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 import jalview.ws.EBIFetchClient;
  37
  38 import org.jmol.api.*;
  39 import org.jmol.adapter.smarter.SmarterJmolAdapter;
  40 import org.jmol.popup.*;
  41
  42
  43 public class AppJmol
  44     extends GStructureViewer
  45     implements StructureListener, JmolStatusListener, Runnable
  46
  47 {
  48   JmolViewer viewer;
  49   JmolPopup jmolpopup;
  50   ScriptWindow scriptWindow;
  51   PDBEntry pdbentry;
  52   SequenceI[] sequence;
  53   String [] chains;
  54   StructureSelectionManager ssm;
  55   JSplitPane splitPane;
  56   RenderPanel renderPanel;
  57   AlignmentPanel ap;
  58   String fileLoadingError;
  59   boolean colourBySequence = true;
  60   boolean loadingFromArchive = false;
  61   Vector atomsPicked = new Vector();
  62
  63   public AppJmol(String file, String id,
  64                  SequenceI[] seq,
  65                  AlignmentPanel ap,
  66                  String loadStatus,
  67                  Rectangle bounds)
  68   {
  69     loadingFromArchive = true;
  70     pdbentry = new PDBEntry();
  71     pdbentry.setFile(file);
  72     pdbentry.setId(id);
  73     this.chains = chains;
  74     this.sequence = seq;
  75     this.ap = ap;
  76     this.setBounds(bounds);
  77
  78     colourBySequence = false;
  79     seqColour.setSelected(false);
  80
  81     jalview.gui.Desktop.addInternalFrame(this, "Loading File",
  82                                          bounds.width,bounds.height);
  83
  84     initJmol(loadStatus);
  85
  86     this.addInternalFrameListener(new InternalFrameAdapter()
  87     {
  88       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
  89       {
  90         closeViewer();
  91       }
  92     });
  93   }
  94
  95 public synchronized void addSequence(SequenceI [] seq)
  96    {
  97     Vector v = new Vector();
  98      for(int i=0; i<sequence.length; i++)
  99        v.addElement(sequence[i]);
 100
 101      for(int i=0; i<seq.length; i++)
 102       if(!v.contains(seq[i]))
 103           v.addElement(seq[i]);
 104
 105      SequenceI [] tmp = new SequenceI[v.size()];
 106      v.copyInto(tmp);
 107      sequence = tmp;
 108    }
 109
 110   public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String [] chains, AlignmentPanel ap)
 111   {
 112     //////////////////////////////////
 113     //Is the pdb file already loaded?
 114     String alreadyMapped = StructureSelectionManager
 115         .getStructureSelectionManager()
 116         .alreadyMappedToFile(pdbentry.getId());
 117
 118     if (alreadyMapped != null)
 119     {
 120       int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
 121           pdbentry.getId() + " is already displayed."
