src/jalview/gui/StructureChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21
  22 package jalview.gui;
  23
  24 import jalview.api.structures.JalviewStructureDisplayI;
  25 import jalview.bin.Cache;
  26 import jalview.bin.Jalview;
  27 import jalview.datamodel.DBRefEntry;
  28 import jalview.datamodel.DBRefSource;
  29 import jalview.datamodel.PDBEntry;
  30 import jalview.datamodel.SequenceI;
  31 import jalview.fts.api.FTSData;
  32 import jalview.fts.api.FTSDataColumnI;
  33 import jalview.fts.api.FTSRestClientI;
  34 import jalview.fts.core.FTSRestRequest;
  35 import jalview.fts.core.FTSRestResponse;
  36 import jalview.fts.service.pdb.PDBFTSRestClient;
  37 import jalview.io.DataSourceType;
  38 import jalview.jbgui.GStructureChooser;
  39 import jalview.structure.StructureMapping;
  40 import jalview.structure.StructureSelectionManager;
  41 import jalview.util.MessageManager;
  42 import jalview.ws.DBRefFetcher;
  43 import jalview.ws.sifts.SiftsSettings;
  44
  45 import java.awt.event.ItemEvent;
  46 import java.util.ArrayList;
  47 import java.util.Collection;
  48 import java.util.HashSet;
  49 import java.util.LinkedHashSet;
  50 import java.util.List;
  51 import java.util.Objects;
  52 import java.util.Set;
  53 import java.util.Vector;
  54
  55 import javax.swing.JCheckBox;
  56 import javax.swing.JComboBox;
  57 import javax.swing.JLabel;
  58 import javax.swing.JTable;
  59 import javax.swing.SwingUtilities;
  60 import javax.swing.table.AbstractTableModel;
  61
  62 /**
  63  * Provides the behaviors for the Structure chooser Panel
  64  *
  65  * @author tcnofoegbu
  66  *
  67  */
  68 @SuppressWarnings("serial")
  69 public class StructureChooser extends GStructureChooser
  70         implements IProgressIndicator
  71 {
  72   private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
  73
  74   private static int MAX_QLENGTH = 7820;
  75
  76   private SequenceI selectedSequence;
  77
  78   private SequenceI[] selectedSequences;
  79
  80   private IProgressIndicator progressIndicator;
  81
  82   private Collection<FTSData> discoveredStructuresSet;
  83
  84   private FTSRestRequest lastPdbRequest;
  85
  86   private FTSRestClientI pdbRestCleint;
  87
  88   private String selectedPdbFileName;
  89
  90   private boolean isValidPBDEntry;
  91
  92   private boolean cachedPDBExists;
  93
  94   private static StructureViewer lastTargetedView = null;
  95
  96   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
  97           AlignmentPanel ap)
  98   {
  99     this.ap = ap;
 100     this.selectedSequence = selectedSeq;
 101     this.selectedSequences = selectedSeqs;
 102     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
 103     init();
 104   }
 105
 106   /**
 107    * Initializes parameters used by the Structure Chooser Panel
 108    */
 109   protected void init()
 110   {
 111     if (!Jalview.isHeadlessMode())
 112     {
 113       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 114     }
 115
 116     chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
 117
 118     // ensure a filter option is in force for search
 119     populateFilterComboBox(true, cachedPDBExists);
 120     Thread discoverPDBStructuresThread = new Thread(new Runnable()
 121     {
 122       @Override
 123       public void run()
 124       {
 125         long startTime = System.currentTimeMillis();
 126         updateProgressIndicator(MessageManager
 127                 .getString("status.loading_cached_pdb_entries"), startTime);
 128         loadLocalCachedPDBEntries();
 129         updateProgressIndicator(null, startTime);
 130         updateProgressIndicator(MessageManager.getString(
 131                 "status.searching_for_pdb_structures"), startTime);
 132         fetchStructuresMetaData();
 133         // revise filter options if no results were found
 134         populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
 135         discoverStructureViews();
 136         updateProgressIndicator(null, startTime);
 137         mainFrame.setVisible(true);
 138         updateCurrentView();
 139       }
 140     });
 141     discoverPDBStructuresThread.start();
 142   }
 143
 144   /**
 145    * Builds a drop-down choice list of existing structure viewers to which new
 146    * structures may be added. If this list is empty then it, and the 'Add'
 147    * button, are hidden.
