src/jalview/gui/AppJmol.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import java.util.regex.*;
  22 import java.util.*;
  23 import java.awt.*;
  24 import javax.swing.*;
  25 import javax.swing.event.*;
  26 import java.awt.event.*;
  27 import java.io.*;
  28
  29 import jalview.jbgui.GStructureViewer;
  30 import jalview.datamodel.*;
  31 import jalview.gui.*;
  32 import jalview.structure.*;
  33 import jalview.datamodel.PDBEntry;
  34 import jalview.io.*;
  35 import jalview.schemes.*;
  36 import jalview.ws.ebi.EBIFetchClient;
  37
  38 import org.jmol.api.*;
  39 import org.jmol.adapter.smarter.SmarterJmolAdapter;
  40 import org.jmol.popup.*;
  41
  42
  43 public class AppJmol
  44     extends GStructureViewer
  45     implements StructureListener, JmolStatusListener, Runnable
  46
  47 {
  48   JmolViewer viewer;
  49   JmolPopup jmolpopup;
  50   ScriptWindow scriptWindow;
  51   PDBEntry pdbentry;
  52   SequenceI[] sequence;
  53   String [] chains;
  54   StructureSelectionManager ssm;
  55   JSplitPane splitPane;
  56   RenderPanel renderPanel;
  57   AlignmentPanel ap;
  58   String fileLoadingError;
  59   boolean colourBySequence = true;
  60   boolean loadingFromArchive = false;
  61   Vector atomsPicked = new Vector();
  62
  63   public AppJmol(String file, String id,
  64                  SequenceI[] seq,
  65                  AlignmentPanel ap,
  66                  String loadStatus,
  67                  Rectangle bounds)
  68   {
  69     loadingFromArchive = true;
  70     pdbentry = new PDBEntry();
  71     pdbentry.setFile(file);
  72     pdbentry.setId(id);
  73     this.chains = chains;
  74     this.sequence = seq;
  75     this.ap = ap;
  76     this.setBounds(bounds);
  77     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
 134         //Now this AppJmol is mapped to new sequences. We must add them to
 135         // the exisiting array
 136         JInternalFrame [] frames = Desktop.instance.getAllFrames();
 137
 138         for(int i=0; i<frames.length; i++)
 139         {
 140           if(frames[i] instanceof AppJmol)
 141           {
 142            AppJmol topJmol = ((AppJmol)frames[i]);
 143            if(topJmol.pdbentry.getFile().equals(alreadyMapped))
 144            {
 145              topJmol.addSequence(seq);
 146              break;
 147            }
 148           }
 149         }
 150
 151         return;
 152       }
 153     }
 154     ///////////////////////////////////
 155
 156     this.ap = ap;
 157     this.pdbentry = pdbentry;
 158     this.sequence = seq;
 159     this.setSize(400,400);
 160     //jalview.gui.Desktop.addInternalFrame(this, "Jmol View"+(pdbentry.getId()!=null ? "for "+pdbentry.getId()
 161     //          : ""), 400, 400);
 162
 163     if (pdbentry.getFile() != null)
 164     {
 165       initJmol("load \""+pdbentry.getFile()+"\"");
 166     }
 167     else
 168     {
 169       Thread worker = new Thread(this);
 170       worker.start();
 171     }
 172
 173     this.addInternalFrameListener(new InternalFrameAdapter()
 174     {
 175       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
 176       {
 177         closeViewer();
 178       }
 179     });
 180   }
 181
 182
 183   void initJmol(String command)
 184   {
 185     renderPanel = new RenderPanel();
 186
 187     this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
 188
 189     StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +
 190                                           pdbentry.getId());
 191
 192     if (pdbentry.getProperty() != null)
 193     {
 194       if (pdbentry.getProperty().get("method") != null)
 195       {
 196         title.append(" Method: ");
 197         title.append(pdbentry.getProperty().get("method"));
 198       }
 199       if (pdbentry.getProperty().get("chains") != null)
 200       {
 201         title.append(" Chain:");
 202         title.append(pdbentry.getProperty().get("chains"));
 203       }
 204     }
 205
 206     this.setTitle(title.toString());
 207     jalview.gui.Desktop.addInternalFrame(this, title.toString(),
 208                                          getBounds().width,getBounds().height);
 209
 210     viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
 211         new SmarterJmolAdapter());
 212
 213
 214     viewer.setAppletContext("", null, null, "");
 215
 216     viewer.setJmolStatusListener(this);
 217
 218     jmolpopup = JmolPopup.newJmolPopup(viewer);
 219
 220     viewer.evalStringQuiet(command);
 221   }
 222
 223
 224   void setChainMenuItems(Vector chains)
 225   {
