src/MCview/PDBViewer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2006 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 import java.io.*;
  30 import jalview.io.JalviewFileChooser;
  31 import jalview.io.JalviewFileView;
  32
  33 public class PDBViewer extends JInternalFrame implements Runnable
  34 {
  35   PDBEntry pdb;
  36   Sequence sequence;
  37   PDBCanvas pdbcanvas;
  38   String tmpPDBFile;
  39
  40
  41   public PDBViewer(PDBEntry entry,
  42                    Sequence seq,
  43                    SeqCanvas seqcanvas)
  44   {
  45     try
  46     {
  47       jbInit();
  48     }
  49     catch (Exception ex)
  50     {
  51       ex.printStackTrace();
  52     }
  53
  54
  55     if (entry==null)
  56       return;
  57     pdb = entry;
  58     sequence = seq;
  59     pdbcanvas = new PDBCanvas(seqcanvas, sequence);
  60
  61     if(pdb.getFile()!=null)
  62     {
  63         try{
  64           tmpPDBFile = pdb.getFile();
  65           PDBfile pdbfile = new PDBfile(tmpPDBFile,
  66                                         jalview.io.AppletFormatAdapter.FILE);
  67           pdbcanvas.setPDBFile(pdbfile);
  68
  69         }catch(java.io.IOException ex)
  70         {
  71           ex.printStackTrace();
  72         }
  73     }
  74     else
  75     {
  76       Thread worker = new Thread(this);
  77       worker.start();
  78     }
  79
  80
  81
  82     setContentPane(pdbcanvas);
  83     StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
  84     if(pdb.getProperty()!=null)
  85     {
  86       if (pdb.getProperty().get("method")!=null)
  87       {
  88         title.append(" Method: ");
  89         title.append(pdb.getProperty().get("method"));
  90       }
  91       if (pdb.getProperty().get("chains") != null)
  92       {
  93         title.append(" Chain:");
  94         title.append(pdb.getProperty().get("chains"));
  95       }
  96     }
  97      Desktop.addInternalFrame(this,title.toString(),400, 400);
  98   }
  99
 100   public void run()
 101   {
 102     try
 103     {
 104         EBIFetchClient ebi = new EBIFetchClient();
 105         String query = "pdb:" + pdb.getId();
 106         tmpPDBFile = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
 107         if (tmpPDBFile != null)
 108         {
 109           PDBfile pdbfile = new PDBfile(tmpPDBFile, jalview.io.AppletFormatAdapter.FILE);
 110           pdbcanvas.setPDBFile(pdbfile);
 111         }
 112         else
 113         {
 114           throw new Exception("Empty result for WSDbFetch Query: " + query);
 115         }
 116     }
 117     catch (Exception ex)
 118     {
 119       ex.printStackTrace();
 120       showErrorMessage("Failed to retrieve PDB structure.");
 121 //      this.dispose();
 122     }
 123   }
 124
 125   private void jbInit()
 126       throws Exception
 127   {
 128     this.addKeyListener(new KeyAdapter()
 129         {
 130             public void keyPressed(KeyEvent evt)
 131             {
 132               pdbcanvas.keyPressed(evt);
 133             }
 134         });
 135
 136     this.setJMenuBar(jMenuBar1);
 137     fileMenu.setText("File");
 138     coloursMenu.setText("Colours");
 139     saveMenu.setActionCommand("Save Image");
 140     saveMenu.setText("Save As");
 141     png.setText("PNG");
 142     png.addActionListener(new ActionListener()
 143     {
 144       public void actionPerformed(ActionEvent e)
 145       {
 146         png_actionPerformed(e);
 147       }
 148     });
 149     eps.setText("EPS");
 150     eps.addActionListener(new ActionListener()
 151     {
 152       public void actionPerformed(ActionEvent e)
 153       {
 154         eps_actionPerformed(e);
 155       }
 156     });
 157     mapping.setText("View Mapping");
 158     mapping.addActionListener(new ActionListener()
 159     {
 160       public void actionPerformed(ActionEvent e)
 161       {
 162         mapping_actionPerformed(e);
 163       }
 164     });
 165     wire.setText("Wireframe");
 166     wire.addActionListener(new ActionListener()
 167     {
 168       public void actionPerformed(ActionEvent e)
 169       {
 170         wire_actionPerformed(e);
 171       }
 172     });
