src/MCview/PDBViewer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   3  * Copyright (C) 2014 The Jalview Authors
   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  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package MCview;
  20
  21 import java.io.*;
  22
  23 import java.awt.event.*;
  24 import javax.swing.*;
  25
  26 import jalview.datamodel.*;
  27 import jalview.gui.*;
  28 import jalview.io.*;
  29 import jalview.schemes.*;
  30 import jalview.ws.ebi.EBIFetchClient;
  31
  32 public class PDBViewer extends JInternalFrame implements Runnable
  33 {
  34
  35   /**
  36    * The associated sequence in an alignment
  37    */
  38   PDBCanvas pdbcanvas;
  39
  40   PDBEntry pdbentry;
  41
  42   SequenceI[] seq;
  43
  44   String[] chains;
  45
  46   AlignmentPanel ap;
  47
  48   String protocol;
  49
  50   String tmpPDBFile;
  51
  52   public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
  53           AlignmentPanel ap, String protocol)
  54
  55   {
  56     this.pdbentry = pdbentry;
  57     this.seq = seq;
  58     this.chains = chains;
  59     this.ap = ap;
  60     this.protocol = protocol;
  61
  62     try
  63     {
  64       jbInit();
  65     } catch (Exception ex)
  66     {
  67       ex.printStackTrace();
  68     }
  69
  70     StringBuffer title = new StringBuffer(seq[0].getName() + ":"
  71             + pdbentry.getFile());
  72
  73     pdbcanvas = new PDBCanvas();
  74
  75     setContentPane(pdbcanvas);
  76
  77     if (pdbentry.getFile() != null)
  78     {
  79       try
  80       {
  81         tmpPDBFile = pdbentry.getFile();
  82         PDBfile pdbfile = new PDBfile(tmpPDBFile,
  83                 jalview.io.AppletFormatAdapter.FILE);
  84
  85         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
  86
  87       } catch (java.io.IOException ex)
  88       {
  89         ex.printStackTrace();
  90       }
  91     }
  92     else
  93     {
  94       Thread worker = new Thread(this);
  95       worker.start();
  96     }
  97
  98     if (pdbentry.getProperty() != null)
  99     {
 100       if (pdbentry.getProperty().get("method") != null)
 101       {
 102         title.append(" Method: ");
 103         title.append(pdbentry.getProperty().get("method"));
 104       }
 105       if (pdbentry.getProperty().get("chains") != null)
 106       {
 107         title.append(" Chain:");
 108         title.append(pdbentry.getProperty().get("chains"));
 109       }
 110     }
 111     Desktop.addInternalFrame(this, title.toString(), 400, 400);
 112   }
 113
 114   public void run()
 115   {
 116     try
 117     {
 118       EBIFetchClient ebi = new EBIFetchClient();
 119       String query = "pdb:" + pdbentry.getId();
 120       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
 121               .getAbsolutePath());
 122
 123       if (pdbentry.getFile() != null)
 124         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 125     } catch (Exception ex)
 126     {
 127       pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
 128       ex.printStackTrace();
 129     }
 130   }
 131
 132   private void jbInit() throws Exception
 133   {
 134     this.addKeyListener(new KeyAdapter()
 135     {
 136       public void keyPressed(KeyEvent evt)
 137       {
 138         pdbcanvas.keyPressed(evt);
 139       }
 140     });
 141
 142     this.setJMenuBar(jMenuBar1);
 143     fileMenu.setText("File");
 144     coloursMenu.setText("Colours");
 145     saveMenu.setActionCommand("Save Image");
 146     saveMenu.setText("Save As");
 147     png.setText("PNG");
 148     png.addActionListener(new ActionListener()
 149     {
 150       public void actionPerformed(ActionEvent e)
 151       {
 152         png_actionPerformed(e);
 153       }
 154     });
 155     eps.setText("EPS");
 156     eps.addActionListener(new ActionListener()
 157     {
 158       public void actionPerformed(ActionEvent e)
 159       {
 160         eps_actionPerformed(e);
 161       }
 162     });
 163     mapping.setText("View Mapping");
 164     mapping.addActionListener(new ActionListener()
 165     {
 166       public void actionPerformed(ActionEvent e)
 167       {
 168         mapping_actionPerformed(e);
 169       }
 170     });
 171     wire.setText("Wireframe");
 172     wire.addActionListener(new ActionListener()
 173     {
 174       public void actionPerformed(ActionEvent e)
