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 final int MAX_QLENGTH = 7820;
  75
  76   protected SequenceI selectedSequence;
  77
  78   public SequenceI[] selectedSequences;
  79
  80   private IProgressIndicator progressIndicator;
  81
  82   protected Collection<FTSData> discoveredStructuresSet;
  83
  84   protected FTSRestRequest lastPdbRequest;
  85
  86   protected FTSRestClientI pdbRestClient;
  87
  88   protected String selectedPdbFileName;
  89
  90   protected boolean isValidPBDEntry;
  91
  92   protected boolean cachedPDBExists;
  93
  94   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
  95           AlignmentPanel ap)
  96   {
  97     this.ap = ap;
  98     this.selectedSequence = selectedSeq;
  99     this.selectedSequences = selectedSeqs;
 100     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
 101     init();
 102   }
 103
 104   /**
 105    * Initializes parameters used by the Structure Chooser Panel
 106    */
 107   protected void init()
 108   {
 109     if (!Jalview.isHeadlessMode())
 110     {
 111       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 112     }
 113
 114     chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
 115
 116     // ensure a filter option is in force for search
 117     populateFilterComboBox(true, cachedPDBExists);
 118     Thread discoverPDBStructuresThread = new Thread(new Runnable()
 119     {
 120       @Override
 121       public void run()
 122       {
 123         long startTime = System.currentTimeMillis();
 124         updateProgressIndicator(MessageManager
 125                 .getString("status.loading_cached_pdb_entries"), startTime);
 126         loadLocalCachedPDBEntries();
 127         updateProgressIndicator(null, startTime);
 128         updateProgressIndicator(MessageManager.getString(
 129                 "status.searching_for_pdb_structures"), startTime);
 130         fetchStructuresMetaData();
 131         // revise filter options if no results were found
 132         populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
 133         discoverStructureViews();
 134         updateProgressIndicator(null, startTime);
 135         mainFrame.setVisible(true);
 136         updateCurrentView();
 137       }
 138     });
 139     discoverPDBStructuresThread.start();
 140   }
 141
 142   /**
 143    * Builds a drop-down choice list of existing structure viewers to which new
 144    * structures may be added. If this list is empty then it, and the 'Add'
 145    * button, are hidden.
 146    */
 147   protected void discoverStructureViews()
 148   {
 149     if (Desktop.getInstance() != null)
 150     {
 151       targetView.removeAllItems();
 152       Desktop d = Desktop.getInstance();
 153       if (d.lastTargetedView != null && !d.lastTargetedView.isVisible())
 154       {
 155         d.lastTargetedView = null;
 156       }
 157       int linkedViewsAt = 0;
 158       for (StructureViewerBase view : Desktop.getInstance()
 159               .getStructureViewers(null, null))
 160       {
 161         StructureViewer viewHandler = (d.lastTargetedView != null
 162                 && d.lastTargetedView.sview == view) ? d.lastTargetedView
 163                         : StructureViewer.reconfigure(view);
 164
 165         if (view.isLinkedWith(ap))
 166         {
 167           targetView.insertItemAt(viewHandler,
 168                   linkedViewsAt++);
 169         }
 170         else
 171         {
 172           targetView.addItem(viewHandler);
 173         }
 174       }
 175
 176       /*
 177        * show option to Add to viewer if at least 1 viewer found
 178        */
 179       targetView.setVisible(false);
 180       if (targetView.getItemCount() > 0)
 181       {
 182         targetView.setVisible(true);
 183         if (d.lastTargetedView != null)
 184         {
 185           targetView.setSelectedItem(d.lastTargetedView);
 186         }
 187         else
 188         {
 189           targetView.setSelectedIndex(0);
 190         }
 191       }
 192       btn_add.setVisible(targetView.isVisible());
 193     }
 194   }
 195
 196   /**
 197    * Updates the progress indicator with the specified message
 198    *
 199    * @param message
 200    *          displayed message for the operation
 201    * @param id
 202    *          unique handle for this indicator
 203    */
 204   protected void updateProgressIndicator(String message, long id)
 205   {
 206     if (progressIndicator != null)
 207     {
 208       progressIndicator.setProgressBar(message, id);
 209     }
 210   }
 211
 212   /**
 213    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
 214    * selection group
 215    */
 216   void fetchStructuresMetaData()
 217   {
 218     long startTime = System.currentTimeMillis();
 219     pdbRestClient = PDBFTSRestClient.getInstance();
 220     Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
 221             .getStructureSummaryFields();
 222
 223     discoveredStructuresSet = new LinkedHashSet<>();
 224     HashSet<String> errors = new HashSet<>();
 225     for (SequenceI seq : selectedSequences)
 226     {
 227       FTSRestRequest pdbRequest = new FTSRestRequest();
 228       pdbRequest.setAllowEmptySeq(false);
 229       pdbRequest.setResponseSize(500);
 230       pdbRequest.setFieldToSearchBy("(");
 231       FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 232               .getSelectedItem());
 233       pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
 234               !chk_invertFilter.isSelected());
 235       pdbRequest.setWantedFields(wantedFields);
