src/MCview/PDBViewer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
   3  * Copyright (C) 2008 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.ebi.EBIFetchClient;
  31
  32 import java.awt.BorderLayout;
  33
  34 public class PDBViewer extends JInternalFrame implements Runnable
  35 {
  36
  37   /**
  38    * The associated sequence in an alignment
  39    */
  40   PDBCanvas pdbcanvas;
  41
  42   PDBEntry pdbentry;
  43
  44   SequenceI[] seq;
  45
  46   String[] chains;
  47
  48   AlignmentPanel ap;
  49
  50   String protocol;
  51
  52   String tmpPDBFile;
  53
  54   public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
  55           AlignmentPanel ap, String protocol)
  56
  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("File");
 146     coloursMenu.setText("Colours");
 147     saveMenu.setActionCommand("Save Image");
 148     saveMenu.setText("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("View Mapping");
 166     mapping.addActionListener(new ActionListener()
 167     {
 168       public void actionPerformed(ActionEvent e)
 169       {
 170         mapping_actionPerformed(e);
 171       }
 172     });
 173     wire.setText("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("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("Z Buffering");
 192     zbuffer.addActionListener(new ActionListener()
 193     {
 194       public void actionPerformed(ActionEvent e)
 195       {
 196         zbuffer_actionPerformed(e);
 197       }
 198     });
 199     charge.setText("Charge & Cysteine");
 200     charge.addActionListener(new ActionListener()
 201     {
 202       public void actionPerformed(ActionEvent e)
 203       {
 204         charge_actionPerformed(e);
 205       }
 206     });
 207     chain.setText("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("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("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("Zappo");
 234     zappo.addActionListener(new ActionListener()
 235     {
 236       public void actionPerformed(ActionEvent e)
 237       {
 238         zappo_actionPerformed(e);
 239       }
 240     });
 241     taylor.setText("Taylor");
 242     taylor.addActionListener(new ActionListener()
 243     {
 244       public void actionPerformed(ActionEvent e)
 245       {
 246         taylor_actionPerformed(e);
 247       }
 248     });
 249     hydro.setText("Hydro");
 250     hydro.addActionListener(new ActionListener()
 251     {
 252       public void actionPerformed(ActionEvent e)
 253       {
 254         hydro_actionPerformed(e);
 255       }
 256     });
 257     helix.setText("Helix");
 258     helix.addActionListener(new ActionListener()
 259     {
 260       public void actionPerformed(ActionEvent e)
 261       {
 262         helix_actionPerformed(e);
 263       }
 264     });
 265     strand.setText("Strand");
 266     strand.addActionListener(new ActionListener()
 267     {
 268       public void actionPerformed(ActionEvent e)
 269       {
 270         strand_actionPerformed(e);
 271       }
 272     });
 273     turn.setText("Turn");
 274     turn.addActionListener(new ActionListener()
 275     {
 276       public void actionPerformed(ActionEvent e)
 277       {
 278         turn_actionPerformed(e);
 279       }
 280     });
 281     buried.setText("Buried");
 282     buried.addActionListener(new ActionListener()
 283     {
 284       public void actionPerformed(ActionEvent e)
 285       {
 286         buried_actionPerformed(e);
 287       }
 288     });
 289     user.setText("User Defined...");
 290     user.addActionListener(new ActionListener()
 291     {
 292       public void actionPerformed(ActionEvent e)
 293       {
 294         user_actionPerformed(e);
 295       }
 296     });
 297     viewMenu.setText("View");
 298     background.setText("Background Colour...");
 299     background.addActionListener(new ActionListener()
 300     {
 301       public void actionPerformed(ActionEvent e)
 302       {
 303         background_actionPerformed(e);
 304       }
 305     });
 306     savePDB.setText("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
 365                       .removeActionListener(radioItem.getActionListeners()[0]);
 366
 367               int option = JOptionPane.showInternalConfirmDialog(
 368                       jalview.gui.Desktop.desktop,
 369                       "Remove from default list?",
 370                       "Remove user defined colour",
 371                       JOptionPane.YES_NO_OPTION);
 372               if (option == JOptionPane.YES_OPTION)
 373               {
 374                 jalview.gui.UserDefinedColours