 226     chainMenu.removeAll();
 227
 228     JMenuItem menuItem = new JMenuItem("All");
 229     menuItem.addActionListener(new ActionListener()
 230         {
 231           public void actionPerformed(ActionEvent evt)
 232           {
 233             allChainsSelected = true;
 234             for(int i=0; i<chainMenu.getItemCount(); i++)
 235             {
 236               if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
 237                 ( (JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
 238             }
 239             centerViewer();
 240             allChainsSelected = false;
 241           }
 242         });
 243
 244     chainMenu.add(menuItem);
 245
 246     for (int c = 0; c < chains.size(); c++)
 247     {
 248       menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
 249       menuItem.addItemListener(new ItemListener()
 250       {
 251         public void itemStateChanged(ItemEvent evt)
 252         {
 253           if (!allChainsSelected)
 254             centerViewer();
 255         }
 256       });
 257
 258       chainMenu.add(menuItem);
 259     }
 260   }
 261
 262   boolean allChainsSelected = false;
 263   void centerViewer()
 264   {
 265     StringBuffer cmd = new StringBuffer();
 266     for(int i=0; i<chainMenu.getItemCount(); i++)
 267     {
 268       if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
 269       {
 270        JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
 271        if(item.isSelected())
 272          cmd.append(":"+item.getText()+" or ");
 273       }
 274     }
 275
 276     if (cmd.length() > 0)
 277       cmd.setLength(cmd.length() - 4);
 278
 279     viewer.evalStringQuiet("select *;restrict "
 280                       +cmd+";cartoon;center "+cmd);
 281   }
 282
 283   void closeViewer()
 284   {
 285     viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
 286     viewer.evalStringQuiet("zap");
 287     viewer.setJmolStatusListener(null);
 288     viewer = null;
 289
 290     //We'll need to find out what other
 291     // listeners need to be shut down in Jmol
 292     StructureSelectionManager
 293         .getStructureSelectionManager()
 294         .removeStructureViewerListener(this, pdbentry.getFile());
 295   }
 296
 297   public void run()
 298   {
 299     try
 300     {
 301       EBIFetchClient ebi = new EBIFetchClient();
 302       String query = "pdb:" + pdbentry.getId();
 303       pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
 304                        .getAbsolutePath());
 305       initJmol("load "+pdbentry.getFile());
 306     }
 307     catch (Exception ex)
 308     {
 309       ex.printStackTrace();
 310     }
 311   }
 312
 313   public void pdbFile_actionPerformed(ActionEvent actionEvent)
 314   {
 315     JalviewFileChooser chooser = new JalviewFileChooser(
 316         jalview.bin.Cache.getProperty(
 317             "LAST_DIRECTORY"));
 318
 319     chooser.setFileView(new JalviewFileView());
 320     chooser.setDialogTitle("Save PDB File");
 321     chooser.setToolTipText("Save");
 322
 323     int value = chooser.showSaveDialog(this);
 324
 325     if (value == JalviewFileChooser.APPROVE_OPTION)
 326     {
 327       try
 328       {
 329         BufferedReader in = new BufferedReader(new FileReader(pdbentry.getFile()));
 330         File outFile = chooser.getSelectedFile();
 331
 332         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
 333         String data;
 334         while ( (data = in.readLine()) != null)
 335         {
 336           if (
 337               ! (data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
 338               )
 339           {
 340             out.println(data);
 341           }
 342         }
 343         out.close();
 344       }
 345       catch (Exception ex)
 346       {
 347         ex.printStackTrace();
 348       }
 349     }
 350   }
 351
 352   public void viewMapping_actionPerformed(ActionEvent actionEvent)
 353   {
 354     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
 355     jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550,
 356                                          600);
 357     cap.setText(
 358         StructureSelectionManager.getStructureSelectionManager().printMapping(
 359             pdbentry.getFile())
 360         );
 361   }
 362
 363   /**
 364    * DOCUMENT ME!
 365    *
 366    * @param e DOCUMENT ME!
 367    */
 368   public void eps_actionPerformed(ActionEvent e)
 369   {
 370     makePDBImage(jalview.util.ImageMaker.EPS);
 371   }
 372
 373   /**
 374    * DOCUMENT ME!
