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