src/MCview/PDBViewer.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 MCview;
  22
  23 import jalview.datamodel.PDBEntry;
  24 import jalview.datamodel.SequenceI;
  25 import jalview.gui.AlignmentPanel;
  26 import jalview.gui.Desktop;
  27 import jalview.gui.OOMWarning;
  28 import jalview.gui.UserDefinedColours;
  29 import jalview.io.JalviewFileChooser;
  30 import jalview.io.JalviewFileView;
  31 import jalview.schemes.BuriedColourScheme;
  32 import jalview.schemes.HelixColourScheme;
  33 import jalview.schemes.HydrophobicColourScheme;
  34 import jalview.schemes.StrandColourScheme;
  35 import jalview.schemes.TaylorColourScheme;
  36 import jalview.schemes.TurnColourScheme;
  37 import jalview.schemes.UserColourScheme;
  38 import jalview.schemes.ZappoColourScheme;
  39 import jalview.util.MessageManager;
  40 import jalview.ws.ebi.EBIFetchClient;
  41
  42 import java.awt.event.ActionEvent;
  43 import java.awt.event.ActionListener;
  44 import java.awt.event.ItemEvent;
  45 import java.awt.event.ItemListener;
  46 import java.awt.event.KeyAdapter;
  47 import java.awt.event.KeyEvent;
  48 import java.awt.event.MouseAdapter;
  49 import java.awt.event.MouseEvent;
  50 import java.io.BufferedReader;
  51 import java.io.File;
  52 import java.io.FileOutputStream;
  53 import java.io.FileReader;
  54 import java.io.PrintWriter;
  55
  56 import javax.swing.ButtonGroup;
  57 import javax.swing.JCheckBoxMenuItem;
  58 import javax.swing.JColorChooser;
  59 import javax.swing.JInternalFrame;
  60 import javax.swing.JMenu;
  61 import javax.swing.JMenuBar;
  62 import javax.swing.JMenuItem;
  63 import javax.swing.JOptionPane;
  64 import javax.swing.JRadioButtonMenuItem;
  65
  66 public class PDBViewer extends JInternalFrame implements Runnable
  67 {
  68
  69   /**
  70    * The associated sequence in an alignment
  71    */
  72   PDBCanvas pdbcanvas;
  73
  74   PDBEntry pdbentry;
  75
  76   SequenceI[] seq;
  77
  78   String[] chains;
  79
  80   AlignmentPanel ap;
  81
  82   String protocol;
  83
  84   String tmpPDBFile;
  85
  86   public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
  87           AlignmentPanel ap, String protocol)
  88   {
  89     this.pdbentry = pdbentry;
  90     this.seq = seq;
  91     this.chains = chains;
  92     this.ap = ap;
  93     this.protocol = protocol;
  94
  95     try
  96     {
  97       jbInit();
  98     } catch (Exception ex)
  99     {
 100       ex.printStackTrace();
 101     }
 102
 103     StringBuffer title = new StringBuffer(seq[0].getName() + ":"
 104             + pdbentry.getFile());
 105
 106     pdbcanvas = new PDBCanvas();
 107
 108     setContentPane(pdbcanvas);
 109
 110     if (pdbentry.getFile() != null)
 111     {
 112       try
 113       {
 114         tmpPDBFile = pdbentry.getFile();
 115         PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
 116                 jalview.io.AppletFormatAdapter.FILE);
 117
 118         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 119
 120       } catch (java.io.IOException ex)
 121       {
 122         ex.printStackTrace();
 123       }
 124     }
 125     else
 126     {
 127       Thread worker = new Thread(this);
 128       worker.start();
 129     }
 130
 131     if (pdbentry.getProperty() != null)
 132     {
 133       if (pdbentry.getProperty().get("method") != null)
 134       {
 135         title.append(" Method: ");
 136         title.append(pdbentry.getProperty().get("method"));
 137       }
 138       if (pdbentry.getProperty().get("chains") != null)
 139       {
 140         title.append(" Chain:");
 141         title.append(pdbentry.getProperty().get("chains"));
 142       }
 143     }
 144     Desktop.addInternalFrame(this, title.toString(), 400, 400);
 145   }
 146
 147   @Override
 148   public void run()
 149   {
 150     try
 151     {
 152       EBIFetchClient ebi = new EBIFetchClient();
 153       String query = "pdb:" + pdbentry.getId();
 154       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw", ".xml")
 155               .getAbsolutePath());
 156
 157       if (pdbentry.getFile() != null)
 158       {
 159         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 160       }
 161     } catch (Exception ex)
 162     {
 163       pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
 164       ex.printStackTrace();
 165     }
 166   }
 167
 168   private void jbInit() throws Exception
 169   {
 170     this.addKeyListener(new KeyAdapter()
 171     {
 172       @Override
 173       public void keyPressed(KeyEvent evt)
 174       {
 175         pdbcanvas.keyPressed(evt);
 176       }
 177     });
 178
 179     this.setJMenuBar(jMenuBar1);
