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
  66 public class PDBViewer extends JInternalFrame implements Runnable
  67 {
  68
  69   /**
  70    * The associated sequence in an alignment
  71    */
  72   PDBCanvas pdbcanvas;
  73
  74   PDBEntry pdbentry;
  75
  76   SequenceI[] seq;
  77
  78   String[] chains;
  79
  80   AlignmentPanel ap;
  81
  82   String protocol;
  83
  84   String tmpPDBFile;
  85
  86   public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
  87           AlignmentPanel ap, String protocol)
  88   {
  89     this.pdbentry = pdbentry;
  90     this.seq = seq;
  91     this.chains = chains;
  92     this.ap = ap;
  93     this.protocol = protocol;
  94
  95     try
  96     {
  97       jbInit();
  98     } catch (Exception ex)
  99     {
 100       ex.printStackTrace();
 101     }
 102
 103     StringBuffer title = new StringBuffer(seq[0].getName() + ":"
 104             + pdbentry.getFile());
 105
 106     pdbcanvas = new PDBCanvas();
 107
 108     setContentPane(pdbcanvas);
 109
 110     if (pdbentry.getFile() != null)
 111     {
 112       try
 113       {
 114         tmpPDBFile = pdbentry.getFile();
 115         PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
 116                 jalview.io.AppletFormatAdapter.FILE);
 117
 118         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 119
 120       } catch (java.io.IOException ex)
 121       {
 122         ex.printStackTrace();
 123       }
 124     }
 125     else
 126     {
 127       Thread worker = new Thread(this);
 128       worker.start();
 129     }
 130
 131     String method = (String) pdbentry.getProperty("method");
 132     if (method != null)
 133     {
 134       title.append(" Method: ");
 135       title.append(method);
 136     }
 137     String ch = (String) pdbentry.getProperty("chains");
 138     if (ch != null)
 139     {
 140       title.append(" Chain:");
 141       title.append(ch);
 142     }
 143     Desktop.addInternalFrame(this, title.toString(), 400, 400);
 144   }
 145
 146   @Override
 147   public void run()
 148   {
 149     try
 150     {
 151       EBIFetchClient ebi = new EBIFetchClient();
 152       String query = "pdb:" + pdbentry.getId();
 153       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", ".xml")
 154               .getAbsolutePath());
 155
 156       if (pdbentry.getFile() != null)
 157       {
 158         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 159       }
 160     } catch (Exception ex)
 161     {
 162       pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
 163       ex.printStackTrace();
 164     }
 165   }
 166
 167   private void jbInit() throws Exception
 168   {
 169     this.addKeyListener(new KeyAdapter()
 170     {
 171       @Override
 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       @Override
 187       public void actionPerformed(ActionEvent e)
 188       {
 189         png_actionPerformed(e);
 190       }
 191     });
 192     eps.setText("EPS");
 193     eps.addActionListener(new ActionListener()
 194     {
 195       @Override
 196       public void actionPerformed(ActionEvent e)
 197       {
 198         eps_actionPerformed(e);
 199       }
 200     });
 201     mapping.setText(MessageManager.getString("label.view_mapping"));
 202     mapping.addActionListener(new ActionListener()
 203     {
 204       @Override
 205       public void actionPerformed(ActionEvent e)
 206       {
 207         mapping_actionPerformed(e);
 208       }
 209     });
 210     wire.setText(MessageManager.getString("label.wireframe"));
 211     wire.addActionListener(new ActionListener()
 212     {
 213       @Override
 214       public void actionPerformed(ActionEvent e)
 215       {
 216         wire_actionPerformed(e);
 217       }
 218     });
 219     depth.setSelected(true);
 220     depth.setText(MessageManager.getString("label.depthcue"));
 221     depth.addActionListener(new ActionListener()
 222     {
 223       @Override
 224       public void actionPerformed(ActionEvent e)
 225       {
 226         depth_actionPerformed(e);
 227       }
 228     });
 229     zbuffer.setSelected(true);
 230     zbuffer.setText(MessageManager.getString("label.z_buffering"));
 231     zbuffer.addActionListener(new ActionListener()
 232     {
 233       @Override
 234       public void actionPerformed(ActionEvent e)
 235       {
 236         zbuffer_actionPerformed(e);
 237       }
 238     });
 239     charge.setText(MessageManager.getString("label.charge_cysteine"));
 240     charge.addActionListener(new ActionListener()
 241     {
 242       @Override
 243       public void actionPerformed(ActionEvent e)
