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
  31 public class PDBViewer
  32     extends JInternalFrame implements Runnable
  33 {
  34   PDBEntry pdb;
  35   /**
  36    * The associated sequence in an alignment
  37    */
  38   Sequence sequence;
  39   PDBCanvas pdbcanvas;
  40   String tmpPDBFile;
  41
  42   public PDBViewer(PDBEntry entry,
  43                    Sequence seq,
  44                    SeqCanvas seqcanvas)
  45   {
  46     try
  47     {
  48       jbInit();
  49     }
  50     catch (Exception ex)
  51     {
  52       ex.printStackTrace();
  53     }
  54
  55     if (entry == null)
  56     {
  57       return;
  58     }
  59     pdb = entry;
  60     sequence = seq;
  61     pdbcanvas = new PDBCanvas(seqcanvas, sequence);
  62
  63     if (pdb.getFile() != null)
  64     {
  65       try
  66       {
  67         tmpPDBFile = pdb.getFile();
  68         PDBfile pdbfile = new PDBfile(tmpPDBFile,
  69                                       jalview.io.AppletFormatAdapter.FILE);
  70         pdbcanvas.setPDBFile(pdbfile);
  71
  72       }
  73       catch (java.io.IOException ex)
  74       {
  75         ex.printStackTrace();
  76       }
  77     }
  78     else
  79     {
  80       Thread worker = new Thread(this);
  81       worker.start();
  82     }
  83
  84     setContentPane(pdbcanvas);
  85     StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
  86     if (pdb.getProperty() != null)
  87     {
  88       if (pdb.getProperty().get("method") != null)
  89       {
  90         title.append(" Method: ");
  91         title.append(pdb.getProperty().get("method"));
  92       }
  93       if (pdb.getProperty().get("chains") != null)
  94       {
  95         title.append(" Chain:");
  96         title.append(pdb.getProperty().get("chains"));
  97       }
  98     }
  99     Desktop.addInternalFrame(this, title.toString(), 400, 400);
 100   }
 101
 102   public void run()
 103   {
 104     try
 105     {
 106       EBIFetchClient ebi = new EBIFetchClient();
 107       String query = "pdb:" + pdb.getId();
 108       tmpPDBFile = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
 109       if (tmpPDBFile != null)
 110       {
 111         PDBfile pdbfile = new PDBfile(tmpPDBFile,
 112                                       jalview.io.AppletFormatAdapter.FILE);
 113         pdbcanvas.setPDBFile(pdbfile);
 114       }
 115       else
 116       {
 117         throw new Exception("Empty result for WSDbFetch Query: " + query);
 118       }
 119     }
 120     catch (Exception ex)
 121     {
 122       ex.printStackTrace();
 123       showErrorMessage("Failed to retrieve PDB structure.");
 124 //      this.dispose();
 125     }
 126   }
 127
 128   private void jbInit()
 129       throws Exception
 130   {
 131     this.addKeyListener(new KeyAdapter()
 132     {
 133       public void keyPressed(KeyEvent evt)
 134       {
 135         pdbcanvas.keyPressed(evt);
 136       }
 137     });
 138
 139     this.setJMenuBar(jMenuBar1);
 140     fileMenu.setText("File");
 141     coloursMenu.setText("Colours");
 142     saveMenu.setActionCommand("Save Image");
 143     saveMenu.setText("Save As");
 144     png.setText("PNG");
 145     png.addActionListener(new ActionListener()
 146     {
 147       public void actionPerformed(ActionEvent e)
 148       {
 149         png_actionPerformed(e);
 150       }
 151     });
 152     eps.setText("EPS");
 153     eps.addActionListener(new ActionListener()
 154     {
 155       public void actionPerformed(ActionEvent e)
 156       {
 157         eps_actionPerformed(e);
 158       }
 159     });
 160     mapping.setText("View Mapping");
 161     mapping.addActionListener(new ActionListener()
 162     {
 163       public void actionPerformed(ActionEvent e)
 164       {
 165         mapping_actionPerformed(e);
 166       }
 167     });
 168     wire.setText("Wireframe");
 169     wire.addActionListener(new ActionListener()
 170     {
 171       public void actionPerformed(ActionEvent e)
 172       {
 173         wire_actionPerformed(e);
 174       }
 175     });
 176     depth.setSelected(true);
 177     depth.setText("Depthcue");
 178     depth.addActionListener(new ActionListener()
