src/jalview/gui/TreePanel.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   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.
  11  *
  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.
  16  *
  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.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.NJTree;
  25 import jalview.analysis.scoremodels.ScoreModels;
  26 import jalview.api.analysis.ScoreModelI;
  27 import jalview.api.analysis.ViewBasedAnalysisI;
  28 import jalview.bin.Cache;
  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.ColumnSelection;
  36 import jalview.datamodel.DBRefEntry;
  37 import jalview.datamodel.NodeTransformI;
  38 import jalview.datamodel.SequenceFeature;
  39 import jalview.datamodel.SequenceI;
  40 import jalview.datamodel.SequenceNode;
  41 import jalview.io.JalviewFileChooser;
  42 import jalview.io.JalviewFileView;
  43 import jalview.io.NewickFile;
  44 import jalview.jbgui.GTreePanel;
  45 import jalview.util.ImageMaker;
  46 import jalview.util.MessageManager;
  47 import jalview.viewmodel.AlignmentViewport;
  48
  49 import java.awt.Font;
  50 import java.awt.Graphics;
  51 import java.awt.event.ActionEvent;
  52 import java.awt.event.ActionListener;
  53 import java.awt.image.BufferedImage;
  54 import java.beans.PropertyChangeEvent;
  55 import java.io.FileOutputStream;
  56 import java.util.ArrayList;
  57 import java.util.List;
  58
  59 import javax.imageio.ImageIO;
  60 import javax.swing.ButtonGroup;
  61 import javax.swing.JMenuItem;
  62 import javax.swing.JRadioButtonMenuItem;
  63
  64 import org.jibble.epsgraphics.EpsGraphics2D;
  65
  66 /**
  67  * DOCUMENT ME!
  68  *
  69  * @author $author$
  70  * @version $Revision$
  71  */
  72 public class TreePanel extends GTreePanel
  73 {
  74   String type;
  75
  76   String pwtype;
  77
  78   TreeCanvas treeCanvas;
  79
  80   NJTree tree;
  81
  82   AlignViewport av;
  83
  84   /**
  85    * Creates a new TreePanel object.
  86    *
  87    * @param av
  88    *          DOCUMENT ME!
  89    * @param seqVector
  90    *          DOCUMENT ME!
  91    * @param type
  92    *          DOCUMENT ME!
  93    * @param pwtype
  94    *          DOCUMENT ME!
  95    * @param s
  96    *          DOCUMENT ME!
  97    * @param e
  98    *          DOCUMENT ME!
  99    */
 100   public TreePanel(AlignmentPanel ap, String type, String pwtype)
 101   {
 102     super();
 103     initTreePanel(ap, type, pwtype, null, null);
 104
 105     // We know this tree has distances. JBPNote TODO: prolly should add this as
 106     // a userdefined default
 107     // showDistances(true);
 108   }
 109
 110   /**
 111    * Creates a new TreePanel object.
 112    *
 113    * @param av
 114    *          DOCUMENT ME!
 115    * @param seqVector
 116    *          DOCUMENT ME!
 117    * @param newtree
 118    *          DOCUMENT ME!
 119    * @param type
 120    *          DOCUMENT ME!
 121    * @param pwtype
 122    *          DOCUMENT ME!
 123    */
 124   public TreePanel(AlignmentPanel ap, String type, String pwtype,
 125           NewickFile newtree)
 126   {
 127     super();
 128     initTreePanel(ap, type, pwtype, newtree, null);
 129   }
 130
 131   public TreePanel(AlignmentPanel av, String type, String pwtype,
 132           NewickFile newtree, AlignmentView inputData)
 133   {
 134     super();
 135     initTreePanel(av, type, pwtype, newtree, inputData);
 136   }
 137
 138   public AlignmentI getAlignment()
 139   {
 140     return treeCanvas.av.getAlignment();
 141   }
 142
 143   public AlignmentViewport getViewPort()
 144   {
 145     return treeCanvas.av;
 146   }
 147
 148   void initTreePanel(AlignmentPanel ap, String type, String pwtype,
 149           NewickFile newTree, AlignmentView inputData)
 150   {
 151
 152     av = ap.av;
 153     this.type = type;
 154     this.pwtype = pwtype;
 155
 156     treeCanvas = new TreeCanvas(this, ap, scrollPane);
 157     scrollPane.setViewportView(treeCanvas);
 158
 159     PaintRefresher.Register(this, ap.av.getSequenceSetId());
 160
 161     buildAssociatedViewMenu();
 162
 163     av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
 164     {
 165       @Override
 166       public void propertyChange(PropertyChangeEvent evt)
 167       {
 168         if (evt.getPropertyName().equals("alignment"))
 169         {
 170           if (tree == null)
 171           {
 172             System.out.println("tree is null");
 173             // TODO: deal with case when a change event is received whilst a
 174             // tree is still being calculated - should save reference for
 175             // processing message later.
