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 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   @Override
 149   public void run()
 150   {
 151     try
 152     {
 153       EBIFetchClient ebi = new EBIFetchClient();
 154       String query = "pdb:" + pdbentry.getId();
 155       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw", ".xml")
 156               .getAbsolutePath());
 157
 158       if (pdbentry.getFile() != null)
 159       {
 160         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 161       }
 162     } catch (Exception ex)
 163     {
 164       pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
 165       ex.printStackTrace();
 166     }
 167   }
 168
 169   private void jbInit() throws Exception
 170   {
 171     this.addKeyListener(new KeyAdapter()
 172     {
 173       @Override
 174       public void keyPressed(KeyEvent evt)
 175       {
 176         pdbcanvas.keyPressed(evt);
 177       }
 178     });
 179
 180     this.setJMenuBar(jMenuBar1);
 181     fileMenu.setText(MessageManager.getString("action.file"));
 182     coloursMenu.setText(MessageManager.getString("label.colours"));
 183     saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
 184     saveMenu.setText(MessageManager.getString("action.save_as"));
 185     png.setText("PNG");
 186     png.addActionListener(new ActionListener()
 187     {
 188       @Override
 189       public void actionPerformed(ActionEvent e)
 190       {
 191         png_actionPerformed(e);
 192       }
 193     });
 194     eps.setText("EPS");
 195     eps.addActionListener(new ActionListener()
 196     {
 197       @Override
 198       public void actionPerformed(ActionEvent e)
 199       {
 200         eps_actionPerformed(e);
 201       }
 202     });
 203     mapping.setText(MessageManager.getString("label.view_mapping"));
 204     mapping.addActionListener(new ActionListener()
 205     {
 206       @Override
 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       @Override
 216       public void actionPerformed(ActionEvent e)
 217       {
 218         wire_actionPerformed(e);
 219       }
 220     });
 221     depth.setSelected(true);
 222     depth.setText(MessageManager.getString("label.depthcue"));
 223     depth.addActionListener(new ActionListener()
 224     {
 225       @Override
 226       public void actionPerformed(ActionEvent e)
 227       {
 228         depth_actionPerformed(e);
 229       }
 230     });
 231     zbuffer.setSelected(true);
 232     zbuffer.setText(MessageManager.getString("label.z_buffering"));
 233     zbuffer.addActionListener(new ActionListener()
 234     {
 235       @Override
 236       public void actionPerformed(ActionEvent e)
 237       {
 238         zbuffer_actionPerformed(e);
 239       }
 240     });
 241     charge.setText(MessageManager.getString("label.charge_cysteine"));
 242     charge.addActionListener(new ActionListener()
 243     {
 244       @Override
 245       public void actionPerformed(ActionEvent e)
 246       {
 247         charge_actionPerformed(e);
 248       }
 249     });
 250     chain.setText(MessageManager.getString("action.by_chain"));
 251     chain.addActionListener(new ActionListener()
 252     {
 253       @Override
 254       public void actionPerformed(ActionEvent e)
 255       {
 256         chain_actionPerformed(e);
 257       }
 258     });
 259     seqButton.setSelected(true);
 260     seqButton.setText(MessageManager.getString("action.by_sequence"));
 261     seqButton.addActionListener(new ActionListener()
 262     {
 263       @Override
 264       public void actionPerformed(ActionEvent e)
 265       {
 266         seqButton_actionPerformed(e);
 267       }
 268     });
 269     allchains.setSelected(true);
 270     allchains.setText(MessageManager.getString("label.show_all_chains"));
 271     allchains.addItemListener(new ItemListener()
 272     {
 273       @Override
 274       public void itemStateChanged(ItemEvent e)
 275       {
 276         allchains_itemStateChanged(e);
 277       }
 278     });
 279     zappo.setText(MessageManager.getString("label.zappo"));
 280     zappo.addActionListener(new ActionListener()
 281     {
 282       @Override
 283       public void actionPerformed(ActionEvent e)
 284       {
 285         zappo_actionPerformed(e);
 286       }
 287     });
 288     taylor.setText(MessageManager.getString("label.taylor"));
 289     taylor.addActionListener(new ActionListener()
 290     {
 291       @Override
 292       public void actionPerformed(ActionEvent e)
 293       {
 294         taylor_actionPerformed(e);
 295       }
 296     });
 297     hydro.setText(MessageManager.getString("label.hydrophobicity"));
 298     hydro.addActionListener(new ActionListener()
 299     {
 300       @Override
 301       public void actionPerformed(ActionEvent e)
 302       {
 303         hydro_actionPerformed(e);
 304       }
 305     });
