src/MCview/PDBViewer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package 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 import javax.swing.SwingUtilities;
  66
  67 public class PDBViewer extends JInternalFrame implements Runnable
  68 {
  69
  70   /**
  71    * The associated sequence in an alignment
  72    */
  73   PDBCanvas pdbcanvas;
  74
  75   PDBEntry pdbentry;
  76
  77   SequenceI[] seq;
  78
  79   String[] chains;
  80
  81   AlignmentPanel ap;
  82
  83   String protocol;
  84
  85   String tmpPDBFile;
  86
  87   public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
  88           AlignmentPanel ap, String protocol)
  89   {
  90     this.pdbentry = pdbentry;
  91     this.seq = seq;
  92     this.chains = chains;
  93     this.ap = ap;
  94     this.protocol = protocol;
  95
  96     try
  97     {
  98       jbInit();
  99     } catch (Exception ex)
 100     {
 101       ex.printStackTrace();
 102     }
 103
 104     StringBuffer title = new StringBuffer(seq[0].getName() + ":"
 105             + pdbentry.getFile());
 106
 107     pdbcanvas = new PDBCanvas();
 108
 109     setContentPane(pdbcanvas);
 110
 111     if (pdbentry.getFile() != null)
 112     {
 113       try
 114       {
 115         tmpPDBFile = pdbentry.getFile();
 116         PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
 117                 jalview.io.AppletFormatAdapter.FILE);
 118
 119         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 120
 121       } catch (java.io.IOException ex)
 122       {
 123         ex.printStackTrace();
 124       }
 125     }
 126     else
 127     {
 128       Thread worker = new Thread(this);
 129       worker.start();
 130     }
 131
 132     if (pdbentry.getProperty() != null)
 133     {
 134       if (pdbentry.getProperty().get("method") != null)
 135       {
 136         title.append(" Method: ");
 137         title.append(pdbentry.getProperty().get("method"));
 138       }
 139       if (pdbentry.getProperty().get("chains") != null)
 140       {
 141         title.append(" Chain:");
 142         title.append(pdbentry.getProperty().get("chains"));
 143       }
 144     }
 145     Desktop.addInternalFrame(this, title.toString(), 400, 400);
 146   }
 147
 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")
 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       public void keyPressed(KeyEvent evt)
 173       {
 174         pdbcanvas.keyPressed(evt);
 175       }
 176     });
 177
 178     this.setJMenuBar(jMenuBar1);
 179     fileMenu.setText(MessageManager.getString("action.file"));
 180     coloursMenu.setText(MessageManager.getString("label.colours"));
 181     saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
 182     saveMenu.setText(MessageManager.getString("action.save_as"));
 183     png.setText("PNG");
 184     png.addActionListener(new ActionListener()
 185     {
 186       public void actionPerformed(ActionEvent e)
 187       {
 188         png_actionPerformed(e);
 189       }
 190     });
 191     eps.setText("EPS");
 192     eps.addActionListener(new ActionListener()
 193     {
 194       public void actionPerformed(ActionEvent e)
 195       {
 196         eps_actionPerformed(e);
 197       }
 198     });
 199     mapping.setText(MessageManager.getString("label.view_mapping"));
 200     mapping.addActionListener(new ActionListener()
 201     {
 202       public void actionPerformed(ActionEvent e)
 203       {
 204         mapping_actionPerformed(e);
 205       }
 206     });
 207     wire.setText(MessageManager.getString("label.wireframe"));
 208     wire.addActionListener(new ActionListener()
 209     {
 210       public void actionPerformed(ActionEvent e)
 211       {
 212         wire_actionPerformed(e);
 213       }
 214     });
 215     depth.setSelected(true);
 216     depth.setText(MessageManager.getString("label.depthcue"));
 217     depth.addActionListener(new ActionListener()
 218     {
 219       public void actionPerformed(ActionEvent e)
 220       {
 221         depth_actionPerformed(e);
 222       }
 223     });
 224     zbuffer.setSelected(true);
 225     zbuffer.setText(MessageManager.getString("label.z_buffering"));
 226     zbuffer.addActionListener(new ActionListener()
 227     {
 228       public void actionPerformed(ActionEvent e)
 229       {
 230         zbuffer_actionPerformed(e);
 231       }
 232     });