 148    */
 149   private void discoverStructureViews()
 150   {
 151     if (Desktop.instance != null)
 152     {
 153       targetView.removeAllItems();
 154       if (lastTargetedView != null && !lastTargetedView.isVisible())
 155       {
 156         lastTargetedView = null;
 157       }
 158       int linkedViewsAt = 0;
 159       for (StructureViewerBase view : Desktop.instance
 160               .getStructureViewers(null, null))
 161       {
 162         StructureViewer viewHandler = (lastTargetedView != null
 163                 && lastTargetedView.sview == view) ? lastTargetedView
 164                         : StructureViewer.reconfigure(view);
 165
 166         if (view.isLinkedWith(ap))
 167         {
 168           targetView.insertItemAt(viewHandler,
 169                   linkedViewsAt++);
 170         }
 171         else
 172         {
 173           targetView.addItem(viewHandler);
 174         }
 175       }
 176
 177       /*
 178        * show option to Add to viewer if at least 1 viewer found
 179        */
 180       targetView.setVisible(false);
 181       if (targetView.getItemCount() > 0)
 182       {
 183         targetView.setVisible(true);
 184         if (lastTargetedView != null)
 185         {
 186           targetView.setSelectedItem(lastTargetedView);
 187         }
 188         else
 189         {
 190           targetView.setSelectedIndex(0);
 191         }
 192       }
 193       btn_add.setVisible(targetView.isVisible());
 194     }
 195   }
 196
 197   /**
 198    * Updates the progress indicator with the specified message
 199    *
 200    * @param message
 201    *          displayed message for the operation
 202    * @param id
 203    *          unique handle for this indicator
 204    */
 205   protected void updateProgressIndicator(String message, long id)
 206   {
 207     if (progressIndicator != null)
 208     {
 209       progressIndicator.setProgressBar(message, id);
 210     }
 211   }
 212
 213   /**
 214    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
 215    * selection group
 216    */
 217   void fetchStructuresMetaData()
 218   {
 219     long startTime = System.currentTimeMillis();
 220     pdbRestCleint = PDBFTSRestClient.getInstance();
 221     Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
 222             .getStructureSummaryFields();
 223
 224     discoveredStructuresSet = new LinkedHashSet<>();
 225     HashSet<String> errors = new HashSet<>();
 226     for (SequenceI seq : selectedSequences)
 227     {
 228       FTSRestRequest pdbRequest = new FTSRestRequest();
 229       pdbRequest.setAllowEmptySeq(false);
 230       pdbRequest.setResponseSize(500);
 231       pdbRequest.setFieldToSearchBy("(");
 232       FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 233               .getSelectedItem());
 234       pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
 235               !chk_invertFilter.isSelected());
 236       pdbRequest.setWantedFields(wantedFields);
 237       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 238       pdbRequest.setAssociatedSequence(seq);
 239       FTSRestResponse resultList;
 240       try
 241       {
 242         resultList = pdbRestCleint.executeRequest(pdbRequest);
 243       } catch (Exception e)
 244       {
 245         e.printStackTrace();
 246         errors.add(e.getMessage());
 247         continue;
 248       }
 249       lastPdbRequest = pdbRequest;
 250       if (resultList.getSearchSummary() != null
 251               && !resultList.getSearchSummary().isEmpty())
 252       {
 253         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 254       }
 255     }
 256
 257     int noOfStructuresFound = 0;
 258     String totalTime = (System.currentTimeMillis() - startTime)
 259             + " milli secs";
 260     if (discoveredStructuresSet != null
 261             && !discoveredStructuresSet.isEmpty())
 262     {
 263       getResultTable().setModel(FTSRestResponse
 264               .getTableModel(lastPdbRequest, discoveredStructuresSet));
 265       noOfStructuresFound = discoveredStructuresSet.size();
 266       mainFrame.setTitle(MessageManager.formatMessage(
 267               "label.structure_chooser_no_of_structures",
 268               noOfStructuresFound, totalTime));
 269     }
 270     else
 271     {
 272       mainFrame.setTitle(MessageManager
 273               .getString("label.structure_chooser_manual_association"));
 274       if (errors.size() > 0)
 275       {
 276         StringBuilder errorMsg = new StringBuilder();
 277         for (String error : errors)
 278         {
 279           errorMsg.append(error).append("\n");
 280         }
 281         JvOptionPane.showMessageDialog(this, errorMsg.toString(),
 282                 MessageManager.getString("label.pdb_web-service_error"),
 283                 JvOptionPane.ERROR_MESSAGE);
 284       }
 285     }
 286   }
 287
 288   protected void loadLocalCachedPDBEntries()
 289   {
 290     ArrayList<CachedPDB> entries = new ArrayList<>();
 291     for (SequenceI seq : selectedSequences)
 292     {
 293       if (seq.getDatasetSequence() != null
 294               && seq.getDatasetSequence().getAllPDBEntries() != null)
 295       {
 296         for (PDBEntry pdbEntry : seq.getDatasetSequence()
 297                 .getAllPDBEntries())
 298         {
 299           if (pdbEntry.getFile() != null)
 300           {
 301             entries.add(new CachedPDB(seq, pdbEntry));
 302           }
 303         }
 304       }
 305     }
 306     cachedPDBExists = !entries.isEmpty();
 307     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
 308     tbl_local_pdb.setModel(tableModelx);
 309   }
 310
 311   /**
 312    * Builds a query string for a given sequences using its DBRef entries
 313    *
 314    * @param seq
 315    *          the sequences to build a query for
 316    * @return the built query string
 317    */
 318
 319   static String buildQuery(SequenceI seq)
 320   {
 321     boolean isPDBRefsFound = false;
 322     boolean isUniProtRefsFound = false;
 323     StringBuilder queryBuilder = new StringBuilder();
 324     Set<String> seqRefs = new LinkedHashSet<>();
 325
 326     /*
 327      * note PDBs as DBRefEntry so they are not duplicated in query
 328      */
 329     Set<String> pdbids = new HashSet<>();
 330
 331     if (seq.getAllPDBEntries() != null
 332             && queryBuilder.length() < MAX_QLENGTH)
 333     {
 334       for (PDBEntry entry : seq.getAllPDBEntries())
 335       {
 336         if (isValidSeqName(entry.getId()))
 337         {
