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   /**
  37    * The associated sequence in an alignment
  38    */
  39   Sequence sequence;
  40   PDBCanvas pdbcanvas;
  41   String tmpPDBFile;
  42
  43
  44   public PDBViewer(PDBEntry entry,
  45                    Sequence seq,
  46                    SeqCanvas seqcanvas)
  47   {
  48     try
  49     {
  50       jbInit();
  51     }
  52     catch (Exception ex)
  53     {
  54       ex.printStackTrace();
  55     }
  56
  57
  58     if (entry==null)
  59       return;
  60     pdb = entry;
  61     sequence = seq;
  62     pdbcanvas = new PDBCanvas(seqcanvas, sequence);
  63
  64     if(pdb.getFile()!=null)
  65     {
  66         try{
  67           tmpPDBFile = pdb.getFile();
  68           PDBfile pdbfile = new PDBfile(tmpPDBFile,
  69                                         jalview.io.AppletFormatAdapter.FILE);
  70           pdbcanvas.setPDBFile(pdbfile);
  71
  72         }catch(java.io.IOException ex)
  73         {
  74           ex.printStackTrace();
  75         }
  76     }
  77     else
  78     {
  79       Thread worker = new Thread(this);
  80       worker.start();
  81     }
  82
  83
  84
  85     setContentPane(pdbcanvas);
  86     StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
  87     if(pdb.getProperty()!=null)
  88     {
  89       if (pdb.getProperty().get("method")!=null)
  90       {
  91         title.append(" Method: ");
  92         title.append(pdb.getProperty().get("method"));
  93       }
  94       if (pdb.getProperty().get("chains") != null)
  95       {
  96         title.append(" Chain:");
  97         title.append(pdb.getProperty().get("chains"));
  98       }
  99     }
 100      Desktop.addInternalFrame(this,title.toString(),400, 400);
 101   }
 102
 103   public void run()
 104   {
 105     try
 106     {
 107         EBIFetchClient ebi = new EBIFetchClient();
 108         String query = "pdb:" + pdb.getId();
 109         tmpPDBFile = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
 110         if (tmpPDBFile != null)
 111         {
 112           PDBfile pdbfile = new PDBfile(tmpPDBFile, jalview.io.AppletFormatAdapter.FILE);
 113           pdbcanvas.setPDBFile(pdbfile);
 114         }
 115         else
 116         {
 117           throw new Exception("Empty result for WSDbFetch Query: " + query);
 118         }
 119     }
 120     catch (Exception ex)
 121     {
 122       ex.printStackTrace();
 123       showErrorMessage("Failed to retrieve PDB structure.");
 124 //      this.dispose();
 125     }
 126   }
 127
 128   private void jbInit()
 129       throws Exception
 130   {
 131     this.addKeyListener(new KeyAdapter()
 132         {
 133             public void keyPressed(KeyEvent evt)
 134             {
 135               pdbcanvas.keyPressed(evt);
 136             }
 137         });
 138
 139     this.setJMenuBar(jMenuBar1);
 140     fileMenu.setText("File");
 141     coloursMenu.setText("Colours");
 142     saveMenu.setActionCommand("Save Image");
 143     saveMenu.setText("Save As");
 144     png.setText("PNG");
 145     png.addActionListener(new ActionListener()
 146     {
 147       public void actionPerformed(ActionEvent e)
 148       {
 149         png_actionPerformed(e);
 150       }
 151     });
 152     eps.setText("EPS");
 153     eps.addActionListener(new ActionListener()
 154     {
 155       public void actionPerformed(ActionEvent e)
 156       {
 157         eps_actionPerformed(e);
 158       }
 159     });
 160     mapping.setText("View Mapping");
 161     mapping.addActionListener(new ActionListener()
 162     {
 163       public void actionPerformed(ActionEvent e)
 164       {
 165         mapping_actionPerformed(e);
 166       }
 167     });
 168     wire.setText("Wireframe");
 169     wire.addActionListener(new ActionListener()
 170     {
 171       public void actionPerformed(ActionEvent e)
 172       {
 173         wire_actionPerformed(e);
 174       }
 175     });
 176     depth.setSelected(true);
 177     depth.setText("Depthcue");
 178     depth.addActionListener(new ActionListener()
 179     {