 179     {
 180       public void actionPerformed(ActionEvent e)
 181       {
 182         depth_actionPerformed(e);
 183       }
 184     });
 185     zbuffer.setSelected(true);
 186     zbuffer.setText("Z Buffering");
 187     zbuffer.addActionListener(new ActionListener()
 188     {
 189       public void actionPerformed(ActionEvent e)
 190       {
 191         zbuffer_actionPerformed(e);
 192       }
 193     });
 194     charge.setText("Charge & Cysteine");
 195     charge.addActionListener(new ActionListener()
 196     {
 197       public void actionPerformed(ActionEvent e)
 198       {
 199         charge_actionPerformed(e);
 200       }
 201     });
 202     chain.setText("By Chain");
 203     chain.addActionListener(new ActionListener()
 204     {
 205       public void actionPerformed(ActionEvent e)
 206       {
 207         chain_actionPerformed(e);
 208       }
 209     });
 210     seqButton.setSelected(true);
 211     seqButton.setText("By Sequence");
 212     seqButton.addActionListener(new ActionListener()
 213     {
 214       public void actionPerformed(ActionEvent e)
 215       {
 216         seqButton_actionPerformed(e);
 217       }
 218     });
 219     allchains.setSelected(true);
 220     allchains.setText("Show All Chains");
 221     allchains.addItemListener(new ItemListener()
 222     {
 223       public void itemStateChanged(ItemEvent e)
 224       {
 225         allchains_itemStateChanged(e);
 226       }
 227     });
 228     zappo.setText("Zappo");
 229     zappo.addActionListener(new ActionListener()
 230     {
 231       public void actionPerformed(ActionEvent e)
 232       {
 233         zappo_actionPerformed(e);
 234       }
 235     });
 236     taylor.setText("Taylor");
 237     taylor.addActionListener(new ActionListener()
 238     {
 239       public void actionPerformed(ActionEvent e)
 240       {
 241         taylor_actionPerformed(e);
 242       }
 243     });
 244     hydro.setText("Hydro");
 245     hydro.addActionListener(new ActionListener()
 246     {
 247       public void actionPerformed(ActionEvent e)
 248       {
 249         hydro_actionPerformed(e);
 250       }
 251     });
 252     helix.setText("Helix");
 253     helix.addActionListener(new ActionListener()
 254     {
 255       public void actionPerformed(ActionEvent e)
 256       {
 257         helix_actionPerformed(e);
 258       }
 259     });
 260     strand.setText("Strand");
 261     strand.addActionListener(new ActionListener()
 262     {
 263       public void actionPerformed(ActionEvent e)
 264       {
 265         strand_actionPerformed(e);
 266       }
 267     });
 268     turn.setText("Turn");
 269     turn.addActionListener(new ActionListener()
 270     {
 271       public void actionPerformed(ActionEvent e)
 272       {
 273         turn_actionPerformed(e);
 274       }
 275     });
 276     buried.setText("Buried");
 277     buried.addActionListener(new ActionListener()
 278     {
 279       public void actionPerformed(ActionEvent e)
 280       {
 281         buried_actionPerformed(e);
 282       }
 283     });
 284     user.setText("User Defined...");
 285     user.addActionListener(new ActionListener()
 286     {
 287       public void actionPerformed(ActionEvent e)
 288       {
 289         user_actionPerformed(e);
 290       }
 291     });
 292     viewMenu.setText("View");
 293     background.setText("Background Colour...");
 294     background.addActionListener(new ActionListener()
 295     {
 296       public void actionPerformed(ActionEvent e)
 297       {
 298         background_actionPerformed(e);
 299       }
 300     });
 301     savePDB.setText("PDB File");
 302     savePDB.addActionListener(new ActionListener()
 303     {
 304       public void actionPerformed(ActionEvent e)
 305       {
 306         savePDB_actionPerformed(e);
 307       }
 308     });
 309     jMenuBar1.add(fileMenu);
 310     jMenuBar1.add(coloursMenu);
 311     jMenuBar1.add(viewMenu);
 312     fileMenu.add(saveMenu);
 313     fileMenu.add(mapping);
 314     saveMenu.add(savePDB);
 315     saveMenu.add(png);
 316     saveMenu.add(eps);
 317     coloursMenu.add(seqButton);
 318     coloursMenu.add(chain);
