src/MCview/PDBViewer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package MCview;
  22
  23 import java.io.*;
  24
  25 import java.awt.event.*;
  26 import javax.swing.*;
  27
  28 import jalview.datamodel.*;
  29 import jalview.gui.*;
  30 import jalview.io.*;
  31 import jalview.schemes.*;
  32 import jalview.util.MessageManager;
  33 import jalview.ws.ebi.EBIFetchClient;
  34
  35 public class PDBViewer extends JInternalFrame implements Runnable
  36 {
  37
  38   /**
  39    * The associated sequence in an alignment
  40    */
  41   PDBCanvas pdbcanvas;
  42
  43   PDBEntry pdbentry;
  44
  45   SequenceI[] seq;
  46
  47   String[] chains;
  48
  49   AlignmentPanel ap;
  50
  51   String protocol;
  52
  53   String tmpPDBFile;
  54
  55   public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
  56           AlignmentPanel ap, String protocol)
  57   {
  58     this.pdbentry = pdbentry;
  59     this.seq = seq;
  60     this.chains = chains;
  61     this.ap = ap;
  62     this.protocol = protocol;
  63
  64     try
  65     {
  66       jbInit();
  67     } catch (Exception ex)
  68     {
  69       ex.printStackTrace();
  70     }
  71
  72     StringBuffer title = new StringBuffer(seq[0].getName() + ":"
  73             + pdbentry.getFile());
  74
  75     pdbcanvas = new PDBCanvas();
  76
  77     setContentPane(pdbcanvas);
  78
  79     if (pdbentry.getFile() != null)
  80     {
  81       try
  82       {
  83         tmpPDBFile = pdbentry.getFile();
  84         PDBfile pdbfile = new PDBfile(tmpPDBFile,
  85                 jalview.io.AppletFormatAdapter.FILE);
  86
  87         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
  88
  89       } catch (java.io.IOException ex)
  90       {
  91         ex.printStackTrace();
  92       }
  93     }
  94     else
  95     {
  96       Thread worker = new Thread(this);
  97       worker.start();
  98     }
  99
 100     if (pdbentry.getProperty() != null)
 101     {
 102       if (pdbentry.getProperty().get("method") != null)
 103       {
 104         title.append(" Method: ");
 105         title.append(pdbentry.getProperty().get("method"));
 106       }
 107       if (pdbentry.getProperty().get("chains") != null)
 108       {
 109         title.append(" Chain:");
 110         title.append(pdbentry.getProperty().get("chains"));
 111       }
 112     }
 113     Desktop.addInternalFrame(this, title.toString(), 400, 400);
 114   }
 115
 116   public void run()
 117   {
 118     try
 119     {
 120       EBIFetchClient ebi = new EBIFetchClient();
 121       String query = "pdb:" + pdbentry.getId();
 122       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
 123               .getAbsolutePath());
 124
 125       if (pdbentry.getFile() != null)
 126         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 127     } catch (Exception ex)
 128     {
 129       pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
 130       ex.printStackTrace();
 131     }
 132   }
 133
 134   private void jbInit() throws Exception
 135   {
 136     this.addKeyListener(new KeyAdapter()
 137     {
 138       public void keyPressed(KeyEvent evt)
 139       {
 140         pdbcanvas.keyPressed(evt);
 141       }
 142     });
 143
 144     this.setJMenuBar(jMenuBar1);
 145     fileMenu.setText(MessageManager.getString("action.file"));
 146     coloursMenu.setText(MessageManager.getString("label.colours"));
 147     saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
 148     saveMenu.setText(MessageManager.getString("action.save_as"));
 149     png.setText("PNG");
 150     png.addActionListener(new ActionListener()
 151     {
 152       public void actionPerformed(ActionEvent e)
 153       {
 154         png_actionPerformed(e);
 155       }
 156     });
 157     eps.setText("EPS");
 158     eps.addActionListener(new ActionListener()
 159     {
 160       public void actionPerformed(ActionEvent e)
 161       {
 162         eps_actionPerformed(e);
 163       }
 164     });
 165     mapping.setText(MessageManager.getString("label.view_mapping"));
 166     mapping.addActionListener(new ActionListener()
 167     {
 168       public void actionPerformed(ActionEvent e)
 169       {
 170         mapping_actionPerformed(e);
 171       }
 172     });
 173     wire.setText(MessageManager.getString("label.wireframe"));
 174     wire.addActionListener(new ActionListener()
 175     {
 176       public void actionPerformed(ActionEvent e)
 177       {
 178         wire_actionPerformed(e);
 179       }
 180     });
 181     depth.setSelected(true);
 182     depth.setText(MessageManager.getString("label.depthcue"));