 173     depth.setSelected(true);
 174     depth.setText("Depthcue");
 175     depth.addActionListener(new ActionListener()
 176     {
 177       public void actionPerformed(ActionEvent e)
 178       {
 179         depth_actionPerformed(e);
 180       }
 181     });
 182     zbuffer.setSelected(true);
 183     zbuffer.setText("Z Buffering");
 184     zbuffer.addActionListener(new ActionListener()
 185     {
 186       public void actionPerformed(ActionEvent e)
 187       {
 188         zbuffer_actionPerformed(e);
 189       }
 190     });
 191     charge.setText("Charge & Cysteine");
 192     charge.addActionListener(new ActionListener()
 193     {
 194       public void actionPerformed(ActionEvent e)
 195       {
 196         charge_actionPerformed(e);
 197       }
 198     });
 199     chain.setText("By Chain");
 200     chain.addActionListener(new ActionListener()
 201     {
 202       public void actionPerformed(ActionEvent e)
 203       {
 204         chain_actionPerformed(e);
 205       }
 206     });
 207     seqButton.setSelected(true);
 208     seqButton.setText("By Sequence");
 209     seqButton.addActionListener(new ActionListener()
 210     {
 211       public void actionPerformed(ActionEvent e)
 212       {
 213         seqButton_actionPerformed(e);
 214       }
 215     });
 216     allchains.setSelected(true);
 217     allchains.setText("Show All Chains");
 218     allchains.addItemListener(new ItemListener()
 219     {
 220       public void itemStateChanged(ItemEvent e)
 221       {
 222         allchains_itemStateChanged(e);
 223       }
 224     });
 225     zappo.setText("Zappo");
 226     zappo.addActionListener(new ActionListener()
 227     {
 228       public void actionPerformed(ActionEvent e)
 229       {
 230         zappo_actionPerformed(e);
 231       }
 232     });
 233     taylor.setText("Taylor");
 234     taylor.addActionListener(new ActionListener()
 235     {
 236       public void actionPerformed(ActionEvent e)
 237       {
 238         taylor_actionPerformed(e);
 239       }
 240     });
 241     hydro.setText("Hydro");
 242     hydro.addActionListener(new ActionListener()
 243     {
 244       public void actionPerformed(ActionEvent e)
 245       {
 246         hydro_actionPerformed(e);
 247       }
 248     });
 249     helix.setText("Helix");
 250     helix.addActionListener(new ActionListener()
 251     {
 252       public void actionPerformed(ActionEvent e)
 253       {
 254         helix_actionPerformed(e);
 255       }
 256     });
 257     strand.setText("Strand");
 258     strand.addActionListener(new ActionListener()
 259     {
 260       public void actionPerformed(ActionEvent e)
 261       {
 262         strand_actionPerformed(e);
 263       }
 264     });
 265     turn.setText("Turn");
 266     turn.addActionListener(new ActionListener()
 267     {
 268       public void actionPerformed(ActionEvent e)
 269       {
 270         turn_actionPerformed(e);
 271       }
 272     });
 273     buried.setText("Buried");
 274     buried.addActionListener(new ActionListener()
 275     {
 276       public void actionPerformed(ActionEvent e)
 277       {
 278         buried_actionPerformed(e);
 279       }
 280     });
 281     user.setText("User Defined...");
 282     user.addActionListener(new ActionListener()
 283     {
 284       public void actionPerformed(ActionEvent e)
 285       {
 286         user_actionPerformed(e);
 287       }
 288     });
 289     viewMenu.setText("View");
 290     background.setText("Background Colour...");
 291     background.addActionListener(new ActionListener()
 292     {
 293       public void actionPerformed(ActionEvent e)
 294       {
 295         background_actionPerformed(e);
 296       }
 297     });
 298     savePDB.setText("PDB File");
 299     savePDB.addActionListener(new ActionListener()
 300     {
 301       public void actionPerformed(ActionEvent e)
 302       {
 303         savePDB_actionPerformed(e);
 304       }
 305     });
 306     jMenuBar1.add(fileMenu);
 307     jMenuBar1.add(coloursMenu);
 308     jMenuBar1.add(viewMenu);
 309     fileMenu.add(saveMenu);
 310     fileMenu.add(mapping);
 311     saveMenu.add(savePDB);
 312     saveMenu.add(png);
