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