 306     helix.setText(MessageManager.getString("label.helix_propensity"));
 307     helix.addActionListener(new ActionListener()
 308     {
 309       @Override
 310       public void actionPerformed(ActionEvent e)
 311       {
 312         helix_actionPerformed(e);
 313       }
 314     });
 315     strand.setText(MessageManager.getString("label.strand_propensity"));
 316     strand.addActionListener(new ActionListener()
 317     {
 318       @Override
 319       public void actionPerformed(ActionEvent e)
 320       {
 321         strand_actionPerformed(e);
 322       }
 323     });
 324     turn.setText(MessageManager.getString("label.turn_propensity"));
 325     turn.addActionListener(new ActionListener()
 326     {
 327       @Override
 328       public void actionPerformed(ActionEvent e)
 329       {
 330         turn_actionPerformed(e);
 331       }
 332     });
 333     buried.setText(MessageManager.getString("label.buried_index"));
 334     buried.addActionListener(new ActionListener()
 335     {
 336       @Override
 337       public void actionPerformed(ActionEvent e)
 338       {
 339         buried_actionPerformed(e);
 340       }
 341     });
 342     user.setText(MessageManager.getString("action.user_defined"));
 343     user.addActionListener(new ActionListener()
 344     {
 345       @Override
 346       public void actionPerformed(ActionEvent e)
 347       {
 348         user_actionPerformed(e);
 349       }
 350     });
 351     viewMenu.setText(MessageManager.getString("action.view"));
 352     background
 353             .setText(MessageManager.getString("action.background_colour"));
 354     background.addActionListener(new ActionListener()
 355     {
 356       @Override
 357       public void actionPerformed(ActionEvent e)
 358       {
 359         background_actionPerformed(e);
 360       }
 361     });
 362     savePDB.setText(MessageManager.getString("label.pdb_file"));
 363     savePDB.addActionListener(new ActionListener()
 364     {
 365       @Override
 366       public void actionPerformed(ActionEvent e)
 367       {
 368         savePDB_actionPerformed(e);
 369       }
 370     });
 371     jMenuBar1.add(fileMenu);
 372     jMenuBar1.add(coloursMenu);
 373     jMenuBar1.add(viewMenu);
 374     fileMenu.add(saveMenu);
 375     fileMenu.add(mapping);
 376     saveMenu.add(savePDB);
 377     saveMenu.add(png);
 378     saveMenu.add(eps);
 379     coloursMenu.add(seqButton);
 380     coloursMenu.add(chain);
 381     coloursMenu.add(charge);
 382     coloursMenu.add(zappo);
 383     coloursMenu.add(taylor);
 384     coloursMenu.add(hydro);
 385     coloursMenu.add(helix);
 386     coloursMenu.add(strand);
 387     coloursMenu.add(turn);
 388     coloursMenu.add(buried);
 389     coloursMenu.add(user);
 390     coloursMenu.add(background);
 391     ButtonGroup bg = new ButtonGroup();
 392     bg.add(seqButton);
 393     bg.add(chain);
 394     bg.add(charge);
 395     bg.add(zappo);
 396     bg.add(taylor);
 397     bg.add(hydro);
 398     bg.add(helix);
 399     bg.add(strand);
 400     bg.add(turn);
 401     bg.add(buried);
 402     bg.add(user);
 403
 404     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 405     {
 406       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 407               .getUserColourSchemes().keys();
 408
 409       while (userColours.hasMoreElements())
 410       {
 411         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 412                 userColours.nextElement().toString());
 413         radioItem.setName("USER_DEFINED");
 414         radioItem.addMouseListener(new MouseAdapter()
 415         {
 416           @Override
 417           public void mousePressed(MouseEvent evt)
 418           {
 419             if (evt.isControlDown()
 420                     || SwingUtilities.isRightMouseButton(evt))
 421             {
 422               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 423
 424               int option = JOptionPane.showInternalConfirmDialog(
 425                       jalview.gui.Desktop.desktop,
 426                       MessageManager
 427                               .getString("label.remove_from_default_list"),
 428                       MessageManager
 429                               .getString("label.remove_user_defined_colour"),
 430                       JOptionPane.YES_NO_OPTION);
 431               if (option == JOptionPane.YES_OPTION)
 432               {
 433                 jalview.gui.UserDefinedColours
 434                         .removeColourFromDefaults(radioItem.getText());
 435                 coloursMenu.remove(radioItem);
 436               }
 437               else
 438               {
 439                 radioItem.addActionListener(new ActionListener()
 440                 {
 441                   @Override
 442                   public void actionPerformed(ActionEvent evt)
 443                   {
