src/MCview/PDBViewer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package MCview;
  20
  21 import java.io.*;
  22
  23 import java.awt.event.*;
  24 import javax.swing.*;
  25
  26 import jalview.datamodel.*;
  27 import jalview.gui.*;
  28 import jalview.io.*;
  29 import jalview.schemes.*;
  30 import jalview.ws.EBIFetchClient;
  31
  32 import java.awt.BorderLayout;
  33
  34 public class PDBViewer
  35     extends JInternalFrame implements Runnable
  36 {
  37
  38   /**
  39    * The associated sequence in an alignment
  40    */
  41   PDBCanvas pdbcanvas;
  42
  43   PDBEntry pdbentry;
  44   SequenceI[]seq;
  45   String[]chains;
  46   AlignmentPanel ap;
  47   String protocol;
  48   String tmpPDBFile;
  49
  50   public PDBViewer(PDBEntry pdbentry,
  51                    SequenceI[] seq,
  52                    String[] chains,
  53                    AlignmentPanel ap,
  54                    String protocol)
  55
  56   {
  57     this.pdbentry = pdbentry;
  58     this.seq = seq;
  59     this.chains = chains;
  60     this.ap = ap;
  61     this.protocol = protocol;
  62
  63     try
  64     {
  65       jbInit();
  66     }
  67     catch (Exception ex)
  68     {
  69       ex.printStackTrace();
  70     }
  71
  72
  73     StringBuffer title = new StringBuffer(seq[0].getName()
  74                                           + ":"
  75                                           + pdbentry.getFile());
  76
  77     pdbcanvas = new PDBCanvas();
  78
  79     setContentPane(pdbcanvas);
  80
  81     if (pdbentry.getFile() != null)
  82     {
  83       try
  84       {
  85         tmpPDBFile = pdbentry.getFile();
  86         PDBfile pdbfile = new PDBfile(tmpPDBFile,
  87                                       jalview.io.AppletFormatAdapter.FILE);
  88
  89         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
  90
  91       }
  92       catch (java.io.IOException ex)
  93       {
  94         ex.printStackTrace();
  95       }
  96     }
  97     else
  98     {
  99       Thread worker = new Thread(this);
 100       worker.start();
 101     }
 102
 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     }
 133     catch (Exception ex)
 134     {
 135       pdbcanvas.errorMessage = "Error retrieving file: "+pdbentry.getId();
 136       ex.printStackTrace();
 137     }
 138   }
 139
 140   private void jbInit()
 141       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.
 363             nextElement().toString());
 364         radioItem.setName("USER_DEFINED");
 365         radioItem.addMouseListener(new MouseAdapter()
 366         {
 367           public void mousePressed(MouseEvent evt)
 368           {
 369             if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
 370             {
 371               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 372
 373               int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
 374                   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.removeColourFromDefaults(
 381                     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   JMenu fileMenu = new JMenu();
 417   JMenu coloursMenu = new JMenu();
 418   JMenu saveMenu = new JMenu();
 419   JMenuItem png = new JMenuItem();
 420   JMenuItem eps = new JMenuItem();
 421   JMenuItem mapping = new JMenuItem();
 422   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 423   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 424   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 425   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 426
 427   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 428   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 429   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 430   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 431   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 432   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 433   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 434   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 435   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 436   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 437   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 438   JMenu viewMenu = new JMenu();
 439   JMenuItem background = new JMenuItem();
 440   JMenuItem savePDB = new JMenuItem();
 441
 442   /**
 443    * DOCUMENT ME!
 444    *
 445    * @param e DOCUMENT ME!
 446    */
 447   public void eps_actionPerformed(ActionEvent e)
 448   {
 449     makePDBImage(jalview.util.ImageMaker.EPS);
 450   }
 451
 452   /**
 453    * DOCUMENT ME!
 454    *
 455    * @param e DOCUMENT ME!
