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.JvOptionPane;
  28 import jalview.gui.OOMWarning;
  29 import jalview.gui.UserDefinedColours;
  30 import jalview.io.DataSourceType;
  31 import jalview.io.JalviewFileChooser;
  32 import jalview.io.JalviewFileView;
  33 import jalview.schemes.BuriedColourScheme;
  34 import jalview.schemes.HelixColourScheme;
  35 import jalview.schemes.HydrophobicColourScheme;
  36 import jalview.schemes.StrandColourScheme;
  37 import jalview.schemes.TaylorColourScheme;
  38 import jalview.schemes.TurnColourScheme;
  39 import jalview.schemes.UserColourScheme;
  40 import jalview.schemes.ZappoColourScheme;
  41 import jalview.util.MessageManager;
  42 import jalview.ws.ebi.EBIFetchClient;
  43
  44 import java.awt.Color;
  45 import java.awt.event.ActionEvent;
  46 import java.awt.event.ActionListener;
  47 import java.awt.event.ItemEvent;
  48 import java.awt.event.ItemListener;
  49 import java.awt.event.KeyAdapter;
  50 import java.awt.event.KeyEvent;
  51 import java.awt.event.MouseAdapter;
  52 import java.awt.event.MouseEvent;
  53 import java.io.BufferedReader;
  54 import java.io.File;
  55 import java.io.FileOutputStream;
  56 import java.io.FileReader;
  57 import java.io.PrintWriter;
  58 import java.util.Map;
  59
  60 import javax.swing.ButtonGroup;
  61 import javax.swing.JCheckBoxMenuItem;
  62 import javax.swing.JColorChooser;
  63 import javax.swing.JInternalFrame;
  64 import javax.swing.JMenu;
  65 import javax.swing.JMenuBar;
  66 import javax.swing.JMenuItem;
  67 import javax.swing.JRadioButtonMenuItem;
  68
  69 public class PDBViewer extends JInternalFrame implements Runnable
  70 {
  71
  72   /**
  73    * The associated sequence in an alignment
  74    */
  75   PDBCanvas pdbcanvas;
  76
  77   PDBEntry pdbentry;
  78
  79   SequenceI[] seq;
  80
  81   String[] chains;
  82
  83   AlignmentPanel ap;
  84
  85   DataSourceType protocol;
  86
  87   String tmpPDBFile;
  88
  89   public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
  90           AlignmentPanel ap, DataSourceType protocol)
  91   {
  92     this.pdbentry = pdbentry;
  93     this.seq = seq;
  94     this.chains = chains;
  95     this.ap = ap;
  96     this.protocol = protocol;
  97
  98     try
  99     {
 100       jbInit();
 101     } catch (Exception ex)
 102     {
 103       ex.printStackTrace();
 104     }
 105
 106     StringBuffer title = new StringBuffer(seq[0].getName() + ":"
 107             + pdbentry.getFile());
 108
 109     pdbcanvas = new PDBCanvas();
 110
 111     setContentPane(pdbcanvas);
 112
 113     if (pdbentry.getFile() != null)
 114     {
 115       try
 116       {
 117         tmpPDBFile = pdbentry.getFile();
 118         PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
 119                 DataSourceType.FILE);
 120
 121         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 122
 123       } catch (java.io.IOException ex)
 124       {
 125         ex.printStackTrace();
 126       }
 127     }
 128     else
 129     {
 130       Thread worker = new Thread(this);
 131       worker.start();
 132     }
 133
 134     String method = (String) pdbentry.getProperty("method");
 135     if (method != null)
 136     {
 137       title.append(" Method: ");
 138       title.append(method);
 139     }
 140     String ch = (String) pdbentry.getProperty("chains");
 141     if (ch != null)
 142     {
 143       title.append(" Chain:");
 144       title.append(ch);
 145     }
 146     Desktop.addInternalFrame(this, title.toString(), 400, 400);
 147   }
 148
 149   @Override
 150   public void run()
 151   {
 152     try
 153     {
 154       EBIFetchClient ebi = new EBIFetchClient();
 155       String query = "pdb:" + pdbentry.getId();
 156       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "xml")
 157               .getAbsolutePath());
 158
 159       if (pdbentry.getFile() != null)
 160       {
 161         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 162       }
 163     } catch (Exception ex)
 164     {
 165       pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
 166       ex.printStackTrace();
 167     }
 168   }
 169
 170   private void jbInit() throws Exception
 171   {
 172     this.addKeyListener(new KeyAdapter()
 173     {
 174       @Override
 175       public void keyPressed(KeyEvent evt)
 176       {
 177         pdbcanvas.keyPressed(evt);
 178       }
 179     });
 180
 181     this.setJMenuBar(jMenuBar1);
 182     fileMenu.setText(MessageManager.getString("action.file"));
 183     coloursMenu.setText(MessageManager.getString("label.colours"));
 184     saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
