src/jalview/gui/TreePanel.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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.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
  47 import java.awt.Font;
  48 import java.awt.Graphics;
  49 import java.awt.event.ActionEvent;
  50 import java.awt.event.ActionListener;
  51 import java.awt.image.BufferedImage;
  52 import java.beans.PropertyChangeEvent;
  53 import java.io.FileOutputStream;
  54 import java.util.ArrayList;
  55 import java.util.List;
  56
  57 import javax.imageio.ImageIO;
  58 import javax.swing.ButtonGroup;
  59 import javax.swing.JMenuItem;
  60 import javax.swing.JRadioButtonMenuItem;
  61
  62 import org.jibble.epsgraphics.EpsGraphics2D;
  63
  64 /**
  65  * DOCUMENT ME!
  66  *
  67  * @author $author$
  68  * @version $Revision$
  69  */
  70 public class TreePanel extends GTreePanel
  71 {
  72   String type;
  73
  74   String pwtype;
  75
  76   TreeCanvas treeCanvas;
  77
  78   NJTree tree;
  79
  80   AlignViewport av;
  81
  82   /**
  83    * Creates a new TreePanel object.
  84    *
  85    * @param av
  86    *          DOCUMENT ME!
  87    * @param seqVector
  88    *          DOCUMENT ME!
  89    * @param type
  90    *          DOCUMENT ME!
  91    * @param pwtype
  92    *          DOCUMENT ME!
  93    * @param s
  94    *          DOCUMENT ME!
  95    * @param e
  96    *          DOCUMENT ME!
  97    */
  98   public TreePanel(AlignmentPanel ap, String type, String pwtype)
  99   {
 100     super();
 101     initTreePanel(ap, type, pwtype, null, null);
 102
 103     // We know this tree has distances. JBPNote TODO: prolly should add this as
 104     // a userdefined default
 105     // showDistances(true);
 106   }
 107
 108   /**
 109    * Creates a new TreePanel object.
 110    *
 111    * @param av
 112    *          DOCUMENT ME!
 113    * @param seqVector
 114    *          DOCUMENT ME!
 115    * @param newtree
 116    *          DOCUMENT ME!
 117    * @param type
 118    *          DOCUMENT ME!
 119    * @param pwtype
 120    *          DOCUMENT ME!
 121    */
 122   public TreePanel(AlignmentPanel ap, String type, String pwtype,
 123           NewickFile newtree)
 124   {
 125     super();
 126     initTreePanel(ap, type, pwtype, newtree, null);
 127   }
 128
 129   public TreePanel(AlignmentPanel av, String type, String pwtype,
 130           NewickFile newtree, AlignmentView inputData)
 131   {
 132     super();
 133     initTreePanel(av, type, pwtype, newtree, inputData);
 134   }
 135
 136   public AlignmentI getAlignment()
 137   {
 138     return treeCanvas.av.getAlignment();
 139   }
 140
 141   public AlignViewport getViewPort()
 142   {
 143     return treeCanvas.av;
 144   }
 145
 146   void initTreePanel(AlignmentPanel ap, String type, String pwtype,
 147           NewickFile newTree, AlignmentView inputData)
 148   {
 149
 150     av = ap.av;
 151     this.type = type;
 152     this.pwtype = pwtype;
 153
 154     treeCanvas = new TreeCanvas(this, ap, scrollPane);
 155     scrollPane.setViewportView(treeCanvas);
 156
 157     PaintRefresher.Register(this, ap.av.getSequenceSetId());
 158
 159     buildAssociatedViewMenu();
 160
 161     av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
 162     {
 163       public void propertyChange(PropertyChangeEvent evt)
 164       {
 165         if (evt.getPropertyName().equals("alignment"))
 166         {
 167           if (tree == null)
 168           {
 169             System.out.println("tree is null");
 170             // TODO: deal with case when a change event is received whilst a
 171             // tree is still being calculated - should save reference for
 172             // processing message later.
