PDBViewer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2005 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 javax.swing.*;
  22 import java.awt.event.*;
  23 import jalview.datamodel.*;
  24 import jalview.schemes.*;
  25 import jalview.gui.*;
  26 import jalview.io.EBIFetchClient;
  27 import java.awt.event.ActionListener;
  28 import java.awt.event.ActionEvent;
  29
  30 public class PDBViewer extends JInternalFrame implements Runnable
  31 {
  32   PDBEntry pdb;
  33   Sequence sequence;
  34   PDBCanvas pdbcanvas;
  35
  36
  37   public PDBViewer(PDBEntry entry,
  38                    Sequence seq,
  39                    SeqCanvas seqcanvas)
  40   {
  41     /*Uncomment this to modify in Jbuilder
  42     try
  43     {
  44       jbInit();
  45     }
  46     catch (Exception ex)
  47     {
  48       ex.printStackTrace();
  49     }*/
  50
  51     if (entry==null)
  52       return;
  53     pdb = entry;
  54     sequence = seq;
  55
  56     Thread worker = new Thread(this);
  57     worker.start();
  58
  59     pdbcanvas = new PDBCanvas(seqcanvas, seq);
  60
  61     setContentPane(pdbcanvas);
  62     StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
  63     if(pdb.getProperty()!=null)
  64     {
  65       if (pdb.getProperty().get("method")!=null)
  66       {
  67         title.append(" Method: ");
  68         title.append(pdb.getProperty().get("method"));
  69       }
  70       if (pdb.getProperty().get("chains") != null)
  71       {
  72         title.append(" Chain:");
  73         title.append(pdb.getProperty().get("chains"));
  74       }
  75     }
  76      Desktop.addInternalFrame(this,title.toString(),400, 400);
  77   }
  78
  79   public void run()
  80   {
  81     try
  82     {
  83       EBIFetchClient ebi = new EBIFetchClient();
  84       String query = "pdb:" + pdb.getId();
  85       String[] result = ebi.fetchData(query, "default","raw");
  86       if (result!=null) {
  87         PDBfile pdbfile = new PDBfile(result);
  88         pdbcanvas.setPDBFile(pdbfile);
  89       } else {
  90         throw new Exception("Empty result for WSDbFetch Query: "+query);
  91       }
  92
  93       try
  94       {
  95         jbInit();
  96       }
  97       catch (Exception ex)
  98       {
  99         ex.printStackTrace();
 100       }
 101     }
 102     catch (Exception ex)
 103     {
 104       ex.printStackTrace();
 105       showErrorMessage("Failed to retrieve PDB structure.");
 106 //      this.dispose();
 107     }
 108   }
 109
 110   private void jbInit()
 111       throws Exception
 112   {
 113     this.addKeyListener(new KeyAdapter()
 114         {
 115             public void keyPressed(KeyEvent evt)
 116             {
 117               pdbcanvas.keyPressed(evt);
 118             }
 119         });
 120
 121     this.setJMenuBar(jMenuBar1);
 122     fileMenu.setText("File");
 123     coloursMenu.setText("Colours");
 124     saveMenu.setActionCommand("Save Image");
 125     saveMenu.setText("Save As");
 126     png.setText("PNG");
 127     png.addActionListener(new ActionListener()
 128     {
 129       public void actionPerformed(ActionEvent e)
 130       {
 131         png_actionPerformed(e);
 132       }
 133     });
 134     eps.setText("EPS");
 135     eps.addActionListener(new ActionListener()
 136     {
 137       public void actionPerformed(ActionEvent e)
 138       {
 139         eps_actionPerformed(e);
 140       }
 141     });
 142     mapping.setText("View Mapping");
 143     mapping.addActionListener(new ActionListener()
 144     {
 145       public void actionPerformed(ActionEvent e)
 146       {
 147         mapping_actionPerformed(e);
 148       }
 149     });
 150     wire.setText("Wireframe");
 151     wire.addActionListener(new ActionListener()
 152     {
 153       public void actionPerformed(ActionEvent e)
 154       {
 155         wire_actionPerformed(e);
 156       }
 157     });
 158     depth.setSelected(true);
 159     depth.setText("Depthcue");
 160     depth.addActionListener(new ActionListener()
 161     {
 162       public void actionPerformed(ActionEvent e)
 163       {
 164         depth_actionPerformed(e);
 165       }
 166     });
 167     zbuffer.setSelected(true);
 168     zbuffer.setText("Z Buffering");
 169     zbuffer.addActionListener(new ActionListener()
 170     {