 236       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 237       pdbRequest.setAssociatedSequence(seq);
 238       FTSRestResponse resultList;
 239       try
 240       {
 241         resultList = pdbRestClient.executeRequest(pdbRequest);
 242       } catch (Exception e)
 243       {
 244         e.printStackTrace();
 245         errors.add(e.getMessage());
 246         continue;
 247       }
 248       lastPdbRequest = pdbRequest;
 249       if (resultList.getSearchSummary() != null
 250               && !resultList.getSearchSummary().isEmpty())
 251       {
 252         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 253       }
 254     }
 255
 256     int noOfStructuresFound = 0;
 257     String totalTime = (System.currentTimeMillis() - startTime)
 258             + " milli secs";
 259     if (discoveredStructuresSet != null
 260             && !discoveredStructuresSet.isEmpty())
 261     {
 262       getResultTable().setModel(FTSRestResponse
 263               .getTableModel(lastPdbRequest, discoveredStructuresSet));
 264       noOfStructuresFound = discoveredStructuresSet.size();
 265       mainFrame.setTitle(MessageManager.formatMessage(
 266               "label.structure_chooser_no_of_structures",
 267               noOfStructuresFound, totalTime));
 268     }
 269     else
 270     {
 271       mainFrame.setTitle(MessageManager
 272               .getString("label.structure_chooser_manual_association"));
 273       if (errors.size() > 0)
 274       {
 275         StringBuilder errorMsg = new StringBuilder();
 276         for (String error : errors)
 277         {
 278           errorMsg.append(error).append("\n");
 279         }
 280         JvOptionPane.showMessageDialog(this, errorMsg.toString(),
 281                 MessageManager.getString("label.pdb_web-service_error"),
 282                 JvOptionPane.ERROR_MESSAGE);
 283       }
 284     }
 285   }
 286
 287   protected void loadLocalCachedPDBEntries()
 288   {
 289     ArrayList<CachedPDB> entries = new ArrayList<>();
 290     for (SequenceI seq : selectedSequences)
 291     {
 292       if (seq.getDatasetSequence() != null
 293               && seq.getDatasetSequence().getAllPDBEntries() != null)
 294       {
 295         for (PDBEntry pdbEntry : seq.getDatasetSequence()
 296                 .getAllPDBEntries())
 297         {
 298           if (pdbEntry.getFile() != null)
 299           {
 300             entries.add(new CachedPDB(seq, pdbEntry));
 301           }
 302         }
 303       }
 304     }
 305     cachedPDBExists = !entries.isEmpty();
 306     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
 307     tbl_local_pdb.setModel(tableModelx);
 308   }
 309
 310   /**
 311    * Builds a query string for a given sequences using its DBRef entries
 312    *
 313    * @param seq
 314    *          the sequences to build a query for
 315    * @return the built query string
 316    */
 317
 318   static String buildQuery(SequenceI seq)
 319   {
 320     boolean isPDBRefsFound = false;
 321     boolean isUniProtRefsFound = false;
 322     StringBuilder queryBuilder = new StringBuilder();
 323     Set<String> seqRefs = new LinkedHashSet<>();
 324
 325     if (seq.getAllPDBEntries() != null
 326             && queryBuilder.length() < MAX_QLENGTH)
 327     {
 328       for (PDBEntry entry : seq.getAllPDBEntries())
 329       {
 330         if (isValidSeqName(entry.getId()))
 331         {
 332           queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase())
 333                   .append(" OR ");
 334           isPDBRefsFound = true;
 335         }
 336       }
 337     }
 338
 339     List<DBRefEntry> refs = seq.getDBRefs();
 340     if (refs != null && refs.size() != 0)
 341     {
 342       for (int ib = 0, nb = refs.size(); ib < nb; ib++)
 343       {
 344           DBRefEntry dbRef = refs.get(ib);
 345         if (isValidSeqName(getDBRefId(dbRef))
 346                 && queryBuilder.length() < MAX_QLENGTH)
 347         {
 348           if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
 349           {
 350             queryBuilder.append("uniprot_accession:")
 351                     .append(getDBRefId(dbRef)).append(" OR ");
 352             queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
 353                     .append(" OR ");
 354             isUniProtRefsFound = true;
 355           }
 356           else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
 357           {
 358
 359             queryBuilder.append("pdb_id:")
 360                     .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
 361             isPDBRefsFound = true;
 362           }
 363           else
 364           {
 365             seqRefs.add(getDBRefId(dbRef));
 366           }
 367         }
 368       }
 369     }
 370
 371     if (!isPDBRefsFound && !isUniProtRefsFound)
 372     {
 373       String seqName = seq.getName();
 374       seqName = sanitizeSeqName(seqName);
 375       String[] names = seqName.toLowerCase().split("\\|");
 376       for (String name : names)
 377       {
 378         // System.out.println("Found name : " + name);
 379         name.trim();
 380         if (isValidSeqName(name))
 381         {
 382           seqRefs.add(name);
 383         }
 384       }
 385
 386       for (String seqRef : seqRefs)
 387       {
 388         queryBuilder.append("text:").append(seqRef).append(" OR ");
 389       }
 390     }
 391
 392     int endIndex = queryBuilder.lastIndexOf(" OR ");
 393     if (queryBuilder.toString().length() < 6)
 394     {
 395       return null;
 396     }
 397     String query = queryBuilder.toString().substring(0, endIndex);