 180       public void actionPerformed(ActionEvent e)
 181       {
 182         depth_actionPerformed(e);
 183       }
 184     });
 185     zbuffer.setSelected(true);
 186     zbuffer.setText("Z Buffering");
 187     zbuffer.addActionListener(new ActionListener()
 188     {
 189       public void actionPerformed(ActionEvent e)
 190       {
 191         zbuffer_actionPerformed(e);
 192       }
 193     });
 194     charge.setText("Charge & Cysteine");
 195     charge.addActionListener(new ActionListener()
 196     {
 197       public void actionPerformed(ActionEvent e)
 198       {
 199         charge_actionPerformed(e);
 200       }
 201     });
 202     chain.setText("By Chain");
 203     chain.addActionListener(new ActionListener()
 204     {
 205       public void actionPerformed(ActionEvent e)
 206       {
 207         chain_actionPerformed(e);
 208       }
 209     });
 210     seqButton.setSelected(true);
 211     seqButton.setText("By Sequence");
 212     seqButton.addActionListener(new ActionListener()
 213     {
 214       public void actionPerformed(ActionEvent e)
 215       {
 216         seqButton_actionPerformed(e);
 217       }
 218     });
 219     allchains.setSelected(true);
 220     allchains.setText("Show All Chains");
 221     allchains.addItemListener(new ItemListener()
 222     {
 223       public void itemStateChanged(ItemEvent e)
 224       {
 225         allchains_itemStateChanged(e);
 226       }
 227     });
 228     zappo.setText("Zappo");
 229     zappo.addActionListener(new ActionListener()
 230     {
 231       public void actionPerformed(ActionEvent e)
 232       {
 233         zappo_actionPerformed(e);
 234       }
 235     });
 236     taylor.setText("Taylor");
 237     taylor.addActionListener(new ActionListener()
 238     {
 239       public void actionPerformed(ActionEvent e)
 240       {
 241         taylor_actionPerformed(e);
 242       }
 243     });
 244     hydro.setText("Hydro");
 245     hydro.addActionListener(new ActionListener()
 246     {
 247       public void actionPerformed(ActionEvent e)
 248       {
 249         hydro_actionPerformed(e);
 250       }
 251     });
 252     helix.setText("Helix");
 253     helix.addActionListener(new ActionListener()
 254     {
 255       public void actionPerformed(ActionEvent e)
 256       {
 257         helix_actionPerformed(e);
 258       }
 259     });
 260     strand.setText("Strand");
 261     strand.addActionListener(new ActionListener()
 262     {
 263       public void actionPerformed(ActionEvent e)
 264       {
 265         strand_actionPerformed(e);
 266       }
 267     });
 268     turn.setText("Turn");
 269     turn.addActionListener(new ActionListener()
 270     {
 271       public void actionPerformed(ActionEvent e)
 272       {
 273         turn_actionPerformed(e);
 274       }
 275     });
 276     buried.setText("Buried");
 277     buried.addActionListener(new ActionListener()
 278     {
 279       public void actionPerformed(ActionEvent e)
 280       {
 281         buried_actionPerformed(e);
 282       }
 283     });
 284     user.setText("User Defined...");
 285     user.addActionListener(new ActionListener()
 286     {
 287       public void actionPerformed(ActionEvent e)
 288       {
 289         user_actionPerformed(e);
 290       }
 291     });
 292     viewMenu.setText("View");
 293     background.setText("Background Colour...");
 294     background.addActionListener(new ActionListener()
 295     {
 296       public void actionPerformed(ActionEvent e)
 297       {
 298         background_actionPerformed(e);
 299       }
 300     });
 301     savePDB.setText("PDB File");
 302     savePDB.addActionListener(new ActionListener()
 303     {
 304       public void actionPerformed(ActionEvent e)
 305       {
 306         savePDB_actionPerformed(e);
 307       }
 308     });
 309     jMenuBar1.add(fileMenu);
 310     jMenuBar1.add(coloursMenu);
 311     jMenuBar1.add(viewMenu);
 312     fileMenu.add(saveMenu);
 313     fileMenu.add(mapping);
 314     saveMenu.add(savePDB);
 315     saveMenu.add(png);
 316     saveMenu.add(eps);
 317     coloursMenu.add(seqButton);
 318     coloursMenu.add(chain);
