src/MCview/PDBViewer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 import java.awt.BorderLayout;
  40
  41 public class PDBViewer extends JInternalFrame implements Runnable
  42 {
  43
  44   /**
  45    * The associated sequence in an alignment
  46    */
  47   PDBCanvas pdbcanvas;
  48
  49   PDBEntry pdbentry;
  50
  51   SequenceI[] seq;
  52
  53   String[] chains;
  54
  55   AlignmentPanel ap;
  56
  57   String protocol;
  58
  59   String tmpPDBFile;
  60
  61   public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
  62           AlignmentPanel ap, String protocol) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
  63
  64   {
  65     this.pdbentry = pdbentry;
  66     this.seq = seq;
  67     this.chains = chains;
  68     this.ap = ap;
  69     this.protocol = protocol;
  70
  71     try
  72     {
  73       jbInit();
  74     } catch (Exception ex)
  75     {
  76       ex.printStackTrace();
  77     }
  78
  79     StringBuffer title = new StringBuffer(seq[0].getName() + ":"
  80             + pdbentry.getFile());
  81
  82     pdbcanvas = new PDBCanvas();
  83
  84     setContentPane(pdbcanvas);
  85
  86     if (pdbentry.getFile() != null)
  87     {
  88       try
  89       {
  90         tmpPDBFile = pdbentry.getFile();
  91         PDBfile pdbfile = new PDBfile(tmpPDBFile,
  92                 jalview.io.AppletFormatAdapter.FILE);
  93
  94         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
  95
  96       } catch (java.io.IOException ex)
  97       {
  98         ex.printStackTrace();
  99       }
 100     }
 101     else
 102     {
 103       Thread worker = new Thread(this);
 104       worker.start();
 105     }
 106
 107     if (pdbentry.getProperty() != null)
 108     {
 109       if (pdbentry.getProperty().get("method") != null)
 110       {
 111         title.append(" Method: ");
 112         title.append(pdbentry.getProperty().get("method"));
 113       }
 114       if (pdbentry.getProperty().get("chains") != null)
 115       {
 116         title.append(" Chain:");
 117         title.append(pdbentry.getProperty().get("chains"));
 118       }
 119     }
 120     Desktop.addInternalFrame(this, title.toString(), 400, 400);
 121   }
 122
 123   public void run()
 124   {
 125     try
 126     {
 127       EBIFetchClient ebi = new EBIFetchClient();
 128       String query = "pdb:" + pdbentry.getId();
 129       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
 130               .getAbsolutePath());
 131
 132       if (pdbentry.getFile() != null)
 133         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 134     } catch (Exception ex)
 135     {
 136       pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
 137       ex.printStackTrace();
 138     }
 139   }
 140
 141   private void jbInit() throws Exception
 142   {
 143     this.addKeyListener(new KeyAdapter()
 144     {
 145       public void keyPressed(KeyEvent evt)
 146       {
 147         pdbcanvas.keyPressed(evt);
 148       }
 149     });
 150
 151     this.setJMenuBar(jMenuBar1);
 152     fileMenu.setText("File");
 153     coloursMenu.setText("Colours");
 154     saveMenu.setActionCommand("Save Image");
 155     saveMenu.setText("Save As");
 156     png.setText("PNG");
 157     png.addActionListener(new ActionListener()
 158     {
 159       public void actionPerformed(ActionEvent e)
 160       {
 161         png_actionPerformed(e);
 162       }
 163     });
 164     eps.setText("EPS");
 165     eps.addActionListener(new ActionListener()
 166     {
 167       public void actionPerformed(ActionEvent e)
 168       {
 169         eps_actionPerformed(e);
 170       }
 171     });
 172     mapping.setText("View Mapping");
 173     mapping.addActionListener(new ActionListener()
 174     {
 175       public void actionPerformed(ActionEvent e)
 176       {
 177         mapping_actionPerformed(e);
 178       }
 179     });
 180     wire.setText("Wireframe");
 181     wire.addActionListener(new ActionListener()
 182     {
 183       public void actionPerformed(ActionEvent e)
 184       {
 185         wire_actionPerformed(e);
 186       }
 187     });
 188     depth.setSelected(true);
 189     depth.setText("Depthcue");
 190     depth.addActionListener(new ActionListener()
 191     {
 192       public void actionPerformed(ActionEvent e)
 193       {
 194         depth_actionPerformed(e);
