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     background.addActionListener(new ActionListener()
 300     {
 301       public void actionPerformed(ActionEvent e)
 302       {
 303         background_actionPerformed(e);
 304       }
 305     });
 306     savePDB.setText(MessageManager.getString("label.pdb_file"));
 307     savePDB.addActionListener(new ActionListener()
 308     {
 309       public void actionPerformed(ActionEvent e)
 310       {
 311         savePDB_actionPerformed(e);
 312       }
 313     });
 314     jMenuBar1.add(fileMenu);
 315     jMenuBar1.add(coloursMenu);
 316     jMenuBar1.add(viewMenu);
 317     fileMenu.add(saveMenu);
 318     fileMenu.add(mapping);
 319     saveMenu.add(savePDB);
 320     saveMenu.add(png);
 321     saveMenu.add(eps);
 322     coloursMenu.add(seqButton);
 323     coloursMenu.add(chain);
 324     coloursMenu.add(charge);
 325     coloursMenu.add(zappo);
 326     coloursMenu.add(taylor);
 327     coloursMenu.add(hydro);
 328     coloursMenu.add(helix);
 329     coloursMenu.add(strand);
 330     coloursMenu.add(turn);
 331     coloursMenu.add(buried);
 332     coloursMenu.add(user);
 333     coloursMenu.add(background);
 334     ButtonGroup bg = new ButtonGroup();
 335     bg.add(seqButton);
 336     bg.add(chain);
 337     bg.add(charge);
 338     bg.add(zappo);
 339     bg.add(taylor);
 340     bg.add(hydro);
 341     bg.add(helix);
 342     bg.add(strand);
 343     bg.add(turn);
 344     bg.add(buried);
 345     bg.add(user);
 346
 347     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 348     {
 349       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 350               .getUserColourSchemes().keys();
 351
 352       while (userColours.hasMoreElements())
 353       {
 354         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 355                 userColours.nextElement().toString());
 356         radioItem.setName("USER_DEFINED");
 357         radioItem.addMouseListener(new MouseAdapter()
 358         {
 359           public void mousePressed(MouseEvent evt)
 360           {
 361             if (evt.isControlDown()
 362                     || SwingUtilities.isRightMouseButton(evt))
 363             {
 364               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 365
 366               int option = JOptionPane.showInternalConfirmDialog(
 367                       jalview.gui.Desktop.desktop,
 368                       MessageManager.getString("label.remove_from_default_list"),
 369                       MessageManager.getString("label.remove_user_defined_colour"),
 370                       JOptionPane.YES_NO_OPTION);
 371               if (option == JOptionPane.YES_OPTION)
 372               {
 373                 jalview.gui.UserDefinedColours
 374                         .removeColourFromDefaults(radioItem.getText());
 375                 coloursMenu.remove(radioItem);
 376               }
 377               else
 378               {
 379                 radioItem.addActionListener(new ActionListener()
 380                 {
 381                   public void actionPerformed(ActionEvent evt)
 382                   {
 383                     user_actionPerformed(evt);
 384                   }
 385                 });
 386               }
 387             }
 388           }
 389         });
 390         radioItem.addActionListener(new ActionListener()
 391         {
 392           public void actionPerformed(ActionEvent evt)
 393           {
 394             user_actionPerformed(evt);
 395           }
 396         });
 397         coloursMenu.add(radioItem);
 398         bg.add(radioItem);
 399       }
 400     }
 401
 402     viewMenu.add(wire);
 403     viewMenu.add(depth);
 404     viewMenu.add(zbuffer);
 405     viewMenu.add(allchains);
 406   }
 407
 408   JMenuBar jMenuBar1 = new JMenuBar();
 409
 410   JMenu fileMenu = new JMenu();
 411
 412   JMenu coloursMenu = new JMenu();
 413
 414   JMenu saveMenu = new JMenu();
 415
 416   JMenuItem png = new JMenuItem();
 417
 418   JMenuItem eps = new JMenuItem();
 419
 420   JMenuItem mapping = new JMenuItem();
 421
 422   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 423
 424   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 425
 426   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 427
 428   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 429
 430   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 431
 432   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 433
 434   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 435
 436   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 437
 438   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 439
 440   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 441
 442   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 443
 444   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 445
 446   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 447
 448   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 449
 450   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 451
 452   JMenu viewMenu = new JMenu();
 453
 454   JMenuItem background = new JMenuItem();
 455
 456   JMenuItem savePDB = new JMenuItem();
 457
 458   /**
 459    * DOCUMENT ME!
