src/jalview/gui/AppJmol.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2007 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 jalview.gui;
  20
  21 import java.util.regex.*;
  22 import java.util.*;
  23 import java.awt.*;
  24 import javax.swing.*;
  25 import javax.swing.event.*;
  26 import java.awt.event.*;
  27 import java.io.*;
  28
  29 import jalview.jbgui.GStructureViewer;
  30 import jalview.datamodel.*;
  31 import jalview.gui.*;
  32 import jalview.structure.*;
  33 import jalview.datamodel.PDBEntry;
  34 import jalview.io.*;
  35 import jalview.schemes.*;
  36
  37 import org.jmol.api.*;
  38 import org.jmol.adapter.smarter.SmarterJmolAdapter;
  39 import org.jmol.popup.*;
  40
  41
  42 public class AppJmol
  43     extends GStructureViewer
  44     implements StructureListener, JmolStatusListener, Runnable
  45
  46 {
  47   JmolViewer viewer;
  48   JmolPopup jmolpopup;
  49   ScriptWindow scriptWindow;
  50   PDBEntry pdbentry;
  51   SequenceI[] sequence;
  52   String [] chains;
  53   StructureSelectionManager ssm;
  54   JSplitPane splitPane;
  55   RenderPanel renderPanel;
  56   AlignmentPanel ap;
  57   String fileLoadingError;
  58   boolean colourBySequence = true;
  59   boolean loadingFromArchive = false;
  60   Vector atomsPicked = new Vector();
  61
  62   public AppJmol(String file, String id,
  63                  SequenceI[] seq,
  64                  AlignmentPanel ap,
  65                  String loadStatus,
  66                  Rectangle bounds)
  67   {
  68     loadingFromArchive = true;
  69     pdbentry = new PDBEntry();
  70     pdbentry.setFile(file);
  71     pdbentry.setId(id);
  72     this.chains = chains;
  73     this.sequence = seq;
  74     this.ap = ap;
  75     this.setBounds(bounds);
  76
  77     colourBySequence = false;
  78     seqColour.setSelected(false);
  79
  80     jalview.gui.Desktop.addInternalFrame(this, "Loading File",
  81                                          bounds.width,bounds.height);
  82
  83     initJmol(loadStatus);
  84
  85     this.addInternalFrameListener(new InternalFrameAdapter()
  86     {
  87       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
  88       {
  89         closeViewer();
  90       }
  91     });
  92   }
  93
  94 public synchronized void addSequence(SequenceI [] seq)
  95    {
  96     Vector v = new Vector();
  97      for(int i=0; i<sequence.length; i++)
  98        v.addElement(sequence[i]);
  99
 100      for(int i=0; i<seq.length; i++)
 101       if(!v.contains(seq[i]))
 102           v.addElement(seq[i]);
 103
 104      SequenceI [] tmp = new SequenceI[v.size()];
 105      v.copyInto(tmp);
 106      sequence = tmp;
 107    }
 108
 109   public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String [] chains, AlignmentPanel ap)
 110   {
 111     //////////////////////////////////
 112     //Is the pdb file already loaded?
 113     String alreadyMapped = StructureSelectionManager
 114         .getStructureSelectionManager()
 115         .alreadyMappedToFile(pdbentry.getId());
 116
 117     if (alreadyMapped != null)
 118     {
 119       int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
 120           pdbentry.getId() + " is already displayed."