 180     fileMenu.setText(MessageManager.getString("action.file"));
 181     coloursMenu.setText(MessageManager.getString("label.colours"));
 182     saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
 183     saveMenu.setText(MessageManager.getString("action.save_as"));
 184     png.setText("PNG");
 185     png.addActionListener(new ActionListener()
 186     {
 187       @Override
 188       public void actionPerformed(ActionEvent e)
 189       {
 190         png_actionPerformed(e);
 191       }
 192     });
 193     eps.setText("EPS");
 194     eps.addActionListener(new ActionListener()
 195     {
 196       @Override
 197       public void actionPerformed(ActionEvent e)
 198       {
 199         eps_actionPerformed(e);
 200       }
 201     });
 202     mapping.setText(MessageManager.getString("label.view_mapping"));
 203     mapping.addActionListener(new ActionListener()
 204     {
 205       @Override
 206       public void actionPerformed(ActionEvent e)
 207       {
 208         mapping_actionPerformed(e);
 209       }
 210     });
 211     wire.setText(MessageManager.getString("label.wireframe"));
 212     wire.addActionListener(new ActionListener()
 213     {
 214       @Override
 215       public void actionPerformed(ActionEvent e)
 216       {
 217         wire_actionPerformed(e);
 218       }
 219     });
 220     depth.setSelected(true);
 221     depth.setText(MessageManager.getString("label.depthcue"));
 222     depth.addActionListener(new ActionListener()
 223     {
 224       @Override
 225       public void actionPerformed(ActionEvent e)
 226       {
 227         depth_actionPerformed(e);
 228       }
 229     });
 230     zbuffer.setSelected(true);
 231     zbuffer.setText(MessageManager.getString("label.z_buffering"));
 232     zbuffer.addActionListener(new ActionListener()
 233     {
 234       @Override
 235       public void actionPerformed(ActionEvent e)
 236       {
 237         zbuffer_actionPerformed(e);
 238       }
 239     });
 240     charge.setText(MessageManager.getString("label.charge_cysteine"));
 241     charge.addActionListener(new ActionListener()
 242     {
 243       @Override
 244       public void actionPerformed(ActionEvent e)
 245       {
 246         charge_actionPerformed(e);
 247       }
 248     });
 249     chain.setText(MessageManager.getString("action.by_chain"));
 250     chain.addActionListener(new ActionListener()
 251     {
 252       @Override
 253       public void actionPerformed(ActionEvent e)
 254       {
 255         chain_actionPerformed(e);
 256       }
 257     });
 258     seqButton.setSelected(true);
 259     seqButton.setText(MessageManager.getString("action.by_sequence"));
 260     seqButton.addActionListener(new ActionListener()
 261     {
 262       @Override
 263       public void actionPerformed(ActionEvent e)
 264       {
 265         seqButton_actionPerformed(e);
 266       }
 267     });
 268     allchains.setSelected(true);
 269     allchains.setText(MessageManager.getString("label.show_all_chains"));
 270     allchains.addItemListener(new ItemListener()
 271     {
 272       @Override
 273       public void itemStateChanged(ItemEvent e)
 274       {
 275         allchains_itemStateChanged(e);
 276       }
 277     });
 278     zappo.setText(MessageManager.getString("label.zappo"));
 279     zappo.addActionListener(new ActionListener()
 280     {
 281       @Override
 282       public void actionPerformed(ActionEvent e)
 283       {
 284         zappo_actionPerformed(e);
 285       }
 286     });
 287     taylor.setText(MessageManager.getString("label.taylor"));
 288     taylor.addActionListener(new ActionListener()
 289     {
 290       @Override
 291       public void actionPerformed(ActionEvent e)
 292       {
 293         taylor_actionPerformed(e);
 294       }
 295     });
 296     hydro.setText(MessageManager.getString("label.hydrophobicity"));
 297     hydro.addActionListener(new ActionListener()
 298     {
 299       @Override
 300       public void actionPerformed(ActionEvent e)
 301       {
 302         hydro_actionPerformed(e);
 303       }
 304     });
 305     helix.setText(MessageManager.getString("label.helix_propensity"));
 306     helix.addActionListener(new ActionListener()
 307     {
 308       @Override
 309       public void actionPerformed(ActionEvent e)
 310       {
 311         helix_actionPerformed(e);
 312       }
 313     });
 314     strand.setText(MessageManager.getString("label.strand_propensity"));
 315     strand.addActionListener(new ActionListener()
 316     {
 317       @Override
 318       public void actionPerformed(ActionEvent e)
 319       {
 320         strand_actionPerformed(e);
 321       }
