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 java.awt.BorderLayout;
  31
  32 public class PDBViewer
  33     extends JInternalFrame implements Runnable
  34 {
  35
  36   /**
  37    * The associated sequence in an alignment
  38    */
  39   PDBCanvas pdbcanvas;
  40
  41   PDBEntry pdbentry;
  42   SequenceI[]seq;
  43   String[]chains;
  44   AlignmentPanel ap;
  45   String protocol;
  46   String tmpPDBFile;
  47
  48   public PDBViewer(PDBEntry pdbentry,
  49                    SequenceI[] seq,
  50                    String[] chains,
  51                    AlignmentPanel ap,
  52                    String protocol)
  53
  54   {
  55     this.pdbentry = pdbentry;
  56     this.seq = seq;
  57     this.chains = chains;
  58     this.ap = ap;
  59     this.protocol = protocol;
  60
  61     try
  62     {
  63       jbInit();
  64     }
  65     catch (Exception ex)
  66     {
  67       ex.printStackTrace();
  68     }
  69
  70
  71     StringBuffer title = new StringBuffer(seq[0].getName()
  72                                           + ":"
  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       }
  90       catch (java.io.IOException ex)
  91       {
  92         ex.printStackTrace();
  93       }
  94     }
  95     else
  96     {
  97       Thread worker = new Thread(this);
  98       worker.start();
  99     }
 100
 101
 102
 103     if (pdbentry.getProperty() != null)
 104     {
 105       if (pdbentry.getProperty().get("method") != null)
 106       {
 107         title.append(" Method: ");
 108         title.append(pdbentry.getProperty().get("method"));
 109       }
 110       if (pdbentry.getProperty().get("chains") != null)
 111       {
 112         title.append(" Chain:");
 113         title.append(pdbentry.getProperty().get("chains"));
 114       }
 115     }
 116     Desktop.addInternalFrame(this, title.toString(), 400, 400);
 117   }
 118
 119   public void run()
 120   {
 121     try
 122     {
 123       EBIFetchClient ebi = new EBIFetchClient();
 124       String query = "pdb:" + pdbentry.getId();
 125       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
 126                        .getAbsolutePath());
 127
 128       if(pdbentry.getFile()!=null)
 129         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 130     }
 131     catch (Exception ex)
 132     {
 133       pdbcanvas.errorMessage = "Error retrieving file: "+pdbentry.getId();
 134       ex.printStackTrace();
 135     }
 136   }
 137
 138   private void jbInit()
 139       throws Exception
 140   {
 141     this.addKeyListener(new KeyAdapter()
 142     {
 143       public void keyPressed(KeyEvent evt)
 144       {
 145         pdbcanvas.keyPressed(evt);
 146       }
 147     });
 148
 149     this.setJMenuBar(jMenuBar1);
 150     fileMenu.setText("File");
 151     coloursMenu.setText("Colours");
 152     saveMenu.setActionCommand("Save Image");
 153     saveMenu.setText("Save As");
 154     png.setText("PNG");
 155     png.addActionListener(new ActionListener()
 156     {
 157       public void actionPerformed(ActionEvent e)
 158       {
 159         png_actionPerformed(e);
 160       }
 161     });
 162     eps.setText("EPS");
 163     eps.addActionListener(new ActionListener()
 164     {
 165       public void actionPerformed(ActionEvent e)
 166       {
 167         eps_actionPerformed(e);
 168       }
 169     });
 170     mapping.setText("View Mapping");
 171     mapping.addActionListener(new ActionListener()
 172     {
 173       public void actionPerformed(ActionEvent e)
 174       {
 175         mapping_actionPerformed(e);
 176       }
 177     });
 178     wire.setText("Wireframe");
 179     wire.addActionListener(new ActionListener()
 180     {
 181       public void actionPerformed(ActionEvent e)
 182       {
 183         wire_actionPerformed(e);
 184       }
 185     });
 186     depth.setSelected(true);
 187     depth.setText("Depthcue");
 188     depth.addActionListener(new ActionListener()
 189     {
 190       public void actionPerformed(ActionEvent e)
 191       {
 192         depth_actionPerformed(e);
 193       }
 194     });
 195     zbuffer.setSelected(true);
 196     zbuffer.setText("Z Buffering");
 197     zbuffer.addActionListener(new ActionListener()
 198     {
 199       public void actionPerformed(ActionEvent e)
 200       {
 201         zbuffer_actionPerformed(e);
 202       }
 203     });
 204     charge.setText("Charge & Cysteine");
 205     charge.addActionListener(new ActionListener()
 206     {
 207       public void actionPerformed(ActionEvent e)
 208       {
