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.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.DBRefUtils;
  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       public void propertyChange(PropertyChangeEvent evt)
 166       {
 167         if (evt.getPropertyName().equals("alignment"))
 168         {
 169           if (tree == null)
 170           {
 171             System.out.println("tree is null");
 172             // TODO: deal with case when a change event is received whilst a
 173             // tree is still being calculated - should save reference for
 174             // processing message later.
 175             return;
 176           }
 177           if (evt.getNewValue() == null)
 178           {
 179             System.out
 180                     .println("new alignment sequences vector value is null");
 181           }
 182
 183           tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
 184           treeCanvas.nameHash.clear(); // reset the mapping between canvas
 185           // rectangles and leafnodes
 186           repaint();
 187         }
 188       }
 189     });
 190
 191     TreeLoader tl = new TreeLoader(newTree);
 192     if (inputData != null)
 193     {
 194       tl.odata = inputData;
 195     }
 196     tl.start();
 197
 198   }
 199
 200   public void viewMenu_menuSelected()
 201   {
 202     buildAssociatedViewMenu();
 203   }
 204
 205   void buildAssociatedViewMenu()
 206   {
 207     AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
 208             .getSequenceSetId());
 209     if (aps.length == 1 && treeCanvas.ap == aps[0])
 210     {
 211       associateLeavesMenu.setVisible(false);
 212       return;
 213     }
 214
 215     associateLeavesMenu.setVisible(true);
 216
 217     if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
 218     {
 219       viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
 220     }
 221
 222     associateLeavesMenu.removeAll();
 223
 224     JRadioButtonMenuItem item;
 225     ButtonGroup buttonGroup = new ButtonGroup();
 226     int i, iSize = aps.length;
 227     final TreePanel thisTreePanel = this;
 228     for (i = 0; i < iSize; i++)
 229     {
 230       final AlignmentPanel ap = aps[i];
 231       item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
 232       buttonGroup.add(item);
 233       item.addActionListener(new ActionListener()
 234       {
 235         public void actionPerformed(ActionEvent evt)
 236         {
 237           treeCanvas.applyToAllViews = false;
 238           treeCanvas.ap = ap;
 239           treeCanvas.av = ap.av;
 240           PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
 241         }
 242       });
 243
 244       associateLeavesMenu.add(item);
 245     }
 246
 247     final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
 248             "label.all_views");
 249     buttonGroup.add(itemf);
 250     itemf.setSelected(treeCanvas.applyToAllViews);
 251     itemf.addActionListener(new ActionListener()
 252     {
 253       public void actionPerformed(ActionEvent evt)
 254       {
 255         treeCanvas.applyToAllViews = itemf.isSelected();
 256       }
 257     });
 258     associateLeavesMenu.add(itemf);
 259
 260   }
 261
 262   class TreeLoader extends Thread
 263   {
 264     NewickFile newtree;
 265
 266     AlignmentView odata = null;
 267
 268     public TreeLoader(NewickFile newtree)
 269     {
 270       this.newtree = newtree;
 271       if (newtree != null)
 272       {
 273         // Must be outside run(), as Jalview2XML tries to
 274         // update distance/bootstrap visibility at the same time
 275         showBootstrap(newtree.HasBootstrap());
 276         showDistances(newtree.HasDistances());
 277       }
 278     }
 279
 280     public void run()
 281     {
 282
 283       if (newtree != null)
 284       {
 285         if (odata == null)
 286         {
 287           tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
 288         }
 289         else
 290         {
 291           tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
 292                   newtree);
 293         }
 294         if (!tree.hasOriginalSequenceData())
 295         {
 296           allowOriginalSeqData(false);
 297         }
 298       }
 299       else
 300       {
 301         int start, end;
 302         SequenceI[] seqs;
 303         boolean selview = av.getSelectionGroup() != null
 304                 && av.getSelectionGroup().getSize() > 1;
 305         AlignmentView seqStrings = av.getAlignmentView(selview);
 306         if (!selview)
 307         {
 308           start = 0;
 309           end = av.getAlignment().getWidth();
 310           seqs = av.getAlignment().getSequencesArray();