 444                     user_actionPerformed(evt);
 445                   }
 446                 });
 447               }
 448             }
 449           }
 450         });
 451         radioItem.addActionListener(new ActionListener()
 452         {
 453           @Override
 454           public void actionPerformed(ActionEvent evt)
 455           {
 456             user_actionPerformed(evt);
 457           }
 458         });
 459         coloursMenu.add(radioItem);
 460         bg.add(radioItem);
 461       }
 462     }
 463
 464     viewMenu.add(wire);
 465     viewMenu.add(depth);
 466     viewMenu.add(zbuffer);
 467     viewMenu.add(allchains);
 468   }
 469
 470   JMenuBar jMenuBar1 = new JMenuBar();
 471
 472   JMenu fileMenu = new JMenu();
 473
 474   JMenu coloursMenu = new JMenu();
 475
 476   JMenu saveMenu = new JMenu();
 477
 478   JMenuItem png = new JMenuItem();
 479
 480   JMenuItem eps = new JMenuItem();
 481
 482   JMenuItem mapping = new JMenuItem();
 483
 484   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 485
 486   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 487
 488   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 489
 490   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 491
 492   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 493
 494   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 495
 496   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 497
 498   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 499
 500   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 501
 502   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 503
 504   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 505
 506   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 507
 508   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 509
 510   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 511
 512   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 513
 514   JMenu viewMenu = new JMenu();
 515
 516   JMenuItem background = new JMenuItem();
 517
 518   JMenuItem savePDB = new JMenuItem();
 519
 520   /**
 521    * DOCUMENT ME!
 522    *
 523    * @param e
 524    *          DOCUMENT ME!
 525    */
 526   public void eps_actionPerformed(ActionEvent e)
 527   {
 528     makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
 529   }
 530
 531   /**
 532    * DOCUMENT ME!
 533    *
 534    * @param e
 535    *          DOCUMENT ME!
 536    */
 537   public void png_actionPerformed(ActionEvent e)
 538   {
 539     makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
 540   }
 541
 542   void makePDBImage(jalview.util.ImageMaker.TYPE type)
 543   {
 544     int width = pdbcanvas.getWidth();
 545     int height = pdbcanvas.getHeight();
 546
 547     jalview.util.ImageMaker im;
 548
 549     if (type == jalview.util.ImageMaker.TYPE.PNG)
 550     {
 551       im = new jalview.util.ImageMaker(this,
 552               jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
 553               width, height, null, null, null, 0, false);
 554     }
 555     else if (type == jalview.util.ImageMaker.TYPE.EPS)
 556     {
 557       im = new jalview.util.ImageMaker(this,
 558               jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
 559               width, height, null, this.getTitle(), null, 0, false);
 560     }
 561     else
 562     {
 563
 564       im = new jalview.util.ImageMaker(this,
 565               jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
 566               width, height, null, this.getTitle(), null, 0, false);
 567     }
 568
 569     if (im.getGraphics() != null)
 570     {
 571       pdbcanvas.drawAll(im.getGraphics(), width, height);
 572       im.writeImage();
 573     }
 574   }
 575
 576   public void charge_actionPerformed(ActionEvent e)
 577   {
 578     pdbcanvas.bysequence = false;
 579     pdbcanvas.pdb.setChargeColours();
 580     pdbcanvas.redrawneeded = true;
 581     pdbcanvas.repaint();
 582   }
 583
 584   public void hydro_actionPerformed(ActionEvent e)
 585   {
 586     pdbcanvas.bysequence = false;
 587     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 588     pdbcanvas.redrawneeded = true;
 589     pdbcanvas.repaint();
 590   }
 591
 592   public void chain_actionPerformed(ActionEvent e)
 593   {
 594     pdbcanvas.bysequence = false;
 595     pdbcanvas.pdb.setChainColours();
 596     pdbcanvas.redrawneeded = true;
 597     pdbcanvas.repaint();
 598   }
 599
 600   public void zbuffer_actionPerformed(ActionEvent e)
 601   {
 602     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 603     pdbcanvas.redrawneeded = true;
 604     pdbcanvas.repaint();
 605   }
 606
 607   public void molecule_actionPerformed(ActionEvent e)
 608   {
 609     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 610     pdbcanvas.redrawneeded = true;
 611     pdbcanvas.repaint();
 612   }
 613