 121           + "\nDo you want to map sequences to the visible structure?",
 122           "Map Sequences to Visible Window: " + pdbentry.getId(),
 123           JOptionPane.YES_NO_OPTION);
 124
 125       if (option == JOptionPane.YES_OPTION)
 126       {
 127         StructureSelectionManager.getStructureSelectionManager()
 128             .setMapping(seq, chains, alreadyMapped, AppletFormatAdapter.FILE);
 129         if (ap.seqPanel.seqCanvas.fr!=null) {
 130           ap.seqPanel.seqCanvas.fr.featuresAdded();
 131           ap.paintAlignment(true);
 132         }
 133
 134         //Now this AppJmol is mapped to new sequences. We must add them to
 135         // the exisiting array
 136         JInternalFrame [] frames = Desktop.instance.getAllFrames();
 137
 138         for(int i=0; i<frames.length; i++)
 139         {
 140           if(frames[i] instanceof AppJmol)
 141           {
 142            AppJmol topJmol = ((AppJmol)frames[i]);
 143            if(topJmol.pdbentry.getFile().equals(alreadyMapped))
 144            {
 145              topJmol.addSequence(seq);
 146              break;
 147            }
 148           }
 149         }
 150
 151         return;
 152       }
 153     }
 154     ///////////////////////////////////
 155
 156     this.ap = ap;
 157     this.pdbentry = pdbentry;
 158     this.sequence = seq;
 159
 160     jalview.gui.Desktop.addInternalFrame(this, "Loading File", 400, 400);
 161
 162     if (pdbentry.getFile() != null)
 163     {
 164       initJmol("load \""+pdbentry.getFile()+"\"");
 165     }
 166     else
 167     {
 168       Thread worker = new Thread(this);
 169       worker.start();
 170     }
 171
 172     this.addInternalFrameListener(new InternalFrameAdapter()
 173     {
 174       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
 175       {
 176         closeViewer();
 177       }
 178     });
 179   }
 180
 181
 182   void initJmol(String command)
 183   {
 184     renderPanel = new RenderPanel();
 185
 186     this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
 187
 188     StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +
 189                                           pdbentry.getId());
 190
 191     if (pdbentry.getProperty() != null)
 192     {
 193       if (pdbentry.getProperty().get("method") != null)
 194       {
 195         title.append(" Method: ");
 196         title.append(pdbentry.getProperty().get("method"));
 197       }
 198       if (pdbentry.getProperty().get("chains") != null)
 199       {
 200         title.append(" Chain:");
 201         title.append(pdbentry.getProperty().get("chains"));
 202       }
 203     }
 204
 205     this.setTitle(title.toString());
 206
 207     viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
 208         new SmarterJmolAdapter());
 209
 210
 211     viewer.setAppletContext("", null, null, "");
 212
 213     viewer.setJmolStatusListener(this);
 214
 215     jmolpopup = JmolPopup.newJmolPopup(viewer);
 216
 217     viewer.evalStringQuiet(command);
 218   }
 219
 220
 221   void setChainMenuItems(Vector chains)
 222   {
 223     chainMenu.removeAll();
 224
 225     JMenuItem menuItem = new JMenuItem("All");
 226     menuItem.addActionListener(new ActionListener()
 227         {
 228           public void actionPerformed(ActionEvent evt)
 229           {
 230             allChainsSelected = true;
 231             for(int i=0; i<chainMenu.getItemCount(); i++)
 232             {
 233               if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
 234                 ( (JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
 235             }
 236             centerViewer();
 237             allChainsSelected = false;
 238           }
 239         });
 240
 241     chainMenu.add(menuItem);
 242
 243     for (int c = 0; c < chains.size(); c++)
 244     {
 245       menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
 246       menuItem.addItemListener(new ItemListener()
 247       {
 248         public void itemStateChanged(ItemEvent evt)
 249         {
 250           if (!allChainsSelected)
 251             centerViewer();
 252         }
 253       });
 254
 255       chainMenu.add(menuItem);
 256     }
 257   }
 258
 259   boolean allChainsSelected = false;
 260   void centerViewer()
 261   {
 262     StringBuffer cmd = new StringBuffer();
