src/MCview/PDBViewer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package MCview;
  19
  20 import java.io.*;
  21
  22 import java.awt.event.*;
  23 import javax.swing.*;
  24 import javax.xml.parsers.ParserConfigurationException;
  25
  26 import org.xml.sax.SAXException;
  27
  28 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  29 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  30 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
  31 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  32
  33 import jalview.datamodel.*;
  34 import jalview.gui.*;
  35 import jalview.io.*;
  36 import jalview.schemes.*;
  37 import jalview.ws.ebi.EBIFetchClient;
  38
  39 public class PDBViewer extends JInternalFrame implements Runnable
  40 {
  41
  42   /**
  43    * The associated sequence in an alignment
  44    */
  45   PDBCanvas pdbcanvas;
  46
  47   PDBEntry pdbentry;
  48
  49   SequenceI[] seq;
  50
  51   String[] chains;
  52
  53   AlignmentPanel ap;
  54
  55   String protocol;
  56
  57   String tmpPDBFile;
  58
  59   public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
  60           AlignmentPanel ap, String protocol) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
  61
  62   {
  63     this.pdbentry = pdbentry;
  64     this.seq = seq;
  65     this.chains = chains;
  66     this.ap = ap;
  67     this.protocol = protocol;
  68
  69     try
  70     {
  71       jbInit();
  72     } catch (Exception ex)
  73     {
  74       ex.printStackTrace();
  75     }
  76
  77     StringBuffer title = new StringBuffer(seq[0].getName() + ":"
  78             + pdbentry.getFile());
  79
  80     pdbcanvas = new PDBCanvas();
  81
  82     setContentPane(pdbcanvas);
  83
  84     if (pdbentry.getFile() != null)
  85     {
  86       try
  87       {
  88         tmpPDBFile = pdbentry.getFile();
  89         PDBfile pdbfile = new PDBfile(tmpPDBFile,
  90                 jalview.io.AppletFormatAdapter.FILE);
  91
  92         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
  93
  94       } catch (java.io.IOException ex)
  95       {
  96         ex.printStackTrace();
  97       }
  98     }
  99     else
 100     {
 101       Thread worker = new Thread(this);
 102       worker.start();
 103     }
 104
 105     if (pdbentry.getProperty() != null)
 106     {
 107       if (pdbentry.getProperty().get("method") != null)
 108       {
 109         title.append(" Method: ");
 110         title.append(pdbentry.getProperty().get("method"));
 111       }
 112       if (pdbentry.getProperty().get("chains") != null)
 113       {
 114         title.append(" Chain:");
 115         title.append(pdbentry.getProperty().get("chains"));
 116       }
 117     }
 118     Desktop.addInternalFrame(this, title.toString(), 400, 400);
 119   }
 120
 121   public void run()
 122   {
 123     try
 124     {
 125       EBIFetchClient ebi = new EBIFetchClient();
 126       String query = "pdb:" + pdbentry.getId();
 127       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
 128               .getAbsolutePath());
 129
 130       if (pdbentry.getFile() != null)
 131         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 132     } catch (Exception ex)
 133     {
 134       pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
 135       ex.printStackTrace();
 136     }
 137   }
 138
 139   private void jbInit() throws Exception
 140   {
 141     this.addKeyListener(new KeyAdapter()
 142     {
 143       public void keyPressed(KeyEvent evt)
 144       {
 145         pdbcanvas.keyPressed(evt);
 146       }
 147     });
 148
 149     this.setJMenuBar(jMenuBar1);
 150     fileMenu.setText("File");
 151     coloursMenu.setText("Colours");
 152     saveMenu.setActionCommand("Save Image");
 153     saveMenu.setText("Save As");
 154     png.setText("PNG");
 155     png.addActionListener(new ActionListener()
 156     {
 157       public void actionPerformed(ActionEvent e)
 158       {
 159         png_actionPerformed(e);
 160       }
 161     });
 162     eps.setText("EPS");
 163     eps.addActionListener(new ActionListener()
 164     {
 165       public void actionPerformed(ActionEvent e)
 166       {
 167         eps_actionPerformed(e);
 168       }
 169     });
 170     mapping.setText("View Mapping");
 171     mapping.addActionListener(new ActionListener()
 172     {
 173       public void actionPerformed(ActionEvent e)
 174       {
 175         mapping_actionPerformed(e);
 176       }
 177     });
 178     wire.setText("Wireframe");
 179     wire.addActionListener(new ActionListener()