 209         charge_actionPerformed(e);
 210       }
 211     });
 212     chain.setText("By Chain");
 213     chain.addActionListener(new ActionListener()
 214     {
 215       public void actionPerformed(ActionEvent e)
 216       {
 217         chain_actionPerformed(e);
 218       }
 219     });
 220     seqButton.setSelected(true);
 221     seqButton.setText("By Sequence");
 222     seqButton.addActionListener(new ActionListener()
 223     {
 224       public void actionPerformed(ActionEvent e)
 225       {
 226         seqButton_actionPerformed(e);
 227       }
 228     });
 229     allchains.setSelected(true);
 230     allchains.setText("Show All Chains");
 231     allchains.addItemListener(new ItemListener()
 232     {
 233       public void itemStateChanged(ItemEvent e)
 234       {
 235         allchains_itemStateChanged(e);
 236       }
 237     });
 238     zappo.setText("Zappo");
 239     zappo.addActionListener(new ActionListener()
 240     {
 241       public void actionPerformed(ActionEvent e)
 242       {
 243         zappo_actionPerformed(e);
 244       }
 245     });
 246     taylor.setText("Taylor");
 247     taylor.addActionListener(new ActionListener()
 248     {
 249       public void actionPerformed(ActionEvent e)
 250       {
 251         taylor_actionPerformed(e);
 252       }
 253     });
 254     hydro.setText("Hydro");
 255     hydro.addActionListener(new ActionListener()
 256     {
 257       public void actionPerformed(ActionEvent e)
 258       {
 259         hydro_actionPerformed(e);
 260       }
 261     });
 262     helix.setText("Helix");
 263     helix.addActionListener(new ActionListener()
 264     {
 265       public void actionPerformed(ActionEvent e)
 266       {
 267         helix_actionPerformed(e);
 268       }
 269     });
 270     strand.setText("Strand");
 271     strand.addActionListener(new ActionListener()
 272     {
 273       public void actionPerformed(ActionEvent e)
 274       {
 275         strand_actionPerformed(e);
 276       }
 277     });
 278     turn.setText("Turn");
 279     turn.addActionListener(new ActionListener()
 280     {
 281       public void actionPerformed(ActionEvent e)
 282       {
 283         turn_actionPerformed(e);
 284       }
 285     });
 286     buried.setText("Buried");
 287     buried.addActionListener(new ActionListener()
 288     {
 289       public void actionPerformed(ActionEvent e)
 290       {
 291         buried_actionPerformed(e);
 292       }
 293     });
 294     user.setText("User Defined...");
 295     user.addActionListener(new ActionListener()
 296     {
 297       public void actionPerformed(ActionEvent e)
 298       {
 299         user_actionPerformed(e);
 300       }
 301     });
 302     viewMenu.setText("View");
 303     background.setText("Background Colour...");
 304     background.addActionListener(new ActionListener()
 305     {
 306       public void actionPerformed(ActionEvent e)
 307       {
 308         background_actionPerformed(e);
 309       }
 310     });
 311     savePDB.setText("PDB File");
 312     savePDB.addActionListener(new ActionListener()
 313     {
 314       public void actionPerformed(ActionEvent e)
 315       {
 316         savePDB_actionPerformed(e);
 317       }
 318     });
 319     jMenuBar1.add(fileMenu);
 320     jMenuBar1.add(coloursMenu);
 321     jMenuBar1.add(viewMenu);
 322     fileMenu.add(saveMenu);
 323     fileMenu.add(mapping);
 324     saveMenu.add(savePDB);
 325     saveMenu.add(png);
 326     saveMenu.add(eps);
 327     coloursMenu.add(seqButton);
 328     coloursMenu.add(chain);
 329     coloursMenu.add(charge);
 330     coloursMenu.add(zappo);
 331     coloursMenu.add(taylor);
 332     coloursMenu.add(hydro);
 333     coloursMenu.add(helix);
 334     coloursMenu.add(strand);
 335     coloursMenu.add(turn);
 336     coloursMenu.add(buried);
 337     coloursMenu.add(user);
 338     coloursMenu.add(background);
 339     ButtonGroup bg = new ButtonGroup();
 340     bg.add(seqButton);
 341     bg.add(chain);
 342     bg.add(charge);
 343     bg.add(zappo);
 344     bg.add(taylor);
 345     bg.add(hydro);
 346     bg.add(helix);
 347     bg.add(strand);
 348     bg.add(turn);
 349     bg.add(buried);
 350     bg.add(user);
 351
 352     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 353     {
 354       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
 355           getUserColourSchemes().keys();
 356
 357       while (userColours.hasMoreElements())
 358       {
 359         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 360             userColours.