 176             return;
 177           }
 178           if (evt.getNewValue() == null)
 179           {
 180             System.out
 181                     .println("new alignment sequences vector value is null");
 182           }
 183
 184           tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
 185           treeCanvas.nameHash.clear(); // reset the mapping between canvas
 186           // rectangles and leafnodes
 187           repaint();
 188         }
 189       }
 190     });
 191
 192     TreeLoader tl = new TreeLoader(newTree);
 193     if (inputData != null)
 194     {
 195       tl.odata = inputData;
 196     }
 197     tl.start();
 198
 199   }
 200
 201   @Override
 202   public void viewMenu_menuSelected()
 203   {
 204     buildAssociatedViewMenu();
 205   }
 206
 207   void buildAssociatedViewMenu()
 208   {
 209     AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
 210             .getSequenceSetId());
 211     if (aps.length == 1 && treeCanvas.ap == aps[0])
 212     {
 213       associateLeavesMenu.setVisible(false);
 214       return;
 215     }
 216
 217     associateLeavesMenu.setVisible(true);
 218
 219     if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
 220     {
 221       viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
 222     }
 223
 224     associateLeavesMenu.removeAll();
 225
 226     JRadioButtonMenuItem item;
 227     ButtonGroup buttonGroup = new ButtonGroup();
 228     int i, iSize = aps.length;
 229     final TreePanel thisTreePanel = this;
 230     for (i = 0; i < iSize; i++)
 231     {
 232       final AlignmentPanel ap = aps[i];
 233       item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
 234       buttonGroup.add(item);
 235       item.addActionListener(new ActionListener()
 236       {
 237         @Override
 238         public void actionPerformed(ActionEvent evt)
 239         {
 240           treeCanvas.applyToAllViews = false;
 241           treeCanvas.ap = ap;
 242           treeCanvas.av = ap.av;
 243           PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
 244         }
 245       });
 246
 247       associateLeavesMenu.add(item);
 248     }
 249
 250     final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
 251             MessageManager.getString("label.all_views"));
 252     buttonGroup.add(itemf);
 253     itemf.setSelected(treeCanvas.applyToAllViews);
 254     itemf.addActionListener(new ActionListener()
 255     {
 256       @Override
 257       public void actionPerformed(ActionEvent evt)
 258       {
 259         treeCanvas.applyToAllViews = itemf.isSelected();
 260       }
 261     });
 262     associateLeavesMenu.add(itemf);
 263
 264   }
 265
 266   class TreeLoader extends Thread
 267   {
 268     NewickFile newtree;
 269
 270     jalview.datamodel.AlignmentView odata = null;
 271
 272     public TreeLoader(NewickFile newtree)
 273     {
 274       this.newtree = newtree;
 275       if (newtree != null)
 276       {
 277         // Must be outside run(), as Jalview2XML tries to
 278         // update distance/bootstrap visibility at the same time
 279         showBootstrap(newtree.HasBootstrap());
 280         showDistances(newtree.HasDistances());
 281       }
 282     }
 283
 284     @Override
 285     public void run()
 286     {
 287
 288       if (newtree != null)
 289       {
 290         if (odata == null)
 291         {
 292           tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
 293         }
 294         else
 295         {
 296           tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
 297                   newtree);
 298         }
 299         if (!tree.hasOriginalSequenceData())
 300         {
 301           allowOriginalSeqData(false);
 302         }
 303       }
 304       else
