src/MCview/PDBViewer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package MCview;
  19
  20 import java.io.*;
  21
  22 import java.awt.event.*;
  23 import javax.swing.*;
  24
  25 import jalview.datamodel.*;
  26 import jalview.gui.*;
  27 import jalview.io.*;
  28 import jalview.schemes.*;
  29 import jalview.ws.ebi.EBIFetchClient;
  30
  31 public class PDBViewer extends JInternalFrame implements Runnable
  32 {
  33
  34   /**
  35    * The associated sequence in an alignment
  36    */
  37   PDBCanvas pdbcanvas;
  38
  39   PDBEntry pdbentry;
  40
  41   SequenceI[] seq;
  42
  43   String[] chains;
  44
  45   AlignmentPanel ap;
  46
  47   String protocol;
  48
  49   String tmpPDBFile;
  50
  51   public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
  52           AlignmentPanel ap, String protocol)
  53
  54   {
  55     this.pdbentry = pdbentry;
  56     this.seq = seq;
  57     this.chains = chains;
  58     this.ap = ap;
  59     this.protocol = protocol;
  60
  61     try
  62     {
  63       jbInit();
  64     } catch (Exception ex)
  65     {
  66       ex.printStackTrace();
  67     }
  68
  69     StringBuffer title = new StringBuffer(seq[0].getName() + ":"
  70             + pdbentry.getFile());
  71
  72     pdbcanvas = new PDBCanvas();
  73
  74     setContentPane(pdbcanvas);
  75
  76     if (pdbentry.getFile() != null)
  77     {
  78       try
  79       {
  80         tmpPDBFile = pdbentry.getFile();
  81         PDBfile pdbfile = new PDBfile(tmpPDBFile,
  82                 jalview.io.AppletFormatAdapter.FILE);
  83
  84         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
  85
  86       } catch (java.io.IOException ex)
  87       {
  88         ex.printStackTrace();
  89       }
  90     }
  91     else
  92     {
  93       Thread worker = new Thread(this);
  94       worker.start();
  95     }
  96
  97     if (pdbentry.getProperty() != null)
  98     {
  99       if (pdbentry.getProperty().get("method") != null)
 100       {
 101         title.append(" Method: ");
 102         title.append(pdbentry.getProperty().get("method"));
 103       }
 104       if (pdbentry.getProperty().get("chains") != null)
 105       {
 106         title.append(" Chain:");
 107         title.append(pdbentry.getProperty().get("chains"));
 108       }
 109     }
 110     Desktop.addInternalFrame(this, title.toString(), 400, 400);
 111   }
 112
 113   public void run()
 114   {
 115     try
 116     {
 117       EBIFetchClient ebi = new EBIFetchClient();
 118       String query = "pdb:" + pdbentry.getId();
 119       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
 120               .getAbsolutePath());
 121
 122       if (pdbentry.getFile() != null)
 123         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 124     } catch (Exception ex)
 125     {
 126       pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
 127       ex.printStackTrace();
 128     }
 129   }
 130
 131   private void jbInit() throws Exception
 132   {
 133     this.addKeyListener(new KeyAdapter()
 134     {
 135       public void keyPressed(KeyEvent evt)
 136       {
 137         pdbcanvas.keyPressed(evt);
 138       }
 139     });
 140
 141     this.setJMenuBar(jMenuBar1);
 142     fileMenu.setText("File");
 143     coloursMenu.setText("Colours");
 144     saveMenu.setActionCommand("Save Image");
 145     saveMenu.setText("Save As");
 146     png.setText("PNG");
 147     png.addActionListener(new ActionListener()
 148     {
 149       public void actionPerformed(ActionEvent e)
 150       {
 151         png_actionPerformed(e);
 152       }
 153     });
 154     eps.setText("EPS");
 155     eps.addActionListener(new ActionListener()
 156     {
 157       public void actionPerformed(ActionEvent e)
 158       {
 159         eps_actionPerformed(e);
 160       }
 161     });
 162     mapping.setText("View Mapping");
 163     mapping.addActionListener(new ActionListener()
 164     {
 165       public void actionPerformed(ActionEvent e)
 166       {
 167         mapping_actionPerformed(e);
 168       }
 169     });
 170     wire.setText("Wireframe");
 171     wire.addActionListener(new ActionListener()
 172     {
 173       public void actionPerformed(ActionEvent e)
 174       {
 175         wire_actionPerformed(e);
 176       }
 177     });