 180     {
 181       public void actionPerformed(ActionEvent e)
 182       {
 183         wire_actionPerformed(e);
 184       }
 185     });
 186     depth.setSelected(true);
 187     depth.setText("Depthcue");
 188     depth.addActionListener(new ActionListener()
 189     {
 190       public void actionPerformed(ActionEvent e)
 191       {
 192         depth_actionPerformed(e);
 193       }
 194     });
 195     zbuffer.setSelected(true);
 196     zbuffer.setText("Z Buffering");
 197     zbuffer.addActionListener(new ActionListener()
 198     {
 199       public void actionPerformed(ActionEvent e)
 200       {
 201         zbuffer_actionPerformed(e);
 202       }
 203     });
 204     charge.setText("Charge & Cysteine");
 205     charge.addActionListener(new ActionListener()
 206     {
 207       public void actionPerformed(ActionEvent e)
 208       {
 209         charge_actionPerformed(e);
 210       }
 211     });
 212     chain.setText("By Chain");
 213     chain.addActionListener(new ActionListener()
 214     {
 215       public void actionPerformed(ActionEvent e)
 216       {
 217         chain_actionPerformed(e);
 218       }
 219     });
 220     seqButton.setSelected(true);
 221     seqButton.setText("By Sequence");
 222     seqButton.addActionListener(new ActionListener()
 223     {
 224       public void actionPerformed(ActionEvent e)
 225       {
 226         seqButton_actionPerformed(e);
 227       }
 228     });
 229     allchains.setSelected(true);
 230     allchains.setText("Show All Chains");
 231     allchains.addItemListener(new ItemListener()
 232     {
 233       public void itemStateChanged(ItemEvent e)
 234       {
 235         allchains_itemStateChanged(e);
 236       }
 237     });
 238     zappo.setText("Zappo");
 239     zappo.addActionListener(new ActionListener()
 240     {
 241       public void actionPerformed(ActionEvent e)
 242       {
 243         zappo_actionPerformed(e);
 244       }
 245     });
 246     taylor.setText("Taylor");
 247     taylor.addActionListener(new ActionListener()
 248     {
 249       public void actionPerformed(ActionEvent e)
 250       {
 251         taylor_actionPerformed(e);
 252       }
 253     });
 254     hydro.setText("Hydro");
 255     hydro.addActionListener(new ActionListener()
 256     {
 257       public void actionPerformed(ActionEvent e)
 258       {
 259         hydro_actionPerformed(e);
 260       }
 261     });
 262     helix.setText("Helix");
 263     helix.addActionListener(new ActionListener()
 264     {
 265       public void actionPerformed(ActionEvent e)
 266       {
 267         helix_actionPerformed(e);
 268       }
 269     });
 270     strand.setText("Strand");
 271     strand.addActionListener(new ActionListener()
 272     {
 273       public void actionPerformed(ActionEvent e)
 274       {
 275         strand_actionPerformed(e);
 276       }
 277     });
 278     turn.setText("Turn");
 279     turn.addActionListener(new ActionListener()
 280     {
 281       public void actionPerformed(ActionEvent e)
 282       {
 283         turn_actionPerformed(e);
 284       }
 285     });
 286     buried.setText("Buried");
 287     buried.addActionListener(new ActionListener()
 288     {
 289       public void actionPerformed(ActionEvent e)
 290       {
 291         buried_actionPerformed(e);
 292       }
 293     });
 294     user.setText("User Defined...");
 295     user.addActionListener(new ActionListener()
 296     {
 297       public void actionPerformed(ActionEvent e)
 298       {
 299         user_actionPerformed(e);
 300       }
 301     });
 302     viewMenu.setText("View");
 303     background.setText("Background Colour...");
 304     background.addActionListener(new ActionListener()
 305     {
 306       public void actionPerformed(ActionEvent e)
 307       {
 308         background_actionPerformed(e);
 309       }
 310     });
 311     savePDB.setText("PDB File");
 312     savePDB.addActionListener(new ActionListener()
 313     {
 314       public void actionPerformed(ActionEvent e)
 315       {
 316         savePDB_actionPerformed(e);
 317       }
 318     });
 319     jMenuBar1.add(fileMenu);
 320     jMenuBar1.add(coloursMenu);
 321     jMenuBar1.add(viewMenu);
 322     fileMenu.add(saveMenu);
 323     fileMenu.add(mapping);
 324     saveMenu.add(savePDB);
 325     saveMenu.add(png);
 326     saveMenu.add(eps);
 327     coloursMenu.add(seqButton);
 328     coloursMenu.add(chain);
 329     coloursMenu.add(charge);
 330     coloursMenu.add(zappo);
 331     coloursMenu.add(taylor);