 173             return;
 174           }
 175           if (evt.getNewValue() == null)
 176           {
 177             System.out
 178                     .println("new alignment sequences vector value is null");
 179           }
 180
 181           tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
 182           treeCanvas.nameHash.clear(); // reset the mapping between canvas
 183           // rectangles and leafnodes
 184           repaint();
 185         }
 186       }
 187     });
 188
 189     TreeLoader tl = new TreeLoader(newTree);
 190     if (inputData != null)
 191     {
 192       tl.odata = inputData;
 193     }
 194     tl.start();
 195
 196   }
 197
 198   public void viewMenu_menuSelected()
 199   {
 200     buildAssociatedViewMenu();
 201   }
 202
 203   void buildAssociatedViewMenu()
 204   {
 205     AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
 206             .getSequenceSetId());
 207     if (aps.length == 1 && treeCanvas.ap == aps[0])
 208     {
 209       associateLeavesMenu.setVisible(false);
 210       return;
 211     }
 212
 213     associateLeavesMenu.setVisible(true);
 214
 215     if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
 216     {
 217       viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
 218     }
 219
 220     associateLeavesMenu.removeAll();
 221
 222     JRadioButtonMenuItem item;
 223     ButtonGroup buttonGroup = new ButtonGroup();
 224     int i, iSize = aps.length;
 225     final TreePanel thisTreePanel = this;
 226     for (i = 0; i < iSize; i++)
 227     {
 228       final AlignmentPanel ap = aps[i];
 229       item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
 230       buttonGroup.add(item);
 231       item.addActionListener(new ActionListener()
 232       {
 233         public void actionPerformed(ActionEvent evt)
 234         {
 235           treeCanvas.applyToAllViews = false;
 236           treeCanvas.ap = ap;
 237           treeCanvas.av = ap.av;
 238           PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
 239         }
 240       });
 241
 242       associateLeavesMenu.add(item);
 243     }
 244
 245     final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
 246             "label.all_views");
 247     buttonGroup.add(itemf);
 248     itemf.setSelected(treeCanvas.applyToAllViews);
 249     itemf.addActionListener(new ActionListener()
 250     {
 251       public void actionPerformed(ActionEvent evt)
 252       {
 253         treeCanvas.applyToAllViews = itemf.isSelected();
 254       }
 255     });
 256     associateLeavesMenu.add(itemf);
 257
 258   }
 259
 260   class TreeLoader extends Thread
 261   {
 262     NewickFile newtree;
 263
 264     jalview.datamodel.AlignmentView odata = null;
 265
 266     public TreeLoader(NewickFile newtree)
 267     {
 268       this.newtree = newtree;
 269       if (newtree != null)
 270       {
 271         // Must be outside run(), as Jalview2XML tries to
 272         // update distance/bootstrap visibility at the same time
 273         showBootstrap(newtree.HasBootstrap());
 274         showDistances(newtree.HasDistances());
 275       }
 276     }
 277
 278     public void run()
 279     {
 280
 281       if (newtree != null)
 282       {
 283         if (odata == null)
 284         {
 285           tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
 286         }
 287         else
 288         {
 289           tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
 290                   newtree);
 291         }
 292         if (!tree.hasOriginalSequenceData())
 293         {
 294           allowOriginalSeqData(false);
 295         }
 296       }
 297       else
 298       {
 299         int start, end;
 300         SequenceI[] seqs;
 301         boolean selview = av.getSelectionGroup() != null
 302                 && av.getSelectionGroup().getSize() > 1;
 303         AlignmentView seqStrings = av.getAlignmentView(selview);
 304         if (!selview)
 305         {
 306           start = 0;
 307           end = av.getAlignment().getWidth();
 308           seqs = av.getAlignment().getSequencesArray();
 309         }
 310         else
 311         {
 312           start = av.getSelectionGroup().getStartRes();
 313           end = av.getSelectionGroup().getEndRes() + 1;
 314           seqs = av.getSelectionGroup().getSequencesInOrder(
 315                   av.getAlignment());
 316         }
