src/MCview/PDBViewer.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package MCview;\r
  20 \r
  21 import javax.swing.*;\r
  22 import java.awt.event.*;\r
  23 import jalview.datamodel.*;\r
  24 import jalview.schemes.*;\r
  25 import jalview.gui.*;\r
  26 import jalview.io.EBIFetchClient;\r
  27 import java.awt.event.ActionListener;\r
  28 import java.awt.event.ActionEvent;\r
  29 \r
  30 public class PDBViewer extends JInternalFrame implements Runnable\r
  31 {\r
  32   PDBEntry pdb;\r
  33   Sequence sequence;\r
  34   PDBCanvas pdbcanvas;\r
  35 \r
  36 \r
  37   public PDBViewer(PDBEntry entry,\r
  38                    Sequence seq,\r
  39                    SeqCanvas seqcanvas)\r
  40   {\r
  41     /*Uncomment this to modify in Jbuilder\r
  42     try\r
  43     {\r
  44       jbInit();\r
  45     }\r
  46     catch (Exception ex)\r
  47     {\r
  48       ex.printStackTrace();\r
  49     }*/\r
  50 \r
  51 \r
  52     pdb = entry;\r
  53     sequence = seq;\r
  54 \r
  55     Thread worker = new Thread(this);\r
  56     worker.start();\r
  57 \r
  58     pdbcanvas = new PDBCanvas(seqcanvas, seq);\r
  59 \r
  60     setContentPane(pdbcanvas);\r
  61     StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());\r
  62     if(pdb.getProperty()!=null)\r
  63     {\r
  64       title.append( " Method: " );\r
  65       title.append(pdb.getProperty().get("method"));\r
  66       title.append( " Chain:" );\r
  67       title.append( pdb.getProperty().get("chains"));\r
  68     }\r
  69 \r
  70      Desktop.addInternalFrame(this,title.toString(),400, 400);\r
  71   }\r
  72 \r
  73   public void run()\r
  74   {\r
  75     try\r
  76     {\r
  77       EBIFetchClient ebi = new EBIFetchClient();\r
  78       String[] result = ebi.fetchData("pdb:" + pdb.getId(), "default","raw");\r
  79 \r
  80       PDBfile pdbfile = new PDBfile(result);\r
  81 \r
  82       pdbcanvas.setPDBFile(pdbfile);\r
  83 \r
  84       try\r
  85       {\r
  86         jbInit();\r
  87       }\r
  88       catch (Exception ex)\r
  89       {\r
  90         ex.printStackTrace();\r
  91       }\r
  92     }\r
  93     catch (Exception ex)\r
  94     {\r
  95       ex.printStackTrace();\r
  96     }\r
  97   }\r
  98 \r
  99   private void jbInit()\r
 100       throws Exception\r
 101   {\r
 102     this.addKeyListener(new KeyAdapter()\r
 103         {\r
 104             public void keyPressed(KeyEvent evt)\r
 105             {\r
 106               pdbcanvas.keyPressed(evt);\r
 107             }\r
 108         });\r
 109 \r
 110     this.setJMenuBar(jMenuBar1);\r
 111     fileMenu.setText("File");\r
 112     coloursMenu.setText("Colours");\r
 113     saveMenu.setActionCommand("Save Image");\r
 114     saveMenu.setText("Save As");\r
 115     png.setText("PNG");\r
 116     png.addActionListener(new ActionListener()\r
 117     {\r
 118       public void actionPerformed(ActionEvent e)\r
 119       {\r
 120         png_actionPerformed(e);\r
 121       }\r
 122     });\r
 123     eps.setText("EPS");\r
 124     eps.addActionListener(new ActionListener()\r
 125     {\r
 126       public void actionPerformed(ActionEvent e)\r
 127       {\r
 128         eps_actionPerformed(e);\r
 129       }\r
 130     });\r
 131     mapping.setText("View Mapping");\r
 132     mapping.addActionListener(new ActionListener()\r
 133     {\r
 134       public void actionPerformed(ActionEvent e)\r
 135       {\r
 136         mapping_actionPerformed(e);\r
 137       }\r
 138     });\r
 139     wire.setText("Wireframe");\r
 140     wire.addActionListener(new ActionListener()\r