 338           String id = entry.getId().toLowerCase();
 339           queryBuilder.append("pdb_id:").append(id).append(" OR ");
 340           isPDBRefsFound = true;
 341           pdbids.add(id);
 342         }
 343       }
 344     }
 345
 346     if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
 347     {
 348       for (DBRefEntry dbRef : seq.getDBRefs())
 349       {
 350         if (isValidSeqName(getDBRefId(dbRef))
 351                 && queryBuilder.length() < MAX_QLENGTH)
 352         {
 353           if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
 354           {
 355             queryBuilder.append("uniprot_accession:")
 356                     .append(getDBRefId(dbRef)).append(" OR ");
 357             queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
 358                     .append(" OR ");
 359             isUniProtRefsFound = true;
 360           }
 361           else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
 362           {
 363
 364             String id = getDBRefId(dbRef).toLowerCase();
 365             if (!pdbids.contains(id))
 366             {
 367               queryBuilder.append("pdb_id:").append(id).append(" OR ");
 368               isPDBRefsFound = true;
 369               pdbids.add(id);
 370             }
 371           }
 372           else
 373           {
 374             seqRefs.add(getDBRefId(dbRef));
 375           }
 376         }
 377       }
 378     }
 379
 380     if (!isPDBRefsFound && !isUniProtRefsFound)
 381     {
 382       String seqName = seq.getName();
 383       seqName = sanitizeSeqName(seqName);
 384       String[] names = seqName.toLowerCase().split("\\|");
 385       for (String name : names)
 386       {
 387         // System.out.println("Found name : " + name);
 388         name.trim();
 389         if (isValidSeqName(name))
 390         {
 391           seqRefs.add(name);
 392         }
 393       }
 394
 395       for (String seqRef : seqRefs)
 396       {
 397         queryBuilder.append("text:").append(seqRef).append(" OR ");
 398       }
 399     }
 400
 401     int endIndex = queryBuilder.lastIndexOf(" OR ");
 402     if (queryBuilder.toString().length() < 6)
 403     {
 404       return null;
 405     }
 406     String query = queryBuilder.toString().substring(0, endIndex);
 407     return query;
 408   }
 409
 410   /**
 411    * Remove the following special characters from input string +, -, &, !, (, ),
 412    * {, }, [, ], ^, ", ~, *, ?, :, \
 413    *
 414    * @param seqName
 415    * @return
 416    */
 417   static String sanitizeSeqName(String seqName)
 418   {
 419     Objects.requireNonNull(seqName);
 420     return seqName.replaceAll("\\[\\d*\\]", "")
 421             .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
 422   }
 423
 424   /**
 425    * Ensures sequence ref names are not less than 3 characters and does not
 426    * contain a database name
 427    *
 428    * @param seqName
 429    * @return
 430    */
 431   static boolean isValidSeqName(String seqName)
 432   {
 433     // System.out.println("seqName : " + seqName);
 434     String ignoreList = "pdb,uniprot,swiss-prot";
 435     if (seqName.length() < 3)
 436     {
 437       return false;
 438     }
 439     if (seqName.contains(":"))
 440     {
 441       return false;
 442     }
 443     seqName = seqName.toLowerCase();
 444     for (String ignoredEntry : ignoreList.split(","))
 445     {
 446       if (seqName.contains(ignoredEntry))
 447       {
 448         return false;
 449       }
 450     }
 451     return true;
 452   }
 453
 454   static String getDBRefId(DBRefEntry dbRef)
 455   {
 456     String ref = dbRef.getAccessionId().replaceAll("GO:", "");
 457     return ref;
 458   }
 459
 460   /**
 461    * Filters a given list of discovered structures based on supplied argument
 462    *
 463    * @param fieldToFilterBy
 464    *          the field to filter by
 465    */
 466   void filterResultSet(final String fieldToFilterBy)
 467   {
 468     Thread filterThread = new Thread(new Runnable()
 469     {
 470       @Override
 471       public void run()
 472       {
 473         long startTime = System.currentTimeMillis();
 474         pdbRestCleint = PDBFTSRestClient.getInstance();
 475         lbl_loading.setVisible(true);
 476         Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
 477                 .getStructureSummaryFields();
 478         Collection<FTSData> filteredResponse = new HashSet<>();
 479         HashSet<String> errors = new HashSet<>();
 480
 481         for (SequenceI seq : selectedSequences)
 482         {
 483           FTSRestRequest pdbRequest = new FTSRestRequest();
 484           if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
 485           {
 486             pdbRequest.setAllowEmptySeq(false);
 487             pdbRequest.setResponseSize(1);
 488             pdbRequest.setFieldToSearchBy("(");
 489             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 490             pdbRequest.setWantedFields(wantedFields);
 491             pdbRequest.setAssociatedSequence(seq);
 492             pdbRequest.setFacet(true);
 493             pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
 494             pdbRequest.setFacetPivotMinCount(1);
 495           }
 496           else
 497           {
 498             pdbRequest.setAllowEmptySeq(false);
 499             pdbRequest.setResponseSize(1);
 500             pdbRequest.setFieldToSearchBy("(");
 501             pdbRequest.setFieldToSortBy(fieldToFilterBy,
 502                     !chk_invertFilter.isSelected());
 503             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 504             pdbRequest.setWantedFields(wantedFields);
 505             pdbRequest.setAssociatedSequence(seq);
 506           }
 507           FTSRestResponse resultList;
 508           try
 509           {
 510             resultList = pdbRestCleint.executeRequest(pdbRequest);
 511           } catch (Exception e)
 512           {
 513             e.printStackTrace();
 514             errors.add(e.getMessage());
 515             continue;
 516           }
 517           lastPdbRequest = pdbRequest;
 518           if (resultList.getSearchSummary() != null
 519                   && !resultList.getSearchSummary().isEmpty())
 520           {
 521             filteredResponse.addAll(resultList.getSearchSummary());
 522           }
 523         }
 524
 525         String totalTime = (System.currentTimeMillis() - startTime)
 526                 + " milli secs";
 527         if (!filteredResponse.isEmpty())