 263     for(int i=0; i<chainMenu.getItemCount(); i++)
 264     {
 265       if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
 266       {
 267        JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
 268        if(item.isSelected())
 269          cmd.append(":"+item.getText()+" or ");
 270       }
 271     }
 272
 273     if (cmd.length() > 0)
 274       cmd.setLength(cmd.length() - 4);
 275
 276     viewer.evalStringQuiet("select *;restrict "
 277                       +cmd+";cartoon;center "+cmd);
 278   }
 279
 280   void closeViewer()
 281   {
 282     viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
 283     viewer.evalStringQuiet("zap");
 284     viewer.setJmolStatusListener(null);
 285     viewer = null;
 286
 287     //We'll need to find out what other
 288     // listeners need to be shut down in Jmol
 289     StructureSelectionManager
 290         .getStructureSelectionManager()
 291         .removeStructureViewerListener(this, pdbentry.getFile());
 292   }
 293
 294   public void run()
 295   {
 296     try
 297     {
 298       EBIFetchClient ebi = new EBIFetchClient();
 299       String query = "pdb:" + pdbentry.getId();
 300       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
 301                        .getAbsolutePath());
 302       initJmol("load "+pdbentry.getFile());
 303     }
 304     catch (Exception ex)
 305     {
 306       ex.printStackTrace();
 307     }
 308   }
 309
 310   public void pdbFile_actionPerformed(ActionEvent actionEvent)
 311   {
 312     JalviewFileChooser chooser = new JalviewFileChooser(
 313         jalview.bin.Cache.getProperty(
 314             "LAST_DIRECTORY"));
 315
 316     chooser.setFileView(new JalviewFileView());
 317     chooser.setDialogTitle("Save PDB File");
 318     chooser.setToolTipText("Save");
 319
 320     int value = chooser.showSaveDialog(this);
 321
 322     if (value == JalviewFileChooser.APPROVE_OPTION)
 323     {
 324       try
 325       {
 326         BufferedReader in = new BufferedReader(new FileReader(pdbentry.getFile()));
 327         File outFile = chooser.getSelectedFile();
 328
 329         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 330         String data;
 331         while ( (data = in.readLine()) != null)
 332         {
 333           if (
 334               ! (data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
 335               )
 336           {
 337             out.println(data);
 338           }
 339         }
 340         out.close();
 341       }
 342       catch (Exception ex)
 343       {
 344         ex.printStackTrace();
 345       }
 346     }
 347   }
 348
 349   public void viewMapping_actionPerformed(ActionEvent actionEvent)
 350   {
 351     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 352     jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550,
 353                                          600);
 354     cap.setText(
 355         StructureSelectionManager.getStructureSelectionManager().printMapping(
 356             pdbentry.getFile())
 357         );
 358   }
 359
 360   /**
 361    * DOCUMENT ME!
 362    *
 363    * @param e DOCUMENT ME!
 364    */
 365   public void eps_actionPerformed(ActionEvent e)
 366   {
 367     makePDBImage(jalview.util.ImageMaker.EPS);
 368   }
 369
 370   /**
 371    * DOCUMENT ME!
 372    *
 373    * @param e DOCUMENT ME!
 374    */
 375   public void png_actionPerformed(ActionEvent e)
 376   {
 377     makePDBImage(jalview.util.ImageMaker.PNG);
 378   }
 379
 380   void makePDBImage(int type)
 381   {
 382     int width = getWidth();
 383     int height = getHeight();
 384
 385     jalview.util.ImageMaker im;
 386
 387     if (type == jalview.util.ImageMaker.PNG)
 388     {
 389       im = new jalview.util.ImageMaker(this,
 390                                        jalview.util.ImageMaker.PNG,
 391                                        "Make PNG image from view",
 392                                        width, height,
 393                                        null, null);
 394     }
 395     else
 396     {
 397       im = new jalview.util.ImageMaker(this,
 398                                        jalview.util.ImageMaker.EPS,
 399                                        "Make EPS file from view",
 400                                        width, height,
 401                                        null, this.getTitle());