 311         }
 312         else
 313         {
 314           start = av.getSelectionGroup().getStartRes();
 315           end = av.getSelectionGroup().getEndRes() + 1;
 316           seqs = av.getSelectionGroup().getSequencesInOrder(
 317                   av.getAlignment());
 318         }
 319         ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
 320         if (sm instanceof ViewBasedAnalysisI)
 321         {
 322           try
 323           {
 324             sm = sm.getClass().newInstance();
 325             ((ViewBasedAnalysisI) sm)
 326                     .configureFromAlignmentView(treeCanvas.ap);
 327           } catch (Exception q)
 328           {
 329             Cache.log.error("Couldn't create a scoremodel instance for "
 330                     + sm.getName());
 331           }
 332           tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
 333         }
 334         else
 335         {
 336           tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
 337                   end);
 338         }
 339         showDistances(true);
 340       }
 341
 342       tree.reCount(tree.getTopNode());
 343       tree.findHeight(tree.getTopNode());
 344       treeCanvas.setTree(tree);
 345       treeCanvas.repaint();
 346       av.setCurrentTree(tree);
 347       if (av.getSortByTree())
 348       {
 349         sortByTree_actionPerformed();
 350       }
 351     }
 352   }
 353
 354   public void showDistances(boolean b)
 355   {
 356     treeCanvas.setShowDistances(b);
 357     distanceMenu.setSelected(b);
 358   }
 359
 360   public void showBootstrap(boolean b)
 361   {
 362     treeCanvas.setShowBootstrap(b);
 363     bootstrapMenu.setSelected(b);
 364   }
 365
 366   public void showPlaceholders(boolean b)
 367   {
 368     placeholdersMenu.setState(b);
 369     treeCanvas.setMarkPlaceholders(b);
 370   }
 371
 372   private void allowOriginalSeqData(boolean b)
 373   {
 374     originalSeqData.setVisible(b);
 375   }
 376
 377   /**
 378    * DOCUMENT ME!
 379    *
 380    * @return DOCUMENT ME!
 381    */
 382   public NJTree getTree()
 383   {
 384     return tree;
 385   }
 386
 387   /**
 388    * DOCUMENT ME!
 389    *
 390    * @param e
 391    *          DOCUMENT ME!
 392    */
 393   public void textbox_actionPerformed(ActionEvent e)
 394   {
 395     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 396
 397     StringBuffer buffer = new StringBuffer();
 398
 399     if (type.equals("AV"))
 400     {
 401       buffer.append("Average distance tree using ");
 402     }
 403     else
 404     {
 405       buffer.append("Neighbour joining tree using ");
 406     }
 407
 408     if (pwtype.equals("BL"))
 409     {
 410       buffer.append("BLOSUM62");
 411     }
 412     else
 413     {
 414       buffer.append("PID");
 415     }
 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   public void saveAsNewick_actionPerformed(ActionEvent e)
 438   {
 439     JalviewFileChooser chooser = new JalviewFileChooser(
 440             Cache.getProperty("LAST_DIRECTORY"));
 441     chooser.setFileView(new JalviewFileView());
 442     chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
 443     chooser.setToolTipText(MessageManager.getString("action.save"));
 444
 445     int value = chooser.showSaveDialog(null);
 446
 447     if (value == JalviewFileChooser.APPROVE_OPTION)
 448     {
 449       String choice = chooser.getSelectedFile().getPath();
 450       Cache.setProperty("LAST_DIRECTORY", chooser
 451               .getSelectedFile().getParent());
 452
 453       try
 454       {
 455         NewickFile fout = new NewickFile(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       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     AlignmentViewport 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 = 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       JalviewFileChooser chooser = new JalviewFileChooser(
 734               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 != JalviewFileChooser.APPROVE_OPTION)
 744       {
 745         return;
 746       }
 747
 748       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       JalviewFileChooser chooser = new JalviewFileChooser(
 780               Cache.getProperty("LAST_DIRECTORY"), new String[]
 781               { "png" }, new String[]
 782               { "Portable network graphics" }, "Portable network graphics");
 783
 784       chooser.setFileView(new 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 != JalviewFileChooser.APPROVE_OPTION)
 791       {
 792         return;
 793       }
 794
 795       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 = 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 }