 361             nextElement().toString());
 362         radioItem.setName("USER_DEFINED");
 363         radioItem.addMouseListener(new MouseAdapter()
 364         {
 365           public void mousePressed(MouseEvent evt)
 366           {
 367             if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
 368             {
 369               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 370
 371               int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
 372                   Desktop.desktop,
 373                   "Remove from default list?",
 374                   "Remove user defined colour",
 375                   JOptionPane.YES_NO_OPTION);
 376               if (option == JOptionPane.YES_OPTION)
 377               {
 378                 jalview.gui.UserDefinedColours.removeColourFromDefaults(
 379                     radioItem.getText());
 380                 coloursMenu.remove(radioItem);
 381               }
 382               else
 383               {
 384                 radioItem.addActionListener(new ActionListener()
 385                 {
 386                   public void actionPerformed(ActionEvent evt)
 387                   {
 388                     user_actionPerformed(evt);
 389                   }
 390                 });
 391               }
 392             }
 393           }
 394         });
 395         radioItem.addActionListener(new ActionListener()
 396         {
 397           public void actionPerformed(ActionEvent evt)
 398           {
 399             user_actionPerformed(evt);
 400           }
 401         });
 402         coloursMenu.add(radioItem);
 403         bg.add(radioItem);
 404       }
 405     }
 406
 407     viewMenu.add(wire);
 408     viewMenu.add(depth);
 409     viewMenu.add(zbuffer);
 410     viewMenu.add(allchains);
 411   }
 412
 413   JMenuBar jMenuBar1 = new JMenuBar();
 414   JMenu fileMenu = new JMenu();
 415   JMenu coloursMenu = new JMenu();
 416   JMenu saveMenu = new JMenu();
 417   JMenuItem png = new JMenuItem();
 418   JMenuItem eps = new JMenuItem();
 419   JMenuItem mapping = new JMenuItem();
 420   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 421   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 422   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 423   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 424
 425   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 426   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 427   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 428   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 429   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 430   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 431   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 432   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 433   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 434   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 435   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 436   JMenu viewMenu = new JMenu();
 437   JMenuItem background = new JMenuItem();
 438   JMenuItem savePDB = new JMenuItem();
 439
 440   /**
 441    * DOCUMENT ME!
 442    *
 443    * @param e DOCUMENT ME!
 444    */
 445   public void eps_actionPerformed(ActionEvent e)
 446   {
 447     makePDBImage(jalview.util.ImageMaker.EPS);
 448   }
 449
 450   /**
 451    * DOCUMENT ME!
 452    *
 453    * @param e DOCUMENT ME!
 454    */
 455   public void png_actionPerformed(ActionEvent e)
 456   {
 457     makePDBImage(jalview.util.ImageMaker.PNG);
 458   }
 459
 460   void makePDBImage(int type)
 461   {
 462     int width = pdbcanvas.getWidth();
 463     int height = pdbcanvas.getHeight();
 464
 465     jalview.util.ImageMaker im;
 466
 467     if (type == jalview.util.ImageMaker.PNG)
 468     {
 469       im = new jalview.util.ImageMaker(this,
 470                                        jalview.util.ImageMaker.PNG,
 471                                        "Make PNG image from view",
 472                                        width, height,
 473                                        null, null);
 474     }
 475     else
 476     {
 477       im = new jalview.util.ImageMaker(this,
 478                                        jalview.util.ImageMaker.EPS,
 479                                        "Make EPS file from view",
 480                                        width, height,
 481                                        null, this.getTitle());
 482     }
 483
 484     if (im.getGraphics() != null)
 485     {
 486       pdbcanvas.drawAll(im.getGraphics(), width, height);
 487       im.writeImage();
 488     }
 489   }
 490
 491   public void charge_actionPerformed(ActionEvent e)
 492   {
 493     pdbcanvas.bysequence = false;
 494     pdbcanvas.pdb.setChargeColours();
 495     pdbcanvas.redrawneeded = true;
 496     pdbcanvas.repaint();
 497   }
 498
 499   public void hydro_actionPerformed(ActionEvent e)
 500   {
 501     pdbcanvas.bysequence = false;
 502     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 503     pdbcanvas.redrawneeded = true;
 504     pdbcanvas.repaint();
 505   }
 506
 507   public void chain_actionPerformed(ActionEvent e)
 508   {