 317         ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
 318         if (sm instanceof ViewBasedAnalysisI)
 319         {
 320           try
 321           {
 322             sm = sm.getClass().newInstance();
 323             ((ViewBasedAnalysisI) sm)
 324                     .configureFromAlignmentView(treeCanvas.ap);
 325           } catch (Exception q)
 326           {
 327             Cache.log.error("Couldn't create a scoremodel instance for "
 328                     + sm.getName());
 329           }
 330           tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
 331         }
 332         else
 333         {
 334           tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
 335                   end);
 336         }
 337         showDistances(true);
 338       }
 339
 340       tree.reCount(tree.getTopNode());
 341       tree.findHeight(tree.getTopNode());
 342       treeCanvas.setTree(tree);
 343       treeCanvas.repaint();
 344       av.setCurrentTree(tree);
 345       if (av.getSortByTree())
 346       {
 347         sortByTree_actionPerformed();
 348       }
 349     }
 350   }
 351
 352   public void showDistances(boolean b)
 353   {
 354     treeCanvas.setShowDistances(b);
 355     distanceMenu.setSelected(b);
 356   }
 357
 358   public void showBootstrap(boolean b)
 359   {
 360     treeCanvas.setShowBootstrap(b);
 361     bootstrapMenu.setSelected(b);
 362   }
 363
 364   public void showPlaceholders(boolean b)
 365   {
 366     placeholdersMenu.setState(b);
 367     treeCanvas.setMarkPlaceholders(b);
 368   }
 369
 370   private void allowOriginalSeqData(boolean b)
 371   {
 372     originalSeqData.setVisible(b);
 373   }
 374
 375   /**
 376    * DOCUMENT ME!
 377    *
 378    * @return DOCUMENT ME!
 379    */
 380   public NJTree getTree()
 381   {
 382     return tree;
 383   }
 384
 385   /**
 386    * DOCUMENT ME!
 387    *
 388    * @param e
 389    *          DOCUMENT ME!
 390    */
 391   public void textbox_actionPerformed(ActionEvent e)
 392   {
 393     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 394
 395     StringBuffer buffer = new StringBuffer();
 396
 397     if (type.equals("AV"))
 398     {
 399       buffer.append("Average distance tree using ");
 400     }
 401     else
 402     {
 403       buffer.append("Neighbour joining tree using ");
 404     }
 405
 406     if (pwtype.equals("BL"))
 407     {
 408       buffer.append("BLOSUM62");
 409     }
 410     else
 411     {
 412       buffer.append("PID");
 413     }
 414
 415     jalview.io.NewickFile fout = new jalview.io.NewickFile(
 416             tree.getTopNode());
 417     try
 418     {
 419       cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
 420               tree.isHasRootDistance()));
 421       Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 422     } catch (OutOfMemoryError oom)
 423     {
 424       new OOMWarning("generating newick tree file", oom);
 425       cap.dispose();
 426     }
 427
 428   }
 429
 430   /**
 431    * DOCUMENT ME!
 432    *
 433    * @param e
 434    *          DOCUMENT ME!
 435    */
 436   public void saveAsNewick_actionPerformed(ActionEvent e)
 437   {
 438     JalviewFileChooser chooser = new JalviewFileChooser(
 439             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 440     chooser.setFileView(new JalviewFileView());
 441     chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
 442     chooser.setToolTipText(MessageManager.getString("action.save"));
 443
 444     int value = chooser.showSaveDialog(null);
 445
 446     if (value == JalviewFileChooser.APPROVE_OPTION)
 447     {
 448       String choice = chooser.getSelectedFile().getPath();
 449       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
 450               .getSelectedFile().getParent());
 451
 452       try
 453       {
 454         jalview.io.NewickFile fout = new jalview.io.NewickFile(
 455                 tree.getTopNode());
 456         String output = fout.print(tree.isHasBootstrap(),
 457                 tree.isHasDistances(), tree.isHasRootDistance());
 458         java.io.PrintWriter out = new java.io.PrintWriter(
 459                 new java.io.FileWriter(choice));
 460         out.println(output);
 461         out.close();
 462       } catch (Exception ex)
 463       {
 464         ex.printStackTrace();
 465       }
 466     }
 467   }
 468
 469   /**
 470    * DOCUMENT ME!