 322     });
 323     turn.setText(MessageManager.getString("label.turn_propensity"));
 324     turn.addActionListener(new ActionListener()
 325     {
 326       @Override
 327       public void actionPerformed(ActionEvent e)
 328       {
 329         turn_actionPerformed(e);
 330       }
 331     });
 332     buried.setText(MessageManager.getString("label.buried_index"));
 333     buried.addActionListener(new ActionListener()
 334     {
 335       @Override
 336       public void actionPerformed(ActionEvent e)
 337       {
 338         buried_actionPerformed(e);
 339       }
 340     });
 341     user.setText(MessageManager.getString("action.user_defined"));
 342     user.addActionListener(new ActionListener()
 343     {
 344       @Override
 345       public void actionPerformed(ActionEvent e)
 346       {
 347         user_actionPerformed(e);
 348       }
 349     });
 350     viewMenu.setText(MessageManager.getString("action.view"));
 351     background
 352             .setText(MessageManager.getString("action.background_colour"));
 353     background.addActionListener(new ActionListener()
 354     {
 355       @Override
 356       public void actionPerformed(ActionEvent e)
 357       {
 358         background_actionPerformed(e);
 359       }
 360     });
 361     savePDB.setText(MessageManager.getString("label.pdb_file"));
 362     savePDB.addActionListener(new ActionListener()
 363     {
 364       @Override
 365       public void actionPerformed(ActionEvent e)
 366       {
 367         savePDB_actionPerformed(e);
 368       }
 369     });
 370     jMenuBar1.add(fileMenu);
 371     jMenuBar1.add(coloursMenu);
 372     jMenuBar1.add(viewMenu);
 373     fileMenu.add(saveMenu);
 374     fileMenu.add(mapping);
 375     saveMenu.add(savePDB);
 376     saveMenu.add(png);
 377     saveMenu.add(eps);
 378     coloursMenu.add(seqButton);
 379     coloursMenu.add(chain);
 380     coloursMenu.add(charge);
 381     coloursMenu.add(zappo);
 382     coloursMenu.add(taylor);
 383     coloursMenu.add(hydro);
 384     coloursMenu.add(helix);
 385     coloursMenu.add(strand);
 386     coloursMenu.add(turn);
 387     coloursMenu.add(buried);
 388     coloursMenu.add(user);
 389     coloursMenu.add(background);
 390     ButtonGroup bg = new ButtonGroup();
 391     bg.add(seqButton);
 392     bg.add(chain);
 393     bg.add(charge);
 394     bg.add(zappo);
 395     bg.add(taylor);
 396     bg.add(hydro);
 397     bg.add(helix);
 398     bg.add(strand);
 399     bg.add(turn);
 400     bg.add(buried);
 401     bg.add(user);
 402
 403     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 404     {
 405       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 406               .getUserColourSchemes().keys();
 407
 408       while (userColours.hasMoreElements())
 409       {
 410         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 411                 userColours.nextElement().toString());
 412         radioItem.setName("USER_DEFINED");
 413         radioItem.addMouseListener(new MouseAdapter()
 414         {
 415           @Override
 416           public void mousePressed(MouseEvent evt)
 417           {
 418             if (evt.isPopupTrigger())
 419             {
 420               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 421
 422               int option = JOptionPane.showInternalConfirmDialog(
 423                       jalview.gui.Desktop.desktop,
 424                       MessageManager
 425                               .getString("label.remove_from_default_list"),
 426                       MessageManager
 427                               .getString("label.remove_user_defined_colour"),
 428                       JOptionPane.YES_NO_OPTION);
 429               if (option == JOptionPane.YES_OPTION)
 430               {
 431                 jalview.gui.UserDefinedColours
 432                         .removeColourFromDefaults(radioItem.getText());
 433                 coloursMenu.remove(radioItem);
 434               }
 435               else
 436               {
 437                 radioItem.addActionListener(new ActionListener()
 438                 {
 439                   @Override
 440                   public void actionPerformed(ActionEvent evt)
 441                   {
 442                     user_actionPerformed(evt);
 443                   }
 444                 });
 445               }
 446             }
 447           }
 448         });
 449         radioItem.addActionListener(new ActionListener()
 450         {
 451           @Override
 452           public void actionPerformed(ActionEvent evt)
 453           {
 454             user_actionPerformed(evt);
 455           }
