src/jalview/gui/AppJMol.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import java.util.regex.*;
  22 import java.util.*;
  23 import java.awt.*;
  24 import javax.swing.*;
  25 import javax.swing.event.*;
  26 import java.awt.event.*;
  27 import java.io.*;
  28
  29 import jalview.jbgui.GStructureViewer;
  30 import jalview.datamodel.*;
  31 import jalview.gui.*;
  32 import jalview.structure.*;
  33 import jalview.datamodel.PDBEntry;
  34 import jalview.io.*;
  35 import jalview.schemes.*;
  36
  37 import org.jmol.api.*;
  38 import org.jmol.adapter.smarter.SmarterJmolAdapter;
  39 import org.jmol.popup.*;
  40
  41
  42 public class AppJMol
  43     extends GStructureViewer
  44     implements StructureListener, JmolStatusListener, Runnable
  45
  46 {
  47   JmolViewer viewer;
  48   JmolPopup jmolpopup;
  49   ScriptWindow scriptWindow;
  50   PDBEntry pdbentry;
  51   SequenceI[] sequence;
  52   String [] chains;
  53   StructureSelectionManager ssm;
  54   JSplitPane splitPane;
  55   RenderPanel renderPanel;
  56   AlignmentPanel ap;
  57   String fileLoadingError;
  58   boolean colourBySequence = true;
  59   boolean loadingFromArchive = false;
  60   Vector atomsPicked = new Vector();
  61
  62   public AppJMol(String file, String id,
  63                  SequenceI[] seq,
  64                  AlignmentPanel ap,
  65                  String loadStatus,
  66                  Rectangle bounds)
  67   {
  68     loadingFromArchive = true;
  69     pdbentry = new PDBEntry();
  70     pdbentry.setFile(file);
  71     pdbentry.setId(id);
  72     this.chains = chains;
  73     this.sequence = seq;
  74     this.ap = ap;
  75     this.setBounds(bounds);
  76
  77     colourBySequence = false;
  78     seqColour.setSelected(false);
  79
  80     jalview.gui.Desktop.addInternalFrame(this, "Loading File",
  81                                          bounds.width,bounds.height);
  82
  83     initJmol(loadStatus);
  84
  85     this.addInternalFrameListener(new InternalFrameAdapter()
  86     {
  87       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
  88       {
  89         closeViewer();
  90       }
  91     });
  92   }
  93
  94 public synchronized void addSequence(SequenceI [] seq)
  95    {
  96     Vector v = new Vector();
  97      for(int i=0; i<sequence.length; i++)
  98        v.addElement(sequence[i]);
  99
 100      for(int i=0; i<seq.length; i++)
 101       if(!v.contains(seq[i]))
 102           v.addElement(seq[i]);
 103
 104      SequenceI [] tmp = new SequenceI[v.size()];
 105      v.copyInto(tmp);
 106      sequence = tmp;
 107    }
 108
 109   public AppJMol(PDBEntry pdbentry, SequenceI[] seq, String [] chains, AlignmentPanel ap)
 110   {
 111     //////////////////////////////////
 112     //Is the pdb file already loaded?
 113     String alreadyMapped = StructureSelectionManager
 114         .getStructureSelectionManager()
 115         .alreadyMappedToFile(pdbentry.getId());
 116
 117     if (alreadyMapped != null)
 118     {
 119       int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
 120           pdbentry.getId() + " is already displayed."