 244       {
 245         charge_actionPerformed(e);
 246       }
 247     });
 248     chain.setText(MessageManager.getString("action.by_chain"));
 249     chain.addActionListener(new ActionListener()
 250     {
 251       @Override
 252       public void actionPerformed(ActionEvent e)
 253       {
 254         chain_actionPerformed(e);
 255       }
 256     });
 257     seqButton.setSelected(true);
 258     seqButton.setText(MessageManager.getString("action.by_sequence"));
 259     seqButton.addActionListener(new ActionListener()
 260     {
 261       @Override
 262       public void actionPerformed(ActionEvent e)
 263       {
 264         seqButton_actionPerformed(e);
 265       }
 266     });
 267     allchains.setSelected(true);
 268     allchains.setText(MessageManager.getString("label.show_all_chains"));
 269     allchains.addItemListener(new ItemListener()
 270     {
 271       @Override
 272       public void itemStateChanged(ItemEvent e)
 273       {
 274         allchains_itemStateChanged(e);
 275       }
 276     });
 277     zappo.setText(MessageManager.getString("label.zappo"));
 278     zappo.addActionListener(new ActionListener()
 279     {
 280       @Override
 281       public void actionPerformed(ActionEvent e)
 282       {
 283         zappo_actionPerformed(e);
 284       }
 285     });
 286     taylor.setText(MessageManager.getString("label.taylor"));
 287     taylor.addActionListener(new ActionListener()
 288     {
 289       @Override
 290       public void actionPerformed(ActionEvent e)
 291       {
 292         taylor_actionPerformed(e);
 293       }
 294     });
 295     hydro.setText(MessageManager.getString("label.hydrophobicity"));
 296     hydro.addActionListener(new ActionListener()
 297     {
 298       @Override
 299       public void actionPerformed(ActionEvent e)
 300       {
 301         hydro_actionPerformed(e);
 302       }
 303     });
 304     helix.setText(MessageManager.getString("label.helix_propensity"));
 305     helix.addActionListener(new ActionListener()
 306     {
 307       @Override
 308       public void actionPerformed(ActionEvent e)
 309       {
 310         helix_actionPerformed(e);
 311       }
 312     });
 313     strand.setText(MessageManager.getString("label.strand_propensity"));
 314     strand.addActionListener(new ActionListener()
 315     {
 316       @Override
 317       public void actionPerformed(ActionEvent e)
 318       {
 319         strand_actionPerformed(e);
 320       }
 321     });
 322     turn.setText(MessageManager.getString("label.turn_propensity"));
 323     turn.addActionListener(new ActionListener()
 324     {
 325       @Override
 326       public void actionPerformed(ActionEvent e)
 327       {
 328         turn_actionPerformed(e);
 329       }
 330     });
 331     buried.setText(MessageManager.getString("label.buried_index"));
 332     buried.addActionListener(new ActionListener()
 333     {
 334       @Override
 335       public void actionPerformed(ActionEvent e)
 336       {
 337         buried_actionPerformed(e);
 338       }
 339     });
 340     user.setText(MessageManager.getString("action.user_defined"));
 341     user.addActionListener(new ActionListener()
 342     {
 343       @Override
 344       public void actionPerformed(ActionEvent e)
 345       {
 346         user_actionPerformed(e);
 347       }
 348     });
 349     viewMenu.setText(MessageManager.getString("action.view"));
 350     background
 351             .setText(MessageManager.getString("action.background_colour"));
 352     background.addActionListener(new ActionListener()
 353     {
 354       @Override
 355       public void actionPerformed(ActionEvent e)
 356       {
 357         background_actionPerformed(e);
 358       }
 359     });
 360     savePDB.setText(MessageManager.getString("label.pdb_file"));
 361     savePDB.addActionListener(new ActionListener()
 362     {
 363       @Override
 364       public void actionPerformed(ActionEvent e)
 365       {
 366         savePDB_actionPerformed(e);
 367       }
 368     });
 369     jMenuBar1.add(fileMenu);
 370     jMenuBar1.add(coloursMenu);
 371     jMenuBar1.add(viewMenu);
 372     fileMenu.add(saveMenu);
 373     fileMenu.add(mapping);
 374     saveMenu.add(savePDB);
 375     saveMenu.add(png);
 376     saveMenu.add(eps);
 377     coloursMenu.add(seqButton);
 378     coloursMenu.add(chain);
 379     coloursMenu.add(charge);
 380     coloursMenu.add(zappo);
 381     coloursMenu.add(taylor);
 382     coloursMenu.add(hydro);
 383     coloursMenu.add(helix);
 384     coloursMenu.add(strand);
 385     coloursMenu.add(turn);
 386     coloursMenu.add(buried);
 387     coloursMenu.add(user);