 141     {\r
 142       public void actionPerformed(ActionEvent e)\r
 143       {\r
 144         wire_actionPerformed(e);\r
 145       }\r
 146     });\r
 147     depth.setSelected(true);\r
 148     depth.setText("Depthcue");\r
 149     depth.addActionListener(new ActionListener()\r
 150     {\r
 151       public void actionPerformed(ActionEvent e)\r
 152       {\r
 153         depth_actionPerformed(e);\r
 154       }\r
 155     });\r
 156     zbuffer.setSelected(true);\r
 157     zbuffer.setText("Z Buffering");\r
 158     zbuffer.addActionListener(new ActionListener()\r
 159     {\r
 160       public void actionPerformed(ActionEvent e)\r
 161       {\r
 162         zbuffer_actionPerformed(e);\r
 163       }\r
 164     });\r
 165     charge.setText("Charge & Cysteine");\r
 166     charge.addActionListener(new ActionListener()\r
 167     {\r
 168       public void actionPerformed(ActionEvent e)\r
 169       {\r
 170         charge_actionPerformed(e);\r
 171       }\r
 172     });\r
 173     chain.setText("By Chain");\r
 174     chain.addActionListener(new ActionListener()\r
 175     {\r
 176       public void actionPerformed(ActionEvent e)\r
 177       {\r
 178         chain_actionPerformed(e);\r
 179       }\r
 180     });\r
 181     seqButton.setSelected(true);\r
 182     seqButton.setText("By Sequence");\r
 183     seqButton.addActionListener(new ActionListener()\r
 184     {\r
 185       public void actionPerformed(ActionEvent e)\r
 186       {\r
 187         seqButton_actionPerformed(e);\r
 188       }\r
 189     });\r
 190     allchains.setSelected(true);\r
 191     allchains.setText("Show All Chains");\r
 192     allchains.addItemListener(new ItemListener()\r
 193     {\r
 194       public void itemStateChanged(ItemEvent e)\r
 195       {\r
 196         allchains_itemStateChanged(e);\r
 197       }\r
 198     });\r
 199     zappo.setText("Zappo");\r
 200     zappo.addActionListener(new ActionListener()\r
 201     {\r
 202       public void actionPerformed(ActionEvent e)\r
 203       {\r
 204         zappo_actionPerformed(e);\r
 205       }\r
 206     });\r
 207     taylor.setText("Taylor");\r
 208     taylor.addActionListener(new ActionListener()\r
 209     {\r
 210       public void actionPerformed(ActionEvent e)\r
 211       {\r
 212         taylor_actionPerformed(e);\r
 213       }\r
 214     });\r
 215     hydro.setText("Hydro");\r
 216     hydro.addActionListener(new ActionListener()\r
 217     {\r
 218       public void actionPerformed(ActionEvent e)\r
 219       {\r
 220         hydro_actionPerformed(e);\r
 221       }\r
 222     });\r
 223     helix.setText("Helix");\r
 224     helix.addActionListener(new ActionListener()\r
 225     {\r
 226       public void actionPerformed(ActionEvent e)\r
 227       {\r
 228         helix_actionPerformed(e);\r
 229       }\r
 230     });\r
 231     strand.setText("Strand");\r
 232     strand.addActionListener(new ActionListener()\r
 233     {\r
 234       public void actionPerformed(ActionEvent e)\r
 235       {\r
 236         strand_actionPerformed(e);\r
 237       }\r
 238     });\r
 239     turn.setText("Turn");\r
 240     turn.addActionListener(new ActionListener()\r
 241     {\r
 242       public void actionPerformed(ActionEvent e)\r
 243       {\r
 244         turn_actionPerformed(e);\r
 245       }\r
 246     });\r
 247     buried.setText("Buried");\r
 248     buried.addActionListener(new ActionListener()\r
 249     {\r
 250       public void actionPerformed(ActionEvent e)\r
 251       {\r
 252         buried_actionPerformed(e);\r
 253       }\r
 254     });\r