 319     coloursMenu.add(charge);
 320     coloursMenu.add(zappo);
 321     coloursMenu.add(taylor);
 322     coloursMenu.add(hydro);
 323     coloursMenu.add(helix);
 324     coloursMenu.add(strand);
 325     coloursMenu.add(turn);
 326     coloursMenu.add(buried);
 327     coloursMenu.add(user);
 328     coloursMenu.add(background);
 329     ButtonGroup bg = new ButtonGroup();
 330     bg.add(seqButton);
 331     bg.add(chain);
 332     bg.add(charge);
 333     bg.add(zappo);
 334     bg.add(taylor);
 335     bg.add(hydro);
 336     bg.add(helix);
 337     bg.add(strand);
 338     bg.add(turn);
 339     bg.add(buried);
 340     bg.add(user);
 341
 342
 343     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
 344     {
 345       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
 346           getUserColourSchemes().keys();
 347
 348       while (userColours.hasMoreElements())
 349       {
 350         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
 351             nextElement().toString());
 352         radioItem.setName("USER_DEFINED");
 353         radioItem.addMouseListener(new MouseAdapter()
 354             {
 355               public void mousePressed(MouseEvent evt)
 356               {
 357                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
 358                 {
 359                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 360
 361                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
 362                       "Remove from default list?",
 363                       "Remove user defined colour",
 364                       JOptionPane.YES_NO_OPTION);
 365                   if(option == JOptionPane.YES_OPTION)
 366                   {
 367                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
 368                     coloursMenu.remove(radioItem);
 369                   }
 370                   else
 371                     radioItem.addActionListener(new ActionListener()
 372                     {
 373                       public void actionPerformed(ActionEvent evt)
 374                       {
 375                         user_actionPerformed(evt);
 376                       }
 377                     });
 378                 }
 379               }
 380             });
 381         radioItem.addActionListener(new ActionListener()
 382         {
 383           public void actionPerformed(ActionEvent evt)
 384           {
 385             user_actionPerformed(evt);
 386           }
 387         });
 388         coloursMenu.add(radioItem);
 389         bg.add(radioItem);
 390       }
 391     }
 392
 393     viewMenu.add(wire);
 394     viewMenu.add(depth);
 395     viewMenu.add(zbuffer);
 396     viewMenu.add(allchains);
 397   }
 398
 399   JMenuBar jMenuBar1 = new JMenuBar();
 400   JMenu fileMenu = new JMenu();
 401   JMenu coloursMenu = new JMenu();
 402   JMenu saveMenu = new JMenu();
 403   JMenuItem png = new JMenuItem();
 404   JMenuItem eps = new JMenuItem();
 405   JMenuItem mapping = new JMenuItem();
 406   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 407   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 408   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 409   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 410
 411   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 412   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 413   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 414   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 415   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 416   JRadioButtonMenuItem zappo = new  JRadioButtonMenuItem();
 417   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 418   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 419   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 420   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 421   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 422   JMenu viewMenu = new JMenu();
 423   JMenuItem background = new JMenuItem();
 424   JMenuItem savePDB = new JMenuItem();
 425
 426   /**
 427    * DOCUMENT ME!
