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