 528         {
 529           final int filterResponseCount = filteredResponse.size();
 530           Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
 531           reorderedStructuresSet.addAll(filteredResponse);
 532           reorderedStructuresSet.addAll(discoveredStructuresSet);
 533           getResultTable().setModel(FTSRestResponse
 534                   .getTableModel(lastPdbRequest, reorderedStructuresSet));
 535
 536           FTSRestResponse.configureTableColumn(getResultTable(),
 537                   wantedFields, tempUserPrefs);
 538           getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
 539           getResultTable().getColumn("Ref Sequence").setMinWidth(100);
 540           getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
 541           // Update table selection model here
 542           getResultTable().addRowSelectionInterval(0,
 543                   filterResponseCount - 1);
 544           mainFrame.setTitle(MessageManager.formatMessage(
 545                   "label.structure_chooser_filter_time", totalTime));
 546         }
 547         else
 548         {
 549           mainFrame.setTitle(MessageManager.formatMessage(
 550                   "label.structure_chooser_filter_time", totalTime));
 551           if (errors.size() > 0)
 552           {
 553             StringBuilder errorMsg = new StringBuilder();
 554             for (String error : errors)
 555             {
 556               errorMsg.append(error).append("\n");
 557             }
 558             JvOptionPane.showMessageDialog(null, errorMsg.toString(),
 559                     MessageManager.getString("label.pdb_web-service_error"),
 560                     JvOptionPane.ERROR_MESSAGE);
 561           }
 562         }
 563
 564         lbl_loading.setVisible(false);
 565
 566         validateSelections();
 567       }
 568     });
 569     filterThread.start();
 570   }
 571
 572   /**
 573    * Handles action event for btn_pdbFromFile
 574    */
 575   @Override
 576   protected void pdbFromFile_actionPerformed()
 577   {
 578     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 579             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 580     chooser.setFileView(new jalview.io.JalviewFileView());
 581     chooser.setDialogTitle(
 582             MessageManager.formatMessage("label.select_pdb_file_for",
 583                     selectedSequence.getDisplayId(false)));
 584     chooser.setToolTipText(MessageManager.formatMessage(
 585             "label.load_pdb_file_associate_with_sequence",
 586             selectedSequence.getDisplayId(false)));
 587
 588     int value = chooser.showOpenDialog(null);
 589     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
 590     {
 591       selectedPdbFileName = chooser.getSelectedFile().getPath();
 592       jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
 593       validateSelections();
 594     }
 595   }
 596
 597   /**
 598    * Populates the filter combo-box options dynamically depending on discovered
 599    * structures
 600    */
 601   protected void populateFilterComboBox(boolean haveData,
 602           boolean cachedPDBExist)
 603   {
 604     /*
 605      * temporarily suspend the change listener behaviour
 606      */
 607     cmb_filterOption.removeItemListener(this);
 608
 609     cmb_filterOption.removeAllItems();
 610     if (haveData)
 611     {
 612       cmb_filterOption.addItem(new FilterOption(
 613               MessageManager.getString("label.best_quality"),
 614               "overall_quality", VIEWS_FILTER, false));
 615       cmb_filterOption.addItem(new FilterOption(
 616               MessageManager.getString("label.best_resolution"),
 617               "resolution", VIEWS_FILTER, false));
 618       cmb_filterOption.addItem(new FilterOption(
 619               MessageManager.getString("label.most_protein_chain"),
 620               "number_of_protein_chains", VIEWS_FILTER, false));
 621       cmb_filterOption.addItem(new FilterOption(
 622               MessageManager.getString("label.most_bound_molecules"),
 623               "number_of_bound_molecules", VIEWS_FILTER, false));
 624       cmb_filterOption.addItem(new FilterOption(
 625               MessageManager.getString("label.most_polymer_residues"),
 626               "number_of_polymer_residues", VIEWS_FILTER, true));
 627     }
 628     cmb_filterOption.addItem(
 629             new FilterOption(MessageManager.getString("label.enter_pdb_id"),
 630                     "-", VIEWS_ENTER_ID, false));
 631     cmb_filterOption.addItem(
 632             new FilterOption(MessageManager.getString("label.from_file"),
 633                     "-", VIEWS_FROM_FILE, false));
 634
 635     if (cachedPDBExist)
 636     {
 637       FilterOption cachedOption = new FilterOption(
 638               MessageManager.getString("label.cached_structures"),
 639               "-", VIEWS_LOCAL_PDB, false);
 640       cmb_filterOption.addItem(cachedOption);
 641       cmb_filterOption.setSelectedItem(cachedOption);
 642     }
 643
 644     cmb_filterOption.addItemListener(this);
 645   }
 646
 647   /**
 648    * Updates the displayed view based on the selected filter option
 649    */
 650   protected void updateCurrentView()
 651   {
 652     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 653             .getSelectedItem());
 654     layout_switchableViews.show(pnl_switchableViews,
 655             selectedFilterOpt.getView());
 656     String filterTitle = mainFrame.getTitle();
 657     mainFrame.setTitle(frameTitle);
 658     chk_invertFilter.setVisible(false);
 659     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 660     {
 661       mainFrame.setTitle(filterTitle);
 662       chk_invertFilter.setVisible(true);
 663       filterResultSet(selectedFilterOpt.getValue());
 664     }
 665     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 666             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 667     {
 668       mainFrame.setTitle(MessageManager
 669               .getString("label.structure_chooser_manual_association"));
 670       idInputAssSeqPanel.loadCmbAssSeq();
 671       fileChooserAssSeqPanel.loadCmbAssSeq();
 672     }
 673     validateSelections();
 674   }
 675
 676   /**
 677    * Validates user selection and enables the 'Add' and 'New View' buttons if
 678    * all parameters are correct (the Add button will only be visible if there is
 679    * at least one existing structure viewer open). This basically means at least
 680    * one structure selected and no error messages.
