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