 375    *
 376    * @param e DOCUMENT ME!
 377    */
 378   public void png_actionPerformed(ActionEvent e)
 379   {
 380     makePDBImage(jalview.util.ImageMaker.PNG);
 381   }
 382
 383   void makePDBImage(int type)
 384   {
 385     int width = getWidth();
 386     int height = getHeight();
 387
 388     jalview.util.ImageMaker im;
 389
 390     if (type == jalview.util.ImageMaker.PNG)
 391     {
 392       im = new jalview.util.ImageMaker(this,
 393                                        jalview.util.ImageMaker.PNG,
 394                                        "Make PNG image from view",
 395                                        width, height,
 396                                        null, null);
 397     }
 398     else
 399     {
 400       im = new jalview.util.ImageMaker(this,
 401                                        jalview.util.ImageMaker.EPS,
 402                                        "Make EPS file from view",
 403                                        width, height,
 404                                        null, this.getTitle());
 405     }
 406
 407     if (im.getGraphics() != null)
 408     {
 409       Rectangle rect = new Rectangle(width, height);
 410       viewer.renderScreenImage(im.getGraphics(),
 411                                rect.getSize(), rect);
 412       im.writeImage();
 413     }
 414   }
 415
 416
 417   public void seqColour_actionPerformed(ActionEvent actionEvent)
 418   {
 419     lastCommand = null;
 420     colourBySequence = seqColour.isSelected();
 421     colourBySequence(ap.alignFrame.alignPanel);
 422   }
 423
 424   public void chainColour_actionPerformed(ActionEvent actionEvent)
 425   {
 426     colourBySequence = false;
 427     seqColour.setSelected(false);
 428     viewer.evalStringQuiet("select *;color chain");
 429   }
 430
 431   public void chargeColour_actionPerformed(ActionEvent actionEvent)
 432   {
 433     colourBySequence = false;
 434     seqColour.setSelected(false);
 435     viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
 436                       +"select LYS,ARG;color blue;select CYS;color yellow");
 437   }
 438
 439   public void zappoColour_actionPerformed(ActionEvent actionEvent)
 440   {
 441     setJalviewColourScheme(new ZappoColourScheme());
 442   }
 443
 444   public void taylorColour_actionPerformed(ActionEvent actionEvent)
 445   {
 446     setJalviewColourScheme(new TaylorColourScheme());
 447   }
 448
 449   public void hydroColour_actionPerformed(ActionEvent actionEvent)
 450   {
 451     setJalviewColourScheme(new HydrophobicColourScheme());
 452   }
 453
 454   public void helixColour_actionPerformed(ActionEvent actionEvent)
 455   {
 456     setJalviewColourScheme(new HelixColourScheme());
 457   }
 458
 459   public void strandColour_actionPerformed(ActionEvent actionEvent)
 460   {
 461     setJalviewColourScheme(new StrandColourScheme());
 462   }
 463
 464   public void turnColour_actionPerformed(ActionEvent actionEvent)
 465   {
 466     setJalviewColourScheme(new TurnColourScheme());
 467   }
 468
 469   public void buriedColour_actionPerformed(ActionEvent actionEvent)
 470   {
 471     setJalviewColourScheme(new BuriedColourScheme());
 472   }
 473
 474   public void setJalviewColourScheme(ColourSchemeI cs)
 475   {
 476     colourBySequence = false;
 477     seqColour.setSelected(false);
 478
 479     if(cs==null)
 480       return;
 481
 482     String res;
 483     int index;
 484     Color col;
 485
 486     Enumeration en = ResidueProperties.aa3Hash.keys();
 487     StringBuffer command = new StringBuffer("select *;color white;");
 488     while(en.hasMoreElements())
 489     {
 490       res = en.nextElement().toString();
 491       index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
 492       if(index>20)
 493         continue;
 494
 495       col = cs.findColour(ResidueProperties.aa[index].charAt(0));
 496
 497       command.append("select "+res+";color["
 498                         + col.getRed() + ","
 499                         + col.getGreen() + ","
 500                         + col.getBlue() + "];");
 501     }
 502
 503     viewer.evalStringQuiet(command.toString());
 504   }
 505
 506   public void userColour_actionPerformed(ActionEvent actionEvent)
 507   {
 508     new UserDefinedColours(this, null);
 509   }
 510
 511   public void backGround_actionPerformed(ActionEvent actionEvent)
 512   {
 513     java.awt.Color col = JColorChooser.showDialog(this,
 514                                                   "Select Background Colour",
 515                                                   null);
 516
 517     if (col != null)
 518     {
 519       viewer.evalStringQuiet("background ["
 520                         + col.getRed() + ","
 521                         + col.getGreen() + ","
 522                         + col.getBlue() + "];");
 523     }
 524   }
 525
 526
 527   public void jmolHelp_actionPerformed(ActionEvent actionEvent)
 528   {
 529        try{
 530          jalview.util.BrowserLauncher.openURL(
 531              "http://jmol.sourceforge.net/docs/JmolUserGuide/");
 532        }catch(Exception ex){}
 533    }
 534
 535
 536   //////////////////////////////////
 537   ///StructureListener
 538   public String getPdbFile()
 539   {
 540     return pdbentry.getFile();
 541   }
 542
 543   Pattern pattern = Pattern.compile(
 544       "\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?"