 255     user.setText("User Defined...");\r
 256     user.addActionListener(new ActionListener()\r
 257     {\r
 258       public void actionPerformed(ActionEvent e)\r
 259       {\r
 260         user_actionPerformed(e);\r
 261       }\r
 262     });\r
 263     viewMenu.setText("View");\r
 264     jMenuBar1.add(fileMenu);\r
 265     jMenuBar1.add(coloursMenu);\r
 266     jMenuBar1.add(viewMenu);\r
 267     fileMenu.add(saveMenu);\r
 268     fileMenu.add(mapping);\r
 269     saveMenu.add(png);\r
 270     saveMenu.add(eps);\r
 271     coloursMenu.add(seqButton);\r
 272     coloursMenu.add(chain);\r
 273     coloursMenu.add(charge);\r
 274     coloursMenu.add(zappo);\r
 275     coloursMenu.add(taylor);\r
 276     coloursMenu.add(hydro);\r
 277     coloursMenu.add(helix);\r
 278     coloursMenu.add(strand);\r
 279     coloursMenu.add(turn);\r
 280     coloursMenu.add(buried);\r
 281     coloursMenu.add(user);\r
 282     ButtonGroup bg = new ButtonGroup();\r
 283     bg.add(seqButton);\r
 284     bg.add(chain);\r
 285     bg.add(charge);\r
 286     bg.add(zappo);\r
 287     bg.add(taylor);\r
 288     bg.add(hydro);\r
 289     bg.add(helix);\r
 290     bg.add(strand);\r
 291     bg.add(turn);\r
 292     bg.add(buried);\r
 293     bg.add(user);\r
 294 \r
 295 \r
 296     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 297     {\r
 298       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 299           getUserColourSchemes().keys();\r
 300 \r
 301       while (userColours.hasMoreElements())\r
 302       {\r
 303         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
 304             nextElement().toString());\r
 305         radioItem.setName("USER_DEFINED");\r
 306         radioItem.addMouseListener(new MouseAdapter()\r
 307             {\r
 308               public void mousePressed(MouseEvent evt)\r
 309               {\r
 310                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 311                 {\r
 312                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 313 \r
 314                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
 315                       "Remove from default list?",\r
 316                       "Remove user defined colour",\r
 317                       JOptionPane.YES_NO_OPTION);\r
 318                   if(option == JOptionPane.YES_OPTION)\r
 319                   {\r
 320                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
 321                     coloursMenu.remove(radioItem);\r
 322                   }\r
 323                   else\r
 324                     radioItem.addActionListener(new ActionListener()\r
 325                     {\r
 326                       public void actionPerformed(ActionEvent evt)\r
 327                       {\r
 328                         user_actionPerformed(evt);\r
 329                       }\r
 330                     });\r
 331                 }\r
 332               }\r
 333             });\r
 334         radioItem.addActionListener(new ActionListener()\r
 335         {\r
 336           public void actionPerformed(ActionEvent evt)\r
 337           {\r
 338             user_actionPerformed(evt);\r
 339           }\r
 340         });\r
 341         coloursMenu.add(radioItem);\r
 342         bg.add(radioItem);\r
 343       }\r
 344     }\r
 345 \r
 346     viewMenu.add(wire);\r
 347     viewMenu.add(depth);\r
 348     viewMenu.add(zbuffer);\r
 349     viewMenu.add(allchains);\r
 350   }\r
 351 \r
 352   JMenuBar jMenuBar1 = new JMenuBar();\r
 353   JMenu fileMenu = new JMenu();\r
 354   JMenu coloursMenu = new JMenu();\r
