src/MCview/PDBViewer.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package MCview;\r
  20 \r
  21 import javax.swing.*;\r
  22 import java.awt.event.*;\r
  23 import jalview.datamodel.*;\r
  24 import jalview.schemes.*;\r
  25 import jalview.gui.*;\r
  26 import jalview.io.EBIFetchClient;\r
  27 import java.awt.event.ActionListener;\r
  28 import java.awt.event.ActionEvent;\r
  29 import java.io.*;\r
  30 import jalview.io.JalviewFileChooser;\r
  31 import jalview.io.JalviewFileView;\r
  32 \r
  33 public class PDBViewer extends JInternalFrame implements Runnable\r
  34 {\r
  35   PDBEntry pdb;\r
  36   Sequence sequence;\r
  37   PDBCanvas pdbcanvas;\r
  38   String tmpPDBFile;\r
  39 \r
  40 \r
  41   public PDBViewer(PDBEntry entry,\r
  42                    Sequence seq,\r
  43                    SeqCanvas seqcanvas)\r
  44   {\r
  45     try\r
  46     {\r
  47       jbInit();\r
  48     }\r
  49     catch (Exception ex)\r
  50     {\r
  51       ex.printStackTrace();\r
  52     }\r
  53 \r
  54 \r
  55     if (entry==null)\r
  56       return;\r
  57     pdb = entry;\r
  58     sequence = seq;\r
  59     pdbcanvas = new PDBCanvas(seqcanvas, sequence);\r
  60 \r
  61     if(pdb.getFile()!=null)\r
  62     {\r
  63         try{\r
  64           tmpPDBFile = pdb.getFile();\r
  65           PDBfile pdbfile = new PDBfile(tmpPDBFile,\r
  66                                         jalview.io.AppletFormatAdapter.FILE);\r
  67           pdbcanvas.setPDBFile(pdbfile);\r
  68 \r
  69         }catch(java.io.IOException ex)\r
  70         {\r
  71           ex.printStackTrace();\r
  72         }\r
  73     }\r
  74     else\r
  75     {\r
  76       Thread worker = new Thread(this);\r
  77       worker.start();\r
  78     }\r
  79 \r
  80 \r
  81 \r
  82     setContentPane(pdbcanvas);\r
  83     StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());\r
  84     if(pdb.getProperty()!=null)\r
  85     {\r
  86       if (pdb.getProperty().get("method")!=null)\r
  87       {\r
  88         title.append(" Method: ");\r
  89         title.append(pdb.getProperty().get("method"));\r
  90       }\r
  91       if (pdb.getProperty().get("chains") != null)\r
  92       {\r
  93         title.append(" Chain:");\r
  94         title.append(pdb.getProperty().get("chains"));\r
  95       }\r
  96     }\r
  97      Desktop.addInternalFrame(this,title.toString(),400, 400);\r
  98   }\r
  99 \r
 100   public void run()\r
 101   {\r
 102     try\r
 103     {\r
 104         EBIFetchClient ebi = new EBIFetchClient();\r
 105         String query = "pdb:" + pdb.getId();\r
 106         tmpPDBFile = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();\r
 107         if (tmpPDBFile != null)\r
 108         {\r
 109           PDBfile pdbfile = new PDBfile(tmpPDBFile, jalview.io.AppletFormatAdapter.FILE);\r
 110           pdbcanvas.setPDBFile(pdbfile);\r
 111         }\r
 112         else\r
 113         {\r
 114           throw new Exception("Empty result for WSDbFetch Query: " + query);\r
 115         }\r
 116     }\r
 117     catch (Exception ex)\r
 118     {\r
 119       ex.printStackTrace();\r
 120       showErrorMessage("Failed to retrieve PDB structure.");\r
 121 //      this.dispose();\r
 122     }\r
 123   }\r
 124 \r
 125   private void jbInit()\r
 126       throws Exception\r
 127   {\r
 128     this.addKeyListener(new KeyAdapter()\r
 129         {\r
 130             public void keyPressed(KeyEvent evt)\r
 131             {\r
 132               pdbcanvas.keyPressed(evt);\r
 133             }\r
 134         });\r
 135 \r
 136     this.setJMenuBar(jMenuBar1);\r