 175       {
 176         wire_actionPerformed(e);
 177       }
 178     });
 179     depth.setSelected(true);
 180     depth.setText("Depthcue");
 181     depth.addActionListener(new ActionListener()
 182     {
 183       public void actionPerformed(ActionEvent e)
 184       {
 185         depth_actionPerformed(e);
 186       }
 187     });
 188     zbuffer.setSelected(true);
 189     zbuffer.setText("Z Buffering");
 190     zbuffer.addActionListener(new ActionListener()
 191     {
 192       public void actionPerformed(ActionEvent e)
 193       {
 194         zbuffer_actionPerformed(e);
 195       }
 196     });
 197     charge.setText("Charge & Cysteine");
 198     charge.addActionListener(new ActionListener()
 199     {
 200       public void actionPerformed(ActionEvent e)
 201       {
 202         charge_actionPerformed(e);
 203       }
 204     });
 205     chain.setText("By Chain");
 206     chain.addActionListener(new ActionListener()
 207     {
 208       public void actionPerformed(ActionEvent e)
 209       {
 210         chain_actionPerformed(e);
 211       }
 212     });
 213     seqButton.setSelected(true);
 214     seqButton.setText("By Sequence");
 215     seqButton.addActionListener(new ActionListener()
 216     {
 217       public void actionPerformed(ActionEvent e)
 218       {
 219         seqButton_actionPerformed(e);
 220       }
 221     });
 222     allchains.setSelected(true);
 223     allchains.setText("Show All Chains");
 224     allchains.addItemListener(new ItemListener()
 225     {
 226       public void itemStateChanged(ItemEvent e)
 227       {
 228         allchains_itemStateChanged(e);
 229       }
 230     });
 231     zappo.setText("Zappo");
 232     zappo.addActionListener(new ActionListener()
 233     {
 234       public void actionPerformed(ActionEvent e)
 235       {
 236         zappo_actionPerformed(e);
 237       }
 238     });
 239     taylor.setText("Taylor");
 240     taylor.addActionListener(new ActionListener()
 241     {
 242       public void actionPerformed(ActionEvent e)
 243       {
 244         taylor_actionPerformed(e);
 245       }
 246     });
 247     hydro.setText("Hydro");
 248     hydro.addActionListener(new ActionListener()
 249     {
 250       public void actionPerformed(ActionEvent e)
 251       {
 252         hydro_actionPerformed(e);
 253       }
 254     });
 255     helix.setText("Helix");
 256     helix.addActionListener(new ActionListener()
 257     {
 258       public void actionPerformed(ActionEvent e)
 259       {
 260         helix_actionPerformed(e);
 261       }
 262     });
 263     strand.setText("Strand");
 264     strand.addActionListener(new ActionListener()
 265     {
 266       public void actionPerformed(ActionEvent e)
 267       {
 268         strand_actionPerformed(e);
 269       }
 270     });
 271     turn.setText("Turn");
 272     turn.addActionListener(new ActionListener()
 273     {
 274       public void actionPerformed(ActionEvent e)
 275       {
 276         turn_actionPerformed(e);
 277       }
 278     });
 279     buried.setText("Buried");
 280     buried.addActionListener(new ActionListener()
 281     {
 282       public void actionPerformed(ActionEvent e)
 283       {
 284         buried_actionPerformed(e);
 285       }
 286     });
 287     user.setText("User Defined...");
 288     user.addActionListener(new ActionListener()
 289     {
 290       public void actionPerformed(ActionEvent e)
 291       {
 292         user_actionPerformed(e);
 293       }
 294     });
 295     viewMenu.setText("View");
 296     background.setText("Background Colour...");
 297     background.addActionListener(new ActionListener()
 298     {
 299       public void actionPerformed(ActionEvent e)
 300       {
 301         background_actionPerformed(e);
 302       }
 303     });
 304     savePDB.setText("PDB File");
 305     savePDB.addActionListener(new ActionListener()
 306     {
 307       public void actionPerformed(ActionEvent e)
 308       {
 309         savePDB_actionPerformed(e);
 310       }
 311     });
 312     jMenuBar1.add(fileMenu);
 313     jMenuBar1.add(coloursMenu);
 314     jMenuBar1.add(viewMenu);
 315     fileMenu.add(saveMenu);
 316     fileMenu.add(mapping);
 317     saveMenu.add(savePDB);
 318     saveMenu.add(png);
 319     saveMenu.add(eps);
 320     coloursMenu.add(seqButton);