 195       }
 196     });
 197     zbuffer.setSelected(true);
 198     zbuffer.setText("Z Buffering");
 199     zbuffer.addActionListener(new ActionListener()
 200     {
 201       public void actionPerformed(ActionEvent e)
 202       {
 203         zbuffer_actionPerformed(e);
 204       }
 205     });
 206     charge.setText("Charge & Cysteine");
 207     charge.addActionListener(new ActionListener()
 208     {
 209       public void actionPerformed(ActionEvent e)
 210       {
 211         charge_actionPerformed(e);
 212       }
 213     });
 214     chain.setText("By Chain");
 215     chain.addActionListener(new ActionListener()
 216     {
 217       public void actionPerformed(ActionEvent e)
 218       {
 219         chain_actionPerformed(e);
 220       }
 221     });
 222     seqButton.setSelected(true);
 223     seqButton.setText("By Sequence");
 224     seqButton.addActionListener(new ActionListener()
 225     {
 226       public void actionPerformed(ActionEvent e)
 227       {
 228         seqButton_actionPerformed(e);
 229       }
 230     });
 231     allchains.setSelected(true);
 232     allchains.setText("Show All Chains");
 233     allchains.addItemListener(new ItemListener()
 234     {
 235       public void itemStateChanged(ItemEvent e)
 236       {
 237         allchains_itemStateChanged(e);
 238       }
 239     });
 240     zappo.setText("Zappo");
 241     zappo.addActionListener(new ActionListener()
 242     {
 243       public void actionPerformed(ActionEvent e)
 244       {
 245         zappo_actionPerformed(e);
 246       }
 247     });
 248     taylor.setText("Taylor");
 249     taylor.addActionListener(new ActionListener()
 250     {
 251       public void actionPerformed(ActionEvent e)
 252       {
 253         taylor_actionPerformed(e);
 254       }
 255     });
 256     hydro.setText("Hydro");
 257     hydro.addActionListener(new ActionListener()
 258     {
 259       public void actionPerformed(ActionEvent e)
 260       {
 261         hydro_actionPerformed(e);
 262       }
 263     });
 264     helix.setText("Helix");
 265     helix.addActionListener(new ActionListener()
 266     {
 267       public void actionPerformed(ActionEvent e)
 268       {
 269         helix_actionPerformed(e);
 270       }
 271     });
 272     strand.setText("Strand");
 273     strand.addActionListener(new ActionListener()
 274     {
 275       public void actionPerformed(ActionEvent e)
 276       {
 277         strand_actionPerformed(e);
 278       }
 279     });
 280     turn.setText("Turn");
 281     turn.addActionListener(new ActionListener()
 282     {
 283       public void actionPerformed(ActionEvent e)
 284       {
 285         turn_actionPerformed(e);
 286       }
 287     });
 288     buried.setText("Buried");
 289     buried.addActionListener(new ActionListener()
 290     {
 291       public void actionPerformed(ActionEvent e)
 292       {
 293         buried_actionPerformed(e);
 294       }
 295     });
 296     user.setText("User Defined...");
 297     user.addActionListener(new ActionListener()
 298     {
 299       public void actionPerformed(ActionEvent e)
 300       {
 301         user_actionPerformed(e);
 302       }
 303     });
 304     viewMenu.setText("View");
 305     background.setText("Background Colour...");
 306     background.addActionListener(new ActionListener()
 307     {
 308       public void actionPerformed(ActionEvent e)
 309       {
 310         background_actionPerformed(e);
 311       }
 312     });
 313     savePDB.setText("PDB File");
 314     savePDB.addActionListener(new ActionListener()
 315     {
 316       public void actionPerformed(ActionEvent e)
 317       {
 318         savePDB_actionPerformed(e);
 319       }
 320     });
 321     jMenuBar1.add(fileMenu);
 322     jMenuBar1.add(coloursMenu);
 323     jMenuBar1.add(viewMenu);
 324     fileMenu.add(saveMenu);
 325     fileMenu.add(mapping);
 326     saveMenu.add(savePDB);
 327     saveMenu.add(png);
 328     saveMenu.add(eps);
 329     coloursMenu.add(seqButton);
 330     coloursMenu.add(chain);
 331     coloursMenu.add(charge);
 332     coloursMenu.add(zappo);
 333     coloursMenu.add(taylor);
 334     coloursMenu.add(hydro);
 335     coloursMenu.add(helix);
 336     coloursMenu.add(strand);
 337     coloursMenu.add(turn);
 338     coloursMenu.add(buried);
 339     coloursMenu.add(user);
