src/jalview/gui/TreePanel.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   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("All Views");
 246     buttonGroup.add(itemf);
 247     itemf.setSelected(treeCanvas.applyToAllViews);
 248     itemf.addActionListener(new ActionListener()
 249     {
 250       public void actionPerformed(ActionEvent evt)
 251       {
 252         treeCanvas.applyToAllViews = itemf.isSelected();
 253       }
 254     });
 255     associateLeavesMenu.add(itemf);
 256
 257   }
 258
 259   class TreeLoader extends Thread
 260   {
 261     NewickFile newtree;
 262
 263     jalview.datamodel.AlignmentView odata = null;
 264
 265     public TreeLoader(NewickFile newtree)
 266     {
 267       this.newtree = newtree;
 268       if (newtree != null)
 269       {
 270         // Must be outside run(), as Jalview2XML tries to
 271         // update distance/bootstrap visibility at the same time
 272         showBootstrap(newtree.HasBootstrap());
 273         showDistances(newtree.HasDistances());
 274       }
 275     }
 276
 277     public void run()
 278     {
 279
 280       if (newtree != null)
 281       {
 282         if (odata == null)
 283         {
 284           tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
 285         }
 286         else
 287         {
 288           tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
 289                   newtree);
 290         }
 291         if (!tree.hasOriginalSequenceData())
 292         {
 293           allowOriginalSeqData(false);
 294         }
 295       }
 296       else
 297       {
 298         int start, end;
 299         SequenceI[] seqs;
 300         boolean selview = av.getSelectionGroup() != null
 301                 && av.getSelectionGroup().getSize() > 1;
 302         AlignmentView seqStrings = av.getAlignmentView(selview);
 303         if (!selview)
 304         {
 305           start = 0;
 306           end = av.getAlignment().getWidth();
 307           seqs = av.getAlignment().getSequencesArray();
 308         }
 309         else
 310         {
 311           start = av.getSelectionGroup().getStartRes();
 312           end = av.getSelectionGroup().getEndRes() + 1;
 313           seqs = av.getSelectionGroup().getSequencesInOrder(
 314                   av.getAlignment());
 315         }
 316         ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
 317         if (sm instanceof ViewBasedAnalysisI)
 318         {
 319           try
 320           {
 321             sm = sm.getClass().newInstance();
 322             ((ViewBasedAnalysisI) sm)
 323                     .configureFromAlignmentView(treeCanvas.ap);
 324           } catch (Exception q)
 325           {
 326             Cache.log.error("Couldn't create a scoremodel instance for "
 327                     + sm.getName());
 328           }
 329           tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
 330         }
 331         else
 332         {
 333           tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
 334                   end);
 335         }
 336         showDistances(true);
 337       }
 338
 339       tree.reCount(tree.getTopNode());
 340       tree.findHeight(tree.getTopNode());
 341       treeCanvas.setTree(tree);
 342       treeCanvas.repaint();
 343       av.setCurrentTree(tree);
 344       if (av.getSortByTree())
 345       {
 346         sortByTree_actionPerformed(null);
 347       }
 348     }
 349   }
 350
 351   public void showDistances(boolean b)
 352   {
 353     treeCanvas.setShowDistances(b);
 354     distanceMenu.setSelected(b);
 355   }
 356
 357   public void showBootstrap(boolean b)
 358   {
 359     treeCanvas.setShowBootstrap(b);
 360     bootstrapMenu.setSelected(b);
 361   }
 362
 363   public void showPlaceholders(boolean b)
 364   {
 365     placeholdersMenu.setState(b);
 366     treeCanvas.setMarkPlaceholders(b);
 367   }
 368
 369   private void allowOriginalSeqData(boolean b)
 370   {
 371     originalSeqData.setVisible(b);
 372   }
 373
 374   /**
 375    * DOCUMENT ME!
 376    *
 377    * @return DOCUMENT ME!
 378    */
 379   public NJTree getTree()
 380   {
 381     return tree;
 382   }
 383
 384   /**
 385    * DOCUMENT ME!
 386    *
 387    * @param e
 388    *          DOCUMENT ME!