 137     fileMenu.setText("File");\r
 138     coloursMenu.setText("Colours");\r
 139     saveMenu.setActionCommand("Save Image");\r
 140     saveMenu.setText("Save As");\r
 141     png.setText("PNG");\r
 142     png.addActionListener(new ActionListener()\r
 143     {\r
 144       public void actionPerformed(ActionEvent e)\r
 145       {\r
 146         png_actionPerformed(e);\r
 147       }\r
 148     });\r
 149     eps.setText("EPS");\r
 150     eps.addActionListener(new ActionListener()\r
 151     {\r
 152       public void actionPerformed(ActionEvent e)\r
 153       {\r
 154         eps_actionPerformed(e);\r
 155       }\r
 156     });\r
 157     mapping.setText("View Mapping");\r
 158     mapping.addActionListener(new ActionListener()\r
 159     {\r
 160       public void actionPerformed(ActionEvent e)\r
 161       {\r
 162         mapping_actionPerformed(e);\r
 163       }\r
 164     });\r
 165     wire.setText("Wireframe");\r
 166     wire.addActionListener(new ActionListener()\r
 167     {\r
 168       public void actionPerformed(ActionEvent e)\r
 169       {\r
 170         wire_actionPerformed(e);\r
 171       }\r
 172     });\r
 173     depth.setSelected(true);\r
 174     depth.setText("Depthcue");\r
 175     depth.addActionListener(new ActionListener()\r
 176     {\r
 177       public void actionPerformed(ActionEvent e)\r
 178       {\r
 179         depth_actionPerformed(e);\r
 180       }\r
 181     });\r
 182     zbuffer.setSelected(true);\r
 183     zbuffer.setText("Z Buffering");\r
 184     zbuffer.addActionListener(new ActionListener()\r
 185     {\r
 186       public void actionPerformed(ActionEvent e)\r
 187       {\r
 188         zbuffer_actionPerformed(e);\r
 189       }\r
 190     });\r
 191     charge.setText("Charge & Cysteine");\r
 192     charge.addActionListener(new ActionListener()\r
 193     {\r
 194       public void actionPerformed(ActionEvent e)\r
 195       {\r
 196         charge_actionPerformed(e);\r
 197       }\r
 198     });\r
 199     chain.setText("By Chain");\r
 200     chain.addActionListener(new ActionListener()\r
 201     {\r
 202       public void actionPerformed(ActionEvent e)\r
 203       {\r
 204         chain_actionPerformed(e);\r
 205       }\r
 206     });\r
 207     seqButton.setSelected(true);\r
 208     seqButton.setText("By Sequence");\r
 209     seqButton.addActionListener(new ActionListener()\r
 210     {\r
 211       public void actionPerformed(ActionEvent e)\r
 212       {\r
 213         seqButton_actionPerformed(e);\r
 214       }\r
 215     });\r
 216     allchains.setSelected(true);\r
 217     allchains.setText("Show All Chains");\r
 218     allchains.addItemListener(new ItemListener()\r
 219     {\r
 220       public void itemStateChanged(ItemEvent e)\r
 221       {\r
 222         allchains_itemStateChanged(e);\r
 223       }\r
 224     });\r
 225     zappo.setText("Zappo");\r
 226     zappo.addActionListener(new ActionListener()\r
 227     {\r
 228       public void actionPerformed(ActionEvent e)\r
 229       {\r
 230         zappo_actionPerformed(e);\r
 231       }\r
 232     });\r
 233     taylor.setText("Taylor");\r
 234     taylor.addActionListener(new ActionListener()\r
 235     {\r
 236       public void actionPerformed(ActionEvent e)\r
 237       {\r
 238         taylor_actionPerformed(e);\r
 239       }\r
 240     });\r
 241     hydro.setText("Hydro");\r
 242     hydro.addActionListener(new ActionListener()\r
 243     {\r
 244       public void actionPerformed(ActionEvent e)\r
 245       {\r
 246         hydro_actionPerformed(e);\r
 247       }\r