 460    *
 461    * @param e
 462    *          DOCUMENT ME!
 463    */
 464   public void eps_actionPerformed(ActionEvent e)
 465   {
 466     makePDBImage(jalview.util.ImageMaker.EPS);
 467   }
 468
 469   /**
 470    * DOCUMENT ME!
 471    *
 472    * @param e
 473    *          DOCUMENT ME!
 474    */
 475   public void png_actionPerformed(ActionEvent e)
 476   {
 477     makePDBImage(jalview.util.ImageMaker.PNG);
 478   }
 479
 480   void makePDBImage(int type)
 481   {
 482     int width = pdbcanvas.getWidth();
 483     int height = pdbcanvas.getHeight();
 484
 485     jalview.util.ImageMaker im;
 486
 487     if (type == jalview.util.ImageMaker.PNG)
 488     {
 489       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
 490               "Make PNG image from view", width, height, null, null);
 491     }
 492     else
 493     {
 494       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
 495               "Make EPS file from view", width, height, null,
 496               this.getTitle());
 497     }
 498
 499     if (im.getGraphics() != null)
 500     {
 501       pdbcanvas.drawAll(im.getGraphics(), width, height);
 502       im.writeImage();
 503     }
 504   }
 505
 506   public void charge_actionPerformed(ActionEvent e)
 507   {
 508     pdbcanvas.bysequence = false;
 509     pdbcanvas.pdb.setChargeColours();
 510     pdbcanvas.redrawneeded = true;
 511     pdbcanvas.repaint();
 512   }
 513
 514   public void hydro_actionPerformed(ActionEvent e)
 515   {
 516     pdbcanvas.bysequence = false;
 517     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 518     pdbcanvas.redrawneeded = true;
 519     pdbcanvas.repaint();
 520   }
 521
 522   public void chain_actionPerformed(ActionEvent e)
 523   {
 524     pdbcanvas.bysequence = false;
 525     pdbcanvas.pdb.setChainColours();
 526     pdbcanvas.redrawneeded = true;
 527     pdbcanvas.repaint();
 528   }
 529
 530   public void zbuffer_actionPerformed(ActionEvent e)
 531   {
 532     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 533     pdbcanvas.redrawneeded = true;
 534     pdbcanvas.repaint();
 535   }
 536
 537   public void molecule_actionPerformed(ActionEvent e)
 538   {
 539     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 540     pdbcanvas.redrawneeded = true;
 541     pdbcanvas.repaint();
 542   }
 543
 544   public void depth_actionPerformed(ActionEvent e)
 545   {
 546     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 547     pdbcanvas.redrawneeded = true;
 548     pdbcanvas.repaint();
 549   }
 550
 551   public void wire_actionPerformed(ActionEvent e)
 552   {
 553     pdbcanvas.wire = !pdbcanvas.wire;
 554     pdbcanvas.redrawneeded = true;
 555     pdbcanvas.repaint();
 556   }
 557
 558   public void seqButton_actionPerformed(ActionEvent e)
 559   {
 560     pdbcanvas.bysequence = true;
 561     pdbcanvas.updateSeqColours();
 562   }
 563
 564   public void mapping_actionPerformed(ActionEvent e)
 565   {
 566     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 567     try
 568     {
 569       cap.setText(pdbcanvas.mappingDetails.toString());
 570       Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"), 550, 600);
 571     } catch (OutOfMemoryError oom)
 572     {
 573       new OOMWarning("Opening sequence to structure mapping report", oom);
 574       cap.dispose();
 575     }
 576   }
 577
 578   public void allchains_itemStateChanged(ItemEvent e)
 579   {
 580     pdbcanvas.setAllchainsVisible(allchains.getState());
 581   }
 582
 583   public void zappo_actionPerformed(ActionEvent e)
