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