 509     pdbcanvas.bysequence = false;
 510     pdbcanvas.pdb.setChainColours();
 511     pdbcanvas.redrawneeded = true;
 512     pdbcanvas.repaint();
 513   }
 514
 515   public void zbuffer_actionPerformed(ActionEvent e)
 516   {
 517     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 518     pdbcanvas.redrawneeded = true;
 519     pdbcanvas.repaint();
 520   }
 521
 522   public void molecule_actionPerformed(ActionEvent e)
 523   {
 524     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 525     pdbcanvas.redrawneeded = true;
 526     pdbcanvas.repaint();
 527   }
 528
 529   public void depth_actionPerformed(ActionEvent e)
 530   {
 531     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 532     pdbcanvas.redrawneeded = true;
 533     pdbcanvas.repaint();
 534   }
 535
 536   public void wire_actionPerformed(ActionEvent e)
 537   {
 538     pdbcanvas.wire = !pdbcanvas.wire;
 539     pdbcanvas.redrawneeded = true;
 540     pdbcanvas.repaint();
 541   }
 542
 543   public void seqButton_actionPerformed(ActionEvent e)
 544   {
 545     pdbcanvas.bysequence = true;
 546     pdbcanvas.updateSeqColours();
 547   }
 548
 549   public void mapping_actionPerformed(ActionEvent e)
 550   {
 551     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 552     Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
 553     cap.setText(pdbcanvas.mappingDetails.toString());
 554   }
 555
 556   public void allchains_itemStateChanged(ItemEvent e)
 557   {
 558     pdbcanvas.setAllchainsVisible(allchains.getState());
 559   }
 560
 561
 562   public void zappo_actionPerformed(ActionEvent e)
 563   {
 564     pdbcanvas.bysequence = false;
 565     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 566     pdbcanvas.redrawneeded = true;
 567     pdbcanvas.repaint();
 568   }
 569
 570   public void taylor_actionPerformed(ActionEvent e)
 571   {
 572     pdbcanvas.bysequence = false;
 573     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 574     pdbcanvas.redrawneeded = true;
 575     pdbcanvas.repaint();
 576   }
 577
 578   public void helix_actionPerformed(ActionEvent e)
 579   {
 580     pdbcanvas.bysequence = false;
 581     pdbcanvas.pdb.setColours(new HelixColourScheme());
 582     pdbcanvas.redrawneeded = true;
 583     pdbcanvas.repaint();
 584   }
 585
 586   public void strand_actionPerformed(ActionEvent e)
 587   {
 588     pdbcanvas.bysequence = false;
 589     pdbcanvas.pdb.setColours(new StrandColourScheme());
 590     pdbcanvas.redrawneeded = true;
 591     pdbcanvas.repaint();
 592   }
 593
 594   public void turn_actionPerformed(ActionEvent e)
 595   {
 596     pdbcanvas.bysequence = false;
 597     pdbcanvas.pdb.setColours(new TurnColourScheme());
 598     pdbcanvas.redrawneeded = true;
 599     pdbcanvas.repaint();
 600   }
 601
 602   public void buried_actionPerformed(ActionEvent e)
 603   {
 604     pdbcanvas.bysequence = false;
 605     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 606     pdbcanvas.redrawneeded = true;
 607     pdbcanvas.repaint();
 608   }
 609
 610   public void user_actionPerformed(ActionEvent e)
 611   {
 612     if (e.getActionCommand().equals("User Defined..."))
 613     {
 614      // new UserDefinedColours(pdbcanvas, null);
 615     }
 616     else
 617     {
 618       UserColourScheme udc = (UserColourScheme) UserDefinedColours.
 619           getUserColourSchemes().get(e.getActionCommand());
 620
 621       pdbcanvas.pdb.setColours(udc);
 622       pdbcanvas.redrawneeded = true;
 623       pdbcanvas.repaint();
 624     }
 625   }
 626
 627   public void background_actionPerformed(ActionEvent e)
 628   {
 629     java.awt.Color col = JColorChooser.showDialog(this,
 630                                                   "Select Background Colour",
 631                                                   pdbcanvas.backgroundColour);
 632
 633     if (col != null)
 634     {
 635       pdbcanvas.backgroundColour = col;
 636       pdbcanvas.redrawneeded = true;
 637       pdbcanvas.repaint();
 638     }
 639   }
 640
 641   public void savePDB_actionPerformed(ActionEvent e)
 642   {
 643     JalviewFileChooser chooser = new JalviewFileChooser(
 644         jalview.bin.Cache.getProperty(
 645             "LAST_DIRECTORY"));
 646
 647     chooser.setFileView(new JalviewFileView());
 648     chooser.setDialogTitle("Save PDB File");
 649     chooser.setToolTipText("Save");
 650
 651     int value = chooser.showSaveDialog(this);
 652
 653     if (value == JalviewFileChooser.APPROVE_OPTION)
 654     {
 655       try
 656       {
 657         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 658         File outFile = chooser.getSelectedFile();
 659
 660         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 661         String data;
 662         while ( (data = in.readLine()) != null)
 663         {
 664           if (
 665               ! (data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
 666               )
 667           {
 668             out.println(data);
 669           }
 670         }
 671         out.close();
 672       }
 673       catch (Exception ex)
 674       {
 675         ex.printStackTrace();
 676       }
 677     }
 678   }
 679 }