 178     depth.setSelected(true);
 179     depth.setText("Depthcue");
 180     depth.addActionListener(new ActionListener()
 181     {
 182       public void actionPerformed(ActionEvent e)
 183       {
 184         depth_actionPerformed(e);
 185       }
 186     });
 187     zbuffer.setSelected(true);
 188     zbuffer.setText("Z Buffering");
 189     zbuffer.addActionListener(new ActionListener()
 190     {
 191       public void actionPerformed(ActionEvent e)
 192       {
 193         zbuffer_actionPerformed(e);
 194       }
 195     });
 196     charge.setText("Charge & Cysteine");
 197     charge.addActionListener(new ActionListener()
 198     {
 199       public void actionPerformed(ActionEvent e)
 200       {
 201         charge_actionPerformed(e);
 202       }
 203     });
 204     chain.setText("By Chain");
 205     chain.addActionListener(new ActionListener()
 206     {
 207       public void actionPerformed(ActionEvent e)
 208       {
 209         chain_actionPerformed(e);
 210       }
 211     });
 212     seqButton.setSelected(true);
 213     seqButton.setText("By Sequence");
 214     seqButton.addActionListener(new ActionListener()
 215     {
 216       public void actionPerformed(ActionEvent e)
 217       {
 218         seqButton_actionPerformed(e);
 219       }
 220     });
 221     allchains.setSelected(true);
 222     allchains.setText("Show All Chains");
 223     allchains.addItemListener(new ItemListener()
 224     {
 225       public void itemStateChanged(ItemEvent e)
 226       {
 227         allchains_itemStateChanged(e);
 228       }
 229     });
 230     zappo.setText("Zappo");
 231     zappo.addActionListener(new ActionListener()
 232     {
 233       public void actionPerformed(ActionEvent e)
 234       {
 235         zappo_actionPerformed(e);
 236       }
 237     });
 238     taylor.setText("Taylor");
 239     taylor.addActionListener(new ActionListener()
 240     {
 241       public void actionPerformed(ActionEvent e)
 242       {
 243         taylor_actionPerformed(e);
 244       }
 245     });
 246     hydro.setText("Hydro");
 247     hydro.addActionListener(new ActionListener()
 248     {
 249       public void actionPerformed(ActionEvent e)
 250       {
 251         hydro_actionPerformed(e);
 252       }
 253     });
 254     helix.setText("Helix");
 255     helix.addActionListener(new ActionListener()
 256     {
 257       public void actionPerformed(ActionEvent e)
 258       {
 259         helix_actionPerformed(e);
 260       }
 261     });
 262     strand.setText("Strand");
 263     strand.addActionListener(new ActionListener()
 264     {
 265       public void actionPerformed(ActionEvent e)
 266       {
 267         strand_actionPerformed(e);
 268       }
 269     });
 270     turn.setText("Turn");
 271     turn.addActionListener(new ActionListener()
 272     {
 273       public void actionPerformed(ActionEvent e)
 274       {
 275         turn_actionPerformed(e);
 276       }
 277     });
 278     buried.setText("Buried");
 279     buried.addActionListener(new ActionListener()
 280     {
 281       public void actionPerformed(ActionEvent e)
 282       {
 283         buried_actionPerformed(e);
 284       }
 285     });
 286     user.setText("User Defined...");
 287     user.addActionListener(new ActionListener()
 288     {
 289       public void actionPerformed(ActionEvent e)
 290       {
 291         user_actionPerformed(e);
 292       }
 293     });
 294     viewMenu.setText("View");
 295     background.setText("Background Colour...");
 296     background.addActionListener(new ActionListener()
 297     {
 298       public void actionPerformed(ActionEvent e)
 299       {
 300         background_actionPerformed(e);
 301       }
 302     });
 303     savePDB.setText("PDB File");
 304     savePDB.addActionListener(new ActionListener()
 305     {
 306       public void actionPerformed(ActionEvent e)
 307       {
 308         savePDB_actionPerformed(e);
 309       }
 310     });
 311     jMenuBar1.add(fileMenu);
 312     jMenuBar1.add(coloursMenu);
 313     jMenuBar1.add(viewMenu);
 314     fileMenu.add(saveMenu);
 315     fileMenu.add(mapping);
 316     saveMenu.add(savePDB);
 317     saveMenu.add(png);
 318     saveMenu.add(eps);
 319     coloursMenu.add(seqButton);
 320     coloursMenu.add(chain);
 321     coloursMenu.add(charge);