 681    * <p>
 682    * The 'Superpose Structures' option is enabled if either more than one
 683    * structure is selected, or the 'Add' to existing view option is enabled, and
 684    * disabled if the only option is to open a new view of a single structure.
 685    */
 686   @Override
 687   protected void validateSelections()
 688   {
 689     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 690             .getSelectedItem());
 691     btn_add.setEnabled(false);
 692     String currentView = selectedFilterOpt.getView();
 693     int selectedCount = 0;
 694     if (currentView == VIEWS_FILTER)
 695     {
 696       selectedCount = getResultTable().getSelectedRows().length;
 697       if (selectedCount > 0)
 698       {
 699         btn_add.setEnabled(true);
 700       }
 701     }
 702     else if (currentView == VIEWS_LOCAL_PDB)
 703     {
 704       selectedCount = tbl_local_pdb.getSelectedRows().length;
 705       if (selectedCount > 0)
 706       {
 707         btn_add.setEnabled(true);
 708       }
 709     }
 710     else if (currentView == VIEWS_ENTER_ID)
 711     {
 712       validateAssociationEnterPdb();
 713     }
 714     else if (currentView == VIEWS_FROM_FILE)
 715     {
 716       validateAssociationFromFile();
 717     }
 718
 719     btn_newView.setEnabled(btn_add.isEnabled());
 720
 721     /*
 722      * enable 'Superpose' option if more than one structure is selected,
 723      * or there are view(s) available to add structure(s) to
 724      */
 725     chk_superpose
 726             .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
 727   }
 728
 729   /**
 730    * Validates inputs from the Manual PDB entry panel
 731    */
 732   protected void validateAssociationEnterPdb()
 733   {
 734     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 735             .getCmb_assSeq().getSelectedItem();
 736     lbl_pdbManualFetchStatus.setIcon(errorImage);
 737     lbl_pdbManualFetchStatus.setToolTipText("");
 738     if (txt_search.getText().length() > 0)
 739     {
 740       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
 741               MessageManager.formatMessage("info.no_pdb_entry_found_for",
 742                       txt_search.getText())));
 743     }
 744
 745     if (errorWarning.length() > 0)
 746     {
 747       lbl_pdbManualFetchStatus.setIcon(warningImage);
 748       lbl_pdbManualFetchStatus.setToolTipText(
 749               JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
 750     }
 751
 752     if (selectedSequences.length == 1 || !assSeqOpt.getName()
 753             .equalsIgnoreCase("-Select Associated Seq-"))
 754     {
 755       txt_search.setEnabled(true);
 756       if (isValidPBDEntry)
 757       {
 758         btn_add.setEnabled(true);
 759         lbl_pdbManualFetchStatus.setToolTipText("");
 760         lbl_pdbManualFetchStatus.setIcon(goodImage);
 761       }
 762     }
 763     else
 764     {
 765       txt_search.setEnabled(false);
 766       lbl_pdbManualFetchStatus.setIcon(errorImage);
 767     }
 768   }
 769
 770   /**
 771    * Validates inputs for the manual PDB file selection options
 772    */
 773   protected void validateAssociationFromFile()
 774   {
 775     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
 776             .getCmb_assSeq().getSelectedItem();
 777     lbl_fromFileStatus.setIcon(errorImage);
 778     if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
 779             .getName().equalsIgnoreCase("-Select Associated Seq-")))
 780     {
 781       btn_pdbFromFile.setEnabled(true);
 782       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
 783       {
 784         btn_add.setEnabled(true);
 785         lbl_fromFileStatus.setIcon(goodImage);
 786       }
 787     }
 788     else
 789     {
 790       btn_pdbFromFile.setEnabled(false);
 791       lbl_fromFileStatus.setIcon(errorImage);
 792     }
 793   }
 794
 795   @Override
 796   protected void cmbAssSeqStateChanged()
 797   {
 798     validateSelections();
 799   }
 800
 801   /**
 802    * Handles the state change event for the 'filter' combo-box and 'invert'
 803    * check-box
 804    */
 805   @Override
 806   protected void stateChanged(ItemEvent e)
 807   {
 808     if (e.getSource() instanceof JCheckBox)
 809     {
 810       updateCurrentView();
 811     }
 812     else
 813     {
 814       if (e.getStateChange() == ItemEvent.SELECTED)
 815       {
 816         updateCurrentView();
 817       }
 818     }
 819
 820   }
 821
 822   /**
 823    * select structures for viewing by their PDB IDs
 824    *
 825    * @param pdbids
 826    * @return true if structures were found and marked as selected
 827    */
 828   public boolean selectStructure(String... pdbids)
 829   {
 830     boolean found = false;
 831
 832     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 833             .getSelectedItem());
 834     String currentView = selectedFilterOpt.getView();
 835     JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
 836             : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
 837
 838     if (restable == null)
 839     {
 840       // can't select (enter PDB ID, or load file - need to also select which
 841       // sequence to associate with)
 842       return false;
 843     }
 844
 845     int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
 846     for (int r = 0; r < restable.getRowCount(); r++)
 847     {
 848       for (int p = 0; p < pdbids.length; p++)
 849       {
 850         if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
 851                 .equalsIgnoreCase(pdbids[p]))
 852         {
 853           restable.setRowSelectionInterval(r, r);
 854           found = true;
 855         }
 856       }
 857     }
 858     return found;
