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