src/MCview/PDBViewer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 import java.awt.BorderLayout;
  32
  33 public class PDBViewer extends JInternalFrame implements Runnable
  34 {
  35
  36   /**
  37    * The associated sequence in an alignment
  38    */
  39   PDBCanvas pdbcanvas;
  40
  41   PDBEntry pdbentry;
  42
  43   SequenceI[] seq;
  44
  45   String[] chains;
  46
  47   AlignmentPanel ap;
  48
  49   String protocol;
  50
  51   String tmpPDBFile;
  52
  53   public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
  54           AlignmentPanel ap, String protocol)
  55
  56   {
  57     this.pdbentry = pdbentry;
  58     this.seq = seq;
  59     this.chains = chains;
  60     this.ap = ap;
  61     this.protocol = protocol;
  62
  63     try
  64     {
  65       jbInit();
  66     } catch (Exception ex)
  67     {
  68       ex.printStackTrace();
  69     }
  70
  71     StringBuffer title = new StringBuffer(seq[0].getName() + ":"
  72             + pdbentry.getFile());
  73
  74     pdbcanvas = new PDBCanvas();
  75
  76     setContentPane(pdbcanvas);
  77
  78     if (pdbentry.getFile() != null)
  79     {
  80       try
  81       {
  82         tmpPDBFile = pdbentry.getFile();
  83         PDBfile pdbfile = new PDBfile(tmpPDBFile,
  84                 jalview.io.AppletFormatAdapter.FILE);
  85
  86         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
  87
  88       } catch (java.io.IOException ex)
  89       {
  90         ex.printStackTrace();
  91       }
  92     }
  93     else
  94     {
  95       Thread worker = new Thread(this);
  96       worker.start();
  97     }
  98
  99     if (pdbentry.getProperty() != null)
 100     {
 101       if (pdbentry.getProperty().get("method") != null)
 102       {
 103         title.append(" Method: ");
 104         title.append(pdbentry.getProperty().get("method"));
 105       }
 106       if (pdbentry.getProperty().get("chains") != null)
 107       {
 108         title.append(" Chain:");
 109         title.append(pdbentry.getProperty().get("chains"));
 110       }
 111     }
 112     Desktop.addInternalFrame(this, title.toString(), 400, 400);
 113   }
 114
 115   public void run()
 116   {
 117     try
 118     {
 119       EBIFetchClient ebi = new EBIFetchClient();
 120       String query = "pdb:" + pdbentry.getId();
 121       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
 122               .getAbsolutePath());
 123
 124       if (pdbentry.getFile() != null)
 125         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 126     } catch (Exception ex)
 127     {
 128       pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
 129       ex.printStackTrace();
 130     }
 131   }
 132
 133   private void jbInit() throws Exception
 134   {
 135     this.addKeyListener(new KeyAdapter()
 136     {
 137       public void keyPressed(KeyEvent evt)
 138       {
 139         pdbcanvas.keyPressed(evt);
 140       }
 141     });
 142
 143     this.setJMenuBar(jMenuBar1);
 144     fileMenu.setText("File");
 145     coloursMenu.setText("Colours");
 146     saveMenu.setActionCommand("Save Image");
 147     saveMenu.setText("Save As");
 148     png.setText("PNG");
 149     png.addActionListener(new ActionListener()
 150     {
 151       public void actionPerformed(ActionEvent e)
 152       {
 153         png_actionPerformed(e);
 154       }
 155     });
 156     eps.setText("EPS");
 157     eps.addActionListener(new ActionListener()
 158     {
 159       public void actionPerformed(ActionEvent e)
 160       {
 161         eps_actionPerformed(e);
 162       }
 163     });
 164     mapping.setText("View Mapping");
 165     mapping.addActionListener(new ActionListener()
 166     {
 167       public void actionPerformed(ActionEvent e)
 168       {
 169         mapping_actionPerformed(e);
 170       }
 171     });
 172     wire.setText("Wireframe");
 173     wire.addActionListener(new ActionListener()
 174     {
 175       public void actionPerformed(ActionEvent e)
 176       {
 177         wire_actionPerformed(e);
 178       }
 179     });
 180     depth.setSelected(true);
 181     depth.setText("Depthcue");
 182     depth.addActionListener(new ActionListener()
 183     {
 184       public void actionPerformed(ActionEvent e)