 388     coloursMenu.add(background);
 389     ButtonGroup bg = new ButtonGroup();
 390     bg.add(seqButton);
 391     bg.add(chain);
 392     bg.add(charge);
 393     bg.add(zappo);
 394     bg.add(taylor);
 395     bg.add(hydro);
 396     bg.add(helix);
 397     bg.add(strand);
 398     bg.add(turn);
 399     bg.add(buried);
 400     bg.add(user);
 401
 402     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 403     {
 404       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 405               .getUserColourSchemes().keys();
 406
 407       while (userColours.hasMoreElements())
 408       {
 409         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 410                 userColours.nextElement().toString());
 411         radioItem.setName("USER_DEFINED");
 412         radioItem.addMouseListener(new MouseAdapter()
 413         {
 414           @Override
 415           public void mousePressed(MouseEvent evt)
 416           {
 417             if (evt.isPopupTrigger()) // Mac
 418             {
 419               offerRemoval(radioItem);
 420             }
 421           }
 422
 423           @Override
 424           public void mouseReleased(MouseEvent evt)
 425           {
 426             if (evt.isPopupTrigger()) // Windows
 427             {
 428               offerRemoval(radioItem);
 429             }
 430           }
 431
 432           /**
 433            * @param radioItem
 434            */
 435           void offerRemoval(final JRadioButtonMenuItem radioItem)
 436           {
 437             radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 438
 439             int option = JOptionPane.showInternalConfirmDialog(
 440                     jalview.gui.Desktop.desktop,
 441                     MessageManager
 442                             .getString("label.remove_from_default_list"),
 443                     MessageManager
 444                             .getString("label.remove_user_defined_colour"),
 445                     JOptionPane.YES_NO_OPTION);
 446             if (option == JOptionPane.YES_OPTION)
 447             {
 448               jalview.gui.UserDefinedColours
 449                       .removeColourFromDefaults(radioItem.getText());
 450               coloursMenu.remove(radioItem);
 451             }
 452             else
 453             {
 454               radioItem.addActionListener(new ActionListener()
 455               {
 456                 @Override
 457                 public void actionPerformed(ActionEvent evt)
 458                 {
 459                   user_actionPerformed(evt);
 460                 }
 461               });
 462             }
 463           }
 464         });
 465         radioItem.addActionListener(new ActionListener()
 466         {
 467           @Override
 468           public void actionPerformed(ActionEvent evt)
 469           {
 470             user_actionPerformed(evt);
 471           }
 472         });
 473         coloursMenu.add(radioItem);
 474         bg.add(radioItem);
 475       }
 476     }
 477
 478     viewMenu.add(wire);
 479     viewMenu.add(depth);
 480     viewMenu.add(zbuffer);
 481     viewMenu.add(allchains);
 482   }
 483
 484   JMenuBar jMenuBar1 = new JMenuBar();
 485
 486   JMenu fileMenu = new JMenu();
 487
 488   JMenu coloursMenu = new JMenu();
 489
 490   JMenu saveMenu = new JMenu();
 491
 492   JMenuItem png = new JMenuItem();
 493
 494   JMenuItem eps = new JMenuItem();
 495
 496   JMenuItem mapping = new JMenuItem();
 497
 498   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 499
 500   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 501
 502   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 503
 504   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 505
 506   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 507
 508   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 509
 510   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 511
 512   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 513
 514   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 515
 516   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 517
 518   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 519
 520   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 521
 522   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 523
 524   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 525
 526   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 527
 528   JMenu viewMenu = new JMenu();
 529
 530   JMenuItem background = new JMenuItem();
 531
 532   JMenuItem savePDB = new JMenuItem();
 533
 534   /**
 535    * DOCUMENT ME!