 398     return query;
 399   }
 400
 401   /**
 402    * Remove the following special characters from input string +, -, &, !, (, ),
 403    * {, }, [, ], ^, ", ~, *, ?, :, \
 404    *
 405    * @param seqName
 406    * @return
 407    */
 408   static String sanitizeSeqName(String seqName)
 409   {
 410     Objects.requireNonNull(seqName);
 411     return seqName.replaceAll("\\[\\d*\\]", "")
 412             .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
 413   }
 414
 415   /**
 416    * Ensures sequence ref names are not less than 3 characters and does not
 417    * contain a database name
 418    *
 419    * @param seqName
 420    * @return
 421    */
 422   static boolean isValidSeqName(String seqName)
 423   {
 424     // System.out.println("seqName : " + seqName);
 425     String ignoreList = "pdb,uniprot,swiss-prot";
 426     if (seqName.length() < 3)
 427     {
 428       return false;
 429     }
 430     if (seqName.contains(":"))
 431     {
 432       return false;
 433     }
 434     seqName = seqName.toLowerCase();
 435     for (String ignoredEntry : ignoreList.split(","))
 436     {
 437       if (seqName.contains(ignoredEntry))
 438       {
 439         return false;
 440       }
 441     }
 442     return true;
 443   }
 444
 445   static String getDBRefId(DBRefEntry dbRef)
 446   {
 447     String ref = dbRef.getAccessionId().replaceAll("GO:", "");
 448     return ref;
 449   }
 450
 451   /**
 452    * Filters a given list of discovered structures based on supplied argument
 453    *
 454    * @param fieldToFilterBy
 455    *          the field to filter by
 456    */
 457   void filterResultSet(final String fieldToFilterBy)
 458   {
 459     Thread filterThread = new Thread(new Runnable()
 460     {
 461       @Override
 462       public void run()
 463       {
 464         long startTime = System.currentTimeMillis();
 465         pdbRestClient = PDBFTSRestClient.getInstance();
 466         lbl_loading.setVisible(true);
 467         Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
 468                 .getStructureSummaryFields();
 469         Collection<FTSData> filteredResponse = new HashSet<>();
 470         HashSet<String> errors = new HashSet<>();
 471
 472         for (SequenceI seq : selectedSequences)
 473         {
 474           FTSRestRequest pdbRequest = new FTSRestRequest();
 475           if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
 476           {
 477             pdbRequest.setAllowEmptySeq(false);
 478             pdbRequest.setResponseSize(1);
 479             pdbRequest.setFieldToSearchBy("(");
 480             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 481             pdbRequest.setWantedFields(wantedFields);
 482             pdbRequest.setAssociatedSequence(seq);
 483             pdbRequest.setFacet(true);
 484             pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
 485             pdbRequest.setFacetPivotMinCount(1);
 486           }
 487           else
 488           {
 489             pdbRequest.setAllowEmptySeq(false);
 490             pdbRequest.setResponseSize(1);
 491             pdbRequest.setFieldToSearchBy("(");
 492             pdbRequest.setFieldToSortBy(fieldToFilterBy,
 493                     !chk_invertFilter.isSelected());
 494             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 495             pdbRequest.setWantedFields(wantedFields);
 496             pdbRequest.setAssociatedSequence(seq);
 497           }
 498           FTSRestResponse resultList;
 499           try
 500           {
 501             resultList = pdbRestClient.executeRequest(pdbRequest);
 502           } catch (Exception e)
 503           {
 504             e.printStackTrace();
 505             errors.add(e.getMessage());
 506             continue;
 507           }
 508           lastPdbRequest = pdbRequest;
 509           if (resultList.getSearchSummary() != null
 510                   && !resultList.getSearchSummary().isEmpty())
 511           {
 512             filteredResponse.addAll(resultList.getSearchSummary());
 513           }
 514         }
 515
 516         String totalTime = (System.currentTimeMillis() - startTime)
 517                 + " milli secs";
 518         if (!filteredResponse.isEmpty())
 519         {
 520           final int filterResponseCount = filteredResponse.size();
 521           Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
 522           reorderedStructuresSet.addAll(filteredResponse);
 523           reorderedStructuresSet.addAll(discoveredStructuresSet);
 524           getResultTable().setModel(FTSRestResponse
 525                   .getTableModel(lastPdbRequest, reorderedStructuresSet));
 526
 527           FTSRestResponse.configureTableColumn(getResultTable(),
 528                   wantedFields, tempUserPrefs);
 529           getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
 530           getResultTable().getColumn("Ref Sequence").setMinWidth(100);
 531           getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
 532           // Update table selection model here
 533           getResultTable().addRowSelectionInterval(0,
 534                   filterResponseCount - 1);
 535           mainFrame.setTitle(MessageManager.formatMessage(
 536                   "label.structure_chooser_filter_time", totalTime));
 537         }
 538         else
 539         {
 540           mainFrame.setTitle(MessageManager.formatMessage(
 541                   "label.structure_chooser_filter_time", totalTime));
 542           if (errors.size() > 0)
 543           {