 389    */
 390   public void textbox_actionPerformed(ActionEvent e)
 391   {
 392     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 393
 394     StringBuffer buffer = new StringBuffer();
 395
 396     if (type.equals("AV"))
 397     {
 398       buffer.append("Average distance tree using ");
 399     }
 400     else
 401     {
 402       buffer.append("Neighbour joining tree using ");
 403     }
 404
 405     if (pwtype.equals("BL"))
 406     {
 407       buffer.append("BLOSUM62");
 408     }
 409     else
 410     {
 411       buffer.append("PID");
 412     }
 413
 414     jalview.io.NewickFile fout = new jalview.io.NewickFile(
 415             tree.getTopNode());
 416     try
 417     {
 418       cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
 419               tree.isHasRootDistance()));
 420       Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 421     } catch (OutOfMemoryError oom)
 422     {
 423       new OOMWarning("generating newick tree file", oom);
 424       cap.dispose();
 425     }
 426
 427   }
 428
 429   /**
 430    * DOCUMENT ME!
 431    *
 432    * @param e
 433    *          DOCUMENT ME!
 434    */
 435   public void saveAsNewick_actionPerformed(ActionEvent e)
 436   {
 437     JalviewFileChooser chooser = new JalviewFileChooser(
 438             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 439     chooser.setFileView(new JalviewFileView());
 440     chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
 441     chooser.setToolTipText(MessageManager.getString("action.save"));
 442
 443     int value = chooser.showSaveDialog(null);
 444
 445     if (value == JalviewFileChooser.APPROVE_OPTION)
 446     {
 447       String choice = chooser.getSelectedFile().getPath();
 448       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
 449               .getSelectedFile().getParent());
 450
 451       try
 452       {
 453         jalview.io.NewickFile fout = new jalview.io.NewickFile(
 454                 tree.getTopNode());
 455         String output = fout.print(tree.isHasBootstrap(),
 456                 tree.isHasDistances(), tree.isHasRootDistance());
 457         java.io.PrintWriter out = new java.io.PrintWriter(
 458                 new java.io.FileWriter(choice));
 459         out.println(output);
 460         out.close();
 461       } catch (Exception ex)
 462       {
 463         ex.printStackTrace();
 464       }
 465     }
 466   }
 467
 468   /**
 469    * DOCUMENT ME!
 470    *
 471    * @param e
 472    *          DOCUMENT ME!
 473    */
 474   public void printMenu_actionPerformed(ActionEvent e)
 475   {
 476     // Putting in a thread avoids Swing painting problems
 477     treeCanvas.startPrinting();
 478   }
 479
 480   public void originalSeqData_actionPerformed(ActionEvent e)
 481   {
 482     if (!tree.hasOriginalSequenceData())
 483     {
 484       jalview.bin.Cache.log
 485               .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
 486       return;
 487     }
 488     // decide if av alignment is sufficiently different to original data to
 489     // warrant a new window to be created
 490     // create new alignmnt window with hidden regions (unhiding hidden regions
 491     // yields unaligned seqs)
 492     // or create a selection box around columns in alignment view
 493     // test Alignment(SeqCigar[])
 494     char gc = '-';
 495     try
 496     {
 497       // we try to get the associated view's gap character
 498       // but this may fail if the view was closed...
 499       gc = av.getGapCharacter();
 500
 501     } catch (Exception ex)
 502     {
 503     }
 504     ;
 505     Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
 506
 507     if (alAndColsel != null && alAndColsel[0] != null)
 508     {
 509       // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 510
 511       Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
 512       Alignment dataset = (av != null && av.getAlignment() != null) ? av
 513               .getAlignment().getDataset() : null;
 514       if (dataset != null)
 515       {
 516         al.setDataset(dataset);
 517       }
 518
 519       if (true)
 520       {
 521         // make a new frame!
 522         AlignFrame af = new AlignFrame(al,
 523                 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
 524                 AlignFrame.DEFAULT_HEIGHT);
 525
 526         // >>>This is a fix for the moment, until a better solution is
 527         // found!!<<<
 528         // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
 529
 530         // af.addSortByOrderMenuItem(ServiceName + " Ordering",
 531         // msaorder);
 532
 533         Desktop.addInternalFrame(af, MessageManager.formatMessage(
 534                 "label.original_data_for_params", new String[]
 535                 { this.title }), AlignFrame.DEFAULT_WIDTH,
 536                 AlignFrame.DEFAULT_HEIGHT);
 537       }
 538     }
 539   }
 540
 541   /**
 542    * DOCUMENT ME!
 543    *
 544    * @param e
 545    *          DOCUMENT ME!