 322     coloursMenu.add(zappo);
 323     coloursMenu.add(taylor);
 324     coloursMenu.add(hydro);
 325     coloursMenu.add(helix);
 326     coloursMenu.add(strand);
 327     coloursMenu.add(turn);
 328     coloursMenu.add(buried);
 329     coloursMenu.add(user);
 330     coloursMenu.add(background);
 331     ButtonGroup bg = new ButtonGroup();
 332     bg.add(seqButton);
 333     bg.add(chain);
 334     bg.add(charge);
 335     bg.add(zappo);
 336     bg.add(taylor);
 337     bg.add(hydro);
 338     bg.add(helix);
 339     bg.add(strand);
 340     bg.add(turn);
 341     bg.add(buried);
 342     bg.add(user);
 343
 344     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 345     {
 346       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 347               .getUserColourSchemes().keys();
 348
 349       while (userColours.hasMoreElements())
 350       {
 351         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 352                 userColours.nextElement().toString());
 353         radioItem.setName("USER_DEFINED");
 354         radioItem.addMouseListener(new MouseAdapter()
 355         {
 356           public void mousePressed(MouseEvent evt)
 357           {
 358             if (evt.isControlDown()
 359                     || SwingUtilities.isRightMouseButton(evt))
 360             {
 361               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 362
 363               int option = JOptionPane.showInternalConfirmDialog(
 364                       jalview.gui.Desktop.desktop,
 365                       "Remove from default list?",
 366                       "Remove user defined colour",
 367                       JOptionPane.YES_NO_OPTION);
 368               if (option == JOptionPane.YES_OPTION)
 369               {
 370                 jalview.gui.UserDefinedColours
 371                         .removeColourFromDefaults(radioItem.getText());
 372                 coloursMenu.remove(radioItem);
 373               }
 374               else
 375               {
 376                 radioItem.addActionListener(new ActionListener()
 377                 {
 378                   public void actionPerformed(ActionEvent evt)
 379                   {
 380                     user_actionPerformed(evt);
 381                   }
 382                 });
 383               }
 384             }
 385           }
 386         });
 387         radioItem.addActionListener(new ActionListener()
 388         {
 389           public void actionPerformed(ActionEvent evt)
 390           {
 391             user_actionPerformed(evt);
 392           }
 393         });
 394         coloursMenu.add(radioItem);
 395         bg.add(radioItem);
 396       }
 397     }
 398
 399     viewMenu.add(wire);
 400     viewMenu.add(depth);
 401     viewMenu.add(zbuffer);
 402     viewMenu.add(allchains);
 403   }
 404
 405   JMenuBar jMenuBar1 = new JMenuBar();
 406
 407   JMenu fileMenu = new JMenu();
 408
 409   JMenu coloursMenu = new JMenu();
 410
 411   JMenu saveMenu = new JMenu();
 412
 413   JMenuItem png = new JMenuItem();
 414
 415   JMenuItem eps = new JMenuItem();
 416
 417   JMenuItem mapping = new JMenuItem();
 418
 419   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 420
 421   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 422
 423   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 424
 425   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 426
 427   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 428
 429   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 430
 431   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 432
 433   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 434
 435   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 436
 437   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 438
 439   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 440
 441   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 442
 443   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 444
 445   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 446
 447   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 448
 449   JMenu viewMenu = new JMenu();
 450
 451   JMenuItem background = new JMenuItem();
 452
 453   JMenuItem savePDB = new JMenuItem();
 454
 455   /**
 456    * DOCUMENT ME!