 121           + "\nDo you want to map sequences to the visible structure?",
 122           "Map Sequences to Visible Window: " + pdbentry.getId(),
 123           JOptionPane.YES_NO_OPTION);
 124
 125       if (option == JOptionPane.YES_OPTION)
 126       {
 127         StructureSelectionManager.getStructureSelectionManager()
 128             .setMapping(seq, chains, alreadyMapped, AppletFormatAdapter.FILE);
 129         if (ap.seqPanel.seqCanvas.fr!=null) {
 130           ap.seqPanel.seqCanvas.fr.featuresAdded();
 131           ap.paintAlignment(true);
 132         }
 133         return;
 134       }
 135     }
 136     ///////////////////////////////////
 137
 138     this.ap = ap;
 139     this.pdbentry = pdbentry;
 140     this.sequence = seq;
 141
 142     jalview.gui.Desktop.addInternalFrame(this, "Loading File", 400, 400);
 143
 144     if (pdbentry.getFile() != null)
 145     {
 146       initJmol("load \""+pdbentry.getFile()+"\"");
 147     }
 148     else
 149     {
 150       Thread worker = new Thread(this);
 151       worker.start();
 152     }
 153
 154     this.addInternalFrameListener(new InternalFrameAdapter()
 155     {
 156       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
 157       {
 158         closeViewer();
 159       }
 160     });
 161   }
 162
 163
 164   void initJmol(String command)
 165   {
 166     renderPanel = new RenderPanel();
 167
 168     this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
 169
 170     StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +
 171                                           pdbentry.getId());
 172
 173     if (pdbentry.getProperty() != null)
 174     {
 175       if (pdbentry.getProperty().get("method") != null)
 176       {
 177         title.append(" Method: ");
 178         title.append(pdbentry.getProperty().get("method"));
 179       }
 180       if (pdbentry.getProperty().get("chains") != null)
 181       {
 182         title.append(" Chain:");
 183         title.append(pdbentry.getProperty().get("chains"));
 184       }
 185     }
 186
 187     this.setTitle(title.toString());
 188
 189     viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
 190         new SmarterJmolAdapter());
 191
 192
 193     viewer.setAppletContext("", null, null, "");
 194
 195     viewer.setJmolStatusListener(this);
 196
 197     jmolpopup = JmolPopup.newJmolPopup(viewer);
 198
 199     viewer.evalStringQuiet(command);
 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 Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
 586   {
 587     if (!pdbfile.equals(pdbentry.getFile()))
 588       return null;
 589
 590     return new Color(viewer.getAtomArgb(atomIndex));
 591   }
 592
 593   public void updateColours(Object source)
 594   {
 595     colourBySequence( (AlignmentPanel) source);
 596   }
 597
 598
 599 //End StructureListener
 600 ////////////////////////////
 601
 602   FeatureRenderer fr=null;
 603   public void colourBySequence(AlignmentPanel ap)
 604   {
 605     if(!colourBySequence)
 606       return;
 607
 608
 609     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 610
 611     if (mapping.length < 1)
 612       return;
 613
 614     SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();
 615
 616     boolean showFeatures = false;
 617
 618     if (ap.av.showSequenceFeatures)
 619     {
 620       showFeatures = true;
 621       if (fr == null)
 622       {
 623         fr = new jalview.gui.FeatureRenderer(ap);
 624       }
 625
 626       fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
 627     }
 628
 629     StringBuffer command = new StringBuffer();
 630
 631     int lastPos = -1;
 632     for (int s = 0; s < sequence.length; s++)
 633     {
 634       for (int m = 0; m < mapping.length; m++)
 635       {
 636         if (mapping[m].getSequence() == sequence[s]
 637             && ap.av.alignment.findIndex(sequence[s])>-1)
 638         {
 639           for (int r = 0; r < sequence[s].getLength(); r++)
 640           {
 641             int pos = mapping[m].getPDBResNum(
 642                 sequence[s].findPosition(r));
 643
 644             if (pos < 1 || pos==lastPos)