 546    */
 547   public void fitToWindow_actionPerformed(ActionEvent e)
 548   {
 549     treeCanvas.fitToWindow = fitToWindow.isSelected();
 550     repaint();
 551   }
 552
 553   /**
 554    * sort the associated alignment view by the current tree.
 555    *
 556    * @param e
 557    */
 558   public void sortByTree_actionPerformed(ActionEvent e)
 559   {
 560
 561     if (treeCanvas.applyToAllViews)
 562     {
 563       final ArrayList<CommandI> commands = new ArrayList<CommandI>();
 564       for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
 565               .getSequenceSetId()))
 566       {
 567         commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
 568       }
 569       av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
 570       {
 571
 572         @Override
 573         public void undoCommand(AlignmentI[] views)
 574         {
 575           for (CommandI tsort : commands)
 576           {
 577             tsort.undoCommand(views);
 578           }
 579         }
 580
 581         @Override
 582         public int getSize()
 583         {
 584           return commands.size();
 585         }
 586
 587         @Override
 588         public String getDescription()
 589         {
 590           return "Tree Sort (many views)";
 591         }
 592
 593         @Override
 594         public void doCommand(AlignmentI[] views)
 595         {
 596
 597           for (CommandI tsort : commands)
 598           {
 599             tsort.doCommand(views);
 600           }
 601         }
 602       });
 603       for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
 604               .getSequenceSetId()))
 605       {
 606         // ensure all the alignFrames refresh their GI after adding an undo item
 607         ap.alignFrame.updateEditMenuBar();
 608       }
 609     }
 610     else
 611     {
 612       treeCanvas.ap.alignFrame
 613               .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
 614     }
 615
 616   }
 617
 618   public CommandI sortAlignmentIn(AlignmentPanel ap)
 619   {
 620     AlignViewport av = ap.av;
 621     SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
 622     AlignmentSorter.sortByTree(av.getAlignment(), tree);
 623     CommandI undo;
 624     undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
 625
 626     ap.paintAlignment(true);
 627     return undo;
 628   }
 629
 630   /**
 631    * DOCUMENT ME!
 632    *
 633    * @param e
 634    *          DOCUMENT ME!
 635    */
 636   public void font_actionPerformed(ActionEvent e)
 637   {
 638     if (treeCanvas == null)
 639     {
 640       return;
 641     }
 642
 643     new FontChooser(this);
 644   }
 645
 646   public Font getTreeFont()
 647   {
 648     return treeCanvas.font;
 649   }
 650
 651   public void setTreeFont(Font font)
 652   {
 653     if (treeCanvas != null)
 654     {
 655       treeCanvas.setFont(font);
 656     }
 657   }
 658
 659   /**
 660    * DOCUMENT ME!
 661    *
 662    * @param e
 663    *          DOCUMENT ME!
 664    */
 665   public void distanceMenu_actionPerformed(ActionEvent e)
 666   {
 667     treeCanvas.setShowDistances(distanceMenu.isSelected());
 668   }
 669
 670   /**
 671    * DOCUMENT ME!
 672    *
 673    * @param e
 674    *          DOCUMENT ME!
 675    */
 676   public void bootstrapMenu_actionPerformed(ActionEvent e)
 677   {
 678     treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
 679   }
 680
 681   /**
 682    * DOCUMENT ME!
 683    *
 684    * @param e
 685    *          DOCUMENT ME!
 686    */
 687   public void placeholdersMenu_actionPerformed(ActionEvent e)
 688   {
 689     treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
 690   }
 691
 692   /**
 693    * DOCUMENT ME!
 694    *
 695    * @param e
 696    *          DOCUMENT ME!