 457    *
 458    * @param e
 459    *          DOCUMENT ME!
 460    */
 461   public void eps_actionPerformed(ActionEvent e)
 462   {
 463     makePDBImage(jalview.util.ImageMaker.EPS);
 464   }
 465
 466   /**
 467    * DOCUMENT ME!
 468    *
 469    * @param e
 470    *          DOCUMENT ME!
 471    */
 472   public void png_actionPerformed(ActionEvent e)
 473   {
 474     makePDBImage(jalview.util.ImageMaker.PNG);
 475   }
 476
 477   void makePDBImage(int type)
 478   {
 479     int width = pdbcanvas.getWidth();
 480     int height = pdbcanvas.getHeight();
 481
 482     jalview.util.ImageMaker im;
 483
 484     if (type == jalview.util.ImageMaker.PNG)
 485     {
 486       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
 487               "Make PNG image from view", width, height, null, null);
 488     }
 489     else
 490     {
 491       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
 492               "Make EPS file from view", width, height, null,
 493               this.getTitle());
 494     }
 495
 496     if (im.getGraphics() != null)
 497     {
 498       pdbcanvas.drawAll(im.getGraphics(), width, height);
 499       im.writeImage();
 500     }
 501   }
 502
 503   public void charge_actionPerformed(ActionEvent e)
 504   {
 505     pdbcanvas.bysequence = false;
 506     pdbcanvas.pdb.setChargeColours();
 507     pdbcanvas.redrawneeded = true;
 508     pdbcanvas.repaint();
 509   }
 510
 511   public void hydro_actionPerformed(ActionEvent e)
 512   {
 513     pdbcanvas.bysequence = false;
 514     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 515     pdbcanvas.redrawneeded = true;
 516     pdbcanvas.repaint();
 517   }
 518
 519   public void chain_actionPerformed(ActionEvent e)
 520   {
 521     pdbcanvas.bysequence = false;
 522     pdbcanvas.pdb.setChainColours();
 523     pdbcanvas.redrawneeded = true;
 524     pdbcanvas.repaint();
 525   }
 526
 527   public void zbuffer_actionPerformed(ActionEvent e)
 528   {
 529     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 530     pdbcanvas.redrawneeded = true;
 531     pdbcanvas.repaint();
 532   }
 533
 534   public void molecule_actionPerformed(ActionEvent e)
 535   {
 536     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 537     pdbcanvas.redrawneeded = true;
 538     pdbcanvas.repaint();
 539   }
 540
 541   public void depth_actionPerformed(ActionEvent e)
 542   {
 543     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 544     pdbcanvas.redrawneeded = true;
 545     pdbcanvas.repaint();
 546   }
 547
 548   public void wire_actionPerformed(ActionEvent e)
 549   {
 550     pdbcanvas.wire = !pdbcanvas.wire;
 551     pdbcanvas.redrawneeded = true;
 552     pdbcanvas.repaint();
 553   }
 554
 555   public void seqButton_actionPerformed(ActionEvent e)
 556   {
 557     pdbcanvas.bysequence = true;
 558     pdbcanvas.updateSeqColours();
 559   }
 560
 561   public void mapping_actionPerformed(ActionEvent e)
 562   {
 563     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 564     try
 565     {
 566       cap.setText(pdbcanvas.mappingDetails.toString());
 567       Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
 568     } catch (OutOfMemoryError oom)
 569     {
 570       new OOMWarning("Opening sequence to structure mapping report", oom);
 571       cap.dispose();
 572     }
 573   }
 574
 575   public void allchains_itemStateChanged(ItemEvent e)
 576   {
 577     pdbcanvas.setAllchainsVisible(allchains.getState());
 578   }
 579