 183     depth.addActionListener(new ActionListener()
 184     {
 185       public void actionPerformed(ActionEvent e)
 186       {
 187         depth_actionPerformed(e);
 188       }
 189     });
 190     zbuffer.setSelected(true);
 191     zbuffer.setText(MessageManager.getString("label.z_buffering"));
 192     zbuffer.addActionListener(new ActionListener()
 193     {
 194       public void actionPerformed(ActionEvent e)
 195       {
 196         zbuffer_actionPerformed(e);
 197       }
 198     });
 199     charge.setText(MessageManager.getString("label.charge_cysteine"));
 200     charge.addActionListener(new ActionListener()
 201     {
 202       public void actionPerformed(ActionEvent e)
 203       {
 204         charge_actionPerformed(e);
 205       }
 206     });
 207     chain.setText(MessageManager.getString("action.by_chain"));
 208     chain.addActionListener(new ActionListener()
 209     {
 210       public void actionPerformed(ActionEvent e)
 211       {
 212         chain_actionPerformed(e);
 213       }
 214     });
 215     seqButton.setSelected(true);
 216     seqButton.setText(MessageManager.getString("action.by_sequence"));
 217     seqButton.addActionListener(new ActionListener()
 218     {
 219       public void actionPerformed(ActionEvent e)
 220       {
 221         seqButton_actionPerformed(e);
 222       }
 223     });
 224     allchains.setSelected(true);
 225     allchains.setText(MessageManager.getString("label.show_all_chains"));
 226     allchains.addItemListener(new ItemListener()
 227     {
 228       public void itemStateChanged(ItemEvent e)
 229       {
 230         allchains_itemStateChanged(e);
 231       }
 232     });
 233     zappo.setText(MessageManager.getString("label.zappo"));
 234     zappo.addActionListener(new ActionListener()
 235     {
 236       public void actionPerformed(ActionEvent e)
 237       {
 238         zappo_actionPerformed(e);
 239       }
 240     });
 241     taylor.setText(MessageManager.getString("label.taylor"));
 242     taylor.addActionListener(new ActionListener()
 243     {
 244       public void actionPerformed(ActionEvent e)
 245       {
 246         taylor_actionPerformed(e);
 247       }
 248     });
 249     hydro.setText(MessageManager.getString("label.hydrophobicity"));
 250     hydro.addActionListener(new ActionListener()
 251     {
 252       public void actionPerformed(ActionEvent e)
 253       {
 254         hydro_actionPerformed(e);
 255       }
 256     });
 257     helix.setText(MessageManager.getString("label.helix_propensity"));
 258     helix.addActionListener(new ActionListener()
 259     {
 260       public void actionPerformed(ActionEvent e)
 261       {
 262         helix_actionPerformed(e);
 263       }
 264     });
 265     strand.setText(MessageManager.getString("label.strand_propensity"));
 266     strand.addActionListener(new ActionListener()
 267     {
 268       public void actionPerformed(ActionEvent e)
 269       {
 270         strand_actionPerformed(e);
 271       }
 272     });
 273     turn.setText(MessageManager.getString("label.turn_propensity"));
 274     turn.addActionListener(new ActionListener()
 275     {
 276       public void actionPerformed(ActionEvent e)
 277       {
 278         turn_actionPerformed(e);
 279       }
 280     });
 281     buried.setText(MessageManager.getString("label.buried_index"));
 282     buried.addActionListener(new ActionListener()
 283     {
 284       public void actionPerformed(ActionEvent e)
 285       {
 286         buried_actionPerformed(e);
 287       }
 288     });
 289     user.setText(MessageManager.getString("action.user_defined"));
 290     user.addActionListener(new ActionListener()
 291     {
 292       public void actionPerformed(ActionEvent e)
 293       {
 294         user_actionPerformed(e);
 295       }
 296     });
 297     viewMenu.setText(MessageManager.getString("action.view"));
 298     background.setText(MessageManager.getString("label.background_colour")
 299             + "...");
 300     background.addActionListener(new ActionListener()
 301     {
 302       public void actionPerformed(ActionEvent e)
 303       {
 304         background_actionPerformed(e);
 305       }
 306     });
 307     savePDB.setText(MessageManager.getString("label.pdb_file"));
 308     savePDB.addActionListener(new ActionListener()
 309     {
 310       public void actionPerformed(ActionEvent e)
 311       {
 312         savePDB_actionPerformed(e);
 313       }
 314     });
 315     jMenuBar1.add(fileMenu);
 316     jMenuBar1.add(coloursMenu);
 317     jMenuBar1.add(viewMenu);
 318     fileMenu.add(saveMenu);
 319     fileMenu.add(mapping);