 536    *
 537    * @param e
 538    *          DOCUMENT ME!
 539    */
 540   public void eps_actionPerformed(ActionEvent e)
 541   {
 542     makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
 543   }
 544
 545   /**
 546    * DOCUMENT ME!
 547    *
 548    * @param e
 549    *          DOCUMENT ME!
 550    */
 551   public void png_actionPerformed(ActionEvent e)
 552   {
 553     makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
 554   }
 555
 556   void makePDBImage(jalview.util.ImageMaker.TYPE type)
 557   {
 558     int width = pdbcanvas.getWidth();
 559     int height = pdbcanvas.getHeight();
 560
 561     jalview.util.ImageMaker im;
 562
 563     if (type == jalview.util.ImageMaker.TYPE.PNG)
 564     {
 565       im = new jalview.util.ImageMaker(this,
 566               jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
 567               width, height, null, null, null, 0, false);
 568     }
 569     else if (type == jalview.util.ImageMaker.TYPE.EPS)
 570     {
 571       im = new jalview.util.ImageMaker(this,
 572               jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
 573               width, height, null, this.getTitle(), null, 0, false);
 574     }
 575     else
 576     {
 577
 578       im = new jalview.util.ImageMaker(this,
 579               jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
 580               width, height, null, this.getTitle(), null, 0, false);
 581     }
 582
 583     if (im.getGraphics() != null)
 584     {
 585       pdbcanvas.drawAll(im.getGraphics(), width, height);
 586       im.writeImage();
 587     }
 588   }
 589
 590   public void charge_actionPerformed(ActionEvent e)
 591   {
 592     pdbcanvas.bysequence = false;
 593     pdbcanvas.pdb.setChargeColours();
 594     pdbcanvas.redrawneeded = true;
 595     pdbcanvas.repaint();
 596   }
 597
 598   public void hydro_actionPerformed(ActionEvent e)
 599   {
 600     pdbcanvas.bysequence = false;
 601     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 602     pdbcanvas.redrawneeded = true;
 603     pdbcanvas.repaint();
 604   }
 605
 606   public void chain_actionPerformed(ActionEvent e)
 607   {
 608     pdbcanvas.bysequence = false;
 609     pdbcanvas.pdb.setChainColours();
 610     pdbcanvas.redrawneeded = true;
 611     pdbcanvas.repaint();
 612   }
 613
 614   public void zbuffer_actionPerformed(ActionEvent e)
 615   {
 616     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 617     pdbcanvas.redrawneeded = true;
 618     pdbcanvas.repaint();
 619   }
 620
 621   public void molecule_actionPerformed(ActionEvent e)
 622   {
 623     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 624     pdbcanvas.redrawneeded = true;
 625     pdbcanvas.repaint();
 626   }
 627
 628   public void depth_actionPerformed(ActionEvent e)
 629   {
 630     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 631     pdbcanvas.redrawneeded = true;
 632     pdbcanvas.repaint();
 633   }
 634
 635   public void wire_actionPerformed(ActionEvent e)
 636   {
 637     pdbcanvas.wire = !pdbcanvas.wire;
 638     pdbcanvas.redrawneeded = true;
 639     pdbcanvas.repaint();
 640   }
 641
 642   public void seqButton_actionPerformed(ActionEvent e)
 643   {
 644     pdbcanvas.bysequence = true;
 645     pdbcanvas.updateSeqColours();
 646   }
 647
 648   public void mapping_actionPerformed(ActionEvent e)
 649   {
 650     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 651     try
 652     {
 653       cap.setText(pdbcanvas.mappingDetails.toString());
 654       Desktop.addInternalFrame(cap,
 655               MessageManager.getString("label.pdb_sequence_mapping"), 550,
 656               600);
 657     } catch (OutOfMemoryError oom)
 658     {
 659       new OOMWarning("Opening sequence to structure mapping report", oom);
 660       cap.dispose();