 545       );
 546
 547   String lastMessage;
 548   public void mouseOverStructure(int atomIndex, String strInfo)
 549   {
 550     Matcher matcher = pattern.matcher(strInfo);
 551     matcher.find();
 552     matcher.group(1);
 553     int pdbResNum = Integer.parseInt(matcher.group(2));
 554     String chainId = matcher.group(3);
 555
 556     if (chainId != null)
 557       chainId = chainId.substring(1, chainId.length());
 558     else
 559     {
 560       chainId = " ";
 561     }
 562
 563     if (lastMessage == null || !lastMessage.equals(strInfo))
 564     {
 565       ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
 566     }
 567     lastMessage = strInfo;
 568   }
 569
 570   StringBuffer resetLastRes = new StringBuffer();
 571   StringBuffer eval = new StringBuffer();
 572
 573   public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
 574   {
 575     if (!pdbfile.equals(pdbentry.getFile()))
 576       return;
 577
 578     if (resetLastRes.length() > 0)
 579     {
 580       viewer.evalStringQuiet(resetLastRes.toString());
 581     }
 582
 583     eval.setLength(0);
 584     eval.append("select " + pdbResNum);
 585
 586     resetLastRes.setLength(0);
 587     resetLastRes.append("select " + pdbResNum);
 588
 589     if (!chain.equals(" "))
 590     {
 591       eval.append(":" + chain);
 592       resetLastRes.append(":" + chain);
 593     }
 594
 595     eval.append(";wireframe 100;"+eval.toString()+".CA;");
 596
 597     resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
 598
 599     eval.append("spacefill 200;select none");
 600
 601     viewer.evalStringQuiet(eval.toString());
 602   }
 603
 604   public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
 605   {
 606     if (!pdbfile.equals(pdbentry.getFile()))
 607       return null;
 608
 609     return new Color(viewer.getAtomArgb(atomIndex));
 610   }
 611
 612   public void updateColours(Object source)
 613   {
 614     colourBySequence( (AlignmentPanel) source);
 615   }
 616
 617
 618 //End StructureListener
 619 ////////////////////////////
 620
 621   String lastCommand;
 622   FeatureRenderer fr=null;
 623   public void colourBySequence(AlignmentPanel sourceap)
 624   {
 625     this.ap = sourceap;
 626
 627     if(!colourBySequence || ap.alignFrame.getCurrentView()!=ap.av)
 628       return;
 629
 630     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 631
 632     if (mapping.length < 1)
 633      return;
 634
 635
 636     SequenceRenderer sr = new SequenceRenderer(ap.av);
 637
 638     boolean showFeatures = false;
 639
 640     if (ap.av.showSequenceFeatures)
 641     {
 642       showFeatures = true;
 643       if (fr == null)
 644       {
 645         fr = new jalview.gui.FeatureRenderer(ap);
 646       }
 647
 648       fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
 649     }
 650
 651     StringBuffer command = new StringBuffer();
 652
 653     int lastPos = -1;
 654     for (int sp,s = 0; s < sequence.length; s++)
 655     {
 656       for (int m = 0; m < mapping.length; m++)
 657       {
 658         if (mapping[m].getSequence() == sequence[s]
 659             && (sp=ap.av.alignment.findIndex(sequence[s]))>-1)
 660         {
 661           SequenceI asp = ap.av.alignment.getSequenceAt(sp);
 662           for (int r = 0; r < asp.getLength(); r++)
 663           {
 664             // No mapping to gaps in sequence.