 645               continue;
 646
 647             lastPos = pos;
 648
 649             Color col = sr.getResidueBoxColour(sequence[s], r);
 650
 651             if (showFeatures)
 652               col = fr.findFeatureColour(col, sequence[s], r);
 653
 654             if (command.toString().endsWith(":" + mapping[m].getChain()+
 655                                             ";color["
 656                                             + col.getRed() + ","
 657                                             + col.getGreen() + ","
 658                                             + col.getBlue() + "]"))
 659             {
 660               command = condenseCommand(command, pos);
 661               continue;
 662             }
 663
 664             command.append(";select " + pos);
 665
 666             if (!mapping[m].getChain().equals(" "))
 667             {
 668               command.append(":" + mapping[m].getChain());
 669             }
 670
 671             command.append(";color["
 672                              + col.getRed() + ","
 673                              + col.getGreen() + ","
 674                              + col.getBlue() + "]");
 675
 676           }
 677           break;
 678         }
 679       }
 680     }
 681
 682     viewer.evalStringQuiet(command.toString());
 683   }
 684
 685   StringBuffer condenseCommand(StringBuffer command, int pos)
 686   {
 687     StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));
 688
 689     command.delete(0, sb.length());
 690
 691     String start;
 692
 693     if (command.indexOf("-") > -1)
 694     {
 695       start = command.substring(0,command.indexOf("-"));
 696     }
 697     else
 698     {
 699       start = command.substring(0, command.indexOf(":"));
 700     }
 701
 702     sb.append(start+"-"+pos+command.substring(command.indexOf(":")));
 703
 704     return sb;
 705   }
 706
 707   /////////////////////////////////
 708   //JmolStatusListener
 709
 710   public String eval(String strEval)
 711   {
 712    // System.out.println(strEval);
 713    //"# 'eval' is implemented only for the applet.";
 714     return null;
 715   }
 716
 717   public void createImage(String file, String type, int quality)
 718   {
 719     System.out.println("JMOL CREATE IMAGE");
 720   }
 721
 722   public void setCallbackFunction(String callbackType,
 723                                   String callbackFunction)
 724   {}
 725
 726   public void notifyFileLoaded(String fullPathName, String fileName,
 727                                String modelName, Object clientFile,
 728                                String errorMsg)
 729   {
 730     if(errorMsg!=null)
 731     {
 732       fileLoadingError = errorMsg;
 733       repaint();
 734       return;
 735     }
 736
 737     fileLoadingError = null;
 738
 739     if (fileName != null)
 740     {
 741
 742       //FILE LOADED OK
 743       ssm = StructureSelectionManager.getStructureSelectionManager();
 744       MCview.PDBfile pdbFile = ssm.setMapping(sequence,chains,pdbentry.getFile(), AppletFormatAdapter.FILE);
 745       ssm.addStructureViewerListener(this);
 746       Vector chains = new Vector();
 747       for(int i=0; i<pdbFile.chains.size(); i++)
 748       {
 749         chains.addElement(((MCview.PDBChain)pdbFile.chains.elementAt(i)).id);
 750       }
 751       setChainMenuItems(chains);
 752
 753       jmolpopup.updateComputedMenus();
 754
 755       if(!loadingFromArchive)
 756       {
 757         viewer.evalStringQuiet(
 758              "select backbone;restrict;cartoon;wireframe off;spacefill off");
 759
 760         colourBySequence(ap);
 761       }
 762       if (fr!=null)
 763         fr.featuresAdded();
 764
 765       loadingFromArchive = false;
 766     }
 767     else
 768       return;
 769   }
 770
 771   public void notifyFrameChanged(int frameNo)
 772   {
 773     boolean isAnimationRunning = (frameNo <= -2);
 774   }
 775
 776   public void notifyScriptStart(String statusMessage, String additionalInfo)
 777   {}
 778
 779   public void sendConsoleEcho(String strEcho)
 780   {
 781     if (scriptWindow != null)