 661     }
 662   }
 663
 664   public void allchains_itemStateChanged(ItemEvent e)
 665   {
 666     pdbcanvas.setAllchainsVisible(allchains.getState());
 667   }
 668
 669   public void zappo_actionPerformed(ActionEvent e)
 670   {
 671     pdbcanvas.bysequence = false;
 672     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 673     pdbcanvas.redrawneeded = true;
 674     pdbcanvas.repaint();
 675   }
 676
 677   public void taylor_actionPerformed(ActionEvent e)
 678   {
 679     pdbcanvas.bysequence = false;
 680     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 681     pdbcanvas.redrawneeded = true;
 682     pdbcanvas.repaint();
 683   }
 684
 685   public void helix_actionPerformed(ActionEvent e)
 686   {
 687     pdbcanvas.bysequence = false;
 688     pdbcanvas.pdb.setColours(new HelixColourScheme());
 689     pdbcanvas.redrawneeded = true;
 690     pdbcanvas.repaint();
 691   }
 692
 693   public void strand_actionPerformed(ActionEvent e)
 694   {
 695     pdbcanvas.bysequence = false;
 696     pdbcanvas.pdb.setColours(new StrandColourScheme());
 697     pdbcanvas.redrawneeded = true;
 698     pdbcanvas.repaint();
 699   }
 700
 701   public void turn_actionPerformed(ActionEvent e)
 702   {
 703     pdbcanvas.bysequence = false;
 704     pdbcanvas.pdb.setColours(new TurnColourScheme());
 705     pdbcanvas.redrawneeded = true;
 706     pdbcanvas.repaint();
 707   }
 708
 709   public void buried_actionPerformed(ActionEvent e)
 710   {
 711     pdbcanvas.bysequence = false;
 712     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 713     pdbcanvas.redrawneeded = true;
 714     pdbcanvas.repaint();
 715   }
 716
 717   public void user_actionPerformed(ActionEvent e)
 718   {
 719     if (e.getActionCommand().equals(
 720             MessageManager.getString("action.user_defined")))
 721     {
 722       // new UserDefinedColours(pdbcanvas, null);
 723     }
 724     else
 725     {
 726       UserColourScheme udc = (UserColourScheme) UserDefinedColours
 727               .getUserColourSchemes().get(e.getActionCommand());
 728
 729       pdbcanvas.pdb.setColours(udc);
 730       pdbcanvas.redrawneeded = true;
 731       pdbcanvas.repaint();
 732     }
 733   }
 734
 735   public void background_actionPerformed(ActionEvent e)
 736   {
 737     java.awt.Color col = JColorChooser.showDialog(this,
 738             MessageManager.getString("label.select_backgroud_colour"),
 739             pdbcanvas.backgroundColour);
 740
 741     if (col != null)
 742     {
 743       pdbcanvas.backgroundColour = col;
 744       pdbcanvas.redrawneeded = true;
 745       pdbcanvas.repaint();
 746     }
 747   }
 748
 749   public void savePDB_actionPerformed(ActionEvent e)
 750   {
 751     JalviewFileChooser chooser = new JalviewFileChooser(
 752             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 753
 754     chooser.setFileView(new JalviewFileView());
 755     chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
 756     chooser.setToolTipText(MessageManager.getString("action.save"));
 757
 758     int value = chooser.showSaveDialog(this);
 759
 760     if (value == JalviewFileChooser.APPROVE_OPTION)
 761     {
 762       try
 763       {
 764         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 765         File outFile = chooser.getSelectedFile();
 766
 767         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 768         String data;
 769         while ((data = in.readLine()) != null)
 770         {
 771           if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
 772           {
 773             out.println(data);
 774           }
 775         }
 776         out.close();
 777         in.close();
 778       } catch (Exception ex)
 779       {
 780         ex.printStackTrace();
 781       }
 782     }
 783   }
 784 }