 428    *
 429    * @param e DOCUMENT ME!
 430    */
 431   public void eps_actionPerformed(ActionEvent e)
 432   {
 433     makePDBImage(jalview.util.ImageMaker.EPS);
 434   }
 435
 436   /**
 437    * DOCUMENT ME!
 438    *
 439    * @param e DOCUMENT ME!
 440    */
 441   public void png_actionPerformed(ActionEvent e)
 442   {
 443      makePDBImage(jalview.util.ImageMaker.PNG);
 444   }
 445
 446   void makePDBImage(int type)
 447   {
 448     int width = pdbcanvas.getWidth();
 449     int height = pdbcanvas.getHeight();
 450
 451     jalview.util.ImageMaker im;
 452
 453     if (type == jalview.util.ImageMaker.PNG)
 454       im = new jalview.util.ImageMaker(this,
 455                                        jalview.util.ImageMaker.PNG,
 456                                        "Make PNG image from view",
 457                                        width, height,
 458                                        null, null);
 459     else
 460       im = new jalview.util.ImageMaker(this,
 461                                        jalview.util.ImageMaker.EPS,
 462                                        "Make EPS file from view",
 463                                        width, height,
 464                                        null, this.getTitle());
 465
 466     if (im.getGraphics() != null)
 467     {
 468       pdbcanvas.drawAll(im.getGraphics(), width, height);
 469       im.writeImage();
 470     }
 471   }
 472   public void charge_actionPerformed(ActionEvent e)
 473   {
 474     pdbcanvas.bysequence = false;
 475     pdbcanvas.pdb.setChargeColours();
 476     pdbcanvas.redrawneeded=true;
 477     pdbcanvas.repaint();
 478   }
 479
 480   public void hydro_actionPerformed(ActionEvent e)
 481   {
 482     pdbcanvas.bysequence = false;
 483     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 484     pdbcanvas.redrawneeded=true;
 485     pdbcanvas.repaint();
 486   }
 487
 488   public void chain_actionPerformed(ActionEvent e)
 489   {
 490     pdbcanvas.bysequence = false;
 491     pdbcanvas.pdb.setChainColours();
 492     pdbcanvas.redrawneeded=true;
 493     pdbcanvas.repaint();
 494   }
 495
 496   public void zbuffer_actionPerformed(ActionEvent e)
 497   {
 498     pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
 499     pdbcanvas.redrawneeded=true;
 500     pdbcanvas.repaint();
 501   }
 502
 503   public void molecule_actionPerformed(ActionEvent e)
 504   {
 505     pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
 506     pdbcanvas.redrawneeded=true;
 507     pdbcanvas.repaint();
 508   }
 509
 510   public void depth_actionPerformed(ActionEvent e)
 511   {
 512   pdbcanvas.depthcue = ! pdbcanvas.depthcue;
 513   pdbcanvas.redrawneeded=true;
 514     pdbcanvas.repaint();
 515   }
 516
 517   public void wire_actionPerformed(ActionEvent e)
 518   {
 519     pdbcanvas.wire = ! pdbcanvas.wire;
 520     pdbcanvas.redrawneeded=true;
 521     pdbcanvas.repaint();
 522   }
 523
 524   public void seqButton_actionPerformed(ActionEvent e)
 525   {
 526     pdbcanvas.bysequence = true;
 527     pdbcanvas.updateSeqColours();
 528   }
 529
 530
 531   public void mapping_actionPerformed(ActionEvent e)
 532   {
 533     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 534     Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
 535     cap.setText(pdbcanvas.mappingDetails.toString());
 536   }
 537
 538   public void allchains_itemStateChanged(ItemEvent e)
 539   {
 540     pdbcanvas.setAllchainsVisible(allchains.getState());
 541   }
 542   void showErrorMessage(String error)
 543   {
 544     JOptionPane.showInternalMessageDialog(Desktop.desktop,