 122           + "\nDo you want to map sequences to the visible structure?",
 123           "Map Sequences to Visible Window: " + pdbentry.getId(),
 124           JOptionPane.YES_NO_OPTION);
 125
 126       if (option == JOptionPane.YES_OPTION)
 127       {
 128         StructureSelectionManager.getStructureSelectionManager()
 129             .setMapping(seq, chains, alreadyMapped, AppletFormatAdapter.FILE);
 130         if (ap.seqPanel.seqCanvas.fr!=null) {
 131           ap.seqPanel.seqCanvas.fr.featuresAdded();
 132           ap.paintAlignment(true);
 133         }
 134
 135         //Now this AppJmol is mapped to new sequences. We must add them to
 136         // the exisiting array
 137         JInternalFrame [] frames = Desktop.instance.getAllFrames();
 138
 139         for(int i=0; i<frames.length; i++)
 140         {
 141           if(frames[i] instanceof AppJmol)
 142           {
 143            AppJmol topJmol = ((AppJmol)frames[i]);
 144            if(topJmol.pdbentry.getFile().equals(alreadyMapped))
 145            {
 146              topJmol.addSequence(seq);
 147              break;
 148            }
 149           }
 150         }
 151
 152         return;
 153       }
 154     }
 155     ///////////////////////////////////
 156
 157     this.ap = ap;
 158     this.pdbentry = pdbentry;
 159     this.sequence = seq;
 160
 161     jalview.gui.Desktop.addInternalFrame(this, "Loading File", 400, 400);
 162
 163     if (pdbentry.getFile() != null)
 164     {
 165       initJmol("load \""+pdbentry.getFile()+"\"");
 166     }
 167     else
 168     {
 169       Thread worker = new Thread(this);
 170       worker.start();
 171     }
 172
 173     this.addInternalFrameListener(new InternalFrameAdapter()
 174     {
 175       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
 176       {
 177         closeViewer();
 178       }
 179     });
 180   }
 181
 182
 183   void initJmol(String command)
 184   {
 185     renderPanel = new RenderPanel();
 186
 187     this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
 188
 189     StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +
 190                                           pdbentry.getId());
 191
 192     if (pdbentry.getProperty() != null)
 193     {
 194       if (pdbentry.getProperty().get("method") != null)
 195       {
 196         title.append(" Method: ");
 197         title.append(pdbentry.getProperty().get("method"));
 198       }
 199       if (pdbentry.getProperty().get("chains") != null)
 200       {
 201         title.append(" Chain:");
 202         title.append(pdbentry.getProperty().get("chains"));
 203       }
 204     }
 205
 206     this.setTitle(title.toString());
 207
 208     viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
 209         new SmarterJmolAdapter());
 210
 211
 212     viewer.setAppletContext("", null, null, "");
 213
 214     viewer.setJmolStatusListener(this);
 215
 216     jmolpopup = JmolPopup.newJmolPopup(viewer);
 217
 218     viewer.evalStringQuiet(command);
 219   }
 220
 221
 222   void setChainMenuItems(Vector chains)
 223   {
 224     chainMenu.removeAll();
 225
 226     JMenuItem menuItem = new JMenuItem("All");
 227     menuItem.addActionListener(new ActionListener()
 228         {
 229           public void actionPerformed(ActionEvent evt)
 230           {
 231             allChainsSelected = true;
 232             for(int i=0; i<chainMenu.getItemCount(); i++)
 233             {
 234               if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
 235                 ( (JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
 236             }
 237             centerViewer();
 238             allChainsSelected = false;
 239           }
 240         });
 241
 242     chainMenu.add(menuItem);
 243
 244     for (int c = 0; c < chains.size(); c++)
 245     {
 246       menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
 247       menuItem.addItemListener(new ItemListener()
 248       {
 249         public void itemStateChanged(ItemEvent evt)
 250         {
 251           if (!allChainsSelected)
 252             centerViewer();
 253         }
 254       });
 255
 256       chainMenu.add(menuItem);
 257     }
 258   }
 259
 260   boolean allChainsSelected = false;
 261   void centerViewer()
 262   {
 263     StringBuffer cmd = new StringBuffer();