 544             StringBuilder errorMsg = new StringBuilder();
 545             for (String error : errors)
 546             {
 547               errorMsg.append(error).append("\n");
 548             }
 549             JvOptionPane.showMessageDialog(null, errorMsg.toString(),
 550                     MessageManager.getString("label.pdb_web-service_error"),
 551                     JvOptionPane.ERROR_MESSAGE);
 552           }
 553         }
 554
 555         lbl_loading.setVisible(false);
 556
 557         validateSelections();
 558       }
 559     });
 560     filterThread.start();
 561   }
 562
 563   /**
 564    * Handles action event for btn_pdbFromFile
 565    */
 566   @Override
 567   protected void pdbFromFile_actionPerformed()
 568   {
 569     // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and StructureChooser
 570     // works
 571     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 572             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 573     chooser.setFileView(new jalview.io.JalviewFileView());
 574     chooser.setDialogTitle(
 575             MessageManager.formatMessage("label.select_pdb_file_for",
 576                     selectedSequence.getDisplayId(false)));
 577     chooser.setToolTipText(MessageManager.formatMessage(
 578             "label.load_pdb_file_associate_with_sequence",
 579             selectedSequence.getDisplayId(false)));
 580
 581     int value = chooser.showOpenDialog(null);
 582     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
 583     {
 584       selectedPdbFileName = chooser.getSelectedFile().getPath();
 585       jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
 586       validateSelections();
 587     }
 588   }
 589
 590   /**
 591    * Populates the filter combo-box options dynamically depending on discovered
 592    * structures
 593    */
 594   protected void populateFilterComboBox(boolean haveData,
 595           boolean cachedPDBExist)
 596   {
 597     /*
 598      * temporarily suspend the change listener behaviour
 599      */
 600     cmb_filterOption.removeItemListener(this);
 601
 602     cmb_filterOption.removeAllItems();
 603     if (haveData)
 604     {
 605       cmb_filterOption.addItem(new FilterOption(
 606               MessageManager.getString("label.best_quality"),
 607               "overall_quality", VIEWS_FILTER, false));
 608       cmb_filterOption.addItem(new FilterOption(
 609               MessageManager.getString("label.best_resolution"),
 610               "resolution", VIEWS_FILTER, false));
 611       cmb_filterOption.addItem(new FilterOption(
 612               MessageManager.getString("label.most_protein_chain"),
 613               "number_of_protein_chains", VIEWS_FILTER, false));
 614       cmb_filterOption.addItem(new FilterOption(
 615               MessageManager.getString("label.most_bound_molecules"),
 616               "number_of_bound_molecules", VIEWS_FILTER, false));
 617       cmb_filterOption.addItem(new FilterOption(
 618               MessageManager.getString("label.most_polymer_residues"),
 619               "number_of_polymer_residues", VIEWS_FILTER, true));
 620     }
 621     cmb_filterOption.addItem(
 622             new FilterOption(MessageManager.getString("label.enter_pdb_id"),
 623                     "-", VIEWS_ENTER_ID, false));
 624     cmb_filterOption.addItem(
 625             new FilterOption(MessageManager.getString("label.from_file"),
 626                     "-", VIEWS_FROM_FILE, false));
 627
 628     if (cachedPDBExist)
 629     {
 630       FilterOption cachedOption = new FilterOption(
 631               MessageManager.getString("label.cached_structures"),
 632               "-", VIEWS_LOCAL_PDB, false);
 633       cmb_filterOption.addItem(cachedOption);
 634       cmb_filterOption.setSelectedItem(cachedOption);
 635     }
 636
 637     cmb_filterOption.addItemListener(this);
 638   }
 639
 640   /**
 641    * Updates the displayed view based on the selected filter option
 642    */
 643   protected void updateCurrentView()
 644   {
 645     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 646             .getSelectedItem());
 647     layout_switchableViews.show(pnl_switchableViews,
 648             selectedFilterOpt.getView());
 649     String filterTitle = mainFrame.getTitle();
 650     mainFrame.setTitle(frameTitle);
 651     chk_invertFilter.setVisible(false);
 652     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 653     {
 654       mainFrame.setTitle(filterTitle);
 655       chk_invertFilter.setVisible(true);
 656       filterResultSet(selectedFilterOpt.getValue());
 657     }
 658     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 659             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 660     {
 661       mainFrame.setTitle(MessageManager
 662               .getString("label.structure_chooser_manual_association"));
 663       idInputAssSeqPanel.loadCmbAssSeq();
 664       fileChooserAssSeqPanel.loadCmbAssSeq();
 665     }
 666     validateSelections();
 667   }
 668
 669   /**
 670    * Validates user selection and enables the 'Add' and 'New View' buttons if
 671    * all parameters are correct (the Add button will only be visible if there is
 672    * at least one existing structure viewer open). This basically means at least
 673    * one structure selected and no error messages.
 674    * <p>
 675    * The 'Superpose Structures' option is enabled if either more than one
 676    * structure is selected, or the 'Add' to existing view option is enabled, and
 677    * disabled if the only option is to open a new view of a single structure.