 185       {
 186         depth_actionPerformed(e);
 187       }
 188     });
 189     zbuffer.setSelected(true);
 190     zbuffer.setText("Z Buffering");
 191     zbuffer.addActionListener(new ActionListener()
 192     {
 193       public void actionPerformed(ActionEvent e)
 194       {
 195         zbuffer_actionPerformed(e);
 196       }
 197     });
 198     charge.setText("Charge & Cysteine");
 199     charge.addActionListener(new ActionListener()
 200     {
 201       public void actionPerformed(ActionEvent e)
 202       {
 203         charge_actionPerformed(e);
 204       }
 205     });
 206     chain.setText("By Chain");
 207     chain.addActionListener(new ActionListener()
 208     {
 209       public void actionPerformed(ActionEvent e)
 210       {
 211         chain_actionPerformed(e);
 212       }
 213     });
 214     seqButton.setSelected(true);
 215     seqButton.setText("By Sequence");
 216     seqButton.addActionListener(new ActionListener()
 217     {
 218       public void actionPerformed(ActionEvent e)
 219       {
 220         seqButton_actionPerformed(e);
 221       }
 222     });
 223     allchains.setSelected(true);
 224     allchains.setText("Show All Chains");
 225     allchains.addItemListener(new ItemListener()
 226     {
 227       public void itemStateChanged(ItemEvent e)
 228       {
 229         allchains_itemStateChanged(e);
 230       }
 231     });
 232     zappo.setText("Zappo");
 233     zappo.addActionListener(new ActionListener()
 234     {
 235       public void actionPerformed(ActionEvent e)
 236       {
 237         zappo_actionPerformed(e);
 238       }
 239     });
 240     taylor.setText("Taylor");
 241     taylor.addActionListener(new ActionListener()
 242     {
 243       public void actionPerformed(ActionEvent e)
 244       {
 245         taylor_actionPerformed(e);
 246       }
 247     });
 248     hydro.setText("Hydro");
 249     hydro.addActionListener(new ActionListener()
 250     {
 251       public void actionPerformed(ActionEvent e)
 252       {
 253         hydro_actionPerformed(e);
 254       }
 255     });
 256     helix.setText("Helix");
 257     helix.addActionListener(new ActionListener()
 258     {
 259       public void actionPerformed(ActionEvent e)
 260       {
 261         helix_actionPerformed(e);
 262       }
 263     });
 264     strand.setText("Strand");
 265     strand.addActionListener(new ActionListener()
 266     {
 267       public void actionPerformed(ActionEvent e)
 268       {
 269         strand_actionPerformed(e);
 270       }
 271     });
 272     turn.setText("Turn");
 273     turn.addActionListener(new ActionListener()
 274     {
 275       public void actionPerformed(ActionEvent e)
 276       {
 277         turn_actionPerformed(e);
 278       }
 279     });
 280     buried.setText("Buried");
 281     buried.addActionListener(new ActionListener()
 282     {
 283       public void actionPerformed(ActionEvent e)
 284       {
 285         buried_actionPerformed(e);
 286       }
 287     });
 288     user.setText("User Defined...");
 289     user.addActionListener(new ActionListener()
 290     {
 291       public void actionPerformed(ActionEvent e)
 292       {
 293         user_actionPerformed(e);
 294       }
 295     });
 296     viewMenu.setText("View");
 297     background.setText("Background Colour...");
 298     background.addActionListener(new ActionListener()
 299     {
 300       public void actionPerformed(ActionEvent e)
 301       {
 302         background_actionPerformed(e);
 303       }
 304     });
 305     savePDB.setText("PDB File");
 306     savePDB.addActionListener(new ActionListener()
 307     {
 308       public void actionPerformed(ActionEvent e)
 309       {
 310         savePDB_actionPerformed(e);
 311       }
 312     });
 313     jMenuBar1.add(fileMenu);
 314     jMenuBar1.add(coloursMenu);
 315     jMenuBar1.add(viewMenu);
 316     fileMenu.add(saveMenu);
 317     fileMenu.add(mapping);
 318     saveMenu.add(savePDB);
 319     saveMenu.add(png);
 320     saveMenu.add(eps);
 321     coloursMenu.add(seqButton);
 322     coloursMenu.add(chain);
 323     coloursMenu.add(charge);
 324     coloursMenu.add(zappo);
 325     coloursMenu.add(taylor);