 320     saveMenu.add(savePDB);
 321     saveMenu.add(png);
 322     saveMenu.add(eps);
 323     coloursMenu.add(seqButton);
 324     coloursMenu.add(chain);
 325     coloursMenu.add(charge);
 326     coloursMenu.add(zappo);
 327     coloursMenu.add(taylor);
 328     coloursMenu.add(hydro);
 329     coloursMenu.add(helix);
 330     coloursMenu.add(strand);
 331     coloursMenu.add(turn);
 332     coloursMenu.add(buried);
 333     coloursMenu.add(user);
 334     coloursMenu.add(background);
 335     ButtonGroup bg = new ButtonGroup();
 336     bg.add(seqButton);
 337     bg.add(chain);
 338     bg.add(charge);
 339     bg.add(zappo);
 340     bg.add(taylor);
 341     bg.add(hydro);
 342     bg.add(helix);
 343     bg.add(strand);
 344     bg.add(turn);
 345     bg.add(buried);
 346     bg.add(user);
 347
 348     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 349     {
 350       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 351               .getUserColourSchemes().keys();
 352
 353       while (userColours.hasMoreElements())
 354       {
 355         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 356                 userColours.nextElement().toString());
 357         radioItem.setName("USER_DEFINED");
 358         radioItem.addMouseListener(new MouseAdapter()
 359         {
 360           public void mousePressed(MouseEvent evt)
 361           {
 362             if (evt.isControlDown()
 363                     || SwingUtilities.isRightMouseButton(evt))
 364             {
 365               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 366
 367               int option = JOptionPane.showInternalConfirmDialog(
 368                       jalview.gui.Desktop.desktop,
 369                       MessageManager
 370                               .getString("label.remove_from_default_list"),
 371                       MessageManager
 372                               .getString("label.remove_user_defined_colour"),
 373                       JOptionPane.YES_NO_OPTION);
 374               if (option == JOptionPane.YES_OPTION)
 375               {
 376                 jalview.gui.UserDefinedColours
 377                         .removeColourFromDefaults(radioItem.getText());
 378                 coloursMenu.remove(radioItem);
 379               }
 380               else
 381               {
 382                 radioItem.addActionListener(new ActionListener()
 383                 {
 384                   public void actionPerformed(ActionEvent evt)
 385                   {
 386                     user_actionPerformed(evt);
 387                   }
 388                 });
 389               }
 390             }
 391           }
 392         });
 393         radioItem.addActionListener(new ActionListener()
 394         {
 395           public void actionPerformed(ActionEvent evt)
 396           {
 397             user_actionPerformed(evt);
 398           }
 399         });
 400         coloursMenu.add(radioItem);
 401         bg.add(radioItem);
 402       }
 403     }
 404
 405     viewMenu.add(wire);
 406     viewMenu.add(depth);
 407     viewMenu.add(zbuffer);
 408     viewMenu.add(allchains);
 409   }
 410
 411   JMenuBar jMenuBar1 = new JMenuBar();
 412
 413   JMenu fileMenu = new JMenu();
 414
 415   JMenu coloursMenu = new JMenu();
 416
 417   JMenu saveMenu = new JMenu();
 418
 419   JMenuItem png = new JMenuItem();
 420
 421   JMenuItem eps = new JMenuItem();
 422
 423   JMenuItem mapping = new JMenuItem();
 424
 425   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 426
 427   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 428
 429   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 430
 431   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 432
 433   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 434
 435   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 436
 437   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 438
 439   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 440
 441   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 442
 443   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 444
 445   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 446
 447   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 448
 449   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 450
 451   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 452
 453   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 454
 455   JMenu viewMenu = new JMenu();
 456
 457   JMenuItem background = new JMenuItem();
 458
 459   JMenuItem savePDB = new JMenuItem();
 460
 461   /**
 462    * DOCUMENT ME!