 697    */
 698   public void epsTree_actionPerformed(ActionEvent e)
 699   {
 700     boolean accurateText = true;
 701
 702     String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
 703             "Prompt each time");
 704
 705     // If we need to prompt, and if the GUI is visible then
 706     // Prompt for EPS rendering style
 707     if (renderStyle.equalsIgnoreCase("Prompt each time")
 708             && !(System.getProperty("java.awt.headless") != null && System
 709                     .getProperty("java.awt.headless").equals("true")))
 710     {
 711       EPSOptions eps = new EPSOptions();
 712       renderStyle = eps.getValue();
 713
 714       if (renderStyle == null || eps.cancelled)
 715       {
 716         return;
 717       }
 718
 719     }
 720
 721     if (renderStyle.equalsIgnoreCase("text"))
 722     {
 723       accurateText = false;
 724     }
 725
 726     int width = treeCanvas.getWidth();
 727     int height = treeCanvas.getHeight();
 728
 729     try
 730     {
 731       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 732               jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
 733               { "eps" }, new String[]
 734               { "Encapsulated Postscript" }, "Encapsulated Postscript");
 735       chooser.setFileView(new jalview.io.JalviewFileView());
 736       chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
 737       chooser.setToolTipText(MessageManager.getString("action.save"));
 738
 739       int value = chooser.showSaveDialog(this);
 740
 741       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
 742       {
 743         return;
 744       }
 745
 746       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
 747               .getSelectedFile().getParent());
 748
 749       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 750       EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
 751
 752       pg.setAccurateTextMode(accurateText);
 753
 754       treeCanvas.draw(pg, width, height);
 755
 756       pg.flush();
 757       pg.close();
 758     } catch (Exception ex)
 759     {
 760       ex.printStackTrace();
 761     }
 762   }
 763
 764   /**
 765    * DOCUMENT ME!
 766    *
 767    * @param e
 768    *          DOCUMENT ME!
 769    */
 770   public void pngTree_actionPerformed(ActionEvent e)
 771   {
 772     int width = treeCanvas.getWidth();
 773     int height = treeCanvas.getHeight();
 774
 775     try
 776     {
 777       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 778               jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
 779               { "png" }, new String[]
 780               { "Portable network graphics" }, "Portable network graphics");
 781
 782       chooser.setFileView(new jalview.io.JalviewFileView());
 783       chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
 784       chooser.setToolTipText(MessageManager.getString("action.save"));
 785
 786       int value = chooser.showSaveDialog(this);
 787
 788       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
 789       {
 790         return;
 791       }
 792
 793       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
 794               .getSelectedFile().getParent());
 795
 796       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 797
 798       BufferedImage bi = new BufferedImage(width, height,
 799               BufferedImage.TYPE_INT_RGB);
 800       Graphics png = bi.getGraphics();
 801
 802       treeCanvas.draw(png, width, height);
 803
 804       ImageIO.write(bi, "png", out);
 805       out.close();
 806     } catch (Exception ex)
 807     {
 808       ex.printStackTrace();
 809     }
 810   }
 811
 812   /**
 813    * change node labels to the annotation referred to by labelClass TODO:
 814    * promote to a datamodel modification that can be undone TODO: make argument
 815    * one case of a generic transformation function ie { undoStep = apply(Tree,
 816    * TransformFunction)};
 817    *
 818    * @param labelClass
 819    */
 820   public void changeNames(final String labelClass)
 821   {
 822     tree.applyToNodes(new NodeTransformI()
 823     {
 824
 825       public void transform(BinaryNode node)
 826       {
 827         if (node instanceof SequenceNode
 828                 && !((SequenceNode) node).isPlaceholder()
 829                 && !((SequenceNode) node).isDummy())
 830         {
 831           String newname = null;
 832           SequenceI sq = (SequenceI) ((SequenceNode) node).element();
 833           if (sq != null)
 834           {
 835             // search dbrefs, features and annotation
 836             DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
 837                     sq.getDBRef(), new String[]
 838                     { labelClass.toUpperCase() });
 839             if (refs != null)
 840             {
 841               for (int i = 0; i < refs.length; i++)
 842               {
 843                 if (newname == null)
 844                 {
 845                   newname = new String(refs[i].getAccessionId());
 846                 }
 847                 else
 848                 {
 849                   newname = newname + "; " + refs[i].getAccessionId();
 850                 }
 851               }
 852             }
 853             if (newname == null)
 854             {
 855               SequenceFeature sf[] = sq.getSequenceFeatures();
 856               for (int i = 0; sf != null && i < sf.length; i++)
 857               {
 858                 if (sf[i].getType().equals(labelClass))
 859                 {
 860                   if (newname == null)
 861                   {
 862                     newname = new String(sf[i].getDescription());
 863                   }
 864                   else
 865                   {
 866                     newname = newname + "; " + sf[i].getDescription();
 867                   }
 868                 }
 869               }
 870             }
 871           }
 872           if (newname != null)
 873           {
 874             String oldname = ((SequenceNode) node).getName();
 875             // TODO : save in the undo object for this modification.
 876             ((SequenceNode) node).setName(newname);
 877           }
 878         }
 879       }
 880     });
 881   }
 882 }