 326     coloursMenu.add(hydro);
 327     coloursMenu.add(helix);
 328     coloursMenu.add(strand);
 329     coloursMenu.add(turn);
 330     coloursMenu.add(buried);
 331     coloursMenu.add(user);
 332     coloursMenu.add(background);
 333     ButtonGroup bg = new ButtonGroup();
 334     bg.add(seqButton);
 335     bg.add(chain);
 336     bg.add(charge);
 337     bg.add(zappo);
 338     bg.add(taylor);
 339     bg.add(hydro);
 340     bg.add(helix);
 341     bg.add(strand);
 342     bg.add(turn);
 343     bg.add(buried);
 344     bg.add(user);
 345
 346     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 347     {
 348       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 349               .getUserColourSchemes().keys();
 350
 351       while (userColours.hasMoreElements())
 352       {
 353         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 354                 userColours.nextElement().toString());
 355         radioItem.setName("USER_DEFINED");
 356         radioItem.addMouseListener(new MouseAdapter()
 357         {
 358           public void mousePressed(MouseEvent evt)
 359           {
 360             if (evt.isControlDown()
 361                     || SwingUtilities.isRightMouseButton(evt))
 362             {
 363               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 364
 365               int option = JOptionPane.showInternalConfirmDialog(
 366                       jalview.gui.Desktop.desktop,
 367                       "Remove from default list?",
 368                       "Remove user defined colour",
 369                       JOptionPane.YES_NO_OPTION);
 370               if (option == JOptionPane.YES_OPTION)
 371               {
 372                 jalview.gui.UserDefinedColours
 373                         .removeColourFromDefaults(radioItem.getText());
 374                 coloursMenu.remove(radioItem);
 375               }
 376               else
 377               {
 378                 radioItem.addActionListener(new ActionListener()
 379                 {
 380                   public void actionPerformed(ActionEvent evt)
 381                   {
 382                     user_actionPerformed(evt);
 383                   }
 384                 });
 385               }
 386             }
 387           }
 388         });
 389         radioItem.addActionListener(new ActionListener()
 390         {
 391           public void actionPerformed(ActionEvent evt)
 392           {
 393             user_actionPerformed(evt);
 394           }
 395         });
 396         coloursMenu.add(radioItem);
 397         bg.add(radioItem);
 398       }
 399     }
 400
 401     viewMenu.add(wire);
 402     viewMenu.add(depth);
 403     viewMenu.add(zbuffer);
 404     viewMenu.add(allchains);
 405   }
 406
 407   JMenuBar jMenuBar1 = new JMenuBar();
 408
 409   JMenu fileMenu = new JMenu();
 410
 411   JMenu coloursMenu = new JMenu();
 412
 413   JMenu saveMenu = new JMenu();
 414
 415   JMenuItem png = new JMenuItem();
 416
 417   JMenuItem eps = new JMenuItem();
 418
 419   JMenuItem mapping = new JMenuItem();
 420
 421   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
 422
 423   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
 424
 425   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
 426
 427   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 428
 429   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
 430
 431   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
 432
 433   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
 434
 435   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
 436
 437   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
 438
 439   JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
 440
 441   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
 442
 443   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
 444
 445   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
 446
 447   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
 448
 449   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
 450
 451   JMenu viewMenu = new JMenu();
 452
 453   JMenuItem background = new JMenuItem();
 454
 455   JMenuItem savePDB = new JMenuItem();
 456
 457   /**
 458    * DOCUMENT ME!