 456         });
 457         coloursMenu.add(radioItem);
 458         bg.add(radioItem);
 459       }
 460     }
 461
 462     viewMenu.add(wire);
 463     viewMenu.add(depth);
 464     viewMenu.add(zbuffer);
 465     viewMenu.add(allchains);
 466   }
 467
 468   JMenuBar jMenuBar1 = new JMenuBar();
 469
 470   JMenu fileMenu = new JMenu();
 471
 472   JMenu coloursMenu = new JMenu();
 473
 474   JMenu saveMenu = new JMenu();
 475
 476   JMenuItem png = new JMenuItem();
 477
 478   JMenuItem eps = new JMenuItem();
 479
 480   JMenuItem mapping = new JMenuItem();
 481
 482   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 483
 484   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 485
 486   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 487
 488   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 489
 490   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 491
 492   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 493
 494   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 495
 496   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 497
 498   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 499
 500   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 501
 502   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 503
 504   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 505
 506   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 507
 508   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 509
 510   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 511
 512   JMenu viewMenu = new JMenu();
 513
 514   JMenuItem background = new JMenuItem();
 515
 516   JMenuItem savePDB = new JMenuItem();
 517
 518   /**
 519    * DOCUMENT ME!
 520    *
 521    * @param e
 522    *          DOCUMENT ME!
 523    */
 524   public void eps_actionPerformed(ActionEvent e)
 525   {
 526     makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
 527   }
 528
 529   /**
 530    * DOCUMENT ME!
 531    *
 532    * @param e
 533    *          DOCUMENT ME!
 534    */
 535   public void png_actionPerformed(ActionEvent e)
 536   {
 537     makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
 538   }
 539
 540   void makePDBImage(jalview.util.ImageMaker.TYPE type)
 541   {
 542     int width = pdbcanvas.getWidth();
 543     int height = pdbcanvas.getHeight();
 544
 545     jalview.util.ImageMaker im;
 546
 547     if (type == jalview.util.ImageMaker.TYPE.PNG)
 548     {
 549       im = new jalview.util.ImageMaker(this,
 550               jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
 551               width, height, null, null, null, 0, false);
 552     }
 553     else if (type == jalview.util.ImageMaker.TYPE.EPS)
 554     {
 555       im = new jalview.util.ImageMaker(this,
 556               jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
 557               width, height, null, this.getTitle(), null, 0, false);
 558     }
 559     else
 560     {
 561
 562       im = new jalview.util.ImageMaker(this,
 563               jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
 564               width, height, null, this.getTitle(), null, 0, false);
 565     }
 566
 567     if (im.getGraphics() != null)
 568     {
 569       pdbcanvas.drawAll(im.getGraphics(), width, height);
 570       im.writeImage();
 571     }
 572   }
 573
 574   public void charge_actionPerformed(ActionEvent e)
 575   {
 576     pdbcanvas.bysequence = false;
 577     pdbcanvas.pdb.setChargeColours();
 578     pdbcanvas.redrawneeded = true;
 579     pdbcanvas.repaint();
 580   }
 581
 582   public void hydro_actionPerformed(ActionEvent e)
 583   {
 584     pdbcanvas.bysequence = false;
 585     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 586     pdbcanvas.redrawneeded = true;
 587     pdbcanvas.repaint();
 588   }
 589
 590   public void chain_actionPerformed(ActionEvent e)
 591   {
 592     pdbcanvas.bysequence = false;
 593     pdbcanvas.pdb.setChainColours();
 594     pdbcanvas.redrawneeded = true;
 595     pdbcanvas.repaint();
 596   }
 597
 598   public void zbuffer_actionPerformed(ActionEvent e)
 599   {
 600     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 601     pdbcanvas.redrawneeded = true;
 602     pdbcanvas.repaint();
 603   }
 604
 605   public void molecule_actionPerformed(ActionEvent e)
 606   {
 607     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 608     pdbcanvas.redrawneeded = true;
 609     pdbcanvas.repaint();
 610   }
 611
 612   public void depth_actionPerformed(ActionEvent e)
 613   {
 614     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 615     pdbcanvas.redrawneeded = true;
 616     pdbcanvas.repaint();
 617   }
 618