 614   public void depth_actionPerformed(ActionEvent e)
 615   {
 616     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 617     pdbcanvas.redrawneeded = true;
 618     pdbcanvas.repaint();
 619   }
 620
 621   public void wire_actionPerformed(ActionEvent e)
 622   {
 623     pdbcanvas.wire = !pdbcanvas.wire;
 624     pdbcanvas.redrawneeded = true;
 625     pdbcanvas.repaint();
 626   }
 627
 628   public void seqButton_actionPerformed(ActionEvent e)
 629   {
 630     pdbcanvas.bysequence = true;
 631     pdbcanvas.updateSeqColours();
 632   }
 633
 634   public void mapping_actionPerformed(ActionEvent e)
 635   {
 636     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 637     try
 638     {
 639       cap.setText(pdbcanvas.mappingDetails.toString());
 640       Desktop.addInternalFrame(cap,
 641               MessageManager.getString("label.pdb_sequence_mapping"), 550,
 642               600);
 643     } catch (OutOfMemoryError oom)
 644     {
 645       new OOMWarning("Opening sequence to structure mapping report", oom);
 646       cap.dispose();
 647     }
 648   }
 649
 650   public void allchains_itemStateChanged(ItemEvent e)
 651   {
 652     pdbcanvas.setAllchainsVisible(allchains.getState());
 653   }
 654
 655   public void zappo_actionPerformed(ActionEvent e)
 656   {
 657     pdbcanvas.bysequence = false;
 658     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 659     pdbcanvas.redrawneeded = true;
 660     pdbcanvas.repaint();
 661   }
 662
 663   public void taylor_actionPerformed(ActionEvent e)
 664   {
 665     pdbcanvas.bysequence = false;
 666     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 667     pdbcanvas.redrawneeded = true;
 668     pdbcanvas.repaint();
 669   }
 670
 671   public void helix_actionPerformed(ActionEvent e)
 672   {
 673     pdbcanvas.bysequence = false;
 674     pdbcanvas.pdb.setColours(new HelixColourScheme());
 675     pdbcanvas.redrawneeded = true;
 676     pdbcanvas.repaint();
 677   }
 678
 679   public void strand_actionPerformed(ActionEvent e)
 680   {
 681     pdbcanvas.bysequence = false;
 682     pdbcanvas.pdb.setColours(new StrandColourScheme());
 683     pdbcanvas.redrawneeded = true;
 684     pdbcanvas.repaint();
 685   }
 686
 687   public void turn_actionPerformed(ActionEvent e)
 688   {
 689     pdbcanvas.bysequence = false;
 690     pdbcanvas.pdb.setColours(new TurnColourScheme());
 691     pdbcanvas.redrawneeded = true;
 692     pdbcanvas.repaint();
 693   }
 694
 695   public void buried_actionPerformed(ActionEvent e)
 696   {
 697     pdbcanvas.bysequence = false;
 698     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 699     pdbcanvas.redrawneeded = true;
 700     pdbcanvas.repaint();
 701   }
 702
 703   public void user_actionPerformed(ActionEvent e)
 704   {
 705     if (e.getActionCommand().equals(
 706             MessageManager.getString("action.user_defined")))
 707     {
 708       // new UserDefinedColours(pdbcanvas, null);
 709     }
 710     else
 711     {
 712       UserColourScheme udc = (UserColourScheme) UserDefinedColours
 713               .getUserColourSchemes().get(e.getActionCommand());
 714
 715       pdbcanvas.pdb.setColours(udc);
 716       pdbcanvas.redrawneeded = true;
 717       pdbcanvas.repaint();
 718     }
 719   }
 720
 721   public void background_actionPerformed(ActionEvent e)
 722   {
 723     java.awt.Color col = JColorChooser.showDialog(this,
 724             MessageManager.getString("label.select_backgroud_colour"),
 725             pdbcanvas.backgroundColour);
 726
 727     if (col != null)
 728     {
 729       pdbcanvas.backgroundColour = col;
 730       pdbcanvas.redrawneeded = true;
 731       pdbcanvas.repaint();
 732     }
 733   }
 734
 735   public void savePDB_actionPerformed(ActionEvent e)
 736   {
 737     JalviewFileChooser chooser = new JalviewFileChooser(
 738             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 739
 740     chooser.setFileView(new JalviewFileView());
 741     chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
 742     chooser.setToolTipText(MessageManager.getString("action.save"));
 743
 744     int value = chooser.showSaveDialog(this);
 745
 746     if (value == JalviewFileChooser.APPROVE_OPTION)
 747     {
 748       try
 749       {
 750         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 751         File outFile = chooser.getSelectedFile();
 752
 753         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 754         String data;
 755         while ((data = in.readLine()) != null)
 756         {
 757           if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
 758           {
 759             out.println(data);
 760           }
 761         }
 762         out.close();
 763         in.close();
 764       } catch (Exception ex)
 765       {
 766         ex.printStackTrace();
 767       }
 768     }
 769   }
 770 }