 402     }
 403
 404     if (im.getGraphics() != null)
 405     {
 406       Rectangle rect = new Rectangle(width, height);
 407       viewer.renderScreenImage(im.getGraphics(),
 408                                rect.getSize(), rect);
 409       im.writeImage();
 410     }
 411   }
 412
 413
 414   public void seqColour_actionPerformed(ActionEvent actionEvent)
 415   {
 416     lastCommand = null;
 417     colourBySequence = seqColour.isSelected();
 418     colourBySequence(ap.alignFrame.alignPanel);
 419   }
 420
 421   public void chainColour_actionPerformed(ActionEvent actionEvent)
 422   {
 423     colourBySequence = false;
 424     seqColour.setSelected(false);
 425     viewer.evalStringQuiet("select *;color chain");
 426   }
 427
 428   public void chargeColour_actionPerformed(ActionEvent actionEvent)
 429   {
 430     colourBySequence = false;
 431     seqColour.setSelected(false);
 432     viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
 433                       +"select LYS,ARG;color blue;select CYS;color yellow");
 434   }
 435
 436   public void zappoColour_actionPerformed(ActionEvent actionEvent)
 437   {
 438     setJalviewColourScheme(new ZappoColourScheme());
 439   }
 440
 441   public void taylorColour_actionPerformed(ActionEvent actionEvent)
 442   {
 443     setJalviewColourScheme(new TaylorColourScheme());
 444   }
 445
 446   public void hydroColour_actionPerformed(ActionEvent actionEvent)
 447   {
 448     setJalviewColourScheme(new HydrophobicColourScheme());
 449   }
 450
 451   public void helixColour_actionPerformed(ActionEvent actionEvent)
 452   {
 453     setJalviewColourScheme(new HelixColourScheme());
 454   }
 455
 456   public void strandColour_actionPerformed(ActionEvent actionEvent)
 457   {
 458     setJalviewColourScheme(new StrandColourScheme());
 459   }
 460
 461   public void turnColour_actionPerformed(ActionEvent actionEvent)
 462   {
 463     setJalviewColourScheme(new TurnColourScheme());
 464   }
 465
 466   public void buriedColour_actionPerformed(ActionEvent actionEvent)
 467   {
 468     setJalviewColourScheme(new BuriedColourScheme());
 469   }
 470
 471   public void setJalviewColourScheme(ColourSchemeI cs)
 472   {
 473     colourBySequence = false;
 474     seqColour.setSelected(false);
 475
 476     if(cs==null)
 477       return;
 478
 479     String res;
 480     int index;
 481     Color col;
 482
 483     Enumeration en = ResidueProperties.aa3Hash.keys();
 484     StringBuffer command = new StringBuffer("select *;color white;");
 485     while(en.hasMoreElements())
 486     {
 487       res = en.nextElement().toString();
 488       index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
 489       if(index>20)
 490         continue;
 491
 492       col = cs.findColour(ResidueProperties.aa[index].charAt(0));
 493
 494       command.append("select "+res+";color["
 495                         + col.getRed() + ","
 496                         + col.getGreen() + ","
 497                         + col.getBlue() + "];");
 498     }
 499
 500     viewer.evalStringQuiet(command.toString());
 501   }
 502
 503   public void userColour_actionPerformed(ActionEvent actionEvent)
 504   {
 505     new UserDefinedColours(this, null);
 506   }
 507
 508   public void backGround_actionPerformed(ActionEvent actionEvent)
 509   {
 510     java.awt.Color col = JColorChooser.showDialog(this,
 511                                                   "Select Background Colour",
 512                                                   null);
 513
 514     if (col != null)
 515     {
 516       viewer.evalStringQuiet("background ["
 517                         + col.getRed() + ","
 518                         + col.getGreen() + ","
 519                         + col.getBlue() + "];");
 520     }
 521   }
 522
 523
 524   public void jmolHelp_actionPerformed(ActionEvent actionEvent)
 525   {
 526        try{
 527          jalview.util.BrowserLauncher.openURL(
 528              "http://jmol.sourceforge.net/docs/JmolUserGuide/");
 529        }catch(Exception ex){}
 530    }
 531
 532
 533   //////////////////////////////////
 534   ///StructureListener
 535   public String getPdbFile()
 536   {
 537     return pdbentry.getFile();
 538   }
 539
 540   Pattern pattern = Pattern.compile(
 541       "\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?"