 375                         .removeColourFromDefaults(radioItem.getText());
 376                 coloursMenu.remove(radioItem);
 377               }
 378               else
 379               {
 380                 radioItem.addActionListener(new ActionListener()
 381                 {
 382                   public void actionPerformed(ActionEvent evt)
 383                   {
 384                     user_actionPerformed(evt);
 385                   }
 386                 });
 387               }
 388             }
 389           }
 390         });
 391         radioItem.addActionListener(new ActionListener()
 392         {
 393           public void actionPerformed(ActionEvent evt)
 394           {
 395             user_actionPerformed(evt);
 396           }
 397         });
 398         coloursMenu.add(radioItem);
 399         bg.add(radioItem);
 400       }
 401     }
 402
 403     viewMenu.add(wire);
 404     viewMenu.add(depth);
 405     viewMenu.add(zbuffer);
 406     viewMenu.add(allchains);
 407   }
 408
 409   JMenuBar jMenuBar1 = new JMenuBar();
 410
 411   JMenu fileMenu = new JMenu();
 412
 413   JMenu coloursMenu = new JMenu();
 414
 415   JMenu saveMenu = new JMenu();
 416
 417   JMenuItem png = new JMenuItem();
 418
 419   JMenuItem eps = new JMenuItem();
 420
 421   JMenuItem mapping = new JMenuItem();
 422
 423   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 424
 425   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 426
 427   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 428
 429   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 430
 431   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 432
 433   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 434
 435   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 436
 437   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 438
 439   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 440
 441   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 442
 443   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 444
 445   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 446
 447   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 448
 449   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 450
 451   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 452
 453   JMenu viewMenu = new JMenu();
 454
 455   JMenuItem background = new JMenuItem();
 456
 457   JMenuItem savePDB = new JMenuItem();
 458
 459   /**
 460    * DOCUMENT ME!
 461    *
 462    * @param e
 463    *                DOCUMENT ME!
 464    */
 465   public void eps_actionPerformed(ActionEvent e)
 466   {
 467     makePDBImage(jalview.util.ImageMaker.EPS);
 468   }
 469
 470   /**
 471    * DOCUMENT ME!
 472    *
 473    * @param e
 474    *                DOCUMENT ME!
 475    */
 476   public void png_actionPerformed(ActionEvent e)
 477   {
 478     makePDBImage(jalview.util.ImageMaker.PNG);
 479   }
 480
 481   void makePDBImage(int type)
 482   {
 483     int width = pdbcanvas.getWidth();
 484     int height = pdbcanvas.getHeight();
 485
 486     jalview.util.ImageMaker im;
 487
 488     if (type == jalview.util.ImageMaker.PNG)
 489     {
 490       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
 491               "Make PNG image from view", width, height, null, null);
 492     }
 493     else
 494     {
 495       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
 496               "Make EPS file from view", width, height, null, this
 497                       .getTitle());
 498     }
 499
 500     if (im.getGraphics() != null)
 501     {
 502       pdbcanvas.drawAll(im.getGraphics(), width, height);
 503       im.writeImage();
 504     }
 505   }
 506
 507   public void charge_actionPerformed(ActionEvent e)
 508   {
 509     pdbcanvas.bysequence = false;
 510     pdbcanvas.pdb.setChargeColours();
 511     pdbcanvas.redrawneeded = true;
 512     pdbcanvas.repaint();
 513   }
 514
 515   public void hydro_actionPerformed(ActionEvent e)
 516   {
 517     pdbcanvas.bysequence = false;
 518     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 519     pdbcanvas.redrawneeded = true;
 520     pdbcanvas.repaint();
 521   }
 522
 523   public void chain_actionPerformed(ActionEvent e)
 524   {
 525     pdbcanvas.bysequence = false;
 526     pdbcanvas.pdb.setChainColours();
 527     pdbcanvas.redrawneeded = true;
 528     pdbcanvas.repaint();
 529   }
 530
 531   public void zbuffer_actionPerformed(ActionEvent e)
 532   {
 533     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 534     pdbcanvas.redrawneeded = true;
 535     pdbcanvas.repaint();
 536   }
 537