 332     coloursMenu.add(hydro);
 333     coloursMenu.add(helix);
 334     coloursMenu.add(strand);
 335     coloursMenu.add(turn);
 336     coloursMenu.add(buried);
 337     coloursMenu.add(user);
 338     coloursMenu.add(background);
 339     ButtonGroup bg = new ButtonGroup();
 340     bg.add(seqButton);
 341     bg.add(chain);
 342     bg.add(charge);
 343     bg.add(zappo);
 344     bg.add(taylor);
 345     bg.add(hydro);
 346     bg.add(helix);
 347     bg.add(strand);
 348     bg.add(turn);
 349     bg.add(buried);
 350     bg.add(user);
 351
 352     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 353     {
 354       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 355               .getUserColourSchemes().keys();
 356
 357       while (userColours.hasMoreElements())
 358       {
 359         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 360                 userColours.nextElement().toString());
 361         radioItem.setName("USER_DEFINED");
 362         radioItem.addMouseListener(new MouseAdapter()
 363         {
 364           public void mousePressed(MouseEvent evt)
 365           {
 366             if (evt.isControlDown()
 367                     || SwingUtilities.isRightMouseButton(evt))
 368             {
 369               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 370
 371               int option = JOptionPane.showInternalConfirmDialog(
 372                       jalview.gui.Desktop.desktop,
 373                       "Remove from default list?",
 374                       "Remove user defined colour",
 375                       JOptionPane.YES_NO_OPTION);
 376               if (option == JOptionPane.YES_OPTION)
 377               {
 378                 jalview.gui.UserDefinedColours
 379                         .removeColourFromDefaults(radioItem.getText());
 380                 coloursMenu.remove(radioItem);
 381               }
 382               else
 383               {
 384                 radioItem.addActionListener(new ActionListener()
 385                 {
 386                   public void actionPerformed(ActionEvent evt)
 387                   {
 388                     user_actionPerformed(evt);
 389                   }
 390                 });
 391               }
 392             }
 393           }
 394         });
 395         radioItem.addActionListener(new ActionListener()
 396         {
 397           public void actionPerformed(ActionEvent evt)
 398           {
 399             user_actionPerformed(evt);
 400           }
 401         });
 402         coloursMenu.add(radioItem);
 403         bg.add(radioItem);
 404       }
 405     }
 406
 407     viewMenu.add(wire);
 408     viewMenu.add(depth);
 409     viewMenu.add(zbuffer);
 410     viewMenu.add(allchains);
 411   }
 412
 413   JMenuBar jMenuBar1 = new JMenuBar();
 414
 415   JMenu fileMenu = new JMenu();
 416
 417   JMenu coloursMenu = new JMenu();
 418
 419   JMenu saveMenu = new JMenu();
 420
 421   JMenuItem png = new JMenuItem();
 422
 423   JMenuItem eps = new JMenuItem();
 424
 425   JMenuItem mapping = new JMenuItem();
 426
 427   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 428
 429   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 430
 431   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 432
 433   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 434
 435   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 436
 437   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 438
 439   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 440
 441   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 442
 443   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 444
 445   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 446
 447   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 448
 449   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 450
 451   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 452
 453   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 454
 455   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 456
 457   JMenu viewMenu = new JMenu();
 458
 459   JMenuItem background = new JMenuItem();
 460
 461   JMenuItem savePDB = new JMenuItem();
 462
 463   /**
 464    * DOCUMENT ME!
 465    *
 466    * @param e
 467    *          DOCUMENT ME!
 468    */
 469   public void eps_actionPerformed(ActionEvent e)
 470   {
 471     makePDBImage(jalview.util.ImageMaker.EPS);
 472   }
 473
 474   /**
 475    * DOCUMENT ME!
 476    *
 477    * @param e
 478    *          DOCUMENT ME!