 233     charge.setText(MessageManager.getString("label.charge_cysteine"));
 234     charge.addActionListener(new ActionListener()
 235     {
 236       public void actionPerformed(ActionEvent e)
 237       {
 238         charge_actionPerformed(e);
 239       }
 240     });
 241     chain.setText(MessageManager.getString("action.by_chain"));
 242     chain.addActionListener(new ActionListener()
 243     {
 244       public void actionPerformed(ActionEvent e)
 245       {
 246         chain_actionPerformed(e);
 247       }
 248     });
 249     seqButton.setSelected(true);
 250     seqButton.setText(MessageManager.getString("action.by_sequence"));
 251     seqButton.addActionListener(new ActionListener()
 252     {
 253       public void actionPerformed(ActionEvent e)
 254       {
 255         seqButton_actionPerformed(e);
 256       }
 257     });
 258     allchains.setSelected(true);
 259     allchains.setText(MessageManager.getString("label.show_all_chains"));
 260     allchains.addItemListener(new ItemListener()
 261     {
 262       public void itemStateChanged(ItemEvent e)
 263       {
 264         allchains_itemStateChanged(e);
 265       }
 266     });
 267     zappo.setText(MessageManager.getString("label.zappo"));
 268     zappo.addActionListener(new ActionListener()
 269     {
 270       public void actionPerformed(ActionEvent e)
 271       {
 272         zappo_actionPerformed(e);
 273       }
 274     });
 275     taylor.setText(MessageManager.getString("label.taylor"));
 276     taylor.addActionListener(new ActionListener()
 277     {
 278       public void actionPerformed(ActionEvent e)
 279       {
 280         taylor_actionPerformed(e);
 281       }
 282     });
 283     hydro.setText(MessageManager.getString("label.hydrophobicity"));
 284     hydro.addActionListener(new ActionListener()
 285     {
 286       public void actionPerformed(ActionEvent e)
 287       {
 288         hydro_actionPerformed(e);
 289       }
 290     });
 291     helix.setText(MessageManager.getString("label.helix_propensity"));
 292     helix.addActionListener(new ActionListener()
 293     {
 294       public void actionPerformed(ActionEvent e)
 295       {
 296         helix_actionPerformed(e);
 297       }
 298     });
 299     strand.setText(MessageManager.getString("label.strand_propensity"));
 300     strand.addActionListener(new ActionListener()
 301     {
 302       public void actionPerformed(ActionEvent e)
 303       {
 304         strand_actionPerformed(e);
 305       }
 306     });
 307     turn.setText(MessageManager.getString("label.turn_propensity"));
 308     turn.addActionListener(new ActionListener()
 309     {
 310       public void actionPerformed(ActionEvent e)
 311       {
 312         turn_actionPerformed(e);
 313       }
 314     });
 315     buried.setText(MessageManager.getString("label.buried_index"));
 316     buried.addActionListener(new ActionListener()
 317     {
 318       public void actionPerformed(ActionEvent e)
 319       {
 320         buried_actionPerformed(e);
 321       }
 322     });
 323     user.setText(MessageManager.getString("action.user_defined"));
 324     user.addActionListener(new ActionListener()
 325     {
 326       public void actionPerformed(ActionEvent e)
 327       {
 328         user_actionPerformed(e);
 329       }
 330     });
 331     viewMenu.setText(MessageManager.getString("action.view"));
 332     background.setText(MessageManager.getString("label.background_colour")
 333             + "...");
 334     background.addActionListener(new ActionListener()
 335     {
 336       public void actionPerformed(ActionEvent e)
 337       {
 338         background_actionPerformed(e);
 339       }
 340     });
 341     savePDB.setText(MessageManager.getString("label.pdb_file"));
 342     savePDB.addActionListener(new ActionListener()
 343     {
 344       public void actionPerformed(ActionEvent e)
 345       {
 346         savePDB_actionPerformed(e);
 347       }
 348     });
 349     jMenuBar1.add(fileMenu);
 350     jMenuBar1.add(coloursMenu);
 351     jMenuBar1.add(viewMenu);
 352     fileMenu.add(saveMenu);
 353     fileMenu.add(mapping);
 354     saveMenu.add(savePDB);
 355     saveMenu.add(png);
 356     saveMenu.add(eps);
 357     coloursMenu.add(seqButton);
 358     coloursMenu.add(chain);
 359     coloursMenu.add(charge);
 360     coloursMenu.add(zappo);
 361     coloursMenu.add(taylor);