 171       public void actionPerformed(ActionEvent e)
 172       {
 173         zbuffer_actionPerformed(e);
 174       }
 175     });
 176     charge.setText("Charge & Cysteine");
 177     charge.addActionListener(new ActionListener()
 178     {
 179       public void actionPerformed(ActionEvent e)
 180       {
 181         charge_actionPerformed(e);
 182       }
 183     });
 184     chain.setText("By Chain");
 185     chain.addActionListener(new ActionListener()
 186     {
 187       public void actionPerformed(ActionEvent e)
 188       {
 189         chain_actionPerformed(e);
 190       }
 191     });
 192     seqButton.setSelected(true);
 193     seqButton.setText("By Sequence");
 194     seqButton.addActionListener(new ActionListener()
 195     {
 196       public void actionPerformed(ActionEvent e)
 197       {
 198         seqButton_actionPerformed(e);
 199       }
 200     });
 201     allchains.setSelected(true);
 202     allchains.setText("Show All Chains");
 203     allchains.addItemListener(new ItemListener()
 204     {
 205       public void itemStateChanged(ItemEvent e)
 206       {
 207         allchains_itemStateChanged(e);
 208       }
 209     });
 210     zappo.setText("Zappo");
 211     zappo.addActionListener(new ActionListener()
 212     {
 213       public void actionPerformed(ActionEvent e)
 214       {
 215         zappo_actionPerformed(e);
 216       }
 217     });
 218     taylor.setText("Taylor");
 219     taylor.addActionListener(new ActionListener()
 220     {
 221       public void actionPerformed(ActionEvent e)
 222       {
 223         taylor_actionPerformed(e);
 224       }
 225     });
 226     hydro.setText("Hydro");
 227     hydro.addActionListener(new ActionListener()
 228     {
 229       public void actionPerformed(ActionEvent e)
 230       {
 231         hydro_actionPerformed(e);
 232       }
 233     });
 234     helix.setText("Helix");
 235     helix.addActionListener(new ActionListener()
 236     {
 237       public void actionPerformed(ActionEvent e)
 238       {
 239         helix_actionPerformed(e);
 240       }
 241     });
 242     strand.setText("Strand");
 243     strand.addActionListener(new ActionListener()
 244     {
 245       public void actionPerformed(ActionEvent e)
 246       {
 247         strand_actionPerformed(e);
 248       }
 249     });
 250     turn.setText("Turn");
 251     turn.addActionListener(new ActionListener()
 252     {
 253       public void actionPerformed(ActionEvent e)
 254       {
 255         turn_actionPerformed(e);
 256       }
 257     });
 258     buried.setText("Buried");
 259     buried.addActionListener(new ActionListener()
 260     {
 261       public void actionPerformed(ActionEvent e)
 262       {
 263         buried_actionPerformed(e);
 264       }
 265     });
 266     user.setText("User Defined...");
 267     user.addActionListener(new ActionListener()
 268     {
 269       public void actionPerformed(ActionEvent e)
 270       {
 271         user_actionPerformed(e);
 272       }
 273     });
 274     viewMenu.setText("View");
 275     jMenuBar1.add(fileMenu);
 276     jMenuBar1.add(coloursMenu);
 277     jMenuBar1.add(viewMenu);
 278     fileMenu.add(saveMenu);
 279     fileMenu.add(mapping);
 280     saveMenu.add(png);
 281     saveMenu.add(eps);
 282     coloursMenu.add(seqButton);
 283     coloursMenu.add(chain);
 284     coloursMenu.add(charge);
 285     coloursMenu.add(zappo);
 286     coloursMenu.add(taylor);
 287     coloursMenu.add(hydro);
 288     coloursMenu.add(helix);
 289     coloursMenu.add(strand);
 290     coloursMenu.add(turn);
 291     coloursMenu.add(buried);
 292     coloursMenu.add(user);
 293     ButtonGroup bg = new ButtonGroup();
 294     bg.add(seqButton);
 295     bg.add(chain);
 296     bg.add(charge);
 297     bg.add(zappo);
 298     bg.add(taylor);
 299     bg.add(hydro);
 300     bg.add(helix);
 301     bg.add(strand);
 302     bg.add(turn);
 303     bg.add(buried);
 304     bg.add(user);
 305
 306
 307     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
 308     {
 309       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
 310           getUserColourSchemes().keys();
 311
 312       while (userColours.hasMoreElements())
 313       {
 314         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
 315             nextElement().toString());