 471    *
 472    * @param e
 473    *          DOCUMENT ME!
 474    */
 475   public void printMenu_actionPerformed(ActionEvent e)
 476   {
 477     // Putting in a thread avoids Swing painting problems
 478     treeCanvas.startPrinting();
 479   }
 480
 481   public void originalSeqData_actionPerformed(ActionEvent e)
 482   {
 483     if (!tree.hasOriginalSequenceData())
 484     {
 485       jalview.bin.Cache.log
 486               .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
 487       return;
 488     }
 489     // decide if av alignment is sufficiently different to original data to
 490     // warrant a new window to be created
 491     // create new alignmnt window with hidden regions (unhiding hidden regions
 492     // yields unaligned seqs)
 493     // or create a selection box around columns in alignment view
 494     // test Alignment(SeqCigar[])
 495     char gc = '-';
 496     try
 497     {
 498       // we try to get the associated view's gap character
 499       // but this may fail if the view was closed...
 500       gc = av.getGapCharacter();
 501
 502     } catch (Exception ex)
 503     {
 504     }
 505     ;
 506     Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
 507
 508     if (alAndColsel != null && alAndColsel[0] != null)
 509     {
 510       // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 511
 512       Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
 513       Alignment dataset = (av != null && av.getAlignment() != null) ? av
 514               .getAlignment().getDataset() : null;
 515       if (dataset != null)
 516       {
 517         al.setDataset(dataset);
 518       }
 519
 520       if (true)
 521       {
 522         // make a new frame!
 523         AlignFrame af = new AlignFrame(al,
 524                 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
 525                 AlignFrame.DEFAULT_HEIGHT);
 526
 527         // >>>This is a fix for the moment, until a better solution is
 528         // found!!<<<
 529         // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
 530
 531         // af.addSortByOrderMenuItem(ServiceName + " Ordering",
 532         // msaorder);
 533
 534         Desktop.addInternalFrame(af, MessageManager.formatMessage(
 535                 "label.original_data_for_params", new Object[]
 536                 { this.title }), AlignFrame.DEFAULT_WIDTH,
 537                 AlignFrame.DEFAULT_HEIGHT);
 538       }
 539     }
 540   }
 541
 542   /**
 543    * DOCUMENT ME!
 544    *
 545    * @param e
 546    *          DOCUMENT ME!
 547    */
 548   public void fitToWindow_actionPerformed(ActionEvent e)
 549   {
 550     treeCanvas.fitToWindow = fitToWindow.isSelected();
 551     repaint();
 552   }
 553
 554   /**
 555    * sort the associated alignment view by the current tree.