 185     saveMenu.setText(MessageManager.getString("action.save_as"));
 186     png.setText("PNG");
 187     png.addActionListener(new ActionListener()
 188     {
 189       @Override
 190       public void actionPerformed(ActionEvent e)
 191       {
 192         png_actionPerformed(e);
 193       }
 194     });
 195     eps.setText("EPS");
 196     eps.addActionListener(new ActionListener()
 197     {
 198       @Override
 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       @Override
 208       public void actionPerformed(ActionEvent e)
 209       {
 210         mapping_actionPerformed(e);
 211       }
 212     });
 213     wire.setText(MessageManager.getString("label.wireframe"));
 214     wire.addActionListener(new ActionListener()
 215     {
 216       @Override
 217       public void actionPerformed(ActionEvent e)
 218       {
 219         wire_actionPerformed(e);
 220       }
 221     });
 222     depth.setSelected(true);
 223     depth.setText(MessageManager.getString("label.depthcue"));
 224     depth.addActionListener(new ActionListener()
 225     {
 226       @Override
 227       public void actionPerformed(ActionEvent e)
 228       {
 229         depth_actionPerformed(e);
 230       }
 231     });
 232     zbuffer.setSelected(true);
 233     zbuffer.setText(MessageManager.getString("label.z_buffering"));
 234     zbuffer.addActionListener(new ActionListener()
 235     {
 236       @Override
 237       public void actionPerformed(ActionEvent e)
 238       {
 239         zbuffer_actionPerformed(e);
 240       }
 241     });
 242     charge.setText(MessageManager.getString("label.charge_cysteine"));
 243     charge.addActionListener(new ActionListener()
 244     {
 245       @Override
 246       public void actionPerformed(ActionEvent e)
 247       {
 248         charge_actionPerformed(e);
 249       }
 250     });
 251     chain.setText(MessageManager.getString("action.by_chain"));
 252     chain.addActionListener(new ActionListener()
 253     {
 254       @Override
 255       public void actionPerformed(ActionEvent e)
 256       {
 257         chain_actionPerformed(e);
 258       }
 259     });
 260     seqButton.setSelected(true);
 261     seqButton.setText(MessageManager.getString("action.by_sequence"));
 262     seqButton.addActionListener(new ActionListener()
 263     {
 264       @Override
 265       public void actionPerformed(ActionEvent e)
 266       {
 267         seqButton_actionPerformed(e);
 268       }
 269     });
 270     allchains.setSelected(true);
 271     allchains.setText(MessageManager.getString("label.show_all_chains"));
 272     allchains.addItemListener(new ItemListener()
 273     {
 274       @Override
 275       public void itemStateChanged(ItemEvent e)
 276       {
 277         allchains_itemStateChanged(e);
 278       }
 279     });
 280     zappo.setText(MessageManager.getString("label.zappo"));
 281     zappo.addActionListener(new ActionListener()
 282     {
 283       @Override
 284       public void actionPerformed(ActionEvent e)
 285       {
 286         zappo_actionPerformed(e);
 287       }
 288     });
 289     taylor.setText(MessageManager.getString("label.taylor"));
 290     taylor.addActionListener(new ActionListener()
 291     {
 292       @Override
 293       public void actionPerformed(ActionEvent e)
 294       {
 295         taylor_actionPerformed(e);
 296       }
 297     });
 298     hydro.setText(MessageManager.getString("label.hydrophobicity"));
 299     hydro.addActionListener(new ActionListener()
 300     {
 301       @Override
 302       public void actionPerformed(ActionEvent e)
 303       {
 304         hydro_actionPerformed(e);
 305       }
 306     });
 307     helix.setText(MessageManager.getString("label.helix_propensity"));
 308     helix.addActionListener(new ActionListener()
 309     {
 310       @Override
 311       public void actionPerformed(ActionEvent e)
 312       {
 313         helix_actionPerformed(e);
 314       }
 315     });
 316     strand.setText(MessageManager.getString("label.strand_propensity"));
 317     strand.addActionListener(new ActionListener()
 318     {
 319       @Override
 320       public void actionPerformed(ActionEvent e)
 321       {
 322         strand_actionPerformed(e);
 323       }
 324     });
 325     turn.setText(MessageManager.getString("label.turn_propensity"));
 326     turn.addActionListener(new ActionListener()
 327     {
 328       @Override
 329       public void actionPerformed(ActionEvent e)
 330       {
 331         turn_actionPerformed(e);
 332       }
 333     });
 334     buried.setText(MessageManager.getString("label.buried_index"));