 305       {
 306         int start, end;
 307         SequenceI[] seqs;
 308         boolean selview = av.getSelectionGroup() != null
 309                 && av.getSelectionGroup().getSize() > 1;
 310         AlignmentView seqStrings = av.getAlignmentView(selview);
 311         if (!selview)
 312         {
 313           start = 0;
 314           end = av.getAlignment().getWidth();
 315           seqs = av.getAlignment().getSequencesArray();
 316         }
 317         else
 318         {
 319           start = av.getSelectionGroup().getStartRes();
 320           end = av.getSelectionGroup().getEndRes() + 1;
 321           seqs = av.getSelectionGroup().getSequencesInOrder(
 322                   av.getAlignment());
 323         }
 324         ScoreModelI sm = ScoreModels.getInstance().forName(pwtype);
 325         if (sm instanceof ViewBasedAnalysisI)
 326         {
 327           try
 328           {
 329             sm = sm.getClass().newInstance();
 330             ((ViewBasedAnalysisI) sm)
 331                     .configureFromAlignmentView(treeCanvas.ap);
 332           } catch (Exception q)
 333           {
 334             Cache.log.error("Couldn't create a scoremodel instance for "
 335                     + sm.getName());
 336           }
 337           tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
 338         }
 339         else
 340         {
 341           tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
 342                   end);
 343         }
 344         showDistances(true);
 345       }
 346
 347       tree.reCount(tree.getTopNode());
 348       tree.findHeight(tree.getTopNode());
 349       treeCanvas.setTree(tree);
 350       treeCanvas.repaint();
 351       av.setCurrentTree(tree);
 352       if (av.getSortByTree())
 353       {
 354         sortByTree_actionPerformed();
 355       }
 356     }
 357   }
 358
 359   public void showDistances(boolean b)
 360   {
 361     treeCanvas.setShowDistances(b);
 362     distanceMenu.setSelected(b);
 363   }
 364
 365   public void showBootstrap(boolean b)
 366   {
 367     treeCanvas.setShowBootstrap(b);
 368     bootstrapMenu.setSelected(b);
 369   }
 370
 371   public void showPlaceholders(boolean b)
 372   {
 373     placeholdersMenu.setState(b);
 374     treeCanvas.setMarkPlaceholders(b);
 375   }
 376
 377   private void allowOriginalSeqData(boolean b)
 378   {
 379     originalSeqData.setVisible(b);
 380   }
 381
 382   /**
 383    * DOCUMENT ME!
 384    *
 385    * @return DOCUMENT ME!
 386    */
 387   public NJTree getTree()
 388   {
 389     return tree;
 390   }
 391
 392   /**
 393    * DOCUMENT ME!
 394    *
 395    * @param e
 396    *          DOCUMENT ME!
 397    */
 398   @Override
 399   public void textbox_actionPerformed(ActionEvent e)
 400   {
 401     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 402
 403     StringBuffer buffer = new StringBuffer();
 404
 405     if (type.equals(NJTree.AVERAGE_DISTANCE))
 406     {
 407       buffer.append("Average distance tree using ");
 408     }
 409     else
 410     {
 411       buffer.append("Neighbour joining tree using ");
 412     }
 413
 414     ScoreModelI sm = ScoreModels.getInstance().forName(pwtype);
 415     buffer.append(sm.getName());
 416
 417     NewickFile fout = new NewickFile(tree.getTopNode());
 418     try
 419     {
 420       cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
 421               tree.isHasRootDistance()));
 422       Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 423     } catch (OutOfMemoryError oom)
 424     {
 425       new OOMWarning("generating newick tree file", oom);
 426       cap.dispose();
 427     }
 428
 429   }
 430
 431   /**
 432    * DOCUMENT ME!
 433    *
 434    * @param e
 435    *          DOCUMENT ME!