 321     coloursMenu.add(chain);
 322     coloursMenu.add(charge);
 323     coloursMenu.add(zappo);
 324     coloursMenu.add(taylor);
 325     coloursMenu.add(hydro);
 326     coloursMenu.add(helix);
 327     coloursMenu.add(strand);
 328     coloursMenu.add(turn);
 329     coloursMenu.add(buried);
 330     coloursMenu.add(user);
 331     coloursMenu.add(background);
 332     ButtonGroup bg = new ButtonGroup();
 333     bg.add(seqButton);
 334     bg.add(chain);
 335     bg.add(charge);
 336     bg.add(zappo);
 337     bg.add(taylor);
 338     bg.add(hydro);
 339     bg.add(helix);
 340     bg.add(strand);
 341     bg.add(turn);
 342     bg.add(buried);
 343     bg.add(user);
 344
 345     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 346     {
 347       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 348               .getUserColourSchemes().keys();
 349
 350       while (userColours.hasMoreElements())
 351       {
 352         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 353                 userColours.nextElement().toString());
 354         radioItem.setName("USER_DEFINED");
 355         radioItem.addMouseListener(new MouseAdapter()
 356         {
 357           public void mousePressed(MouseEvent evt)
 358           {
 359             if (evt.isControlDown()
 360                     || SwingUtilities.isRightMouseButton(evt))
 361             {
 362               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 363
 364               int option = JOptionPane.showInternalConfirmDialog(
 365                       jalview.gui.Desktop.desktop,
 366                       "Remove from default list?",
 367                       "Remove user defined colour",
 368                       JOptionPane.YES_NO_OPTION);
 369               if (option == JOptionPane.YES_OPTION)
 370               {
 371                 jalview.gui.UserDefinedColours
 372                         .removeColourFromDefaults(radioItem.getText());
 373                 coloursMenu.remove(radioItem);
 374               }
 375               else
 376               {
 377                 radioItem.addActionListener(new ActionListener()
 378                 {
 379                   public void actionPerformed(ActionEvent evt)
 380                   {
 381                     user_actionPerformed(evt);
 382                   }
 383                 });
 384               }
 385             }
 386           }
 387         });
 388         radioItem.addActionListener(new ActionListener()
 389         {
 390           public void actionPerformed(ActionEvent evt)
 391           {
 392             user_actionPerformed(evt);
 393           }
 394         });
 395         coloursMenu.add(radioItem);
 396         bg.add(radioItem);
 397       }
 398     }
 399
 400     viewMenu.add(wire);
 401     viewMenu.add(depth);
 402     viewMenu.add(zbuffer);
 403     viewMenu.add(allchains);
 404   }
 405
 406   JMenuBar jMenuBar1 = new JMenuBar();
 407
 408   JMenu fileMenu = new JMenu();
 409
 410   JMenu coloursMenu = new JMenu();
 411
 412   JMenu saveMenu = new JMenu();
 413
 414   JMenuItem png = new JMenuItem();
 415
 416   JMenuItem eps = new JMenuItem();
 417
 418   JMenuItem mapping = new JMenuItem();
 419
 420   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 421
 422   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 423
 424   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 425
 426   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 427
 428   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 429
 430   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 431
 432   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 433
 434   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 435
 436   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 437
 438   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 439
 440   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 441
 442   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 443
 444   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 445
 446   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 447
 448   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 449
 450   JMenu viewMenu = new JMenu();
 451
 452   JMenuItem background = new JMenuItem();
 453
 454   JMenuItem savePDB = new JMenuItem();
 455
 456   /**
 457    * DOCUMENT ME!