 362     coloursMenu.add(hydro);
 363     coloursMenu.add(helix);
 364     coloursMenu.add(strand);
 365     coloursMenu.add(turn);
 366     coloursMenu.add(buried);
 367     coloursMenu.add(user);
 368     coloursMenu.add(background);
 369     ButtonGroup bg = new ButtonGroup();
 370     bg.add(seqButton);
 371     bg.add(chain);
 372     bg.add(charge);
 373     bg.add(zappo);
 374     bg.add(taylor);
 375     bg.add(hydro);
 376     bg.add(helix);
 377     bg.add(strand);
 378     bg.add(turn);
 379     bg.add(buried);
 380     bg.add(user);
 381
 382     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 383     {
 384       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 385               .getUserColourSchemes().keys();
 386
 387       while (userColours.hasMoreElements())
 388       {
 389         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 390                 userColours.nextElement().toString());
 391         radioItem.setName("USER_DEFINED");
 392         radioItem.addMouseListener(new MouseAdapter()
 393         {
 394           public void mousePressed(MouseEvent evt)
 395           {
 396             if (evt.isControlDown()
 397                     || SwingUtilities.isRightMouseButton(evt))
 398             {
 399               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 400
 401               int option = JOptionPane.showInternalConfirmDialog(
 402                       jalview.gui.Desktop.desktop,
 403                       MessageManager
 404                               .getString("label.remove_from_default_list"),
 405                       MessageManager
 406                               .getString("label.remove_user_defined_colour"),
 407                       JOptionPane.YES_NO_OPTION);
 408               if (option == JOptionPane.YES_OPTION)
 409               {
 410                 jalview.gui.UserDefinedColours
 411                         .removeColourFromDefaults(radioItem.getText());
 412                 coloursMenu.remove(radioItem);
 413               }
 414               else
 415               {
 416                 radioItem.addActionListener(new ActionListener()
 417                 {
 418                   public void actionPerformed(ActionEvent evt)
 419                   {
 420                     user_actionPerformed(evt);
 421                   }
 422                 });
 423               }
 424             }
 425           }
 426         });
 427         radioItem.addActionListener(new ActionListener()
 428         {
 429           public void actionPerformed(ActionEvent evt)
 430           {
 431             user_actionPerformed(evt);
 432           }
 433         });
 434         coloursMenu.add(radioItem);
 435         bg.add(radioItem);
 436       }
 437     }
 438
 439     viewMenu.add(wire);
 440     viewMenu.add(depth);
 441     viewMenu.add(zbuffer);
 442     viewMenu.add(allchains);
 443   }
 444
 445   JMenuBar jMenuBar1 = new JMenuBar();
 446
 447   JMenu fileMenu = new JMenu();
 448
 449   JMenu coloursMenu = new JMenu();
 450
 451   JMenu saveMenu = new JMenu();
 452
 453   JMenuItem png = new JMenuItem();
 454
 455   JMenuItem eps = new JMenuItem();
 456
 457   JMenuItem mapping = new JMenuItem();
 458
 459   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 460
 461   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 462
 463   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 464
 465   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 466
 467   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 468
 469   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 470
 471   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 472
 473   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 474
 475   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 476
 477   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 478
 479   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 480
 481   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 482
 483   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 484
 485   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 486
 487   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 488
 489   JMenu viewMenu = new JMenu();
 490
 491   JMenuItem background = new JMenuItem();
 492
 493   JMenuItem savePDB = new JMenuItem();
 494
 495   /**
 496    * DOCUMENT ME!