 556    *
 557    * @param e
 558    */
 559   @Override
 560   public void sortByTree_actionPerformed()
 561   {
 562
 563     if (treeCanvas.applyToAllViews)
 564     {
 565       final ArrayList<CommandI> commands = new ArrayList<CommandI>();
 566       for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
 567               .getSequenceSetId()))
 568       {
 569         commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
 570       }
 571       av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
 572       {
 573
 574         @Override
 575         public void undoCommand(AlignmentI[] views)
 576         {
 577           for (CommandI tsort : commands)
 578           {
 579             tsort.undoCommand(views);
 580           }
 581         }
 582
 583         @Override
 584         public int getSize()
 585         {
 586           return commands.size();
 587         }
 588
 589         @Override
 590         public String getDescription()
 591         {
 592           return "Tree Sort (many views)";
 593         }
 594
 595         @Override
 596         public void doCommand(AlignmentI[] views)
 597         {
 598
 599           for (CommandI tsort : commands)
 600           {
 601             tsort.doCommand(views);
 602           }
 603         }
 604       });
 605       for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
 606               .getSequenceSetId()))
 607       {
 608         // ensure all the alignFrames refresh their GI after adding an undo item
 609         ap.alignFrame.updateEditMenuBar();
 610       }
 611     }
 612     else
 613     {
 614       treeCanvas.ap.alignFrame
 615               .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
 616     }
 617
 618   }
 619
 620   public CommandI sortAlignmentIn(AlignmentPanel ap)
 621   {
 622     AlignViewport av = ap.av;
 623     SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
 624     AlignmentSorter.sortByTree(av.getAlignment(), tree);
 625     CommandI undo;
 626     undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
 627
 628     ap.paintAlignment(true);
 629     return undo;
 630   }
 631
 632   /**
 633    * DOCUMENT ME!
 634    *
 635    * @param e
 636    *          DOCUMENT ME!
 637    */
 638   public void font_actionPerformed(ActionEvent e)
 639   {
 640     if (treeCanvas == null)
 641     {
 642       return;
 643     }
 644
 645     new FontChooser(this);
 646   }
 647
 648   public Font getTreeFont()
 649   {
 650     return treeCanvas.font;
 651   }
 652
 653   public void setTreeFont(Font font)
 654   {
 655     if (treeCanvas != null)
 656     {
 657       treeCanvas.setFont(font);
 658     }
 659   }
 660
 661   /**
 662    * DOCUMENT ME!
 663    *
 664    * @param e
 665    *          DOCUMENT ME!
 666    */
 667   public void distanceMenu_actionPerformed(ActionEvent e)
 668   {
 669     treeCanvas.setShowDistances(distanceMenu.isSelected());
 670   }
 671
 672   /**
 673    * DOCUMENT ME!
 674    *
 675    * @param e
 676    *          DOCUMENT ME!
 677    */
 678   public void bootstrapMenu_actionPerformed(ActionEvent e)
 679   {
 680     treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
 681   }
 682
 683   /**
 684    * DOCUMENT ME!
 685    *
 686    * @param e
 687    *          DOCUMENT ME!
 688    */
 689   public void placeholdersMenu_actionPerformed(ActionEvent e)
 690   {
 691     treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
 692   }
 693
 694   /**
 695    * DOCUMENT ME!
 696    *
 697    * @param e
 698    *          DOCUMENT ME!
 699    */
 700   public void epsTree_actionPerformed(ActionEvent e)
 701   {
 702     boolean accurateText = true;
 703
 704     String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
 705             "Prompt each time");
 706
 707     // If we need to prompt, and if the GUI is visible then
 708     // Prompt for EPS rendering style
 709     if (renderStyle.equalsIgnoreCase("Prompt each time")
 710             && !(System.getProperty("java.awt.headless") != null && System
 711                     .getProperty("java.awt.headless").equals("true")))
 712     {
 713       EPSOptions eps = new EPSOptions();
 714       renderStyle = eps.getValue();
 715
 716       if (renderStyle == null || eps.cancelled)
 717       {
 718         return;
 719       }
 720
 721     }
 722
 723     if (renderStyle.equalsIgnoreCase("text"))
 724     {
 725       accurateText = false;
 726     }
 727
 728     int width = treeCanvas.getWidth();
 729     int height = treeCanvas.getHeight();
 730
 731     try
 732     {
 733       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 734               jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
 735               { "eps" }, new String[]
 736               { "Encapsulated Postscript" }, "Encapsulated Postscript");
 737       chooser.setFileView(new jalview.io.JalviewFileView());
 738       chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
 739       chooser.setToolTipText(MessageManager.getString("action.save"));
 740
 741       int value = chooser.showSaveDialog(this);
 742
 743       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
 744       {
 745         return;
 746       }
 747
 748       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
 749               .getSelectedFile().getParent());
 750
 751       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 752       EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
 753
 754       pg.setAccurateTextMode(accurateText);
 755
 756       treeCanvas.draw(pg, width, height);
 757
 758       pg.flush();
 759       pg.close();
 760     } catch (Exception ex)
 761     {
 762       ex.printStackTrace();
 763     }
 764   }
 765
 766   /**
 767    * DOCUMENT ME!