 678    */
 679   @Override
 680   protected void validateSelections()
 681   {
 682     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 683             .getSelectedItem());
 684     btn_add.setEnabled(false);
 685     String currentView = selectedFilterOpt.getView();
 686     int selectedCount = 0;
 687     if (currentView == VIEWS_FILTER)
 688     {
 689       selectedCount = getResultTable().getSelectedRows().length;
 690       if (selectedCount > 0)
 691       {
 692         btn_add.setEnabled(true);
 693       }
 694     }
 695     else if (currentView == VIEWS_LOCAL_PDB)
 696     {
 697       selectedCount = tbl_local_pdb.getSelectedRows().length;
 698       if (selectedCount > 0)
 699       {
 700         btn_add.setEnabled(true);
 701       }
 702     }
 703     else if (currentView == VIEWS_ENTER_ID)
 704     {
 705       validateAssociationEnterPdb();
 706     }
 707     else if (currentView == VIEWS_FROM_FILE)
 708     {
 709       validateAssociationFromFile();
 710     }
 711
 712     btn_newView.setEnabled(btn_add.isEnabled());
 713
 714     /*
 715      * enable 'Superpose' option if more than one structure is selected,
 716      * or there are view(s) available to add structure(s) to
 717      */
 718     chk_superpose
 719             .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
 720   }
 721
 722   /**
 723    * Validates inputs from the Manual PDB entry panel
 724    */
 725   protected void validateAssociationEnterPdb()
 726   {
 727     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 728             .getCmb_assSeq().getSelectedItem();
 729     lbl_pdbManualFetchStatus.setIcon(errorImage);
 730     lbl_pdbManualFetchStatus.setToolTipText("");
 731     if (txt_search.getText().length() > 0)
 732     {
 733       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
 734               MessageManager.formatMessage("info.no_pdb_entry_found_for",
 735                       txt_search.getText())));
 736     }
 737
 738     if (errorWarning.length() > 0)
 739     {
 740       lbl_pdbManualFetchStatus.setIcon(warningImage);
 741       lbl_pdbManualFetchStatus.setToolTipText(
 742               JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
 743     }
 744
 745     if (selectedSequences.length == 1 || !assSeqOpt.getName()
 746             .equalsIgnoreCase("-Select Associated Seq-"))
 747     {
 748       txt_search.setEnabled(true);
 749       if (isValidPBDEntry)
 750       {
 751         btn_add.setEnabled(true);
 752         lbl_pdbManualFetchStatus.setToolTipText("");
 753         lbl_pdbManualFetchStatus.setIcon(goodImage);
 754       }
 755     }
 756     else
 757     {
 758       txt_search.setEnabled(false);
 759       lbl_pdbManualFetchStatus.setIcon(errorImage);
 760     }
 761   }
 762
 763   /**
 764    * Validates inputs for the manual PDB file selection options
 765    */
 766   protected void validateAssociationFromFile()
 767   {
 768     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
 769             .getCmb_assSeq().getSelectedItem();
 770     lbl_fromFileStatus.setIcon(errorImage);
 771     if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
 772             .getName().equalsIgnoreCase("-Select Associated Seq-")))
 773     {
 774       btn_pdbFromFile.setEnabled(true);
 775       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
 776       {
 777         btn_add.setEnabled(true);
 778         lbl_fromFileStatus.setIcon(goodImage);
 779       }
 780     }
 781     else
 782     {
 783       btn_pdbFromFile.setEnabled(false);
 784       lbl_fromFileStatus.setIcon(errorImage);
 785     }
 786   }
 787
 788   @Override
 789   protected void cmbAssSeqStateChanged()
 790   {
 791     validateSelections();
 792   }
 793
 794   /**
 795    * Handles the state change event for the 'filter' combo-box and 'invert'
 796    * check-box
 797    */
 798   @Override
 799   protected void stateChanged(ItemEvent e)
 800   {
 801     if (e.getSource() instanceof JCheckBox)
 802     {
 803       updateCurrentView();
 804     }
 805     else
 806     {
 807       if (e.getStateChange() == ItemEvent.SELECTED)
 808       {
 809         updateCurrentView();
 810       }
 811     }
 812
 813   }
 814
 815   /**
 816    * select structures for viewing by their PDB IDs
 817    *
 818    * @param pdbids
 819    * @return true if structures were found and marked as selected
 820    */
 821   public boolean selectStructure(String... pdbids)
 822   {
 823     boolean found = false;
 824
 825     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 826             .getSelectedItem());
 827     String currentView = selectedFilterOpt.getView();
 828     JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
 829             : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
 830
 831     if (restable == null)
 832     {
 833       // can't select (enter PDB ID, or load file - need to also select which
 834       // sequence to associate with)
 835       return false;
 836     }
 837
 838     int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
 839     for (int r = 0; r < restable.getRowCount(); r++)
 840     {
 841       for (int p = 0; p < pdbids.length; p++)
 842       {
 843         if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
 844                 .equalsIgnoreCase(pdbids[p]))
 845         {
 846           restable.setRowSelectionInterval(r, r);
 847           found = true;
 848         }
 849       }
 850     }
 851     return found;
 852   }
 853
 854   /**
 855    * Handles the 'New View' action
 856    */
 857   @Override
 858   protected void newView_ActionPerformed()
 859   {
 860     targetView.setSelectedItem(null);
 861     showStructures(false);
 862   }
 863
 864   /**
 865    * Handles the 'Add to existing viewer' action
 866    */
 867   @Override
 868   protected void add_ActionPerformed()
 869   {
 870     showStructures(false);
 871   }
 872
 873   /**
 874    * structure viewer opened by this dialog, or null
 875    */
 876   protected StructureViewer sViewer = null;
 877
 878   public void showStructures(boolean waitUntilFinished)