 782       scriptWindow.sendConsoleEcho(strEcho);
 783   }
 784
 785   public void sendConsoleMessage(String strStatus)
 786   {
 787     if (scriptWindow != null)
 788       scriptWindow.sendConsoleMessage(strStatus);
 789   }
 790
 791   public void notifyScriptTermination(String strStatus, int msWalltime)
 792   {
 793     if (scriptWindow != null)
 794       scriptWindow.notifyScriptTermination(strStatus, msWalltime);
 795   }
 796
 797   public void handlePopupMenu(int x, int y)
 798   {
 799     jmolpopup.show(x, y);
 800   }
 801
 802   public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
 803   {
 804     notifyAtomPicked(iatom, strMeasure);
 805   }
 806
 807   public void notifyNewDefaultModeMeasurement(int count, String strInfo)
 808   {}
 809
 810   public void notifyAtomPicked(int atomIndex, String strInfo)
 811   {
 812     Matcher matcher = pattern.matcher(strInfo);
 813     matcher.find();
 814
 815     matcher.group(1);
 816     String resnum = new String(matcher.group(2));
 817     String chainId = matcher.group(3);
 818
 819     String picked = resnum;
 820
 821     if (chainId != null)
 822       picked+=(":"+chainId.substring(1, chainId.length()));
 823
 824     picked+=".C";
 825
 826     if (!atomsPicked.contains(picked))
 827     {
 828       if(chainId!=null)
 829       viewer.evalString("select "+picked+";label %n %r:%c");
 830     else
 831       viewer.evalString("select "+picked+";label %n %r");
 832       atomsPicked.addElement(picked);
 833     }
 834     else
 835     {
 836       viewer.evalString("select "+picked+";label off");
 837       atomsPicked.removeElement(picked);
 838     }
 839
 840     if (scriptWindow != null)
 841     {
 842       scriptWindow.sendConsoleMessage(strInfo);
 843       scriptWindow.sendConsoleMessage("\n");
 844     }
 845   }
 846
 847   public void notifyAtomHovered(int atomIndex, String strInfo)
 848   {
 849     mouseOverStructure(atomIndex, strInfo);
 850   }
 851
 852   public void sendSyncScript(String script, String appletName)
 853   {}
 854
 855   public void showUrl(String url)
 856   {}
 857
 858   public void showConsole(boolean showConsole)
 859   {
 860     if (scriptWindow == null)
 861       scriptWindow = new ScriptWindow(this);
 862
 863     if(showConsole)
 864     {
 865       if(splitPane==null)
 866       {
 867         splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
 868         splitPane.setTopComponent(renderPanel);
 869         splitPane.setBottomComponent(scriptWindow);
 870         this.getContentPane().add(splitPane, BorderLayout.CENTER);
 871       }
 872
 873       splitPane.setDividerLocation(getHeight()-200);
 874       splitPane.validate();
 875     }
 876     else
 877     {
 878       if (splitPane != null)
 879         splitPane.setVisible(false);
 880
 881       splitPane = null;
 882
 883       this.getContentPane().add(renderPanel, BorderLayout.CENTER);
 884     }
 885
 886     validate();
 887   }
 888
 889   public float functionXY(String functionName, int x, int y)
 890   {
 891     return 0;
 892   }
 893
 894   ///End JmolStatusListener
 895   ///////////////////////////////
 896
 897
 898   class RenderPanel
 899       extends JPanel
 900   {
 901     final Dimension currentSize = new Dimension();
 902     final Rectangle rectClip = new Rectangle();
 903
 904     public void paintComponent(Graphics g)
 905     {
 906       getSize(currentSize);
 907       g.getClipBounds(rectClip);
 908
 909       if (viewer == 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("Retrieving PDB data....", 20, currentSize.height / 2);
 916       }
 917       else if(fileLoadingError!=null)
 918       {
 919         g.setColor(Color.black);
 920         g.fillRect(0, 0, currentSize.width, currentSize.height);
 921         g.setColor(Color.white);
 922         g.setFont(new Font("Verdana", Font.BOLD, 14));
 923         g.drawString("Error loading file..." + pdbentry.getId(), 20,
 924                      currentSize.height / 2);
 925       }
 926       else
 927       {
 928         viewer.renderScreenImage(g, currentSize, rectClip);
 929       }
 930     }
 931   }
 932
 933 }