 264     for(int i=0; i<chainMenu.getItemCount(); i++)
 265     {
 266       if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
 267       {
 268        JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
 269        if(item.isSelected())
 270          cmd.append(":"+item.getText()+" or ");
 271       }
 272     }
 273
 274     if (cmd.length() > 0)
 275       cmd.setLength(cmd.length() - 4);
 276
 277     viewer.evalStringQuiet("select *;restrict "
 278                       +cmd+";cartoon;center "+cmd);
 279   }
 280
 281   void closeViewer()
 282   {
 283     viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
 284     viewer.evalStringQuiet("zap");
 285     viewer.setJmolStatusListener(null);
 286     viewer = null;
 287
 288     //We'll need to find out what other
 289     // listeners need to be shut down in Jmol
 290     StructureSelectionManager
 291         .getStructureSelectionManager()
 292         .removeStructureViewerListener(this, pdbentry.getFile());
 293   }
 294
 295   public void run()
 296   {
 297     try
 298     {
 299       EBIFetchClient ebi = new EBIFetchClient();
 300       String query = "pdb:" + pdbentry.getId();
 301       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
 302                        .getAbsolutePath());
 303       initJmol("load "+pdbentry.getFile());
 304     }
 305     catch (Exception ex)
 306     {
 307       ex.printStackTrace();
 308     }
 309   }
 310
 311   public void pdbFile_actionPerformed(ActionEvent actionEvent)
 312   {
 313     JalviewFileChooser chooser = new JalviewFileChooser(
 314         jalview.bin.Cache.getProperty(
 315             "LAST_DIRECTORY"));
 316
 317     chooser.setFileView(new JalviewFileView());
 318     chooser.setDialogTitle("Save PDB File");
 319     chooser.setToolTipText("Save");
 320
 321     int value = chooser.showSaveDialog(this);
 322
 323     if (value == JalviewFileChooser.APPROVE_OPTION)
 324     {
 325       try
 326       {
 327         BufferedReader in = new BufferedReader(new FileReader(pdbentry.getFile()));
 328         File outFile = chooser.getSelectedFile();
 329
 330         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 331         String data;
 332         while ( (data = in.readLine()) != null)
 333         {
 334           if (
 335               ! (data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
 336               )
 337           {
 338             out.println(data);
 339           }
 340         }
 341         out.close();
 342       }
 343       catch (Exception ex)
 344       {
 345         ex.printStackTrace();
 346       }
 347     }
 348   }
 349
 350   public void viewMapping_actionPerformed(ActionEvent actionEvent)
 351   {
 352     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 353     jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550,
 354                                          600);
 355     cap.setText(
 356         StructureSelectionManager.getStructureSelectionManager().printMapping(
 357             pdbentry.getFile())
 358         );
 359   }
 360
 361   /**
 362    * DOCUMENT ME!
 363    *
 364    * @param e DOCUMENT ME!
 365    */
 366   public void eps_actionPerformed(ActionEvent e)
 367   {
 368     makePDBImage(jalview.util.ImageMaker.EPS);
 369   }
 370
 371   /**
 372    * DOCUMENT ME!
 373    *
 374    * @param e DOCUMENT ME!
 375    */
 376   public void png_actionPerformed(ActionEvent e)
 377   {
 378     makePDBImage(jalview.util.ImageMaker.PNG);
 379   }
 380
 381   void makePDBImage(int type)
 382   {
 383     int width = getWidth();
 384     int height = getHeight();
 385
 386     jalview.util.ImageMaker im;
 387
 388     if (type == jalview.util.ImageMaker.PNG)
 389     {
 390       im = new jalview.util.ImageMaker(this,
 391                                        jalview.util.ImageMaker.PNG,
 392                                        "Make PNG image from view",
 393                                        width, height,
 394                                        null, null);
 395     }
 396     else
 397     {
 398       im = new jalview.util.ImageMaker(this,
 399                                        jalview.util.ImageMaker.EPS,
 400                                        "Make EPS file from view",
 401                                        width, height,
 402                                        null, this.getTitle());