 768    *
 769    * @param e
 770    *          DOCUMENT ME!
 771    */
 772   public void pngTree_actionPerformed(ActionEvent e)
 773   {
 774     int width = treeCanvas.getWidth();
 775     int height = treeCanvas.getHeight();
 776
 777     try
 778     {
 779       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 780               jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
 781               { "png" }, new String[]
 782               { "Portable network graphics" }, "Portable network graphics");
 783
 784       chooser.setFileView(new jalview.io.JalviewFileView());
 785       chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
 786       chooser.setToolTipText(MessageManager.getString("action.save"));
 787
 788       int value = chooser.showSaveDialog(this);
 789
 790       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
 791       {
 792         return;
 793       }
 794
 795       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
 796               .getSelectedFile().getParent());
 797
 798       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 799
 800       BufferedImage bi = new BufferedImage(width, height,
 801               BufferedImage.TYPE_INT_RGB);
 802       Graphics png = bi.getGraphics();
 803
 804       treeCanvas.draw(png, width, height);
 805
 806       ImageIO.write(bi, "png", out);
 807       out.close();
 808     } catch (Exception ex)
 809     {
 810       ex.printStackTrace();
 811     }
 812   }
 813
 814   /**
 815    * change node labels to the annotation referred to by labelClass TODO:
 816    * promote to a datamodel modification that can be undone TODO: make argument
 817    * one case of a generic transformation function ie { undoStep = apply(Tree,
 818    * TransformFunction)};
 819    *
 820    * @param labelClass
 821    */
 822   public void changeNames(final String labelClass)
 823   {
 824     tree.applyToNodes(new NodeTransformI()
 825     {
 826
 827       public void transform(BinaryNode node)
 828       {
 829         if (node instanceof SequenceNode
 830                 && !((SequenceNode) node).isPlaceholder()
 831                 && !((SequenceNode) node).isDummy())
 832         {
 833           String newname = null;
 834           SequenceI sq = (SequenceI) ((SequenceNode) node).element();
 835           if (sq != null)
 836           {
 837             // search dbrefs, features and annotation
 838             DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
 839                     sq.getDBRef(), new String[]
 840                     { labelClass.toUpperCase() });
 841             if (refs != null)
 842             {
 843               for (int i = 0; i < refs.length; i++)
 844               {
 845                 if (newname == null)
 846                 {
 847                   newname = new String(refs[i].getAccessionId());
 848                 }
 849                 else
 850                 {
 851                   newname = newname + "; " + refs[i].getAccessionId();
 852                 }
 853               }
 854             }
 855             if (newname == null)
 856             {
 857               SequenceFeature sf[] = sq.getSequenceFeatures();
 858               for (int i = 0; sf != null && i < sf.length; i++)
 859               {
 860                 if (sf[i].getType().equals(labelClass))
 861                 {
 862                   if (newname == null)
 863                   {
 864                     newname = new String(sf[i].getDescription());
 865                   }
 866                   else
 867                   {
 868                     newname = newname + "; " + sf[i].getDescription();
 869                   }
 870                 }
 871               }
 872             }
 873           }
 874           if (newname != null)
 875           {
 876             String oldname = ((SequenceNode) node).getName();
 877             // TODO : save in the undo object for this modification.
 878             ((SequenceNode) node).setName(newname);
 879           }
 880         }
 881       }
 882     });
 883   }
 884 }