 340     coloursMenu.add(background);
 341     ButtonGroup bg = new ButtonGroup();
 342     bg.add(seqButton);
 343     bg.add(chain);
 344     bg.add(charge);
 345     bg.add(zappo);
 346     bg.add(taylor);
 347     bg.add(hydro);
 348     bg.add(helix);
 349     bg.add(strand);
 350     bg.add(turn);
 351     bg.add(buried);
 352     bg.add(user);
 353
 354     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 355     {
 356       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 357               .getUserColourSchemes().keys();
 358
 359       while (userColours.hasMoreElements())
 360       {
 361         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 362                 userColours.nextElement().toString());
 363         radioItem.setName("USER_DEFINED");
 364         radioItem.addMouseListener(new MouseAdapter()
 365         {
 366           public void mousePressed(MouseEvent evt)
 367           {
 368             if (evt.isControlDown()
 369                     || SwingUtilities.isRightMouseButton(evt))
 370             {
 371               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 372
 373               int option = JOptionPane.showInternalConfirmDialog(
 374                       jalview.gui.Desktop.desktop,
 375                       "Remove from default list?",
 376                       "Remove user defined colour",
 377                       JOptionPane.YES_NO_OPTION);
 378               if (option == JOptionPane.YES_OPTION)
 379               {
 380                 jalview.gui.UserDefinedColours
 381                         .removeColourFromDefaults(radioItem.getText());
 382                 coloursMenu.remove(radioItem);
 383               }
 384               else
 385               {
 386                 radioItem.addActionListener(new ActionListener()
 387                 {
 388                   public void actionPerformed(ActionEvent evt)
 389                   {
 390                     user_actionPerformed(evt);
 391                   }
 392                 });
 393               }
 394             }
 395           }
 396         });
 397         radioItem.addActionListener(new ActionListener()
 398         {
 399           public void actionPerformed(ActionEvent evt)
 400           {
 401             user_actionPerformed(evt);
 402           }
 403         });
 404         coloursMenu.add(radioItem);
 405         bg.add(radioItem);
 406       }
 407     }
 408
 409     viewMenu.add(wire);
 410     viewMenu.add(depth);
 411     viewMenu.add(zbuffer);
 412     viewMenu.add(allchains);
 413   }
 414
 415   JMenuBar jMenuBar1 = new JMenuBar();
 416
 417   JMenu fileMenu = new JMenu();
 418
 419   JMenu coloursMenu = new JMenu();
 420
 421   JMenu saveMenu = new JMenu();
 422
 423   JMenuItem png = new JMenuItem();
 424
 425   JMenuItem eps = new JMenuItem();
 426
 427   JMenuItem mapping = new JMenuItem();
 428
 429   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 430
 431   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 432
 433   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 434
 435   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 436
 437   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 438
 439   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 440
 441   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 442
 443   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 444
 445   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 446
 447   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 448
 449   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 450
 451   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 452
 453   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 454
 455   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 456
 457   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 458
 459   JMenu viewMenu = new JMenu();
 460
 461   JMenuItem background = new JMenuItem();
 462
 463   JMenuItem savePDB = new JMenuItem();
 464
 465   /**
 466    * DOCUMENT ME!
 467    *
 468    * @param e
 469    *          DOCUMENT ME!
 470    */
 471   public void eps_actionPerformed(ActionEvent e)
 472   {
 473     makePDBImage(jalview.util.ImageMaker.EPS);
 474   }
 475
 476   /**
 477    * DOCUMENT ME!
 478    *
 479    * @param e
 480    *          DOCUMENT ME!