 403     }
 404
 405     if (im.getGraphics() != null)
 406     {
 407       Rectangle rect = new Rectangle(width, height);
 408       viewer.renderScreenImage(im.getGraphics(),
 409                                rect.getSize(), rect);
 410       im.writeImage();
 411     }
 412   }
 413
 414
 415   public void seqColour_actionPerformed(ActionEvent actionEvent)
 416   {
 417     lastCommand = null;
 418     colourBySequence = seqColour.isSelected();
 419     colourBySequence(ap.alignFrame.alignPanel);
 420   }
 421
 422   public void chainColour_actionPerformed(ActionEvent actionEvent)
 423   {
 424     colourBySequence = false;
 425     seqColour.setSelected(false);
 426     viewer.evalStringQuiet("select *;color chain");
 427   }
 428
 429   public void chargeColour_actionPerformed(ActionEvent actionEvent)
 430   {
 431     colourBySequence = false;
 432     seqColour.setSelected(false);
 433     viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
 434                       +"select LYS,ARG;color blue;select CYS;color yellow");
 435   }
 436
 437   public void zappoColour_actionPerformed(ActionEvent actionEvent)
 438   {
 439     setJalviewColourScheme(new ZappoColourScheme());
 440   }
 441
 442   public void taylorColour_actionPerformed(ActionEvent actionEvent)
 443   {
 444     setJalviewColourScheme(new TaylorColourScheme());
 445   }
 446
 447   public void hydroColour_actionPerformed(ActionEvent actionEvent)
 448   {
 449     setJalviewColourScheme(new HydrophobicColourScheme());
 450   }
 451
 452   public void helixColour_actionPerformed(ActionEvent actionEvent)
 453   {
 454     setJalviewColourScheme(new HelixColourScheme());
 455   }
 456
 457   public void strandColour_actionPerformed(ActionEvent actionEvent)
 458   {
 459     setJalviewColourScheme(new StrandColourScheme());
 460   }
 461
 462   public void turnColour_actionPerformed(ActionEvent actionEvent)
 463   {
 464     setJalviewColourScheme(new TurnColourScheme());
 465   }
 466
 467   public void buriedColour_actionPerformed(ActionEvent actionEvent)
 468   {
 469     setJalviewColourScheme(new BuriedColourScheme());
 470   }
 471
 472   public void setJalviewColourScheme(ColourSchemeI cs)
 473   {
 474     colourBySequence = false;
 475     seqColour.setSelected(false);
 476
 477     if(cs==null)
 478       return;
 479
 480     String res;
 481     int index;
 482     Color col;
 483
 484     Enumeration en = ResidueProperties.aa3Hash.keys();
 485     StringBuffer command = new StringBuffer("select *;color white;");
 486     while(en.hasMoreElements())
 487     {
 488       res = en.nextElement().toString();
 489       index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
 490       if(index>20)
 491         continue;
 492
 493       col = cs.findColour(ResidueProperties.aa[index].charAt(0));
 494
 495       command.append("select "+res+";color["
 496                         + col.getRed() + ","
 497                         + col.getGreen() + ","
 498                         + col.getBlue() + "];");
 499     }
 500
 501     viewer.evalStringQuiet(command.toString());
 502   }
 503
 504   public void userColour_actionPerformed(ActionEvent actionEvent)
 505   {
 506     new UserDefinedColours(this, null);
 507   }
 508
 509   public void backGround_actionPerformed(ActionEvent actionEvent)
 510   {
 511     java.awt.Color col = JColorChooser.showDialog(this,
 512                                                   "Select Background Colour",
 513                                                   null);
 514
 515     if (col != null)
 516     {
 517       viewer.evalStringQuiet("background ["
 518                         + col.getRed() + ","
 519                         + col.getGreen() + ","
 520                         + col.getBlue() + "];");
 521     }
 522   }
 523
 524
 525   public void jmolHelp_actionPerformed(ActionEvent actionEvent)
 526   {
 527        try{
 528          jalview.util.BrowserLauncher.openURL(
 529              "http://jmol.sourceforge.net/docs/JmolUserGuide/");
 530        }catch(Exception ex){}
 531    }
 532
 533
 534   //////////////////////////////////
 535   ///StructureListener
 536   public String getPdbFile()
 537   {
 538     return pdbentry.getFile();
 539   }
 540
 541   Pattern pattern = Pattern.compile(
 542       "\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?"
