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