 313     saveMenu.add(eps);
 314     coloursMenu.add(seqButton);
 315     coloursMenu.add(chain);
 316     coloursMenu.add(charge);
 317     coloursMenu.add(zappo);
 318     coloursMenu.add(taylor);
 319     coloursMenu.add(hydro);
 320     coloursMenu.add(helix);
 321     coloursMenu.add(strand);
 322     coloursMenu.add(turn);
 323     coloursMenu.add(buried);
 324     coloursMenu.add(user);
 325     coloursMenu.add(background);
 326     ButtonGroup bg = new ButtonGroup();
 327     bg.add(seqButton);
 328     bg.add(chain);
 329     bg.add(charge);
 330     bg.add(zappo);
 331     bg.add(taylor);
 332     bg.add(hydro);
 333     bg.add(helix);
 334     bg.add(strand);
 335     bg.add(turn);
 336     bg.add(buried);
 337     bg.add(user);
 338
 339
 340     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
 341     {
 342       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
 343           getUserColourSchemes().keys();
 344
 345       while (userColours.hasMoreElements())
 346       {
 347         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
 348             nextElement().toString());
 349         radioItem.setName("USER_DEFINED");
 350         radioItem.addMouseListener(new MouseAdapter()
 351             {
 352               public void mousePressed(MouseEvent evt)
 353               {
 354                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
 355                 {
 356                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 357
 358                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
 359                       "Remove from default list?",
 360                       "Remove user defined colour",
 361                       JOptionPane.YES_NO_OPTION);
 362                   if(option == JOptionPane.YES_OPTION)
 363                   {
 364                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
 365                     coloursMenu.remove(radioItem);
 366                   }
 367                   else
 368                     radioItem.addActionListener(new ActionListener()
 369                     {
 370                       public void actionPerformed(ActionEvent evt)
 371                       {
 372                         user_actionPerformed(evt);
 373                       }
 374                     });
 375                 }
 376               }
 377             });
 378         radioItem.addActionListener(new ActionListener()
 379         {
 380           public void actionPerformed(ActionEvent evt)
 381           {
 382             user_actionPerformed(evt);
 383           }
 384         });
 385         coloursMenu.add(radioItem);
 386         bg.add(radioItem);
 387       }
 388     }
 389
 390     viewMenu.add(wire);
 391     viewMenu.add(depth);
 392     viewMenu.add(zbuffer);
 393     viewMenu.add(allchains);
 394   }
 395
 396   JMenuBar jMenuBar1 = new JMenuBar();
 397   JMenu fileMenu = new JMenu();
 398   JMenu coloursMenu = new JMenu();
 399   JMenu saveMenu = new JMenu();
 400   JMenuItem png = new JMenuItem();
 401   JMenuItem eps = new JMenuItem();
 402   JMenuItem mapping = new JMenuItem();
 403   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 404   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 405   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 406   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 407
 408   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 409   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 410   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 411   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 412   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 413   JRadioButtonMenuItem zappo = new  JRadioButtonMenuItem();
 414   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 415   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 416   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 417   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 418   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 419   JMenu viewMenu = new JMenu();
 420   JMenuItem background = new JMenuItem();
 421   JMenuItem savePDB = new JMenuItem();
 422
 423   /**
 424    * DOCUMENT ME!