 436    */
 437   @Override
 438   public void saveAsNewick_actionPerformed(ActionEvent e)
 439   {
 440     JalviewFileChooser chooser = new JalviewFileChooser(
 441             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 442     chooser.setFileView(new JalviewFileView());
 443     chooser.setDialogTitle(MessageManager
 444             .getString("label.save_tree_as_newick"));
 445     chooser.setToolTipText(MessageManager.getString("action.save"));
 446
 447     int value = chooser.showSaveDialog(null);
 448
 449     if (value == JalviewFileChooser.APPROVE_OPTION)
 450     {
 451       String choice = chooser.getSelectedFile().getPath();
 452       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
 453               .getSelectedFile().getParent());
 454
 455       try
 456       {
 457         jalview.io.NewickFile fout = new jalview.io.NewickFile(
 458                 tree.getTopNode());
 459         String output = fout.print(tree.isHasBootstrap(),
 460                 tree.isHasDistances(), tree.isHasRootDistance());
 461         java.io.PrintWriter out = new java.io.PrintWriter(
 462                 new java.io.FileWriter(choice));
 463         out.println(output);
 464         out.close();
 465       } catch (Exception ex)
 466       {
 467         ex.printStackTrace();
 468       }
 469     }
 470   }
 471
 472   /**
 473    * DOCUMENT ME!
 474    *
 475    * @param e
 476    *          DOCUMENT ME!
 477    */
 478   @Override
 479   public void printMenu_actionPerformed(ActionEvent e)
 480   {
 481     // Putting in a thread avoids Swing painting problems
 482     treeCanvas.startPrinting();
 483   }
 484
 485   @Override
 486   public void originalSeqData_actionPerformed(ActionEvent e)
 487   {
 488     if (!tree.hasOriginalSequenceData())
 489     {
 490       jalview.bin.Cache.log
 491               .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
 492       return;
 493     }
 494     // decide if av alignment is sufficiently different to original data to
 495     // warrant a new window to be created
 496     // create new alignmnt window with hidden regions (unhiding hidden regions
 497     // yields unaligned seqs)
 498     // or create a selection box around columns in alignment view
 499     // test Alignment(SeqCigar[])
 500     char gc = '-';
 501     try
 502     {
 503       // we try to get the associated view's gap character
 504       // but this may fail if the view was closed...
 505       gc = av.getGapCharacter();
 506
 507     } catch (Exception ex)
 508     {
 509     }
 510     ;
 511     Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
 512
 513     if (alAndColsel != null && alAndColsel[0] != null)
 514     {
 515       // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 516
 517       AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
 518       AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
 519               .getAlignment().getDataset() : null;
 520       if (dataset != null)
 521       {
 522         al.setDataset(dataset);
 523       }
 524
 525       if (true)
 526       {
 527         // make a new frame!
 528         AlignFrame af = new AlignFrame(al,
 529                 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
 530                 AlignFrame.DEFAULT_HEIGHT);
 531
 532         // >>>This is a fix for the moment, until a better solution is
 533         // found!!<<<
 534         // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
 535
 536         // af.addSortByOrderMenuItem(ServiceName + " Ordering",
 537         // msaorder);
 538
 539         Desktop.addInternalFrame(af, MessageManager.formatMessage(
 540                 "label.original_data_for_params",
 541                 new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
 542                 AlignFrame.DEFAULT_HEIGHT);
 543       }
 544     }
 545   }
 546
 547   /**
 548    * DOCUMENT ME!
 549    *
 550    * @param e
 551    *          DOCUMENT ME!
 552    */
 553   @Override
 554   public void fitToWindow_actionPerformed(ActionEvent e)
 555   {
 556     treeCanvas.fitToWindow = fitToWindow.isSelected();
 557     repaint();
 558   }
 559
 560   /**
 561    * sort the associated alignment view by the current tree.