 545          error, "PDB Viewer Error", JOptionPane.WARNING_MESSAGE);
 546   }
 547
 548
 549   public void zappo_actionPerformed(ActionEvent e)
 550   {
 551     pdbcanvas.bysequence = false;
 552     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 553     pdbcanvas.redrawneeded=true;
 554     pdbcanvas.repaint();
 555   }
 556
 557   public void taylor_actionPerformed(ActionEvent e)
 558   {
 559     pdbcanvas.bysequence = false;
 560     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 561     pdbcanvas.redrawneeded=true;
 562     pdbcanvas.repaint();
 563   }
 564
 565   public void helix_actionPerformed(ActionEvent e)
 566   {
 567     pdbcanvas.bysequence = false;
 568     pdbcanvas.pdb.setColours(new HelixColourScheme());
 569     pdbcanvas.redrawneeded=true;
 570     pdbcanvas.repaint();
 571   }
 572
 573   public void strand_actionPerformed(ActionEvent e)
 574   {
 575     pdbcanvas.bysequence = false;
 576     pdbcanvas.pdb.setColours(new StrandColourScheme());
 577     pdbcanvas.redrawneeded=true;
 578     pdbcanvas.repaint();
 579   }
 580
 581   public void turn_actionPerformed(ActionEvent e)
 582   {
 583     pdbcanvas.bysequence = false;
 584     pdbcanvas.pdb.setColours(new TurnColourScheme());
 585     pdbcanvas.redrawneeded=true;
 586     pdbcanvas.repaint();
 587   }
 588
 589   public void buried_actionPerformed(ActionEvent e)
 590   {
 591     pdbcanvas.bysequence = false;
 592     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 593     pdbcanvas.redrawneeded=true;
 594     pdbcanvas.repaint();
 595   }
 596
 597   public void user_actionPerformed(ActionEvent e)
 598   {
 599     if (e.getActionCommand().equals("User Defined..."))
 600     {
 601       new UserDefinedColours(pdbcanvas, null);
 602     }
 603     else
 604     {
 605       UserColourScheme udc = (UserColourScheme) UserDefinedColours.
 606           getUserColourSchemes().get(e.getActionCommand());
 607
 608       pdbcanvas.pdb.setColours(udc);
 609       pdbcanvas.redrawneeded=true;
 610       pdbcanvas.repaint();
 611     }
 612   }
 613
 614   public void background_actionPerformed(ActionEvent e)
 615   {
 616       java.awt.Color col = JColorChooser.showDialog(this, "Select Background Colour",
 617                 pdbcanvas.backgroundColour);
 618
 619       if(col!=null)
 620        {
 621          pdbcanvas.backgroundColour = col;
 622          pdbcanvas.redrawneeded = true;
 623          pdbcanvas.repaint();
 624        }
 625   }
 626
 627   public void savePDB_actionPerformed(ActionEvent e)
 628   {
 629     JalviewFileChooser chooser = new JalviewFileChooser(
 630         jalview.bin.Cache.getProperty(
 631             "LAST_DIRECTORY"));
 632
 633     chooser.setFileView(new JalviewFileView());
 634     chooser.setDialogTitle("Save PDB File");
 635     chooser.setToolTipText("Save");
 636
 637     int value = chooser.showSaveDialog(this);
 638
 639     if (value == JalviewFileChooser.APPROVE_OPTION)
 640     {
 641         try
 642         {
 643           BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 644           File outFile = chooser.getSelectedFile();
 645
 646           PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 647           String data;
 648           while ( (data = in.readLine()) != null)
 649           {
 650             if (
 651                 !( data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
 652                 )
 653               out.println(data);
 654           }
 655           out.close();
 656         }
 657         catch (Exception ex)
 658         {
 659           ex.printStackTrace();
 660         }
 661       }
 662   }
 663 }