 543       );
 544
 545   String lastMessage;
 546   public void mouseOverStructure(int atomIndex, String strInfo)
 547   {
 548     Matcher matcher = pattern.matcher(strInfo);
 549     matcher.find();
 550     matcher.group(1);
 551     int pdbResNum = Integer.parseInt(matcher.group(2));
 552     String chainId = matcher.group(3);
 553
 554     if (chainId != null)
 555       chainId = chainId.substring(1, chainId.length());
 556     else
 557     {
 558       chainId = " ";
 559     }
 560
 561     if (lastMessage == null || !lastMessage.equals(strInfo))
 562     {
 563       ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
 564     }
 565     lastMessage = strInfo;
 566   }
 567
 568   StringBuffer resetLastRes = new StringBuffer();
 569   StringBuffer eval = new StringBuffer();
 570
 571   public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
 572   {
 573     if (!pdbfile.equals(pdbentry.getFile()))
 574       return;
 575
 576     if (resetLastRes.length() > 0)
 577     {
 578       viewer.evalStringQuiet(resetLastRes.toString());
 579     }
 580
 581     eval.setLength(0);
 582     eval.append("select " + pdbResNum);
 583
 584     resetLastRes.setLength(0);
 585     resetLastRes.append("select " + pdbResNum);
 586
 587     if (!chain.equals(" "))
 588     {
 589       eval.append(":" + chain);
 590       resetLastRes.append(":" + chain);
 591     }
 592
 593     eval.append(";wireframe 100;"+eval.toString()+".CA;");
 594
 595     resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
 596
 597     eval.append("spacefill 200;select none");
 598
 599     viewer.evalStringQuiet(eval.toString());
 600   }
 601
 602   public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
 603   {
 604     if (!pdbfile.equals(pdbentry.getFile()))
 605       return null;
 606
 607     return new Color(viewer.getAtomArgb(atomIndex));
 608   }
 609
 610   public void updateColours(Object source)
 611   {
 612     colourBySequence( (AlignmentPanel) source);
 613   }
 614
 615
 616 //End StructureListener
 617 ////////////////////////////
 618
 619   String lastCommand;
 620   FeatureRenderer fr=null;
 621   public void colourBySequence(AlignmentPanel sourceap)
 622   {
 623     this.ap = sourceap;
 624
 625     if(!colourBySequence || ap.alignFrame.getCurrentView()!=ap.av)
 626       return;
 627
 628     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 629
 630     if (mapping.length < 1)
 631      return;
 632
 633
 634     SequenceRenderer sr = new SequenceRenderer(ap.av);
 635
 636     boolean showFeatures = false;
 637
 638     if (ap.av.showSequenceFeatures)
 639     {
 640       showFeatures = true;
 641       if (fr == null)
 642       {
 643         fr = new jalview.gui.FeatureRenderer(ap);
 644       }
 645
 646       fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
 647     }
 648
 649     StringBuffer command = new StringBuffer();
 650
 651     int lastPos = -1;
 652     for (int s = 0; s < sequence.length; s++)
 653     {
 654       for (int m = 0; m < mapping.length; m++)
 655       {
 656         if (mapping[m].getSequence() == sequence[s]
 657             && ap.av.alignment.findIndex(sequence[s])>-1)
 658         {
 659           for (int r = 0; r < sequence[s].getLength(); r++)
 660           {
 661             int pos = mapping[m].getPDBResNum(
 662                 sequence[s].findPosition(r));
 663
 664             if (pos < 1 || pos==lastPos)
 665               continue;
 666
 667             lastPos = pos;
 668
 669             Color col = sr.getResidueBoxColour(sequence[s], r);
 670
 671             if (showFeatures)
 672               col = fr.findFeatureColour(col, sequence[s], r);
 673
 674             if (command.toString().endsWith(":" + mapping[m].getChain()+
 675                                             ";color["
 676                                             + col.getRed() + ","
 677                                             + col.getGreen() + ","
 678                                             + col.getBlue() + "]"))