 665             if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
 666             {
 667               continue;
 668             }
 669             int pos = mapping[m].getPDBResNum(
 670                     asp.findPosition(r));
 671
 672             if (pos < 1 || pos==lastPos)
 673               continue;
 674
 675             lastPos = pos;
 676
 677             Color col = sr.getResidueBoxColour(asp, r);
 678
 679             if (showFeatures)
 680               col = fr.findFeatureColour(col, asp, r);
 681
 682             if (command.toString().endsWith(":" + mapping[m].getChain()+
 683                                             ";color["
 684                                             + col.getRed() + ","
 685                                             + col.getGreen() + ","
 686                                             + col.getBlue() + "]"))
 687             {
 688               command = condenseCommand(command, pos);
 689               continue;
 690             }
 691
 692             command.append(";select " + pos);
 693
 694             if (!mapping[m].getChain().equals(" "))
 695             {
 696               command.append(":" + mapping[m].getChain());
 697             }
 698
 699             command.append(";color["
 700                              + col.getRed() + ","
 701                              + col.getGreen() + ","
 702                              + col.getBlue() + "]");
 703
 704           }
 705           break;
 706         }
 707       }
 708     }
 709
 710     if (lastCommand == null || !lastCommand.equals(command.toString()))
 711     {
 712       viewer.evalStringQuiet(command.toString());
 713     }
 714     lastCommand = command.toString();
 715   }
 716
 717   StringBuffer condenseCommand(StringBuffer command, int pos)
 718   {
 719     StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));
 720
 721     command.delete(0, sb.length());
 722
 723     String start;
 724
 725     if (command.indexOf("-") > -1)
 726     {
 727       start = command.substring(0,command.indexOf("-"));
 728     }
 729     else
 730     {
 731       start = command.substring(0, command.indexOf(":"));
 732     }
 733
 734     sb.append(start+"-"+pos+command.substring(command.indexOf(":")));
 735
 736     return sb;
 737   }
 738
 739   /////////////////////////////////
 740   //JmolStatusListener
 741
 742   public String eval(String strEval)
 743   {
 744    // System.out.println(strEval);
 745    //"# 'eval' is implemented only for the applet.";
 746     return null;
 747   }
 748
 749   public void createImage(String file, String type, int quality)
 750   {
 751     System.out.println("JMOL CREATE IMAGE");
 752   }
 753
 754   public void setCallbackFunction(String callbackType,
 755                                   String callbackFunction)
 756   {}
 757
 758   public void notifyFileLoaded(String fullPathName, String fileName,
 759                                String modelName, Object clientFile,
 760                                String errorMsg)
 761   {
 762     if(errorMsg!=null)
 763     {
 764       fileLoadingError = errorMsg;
 765       repaint();
 766       return;
 767     }
 768
 769     fileLoadingError = null;
 770
 771     if (fileName != null)
 772     {
 773
 774       //FILE LOADED OK
 775       ssm = StructureSelectionManager.getStructureSelectionManager();
 776       MCview.PDBfile pdbFile = ssm.setMapping(sequence,chains,pdbentry.getFile(), AppletFormatAdapter.FILE);
 777       ssm.addStructureViewerListener(this);
 778       Vector chains = new Vector();
 779       for(int i=0; i<pdbFile.chains.size(); i++)
 780       {
 781         chains.addElement(((MCview.PDBChain)pdbFile.chains.elementAt(i)).id);
 782       }
 783       setChainMenuItems(chains);
 784
 785       jmolpopup.updateComputedMenus();
 786
 787       if(!loadingFromArchive)
 788       {
 789         viewer.evalStringQuiet(
 790              "select backbone;restrict;cartoon;wireframe off;spacefill off");
 791
 792         colourBySequence(ap);
 793       }
 794       if (fr!=null)
 795         fr.featuresAdded();
 796
 797       loadingFromArchive = false;
 798     }
 799     else
 800       return;
 801   }
 802
 803   public void notifyFrameChanged(int frameNo)
 804   {
 805     boolean isAnimationRunning = (frameNo <= -2);
 806   }
 807
 808   public void notifyScriptStart(String statusMessage, String additionalInfo)
 809   {}