 580   public void zappo_actionPerformed(ActionEvent e)
 581   {
 582     pdbcanvas.bysequence = false;
 583     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 584     pdbcanvas.redrawneeded = true;
 585     pdbcanvas.repaint();
 586   }
 587
 588   public void taylor_actionPerformed(ActionEvent e)
 589   {
 590     pdbcanvas.bysequence = false;
 591     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 592     pdbcanvas.redrawneeded = true;
 593     pdbcanvas.repaint();
 594   }
 595
 596   public void helix_actionPerformed(ActionEvent e)
 597   {
 598     pdbcanvas.bysequence = false;
 599     pdbcanvas.pdb.setColours(new HelixColourScheme());
 600     pdbcanvas.redrawneeded = true;
 601     pdbcanvas.repaint();
 602   }
 603
 604   public void strand_actionPerformed(ActionEvent e)
 605   {
 606     pdbcanvas.bysequence = false;
 607     pdbcanvas.pdb.setColours(new StrandColourScheme());
 608     pdbcanvas.redrawneeded = true;
 609     pdbcanvas.repaint();
 610   }
 611
 612   public void turn_actionPerformed(ActionEvent e)
 613   {
 614     pdbcanvas.bysequence = false;
 615     pdbcanvas.pdb.setColours(new TurnColourScheme());
 616     pdbcanvas.redrawneeded = true;
 617     pdbcanvas.repaint();
 618   }
 619
 620   public void buried_actionPerformed(ActionEvent e)
 621   {
 622     pdbcanvas.bysequence = false;
 623     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 624     pdbcanvas.redrawneeded = true;
 625     pdbcanvas.repaint();
 626   }
 627
 628   public void user_actionPerformed(ActionEvent e)
 629   {
 630     if (e.getActionCommand().equals("User Defined..."))
 631     {
 632       // new UserDefinedColours(pdbcanvas, null);
 633     }
 634     else
 635     {
 636       UserColourScheme udc = (UserColourScheme) UserDefinedColours
 637               .getUserColourSchemes().get(e.getActionCommand());
 638
 639       pdbcanvas.pdb.setColours(udc);
 640       pdbcanvas.redrawneeded = true;
 641       pdbcanvas.repaint();
 642     }
 643   }
 644
 645   public void background_actionPerformed(ActionEvent e)
 646   {
 647     java.awt.Color col = JColorChooser.showDialog(this,
 648             "Select Background Colour", pdbcanvas.backgroundColour);
 649
 650     if (col != null)
 651     {
 652       pdbcanvas.backgroundColour = col;
 653       pdbcanvas.redrawneeded = true;
 654       pdbcanvas.repaint();
 655     }
 656   }
 657
 658   public void savePDB_actionPerformed(ActionEvent e)
 659   {
 660     JalviewFileChooser chooser = new JalviewFileChooser(
 661             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 662
 663     chooser.setFileView(new JalviewFileView());
 664     chooser.setDialogTitle("Save PDB File");
 665     chooser.setToolTipText("Save");
 666
 667     int value = chooser.showSaveDialog(this);
 668
 669     if (value == JalviewFileChooser.APPROVE_OPTION)
 670     {
 671       try
 672       {
 673         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 674         File outFile = chooser.getSelectedFile();
 675
 676         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 677         String data;
 678         while ((data = in.readLine()) != null)
 679         {
 680           if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
 681           {
 682             out.println(data);
 683           }
 684         }
 685         out.close();
 686         in.close();
 687       } catch (Exception ex)
 688       {
 689         ex.printStackTrace();
 690       }
 691     }
 692   }
 693 }