 459    *
 460    * @param e
 461    *          DOCUMENT ME!
 462    */
 463   public void eps_actionPerformed(ActionEvent e)
 464   {
 465     makePDBImage(jalview.util.ImageMaker.EPS);
 466   }
 467
 468   /**
 469    * DOCUMENT ME!
 470    *
 471    * @param e
 472    *          DOCUMENT ME!
 473    */
 474   public void png_actionPerformed(ActionEvent e)
 475   {
 476     makePDBImage(jalview.util.ImageMaker.PNG);
 477   }
 478
 479   void makePDBImage(int type)
 480   {
 481     int width = pdbcanvas.getWidth();
 482     int height = pdbcanvas.getHeight();
 483
 484     jalview.util.ImageMaker im;
 485
 486     if (type == jalview.util.ImageMaker.PNG)
 487     {
 488       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
 489               "Make PNG image from view", width, height, null, null);
 490     }
 491     else
 492     {
 493       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
 494               "Make EPS file from view", width, height, null,
 495               this.getTitle());
 496     }
 497
 498     if (im.getGraphics() != null)
 499     {
 500       pdbcanvas.drawAll(im.getGraphics(), width, height);
 501       im.writeImage();
 502     }
 503   }
 504
 505   public void charge_actionPerformed(ActionEvent e)
 506   {
 507     pdbcanvas.bysequence = false;
 508     pdbcanvas.pdb.setChargeColours();
 509     pdbcanvas.redrawneeded = true;
 510     pdbcanvas.repaint();
 511   }
 512
 513   public void hydro_actionPerformed(ActionEvent e)
 514   {
 515     pdbcanvas.bysequence = false;
 516     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
 517     pdbcanvas.redrawneeded = true;
 518     pdbcanvas.repaint();
 519   }
 520
 521   public void chain_actionPerformed(ActionEvent e)
 522   {
 523     pdbcanvas.bysequence = false;
 524     pdbcanvas.pdb.setChainColours();
 525     pdbcanvas.redrawneeded = true;
 526     pdbcanvas.repaint();
 527   }
 528
 529   public void zbuffer_actionPerformed(ActionEvent e)
 530   {
 531     pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
 532     pdbcanvas.redrawneeded = true;
 533     pdbcanvas.repaint();
 534   }
 535
 536   public void molecule_actionPerformed(ActionEvent e)
 537   {
 538     pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
 539     pdbcanvas.redrawneeded = true;
 540     pdbcanvas.repaint();
 541   }
 542
 543   public void depth_actionPerformed(ActionEvent e)
 544   {
 545     pdbcanvas.depthcue = !pdbcanvas.depthcue;
 546     pdbcanvas.redrawneeded = true;
 547     pdbcanvas.repaint();
 548   }
 549
 550   public void wire_actionPerformed(ActionEvent e)
 551   {
 552     pdbcanvas.wire = !pdbcanvas.wire;
 553     pdbcanvas.redrawneeded = true;
 554     pdbcanvas.repaint();
 555   }
 556
 557   public void seqButton_actionPerformed(ActionEvent e)
 558   {
 559     pdbcanvas.bysequence = true;
 560     pdbcanvas.updateSeqColours();
 561   }
 562
 563   public void mapping_actionPerformed(ActionEvent e)
 564   {
 565     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 566     try
 567     {
 568       cap.setText(pdbcanvas.mappingDetails.toString());
 569       Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
 570     } catch (OutOfMemoryError oom)
 571     {
 572       new OOMWarning("Opening sequence to structure mapping report", oom);
 573       cap.dispose();
 574     }
 575   }
 576
 577   public void allchains_itemStateChanged(ItemEvent e)
 578   {
 579     pdbcanvas.setAllchainsVisible(allchains.getState());
 580   }