 355   JMenu saveMenu = new JMenu();\r
 356   JMenuItem png = new JMenuItem();\r
 357   JMenuItem eps = new JMenuItem();\r
 358   JMenuItem mapping = new JMenuItem();\r
 359   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();\r
 360   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();\r
 361   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();\r
 362   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();\r
 363 \r
 364   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();\r
 365   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();\r
 366   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();\r
 367   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();\r
 368   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();\r
 369   JRadioButtonMenuItem zappo = new  JRadioButtonMenuItem();\r
 370   JRadioButtonMenuItem user = new JRadioButtonMenuItem();\r
 371   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();\r
 372   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();\r
 373   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();\r
 374   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();\r
 375   JMenu viewMenu = new JMenu();\r
 376 \r
 377   /**\r
 378    * DOCUMENT ME!\r
 379    *\r
 380    * @param e DOCUMENT ME!\r
 381    */\r
 382   public void eps_actionPerformed(ActionEvent e)\r
 383   {\r
 384     makePDBImage(jalview.util.ImageMaker.EPS);\r
 385   }\r
 386 \r
 387   /**\r
 388    * DOCUMENT ME!\r
 389    *\r
 390    * @param e DOCUMENT ME!\r
 391    */\r
 392   public void png_actionPerformed(ActionEvent e)\r
 393   {\r
 394      makePDBImage(jalview.util.ImageMaker.PNG);\r
 395   }\r
 396 \r
 397   void makePDBImage(int type)\r
 398   {\r
 399     int width = pdbcanvas.getWidth();\r
 400     int height = pdbcanvas.getHeight();\r
 401 \r
 402     jalview.util.ImageMaker im;\r
 403 \r
 404     if (type == jalview.util.ImageMaker.PNG)\r
 405       im = new jalview.util.ImageMaker(this,\r
 406                                        jalview.util.ImageMaker.PNG,\r
 407                                        "Make PNG image from view",\r
 408                                        width, height,\r
 409                                        null, null);\r
 410     else\r
 411       im = new jalview.util.ImageMaker(this,\r
 412                                        jalview.util.ImageMaker.EPS,\r
 413                                        "Make EPS file from view",\r
 414                                        width, height,\r
 415                                        null, this.getTitle());\r
 416 \r
 417     if (im.getGraphics() != null)\r
 418     {\r
 419       pdbcanvas.drawAll(im.getGraphics(), width, height);\r
 420       im.writeImage();\r
 421     }\r
 422   }\r
 423   public void charge_actionPerformed(ActionEvent e)\r
 424   {\r
 425     pdbcanvas.bysequence = false;\r
 426     pdbcanvas.pdb.setChargeColours();\r
 427     pdbcanvas.redrawneeded=true;\r
 428     pdbcanvas.repaint();\r
 429   }\r
 430 \r
 431   public void hydro_actionPerformed(ActionEvent e)\r
 432   {\r
 433     pdbcanvas.bysequence = false;\r
 434     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());\r
 435     pdbcanvas.redrawneeded=true;\r
 436     pdbcanvas.repaint();\r
 437   }\r
 438 \r
 439   public void chain_actionPerformed(ActionEvent e)\r
 440   {\r
 441     pdbcanvas.bysequence = false;\r
 442     pdbcanvas.pdb.setChainColours();\r
 443     pdbcanvas.redrawneeded=true;\r
 444     pdbcanvas.repaint();\r
 445   }\r
 446 \r