 542       );
 543
 544   String lastMessage;
 545   public void mouseOverStructure(int atomIndex, String strInfo)
 546   {
 547     Matcher matcher = pattern.matcher(strInfo);
 548     matcher.find();
 549     matcher.group(1);
 550     int pdbResNum = Integer.parseInt(matcher.group(2));
 551     String chainId = matcher.group(3);
 552
 553     if (chainId != null)
 554       chainId = chainId.substring(1, chainId.length());
 555     else
 556     {
 557       chainId = " ";
 558     }
 559
 560     if (lastMessage == null || !lastMessage.equals(strInfo))
 561     {
 562       ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
 563     }
 564     lastMessage = strInfo;
 565   }
 566
 567   StringBuffer resetLastRes = new StringBuffer();
 568   StringBuffer eval = new StringBuffer();
 569
 570   public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
 571   {
 572     if (!pdbfile.equals(pdbentry.getFile()))
 573       return;
 574
 575     if (resetLastRes.length() > 0)
 576     {
 577       viewer.evalStringQuiet(resetLastRes.toString());
 578     }
 579
 580     eval.setLength(0);
 581     eval.append("select " + pdbResNum);
 582
 583     resetLastRes.setLength(0);
 584     resetLastRes.append("select " + pdbResNum);
 585
 586     if (!chain.equals(" "))
 587     {
 588       eval.append(":" + chain);
 589       resetLastRes.append(":" + chain);
 590     }
 591
 592     eval.append(";wireframe 100;"+eval.toString()+".CA;");
 593
 594     resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
 595
 596     eval.append("spacefill 200;select none");
 597
 598     viewer.evalStringQuiet(eval.toString());
 599   }
 600
 601   public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
 602   {
 603     if (!pdbfile.equals(pdbentry.getFile()))
 604       return null;
 605
 606     return new Color(viewer.getAtomArgb(atomIndex));
 607   }
 608
 609   public void updateColours(Object source)
 610   {
 611     colourBySequence( (AlignmentPanel) source);
 612   }
 613
 614
 615 //End StructureListener
 616 ////////////////////////////
 617
 618   String lastCommand;
 619   FeatureRenderer fr=null;
 620   public void colourBySequence(AlignmentPanel sourceap)
 621   {
 622     this.ap = sourceap;
 623
 624     if(!colourBySequence || ap.alignFrame.getCurrentView()!=ap.av)
 625       return;
 626
 627     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 628
 629     if (mapping.length < 1)
 630      return;
 631
 632
 633     SequenceRenderer sr = new SequenceRenderer(ap.av);
 634
 635     boolean showFeatures = false;
 636
 637     if (ap.av.showSequenceFeatures)
 638     {
 639       showFeatures = true;
 640       if (fr == null)
 641       {
 642         fr = new jalview.gui.FeatureRenderer(ap);
 643       }
 644
 645       fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
 646     }
 647
 648     StringBuffer command = new StringBuffer();
 649
 650     int lastPos = -1;
 651     for (int s = 0; s < sequence.length; s++)
 652     {
 653       for (int m = 0; m < mapping.length; m++)
 654       {
 655         if (mapping[m].getSequence() == sequence[s]
 656             && ap.av.alignment.findIndex(sequence[s])>-1)
 657         {
 658           for (int r = 0; r < sequence[s].getLength(); r++)
 659           {
 660             int pos = mapping[m].getPDBResNum(
 661                 sequence[s].findPosition(r));
 662
 663             if (pos < 1 || pos==lastPos)
 664               continue;
 665
 666             lastPos = pos;
 667
 668             Color col = sr.getResidueBoxColour(sequence[s], r);
 669
 670             if (showFeatures)
 671               col = fr.findFeatureColour(col, sequence[s], r);
 672
 673             if (command.toString().endsWith(":" + mapping[m].getChain()+
 674                                             ";color["
 675                                             + col.getRed() + ","
 676                                             + col.getGreen() + ","
 677                                             + col.getBlue() + "]"))
