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