 319     coloursMenu.add(charge);
 320     coloursMenu.add(zappo);
 321     coloursMenu.add(taylor);
 322     coloursMenu.add(hydro);
 323     coloursMenu.add(helix);
 324     coloursMenu.add(strand);
 325     coloursMenu.add(turn);
 326     coloursMenu.add(buried);
 327     coloursMenu.add(user);
 328     coloursMenu.add(background);
 329     ButtonGroup bg = new ButtonGroup();
 330     bg.add(seqButton);
 331     bg.add(chain);
 332     bg.add(charge);
 333     bg.add(zappo);
 334     bg.add(taylor);
 335     bg.add(hydro);
 336     bg.add(helix);
 337     bg.add(strand);
 338     bg.add(turn);
 339     bg.add(buried);
 340     bg.add(user);
 341
 342     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 343     {
 344       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
 345           getUserColourSchemes().keys();
 346
 347       while (userColours.hasMoreElements())
 348       {
 349         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 350             userColours.
 351             nextElement().toString());
 352         radioItem.setName("USER_DEFINED");
 353         radioItem.addMouseListener(new MouseAdapter()
 354         {
 355           public void mousePressed(MouseEvent evt)
 356           {
 357             if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
 358             {
 359               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 360
 361               int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
 362                   Desktop.desktop,
 363                   "Remove from default list?",
 364                   "Remove user defined colour",
 365                   JOptionPane.YES_NO_OPTION);
 366               if (option == JOptionPane.YES_OPTION)
 367               {
 368                 jalview.gui.UserDefinedColours.removeColourFromDefaults(
 369                     radioItem.getText());
 370                 coloursMenu.remove(radioItem);
 371               }
 372               else
 373               {
 374                 radioItem.addActionListener(new ActionListener()
 375                 {
 376                   public void actionPerformed(ActionEvent evt)
 377                   {
 378                     user_actionPerformed(evt);
 379                   }
 380                 });
 381               }
 382             }
 383           }
 384         });
 385         radioItem.addActionListener(new ActionListener()
 386         {
 387           public void actionPerformed(ActionEvent evt)
 388           {
 389             user_actionPerformed(evt);
 390           }
 391         });
 392         coloursMenu.add(radioItem);
 393         bg.add(radioItem);
 394       }
 395     }
 396
 397     viewMenu.add(wire);
 398     viewMenu.add(depth);
 399     viewMenu.add(zbuffer);
 400     viewMenu.add(allchains);
 401   }
 402
 403   JMenuBar jMenuBar1 = new JMenuBar();
 404   JMenu fileMenu = new JMenu();
 405   JMenu coloursMenu = new JMenu();
 406   JMenu saveMenu = new JMenu();
 407   JMenuItem png = new JMenuItem();
 408   JMenuItem eps = new JMenuItem();
 409   JMenuItem mapping = new JMenuItem();
 410   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 411   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 412   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 413   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 414
 415   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 416   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 417   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 418   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 419   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 420   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 421   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 422   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 423   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 424   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 425   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 426   JMenu viewMenu = new JMenu();
 427   JMenuItem background = new JMenuItem();
 428   JMenuItem savePDB = new JMenuItem();
 429
 430   /**
 431    * DOCUMENT ME!