 859   }
 860
 861   /**
 862    * Handles the 'New View' action
 863    */
 864   @Override
 865   protected void newView_ActionPerformed()
 866   {
 867     targetView.setSelectedItem(null);
 868     showStructures(false);
 869   }
 870
 871   /**
 872    * Handles the 'Add to existing viewer' action
 873    */
 874   @Override
 875   protected void add_ActionPerformed()
 876   {
 877     showStructures(false);
 878   }
 879
 880   /**
 881    * structure viewer opened by this dialog, or null
 882    */
 883   private StructureViewer sViewer = null;
 884
 885   public void showStructures(boolean waitUntilFinished)
 886   {
 887
 888     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 889
 890     final int preferredHeight = pnl_filter.getHeight();
 891
 892     Runnable viewStruc = new Runnable()
 893     {
 894       @Override
 895       public void run()
 896       {
 897         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 898                 .getSelectedItem());
 899         String currentView = selectedFilterOpt.getView();
 900         JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
 901                 : tbl_local_pdb;
 902
 903         if (currentView == VIEWS_FILTER)
 904         {
 905           int pdbIdColIndex = restable.getColumn("PDB Id")
 906                   .getModelIndex();
 907           int refSeqColIndex = restable.getColumn("Ref Sequence")
 908                   .getModelIndex();
 909           int[] selectedRows = restable.getSelectedRows();
 910           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 911           int count = 0;
 912           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 913           for (int row : selectedRows)
 914           {
 915             String pdbIdStr = restable
 916                     .getValueAt(row, pdbIdColIndex).toString();
 917             SequenceI selectedSeq = (SequenceI) restable
 918                     .getValueAt(row, refSeqColIndex);
 919             selectedSeqsToView.add(selectedSeq);
 920             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
 921             if (pdbEntry == null)
 922             {
 923               pdbEntry = getFindEntry(pdbIdStr,
 924                       selectedSeq.getAllPDBEntries());
 925             }
 926
 927             if (pdbEntry == null)
 928             {
 929               pdbEntry = new PDBEntry();
 930               pdbEntry.setId(pdbIdStr);
 931               pdbEntry.setType(PDBEntry.Type.PDB);
 932               selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
 933             }
 934             pdbEntriesToView[count++] = pdbEntry;
 935           }
 936           SequenceI[] selectedSeqs = selectedSeqsToView
 937                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 938           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 939                   selectedSeqs);
 940         }
 941         else if (currentView == VIEWS_LOCAL_PDB)
 942         {
 943           int[] selectedRows = tbl_local_pdb.getSelectedRows();
 944           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 945           int count = 0;
 946           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
 947                   .getModelIndex();
 948           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
 949                   .getModelIndex();
 950           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 951           for (int row : selectedRows)
 952           {
 953             PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
 954                     pdbIdColIndex);
 955             pdbEntriesToView[count++] = pdbEntry;
 956             SequenceI selectedSeq = (SequenceI) tbl_local_pdb
 957                     .getValueAt(row, refSeqColIndex);
 958             selectedSeqsToView.add(selectedSeq);
 959           }
 960           SequenceI[] selectedSeqs = selectedSeqsToView
 961                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 962           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 963                   selectedSeqs);
 964         }
 965         else if (currentView == VIEWS_ENTER_ID)
 966         {
 967           SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
 968                   .getCmb_assSeq().getSelectedItem()).getSequence();
 969           if (userSelectedSeq != null)
 970           {
 971             selectedSequence = userSelectedSeq;
 972           }
 973           String pdbIdStr = txt_search.getText();
 974           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
 975           if (pdbEntry == null)
 976           {
 977             pdbEntry = new PDBEntry();
 978             if (pdbIdStr.split(":").length > 1)
 979             {
 980               pdbEntry.setId(pdbIdStr.split(":")[0]);
 981               pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
 982             }
 983             else
 984             {
 985               pdbEntry.setId(pdbIdStr);
 986             }
 987             pdbEntry.setType(PDBEntry.Type.PDB);
 988             selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
 989           }
 990
 991           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
 992           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 993                   new SequenceI[]
 994                   { selectedSequence });
 995         }
 996         else if (currentView == VIEWS_FROM_FILE)
 997         {
 998           SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
 999                   .getCmb_assSeq().getSelectedItem()).getSequence();
1000           if (userSelectedSeq != null)
1001           {
1002             selectedSequence = userSelectedSeq;
1003           }
