning("generating newick tree file", oom);
437 public void saveAsNewick_actionPerformed(ActionEvent e)
439 JalviewFileChooser chooser = new JalviewFileChooser(
440 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
441 chooser.setFileView(new JalviewFileView());
442 chooser.setDialogTitle(MessageManager
443 .getString("label.save_tree_as_newick"));
444 chooser.setToolTipText(MessageManager.getString("action.save"));
446 int value = chooser.showSaveDialog(null);
448 if (value == JalviewFileChooser.APPROVE_OPTION)
450 String choice = chooser.getSelectedFile().getPath();
451 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
452 .getSelectedFile().getParent());
456 jalview.io.NewickFile fout = new jalview.io.NewickFile(
458 String output = fout.print(tree.isHasBootstrap(),
459 tree.isHasDistances(), tree.isHasRootDistance());
460 java.io.PrintWriter out = new java.io.PrintWriter(
461 new java.io.FileWriter(choice));
464 } catch (Exception ex)
466 ex.printStackTrace();
477 public void printMenu_actionPerformed(ActionEvent e)
479 // Putting in a thread avoids Swing painting problems
480 treeCanvas.startPrinting();
483 public void originalSeqData_actionPerformed(ActionEvent e)
485 if (!tree.hasOriginalSequenceData())
487 jalview.bin.Cache.log
488 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
491 // decide if av alignment is sufficiently different to original data to
492 // warrant a new window to be created
493 // create new alignmnt window with hidden regions (unhiding hidden regions
494 // yields unaligned seqs)
495 // or create a selection box around columns in alignment view
496 // test Alignment(SeqCigar[])
500 // we try to get the associated view's gap character
501 // but this may fail if the view was closed...
502 gc = av.getGapCharacter();
504 } catch (Exception ex)
508 Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
510 if (alAndColsel != null && alAndColsel[0] != null)
512 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
514 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
515 Alignment dataset = (av != null && av.getAlignment() != null) ? av
516 .getAlignment().getDataset() : null;
519 al.setDataset(dataset);
525 AlignFrame af = new AlignFrame(al,
526 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
527 AlignFrame.DEFAULT_HEIGHT);
529 // >>>This is a fix for the moment, until a better solution is
531 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
533 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
536 Desktop.addInternalFrame(af, MessageManager.formatMessage(
537 "label.original_data_for_params",
538 new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
539 AlignFrame.DEFAULT_HEIGHT);
550 public void fitToWindow_actionPerformed(ActionEvent e)
552 treeCanvas.fitToWindow = fitToWindow.isSelected();
557 * sort the associated alignment view by the current tree.
562 public void sortByTree_actionPerformed()
565 if (treeCanvas.applyToAllViews)
567 final ArrayList<CommandI> commands = new ArrayList<CommandI>();
568 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
569 .getSequenceSetId()))
571 commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
573 av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
577 public void undoCommand(AlignmentI[] views)
579 for (CommandI tsort : commands)
581 tsort.undoCommand(views);
588 return commands.size();
592 public String getDescription()
594 return "Tree Sort (many views)";
598 public void doCommand(AlignmentI[] views)
601 for (CommandI tsort : commands)
603 tsort.doCommand(views);
607 for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
608 .getSequenceSetId()))
610 // ensure all the alignFrames refresh their GI after adding an undo item
611 ap.alignFrame.updateEditMenuBar();
616 treeCanvas.ap.alignFrame
617 .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
622 public CommandI sortAlignmentIn(AlignmentPanel ap)
624 AlignmentViewport av = ap.av;
625 SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
626 AlignmentSorter.sortByTree(av.getAlignment(), tree);
628 undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
630 ap.paintAlignment(true);
640 public void font_actionPerformed(ActionEvent e)
642 if (treeCanvas == null)
647 new FontChooser(this);
650 public Font getTreeFont()
652 return treeCanvas.font;
655 public void setTreeFont(Font font)
657 if (treeCanvas != null)