 810
 811   public void sendConsoleEcho(String strEcho)
 812   {
 813     if (scriptWindow != null)
 814       scriptWindow.sendConsoleEcho(strEcho);
 815   }
 816
 817   public void sendConsoleMessage(String strStatus)
 818   {
 819     if (scriptWindow != null)
 820       scriptWindow.sendConsoleMessage(strStatus);
 821   }
 822
 823   public void notifyScriptTermination(String strStatus, int msWalltime)
 824   {
 825     if (scriptWindow != null)
 826       scriptWindow.notifyScriptTermination(strStatus, msWalltime);
 827   }
 828
 829   public void handlePopupMenu(int x, int y)
 830   {
 831     jmolpopup.show(x, y);
 832   }
 833
 834   public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
 835   {
 836     notifyAtomPicked(iatom, strMeasure);
 837   }
 838
 839   public void notifyNewDefaultModeMeasurement(int count, String strInfo)
 840   {}
 841
 842   public void notifyAtomPicked(int atomIndex, String strInfo)
 843   {
 844     Matcher matcher = pattern.matcher(strInfo);
 845     matcher.find();
 846
 847     matcher.group(1);
 848     String resnum = new String(matcher.group(2));
 849     String chainId = matcher.group(3);
 850
 851     String picked = resnum;
 852
 853     if (chainId != null)
 854       picked+=(":"+chainId.substring(1, chainId.length()));
 855
 856     picked+=".CA";
 857
 858
 859     if (!atomsPicked.contains(picked))
 860     {
 861       if(chainId!=null)
 862       viewer.evalString("select "+picked+";label %n %r:%c");
 863     else
 864       viewer.evalString("select "+picked+";label %n %r");
 865       atomsPicked.addElement(picked);
 866     }
 867     else
 868     {
 869       viewer.evalString("select "+picked+";label off");
 870       atomsPicked.removeElement(picked);
 871     }
 872
 873     if (scriptWindow != null)
 874     {
 875       scriptWindow.sendConsoleMessage(strInfo);
 876       scriptWindow.sendConsoleMessage("\n");
 877     }
 878   }
 879
 880   public void notifyAtomHovered(int atomIndex, String strInfo)
 881   {
 882     mouseOverStructure(atomIndex, strInfo);
 883   }
 884
 885   public void sendSyncScript(String script, String appletName)
 886   {}
 887
 888   public void showUrl(String url)
 889   {}
 890
 891   public void showConsole(boolean showConsole)
 892   {
 893     if (scriptWindow == null)
 894       scriptWindow = new ScriptWindow(this);
 895
 896     if(showConsole)
 897     {
 898       if(splitPane==null)
 899       {
 900         splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
 901         splitPane.setTopComponent(renderPanel);
 902         splitPane.setBottomComponent(scriptWindow);
 903         this.getContentPane().add(splitPane, BorderLayout.CENTER);
 904       }
 905
 906       splitPane.setDividerLocation(getHeight()-200);
 907       splitPane.validate();
 908     }
 909     else
 910     {
 911       if (splitPane != null)
 912         splitPane.setVisible(false);
 913
 914       splitPane = null;
 915
 916       this.getContentPane().add(renderPanel, BorderLayout.CENTER);
 917     }
 918
 919     validate();
 920   }
 921
 922   public float functionXY(String functionName, int x, int y)
 923   {
 924     return 0;
 925   }
 926
 927   ///End JmolStatusListener
 928   ///////////////////////////////
 929
 930
 931   class RenderPanel
 932       extends JPanel
 933   {
 934     final Dimension currentSize = new Dimension();
 935     final Rectangle rectClip = new Rectangle();
 936
 937     public void paintComponent(Graphics g)
 938     {
 939       getSize(currentSize);
 940       g.getClipBounds(rectClip);
 941
 942       if (viewer == null)
 943       {
 944         g.setColor(Color.black);
 945         g.fillRect(0, 0, currentSize.width, currentSize.height);
 946         g.setColor(Color.white);
 947         g.setFont(new Font("Verdana", Font.BOLD, 14));
 948         g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
 949       }
 950       else if(fileLoadingError!=null)
 951       {
 952         g.setColor(Color.black);
 953         g.fillRect(0, 0, currentSize.width, currentSize.height);
 954         g.setColor(Color.white);
 955         g.setFont(new Font("Verdana", Font.BOLD, 14));
 956         g.drawString("Error loading file..." + pdbentry.getId(), 20,
 957                      currentSize.height / 2);
 958       }
 959       else
 960       {
 961         viewer.renderScreenImage(g, currentSize, rectClip);
 962       }
 963     }
 964   }
 965
 966 }