1004           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
1005                   .associatePdbWithSeq(selectedPdbFileName,
1006                           DataSourceType.FILE, selectedSequence, true,
1007                           Desktop.instance);
1008
1009           sViewer = launchStructureViewer(
1010                   ssm, new PDBEntry[]
1011                   { fileEntry }, ap,
1012                   new SequenceI[]
1013                   { selectedSequence });
1014         }
1015         SwingUtilities.invokeLater(new Runnable()
1016         {
1017           @Override
1018           public void run()
1019           {
1020             closeAction(preferredHeight);
1021             mainFrame.dispose();
1022           }
1023         });
1024       }
1025     };
1026     Thread runner = new Thread(viewStruc);
1027     runner.start();
1028     if (waitUntilFinished)
1029     {
1030       while (sViewer == null ? runner.isAlive()
1031               : (sViewer.sview == null ? true
1032                       : !sViewer.sview.hasMapping()))
1033       {
1034         try
1035         {
1036           Thread.sleep(300);
1037         } catch (InterruptedException ie)
1038         {
1039
1040         }
1041       }
1042     }
1043   }
1044
1045   private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
1046   {
1047     Objects.requireNonNull(id);
1048     Objects.requireNonNull(pdbEntries);
1049     PDBEntry foundEntry = null;
1050     for (PDBEntry entry : pdbEntries)
1051     {
1052       if (entry.getId().equalsIgnoreCase(id))
1053       {
1054         return entry;
1055       }
1056     }
1057     return foundEntry;
1058   }
1059
1060   /**
1061    * Answers a structure viewer (new or existing) configured to superimpose
1062    * added structures or not according to the user's choice
1063    *
1064    * @param ssm
1065    * @return
1066    */
1067   StructureViewer getTargetedStructureViewer(
1068           StructureSelectionManager ssm)
1069   {
1070     Object sv = targetView.getSelectedItem();
1071
1072     return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
1073   }
1074
1075   /**
1076    * Adds PDB structures to a new or existing structure viewer
1077    *
1078    * @param ssm
1079    * @param pdbEntriesToView
1080    * @param alignPanel
1081    * @param sequences
1082    * @return
1083    */
1084   private StructureViewer launchStructureViewer(
1085           StructureSelectionManager ssm,
1086           final PDBEntry[] pdbEntriesToView,
1087           final AlignmentPanel alignPanel, SequenceI[] sequences)
1088   {
1089     long progressId = sequences.hashCode();
1090     setProgressBar(MessageManager
1091             .getString("status.launching_3d_structure_viewer"), progressId);
1092     final StructureViewer theViewer = getTargetedStructureViewer(ssm);
1093     boolean superimpose = chk_superpose.isSelected();
1094     theViewer.setSuperpose(superimpose);
1095
1096     /*
1097      * remember user's choice of superimpose or not
1098      */
1099     Cache.setProperty(AUTOSUPERIMPOSE,
1100             Boolean.valueOf(superimpose).toString());
1101
1102     setProgressBar(null, progressId);
1103     if (SiftsSettings.isMapWithSifts())
1104     {
1105       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
1106       int p = 0;
1107       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
1108       // real PDB ID. For moment, we can also safely do this if there is already
1109       // a known mapping between the PDBEntry and the sequence.
1110       for (SequenceI seq : sequences)
1111       {
1112         PDBEntry pdbe = pdbEntriesToView[p++];
1113         if (pdbe != null && pdbe.getFile() != null)
1114         {
1115           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
1116           if (smm != null && smm.length > 0)
1117           {
1118             for (StructureMapping sm : smm)
1119             {
1120               if (sm.getSequence() == seq)
1121               {
1122                 continue;
1123               }
1124             }
1125           }
1126         }
1127         if (seq.getPrimaryDBRefs().isEmpty())
1128         {
1129           seqsWithoutSourceDBRef.add(seq);
1130           continue;
1131         }
1132       }
1133       if (!seqsWithoutSourceDBRef.isEmpty())
1134       {
1135         int y = seqsWithoutSourceDBRef.size();
1136         setProgressBar(MessageManager.formatMessage(
1137                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
1138                 y), progressId);
1139         SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
1140                 .toArray(new SequenceI[y]);
1141         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
1142         dbRefFetcher.fetchDBRefs(true);
1143
1144         setProgressBar("Fetch complete.", progressId); // todo i18n
1145       }
1146     }
1147     if (pdbEntriesToView.length > 1)
1148     {
1149       setProgressBar(MessageManager.getString(
1150               "status.fetching_3d_structures_for_selected_entries"),
1151               progressId);
1152       theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
1153     }
1154     else
1155     {
1156       setProgressBar(MessageManager.formatMessage(
1157               "status.fetching_3d_structures_for",
1158               pdbEntriesToView[0].getId()),progressId);
1159       theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
1160     }
1161     setProgressBar(null, progressId);
1162     // remember the last viewer we used...
1163     lastTargetedView = theViewer;
1164     return theViewer;
1165   }
1166
1167   /**
1168    * Populates the combo-box used in associating manually fetched structures to
1169    * a unique sequence when more than one sequence selection is made.