 584   {
 585     pdbcanvas.bysequence = false;
 586     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 587     pdbcanvas.redrawneeded = true;
 588     pdbcanvas.repaint();
 589   }
 590
 591   public void taylor_actionPerformed(ActionEvent e)
 592   {
 593     pdbcanvas.bysequence = false;
 594     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 595     pdbcanvas.redrawneeded = true;
 596     pdbcanvas.repaint();
 597   }
 598
 599   public void helix_actionPerformed(ActionEvent e)
 600   {
 601     pdbcanvas.bysequence = false;
 602     pdbcanvas.pdb.setColours(new HelixColourScheme());
 603     pdbcanvas.redrawneeded = true;
 604     pdbcanvas.repaint();
 605   }
 606
 607   public void strand_actionPerformed(ActionEvent e)
 608   {
 609     pdbcanvas.bysequence = false;
 610     pdbcanvas.pdb.setColours(new StrandColourScheme());
 611     pdbcanvas.redrawneeded = true;
 612     pdbcanvas.repaint();
 613   }
 614
 615   public void turn_actionPerformed(ActionEvent e)
 616   {
 617     pdbcanvas.bysequence = false;
 618     pdbcanvas.pdb.setColours(new TurnColourScheme());
 619     pdbcanvas.redrawneeded = true;
 620     pdbcanvas.repaint();
 621   }
 622
 623   public void buried_actionPerformed(ActionEvent e)
 624   {
 625     pdbcanvas.bysequence = false;
 626     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 627     pdbcanvas.redrawneeded = true;
 628     pdbcanvas.repaint();
 629   }
 630
 631   public void user_actionPerformed(ActionEvent e)
 632   {
 633     if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))
 634     {
 635       // new UserDefinedColours(pdbcanvas, null);
 636     }
 637     else
 638     {
 639       UserColourScheme udc = (UserColourScheme) UserDefinedColours
 640               .getUserColourSchemes().get(e.getActionCommand());
 641
 642       pdbcanvas.pdb.setColours(udc);
 643       pdbcanvas.redrawneeded = true;
 644       pdbcanvas.repaint();
 645     }
 646   }
 647
 648   public void background_actionPerformed(ActionEvent e)
 649   {
 650     java.awt.Color col = JColorChooser.showDialog(this,
 651             MessageManager.getString("label.select_backgroud_colour"), pdbcanvas.backgroundColour);
 652
 653     if (col != null)
 654     {
 655       pdbcanvas.backgroundColour = col;
 656       pdbcanvas.redrawneeded = true;
 657       pdbcanvas.repaint();
 658     }
 659   }
 660
 661   public void savePDB_actionPerformed(ActionEvent e)
 662   {
 663     JalviewFileChooser chooser = new JalviewFileChooser(
 664             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 665
 666     chooser.setFileView(new JalviewFileView());
 667     chooser.setDialogTitle("Save PDB File");
 668     chooser.setToolTipText(MessageManager.getString("action.save"));
 669
 670     int value = chooser.showSaveDialog(this);
 671
 672     if (value == JalviewFileChooser.APPROVE_OPTION)
 673     {
 674       try
 675       {
 676         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 677         File outFile = chooser.getSelectedFile();
 678
 679         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 680         String data;
 681         while ((data = in.readLine()) != null)
 682         {
 683           if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
 684           {
 685             out.println(data);
 686           }
 687         }
 688         out.close();
 689         in.close();
 690       } catch (Exception ex)
 691       {
 692         ex.printStackTrace();
 693       }
 694     }
 695   }
 696 }