 481    */
 482   public void png_actionPerformed(ActionEvent e)
 483   {
 484     makePDBImage(jalview.util.ImageMaker.PNG);
 485   }
 486
 487   void makePDBImage(int type)
 488   {
 489     int width = pdbcanvas.getWidth();
 490     int height = pdbcanvas.getHeight();
 491
 492     jalview.util.ImageMaker im;
 493
 494     if (type == jalview.util.ImageMaker.PNG)
 495     {
 496       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
 497               "Make PNG image from view", width, height, null, null);
 498     }
 499     else
 500     {
 501       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
 502               "Make EPS file from view", width, height, null,
 503               this.getTitle());
 504     }
 505
 506     if (im.getGraphics() != null)
 507     {
 508       pdbcanvas.drawAll(im.getGraphics(), width, height);
 509       im.writeImage();
 510     }
 511   }
 512
 513   public void charge_actionPerformed(ActionEvent e)
 514   {
 515     pdbcanvas.bysequence = false;
 516     pdbcanvas.pdb.setChargeColours();
 517     pdbcanvas.redrawneeded = true;
 518     pdbcanvas.repaint();
 519   }
 520
 521   public void hydro_actionPerformed(ActionEvent e)
 522   {
 523     pdbcanvas.bysequence = false;
 524     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 525     pdbcanvas.redrawneeded = true;
 526     pdbcanvas.repaint();
 527   }
 528
 529   public void chain_actionPerformed(ActionEvent e)
 530   {
 531     pdbcanvas.bysequence = false;
 532     pdbcanvas.pdb.setChainColours();
 533     pdbcanvas.redrawneeded = true;
 534     pdbcanvas.repaint();
 535   }
 536
 537   public void zbuffer_actionPerformed(ActionEvent e)
 538   {
 539     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 540     pdbcanvas.redrawneeded = true;
 541     pdbcanvas.repaint();
 542   }
 543
 544   public void molecule_actionPerformed(ActionEvent e)
 545   {
 546     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 547     pdbcanvas.redrawneeded = true;
 548     pdbcanvas.repaint();
 549   }
 550
 551   public void depth_actionPerformed(ActionEvent e)
 552   {
 553     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 554     pdbcanvas.redrawneeded = true;
 555     pdbcanvas.repaint();
 556   }
 557
 558   public void wire_actionPerformed(ActionEvent e)
 559   {
 560     pdbcanvas.wire = !pdbcanvas.wire;
 561     pdbcanvas.redrawneeded = true;
 562     pdbcanvas.repaint();
 563   }
 564
 565   public void seqButton_actionPerformed(ActionEvent e)
 566   {
 567     pdbcanvas.bysequence = true;
 568     pdbcanvas.updateSeqColours();
 569   }
 570
 571   public void mapping_actionPerformed(ActionEvent e)
 572   {
 573     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 574     try
 575     {
 576       cap.setText(pdbcanvas.mappingDetails.toString());
 577       Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
 578     } catch (OutOfMemoryError oom)
 579     {
 580       new OOMWarning("Opening sequence to structure mapping report", oom);
 581       cap.dispose();
 582     }
 583   }
 584
 585   public void allchains_itemStateChanged(ItemEvent e)
 586   {
 587     pdbcanvas.setAllchainsVisible(allchains.getState());
 588   }
 589
 590   public void zappo_actionPerformed(ActionEvent e)
 591   {
 592     pdbcanvas.bysequence = false;
 593     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 594     pdbcanvas.redrawneeded = true;
 595     pdbcanvas.repaint();
 596   }
 597
 598   public void taylor_actionPerformed(ActionEvent e)
 599   {
 600     pdbcanvas.bysequence = false;
 601     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 602     pdbcanvas.redrawneeded = true;
 603     pdbcanvas.repaint();
 604   }
 605
 606   public void helix_actionPerformed(ActionEvent e)
 607   {
 608     pdbcanvas.bysequence = false;
 609     pdbcanvas.pdb.setColours(new HelixColourScheme());
 610     pdbcanvas.redrawneeded = true;
 611     pdbcanvas.repaint();
 612   }
 613
 614   public void strand_actionPerformed(ActionEvent e)
 615   {
 616     pdbcanvas.bysequence = false;
 617     pdbcanvas.pdb.setColours(new StrandColourScheme());
 618     pdbcanvas.redrawneeded = true;
 619     pdbcanvas.repaint();
 620   }
 621
 622   public void turn_actionPerformed(ActionEvent e)
 623   {
 624     pdbcanvas.bysequence = false;
 625     pdbcanvas.pdb.setColours(new TurnColourScheme());
 626     pdbcanvas.redrawneeded = true;
 627     pdbcanvas.repaint();
 628   }
 629
 630   public void buried_actionPerformed(ActionEvent e)
 631   {
 632     pdbcanvas.bysequence = false;
 633     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 634     pdbcanvas.redrawneeded = true;
 635     pdbcanvas.repaint();
 636   }
 637
 638   public void user_actionPerformed(ActionEvent e)
 639   {
 640     if (e.getActionCommand().equals("User Defined..."))
 641     {
 642       // new UserDefinedColours(pdbcanvas, null);
 643     }
 644     else
 645     {
 646       UserColourScheme udc = (UserColourScheme) UserDefinedColours
 647               .getUserColourSchemes().get(e.getActionCommand());
 648
 649       pdbcanvas.pdb.setColours(udc);
 650       pdbcanvas.redrawneeded = true;
 651       pdbcanvas.repaint();
 652     }
 653   }
 654
 655   public void background_actionPerformed(ActionEvent e)
 656   {
 657     java.awt.Color col = JColorChooser.showDialog(this,
 658             "Select Background Colour", 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("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       } catch (Exception ex)
 697       {
 698         ex.printStackTrace();
 699       }
 700     }
 701   }
 702 }