 248     });\r
 249     helix.setText("Helix");\r
 250     helix.addActionListener(new ActionListener()\r
 251     {\r
 252       public void actionPerformed(ActionEvent e)\r
 253       {\r
 254         helix_actionPerformed(e);\r
 255       }\r
 256     });\r
 257     strand.setText("Strand");\r
 258     strand.addActionListener(new ActionListener()\r
 259     {\r
 260       public void actionPerformed(ActionEvent e)\r
 261       {\r
 262         strand_actionPerformed(e);\r
 263       }\r
 264     });\r
 265     turn.setText("Turn");\r
 266     turn.addActionListener(new ActionListener()\r
 267     {\r
 268       public void actionPerformed(ActionEvent e)\r
 269       {\r
 270         turn_actionPerformed(e);\r
 271       }\r
 272     });\r
 273     buried.setText("Buried");\r
 274     buried.addActionListener(new ActionListener()\r
 275     {\r
 276       public void actionPerformed(ActionEvent e)\r
 277       {\r
 278         buried_actionPerformed(e);\r
 279       }\r
 280     });\r
 281     user.setText("User Defined...");\r
 282     user.addActionListener(new ActionListener()\r
 283     {\r
 284       public void actionPerformed(ActionEvent e)\r
 285       {\r
 286         user_actionPerformed(e);\r
 287       }\r
 288     });\r
 289     viewMenu.setText("View");\r
 290     background.setText("Background Colour...");\r
 291     background.addActionListener(new ActionListener()\r
 292     {\r
 293       public void actionPerformed(ActionEvent e)\r
 294       {\r
 295         background_actionPerformed(e);\r
 296       }\r
 297     });\r
 298     savePDB.setText("PDB File");\r
 299     savePDB.addActionListener(new ActionListener()\r
 300     {\r
 301       public void actionPerformed(ActionEvent e)\r
 302       {\r
 303         savePDB_actionPerformed(e);\r
 304       }\r
 305     });\r
 306     jMenuBar1.add(fileMenu);\r
 307     jMenuBar1.add(coloursMenu);\r
 308     jMenuBar1.add(viewMenu);\r
 309     fileMenu.add(saveMenu);\r
 310     fileMenu.add(mapping);\r
 311     saveMenu.add(savePDB);\r
 312     saveMenu.add(png);\r
 313     saveMenu.add(eps);\r
 314     coloursMenu.add(seqButton);\r
 315     coloursMenu.add(chain);\r
 316     coloursMenu.add(charge);\r
 317     coloursMenu.add(zappo);\r
 318     coloursMenu.add(taylor);\r
 319     coloursMenu.add(hydro);\r
 320     coloursMenu.add(helix);\r
 321     coloursMenu.add(strand);\r
 322     coloursMenu.add(turn);\r
 323     coloursMenu.add(buried);\r
 324     coloursMenu.add(user);\r
 325     coloursMenu.add(background);\r
 326     ButtonGroup bg = new ButtonGroup();\r
 327     bg.add(seqButton);\r
 328     bg.add(chain);\r
 329     bg.add(charge);\r
 330     bg.add(zappo);\r
 331     bg.add(taylor);\r
 332     bg.add(hydro);\r
 333     bg.add(helix);\r
 334     bg.add(strand);\r
 335     bg.add(turn);\r
 336     bg.add(buried);\r
 337     bg.add(user);\r
 338 \r
 339 \r
 340     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 341     {\r
 342       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 343           getUserColourSchemes().keys();\r
 344 \r
 345       while (userColours.hasMoreElements())\r
 346       {\r
 347         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
 348             nextElement().toString());\r
 349         radioItem.setName("USER_DEFINED");\r
 350         radioItem.addMouseListener(new MouseAdapter()\r
 351             {\r
 352               public void mousePressed(MouseEvent evt)\r
 353               {\r
 354                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 355                 {\r