 538   public void molecule_actionPerformed(ActionEvent e)
 539   {
 540     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 541     pdbcanvas.redrawneeded = true;
 542     pdbcanvas.repaint();
 543   }
 544
 545   public void depth_actionPerformed(ActionEvent e)
 546   {
 547     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 548     pdbcanvas.redrawneeded = true;
 549     pdbcanvas.repaint();
 550   }
 551
 552   public void wire_actionPerformed(ActionEvent e)
 553   {
 554     pdbcanvas.wire = !pdbcanvas.wire;
 555     pdbcanvas.redrawneeded = true;
 556     pdbcanvas.repaint();
 557   }
 558
 559   public void seqButton_actionPerformed(ActionEvent e)
 560   {
 561     pdbcanvas.bysequence = true;
 562     pdbcanvas.updateSeqColours();
 563   }
 564
 565   public void mapping_actionPerformed(ActionEvent e)
 566   {
 567     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 568     Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
 569     cap.setText(pdbcanvas.mappingDetails.toString());
 570   }
 571
 572   public void allchains_itemStateChanged(ItemEvent e)
 573   {
 574     pdbcanvas.setAllchainsVisible(allchains.getState());
 575   }
 576
 577   public void zappo_actionPerformed(ActionEvent e)
 578   {
 579     pdbcanvas.bysequence = false;
 580     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 581     pdbcanvas.redrawneeded = true;
 582     pdbcanvas.repaint();
 583   }
 584
 585   public void taylor_actionPerformed(ActionEvent e)
 586   {
 587     pdbcanvas.bysequence = false;
 588     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 589     pdbcanvas.redrawneeded = true;
 590     pdbcanvas.repaint();
 591   }
 592
 593   public void helix_actionPerformed(ActionEvent e)
 594   {
 595     pdbcanvas.bysequence = false;
 596     pdbcanvas.pdb.setColours(new HelixColourScheme());
 597     pdbcanvas.redrawneeded = true;
 598     pdbcanvas.repaint();
 599   }
 600
 601   public void strand_actionPerformed(ActionEvent e)
 602   {
 603     pdbcanvas.bysequence = false;
 604     pdbcanvas.pdb.setColours(new StrandColourScheme());
 605     pdbcanvas.redrawneeded = true;
 606     pdbcanvas.repaint();
 607   }
 608
 609   public void turn_actionPerformed(ActionEvent e)
 610   {
 611     pdbcanvas.bysequence = false;
 612     pdbcanvas.pdb.setColours(new TurnColourScheme());
 613     pdbcanvas.redrawneeded = true;
 614     pdbcanvas.repaint();
 615   }
 616
 617   public void buried_actionPerformed(ActionEvent e)
 618   {
 619     pdbcanvas.bysequence = false;
 620     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 621     pdbcanvas.redrawneeded = true;
 622     pdbcanvas.repaint();
 623   }
 624
 625   public void user_actionPerformed(ActionEvent e)
 626   {
 627     if (e.getActionCommand().equals("User Defined..."))
 628     {
 629       // new UserDefinedColours(pdbcanvas, null);
 630     }
 631     else
 632     {
 633       UserColourScheme udc = (UserColourScheme) UserDefinedColours
 634               .getUserColourSchemes().get(e.getActionCommand());
 635
 636       pdbcanvas.pdb.setColours(udc);
 637       pdbcanvas.redrawneeded = true;
 638       pdbcanvas.repaint();
 639     }
 640   }
 641
 642   public void background_actionPerformed(ActionEvent e)
 643   {
 644     java.awt.Color col = JColorChooser.showDialog(this,
 645             "Select Background Colour", pdbcanvas.backgroundColour);
 646
 647     if (col != null)
 648     {
 649       pdbcanvas.backgroundColour = col;
 650       pdbcanvas.redrawneeded = true;
 651       pdbcanvas.repaint();
 652     }
 653   }
 654
 655   public void savePDB_actionPerformed(ActionEvent e)
 656   {
 657     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
 658             .getProperty("LAST_DIRECTORY"));
 659
 660     chooser.setFileView(new JalviewFileView());
 661     chooser.setDialogTitle("Save PDB File");
 662     chooser.setToolTipText("Save");
 663
 664     int value = chooser.showSaveDialog(this);
 665
 666     if (value == JalviewFileChooser.APPROVE_OPTION)
 667     {
 668       try
 669       {
 670         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 671         File outFile = chooser.getSelectedFile();
 672
 673         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 674         String data;
 675         while ((data = in.readLine()) != null)
 676         {
 677           if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
 678           {
 679             out.println(data);
 680           }
 681         }
 682         out.close();
 683       } catch (Exception ex)
 684       {
 685         ex.printStackTrace();
 686       }
 687     }
 688   }
 689 }