1170    */
1171   @Override
1172   protected void populateCmbAssociateSeqOptions(
1173           JComboBox<AssociateSeqOptions> cmb_assSeq,
1174           JLabel lbl_associateSeq)
1175   {
1176     cmb_assSeq.removeAllItems();
1177     cmb_assSeq.addItem(
1178             new AssociateSeqOptions("-Select Associated Seq-", null));
1179     lbl_associateSeq.setVisible(false);
1180     if (selectedSequences.length > 1)
1181     {
1182       for (SequenceI seq : selectedSequences)
1183       {
1184         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
1185       }
1186     }
1187     else
1188     {
1189       String seqName = selectedSequence.getDisplayId(false);
1190       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
1191       lbl_associateSeq.setText(seqName);
1192       lbl_associateSeq.setVisible(true);
1193       cmb_assSeq.setVisible(false);
1194     }
1195   }
1196
1197   protected boolean isStructuresDiscovered()
1198   {
1199     return discoveredStructuresSet != null
1200             && !discoveredStructuresSet.isEmpty();
1201   }
1202
1203   @Override
1204   protected void txt_search_ActionPerformed()
1205   {
1206     new Thread()
1207     {
1208       @Override
1209       public void run()
1210       {
1211         errorWarning.setLength(0);
1212         isValidPBDEntry = false;
1213         if (txt_search.getText().length() > 0)
1214         {
1215           String searchTerm = txt_search.getText().toLowerCase();
1216           searchTerm = searchTerm.split(":")[0];
1217           // System.out.println(">>>>> search term : " + searchTerm);
1218           List<FTSDataColumnI> wantedFields = new ArrayList<>();
1219           FTSRestRequest pdbRequest = new FTSRestRequest();
1220           pdbRequest.setAllowEmptySeq(false);
1221           pdbRequest.setResponseSize(1);
1222           pdbRequest.setFieldToSearchBy("(pdb_id:");
1223           pdbRequest.setWantedFields(wantedFields);
1224           pdbRequest.setSearchTerm(searchTerm + ")");
1225           pdbRequest.setAssociatedSequence(selectedSequence);
1226           pdbRestCleint = PDBFTSRestClient.getInstance();
1227           wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
1228           FTSRestResponse resultList;
1229           try
1230           {
1231             resultList = pdbRestCleint.executeRequest(pdbRequest);
1232           } catch (Exception e)
1233           {
1234             errorWarning.append(e.getMessage());
1235             return;
1236           } finally
1237           {
1238             validateSelections();
1239           }
1240           if (resultList.getSearchSummary() != null
1241                   && resultList.getSearchSummary().size() > 0)
1242           {
1243             isValidPBDEntry = true;
1244           }
1245         }
1246         validateSelections();
1247       }
1248     }.start();
1249   }
1250
1251   @Override
1252   protected void tabRefresh()
1253   {
1254     if (selectedSequences != null)
1255     {
1256       Thread refreshThread = new Thread(new Runnable()
1257       {
1258         @Override
1259         public void run()
1260         {
1261           fetchStructuresMetaData();
1262           filterResultSet(
1263                   ((FilterOption) cmb_filterOption.getSelectedItem())
1264                           .getValue());
1265         }
1266       });
1267       refreshThread.start();
1268     }
1269   }
1270
1271   public class PDBEntryTableModel extends AbstractTableModel
1272   {
1273     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1274         "File" };
1275
1276     private List<CachedPDB> pdbEntries;
1277
1278     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1279     {
1280       this.pdbEntries = new ArrayList<>(pdbEntries);
1281     }
1282
1283     @Override
1284     public String getColumnName(int columnIndex)
1285     {
1286       return columns[columnIndex];
1287     }
1288
1289     @Override
1290     public int getRowCount()
1291     {
1292       return pdbEntries.size();
1293     }
1294
1295     @Override
1296     public int getColumnCount()
1297     {
1298       return columns.length;
1299     }
1300
1301     @Override
1302     public boolean isCellEditable(int row, int column)
1303     {
1304       return false;
1305     }
1306
1307     @Override
1308     public Object getValueAt(int rowIndex, int columnIndex)
1309     {
1310       Object value = "??";
1311       CachedPDB entry = pdbEntries.get(rowIndex);
1312       switch (columnIndex)
1313       {
1314       case 0:
1315         value = entry.getSequence();
1316         break;
1317       case 1:
1318         value = entry.getPdbEntry();
1319         break;
1320       case 2:
1321         value = entry.getPdbEntry().getChainCode() == null ? "_"
1322                 : entry.getPdbEntry().getChainCode();
1323         break;
1324       case 3:
1325         value = entry.getPdbEntry().getType();
1326         break;
1327       case 4:
1328         value = entry.getPdbEntry().getFile();
1329         break;
1330       }
1331       return value;
1332     }
1333
1334     @Override
1335     public Class<?> getColumnClass(int columnIndex)
1336     {
1337       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1338     }
1339
1340     public CachedPDB getPDBEntryAt(int row)
1341     {
1342       return pdbEntries.get(row);
1343     }
1344
1345   }
1346
1347   private class CachedPDB
1348   {
1349     private SequenceI sequence;
1350
1351     private PDBEntry pdbEntry;
1352
1353     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1354     {
1355       this.sequence = sequence;
1356       this.pdbEntry = pdbEntry;
1357     }
1358
1359     public SequenceI getSequence()
1360     {
1361       return sequence;
1362     }
1363
1364     public PDBEntry getPdbEntry()
1365     {
1366       return pdbEntry;
1367     }
1368
1369   }
1370
1371   private IProgressIndicator progressBar;
1372
1373   @Override
1374   public void setProgressBar(String message, long id)
1375   {
1376     progressBar.setProgressBar(message, id);
1377   }
1378
1379   @Override
1380   public void registerHandler(long id, IProgressIndicatorHandler handler)
1381   {
1382     progressBar.registerHandler(id, handler);
1383   }
1384
1385   @Override
1386   public boolean operationInProgress()
1387   {
1388     return progressBar.operationInProgress();
1389   }
1390
1391   public JalviewStructureDisplayI getOpenedStructureViewer()
1392   {
1393     return sViewer == null ? null : sViewer.sview;
1394   }
1395 }