 316         radioItem.setName("USER_DEFINED");
 317         radioItem.addMouseListener(new MouseAdapter()
 318             {
 319               public void mousePressed(MouseEvent evt)
 320               {
 321                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
 322                 {
 323                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 324
 325                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
 326                       "Remove from default list?",
 327                       "Remove user defined colour",
 328                       JOptionPane.YES_NO_OPTION);
 329                   if(option == JOptionPane.YES_OPTION)
 330                   {
 331                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
 332                     coloursMenu.remove(radioItem);
 333                   }
 334                   else
 335                     radioItem.addActionListener(new ActionListener()
 336                     {
 337                       public void actionPerformed(ActionEvent evt)
 338                       {
 339                         user_actionPerformed(evt);
 340                       }
 341                     });
 342                 }
 343               }
 344             });
 345         radioItem.addActionListener(new ActionListener()
 346         {
 347           public void actionPerformed(ActionEvent evt)
 348           {
 349             user_actionPerformed(evt);
 350           }
 351         });
 352         coloursMenu.add(radioItem);
 353         bg.add(radioItem);
 354       }
 355     }
 356
 357     viewMenu.add(wire);
 358     viewMenu.add(depth);
 359     viewMenu.add(zbuffer);
 360     viewMenu.add(allchains);
 361   }
 362
 363   JMenuBar jMenuBar1 = new JMenuBar();
 364   JMenu fileMenu = new JMenu();
 365   JMenu coloursMenu = new JMenu();
 366   JMenu saveMenu = new JMenu();
 367   JMenuItem png = new JMenuItem();
 368   JMenuItem eps = new JMenuItem();
 369   JMenuItem mapping = new JMenuItem();
 370   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 371   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 372   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 373   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 374
 375   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 376   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 377   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 378   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 379   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 380   JRadioButtonMenuItem zappo = new  JRadioButtonMenuItem();
 381   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 382   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 383   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 384   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 385   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 386   JMenu viewMenu = new JMenu();
 387
 388   /**
 389    * DOCUMENT ME!
 390    *
 391    * @param e DOCUMENT ME!
 392    */
 393   public void eps_actionPerformed(ActionEvent e)
 394   {
 395     makePDBImage(jalview.util.ImageMaker.EPS);
 396   }
 397
 398   /**
 399    * DOCUMENT ME!
 400    *
 401    * @param e DOCUMENT ME!
 402    */
 403   public void png_actionPerformed(ActionEvent e)
 404   {
 405      makePDBImage(jalview.util.ImageMaker.PNG);
 406   }
 407
 408   void makePDBImage(int type)
 409   {
 410     int width = pdbcanvas.getWidth();
 411     int height = pdbcanvas.getHeight();
 412
 413     jalview.util.ImageMaker im;
 414
 415     if (type == jalview.util.ImageMaker.PNG)
 416       im = new jalview.util.ImageMaker(this,
 417                                        jalview.util.ImageMaker.PNG,
 418                                        "Make PNG image from view",
 419                                        width, height,
 420                                        null, null);
 421     else
 422       im = new jalview.util.ImageMaker(this,
 423                                        jalview.util.ImageMaker.EPS,
 424                                        "Make EPS file from view",
 425                                        width, height,
 426                                        null, this.getTitle());
 427
 428     if (im.getGraphics() != null)
 429     {
 430       pdbcanvas.drawAll(im.getGraphics(), width, height);