 356                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 357 \r
 358                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
 359                       "Remove from default list?",\r
 360                       "Remove user defined colour",\r
 361                       JOptionPane.YES_NO_OPTION);\r
 362                   if(option == JOptionPane.YES_OPTION)\r
 363                   {\r
 364                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
 365                     coloursMenu.remove(radioItem);\r
 366                   }\r
 367                   else\r
 368                     radioItem.addActionListener(new ActionListener()\r
 369                     {\r
 370                       public void actionPerformed(ActionEvent evt)\r
 371                       {\r
 372                         user_actionPerformed(evt);\r
 373                       }\r
 374                     });\r
 375                 }\r
 376               }\r
 377             });\r
 378         radioItem.addActionListener(new ActionListener()\r
 379         {\r
 380           public void actionPerformed(ActionEvent evt)\r
 381           {\r
 382             user_actionPerformed(evt);\r
 383           }\r
 384         });\r
 385         coloursMenu.add(radioItem);\r
 386         bg.add(radioItem);\r
 387       }\r
 388     }\r
 389 \r
 390     viewMenu.add(wire);\r
 391     viewMenu.add(depth);\r
 392     viewMenu.add(zbuffer);\r
 393     viewMenu.add(allchains);\r
 394   }\r
 395 \r
 396   JMenuBar jMenuBar1 = new JMenuBar();\r
 397   JMenu fileMenu = new JMenu();\r
 398   JMenu coloursMenu = new JMenu();\r
 399   JMenu saveMenu = new JMenu();\r
 400   JMenuItem png = new JMenuItem();\r
 401   JMenuItem eps = new JMenuItem();\r
 402   JMenuItem mapping = new JMenuItem();\r
 403   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();\r
 404   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();\r
 405   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();\r
 406   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();\r
 407 \r
 408   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();\r
 409   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();\r
 410   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();\r
 411   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();\r
 412   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();\r
 413   JRadioButtonMenuItem zappo = new  JRadioButtonMenuItem();\r
 414   JRadioButtonMenuItem user = new JRadioButtonMenuItem();\r
 415   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();\r
 416   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();\r
 417   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();\r
 418   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();\r
 419   JMenu viewMenu = new JMenu();\r
 420   JMenuItem background = new JMenuItem();\r
 421   JMenuItem savePDB = new JMenuItem();\r
 422 \r
 423   /**\r
 424    * DOCUMENT ME!\r
 425    *\r
 426    * @param e DOCUMENT ME!\r
 427    */\r
 428   public void eps_actionPerformed(ActionEvent e)\r
 429   {\r
 430     makePDBImage(jalview.util.ImageMaker.EPS);\r
 431   }\r
 432 \r
 433   /**\r
 434    * DOCUMENT ME!\r
 435    *\r
 436    * @param e DOCUMENT ME!\r
 437    */\r
 438   public void png_actionPerformed(ActionEvent e)\r
 439   {\r
 440      makePDBImage(jalview.util.ImageMaker.PNG);\r
 441   }\r
 442 \r
 443   void makePDBImage(int type)\r
 444   {\r
 445     int width = pdbcanvas.getWidth();\r
 446     int height = pdbcanvas.getHeight();\r
 447 \r
 448     jalview.util.ImageMaker im;\r