 879   {
 880
 881     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 882
 883     final int preferredHeight = pnl_filter.getHeight();
 884
 885     Runnable viewStruc = new Runnable()
 886     {
 887       @Override
 888       public void run()
 889       {
 890         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 891                 .getSelectedItem());
 892         String currentView = selectedFilterOpt.getView();
 893         JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
 894                 : tbl_local_pdb;
 895
 896         if (currentView == VIEWS_FILTER)
 897         {
 898           int pdbIdColIndex = restable.getColumn("PDB Id")
 899                   .getModelIndex();
 900           int refSeqColIndex = restable.getColumn("Ref Sequence")
 901                   .getModelIndex();
 902           int[] selectedRows = restable.getSelectedRows();
 903           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 904           int count = 0;
 905           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 906           for (int row : selectedRows)
 907           {
 908             String pdbIdStr = restable
 909                     .getValueAt(row, pdbIdColIndex).toString();
 910             SequenceI selectedSeq = (SequenceI) restable
 911                     .getValueAt(row, refSeqColIndex);
 912             selectedSeqsToView.add(selectedSeq);
 913             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
 914             if (pdbEntry == null)
 915             {
 916               pdbEntry = getFindEntry(pdbIdStr,
 917                       selectedSeq.getAllPDBEntries());
 918             }
 919
 920             if (pdbEntry == null)
 921             {
 922               pdbEntry = new PDBEntry();
 923               pdbEntry.setId(pdbIdStr);
 924               pdbEntry.setType(PDBEntry.Type.PDB);
 925               selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
 926             }
 927             pdbEntriesToView[count++] = pdbEntry;
 928           }
 929           SequenceI[] selectedSeqs = selectedSeqsToView
 930                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 931           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 932                   selectedSeqs);
 933         }
 934         else if (currentView == VIEWS_LOCAL_PDB)
 935         {
 936           int[] selectedRows = tbl_local_pdb.getSelectedRows();
 937           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 938           int count = 0;
 939           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
 940                   .getModelIndex();
 941           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
 942                   .getModelIndex();
 943           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 944           for (int row : selectedRows)
 945           {
 946             PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
 947                     pdbIdColIndex);
 948             pdbEntriesToView[count++] = pdbEntry;
 949             SequenceI selectedSeq = (SequenceI) tbl_local_pdb
 950                     .getValueAt(row, refSeqColIndex);
 951             selectedSeqsToView.add(selectedSeq);
 952           }
 953           SequenceI[] selectedSeqs = selectedSeqsToView
 954                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 955           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 956                   selectedSeqs);
 957         }
 958         else if (currentView == VIEWS_ENTER_ID)
 959         {
 960           SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
 961                   .getCmb_assSeq().getSelectedItem()).getSequence();
 962           if (userSelectedSeq != null)
 963           {
 964             selectedSequence = userSelectedSeq;
 965           }
 966           String pdbIdStr = txt_search.getText();
 967           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
 968           if (pdbEntry == null)
 969           {
 970             pdbEntry = new PDBEntry();
 971             if (pdbIdStr.split(":").length > 1)
 972             {
 973               pdbEntry.setId(pdbIdStr.split(":")[0]);
 974               pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
 975             }
 976             else
 977             {
 978               pdbEntry.setId(pdbIdStr);
 979             }
 980             pdbEntry.setType(PDBEntry.Type.PDB);
 981             selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
 982           }
 983
 984           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
 985           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 986                   new SequenceI[]
 987                   { selectedSequence });
 988         }
 989         else if (currentView == VIEWS_FROM_FILE)
 990         {
 991           SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
 992                   .getCmb_assSeq().getSelectedItem()).getSequence();
 993           if (userSelectedSeq != null)
 994           {
 995             selectedSequence = userSelectedSeq;
 996           }
 997           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 998                   .associatePdbWithSeq(selectedPdbFileName,
 999                           DataSourceType.FILE, selectedSequence, true,
1000                           Desktop.getInstance());
1001
1002           sViewer = launchStructureViewer(
1003                   ssm, new PDBEntry[]
1004                   { fileEntry }, ap,
1005                   new SequenceI[]
1006                   { selectedSequence });
1007         }
1008         SwingUtilities.invokeLater(new Runnable()
1009         {
1010           @Override
1011           public void run()
1012           {
1013             closeAction(preferredHeight);
1014             mainFrame.dispose();
1015           }
1016         });
1017       }
1018     };
1019     Thread runner = new Thread(viewStruc);
1020     runner.start();
1021     if (waitUntilFinished)
1022     {
1023       while (sViewer == null ? runner.isAlive()