 562    *
 563    * @param e
 564    */
 565   @Override
 566   public void sortByTree_actionPerformed()
 567   {
 568
 569     if (treeCanvas.applyToAllViews)
 570     {
 571       final ArrayList<CommandI> commands = new ArrayList<CommandI>();
 572       for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
 573               .getSequenceSetId()))
 574       {
 575         commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
 576       }
 577       av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
 578       {
 579
 580         @Override
 581         public void undoCommand(AlignmentI[] views)
 582         {
 583           for (CommandI tsort : commands)
 584           {
 585             tsort.undoCommand(views);
 586           }
 587         }
 588
 589         @Override
 590         public int getSize()
 591         {
 592           return commands.size();
 593         }
 594
 595         @Override
 596         public String getDescription()
 597         {
 598           return "Tree Sort (many views)";
 599         }
 600
 601         @Override
 602         public void doCommand(AlignmentI[] views)
 603         {
 604
 605           for (CommandI tsort : commands)
 606           {
 607             tsort.doCommand(views);
 608           }
 609         }
 610       });
 611       for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
 612               .getSequenceSetId()))
 613       {
 614         // ensure all the alignFrames refresh their GI after adding an undo item
 615         ap.alignFrame.updateEditMenuBar();
 616       }
 617     }
 618     else
 619     {
 620       treeCanvas.ap.alignFrame
 621               .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
 622     }
 623
 624   }
 625
 626   public CommandI sortAlignmentIn(AlignmentPanel ap)
 627   {
 628     AlignmentViewport av = ap.av;
 629     SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
 630     AlignmentSorter.sortByTree(av.getAlignment(), tree);
 631     CommandI undo;
 632     undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
 633
 634     ap.paintAlignment(true);
 635     return undo;
 636   }
 637
 638   /**
 639    * DOCUMENT ME!
 640    *
 641    * @param e
 642    *          DOCUMENT ME!
 643    */
 644   @Override
 645   public void font_actionPerformed(ActionEvent e)
 646   {
 647     if (treeCanvas == null)
 648     {
 649       return;
 650     }
 651
 652     new FontChooser(this);
 653   }
 654
 655   public Font getTreeFont()
 656   {
 657     return treeCanvas.font;
 658   }
 659
 660   public void setTreeFont(Font font)
 661   {
 662     if (treeCanvas != null)
 663     {
 664       treeCanvas.setFont(font);
 665     }
 666   }
 667
 668   /**
 669    * DOCUMENT ME!
 670    *
 671    * @param e
 672    *          DOCUMENT ME!
 673    */
 674   @Override
 675   public void distanceMenu_actionPerformed(ActionEvent e)
 676   {
 677     treeCanvas.setShowDistances(distanceMenu.isSelected());
 678   }
 679
 680   /**
 681    * DOCUMENT ME!
 682    *
 683    * @param e
 684    *          DOCUMENT ME!
 685    */
 686   @Override
 687   public void bootstrapMenu_actionPerformed(ActionEvent e)
 688   {
 689     treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
 690   }
 691
 692   /**
 693    * DOCUMENT ME!
 694    *
 695    * @param e
 696    *          DOCUMENT ME!
 697    */
 698   @Override
 699   public void placeholdersMenu_actionPerformed(ActionEvent e)
 700   {
 701     treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
 702   }
 703
 704   /**
 705    * DOCUMENT ME!
 706    *
 707    * @param e
 708    *          DOCUMENT ME!
 709    */
 710   @Override
 711   public void epsTree_actionPerformed(ActionEvent e)
 712   {
 713     boolean accurateText = true;
 714
 715     String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
 716             "Prompt each time");
 717
 718     // If we need to prompt, and if the GUI is visible then
 719     // Prompt for EPS rendering style
 720     if (renderStyle.equalsIgnoreCase("Prompt each time")
 721             && !(System.getProperty("java.awt.headless") != null && System
 722                     .getProperty("java.awt.headless").equals("true")))
 723     {
 724       EPSOptions eps = new EPSOptions();
 725       renderStyle = eps.getValue();
 726
 727       if (renderStyle == null || eps.cancelled)
 728       {
 729         return;
 730       }
 731
 732     }
 733
 734     if (renderStyle.equalsIgnoreCase("text"))
 735     {
 736       accurateText = false;
 737     }
 738
 739     int width = treeCanvas.getWidth();
 740     int height = treeCanvas.getHeight();
 741
 742     try
 743     {
 744       JalviewFileChooser chooser = new JalviewFileChooser(
 745               ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
 746       chooser.setFileView(new JalviewFileView());
 747       chooser.setDialogTitle(MessageManager
 748               .getString("label.create_eps_from_tree"));
 749       chooser.setToolTipText(MessageManager.getString("action.save"));
 750
 751       int value = chooser.showSaveDialog(this);
 752
 753       if (value != JalviewFileChooser.APPROVE_OPTION)
 754       {
 755         return;
 756       }
 757
 758       Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile()
 759               .getParent());
 760
 761       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 762       EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
 763
 764       pg.setAccurateTextMode(accurateText);
 765
 766       treeCanvas.draw(pg, width, height);
 767
 768       pg.flush();
 769       pg.close();
 770     } catch (Exception ex)
 771     {
 772       ex.printStackTrace();
 773     }
 774   }
 775
 776   /**
 777    * DOCUMENT ME!