 425    *
 426    * @param e DOCUMENT ME!
 427    */
 428   public void eps_actionPerformed(ActionEvent e)
 429   {
 430     makePDBImage(jalview.util.ImageMaker.EPS);
 431   }
 432
 433   /**
 434    * DOCUMENT ME!
 435    *
 436    * @param e DOCUMENT ME!
 437    */
 438   public void png_actionPerformed(ActionEvent e)
 439   {
 440      makePDBImage(jalview.util.ImageMaker.PNG);
 441   }
 442
 443   void makePDBImage(int type)
 444   {
 445     int width = pdbcanvas.getWidth();
 446     int height = pdbcanvas.getHeight();
 447
 448     jalview.util.ImageMaker im;
 449
 450     if (type == jalview.util.ImageMaker.PNG)
 451       im = new jalview.util.ImageMaker(this,
 452                                        jalview.util.ImageMaker.PNG,
 453                                        "Make PNG image from view",
 454                                        width, height,
 455                                        null, null);
 456     else
 457       im = new jalview.util.ImageMaker(this,
 458                                        jalview.util.ImageMaker.EPS,
 459                                        "Make EPS file from view",
 460                                        width, height,
 461                                        null, this.getTitle());
 462
 463     if (im.getGraphics() != null)
 464     {
 465       pdbcanvas.drawAll(im.getGraphics(), width, height);
 466       im.writeImage();
 467     }
 468   }
 469   public void charge_actionPerformed(ActionEvent e)
 470   {
 471     pdbcanvas.bysequence = false;
 472     pdbcanvas.pdb.setChargeColours();
 473     pdbcanvas.redrawneeded=true;
 474     pdbcanvas.repaint();
 475   }
 476
 477   public void hydro_actionPerformed(ActionEvent e)
 478   {
 479     pdbcanvas.bysequence = false;
 480     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 481     pdbcanvas.redrawneeded=true;
 482     pdbcanvas.repaint();
 483   }
 484
 485   public void chain_actionPerformed(ActionEvent e)
 486   {
 487     pdbcanvas.bysequence = false;
 488     pdbcanvas.pdb.setChainColours();
 489     pdbcanvas.redrawneeded=true;
 490     pdbcanvas.repaint();
 491   }
 492
 493   public void zbuffer_actionPerformed(ActionEvent e)
 494   {
 495     pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
 496     pdbcanvas.redrawneeded=true;
 497     pdbcanvas.repaint();
 498   }
 499
 500   public void molecule_actionPerformed(ActionEvent e)
 501   {
 502     pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
 503     pdbcanvas.redrawneeded=true;
 504     pdbcanvas.repaint();
 505   }
 506
 507   public void depth_actionPerformed(ActionEvent e)
 508   {
 509   pdbcanvas.depthcue = ! pdbcanvas.depthcue;
 510   pdbcanvas.redrawneeded=true;
 511     pdbcanvas.repaint();
 512   }
 513
 514   public void wire_actionPerformed(ActionEvent e)
 515   {
 516     pdbcanvas.wire = ! pdbcanvas.wire;
 517     pdbcanvas.redrawneeded=true;
 518     pdbcanvas.repaint();
 519   }
 520
 521   public void seqButton_actionPerformed(ActionEvent e)
 522   {
 523     pdbcanvas.bysequence = true;
 524     pdbcanvas.updateSeqColours();
 525   }
 526
 527
 528   public void mapping_actionPerformed(ActionEvent e)
 529   {
 530     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 531     Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
 532     cap.setText(pdbcanvas.mappingDetails.toString());
 533   }
 534
 535   public void allchains_itemStateChanged(ItemEvent e)
 536   {
 537     pdbcanvas.setAllchainsVisible(allchains.getState());
 538   }
 539   void showErrorMessage(String error)
 540   {
 541     JOptionPane.showInternalMessageDialog(Desktop.desktop,