1024               : (sViewer.sview == null ? true
1025                       : !sViewer.sview.hasMapping()))
1026       {
1027         try
1028         {
1029           Thread.sleep(300);
1030         } catch (InterruptedException ie)
1031         {
1032
1033         }
1034       }
1035     }
1036   }
1037
1038   protected PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
1039   {
1040     Objects.requireNonNull(id);
1041     Objects.requireNonNull(pdbEntries);
1042     PDBEntry foundEntry = null;
1043     for (PDBEntry entry : pdbEntries)
1044     {
1045       if (entry.getId().equalsIgnoreCase(id))
1046       {
1047         return entry;
1048       }
1049     }
1050     return foundEntry;
1051   }
1052
1053   /**
1054    * Answers a structure viewer (new or existing) configured to superimpose
1055    * added structures or not according to the user's choice
1056    *
1057    * @param ssm
1058    * @return
1059    */
1060   StructureViewer getTargetedStructureViewer(
1061           StructureSelectionManager ssm)
1062   {
1063     Object sv = targetView.getSelectedItem();
1064
1065     return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
1066   }
1067
1068   /**
1069    * Adds PDB structures to a new or existing structure viewer
1070    *
1071    * @param ssm
1072    * @param pdbEntriesToView
1073    * @param alignPanel
1074    * @param sequences
1075    * @return
1076    */
1077   protected StructureViewer launchStructureViewer(
1078           StructureSelectionManager ssm,
1079           final PDBEntry[] pdbEntriesToView,
1080           final AlignmentPanel alignPanel, SequenceI[] sequences)
1081   {
1082     long progressId = sequences.hashCode();
1083     setProgressBar(MessageManager
1084             .getString("status.launching_3d_structure_viewer"), progressId);
1085     final StructureViewer theViewer = getTargetedStructureViewer(ssm);
1086     boolean superimpose = chk_superpose.isSelected();
1087     theViewer.setSuperpose(superimpose);
1088
1089     /*
1090      * remember user's choice of superimpose or not
1091      */
1092     Cache.setProperty(AUTOSUPERIMPOSE,
1093             Boolean.valueOf(superimpose).toString());
1094
1095     setProgressBar(null, progressId);
1096     if (SiftsSettings.isMapWithSifts())
1097     {
1098       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
1099       int p = 0;
1100       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
1101       // real PDB ID. For moment, we can also safely do this if there is already
1102       // a known mapping between the PDBEntry and the sequence.
1103       for (SequenceI seq : sequences)
1104       {
1105         PDBEntry pdbe = pdbEntriesToView[p++];
1106         if (pdbe != null && pdbe.getFile() != null)
1107         {
1108           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
1109           if (smm != null && smm.length > 0)
1110           {
1111             for (StructureMapping sm : smm)
1112             {
1113               if (sm.getSequence() == seq)
1114               {
1115                 continue;
1116               }
1117             }
1118           }
1119         }
1120         if (seq.getPrimaryDBRefs().isEmpty())
1121         {
1122           seqsWithoutSourceDBRef.add(seq);
1123           continue;
1124         }
1125       }
1126       if (!seqsWithoutSourceDBRef.isEmpty())
1127       {
1128         int y = seqsWithoutSourceDBRef.size();
1129         setProgressBar(MessageManager.formatMessage(
1130                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
1131                 y), progressId);
1132         SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
1133                 .toArray(new SequenceI[y]);
1134         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
1135         dbRefFetcher.fetchDBRefs(true);
1136
1137         setProgressBar("Fetch complete.", progressId); // todo i18n
1138       }
1139     }
1140     if (pdbEntriesToView.length > 1)
1141     {
1142       setProgressBar(MessageManager.getString(
1143               "status.fetching_3d_structures_for_selected_entries"),
1144               progressId);
1145       theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
1146     }
1147     else
1148     {
1149       setProgressBar(MessageManager.formatMessage(
1150               "status.fetching_3d_structures_for",
1151               pdbEntriesToView[0].getId()),progressId);
1152       theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
1153     }
1154     setProgressBar(null, progressId);
1155     // remember the last viewer we used...
1156     Desktop.getInstance().lastTargetedView = theViewer;
1157     return theViewer;
1158   }
1159
1160   /**
1161    * Populates the combo-box used in associating manually fetched structures to
1162    * a unique sequence when more than one sequence selection is made.
1163    */
1164   @Override
1165   protected void populateCmbAssociateSeqOptions(
1166           JComboBox<AssociateSeqOptions> cmb_assSeq,
1167           JLabel lbl_associateSeq)
1168   {
1169     cmb_assSeq.removeAllItems();
1170     cmb_assSeq.addItem(
1171             new AssociateSeqOptions("-Select Associated Seq-", null));
1172     lbl_associateSeq.setVisible(false);
1173     if (selectedSequences.length > 1)
1174     {
1175       for (SequenceI seq : selectedSequences)
1176       {
1177         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
1178       }
1179     }
1180     else
1181     {
1182       String seqName = selectedSequence.getDisplayId(false);
1183       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
1184       lbl_associateSeq.setText(seqName);
1185       lbl_associateSeq.setVisible(true);
1186       cmb_assSeq.setVisible(false);
1187     }
1188   }
1189
1190   protected boolean isStructuresDiscovered()
1191   {
1192     return discoveredStructuresSet != null
1193             && !discoveredStructuresSet.isEmpty();
1194   }
1195
1196   protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes this.
1197   // Doing a search for "1" or "1c" is valuable?
1198   // Those work but are enormously slow.