 432    *
 433    * @param e DOCUMENT ME!
 434    */
 435   public void eps_actionPerformed(ActionEvent e)
 436   {
 437     makePDBImage(jalview.util.ImageMaker.EPS);
 438   }
 439
 440   /**
 441    * DOCUMENT ME!
 442    *
 443    * @param e DOCUMENT ME!
 444    */
 445   public void png_actionPerformed(ActionEvent e)
 446   {
 447     makePDBImage(jalview.util.ImageMaker.PNG);
 448   }
 449
 450   void makePDBImage(int type)
 451   {
 452     int width = pdbcanvas.getWidth();
 453     int height = pdbcanvas.getHeight();
 454
 455     jalview.util.ImageMaker im;
 456
 457     if (type == jalview.util.ImageMaker.PNG)
 458     {
 459       im = new jalview.util.ImageMaker(this,
 460                                        jalview.util.ImageMaker.PNG,
 461                                        "Make PNG image from view",
 462                                        width, height,
 463                                        null, null);
 464     }
 465     else
 466     {
 467       im = new jalview.util.ImageMaker(this,
 468                                        jalview.util.ImageMaker.EPS,
 469                                        "Make EPS file from view",
 470                                        width, height,
 471                                        null, this.getTitle());
 472     }
 473
 474     if (im.getGraphics() != null)
 475     {
 476       pdbcanvas.drawAll(im.getGraphics(), width, height);
 477       im.writeImage();
 478     }
 479   }
 480
 481   public void charge_actionPerformed(ActionEvent e)
 482   {
 483     pdbcanvas.bysequence = false;
 484     pdbcanvas.pdb.setChargeColours();
 485     pdbcanvas.redrawneeded = true;
 486     pdbcanvas.repaint();
 487   }
 488
 489   public void hydro_actionPerformed(ActionEvent e)
 490   {
 491     pdbcanvas.bysequence = false;
 492     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 493     pdbcanvas.redrawneeded = true;
 494     pdbcanvas.repaint();
 495   }
 496
 497   public void chain_actionPerformed(ActionEvent e)
 498   {
 499     pdbcanvas.bysequence = false;
 500     pdbcanvas.pdb.setChainColours();
 501     pdbcanvas.redrawneeded = true;
 502     pdbcanvas.repaint();
 503   }
 504
 505   public void zbuffer_actionPerformed(ActionEvent e)
 506   {
 507     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 508     pdbcanvas.redrawneeded = true;
 509     pdbcanvas.repaint();
 510   }
 511
 512   public void molecule_actionPerformed(ActionEvent e)
 513   {
 514     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 515     pdbcanvas.redrawneeded = true;
 516     pdbcanvas.repaint();
 517   }
 518
 519   public void depth_actionPerformed(ActionEvent e)
 520   {
 521     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 522     pdbcanvas.redrawneeded = true;
 523     pdbcanvas.repaint();
 524   }
 525
 526   public void wire_actionPerformed(ActionEvent e)
 527   {
 528     pdbcanvas.wire = !pdbcanvas.wire;
 529     pdbcanvas.redrawneeded = true;
 530     pdbcanvas.repaint();
 531   }
 532
 533   public void seqButton_actionPerformed(ActionEvent e)
 534   {
 535     pdbcanvas.bysequence = true;
 536     pdbcanvas.updateSeqColours();
 537   }
 538
 539   public void mapping_actionPerformed(ActionEvent e)
 540   {
 541     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 542     Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
 543     cap.setText(pdbcanvas.mappingDetails.toString());
 544   }
 545
 546   public void allchains_itemStateChanged(ItemEvent e)
 547   {
 548     pdbcanvas.setAllchainsVisible(allchains.getState());
 549   }
 550
 551   void showErrorMessage(String error)
 552   {
 553     JOptionPane.showInternalMessageDialog(Desktop.desktop,
 554                                           error, "PDB Viewer Error",