 458    *
 459    * @param e
 460    *          DOCUMENT ME!
 461    */
 462   public void eps_actionPerformed(ActionEvent e)
 463   {
 464     makePDBImage(jalview.util.ImageMaker.EPS);
 465   }
 466
 467   /**
 468    * DOCUMENT ME!
 469    *
 470    * @param e
 471    *          DOCUMENT ME!
 472    */
 473   public void png_actionPerformed(ActionEvent e)
 474   {
 475     makePDBImage(jalview.util.ImageMaker.PNG);
 476   }
 477
 478   void makePDBImage(int type)
 479   {
 480     int width = pdbcanvas.getWidth();
 481     int height = pdbcanvas.getHeight();
 482
 483     jalview.util.ImageMaker im;
 484
 485     if (type == jalview.util.ImageMaker.PNG)
 486     {
 487       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
 488               "Make PNG image from view", width, height, null, null);
 489     }
 490     else
 491     {
 492       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
 493               "Make EPS file from view", width, height, null,
 494               this.getTitle());
 495     }
 496
 497     if (im.getGraphics() != null)
 498     {
 499       pdbcanvas.drawAll(im.getGraphics(), width, height);
 500       im.writeImage();
 501     }
 502   }
 503
 504   public void charge_actionPerformed(ActionEvent e)
 505   {
 506     pdbcanvas.bysequence = false;
 507     pdbcanvas.pdb.setChargeColours();
 508     pdbcanvas.redrawneeded = true;
 509     pdbcanvas.repaint();
 510   }
 511
 512   public void hydro_actionPerformed(ActionEvent e)
 513   {
 514     pdbcanvas.bysequence = false;
 515     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 516     pdbcanvas.redrawneeded = true;
 517     pdbcanvas.repaint();
 518   }
 519
 520   public void chain_actionPerformed(ActionEvent e)
 521   {
 522     pdbcanvas.bysequence = false;
 523     pdbcanvas.pdb.setChainColours();
 524     pdbcanvas.redrawneeded = true;
 525     pdbcanvas.repaint();
 526   }
 527
 528   public void zbuffer_actionPerformed(ActionEvent e)
 529   {
 530     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 531     pdbcanvas.redrawneeded = true;
 532     pdbcanvas.repaint();
 533   }
 534
 535   public void molecule_actionPerformed(ActionEvent e)
 536   {
 537     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 538     pdbcanvas.redrawneeded = true;
 539     pdbcanvas.repaint();
 540   }
 541
 542   public void depth_actionPerformed(ActionEvent e)
 543   {
 544     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 545     pdbcanvas.redrawneeded = true;
 546     pdbcanvas.repaint();
 547   }
 548
 549   public void wire_actionPerformed(ActionEvent e)
 550   {
 551     pdbcanvas.wire = !pdbcanvas.wire;
 552     pdbcanvas.redrawneeded = true;
 553     pdbcanvas.repaint();
 554   }
 555
 556   public void seqButton_actionPerformed(ActionEvent e)
 557   {
 558     pdbcanvas.bysequence = true;
 559     pdbcanvas.updateSeqColours();
 560   }
 561
 562   public void mapping_actionPerformed(ActionEvent e)
 563   {
 564     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 565     try
 566     {
 567       cap.setText(pdbcanvas.mappingDetails.toString());
 568       Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
 569     } catch (OutOfMemoryError oom)
 570     {
 571       new OOMWarning("Opening sequence to structure mapping report", oom);
 572       cap.dispose();
 573     }
 574   }
 575
 576   public void allchains_itemStateChanged(ItemEvent e)
 577   {
 578     pdbcanvas.setAllchainsVisible(allchains.getState());
 579   }
 580