1199
1200   @Override
1201   protected void txt_search_ActionPerformed()
1202   {
1203     String text = txt_search.getText().trim();
1204         if (text.length() >= PDB_ID_MIN)
1205   {
1206     new Thread()
1207     {
1208
1209         @Override
1210       public void run()
1211       {
1212         errorWarning.setLength(0);
1213         isValidPBDEntry = false;
1214         if (text.length() > 0)
1215         {
1216           String searchTerm = text.toLowerCase();
1217           searchTerm = searchTerm.split(":")[0];
1218           // System.out.println(">>>>> search term : " + searchTerm);
1219           List<FTSDataColumnI> wantedFields = new ArrayList<>();
1220           FTSRestRequest pdbRequest = new FTSRestRequest();
1221           pdbRequest.setAllowEmptySeq(false);
1222           pdbRequest.setResponseSize(1);
1223           pdbRequest.setFieldToSearchBy("(pdb_id:");
1224           pdbRequest.setWantedFields(wantedFields);
1225           pdbRequest.setSearchTerm(searchTerm + ")");
1226           pdbRequest.setAssociatedSequence(selectedSequence);
1227           pdbRestClient = PDBFTSRestClient.getInstance();
1228           wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
1229           FTSRestResponse resultList;
1230           try
1231           {
1232             resultList = pdbRestClient.executeRequest(pdbRequest);
1233           } catch (Exception e)
1234           {
1235             errorWarning.append(e.getMessage());
1236             return;
1237           } finally
1238           {
1239             validateSelections();
1240           }
1241           if (resultList.getSearchSummary() != null
1242                   && resultList.getSearchSummary().size() > 0)
1243           {
1244             isValidPBDEntry = true;
1245           }
1246         }
1247         validateSelections();
1248       }
1249     }.start();
1250   }
1251   }
1252
1253   @Override
1254   protected void tabRefresh()
1255   {
1256     if (selectedSequences != null)
1257     {
1258       Thread refreshThread = new Thread(new Runnable()
1259       {
1260         @Override
1261         public void run()
1262         {
1263           fetchStructuresMetaData();
1264           filterResultSet(
1265                   ((FilterOption) cmb_filterOption.getSelectedItem())
1266                           .getValue());
1267         }
1268       });
1269       refreshThread.start();
1270     }
1271   }
1272
1273   public class PDBEntryTableModel extends AbstractTableModel
1274   {
1275     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1276         "File" };
1277
1278     private List<CachedPDB> pdbEntries;
1279
1280     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1281     {
1282       this.pdbEntries = new ArrayList<>(pdbEntries);
1283     }
1284
1285     @Override
1286     public String getColumnName(int columnIndex)
1287     {
1288       return columns[columnIndex];
1289     }
1290
1291     @Override
1292     public int getRowCount()
1293     {
1294       return pdbEntries.size();
1295     }
1296
1297     @Override
1298     public int getColumnCount()
1299     {
1300       return columns.length;
1301     }
1302
1303     @Override
1304     public boolean isCellEditable(int row, int column)
1305     {
1306       return false;
1307     }
1308
1309     @Override
1310     public Object getValueAt(int rowIndex, int columnIndex)
1311     {
1312       Object value = "??";
1313       CachedPDB entry = pdbEntries.get(rowIndex);
1314       switch (columnIndex)
1315       {
1316       case 0:
1317         value = entry.getSequence();
1318         break;
1319       case 1:
1320         value = entry.getPdbEntry();
1321         break;
1322       case 2:
1323         value = entry.getPdbEntry().getChainCode() == null ? "_"
1324                 : entry.getPdbEntry().getChainCode();
1325         break;
1326       case 3:
1327         value = entry.getPdbEntry().getType();
1328         break;
1329       case 4:
1330         value = entry.getPdbEntry().getFile();
1331         break;
1332       }
1333       return value;
1334     }
1335
1336     @Override
1337     public Class<?> getColumnClass(int columnIndex)
1338     {
1339       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1340     }
1341
1342     public CachedPDB getPDBEntryAt(int row)
1343     {
1344       return pdbEntries.get(row);
1345     }
1346
1347   }
1348
1349   private class CachedPDB
1350   {
1351     private SequenceI sequence;
1352
1353     private PDBEntry pdbEntry;
1354
1355     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1356     {
1357       this.sequence = sequence;
1358       this.pdbEntry = pdbEntry;
1359     }
1360
1361     public SequenceI getSequence()
1362     {
1363       return sequence;
1364     }
1365
1366     public PDBEntry getPdbEntry()
1367     {
1368       return pdbEntry;
1369     }
1370
1371   }
1372
1373   private IProgressIndicator progressBar;
1374
1375   @Override
1376   public void setProgressBar(String message, long id)
1377   {
1378     progressBar.setProgressBar(message, id);
1379   }
1380
1381   @Override
1382   public void registerHandler(long id, IProgressIndicatorHandler handler)
1383   {
1384     progressBar.registerHandler(id, handler);
1385   }
1386
1387   @Override
1388   public boolean operationInProgress()
1389   {
1390     return progressBar.operationInProgress();
1391   }
1392
1393   public JalviewStructureDisplayI getOpenedStructureViewer()
1394   {
1395     return sViewer == null ? null : sViewer.sview;
1396   }
1397 }