 555                                           JOptionPane.WARNING_MESSAGE);
 556   }
 557
 558   public void zappo_actionPerformed(ActionEvent e)
 559   {
 560     pdbcanvas.bysequence = false;
 561     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 562     pdbcanvas.redrawneeded = true;
 563     pdbcanvas.repaint();
 564   }
 565
 566   public void taylor_actionPerformed(ActionEvent e)
 567   {
 568     pdbcanvas.bysequence = false;
 569     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 570     pdbcanvas.redrawneeded = true;
 571     pdbcanvas.repaint();
 572   }
 573
 574   public void helix_actionPerformed(ActionEvent e)
 575   {
 576     pdbcanvas.bysequence = false;
 577     pdbcanvas.pdb.setColours(new HelixColourScheme());
 578     pdbcanvas.redrawneeded = true;
 579     pdbcanvas.repaint();
 580   }
 581
 582   public void strand_actionPerformed(ActionEvent e)
 583   {
 584     pdbcanvas.bysequence = false;
 585     pdbcanvas.pdb.setColours(new StrandColourScheme());
 586     pdbcanvas.redrawneeded = true;
 587     pdbcanvas.repaint();
 588   }
 589
 590   public void turn_actionPerformed(ActionEvent e)
 591   {
 592     pdbcanvas.bysequence = false;
 593     pdbcanvas.pdb.setColours(new TurnColourScheme());
 594     pdbcanvas.redrawneeded = true;
 595     pdbcanvas.repaint();
 596   }
 597
 598   public void buried_actionPerformed(ActionEvent e)
 599   {
 600     pdbcanvas.bysequence = false;
 601     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 602     pdbcanvas.redrawneeded = true;
 603     pdbcanvas.repaint();
 604   }
 605
 606   public void user_actionPerformed(ActionEvent e)
 607   {
 608     if (e.getActionCommand().equals("User Defined..."))
 609     {
 610       new UserDefinedColours(pdbcanvas, null);
 611     }
 612     else
 613     {
 614       UserColourScheme udc = (UserColourScheme) UserDefinedColours.
 615           getUserColourSchemes().get(e.getActionCommand());
 616
 617       pdbcanvas.pdb.setColours(udc);
 618       pdbcanvas.redrawneeded = true;
 619       pdbcanvas.repaint();
 620     }
 621   }
 622
 623   public void background_actionPerformed(ActionEvent e)
 624   {
 625     java.awt.Color col = JColorChooser.showDialog(this,
 626                                                   "Select Background Colour",
 627                                                   pdbcanvas.backgroundColour);
 628
 629     if (col != null)
 630     {
 631       pdbcanvas.backgroundColour = col;
 632       pdbcanvas.redrawneeded = true;
 633       pdbcanvas.repaint();
 634     }
 635   }
 636
 637   public void savePDB_actionPerformed(ActionEvent e)
 638   {
 639     JalviewFileChooser chooser = new JalviewFileChooser(
 640         jalview.bin.Cache.getProperty(
 641             "LAST_DIRECTORY"));
 642
 643     chooser.setFileView(new JalviewFileView());
 644     chooser.setDialogTitle("Save PDB File");
 645     chooser.setToolTipText("Save");
 646
 647     int value = chooser.showSaveDialog(this);
 648
 649     if (value == JalviewFileChooser.APPROVE_OPTION)
 650     {
 651       try
 652       {
 653         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 654         File outFile = chooser.getSelectedFile();
 655
 656         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 657         String data;
 658         while ( (data = in.readLine()) != null)
 659         {
 660           if (
 661               ! (data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
 662               )
 663           {
 664             out.println(data);
 665           }
 666         }
 667         out.close();
 668       }
 669       catch (Exception ex)
 670       {
 671         ex.printStackTrace();
 672       }
 673     }
 674   }
 675 }