 679             {
 680               command = condenseCommand(command, pos);
 681               continue;
 682             }
 683
 684             command.append(";select " + pos);
 685
 686             if (!mapping[m].getChain().equals(" "))
 687             {
 688               command.append(":" + mapping[m].getChain());
 689             }
 690
 691             command.append(";color["
 692                              + col.getRed() + ","
 693                              + col.getGreen() + ","
 694                              + col.getBlue() + "]");
 695
 696           }
 697           break;
 698         }
 699       }
 700     }
 701
 702     if (lastCommand == null || !lastCommand.equals(command.toString()))
 703     {
 704       viewer.evalStringQuiet(command.toString());
 705     }
 706     lastCommand = command.toString();
 707   }
 708
 709   StringBuffer condenseCommand(StringBuffer command, int pos)
 710   {
 711     StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));
 712
 713     command.delete(0, sb.length());
 714
 715     String start;
 716
 717     if (command.indexOf("-") > -1)
 718     {
 719       start = command.substring(0,command.indexOf("-"));
 720     }
 721     else
 722     {
 723       start = command.substring(0, command.indexOf(":"));
 724     }
 725
 726     sb.append(start+"-"+pos+command.substring(command.indexOf(":")));
 727
 728     return sb;
 729   }
 730
 731   /////////////////////////////////
 732   //JmolStatusListener
 733
 734   public String eval(String strEval)
 735   {
 736    // System.out.println(strEval);
 737    //"# 'eval' is implemented only for the applet.";
 738     return null;
 739   }
 740
 741   public void createImage(String file, String type, int quality)
 742   {
 743     System.out.println("JMOL CREATE IMAGE");
 744   }
 745
 746   public void setCallbackFunction(String callbackType,
 747                                   String callbackFunction)
 748   {}
 749
 750   public void notifyFileLoaded(String fullPathName, String fileName,
 751                                String modelName, Object clientFile,
 752                                String errorMsg)
 753   {
 754     if(errorMsg!=null)
 755     {
 756       fileLoadingError = errorMsg;
 757       repaint();
 758       return;
 759     }
 760
 761     fileLoadingError = null;
 762
 763     if (fileName != null)
 764     {
 765
 766       //FILE LOADED OK
 767       ssm = StructureSelectionManager.getStructureSelectionManager();
 768       MCview.PDBfile pdbFile = ssm.setMapping(sequence,chains,pdbentry.getFile(), AppletFormatAdapter.FILE);
 769       ssm.addStructureViewerListener(this);
 770       Vector chains = new Vector();
 771       for(int i=0; i<pdbFile.chains.size(); i++)
 772       {
 773         chains.addElement(((MCview.PDBChain)pdbFile.chains.elementAt(i)).id);
 774       }
 775       setChainMenuItems(chains);
 776
 777       jmolpopup.updateComputedMenus();
 778
 779       if(!loadingFromArchive)
 780       {
 781         viewer.evalStringQuiet(
 782              "select backbone;restrict;cartoon;wireframe off;spacefill off");
 783
 784         colourBySequence(ap);
 785       }
 786       if (fr!=null)
 787         fr.featuresAdded();
 788
 789       loadingFromArchive = false;
 790     }
 791     else
 792       return;
 793   }
 794
 795   public void notifyFrameChanged(int frameNo)
 796   {
 797     boolean isAnimationRunning = (frameNo <= -2);
 798   }
 799
 800   public void notifyScriptStart(String statusMessage, String additionalInfo)
 801   {}
 802
 803   public void sendConsoleEcho(String strEcho)
 804   {
 805     if (scriptWindow != null)
 806       scriptWindow.sendConsoleEcho(strEcho);
 807   }
 808
 809   public void sendConsoleMessage(String strStatus)
 810   {
 811     if (scriptWindow != null)
 812       scriptWindow.sendConsoleMessage(strStatus);
 813   }
 814
 815   public void notifyScriptTermination(String strStatus, int msWalltime)
 816   {