 581
 582   public void zappo_actionPerformed(ActionEvent e)
 583   {
 584     pdbcanvas.bysequence = false;
 585     pdbcanvas.pdb.setColours(new ZappoColourScheme());
 586     pdbcanvas.redrawneeded = true;
 587     pdbcanvas.repaint();
 588   }
 589
 590   public void taylor_actionPerformed(ActionEvent e)
 591   {
 592     pdbcanvas.bysequence = false;
 593     pdbcanvas.pdb.setColours(new TaylorColourScheme());
 594     pdbcanvas.redrawneeded = true;
 595     pdbcanvas.repaint();
 596   }
 597
 598   public void helix_actionPerformed(ActionEvent e)
 599   {
 600     pdbcanvas.bysequence = false;
 601     pdbcanvas.pdb.setColours(new HelixColourScheme());
 602     pdbcanvas.redrawneeded = true;
 603     pdbcanvas.repaint();
 604   }
 605
 606   public void strand_actionPerformed(ActionEvent e)
 607   {
 608     pdbcanvas.bysequence = false;
 609     pdbcanvas.pdb.setColours(new StrandColourScheme());
 610     pdbcanvas.redrawneeded = true;
 611     pdbcanvas.repaint();
 612   }
 613
 614   public void turn_actionPerformed(ActionEvent e)
 615   {
 616     pdbcanvas.bysequence = false;
 617     pdbcanvas.pdb.setColours(new TurnColourScheme());
 618     pdbcanvas.redrawneeded = true;
 619     pdbcanvas.repaint();
 620   }
 621
 622   public void buried_actionPerformed(ActionEvent e)
 623   {
 624     pdbcanvas.bysequence = false;
 625     pdbcanvas.pdb.setColours(new BuriedColourScheme());
 626     pdbcanvas.redrawneeded = true;
 627     pdbcanvas.repaint();
 628   }
 629
 630   public void user_actionPerformed(ActionEvent e)
 631   {
 632     if (e.getActionCommand().equals("User Defined..."))
 633     {
 634       // new UserDefinedColours(pdbcanvas, null);
 635     }
 636     else
 637     {
 638       UserColourScheme udc = (UserColourScheme) UserDefinedColours
 639               .getUserColourSchemes().get(e.getActionCommand());
 640
 641       pdbcanvas.pdb.setColours(udc);
 642       pdbcanvas.redrawneeded = true;
 643       pdbcanvas.repaint();
 644     }
 645   }
 646
 647   public void background_actionPerformed(ActionEvent e)
 648   {
 649     java.awt.Color col = JColorChooser.showDialog(this,
 650             "Select Background Colour", pdbcanvas.backgroundColour);
 651
 652     if (col != null)
 653     {
 654       pdbcanvas.backgroundColour = col;
 655       pdbcanvas.redrawneeded = true;
 656       pdbcanvas.repaint();
 657     }
 658   }
 659
 660   public void savePDB_actionPerformed(ActionEvent e)
 661   {
 662     JalviewFileChooser chooser = new JalviewFileChooser(
 663             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 664
 665     chooser.setFileView(new JalviewFileView());
 666     chooser.setDialogTitle("Save PDB File");
 667     chooser.setToolTipText("Save");
 668
 669     int value = chooser.showSaveDialog(this);
 670
 671     if (value == JalviewFileChooser.APPROVE_OPTION)
 672     {
 673       try
 674       {
 675         BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
 676         File outFile = chooser.getSelectedFile();
 677
 678         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 679         String data;
 680         while ((data = in.readLine()) != null)
 681         {
 682           if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
 683           {
 684             out.println(data);
 685           }
 686         }
 687         out.close();
 688       } catch (Exception ex)
 689       {
 690         ex.printStackTrace();
 691       }
 692     }
 693   }
 694 }