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