 619   public void wire_actionPerformed(ActionEvent e)
 620   {
 621     pdbcanvas.wire = !pdbcanvas.wire;
 622     pdbcanvas.redrawneeded = true;
 623     pdbcanvas.repaint();
 624   }
 625
 626   public void seqButton_actionPerformed(ActionEvent e)
 627   {
 628     pdbcanvas.bysequence = true;
 629     pdbcanvas.updateSeqColours();
 630   }
 631
 632   public void mapping_actionPerformed(ActionEvent e)
 633   {
 634     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 635     try
 636     {
 637       cap.setText(pdbcanvas.mappingDetails.toString());
 638       Desktop.addInternalFrame(cap,
 639               MessageManager.getString("label.pdb_sequence_mapping"), 550,
 640               600);
 641     } catch (OutOfMemoryError oom)
 642     {
 643       new OOMWarning("Opening sequence to structure mapping report", oom);
 644       cap.dispose();
 645     }
 646   }
 647
 648   public void allchains_itemStateChanged(ItemEvent e)
 649   {
 650     pdbcanvas.setAllchainsVisible(allchains.getState());
 651   }
 652
 653   public void zappo_actionPerformed(ActionEvent e)
 654   {
 655     pdbcanvas.bysequence = false;
 656     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 657     pdbcanvas.redrawneeded = true;
 658     pdbcanvas.repaint();
 659   }
 660
 661   public void taylor_actionPerformed(ActionEvent e)
 662   {
 663     pdbcanvas.bysequence = false;
 664     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 665     pdbcanvas.redrawneeded = true;
 666     pdbcanvas.repaint();
 667   }
 668
 669   public void helix_actionPerformed(ActionEvent e)
 670   {
 671     pdbcanvas.bysequence = false;
 672     pdbcanvas.pdb.setColours(new HelixColourScheme());
 673     pdbcanvas.redrawneeded = true;
 674     pdbcanvas.repaint();
 675   }
 676
 677   public void strand_actionPerformed(ActionEvent e)
 678   {
 679     pdbcanvas.bysequence = false;
 680     pdbcanvas.pdb.setColours(new StrandColourScheme());
 681     pdbcanvas.redrawneeded = true;
 682     pdbcanvas.repaint();
 683   }
 684
 685   public void turn_actionPerformed(ActionEvent e)
 686   {
 687     pdbcanvas.bysequence = false;
 688     pdbcanvas.pdb.setColours(new TurnColourScheme());
 689     pdbcanvas.redrawneeded = true;
 690     pdbcanvas.repaint();
 691   }
 692
 693   public void buried_actionPerformed(ActionEvent e)
 694   {
 695     pdbcanvas.bysequence = false;
 696     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 697     pdbcanvas.redrawneeded = true;
 698     pdbcanvas.repaint();
 699   }
 700
 701   public void user_actionPerformed(ActionEvent e)
 702   {
 703     if (e.getActionCommand().equals(
 704             MessageManager.getString("action.user_defined")))
 705     {
 706       // new UserDefinedColours(pdbcanvas, null);
 707     }
 708     else
 709     {
 710       UserColourScheme udc = (UserColourScheme) UserDefinedColours
 711               .getUserColourSchemes().get(e.getActionCommand());
 712
 713       pdbcanvas.pdb.setColours(udc);
 714       pdbcanvas.redrawneeded = true;
 715       pdbcanvas.repaint();
 716     }
 717   }
 718
 719   public void background_actionPerformed(ActionEvent e)
 720   {
 721     java.awt.Color col = JColorChooser.showDialog(this,
 722             MessageManager.getString("label.select_backgroud_colour"),
 723             pdbcanvas.backgroundColour);
 724
 725     if (col != null)
 726     {
 727       pdbcanvas.backgroundColour = col;
 728       pdbcanvas.redrawneeded = true;
 729       pdbcanvas.repaint();
 730     }
 731   }
 732
 733   public void savePDB_actionPerformed(ActionEvent e)
 734   {
 735     JalviewFileChooser chooser = new JalviewFileChooser(
 736             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 737
 738     chooser.setFileView(new JalviewFileView());
 739     chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
 740     chooser.setToolTipText(MessageManager.getString("action.save"));
 741
 742     int value = chooser.showSaveDialog(this);
 743
 744     if (value == JalviewFileChooser.APPROVE_OPTION)
 745     {
 746       try
 747       {
 748         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 749         File outFile = chooser.getSelectedFile();
 750
 751         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 752         String data;
 753         while ((data = in.readLine()) != null)
 754         {
 755           if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
 756           {
 757             out.println(data);
 758           }
 759         }
 760         out.close();
 761         in.close();
 762       } catch (Exception ex)
 763       {
 764         ex.printStackTrace();
 765       }
 766     }
 767   }
 768 }