659 treeCanvas.setFont(font);
669 public void distanceMenu_actionPerformed(ActionEvent e)
671 treeCanvas.setShowDistances(distanceMenu.isSelected());
680 public void bootstrapMenu_actionPerformed(ActionEvent e)
682 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
691 public void placeholdersMenu_actionPerformed(ActionEvent e)
693 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
702 public void epsTree_actionPerformed(ActionEvent e)
704 boolean accurateText = true;
706 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
709 // If we need to prompt, and if the GUI is visible then
710 // Prompt for EPS rendering style
711 if (renderStyle.equalsIgnoreCase("Prompt each time")
712 && !(System.getProperty("java.awt.headless") != null && System
713 .getProperty("java.awt.headless").equals("true")))
715 EPSOptions eps = new EPSOptions();
716 renderStyle = eps.getValue();
718 if (renderStyle == null || eps.cancelled)
725 if (renderStyle.equalsIgnoreCase("text"))
727 accurateText = false;
730 int width = treeCanvas.getWidth();
731 int height = treeCanvas.getHeight();
735 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
736 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
737 { "eps" }, new String[] { "Encapsulated Postscript" },
738 "Encapsulated Postscript");
739 chooser.setFileView(new jalview.io.JalviewFileView());
740 chooser.setDialogTitle(MessageManager
741 .getString("label.create_eps_from_tree"));
742 chooser.setToolTipText(MessageManager.getString("action.save"));
744 int value = chooser.showSaveDialog(this);
746 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
751 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
752 .getSelectedFile().getParent());
754 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
755 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
757 pg.setAccurateTextMode(accurateText);
759 treeCanvas.draw(pg, width, height);
763 } catch (Exception ex)
765 ex.printStackTrace();
775 public void pngTree_actionPerformed(ActionEvent e)
777 int width = treeCanvas.getWidth();
778 int height = treeCanvas.getHeight();
782 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
783 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
784 { "png" }, new String[] { "Portable network graphics" },
785 "Portable network graphics");
787 chooser.setFileView(new jalview.io.JalviewFileView());
788 chooser.setDialogTitle(MessageManager
789 .getString("label.create_png_from_tree"));
790 chooser.setToolTipText(MessageManager.getString("action.save"));
792 int value = chooser.showSaveDialog(this);
794 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
799 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
800 .getSelectedFile().getParent());
802 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
804 BufferedImage bi = new BufferedImage(width, height,
805 BufferedImage.TYPE_INT_RGB);
806 Graphics png = bi.getGraphics();
808 treeCanvas.draw(png, width, height);
810 ImageIO.write(bi, "png", out);
812 } catch (Exception ex)
814 ex.printStackTrace();
819 * change node labels to the annotation referred to by labelClass TODO:
820 * promote to a datamodel modification that can be undone TODO: make argument
821 * one case of a generic transformation function ie { undoStep = apply(Tree,
822 * TransformFunction)};
826 public void changeNames(final String labelClass)
828 tree.applyToNodes(new NodeTransformI()
831 public void transform(BinaryNode node)
833 if (node instanceof SequenceNode
834 && !((SequenceNode) node).isPlaceholder()
835 && !((SequenceNode) node).isDummy())
837 String newname = null;
838 SequenceI sq = (SequenceI) ((SequenceNode) node).element();
841 // search dbrefs, features and annotation
842 DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
844 new String[] { labelClass.toUpperCase() });
847 for (int i = 0; i < refs.length; i++)
851 newname = new String(refs[i].getAccessionId());
855 newname = newname + "; " + refs[i].getAccessionId();
861 SequenceFeature sf[] = sq.getSequenceFeatures();
862 for (int i = 0; sf != null && i < sf.length; i++)
864 if (sf[i].getType().equals(labelClass))
868 newname = new String(sf[i].getDescription());
872 newname = newname + "; " + sf[i].getDescription();
880 String oldname = ((SequenceNode) node).getName();
881 // TODO : save in the undo object for this modification.
882 ((SequenceNode) node).setName(newname);