 335     buried.addActionListener(new ActionListener()
 336     {
 337       @Override
 338       public void actionPerformed(ActionEvent e)
 339       {
 340         buried_actionPerformed(e);
 341       }
 342     });
 343     user.setText(MessageManager.getString("action.user_defined"));
 344     user.addActionListener(new ActionListener()
 345     {
 346       @Override
 347       public void actionPerformed(ActionEvent e)
 348       {
 349         user_actionPerformed(e);
 350       }
 351     });
 352     viewMenu.setText(MessageManager.getString("action.view"));
 353     background
 354             .setText(MessageManager.getString("action.background_colour"));
 355     background.addActionListener(new ActionListener()
 356     {
 357       @Override
 358       public void actionPerformed(ActionEvent e)
 359       {
 360         background_actionPerformed(e);
 361       }
 362     });
 363     savePDB.setText(MessageManager.getString("label.pdb_file"));
 364     savePDB.addActionListener(new ActionListener()
 365     {
 366       @Override
 367       public void actionPerformed(ActionEvent e)
 368       {
 369         savePDB_actionPerformed(e);
 370       }
 371     });
 372     jMenuBar1.add(fileMenu);
 373     jMenuBar1.add(coloursMenu);
 374     jMenuBar1.add(viewMenu);
 375     fileMenu.add(saveMenu);
 376     fileMenu.add(mapping);
 377     saveMenu.add(savePDB);
 378     saveMenu.add(png);
 379     saveMenu.add(eps);
 380     coloursMenu.add(seqButton);
 381     coloursMenu.add(chain);
 382     coloursMenu.add(charge);
 383     coloursMenu.add(zappo);
 384     coloursMenu.add(taylor);
 385     coloursMenu.add(hydro);
 386     coloursMenu.add(helix);
 387     coloursMenu.add(strand);
 388     coloursMenu.add(turn);
 389     coloursMenu.add(buried);
 390     coloursMenu.add(user);
 391     coloursMenu.add(background);
 392     ButtonGroup bg = new ButtonGroup();
 393     bg.add(seqButton);
 394     bg.add(chain);
 395     bg.add(charge);
 396     bg.add(zappo);
 397     bg.add(taylor);
 398     bg.add(hydro);
 399     bg.add(helix);
 400     bg.add(strand);
 401     bg.add(turn);
 402     bg.add(buried);
 403     bg.add(user);
 404
 405     Map<String, UserColourScheme> userColourSchemes = UserDefinedColours
 406             .getUserColourSchemes();
 407     if (userColourSchemes != null)
 408     {
 409       for (String userColour : userColourSchemes.keySet())
 410       {
 411         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 412                 userColour);
 413         radioItem.setName("USER_DEFINED");
 414         radioItem.addMouseListener(new MouseAdapter()
 415         {
 416           @Override
 417           public void mousePressed(MouseEvent evt)
 418           {
 419             if (evt.isPopupTrigger()) // Mac
 420             {
 421               offerRemoval(radioItem);
 422             }
 423           }
 424
 425           @Override
 426           public void mouseReleased(MouseEvent evt)
 427           {
 428             if (evt.isPopupTrigger()) // Windows
 429             {
 430               offerRemoval(radioItem);
 431             }
 432           }
 433
 434           /**
 435            * @param radioItem
 436            */
 437           void offerRemoval(final JRadioButtonMenuItem radioItem)
 438           {
 439             radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 440
 441             int option = JvOptionPane.showInternalConfirmDialog(
 442                     jalview.gui.Desktop.desktop, MessageManager
 443                             .getString("label.remove_from_default_list"),
 444                     MessageManager
 445                             .getString("label.remove_user_defined_colour"),
 446                     JvOptionPane.YES_NO_OPTION);
 447             if (option == JvOptionPane.YES_OPTION)
 448             {
 449               jalview.gui.UserDefinedColours
 450                       .removeColourFromDefaults(radioItem.getText());
 451               coloursMenu.remove(radioItem);
 452             }
 453             else
 454             {
 455               radioItem.addActionListener(new ActionListener()
 456               {
 457                 @Override
 458                 public void actionPerformed(ActionEvent evt)
 459                 {
 460                   user_actionPerformed(evt);
 461                 }
 462               });
 463             }
 464           }
 465         });
 466         radioItem.addActionListener(new ActionListener()
 467         {
 468           @Override
 469           public void actionPerformed(ActionEvent evt)
 470           {
 471             user_actionPerformed(evt);
 472           }