 497    *
 498    * @param e
 499    *          DOCUMENT ME!
 500    */
 501   public void eps_actionPerformed(ActionEvent e)
 502   {
 503     makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
 504   }
 505
 506   /**
 507    * DOCUMENT ME!
 508    *
 509    * @param e
 510    *          DOCUMENT ME!
 511    */
 512   public void png_actionPerformed(ActionEvent e)
 513   {
 514     makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
 515   }
 516
 517   void makePDBImage(jalview.util.ImageMaker.TYPE type)
 518   {
 519     int width = pdbcanvas.getWidth();
 520     int height = pdbcanvas.getHeight();
 521
 522     jalview.util.ImageMaker im;
 523
 524     if (type == jalview.util.ImageMaker.TYPE.PNG)
 525     {
 526       im = new jalview.util.ImageMaker(this,
 527               jalview.util.ImageMaker.TYPE.PNG,
 528               "Make PNG image from view", width, height, null, null);
 529     }
 530     else if (type == jalview.util.ImageMaker.TYPE.EPS)
 531     {
 532       im = new jalview.util.ImageMaker(this,
 533               jalview.util.ImageMaker.TYPE.EPS,
 534               "Make EPS file from view", width, height, null,
 535               this.getTitle());
 536     }
 537     else
 538     {
 539
 540       im = new jalview.util.ImageMaker(this,
 541               jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
 542               width, height, null, this.getTitle());
 543     }
 544
 545     if (im.getGraphics() != null)
 546     {
 547       pdbcanvas.drawAll(im.getGraphics(), width, height);
 548       im.writeImage();
 549     }
 550   }
 551
 552   public void charge_actionPerformed(ActionEvent e)
 553   {
 554     pdbcanvas.bysequence = false;
 555     pdbcanvas.pdb.setChargeColours();
 556     pdbcanvas.redrawneeded = true;
 557     pdbcanvas.repaint();
 558   }
 559
 560   public void hydro_actionPerformed(ActionEvent e)
 561   {
 562     pdbcanvas.bysequence = false;
 563     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 564     pdbcanvas.redrawneeded = true;
 565     pdbcanvas.repaint();
 566   }
 567
 568   public void chain_actionPerformed(ActionEvent e)
 569   {
 570     pdbcanvas.bysequence = false;
 571     pdbcanvas.pdb.setChainColours();
 572     pdbcanvas.redrawneeded = true;
 573     pdbcanvas.repaint();
 574   }
 575
 576   public void zbuffer_actionPerformed(ActionEvent e)
 577   {
 578     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 579     pdbcanvas.redrawneeded = true;
 580     pdbcanvas.repaint();
 581   }
 582
 583   public void molecule_actionPerformed(ActionEvent e)
 584   {
 585     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 586     pdbcanvas.redrawneeded = true;
 587     pdbcanvas.repaint();
 588   }
 589
 590   public void depth_actionPerformed(ActionEvent e)
 591   {
 592     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 593     pdbcanvas.redrawneeded = true;
 594     pdbcanvas.repaint();
 595   }
 596
 597   public void wire_actionPerformed(ActionEvent e)
 598   {
 599     pdbcanvas.wire = !pdbcanvas.wire;
 600     pdbcanvas.redrawneeded = true;
 601     pdbcanvas.repaint();
 602   }
 603
 604   public void seqButton_actionPerformed(ActionEvent e)
 605   {
 606     pdbcanvas.bysequence = true;
 607     pdbcanvas.updateSeqColours();
 608   }
 609
 610   public void mapping_actionPerformed(ActionEvent e)
 611   {
 612     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 613     try
 614     {
 615       cap.setText(pdbcanvas.mappingDetails.toString());
 616       Desktop.addInternalFrame(cap,
 617               MessageManager.getString("label.pdb_sequence_mapping"), 550,
 618               600);
 619     } catch (OutOfMemoryError oom)
 620     {
 621       new OOMWarning("Opening sequence to structure mapping report", oom);
 622       cap.dispose();