 463    *
 464    * @param e
 465    *          DOCUMENT ME!
 466    */
 467   public void eps_actionPerformed(ActionEvent e)
 468   {
 469     makePDBImage(jalview.util.ImageMaker.EPS);
 470   }
 471
 472   /**
 473    * DOCUMENT ME!
 474    *
 475    * @param e
 476    *          DOCUMENT ME!
 477    */
 478   public void png_actionPerformed(ActionEvent e)
 479   {
 480     makePDBImage(jalview.util.ImageMaker.PNG);
 481   }
 482
 483   void makePDBImage(int type)
 484   {
 485     int width = pdbcanvas.getWidth();
 486     int height = pdbcanvas.getHeight();
 487
 488     jalview.util.ImageMaker im;
 489
 490     if (type == jalview.util.ImageMaker.PNG)
 491     {
 492       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
 493               "Make PNG image from view", width, height, null, null);
 494     }
 495     else
 496     {
 497       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
 498               "Make EPS file from view", width, height, null,
 499               this.getTitle());
 500     }
 501
 502     if (im.getGraphics() != null)
 503     {
 504       pdbcanvas.drawAll(im.getGraphics(), width, height);
 505       im.writeImage();
 506     }
 507   }
 508
 509   public void charge_actionPerformed(ActionEvent e)
 510   {
 511     pdbcanvas.bysequence = false;
 512     pdbcanvas.pdb.setChargeColours();
 513     pdbcanvas.redrawneeded = true;
 514     pdbcanvas.repaint();
 515   }
 516
 517   public void hydro_actionPerformed(ActionEvent e)
 518   {
 519     pdbcanvas.bysequence = false;
 520     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 521     pdbcanvas.redrawneeded = true;
 522     pdbcanvas.repaint();
 523   }
 524
 525   public void chain_actionPerformed(ActionEvent e)
 526   {
 527     pdbcanvas.bysequence = false;
 528     pdbcanvas.pdb.setChainColours();
 529     pdbcanvas.redrawneeded = true;
 530     pdbcanvas.repaint();
 531   }
 532
 533   public void zbuffer_actionPerformed(ActionEvent e)
 534   {
 535     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 536     pdbcanvas.redrawneeded = true;
 537     pdbcanvas.repaint();
 538   }
 539
 540   public void molecule_actionPerformed(ActionEvent e)
 541   {
 542     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 543     pdbcanvas.redrawneeded = true;
 544     pdbcanvas.repaint();
 545   }
 546
 547   public void depth_actionPerformed(ActionEvent e)
 548   {
 549     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 550     pdbcanvas.redrawneeded = true;
 551     pdbcanvas.repaint();
 552   }
 553
 554   public void wire_actionPerformed(ActionEvent e)
 555   {
 556     pdbcanvas.wire = !pdbcanvas.wire;
 557     pdbcanvas.redrawneeded = true;
 558     pdbcanvas.repaint();
 559   }
 560
 561   public void seqButton_actionPerformed(ActionEvent e)
 562   {
 563     pdbcanvas.bysequence = true;
 564     pdbcanvas.updateSeqColours();
 565   }
 566
 567   public void mapping_actionPerformed(ActionEvent e)
 568   {
 569     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 570     try
 571     {
 572       cap.setText(pdbcanvas.mappingDetails.toString());
 573       Desktop.addInternalFrame(cap,
 574               MessageManager.getString("label.pdb_sequence_mapping"), 550,
 575               600);
 576     } catch (OutOfMemoryError oom)
 577     {
 578       new OOMWarning("Opening sequence to structure mapping report", oom);
 579       cap.dispose();
 580     }
 581   }
 582
 583   public void allchains_itemStateChanged(ItemEvent e)
 584   {
 585     pdbcanvas.setAllchainsVisible(allchains.getState());
 586   }
 587
 588   public void zappo_actionPerformed(ActionEvent e)