 473         });
 474         coloursMenu.add(radioItem);
 475         bg.add(radioItem);
 476       }
 477     }
 478
 479     viewMenu.add(wire);
 480     viewMenu.add(depth);
 481     viewMenu.add(zbuffer);
 482     viewMenu.add(allchains);
 483   }
 484
 485   JMenuBar jMenuBar1 = new JMenuBar();
 486
 487   JMenu fileMenu = new JMenu();
 488
 489   JMenu coloursMenu = new JMenu();
 490
 491   JMenu saveMenu = new JMenu();
 492
 493   JMenuItem png = new JMenuItem();
 494
 495   JMenuItem eps = new JMenuItem();
 496
 497   JMenuItem mapping = new JMenuItem();
 498
 499   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 500
 501   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 502
 503   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 504
 505   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 506
 507   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 508
 509   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 510
 511   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 512
 513   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 514
 515   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 516
 517   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 518
 519   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 520
 521   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 522
 523   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 524
 525   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 526
 527   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 528
 529   JMenu viewMenu = new JMenu();
 530
 531   JMenuItem background = new JMenuItem();
 532
 533   JMenuItem savePDB = new JMenuItem();
 534
 535   /**
 536    * DOCUMENT ME!
 537    *
 538    * @param e
 539    *          DOCUMENT ME!
 540    */
 541   public void eps_actionPerformed(ActionEvent e)
 542   {
 543     makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
 544   }
 545
 546   /**
 547    * DOCUMENT ME!
 548    *
 549    * @param e
 550    *          DOCUMENT ME!
 551    */
 552   public void png_actionPerformed(ActionEvent e)
 553   {
 554     makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
 555   }
 556
 557   void makePDBImage(jalview.util.ImageMaker.TYPE type)
 558   {
 559     int width = pdbcanvas.getWidth();
 560     int height = pdbcanvas.getHeight();
 561
 562     jalview.util.ImageMaker im;
 563
 564     if (type == jalview.util.ImageMaker.TYPE.PNG)
 565     {
 566       im = new jalview.util.ImageMaker(this,
 567               jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
 568               width, height, null, null, null, 0, false);
 569     }
 570     else if (type == jalview.util.ImageMaker.TYPE.EPS)
 571     {
 572       im = new jalview.util.ImageMaker(this,
 573               jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
 574               width, height, null, this.getTitle(), null, 0, false);
 575     }
 576     else
 577     {
 578
 579       im = new jalview.util.ImageMaker(this,
 580               jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
 581               width, height, null, this.getTitle(), null, 0, false);
 582     }
 583
 584     if (im.getGraphics() != null)
 585     {
 586       pdbcanvas.drawAll(im.getGraphics(), width, height);
 587       im.writeImage();
 588     }
 589   }
 590
 591   public void charge_actionPerformed(ActionEvent e)
 592   {
 593     pdbcanvas.bysequence = false;
 594     pdbcanvas.pdb.setChargeColours();
 595     pdbcanvas.redrawneeded = true;
 596     pdbcanvas.repaint();
 597   }
 598
 599   public void hydro_actionPerformed(ActionEvent e)
 600   {
 601     pdbcanvas.bysequence = false;
 602     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 603     pdbcanvas.redrawneeded = true;
 604     pdbcanvas.repaint();
 605   }
 606
 607   public void chain_actionPerformed(ActionEvent e)
 608   {
 609     pdbcanvas.bysequence = false;
 610     pdbcanvas.pdb.setChainColours();
 611     pdbcanvas.redrawneeded = true;
 612     pdbcanvas.repaint();
 613   }
 614
 615   public void zbuffer_actionPerformed(ActionEvent e)
 616   {
 617     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 618     pdbcanvas.redrawneeded = true;
 619     pdbcanvas.repaint();
 620   }
 621
 622   public void molecule_actionPerformed(ActionEvent e)
 623   {
 624     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 625     pdbcanvas.redrawneeded = true;
 626     pdbcanvas.repaint();
 627   }
 628
 629   public void depth_actionPerformed(ActionEvent e)
 630   {
 631     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 632     pdbcanvas.redrawneeded = true;
 633     pdbcanvas.repaint();
 634   }