 678             {
 679               command = condenseCommand(command, pos);
 680               continue;
 681             }
 682
 683             command.append(";select " + pos);
 684
 685             if (!mapping[m].getChain().equals(" "))
 686             {
 687               command.append(":" + mapping[m].getChain());
 688             }
 689
 690             command.append(";color["
 691                              + col.getRed() + ","
 692                              + col.getGreen() + ","
 693                              + col.getBlue() + "]");
 694
 695           }
 696           break;
 697         }
 698       }
 699     }
 700
 701     if (lastCommand == null || !lastCommand.equals(command.toString()))
 702     {
 703       viewer.evalStringQuiet(command.toString());
 704     }
 705     lastCommand = command.toString();
 706   }
 707
 708   StringBuffer condenseCommand(StringBuffer command, int pos)
 709   {
 710     StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));
 711
 712     command.delete(0, sb.length());
 713
 714     String start;
 715
 716     if (command.indexOf("-") > -1)
 717     {
 718       start = command.substring(0,command.indexOf("-"));
 719     }
 720     else
 721     {
 722       start = command.substring(0, command.indexOf(":"));
 723     }
 724
 725     sb.append(start+"-"+pos+command.substring(command.indexOf(":")));
 726
 727     return sb;
 728   }
 729
 730   /////////////////////////////////
 731   //JmolStatusListener
 732
 733   public String eval(String strEval)
 734   {
 735    // System.out.println(strEval);
 736    //"# 'eval' is implemented only for the applet.";
 737     return null;
 738   }
 739
 740   public void createImage(String file, String type, int quality)
 741   {
 742     System.out.println("JMOL CREATE IMAGE");
 743   }
 744
 745   public void setCallbackFunction(String callbackType,
 746                                   String callbackFunction)
 747   {}
 748
 749   public void notifyFileLoaded(String fullPathName, String fileName,
 750                                String modelName, Object clientFile,
 751                                String errorMsg)
 752   {
 753     if(errorMsg!=null)
 754     {
 755       fileLoadingError = errorMsg;
 756       repaint();
 757       return;
 758     }
 759
 760     fileLoadingError = null;
 761
 762     if (fileName != null)
 763     {
 764
 765       //FILE LOADED OK
 766       ssm = StructureSelectionManager.getStructureSelectionManager();
 767       MCview.PDBfile pdbFile = ssm.setMapping(sequence,chains,pdbentry.getFile(), AppletFormatAdapter.FILE);
 768       ssm.addStructureViewerListener(this);
 769       Vector chains = new Vector();
 770       for(int i=0; i<pdbFile.chains.size(); i++)
 771       {
 772         chains.addElement(((MCview.PDBChain)pdbFile.chains.elementAt(i)).id);
 773       }
 774       setChainMenuItems(chains);
 775
 776       jmolpopup.updateComputedMenus();
 777
 778       if(!loadingFromArchive)
 779       {
 780         viewer.evalStringQuiet(
 781              "select backbone;restrict;cartoon;wireframe off;spacefill off");
 782
 783         colourBySequence(ap);
 784       }
 785       if (fr!=null)
 786         fr.featuresAdded();
 787
 788       loadingFromArchive = false;
 789     }
 790     else
 791       return;
 792   }
 793
 794   public void notifyFrameChanged(int frameNo)
 795   {
 796     boolean isAnimationRunning = (frameNo <= -2);
 797   }
 798
 799   public void notifyScriptStart(String statusMessage, String additionalInfo)
 800   {}
 801
 802   public void sendConsoleEcho(String strEcho)
 803   {
 804     if (scriptWindow != null)
 805       scriptWindow.sendConsoleEcho(strEcho);
 806   }
 807
 808   public void sendConsoleMessage(String strStatus)
 809   {
 810     if (scriptWindow != null)
 811       scriptWindow.sendConsoleMessage(strStatus);
 812   }
 813
 814   public void notifyScriptTermination(String strStatus, int msWalltime)
 815   {