 449 \r
 450     if (type == jalview.util.ImageMaker.PNG)\r
 451       im = new jalview.util.ImageMaker(this,\r
 452                                        jalview.util.ImageMaker.PNG,\r
 453                                        "Make PNG image from view",\r
 454                                        width, height,\r
 455                                        null, null);\r
 456     else\r
 457       im = new jalview.util.ImageMaker(this,\r
 458                                        jalview.util.ImageMaker.EPS,\r
 459                                        "Make EPS file from view",\r
 460                                        width, height,\r
 461                                        null, this.getTitle());\r
 462 \r
 463     if (im.getGraphics() != null)\r
 464     {\r
 465       pdbcanvas.drawAll(im.getGraphics(), width, height);\r
 466       im.writeImage();\r
 467     }\r
 468   }\r
 469   public void charge_actionPerformed(ActionEvent e)\r
 470   {\r
 471     pdbcanvas.bysequence = false;\r
 472     pdbcanvas.pdb.setChargeColours();\r
 473     pdbcanvas.redrawneeded=true;\r
 474     pdbcanvas.repaint();\r
 475   }\r
 476 \r
 477   public void hydro_actionPerformed(ActionEvent e)\r
 478   {\r
 479     pdbcanvas.bysequence = false;\r
 480     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());\r
 481     pdbcanvas.redrawneeded=true;\r
 482     pdbcanvas.repaint();\r
 483   }\r
 484 \r
 485   public void chain_actionPerformed(ActionEvent e)\r
 486   {\r
 487     pdbcanvas.bysequence = false;\r
 488     pdbcanvas.pdb.setChainColours();\r
 489     pdbcanvas.redrawneeded=true;\r
 490     pdbcanvas.repaint();\r
 491   }\r
 492 \r
 493   public void zbuffer_actionPerformed(ActionEvent e)\r
 494   {\r
 495     pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;\r
 496     pdbcanvas.redrawneeded=true;\r
 497     pdbcanvas.repaint();\r
 498   }\r
 499 \r
 500   public void molecule_actionPerformed(ActionEvent e)\r
 501   {\r
 502     pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;\r
 503     pdbcanvas.redrawneeded=true;\r
 504     pdbcanvas.repaint();\r
 505   }\r
 506 \r
 507   public void depth_actionPerformed(ActionEvent e)\r
 508   {\r
 509   pdbcanvas.depthcue = ! pdbcanvas.depthcue;\r
 510   pdbcanvas.redrawneeded=true;\r
 511     pdbcanvas.repaint();\r
 512   }\r
 513 \r
 514   public void wire_actionPerformed(ActionEvent e)\r
 515   {\r
 516     pdbcanvas.wire = ! pdbcanvas.wire;\r
 517     pdbcanvas.redrawneeded=true;\r
 518     pdbcanvas.repaint();\r
 519   }\r
 520 \r
 521   public void seqButton_actionPerformed(ActionEvent e)\r
 522   {\r
 523     pdbcanvas.bysequence = true;\r
 524     pdbcanvas.updateSeqColours();\r
 525   }\r
 526 \r
 527 \r
 528   public void mapping_actionPerformed(ActionEvent e)\r
 529   {\r
 530     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();\r
 531     Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);\r
 532     cap.setText(pdbcanvas.mappingDetails.toString());\r
 533   }\r
 534 \r
 535   public void allchains_itemStateChanged(ItemEvent e)\r
 536   {\r
 537     pdbcanvas.setAllchainsVisible(allchains.getState());\r
 538   }\r
 539   void showErrorMessage(String error)\r
 540   {\r
 541     JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 542          error, "PDB Viewer Error", JOptionPane.WARNING_MESSAGE);\r
 543   }\r
 544 \r
 545 \r
 546   public void zappo_actionPerformed(ActionEvent e)\r
 547   {\r
 548     pdbcanvas.bysequence = false;\r
 549     pdbcanvas.pdb.setColours(new ZappoColourScheme());\r
 550     pdbcanvas.redrawneeded=true;\r