 635
 636   public void wire_actionPerformed(ActionEvent e)
 637   {
 638     pdbcanvas.wire = !pdbcanvas.wire;
 639     pdbcanvas.redrawneeded = true;
 640     pdbcanvas.repaint();
 641   }
 642
 643   public void seqButton_actionPerformed(ActionEvent e)
 644   {
 645     pdbcanvas.bysequence = true;
 646     pdbcanvas.updateSeqColours();
 647   }
 648
 649   public void mapping_actionPerformed(ActionEvent e)
 650   {
 651     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 652     try
 653     {
 654       cap.setText(pdbcanvas.mappingDetails.toString());
 655       Desktop.addInternalFrame(cap,
 656               MessageManager.getString("label.pdb_sequence_mapping"), 550,
 657               600);
 658     } catch (OutOfMemoryError oom)
 659     {
 660       new OOMWarning("Opening sequence to structure mapping report", oom);
 661       cap.dispose();
 662     }
 663   }
 664
 665   public void allchains_itemStateChanged(ItemEvent e)
 666   {
 667     pdbcanvas.setAllchainsVisible(allchains.getState());
 668   }
 669
 670   public void zappo_actionPerformed(ActionEvent e)
 671   {
 672     pdbcanvas.bysequence = false;
 673     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 674     pdbcanvas.redrawneeded = true;
 675     pdbcanvas.repaint();
 676   }
 677
 678   public void taylor_actionPerformed(ActionEvent e)
 679   {
 680     pdbcanvas.bysequence = false;
 681     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 682     pdbcanvas.redrawneeded = true;
 683     pdbcanvas.repaint();
 684   }
 685
 686   public void helix_actionPerformed(ActionEvent e)
 687   {
 688     pdbcanvas.bysequence = false;
 689     pdbcanvas.pdb.setColours(new HelixColourScheme());
 690     pdbcanvas.redrawneeded = true;
 691     pdbcanvas.repaint();
 692   }
 693
 694   public void strand_actionPerformed(ActionEvent e)
 695   {
 696     pdbcanvas.bysequence = false;
 697     pdbcanvas.pdb.setColours(new StrandColourScheme());
 698     pdbcanvas.redrawneeded = true;
 699     pdbcanvas.repaint();
 700   }
 701
 702   public void turn_actionPerformed(ActionEvent e)
 703   {
 704     pdbcanvas.bysequence = false;
 705     pdbcanvas.pdb.setColours(new TurnColourScheme());
 706     pdbcanvas.redrawneeded = true;
 707     pdbcanvas.repaint();
 708   }
 709
 710   public void buried_actionPerformed(ActionEvent e)
 711   {
 712     pdbcanvas.bysequence = false;
 713     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 714     pdbcanvas.redrawneeded = true;
 715     pdbcanvas.repaint();
 716   }
 717
 718   public void user_actionPerformed(ActionEvent e)
 719   {
 720     if (e.getActionCommand().equals(
 721             MessageManager.getString("action.user_defined")))
 722     {
 723       // new UserDefinedColours(pdbcanvas, null);
 724     }
 725     else
 726     {
 727       UserColourScheme udc = UserDefinedColours
 728               .getUserColourSchemes().get(e.getActionCommand());
 729
 730       pdbcanvas.pdb.setColours(udc);
 731       pdbcanvas.redrawneeded = true;
 732       pdbcanvas.repaint();
 733     }
 734   }
 735
 736   public void background_actionPerformed(ActionEvent e)
 737   {
 738     Color col = JColorChooser.showDialog(this,
 739             MessageManager.getString("label.select_background_colour"),
 740             pdbcanvas.backgroundColour);
 741
 742     if (col != null)
 743     {
 744       pdbcanvas.backgroundColour = col;
 745       pdbcanvas.redrawneeded = true;
 746       pdbcanvas.repaint();
 747     }
 748   }
 749
 750   public void savePDB_actionPerformed(ActionEvent e)
 751   {
 752     JalviewFileChooser chooser = new JalviewFileChooser(
 753             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 754
 755     chooser.setFileView(new JalviewFileView());
 756     chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
 757     chooser.setToolTipText(MessageManager.getString("action.save"));
 758
 759     int value = chooser.showSaveDialog(this);
 760
 761     if (value == JalviewFileChooser.APPROVE_OPTION)
 762     {
 763       try
 764       {
 765         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 766         File outFile = chooser.getSelectedFile();
 767
 768         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 769         String data;
 770         while ((data = in.readLine()) != null)
 771         {
 772           if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
 773           {
 774             out.println(data);
 775           }
 776         }
 777         out.close();
 778         in.close();
 779       } catch (Exception ex)
 780       {
 781         ex.printStackTrace();
 782       }
 783     }
 784   }
 785 }