 816     if (scriptWindow != null)
 817       scriptWindow.notifyScriptTermination(strStatus, msWalltime);
 818   }
 819
 820   public void handlePopupMenu(int x, int y)
 821   {
 822     jmolpopup.show(x, y);
 823   }
 824
 825   public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
 826   {
 827     notifyAtomPicked(iatom, strMeasure);
 828   }
 829
 830   public void notifyNewDefaultModeMeasurement(int count, String strInfo)
 831   {}
 832
 833   public void notifyAtomPicked(int atomIndex, String strInfo)
 834   {
 835     Matcher matcher = pattern.matcher(strInfo);
 836     matcher.find();
 837
 838     matcher.group(1);
 839     String resnum = new String(matcher.group(2));
 840     String chainId = matcher.group(3);
 841
 842     String picked = resnum;
 843
 844     if (chainId != null)
 845       picked+=(":"+chainId.substring(1, chainId.length()));
 846
 847     picked+=".CA";
 848
 849
 850     if (!atomsPicked.contains(picked))
 851     {
 852       if(chainId!=null)
 853       viewer.evalString("select "+picked+";label %n %r:%c");
 854     else
 855       viewer.evalString("select "+picked+";label %n %r");
 856       atomsPicked.addElement(picked);
 857     }
 858     else
 859     {
 860       viewer.evalString("select "+picked+";label off");
 861       atomsPicked.removeElement(picked);
 862     }
 863
 864     if (scriptWindow != null)
 865     {
 866       scriptWindow.sendConsoleMessage(strInfo);
 867       scriptWindow.sendConsoleMessage("\n");
 868     }
 869   }
 870
 871   public void notifyAtomHovered(int atomIndex, String strInfo)
 872   {
 873     mouseOverStructure(atomIndex, strInfo);
 874   }
 875
 876   public void sendSyncScript(String script, String appletName)
 877   {}
 878
 879   public void showUrl(String url)
 880   {}
 881
 882   public void showConsole(boolean showConsole)
 883   {
 884     if (scriptWindow == null)
 885       scriptWindow = new ScriptWindow(this);
 886
 887     if(showConsole)
 888     {
 889       if(splitPane==null)
 890       {
 891         splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
 892         splitPane.setTopComponent(renderPanel);
 893         splitPane.setBottomComponent(scriptWindow);
 894         this.getContentPane().add(splitPane, BorderLayout.CENTER);
 895       }
 896
 897       splitPane.setDividerLocation(getHeight()-200);
 898       splitPane.validate();
 899     }
 900     else
 901     {
 902       if (splitPane != null)
 903         splitPane.setVisible(false);
 904
 905       splitPane = null;
 906
 907       this.getContentPane().add(renderPanel, BorderLayout.CENTER);
 908     }
 909
 910     validate();
 911   }
 912
 913   public float functionXY(String functionName, int x, int y)
 914   {
 915     return 0;
 916   }
 917
 918   ///End JmolStatusListener
 919   ///////////////////////////////
 920
 921
 922   class RenderPanel
 923       extends JPanel
 924   {
 925     final Dimension currentSize = new Dimension();
 926     final Rectangle rectClip = new Rectangle();
 927
 928     public void paintComponent(Graphics g)
 929     {
 930       getSize(currentSize);
 931       g.getClipBounds(rectClip);
 932
 933       if (viewer == null)
 934       {
 935         g.setColor(Color.black);
 936         g.fillRect(0, 0, currentSize.width, currentSize.height);
 937         g.setColor(Color.white);
 938         g.setFont(new Font("Verdana", Font.BOLD, 14));
 939         g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
 940       }
 941       else if(fileLoadingError!=null)
 942       {
 943         g.setColor(Color.black);
 944         g.fillRect(0, 0, currentSize.width, currentSize.height);
 945         g.setColor(Color.white);
 946         g.setFont(new Font("Verdana", Font.BOLD, 14));
 947         g.drawString("Error loading file..." + pdbentry.getId(), 20,
 948                      currentSize.height / 2);
 949       }
 950       else
 951       {
 952         viewer.renderScreenImage(g, currentSize, rectClip);
 953       }
 954     }
 955   }
 956
 957 }