 778    *
 779    * @param e
 780    *          DOCUMENT ME!
 781    */
 782   @Override
 783   public void pngTree_actionPerformed(ActionEvent e)
 784   {
 785     int width = treeCanvas.getWidth();
 786     int height = treeCanvas.getHeight();
 787
 788     try
 789     {
 790       JalviewFileChooser chooser = new JalviewFileChooser(
 791               ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
 792
 793       chooser.setFileView(new jalview.io.JalviewFileView());
 794       chooser.setDialogTitle(MessageManager
 795               .getString("label.create_png_from_tree"));
 796       chooser.setToolTipText(MessageManager.getString("action.save"));
 797
 798       int value = chooser.showSaveDialog(this);
 799
 800       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
 801       {
 802         return;
 803       }
 804
 805       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
 806               .getSelectedFile().getParent());
 807
 808       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 809
 810       BufferedImage bi = new BufferedImage(width, height,
 811               BufferedImage.TYPE_INT_RGB);
 812       Graphics png = bi.getGraphics();
 813
 814       treeCanvas.draw(png, width, height);
 815
 816       ImageIO.write(bi, "png", out);
 817       out.close();
 818     } catch (Exception ex)
 819     {
 820       ex.printStackTrace();
 821     }
 822   }
 823
 824   /**
 825    * change node labels to the annotation referred to by labelClass TODO:
 826    * promote to a datamodel modification that can be undone TODO: make argument
 827    * one case of a generic transformation function ie { undoStep = apply(Tree,
 828    * TransformFunction)};
 829    *
 830    * @param labelClass
 831    */
 832   public void changeNames(final String labelClass)
 833   {
 834     tree.applyToNodes(new NodeTransformI()
 835     {
 836
 837       @Override
 838       public void transform(BinaryNode node)
 839       {
 840         if (node instanceof SequenceNode
 841                 && !((SequenceNode) node).isPlaceholder()
 842                 && !((SequenceNode) node).isDummy())
 843         {
 844           String newname = null;
 845           SequenceI sq = (SequenceI) ((SequenceNode) node).element();
 846           if (sq != null)
 847           {
 848             // search dbrefs, features and annotation
 849             DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
 850                     sq.getDBRefs(),
 851                     new String[] { labelClass.toUpperCase() });
 852             if (refs != null)
 853             {
 854               for (int i = 0; i < refs.length; i++)
 855               {
 856                 if (newname == null)
 857                 {
 858                   newname = new String(refs[i].getAccessionId());
 859                 }
 860                 else
 861                 {
 862                   newname = newname + "; " + refs[i].getAccessionId();
 863                 }
 864               }
 865             }
 866             if (newname == null)
 867             {
 868               SequenceFeature sf[] = sq.getSequenceFeatures();
 869               for (int i = 0; sf != null && i < sf.length; i++)
 870               {
 871                 if (sf[i].getType().equals(labelClass))
 872                 {
 873                   if (newname == null)
 874                   {
 875                     newname = new String(sf[i].getDescription());
 876                   }
 877                   else
 878                   {
 879                     newname = newname + "; " + sf[i].getDescription();
 880                   }
 881                 }
 882               }
 883             }
 884           }
 885           if (newname != null)
 886           {
 887             String oldname = ((SequenceNode) node).getName();
 888             // TODO : save in the undo object for this modification.
 889             ((SequenceNode) node).setName(newname);
 890           }
 891         }
 892       }
 893     });
 894   }
 895 }