 623     }
 624   }
 625
 626   public void allchains_itemStateChanged(ItemEvent e)
 627   {
 628     pdbcanvas.setAllchainsVisible(allchains.getState());
 629   }
 630
 631   public void zappo_actionPerformed(ActionEvent e)
 632   {
 633     pdbcanvas.bysequence = false;
 634     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 635     pdbcanvas.redrawneeded = true;
 636     pdbcanvas.repaint();
 637   }
 638
 639   public void taylor_actionPerformed(ActionEvent e)
 640   {
 641     pdbcanvas.bysequence = false;
 642     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 643     pdbcanvas.redrawneeded = true;
 644     pdbcanvas.repaint();
 645   }
 646
 647   public void helix_actionPerformed(ActionEvent e)
 648   {
 649     pdbcanvas.bysequence = false;
 650     pdbcanvas.pdb.setColours(new HelixColourScheme());
 651     pdbcanvas.redrawneeded = true;
 652     pdbcanvas.repaint();
 653   }
 654
 655   public void strand_actionPerformed(ActionEvent e)
 656   {
 657     pdbcanvas.bysequence = false;
 658     pdbcanvas.pdb.setColours(new StrandColourScheme());
 659     pdbcanvas.redrawneeded = true;
 660     pdbcanvas.repaint();
 661   }
 662
 663   public void turn_actionPerformed(ActionEvent e)
 664   {
 665     pdbcanvas.bysequence = false;
 666     pdbcanvas.pdb.setColours(new TurnColourScheme());
 667     pdbcanvas.redrawneeded = true;
 668     pdbcanvas.repaint();
 669   }
 670
 671   public void buried_actionPerformed(ActionEvent e)
 672   {
 673     pdbcanvas.bysequence = false;
 674     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 675     pdbcanvas.redrawneeded = true;
 676     pdbcanvas.repaint();
 677   }
 678
 679   public void user_actionPerformed(ActionEvent e)
 680   {
 681     if (e.getActionCommand().equals(
 682             MessageManager.getString("action.user_defined")))
 683     {
 684       // new UserDefinedColours(pdbcanvas, null);
 685     }
 686     else
 687     {
 688       UserColourScheme udc = (UserColourScheme) UserDefinedColours
 689               .getUserColourSchemes().get(e.getActionCommand());
 690
 691       pdbcanvas.pdb.setColours(udc);
 692       pdbcanvas.redrawneeded = true;
 693       pdbcanvas.repaint();
 694     }
 695   }
 696
 697   public void background_actionPerformed(ActionEvent e)
 698   {
 699     java.awt.Color col = JColorChooser.showDialog(this,
 700             MessageManager.getString("label.select_backgroud_colour"),
 701             pdbcanvas.backgroundColour);
 702
 703     if (col != null)
 704     {
 705       pdbcanvas.backgroundColour = col;
 706       pdbcanvas.redrawneeded = true;
 707       pdbcanvas.repaint();
 708     }
 709   }
 710
 711   public void savePDB_actionPerformed(ActionEvent e)
 712   {
 713     JalviewFileChooser chooser = new JalviewFileChooser(
 714             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 715
 716     chooser.setFileView(new JalviewFileView());
 717     chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
 718     chooser.setToolTipText(MessageManager.getString("action.save"));
 719
 720     int value = chooser.showSaveDialog(this);
 721
 722     if (value == JalviewFileChooser.APPROVE_OPTION)
 723     {
 724       try
 725       {
 726         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 727         File outFile = chooser.getSelectedFile();
 728
 729         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 730         String data;
 731         while ((data = in.readLine()) != null)
 732         {
 733           if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
 734           {
 735             out.println(data);
 736           }
 737         }
 738         out.close();
 739         in.close();
 740       } catch (Exception ex)
 741       {
 742         ex.printStackTrace();
 743       }
 744     }
 745   }
 746 }