 431       im.writeImage();
 432     }
 433   }
 434   public void charge_actionPerformed(ActionEvent e)
 435   {
 436     pdbcanvas.bysequence = false;
 437     pdbcanvas.pdb.setChargeColours();
 438     pdbcanvas.redrawneeded=true;
 439     pdbcanvas.repaint();
 440   }
 441
 442   public void hydro_actionPerformed(ActionEvent e)
 443   {
 444     pdbcanvas.bysequence = false;
 445     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 446     pdbcanvas.redrawneeded=true;
 447     pdbcanvas.repaint();
 448   }
 449
 450   public void chain_actionPerformed(ActionEvent e)
 451   {
 452     pdbcanvas.bysequence = false;
 453     pdbcanvas.pdb.setChainColours();
 454     pdbcanvas.redrawneeded=true;
 455     pdbcanvas.repaint();
 456   }
 457
 458   public void zbuffer_actionPerformed(ActionEvent e)
 459   {
 460     pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
 461     pdbcanvas.redrawneeded=true;
 462     pdbcanvas.repaint();
 463   }
 464
 465   public void molecule_actionPerformed(ActionEvent e)
 466   {
 467     pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
 468     pdbcanvas.redrawneeded=true;
 469     pdbcanvas.repaint();
 470   }
 471
 472   public void depth_actionPerformed(ActionEvent e)
 473   {
 474   pdbcanvas.depthcue = ! pdbcanvas.depthcue;
 475   pdbcanvas.redrawneeded=true;
 476     pdbcanvas.repaint();
 477   }
 478
 479   public void wire_actionPerformed(ActionEvent e)
 480   {
 481     pdbcanvas.wire = ! pdbcanvas.wire;
 482     pdbcanvas.redrawneeded=true;
 483     pdbcanvas.repaint();
 484   }
 485
 486   public void seqButton_actionPerformed(ActionEvent e)
 487   {
 488     pdbcanvas.bysequence = true;
 489     pdbcanvas.updateSeqColours();
 490   }
 491
 492
 493   public void mapping_actionPerformed(ActionEvent e)
 494   {
 495     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 496     Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
 497     cap.setText(pdbcanvas.mappingDetails.toString());
 498   }
 499
 500   public void allchains_itemStateChanged(ItemEvent e)
 501   {
 502     pdbcanvas.setAllchainsVisible(allchains.getState());
 503   }
 504   void showErrorMessage(String error)
 505   {
 506     JOptionPane.showInternalMessageDialog(Desktop.desktop,
 507          error, "PDB Viewer Error", JOptionPane.WARNING_MESSAGE);
 508   }
 509
 510
 511   public void zappo_actionPerformed(ActionEvent e)
 512   {
 513     pdbcanvas.bysequence = false;
 514     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 515     pdbcanvas.redrawneeded=true;
 516     pdbcanvas.repaint();
 517   }
 518
 519   public void taylor_actionPerformed(ActionEvent e)
 520   {
 521     pdbcanvas.bysequence = false;
 522     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 523     pdbcanvas.redrawneeded=true;
 524     pdbcanvas.repaint();
 525   }
 526
 527   public void helix_actionPerformed(ActionEvent e)
 528   {
 529     pdbcanvas.bysequence = false;
 530     pdbcanvas.pdb.setColours(new HelixColourScheme());
 531     pdbcanvas.redrawneeded=true;
 532     pdbcanvas.repaint();
 533   }
 534
 535   public void strand_actionPerformed(ActionEvent e)
 536   {
 537     pdbcanvas.bysequence = false;
 538     pdbcanvas.pdb.setColours(new StrandColourScheme());
 539     pdbcanvas.redrawneeded=true;
 540     pdbcanvas.repaint();
 541   }
 542
 543   public void turn_actionPerformed(ActionEvent e)
 544   {
 545     pdbcanvas.bysequence = false;
 546     pdbcanvas.pdb.setColours(new TurnColourScheme());
 547     pdbcanvas.redrawneeded=true;
 548     pdbcanvas.repaint();
 549   }
 550
 551   public void buried_actionPerformed(ActionEvent e)
 552   {
 553     pdbcanvas.bysequence = false;
 554     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 555     pdbcanvas.redrawneeded=true;
 556     pdbcanvas.repaint();
 557   }
 558
 559   public void user_actionPerformed(ActionEvent e)
 560   {
 561     if (e.getActionCommand().equals("User Defined..."))
 562     {
 563       new UserDefinedColours(pdbcanvas, null);
 564     }
 565     else
 566     {
 567       UserColourScheme udc = (UserColourScheme) UserDefinedColours.
 568           getUserColourSchemes().get(e.getActionCommand());
 569
 570       pdbcanvas.pdb.setColours(udc);
 571       pdbcanvas.redrawneeded=true;
 572       pdbcanvas.repaint();
 573     }
 574   }
 575 }