 456    */
 457   public void png_actionPerformed(ActionEvent e)
 458   {
 459     makePDBImage(jalview.util.ImageMaker.PNG);
 460   }
 461
 462   void makePDBImage(int type)
 463   {
 464     int width = pdbcanvas.getWidth();
 465     int height = pdbcanvas.getHeight();
 466
 467     jalview.util.ImageMaker im;
 468
 469     if (type == jalview.util.ImageMaker.PNG)
 470     {
 471       im = new jalview.util.ImageMaker(this,
 472                                        jalview.util.ImageMaker.PNG,
 473                                        "Make PNG image from view",
 474                                        width, height,
 475                                        null, null);
 476     }
 477     else
 478     {
 479       im = new jalview.util.ImageMaker(this,
 480                                        jalview.util.ImageMaker.EPS,
 481                                        "Make EPS file from view",
 482                                        width, height,
 483                                        null, this.getTitle());
 484     }
 485
 486     if (im.getGraphics() != null)
 487     {
 488       pdbcanvas.drawAll(im.getGraphics(), width, height);
 489       im.writeImage();
 490     }
 491   }
 492
 493   public void charge_actionPerformed(ActionEvent e)
 494   {
 495     pdbcanvas.bysequence = false;
 496     pdbcanvas.pdb.setChargeColours();
 497     pdbcanvas.redrawneeded = true;
 498     pdbcanvas.repaint();
 499   }
 500
 501   public void hydro_actionPerformed(ActionEvent e)
 502   {
 503     pdbcanvas.bysequence = false;
 504     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 505     pdbcanvas.redrawneeded = true;
 506     pdbcanvas.repaint();
 507   }
 508
 509   public void chain_actionPerformed(ActionEvent e)
 510   {
 511     pdbcanvas.bysequence = false;
 512     pdbcanvas.pdb.setChainColours();
 513     pdbcanvas.redrawneeded = true;
 514     pdbcanvas.repaint();
 515   }
 516
 517   public void zbuffer_actionPerformed(ActionEvent e)
 518   {
 519     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 520     pdbcanvas.redrawneeded = true;
 521     pdbcanvas.repaint();
 522   }
 523
 524   public void molecule_actionPerformed(ActionEvent e)
 525   {
 526     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 527     pdbcanvas.redrawneeded = true;
 528     pdbcanvas.repaint();
 529   }
 530
 531   public void depth_actionPerformed(ActionEvent e)
 532   {
 533     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 534     pdbcanvas.redrawneeded = true;
 535     pdbcanvas.repaint();
 536   }
 537
 538   public void wire_actionPerformed(ActionEvent e)
 539   {
 540     pdbcanvas.wire = !pdbcanvas.wire;
 541     pdbcanvas.redrawneeded = true;
 542     pdbcanvas.repaint();
 543   }
 544
 545   public void seqButton_actionPerformed(ActionEvent e)
 546   {
 547     pdbcanvas.bysequence = true;
 548     pdbcanvas.updateSeqColours();
 549   }
 550
 551   public void mapping_actionPerformed(ActionEvent e)
 552   {
 553     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 554     Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
 555     cap.setText(pdbcanvas.mappingDetails.toString());
 556   }
 557
 558   public void allchains_itemStateChanged(ItemEvent e)
 559   {
 560     pdbcanvas.setAllchainsVisible(allchains.getState());
 561   }
 562
 563
 564   public void zappo_actionPerformed(ActionEvent e)
 565   {
 566     pdbcanvas.bysequence = false;
 567     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 568     pdbcanvas.redrawneeded = true;
 569     pdbcanvas.repaint();
 570   }
 571
 572   public void taylor_actionPerformed(ActionEvent e)
 573   {
 574     pdbcanvas.bysequence = false;
 575     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 576     pdbcanvas.redrawneeded = true;
 577     pdbcanvas.repaint();
 578   }
 579
 580   public void helix_actionPerformed(ActionEvent e)
 581   {
 582     pdbcanvas.bysequence = false;
 583     pdbcanvas.pdb.setColours(new HelixColourScheme());
 584     pdbcanvas.redrawneeded = true;
 585     pdbcanvas.repaint();
 586   }
 587
 588   public void strand_actionPerformed(ActionEvent e)
 589   {
 590     pdbcanvas.bysequence = false;
 591     pdbcanvas.pdb.setColours(new StrandColourScheme());
 592     pdbcanvas.redrawneeded = true;
 593     pdbcanvas.repaint();
 594   }
 595
 596   public void turn_actionPerformed(ActionEvent e)
 597   {
 598     pdbcanvas.bysequence = false;
 599     pdbcanvas.pdb.setColours(new TurnColourScheme());
 600     pdbcanvas.redrawneeded = true;
 601     pdbcanvas.repaint();
 602   }
 603
 604   public void buried_actionPerformed(ActionEvent e)
 605   {
 606     pdbcanvas.bysequence = false;
 607     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 608     pdbcanvas.redrawneeded = true;
 609     pdbcanvas.repaint();
 610   }
 611
 612   public void user_actionPerformed(ActionEvent e)
 613   {
 614     if (e.getActionCommand().equals("User Defined..."))
 615     {
 616      // new UserDefinedColours(pdbcanvas, null);
 617     }
 618     else
 619     {
 620       UserColourScheme udc = (UserColourScheme) UserDefinedColours.
 621           getUserColourSchemes().get(e.getActionCommand());
 622
 623       pdbcanvas.pdb.setColours(udc);
 624       pdbcanvas.redrawneeded = true;
 625       pdbcanvas.repaint();
 626     }
 627   }
 628
 629   public void background_actionPerformed(ActionEvent e)
 630   {
 631     java.awt.Color col = JColorChooser.showDialog(this,
 632                                                   "Select Background Colour",
 633                                                   pdbcanvas.backgroundColour);
 634
 635     if (col != null)
 636     {
 637       pdbcanvas.backgroundColour = col;
 638       pdbcanvas.redrawneeded = true;
 639       pdbcanvas.repaint();
 640     }
 641   }
 642
 643   public void savePDB_actionPerformed(ActionEvent e)
 644   {
 645     JalviewFileChooser chooser = new JalviewFileChooser(
 646         jalview.bin.Cache.getProperty(
 647             "LAST_DIRECTORY"));
 648
 649     chooser.setFileView(new JalviewFileView());
 650     chooser.setDialogTitle("Save PDB File");
 651     chooser.setToolTipText("Save");
 652
 653     int value = chooser.showSaveDialog(this);
 654
 655     if (value == JalviewFileChooser.APPROVE_OPTION)
 656     {
 657       try
 658       {
 659         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 660         File outFile = chooser.getSelectedFile();
 661
 662         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 663         String data;
 664         while ( (data = in.readLine()) != null)
 665         {
 666           if (
 667               ! (data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
 668               )
 669           {
 670             out.println(data);
 671           }
 672         }
 673         out.close();
 674       }
 675       catch (Exception ex)
 676       {
 677         ex.printStackTrace();
 678       }
 679     }
 680   }
 681 }