 447   public void zbuffer_actionPerformed(ActionEvent e)\r
 448   {\r
 449     pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;\r
 450     pdbcanvas.redrawneeded=true;\r
 451     pdbcanvas.repaint();\r
 452   }\r
 453 \r
 454   public void molecule_actionPerformed(ActionEvent e)\r
 455   {\r
 456     pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;\r
 457     pdbcanvas.redrawneeded=true;\r
 458     pdbcanvas.repaint();\r
 459   }\r
 460 \r
 461   public void depth_actionPerformed(ActionEvent e)\r
 462   {\r
 463   pdbcanvas.depthcue = ! pdbcanvas.depthcue;\r
 464   pdbcanvas.redrawneeded=true;\r
 465     pdbcanvas.repaint();\r
 466   }\r
 467 \r
 468   public void wire_actionPerformed(ActionEvent e)\r
 469   {\r
 470     pdbcanvas.wire = ! pdbcanvas.wire;\r
 471     pdbcanvas.redrawneeded=true;\r
 472     pdbcanvas.repaint();\r
 473   }\r
 474 \r
 475   public void seqButton_actionPerformed(ActionEvent e)\r
 476   {\r
 477     pdbcanvas.bysequence = true;\r
 478     pdbcanvas.updateSeqColours();\r
 479   }\r
 480 \r
 481 \r
 482   public void mapping_actionPerformed(ActionEvent e)\r
 483   {\r
 484     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();\r
 485     Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);\r
 486     cap.setText(pdbcanvas.mappingDetails.toString());\r
 487   }\r
 488 \r
 489   public void allchains_itemStateChanged(ItemEvent e)\r
 490   {\r
 491     pdbcanvas.setAllchainsVisible(allchains.getState());\r
 492   }\r
 493 \r
 494   public void zappo_actionPerformed(ActionEvent e)\r
 495   {\r
 496     pdbcanvas.bysequence = false;\r
 497     pdbcanvas.pdb.setColours(new ZappoColourScheme());\r
 498     pdbcanvas.redrawneeded=true;\r
 499     pdbcanvas.repaint();\r
 500   }\r
 501 \r
 502   public void taylor_actionPerformed(ActionEvent e)\r
 503   {\r
 504     pdbcanvas.bysequence = false;\r
 505     pdbcanvas.pdb.setColours(new TaylorColourScheme());\r
 506     pdbcanvas.redrawneeded=true;\r
 507     pdbcanvas.repaint();\r
 508   }\r
 509 \r
 510   public void helix_actionPerformed(ActionEvent e)\r
 511   {\r
 512     pdbcanvas.bysequence = false;\r
 513     pdbcanvas.pdb.setColours(new HelixColourScheme());\r
 514     pdbcanvas.redrawneeded=true;\r
 515     pdbcanvas.repaint();\r
 516   }\r
 517 \r
 518   public void strand_actionPerformed(ActionEvent e)\r
 519   {\r
 520     pdbcanvas.bysequence = false;\r
 521     pdbcanvas.pdb.setColours(new StrandColourScheme());\r
 522     pdbcanvas.redrawneeded=true;\r
 523     pdbcanvas.repaint();\r
 524   }\r
 525 \r
 526   public void turn_actionPerformed(ActionEvent e)\r
 527   {\r
 528     pdbcanvas.bysequence = false;\r
 529     pdbcanvas.pdb.setColours(new TurnColourScheme());\r
 530     pdbcanvas.redrawneeded=true;\r
 531     pdbcanvas.repaint();\r
 532   }\r
 533 \r
 534   public void buried_actionPerformed(ActionEvent e)\r
 535   {\r
 536     pdbcanvas.bysequence = false;\r
 537     pdbcanvas.pdb.setColours(new BuriedColourScheme());\r
 538     pdbcanvas.redrawneeded=true;\r
 539     pdbcanvas.repaint();\r
 540   }\r
 541 \r
 542   public void user_actionPerformed(ActionEvent e)\r
 543   {\r
 544     if (e.getActionCommand().equals("User Defined..."))\r
 545     {\r
 546       new UserDefinedColours(pdbcanvas, null);\r
 547     }\r
 548     else\r
 549     {\r
 550       UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 551           getUserColourSchemes().get(e.getActionCommand());\r
 552 \r
 553       pdbcanvas.pdb.setColours(udc);\r
 554       pdbcanvas.redrawneeded=true;\r
 555       pdbcanvas.repaint();\r
 556     }\r
 557   }\r
 558 }\r