 589   {
 590     pdbcanvas.bysequence = false;
 591     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 592     pdbcanvas.redrawneeded = true;
 593     pdbcanvas.repaint();
 594   }
 595
 596   public void taylor_actionPerformed(ActionEvent e)
 597   {
 598     pdbcanvas.bysequence = false;
 599     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 600     pdbcanvas.redrawneeded = true;
 601     pdbcanvas.repaint();
 602   }
 603
 604   public void helix_actionPerformed(ActionEvent e)
 605   {
 606     pdbcanvas.bysequence = false;
 607     pdbcanvas.pdb.setColours(new HelixColourScheme());
 608     pdbcanvas.redrawneeded = true;
 609     pdbcanvas.repaint();
 610   }
 611
 612   public void strand_actionPerformed(ActionEvent e)
 613   {
 614     pdbcanvas.bysequence = false;
 615     pdbcanvas.pdb.setColours(new StrandColourScheme());
 616     pdbcanvas.redrawneeded = true;
 617     pdbcanvas.repaint();
 618   }
 619
 620   public void turn_actionPerformed(ActionEvent e)
 621   {
 622     pdbcanvas.bysequence = false;
 623     pdbcanvas.pdb.setColours(new TurnColourScheme());
 624     pdbcanvas.redrawneeded = true;
 625     pdbcanvas.repaint();
 626   }
 627
 628   public void buried_actionPerformed(ActionEvent e)
 629   {
 630     pdbcanvas.bysequence = false;
 631     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 632     pdbcanvas.redrawneeded = true;
 633     pdbcanvas.repaint();
 634   }
 635
 636   public void user_actionPerformed(ActionEvent e)
 637   {
 638     if (e.getActionCommand().equals(
 639             MessageManager.getString("action.user_defined")))
 640     {
 641       // new UserDefinedColours(pdbcanvas, null);
 642     }
 643     else
 644     {
 645       UserColourScheme udc = (UserColourScheme) UserDefinedColours
 646               .getUserColourSchemes().get(e.getActionCommand());
 647
 648       pdbcanvas.pdb.setColours(udc);
 649       pdbcanvas.redrawneeded = true;
 650       pdbcanvas.repaint();
 651     }
 652   }
 653
 654   public void background_actionPerformed(ActionEvent e)
 655   {
 656     java.awt.Color col = JColorChooser.showDialog(this,
 657             MessageManager.getString("label.select_backgroud_colour"),
 658             pdbcanvas.backgroundColour);
 659
 660     if (col != null)
 661     {
 662       pdbcanvas.backgroundColour = col;
 663       pdbcanvas.redrawneeded = true;
 664       pdbcanvas.repaint();
 665     }
 666   }
 667
 668   public void savePDB_actionPerformed(ActionEvent e)
 669   {
 670     JalviewFileChooser chooser = new JalviewFileChooser(
 671             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 672
 673     chooser.setFileView(new JalviewFileView());
 674     chooser.setDialogTitle("Save PDB File");
 675     chooser.setToolTipText(MessageManager.getString("action.save"));
 676
 677     int value = chooser.showSaveDialog(this);
 678
 679     if (value == JalviewFileChooser.APPROVE_OPTION)
 680     {
 681       try
 682       {
 683         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 684         File outFile = chooser.getSelectedFile();
 685
 686         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 687         String data;
 688         while ((data = in.readLine()) != null)
 689         {
 690           if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
 691           {
 692             out.println(data);
 693           }
 694         }
 695         out.close();
 696         in.close();
 697       } catch (Exception ex)
 698       {
 699         ex.printStackTrace();
 700       }
 701     }
 702   }
 703 }