 479    */
 480   public void png_actionPerformed(ActionEvent e)
 481   {
 482     makePDBImage(jalview.util.ImageMaker.PNG);
 483   }
 484
 485   void makePDBImage(int type)
 486   {
 487     int width = pdbcanvas.getWidth();
 488     int height = pdbcanvas.getHeight();
 489
 490     jalview.util.ImageMaker im;
 491
 492     if (type == jalview.util.ImageMaker.PNG)
 493     {
 494       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
 495               "Make PNG image from view", width, height, null, null);
 496     }
 497     else
 498     {
 499       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
 500               "Make EPS file from view", width, height, null,
 501               this.getTitle());
 502     }
 503
 504     if (im.getGraphics() != null)
 505     {
 506       pdbcanvas.drawAll(im.getGraphics(), width, height);
 507       im.writeImage();
 508     }
 509   }
 510
 511   public void charge_actionPerformed(ActionEvent e)
 512   {
 513     pdbcanvas.bysequence = false;
 514     pdbcanvas.pdb.setChargeColours();
 515     pdbcanvas.redrawneeded = true;
 516     pdbcanvas.repaint();
 517   }
 518
 519   public void hydro_actionPerformed(ActionEvent e)
 520   {
 521     pdbcanvas.bysequence = false;
 522     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 523     pdbcanvas.redrawneeded = true;
 524     pdbcanvas.repaint();
 525   }
 526
 527   public void chain_actionPerformed(ActionEvent e)
 528   {
 529     pdbcanvas.bysequence = false;
 530     pdbcanvas.pdb.setChainColours();
 531     pdbcanvas.redrawneeded = true;
 532     pdbcanvas.repaint();
 533   }
 534
 535   public void zbuffer_actionPerformed(ActionEvent e)
 536   {
 537     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 538     pdbcanvas.redrawneeded = true;
 539     pdbcanvas.repaint();
 540   }
 541
 542   public void molecule_actionPerformed(ActionEvent e)
 543   {
 544     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 545     pdbcanvas.redrawneeded = true;
 546     pdbcanvas.repaint();
 547   }
 548
 549   public void depth_actionPerformed(ActionEvent e)
 550   {
 551     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 552     pdbcanvas.redrawneeded = true;
 553     pdbcanvas.repaint();
 554   }
 555
 556   public void wire_actionPerformed(ActionEvent e)
 557   {
 558     pdbcanvas.wire = !pdbcanvas.wire;
 559     pdbcanvas.redrawneeded = true;
 560     pdbcanvas.repaint();
 561   }
 562
 563   public void seqButton_actionPerformed(ActionEvent e)
 564   {
 565     pdbcanvas.bysequence = true;
 566     pdbcanvas.updateSeqColours();
 567   }
 568
 569   public void mapping_actionPerformed(ActionEvent e)
 570   {
 571     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 572     try
 573     {
 574       cap.setText(pdbcanvas.mappingDetails.toString());
 575       Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 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("User Defined..."))
 639     {
 640       // new UserDefinedColours(pdbcanvas, null);
 641     }
 642     else
 643     {
 644       UserColourScheme udc = (UserColourScheme) UserDefinedColours
 645               .getUserColourSchemes().get(e.getActionCommand());
 646
 647       pdbcanvas.pdb.setColours(udc);
 648       pdbcanvas.redrawneeded = true;
 649       pdbcanvas.repaint();
 650     }
 651   }
 652
 653   public void background_actionPerformed(ActionEvent e)
 654   {
 655     java.awt.Color col = JColorChooser.showDialog(this,
 656             "Select Background Colour", pdbcanvas.backgroundColour);
 657
 658     if (col != null)
 659     {
 660       pdbcanvas.backgroundColour = col;
 661       pdbcanvas.redrawneeded = true;
 662       pdbcanvas.repaint();
 663     }
 664   }
 665
 666   public void savePDB_actionPerformed(ActionEvent e)
 667   {
 668     JalviewFileChooser chooser = new JalviewFileChooser(
 669             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 670
 671     chooser.setFileView(new JalviewFileView());
 672     chooser.setDialogTitle("Save PDB File");
 673     chooser.setToolTipText("Save");
 674
 675     int value = chooser.showSaveDialog(this);
 676
 677     if (value == JalviewFileChooser.APPROVE_OPTION)
 678     {
 679       try
 680       {
 681         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 682         File outFile = chooser.getSelectedFile();
 683
 684         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 685         String data;
 686         while ((data = in.readLine()) != null)
 687         {
 688           if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
 689           {
 690             out.println(data);
 691           }
 692         }
 693         out.close();
 694         in.close();
 695       } catch (Exception ex)
 696       {
 697         ex.printStackTrace();
 698       }
 699     }
 700   }
 701 }