 542          error, "PDB Viewer Error", JOptionPane.WARNING_MESSAGE);
 543   }
 544
 545
 546   public void zappo_actionPerformed(ActionEvent e)
 547   {
 548     pdbcanvas.bysequence = false;
 549     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 550     pdbcanvas.redrawneeded=true;
 551     pdbcanvas.repaint();
 552   }
 553
 554   public void taylor_actionPerformed(ActionEvent e)
 555   {
 556     pdbcanvas.bysequence = false;
 557     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 558     pdbcanvas.redrawneeded=true;
 559     pdbcanvas.repaint();
 560   }
 561
 562   public void helix_actionPerformed(ActionEvent e)
 563   {
 564     pdbcanvas.bysequence = false;
 565     pdbcanvas.pdb.setColours(new HelixColourScheme());
 566     pdbcanvas.redrawneeded=true;
 567     pdbcanvas.repaint();
 568   }
 569
 570   public void strand_actionPerformed(ActionEvent e)
 571   {
 572     pdbcanvas.bysequence = false;
 573     pdbcanvas.pdb.setColours(new StrandColourScheme());
 574     pdbcanvas.redrawneeded=true;
 575     pdbcanvas.repaint();
 576   }
 577
 578   public void turn_actionPerformed(ActionEvent e)
 579   {
 580     pdbcanvas.bysequence = false;
 581     pdbcanvas.pdb.setColours(new TurnColourScheme());
 582     pdbcanvas.redrawneeded=true;
 583     pdbcanvas.repaint();
 584   }
 585
 586   public void buried_actionPerformed(ActionEvent e)
 587   {
 588     pdbcanvas.bysequence = false;
 589     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 590     pdbcanvas.redrawneeded=true;
 591     pdbcanvas.repaint();
 592   }
 593
 594   public void user_actionPerformed(ActionEvent e)
 595   {
 596     if (e.getActionCommand().equals("User Defined..."))
 597     {
 598       new UserDefinedColours(pdbcanvas, null);
 599     }
 600     else
 601     {
 602       UserColourScheme udc = (UserColourScheme) UserDefinedColours.
 603           getUserColourSchemes().get(e.getActionCommand());
 604
 605       pdbcanvas.pdb.setColours(udc);
 606       pdbcanvas.redrawneeded=true;
 607       pdbcanvas.repaint();
 608     }
 609   }
 610
 611   public void background_actionPerformed(ActionEvent e)
 612   {
 613       java.awt.Color col = JColorChooser.showDialog(this, "Select Background Colour",
 614                 pdbcanvas.backgroundColour);
 615
 616       if(col!=null)
 617        {
 618          pdbcanvas.backgroundColour = col;
 619          pdbcanvas.redrawneeded = true;
 620          pdbcanvas.repaint();
 621        }
 622   }
 623
 624   public void savePDB_actionPerformed(ActionEvent e)
 625   {
 626     JalviewFileChooser chooser = new JalviewFileChooser(
 627         jalview.bin.Cache.getProperty(
 628             "LAST_DIRECTORY"));
 629
 630     chooser.setFileView(new JalviewFileView());
 631     chooser.setDialogTitle("Save PDB File");
 632     chooser.setToolTipText("Save");
 633
 634     int value = chooser.showSaveDialog(this);
 635
 636     if (value == JalviewFileChooser.APPROVE_OPTION)
 637     {
 638         try
 639         {
 640           BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 641           File outFile = chooser.getSelectedFile();
 642
 643           PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 644           String data;
 645           while ( (data = in.readLine()) != null)
 646           {
 647             if (
 648                 !( data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
 649                 )
 650               out.println(data);
 651           }
 652           out.close();
 653         }
 654         catch (Exception ex)
 655         {
 656           ex.printStackTrace();
 657         }
 658       }
 659   }
 660 }