 581   public void zappo_actionPerformed(ActionEvent e)
 582   {
 583     pdbcanvas.bysequence = false;
 584     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 585     pdbcanvas.redrawneeded = true;
 586     pdbcanvas.repaint();
 587   }
 588
 589   public void taylor_actionPerformed(ActionEvent e)
 590   {
 591     pdbcanvas.bysequence = false;
 592     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 593     pdbcanvas.redrawneeded = true;
 594     pdbcanvas.repaint();
 595   }
 596
 597   public void helix_actionPerformed(ActionEvent e)
 598   {
 599     pdbcanvas.bysequence = false;
 600     pdbcanvas.pdb.setColours(new HelixColourScheme());
 601     pdbcanvas.redrawneeded = true;
 602     pdbcanvas.repaint();
 603   }
 604
 605   public void strand_actionPerformed(ActionEvent e)
 606   {
 607     pdbcanvas.bysequence = false;
 608     pdbcanvas.pdb.setColours(new StrandColourScheme());
 609     pdbcanvas.redrawneeded = true;
 610     pdbcanvas.repaint();
 611   }
 612
 613   public void turn_actionPerformed(ActionEvent e)
 614   {
 615     pdbcanvas.bysequence = false;
 616     pdbcanvas.pdb.setColours(new TurnColourScheme());
 617     pdbcanvas.redrawneeded = true;
 618     pdbcanvas.repaint();
 619   }
 620
 621   public void buried_actionPerformed(ActionEvent e)
 622   {
 623     pdbcanvas.bysequence = false;
 624     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 625     pdbcanvas.redrawneeded = true;
 626     pdbcanvas.repaint();
 627   }
 628
 629   public void user_actionPerformed(ActionEvent e)
 630   {
 631     if (e.getActionCommand().equals("User Defined..."))
 632     {
 633       // new UserDefinedColours(pdbcanvas, null);
 634     }
 635     else
 636     {
 637       UserColourScheme udc = (UserColourScheme) UserDefinedColours
 638               .getUserColourSchemes().get(e.getActionCommand());
 639
 640       pdbcanvas.pdb.setColours(udc);
 641       pdbcanvas.redrawneeded = true;
 642       pdbcanvas.repaint();
 643     }
 644   }
 645
 646   public void background_actionPerformed(ActionEvent e)
 647   {
 648     java.awt.Color col = JColorChooser.showDialog(this,
 649             "Select Background Colour", pdbcanvas.backgroundColour);
 650
 651     if (col != null)
 652     {
 653       pdbcanvas.backgroundColour = col;
 654       pdbcanvas.redrawneeded = true;
 655       pdbcanvas.repaint();
 656     }
 657   }
 658
 659   public void savePDB_actionPerformed(ActionEvent e)
 660   {
 661     JalviewFileChooser chooser = new JalviewFileChooser(
 662             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 663
 664     chooser.setFileView(new JalviewFileView());
 665     chooser.setDialogTitle("Save PDB File");
 666     chooser.setToolTipText("Save");
 667
 668     int value = chooser.showSaveDialog(this);
 669
 670     if (value == JalviewFileChooser.APPROVE_OPTION)
 671     {
 672       try
 673       {
 674         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 675         File outFile = chooser.getSelectedFile();
 676
 677         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 678         String data;
 679         while ((data = in.readLine()) != null)
 680         {
 681           if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
 682           {
 683             out.println(data);
 684           }
 685         }
 686         out.close();
 687         in.close();
 688       } catch (Exception ex)
 689       {
 690         ex.printStackTrace();
 691       }
 692     }
 693   }
 694 }