 817     if (scriptWindow != null)
 818       scriptWindow.notifyScriptTermination(strStatus, msWalltime);
 819   }
 820
 821   public void handlePopupMenu(int x, int y)
 822   {
 823     jmolpopup.show(x, y);
 824   }
 825
 826   public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
 827   {
 828     notifyAtomPicked(iatom, strMeasure);
 829   }
 830
 831   public void notifyNewDefaultModeMeasurement(int count, String strInfo)
 832   {}
 833
 834   public void notifyAtomPicked(int atomIndex, String strInfo)
 835   {
 836     Matcher matcher = pattern.matcher(strInfo);
 837     matcher.find();
 838
 839     matcher.group(1);
 840     String resnum = new String(matcher.group(2));
 841     String chainId = matcher.group(3);
 842
 843     String picked = resnum;
 844
 845     if (chainId != null)
 846       picked+=(":"+chainId.substring(1, chainId.length()));
 847
 848     picked+=".CA";
 849
 850
 851     if (!atomsPicked.contains(picked))
 852     {
 853       if(chainId!=null)
 854       viewer.evalString("select "+picked+";label %n %r:%c");
 855     else
 856       viewer.evalString("select "+picked+";label %n %r");
 857       atomsPicked.addElement(picked);
 858     }
 859     else
 860     {
 861       viewer.evalString("select "+picked+";label off");
 862       atomsPicked.removeElement(picked);
 863     }
 864
 865     if (scriptWindow != null)
 866     {
 867       scriptWindow.sendConsoleMessage(strInfo);
 868       scriptWindow.sendConsoleMessage("\n");
 869     }
 870   }
 871
 872   public void notifyAtomHovered(int atomIndex, String strInfo)
 873   {
 874     mouseOverStructure(atomIndex, strInfo);
 875   }
 876
 877   public void sendSyncScript(String script, String appletName)
 878   {}
 879
 880   public void showUrl(String url)
 881   {}
 882
 883   public void showConsole(boolean showConsole)
 884   {
 885     if (scriptWindow == null)
 886       scriptWindow = new ScriptWindow(this);
 887
 888     if(showConsole)
 889     {
 890       if(splitPane==null)
 891       {
 892         splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
 893         splitPane.setTopComponent(renderPanel);
 894         splitPane.setBottomComponent(scriptWindow);
 895         this.getContentPane().add(splitPane, BorderLayout.CENTER);
 896       }
 897
 898       splitPane.setDividerLocation(getHeight()-200);
 899       splitPane.validate();
 900     }
 901     else
 902     {
 903       if (splitPane != null)
 904         splitPane.setVisible(false);
 905
 906       splitPane = null;
 907
 908       this.getContentPane().add(renderPanel, BorderLayout.CENTER);
 909     }
 910
 911     validate();
 912   }
 913
 914   public float functionXY(String functionName, int x, int y)
 915   {
 916     return 0;
 917   }
 918
 919   ///End JmolStatusListener
 920   ///////////////////////////////
 921
 922
 923   class RenderPanel
 924       extends JPanel
 925   {
 926     final Dimension currentSize = new Dimension();
 927     final Rectangle rectClip = new Rectangle();
 928
 929     public void paintComponent(Graphics g)
 930     {
 931       getSize(currentSize);
 932       g.getClipBounds(rectClip);
 933
 934       if (viewer == null)
 935       {
 936         g.setColor(Color.black);
 937         g.fillRect(0, 0, currentSize.width, currentSize.height);
 938         g.setColor(Color.white);
 939         g.setFont(new Font("Verdana", Font.BOLD, 14));
 940         g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
 941       }
 942       else if(fileLoadingError!=null)
 943       {
 944         g.setColor(Color.black);
 945         g.fillRect(0, 0, currentSize.width, currentSize.height);
 946         g.setColor(Color.white);
 947         g.setFont(new Font("Verdana", Font.BOLD, 14));
 948         g.drawString("Error loading file..." + pdbentry.getId(), 20,
 949                      currentSize.height / 2);
 950       }
 951       else
 952       {
 953         viewer.renderScreenImage(g, currentSize, rectClip);
 954       }
 955     }
 956   }
 957
 958 }