 551     pdbcanvas.repaint();\r
 552   }\r
 553 \r
 554   public void taylor_actionPerformed(ActionEvent e)\r
 555   {\r
 556     pdbcanvas.bysequence = false;\r
 557     pdbcanvas.pdb.setColours(new TaylorColourScheme());\r
 558     pdbcanvas.redrawneeded=true;\r
 559     pdbcanvas.repaint();\r
 560   }\r
 561 \r
 562   public void helix_actionPerformed(ActionEvent e)\r
 563   {\r
 564     pdbcanvas.bysequence = false;\r
 565     pdbcanvas.pdb.setColours(new HelixColourScheme());\r
 566     pdbcanvas.redrawneeded=true;\r
 567     pdbcanvas.repaint();\r
 568   }\r
 569 \r
 570   public void strand_actionPerformed(ActionEvent e)\r
 571   {\r
 572     pdbcanvas.bysequence = false;\r
 573     pdbcanvas.pdb.setColours(new StrandColourScheme());\r
 574     pdbcanvas.redrawneeded=true;\r
 575     pdbcanvas.repaint();\r
 576   }\r
 577 \r
 578   public void turn_actionPerformed(ActionEvent e)\r
 579   {\r
 580     pdbcanvas.bysequence = false;\r
 581     pdbcanvas.pdb.setColours(new TurnColourScheme());\r
 582     pdbcanvas.redrawneeded=true;\r
 583     pdbcanvas.repaint();\r
 584   }\r
 585 \r
 586   public void buried_actionPerformed(ActionEvent e)\r
 587   {\r
 588     pdbcanvas.bysequence = false;\r
 589     pdbcanvas.pdb.setColours(new BuriedColourScheme());\r
 590     pdbcanvas.redrawneeded=true;\r
 591     pdbcanvas.repaint();\r
 592   }\r
 593 \r
 594   public void user_actionPerformed(ActionEvent e)\r
 595   {\r
 596     if (e.getActionCommand().equals("User Defined..."))\r
 597     {\r
 598       new UserDefinedColours(pdbcanvas, null);\r
 599     }\r
 600     else\r
 601     {\r
 602       UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 603           getUserColourSchemes().get(e.getActionCommand());\r
 604 \r
 605       pdbcanvas.pdb.setColours(udc);\r
 606       pdbcanvas.redrawneeded=true;\r
 607       pdbcanvas.repaint();\r
 608     }\r
 609   }\r
 610 \r
 611   public void background_actionPerformed(ActionEvent e)\r
 612   {\r
 613       java.awt.Color col = JColorChooser.showDialog(this, "Select Background Colour",\r
 614                 pdbcanvas.backgroundColour);\r
 615 \r
 616       if(col!=null)\r
 617        {\r
 618          pdbcanvas.backgroundColour = col;\r
 619          pdbcanvas.redrawneeded = true;\r
 620          pdbcanvas.repaint();\r
 621        }\r
 622   }\r
 623 \r
 624   public void savePDB_actionPerformed(ActionEvent e)\r
 625   {\r
 626     JalviewFileChooser chooser = new JalviewFileChooser(\r
 627         jalview.bin.Cache.getProperty(\r
 628             "LAST_DIRECTORY"));\r
 629 \r
 630     chooser.setFileView(new JalviewFileView());\r
 631     chooser.setDialogTitle("Save PDB File");\r
 632     chooser.setToolTipText("Save");\r
 633 \r
 634     int value = chooser.showSaveDialog(this);\r
 635 \r
 636     if (value == JalviewFileChooser.APPROVE_OPTION)\r
 637     {\r
 638         try\r
 639         {\r
 640           BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));\r
 641           File outFile = chooser.getSelectedFile();\r
 642 \r
 643           PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
 644           String data;\r
 645           while ( (data = in.readLine()) != null)\r
 646           {\r
 647             if (\r
 648                 !( data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)\r
 649                 )\r
 650               out.println(data);\r
 651           }\r
 652           out.close();\r
 653         }\r
 654         catch (Exception ex)\r
 655         {\r
 656           ex.printStackTrace();\r
 657         }\r
 658       }\r
 659   }\r
 660 }\r