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 java.util.Locale;
  25
  26 import java.awt.event.ItemEvent;
  27 import java.util.ArrayList;
  28 import java.util.Collection;
  29 import java.util.HashSet;
  30 import java.util.LinkedHashSet;
  31 import java.util.List;
  32 import java.util.concurrent.Executors;
  33
  34 import javax.swing.JCheckBox;
  35 import javax.swing.JComboBox;
  36 import javax.swing.JLabel;
  37 import javax.swing.JTable;
  38 import javax.swing.SwingUtilities;
  39 import javax.swing.table.AbstractTableModel;
  40
  41 import jalview.api.structures.JalviewStructureDisplayI;
  42 import jalview.bin.Cache;
  43 import jalview.bin.Jalview;
  44 import jalview.datamodel.PDBEntry;
  45 import jalview.datamodel.SequenceI;
  46 import jalview.fts.api.FTSData;
  47 import jalview.fts.api.FTSDataColumnI;
  48 import jalview.fts.api.FTSRestClientI;
  49 import jalview.fts.core.FTSDataColumnPreferences;
  50 import jalview.fts.core.FTSRestRequest;
  51 import jalview.fts.core.FTSRestResponse;
  52 import jalview.fts.service.pdb.PDBFTSRestClient;
  53 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
  54 import jalview.gui.structurechooser.StructureChooserQuerySource;
  55 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
  56 import jalview.io.DataSourceType;
  57 import jalview.jbgui.FilterOption;
  58 import jalview.jbgui.GStructureChooser;
  59 import jalview.structure.StructureMapping;
  60 import jalview.structure.StructureSelectionManager;
  61 import jalview.util.MessageManager;
  62 import jalview.ws.DBRefFetcher;
  63 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  64 import jalview.ws.seqfetcher.DbSourceProxy;
  65 import jalview.ws.sifts.SiftsSettings;
  66
  67 /**
  68  * Provides the behaviors for the Structure chooser Panel
  69  *
  70  * @author tcnofoegbu
  71  *
  72  */
  73 @SuppressWarnings("serial")
  74 public class StructureChooser extends GStructureChooser
  75         implements IProgressIndicator
  76 {
  77   private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
  78
  79   /**
  80    * transient combo box choice for initiating 3db fetch
  81    */
  82   private static final String VIEWS_QUERYING_TDB = "QUERY_3DB";
  83
  84   private SequenceI selectedSequence;
  85
  86   private SequenceI[] selectedSequences;
  87
  88   private IProgressIndicator progressIndicator;
  89
  90   private Collection<FTSData> discoveredStructuresSet;
  91
  92   private StructureChooserQuerySource data;
  93
  94   @Override
  95   protected FTSDataColumnPreferences getFTSDocFieldPrefs()
  96   {
  97     return data.getDocFieldPrefs();
  98   }
  99
 100   private String selectedPdbFileName;
 101
 102   private boolean isValidPBDEntry;
 103
 104   private boolean cachedPDBExists;
 105
 106   private Collection<FTSData> lastDiscoveredStructuresSet;
 107
 108   private boolean canQueryTDB = false;
 109
 110   private boolean notQueriedTDBYet = true;
 111
 112   List<SequenceI> seqsWithoutSourceDBRef = null;
 113
 114   private static StructureViewer lastTargetedView = null;
 115
 116   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
 117           AlignmentPanel ap)
 118   {
 119     // which FTS engine to use
 120     data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
 121     initDialog();
 122
 123     this.ap = ap;
 124     this.selectedSequence = selectedSeq;
 125     this.selectedSequences = selectedSeqs;
 126     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
 127     init();
 128
 129   }
 130
 131   /**
 132    * sets canQueryTDB if protein sequences without a canonical uniprot ref or at
 133    * least one structure are discovered.
 134    */
 135   private void populateSeqsWithoutSourceDBRef()
 136   {
 137     seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
 138     boolean needCanonical = false;
 139     for (SequenceI seq : selectedSequences)
 140     {
 141       if (seq.isProtein())
 142       {
 143         int dbRef = ThreeDBStructureChooserQuerySource
 144                 .checkUniprotRefs(seq.getDBRefs());
 145         if (dbRef < 0)
 146         {
 147           if (dbRef == -1)
 148           {
 149             // need to retrieve canonicals
 150             needCanonical = true;
 151             seqsWithoutSourceDBRef.add(seq);
 152           }
 153           else
 154           {
 155             // could be a sequence with pdb ref
 156             if (seq.getAllPDBEntries() == null
 157                     || seq.getAllPDBEntries().size() == 0)
 158             {
 159               seqsWithoutSourceDBRef.add(seq);
 160             }
 161           }
 162         }
 163       }
 164     }
 165     // retrieve database refs for protein sequences
 166     if (!seqsWithoutSourceDBRef.isEmpty())
 167     {
 168       canQueryTDB = true;
 169       if (needCanonical)
 170       {
 171         notQueriedTDBYet = false;
 172       }
 173     }
 174   };
 175
 176   /**
 177    * Initializes parameters used by the Structure Chooser Panel
 178    */
 179   protected void init()
 180   {
 181     if (!Jalview.isHeadlessMode())
 182     {
 183       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 184     }
 185
 186     chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
 187
 188     Executors.defaultThreadFactory().newThread(new Runnable()
 189     {
 190       public void run()
 191       {
 192         populateSeqsWithoutSourceDBRef();
 193         initialStructureDiscovery();
 194       }
 195
 196     }).start();
 197
 198   }
 199
 200   // called by init
 201   private void initialStructureDiscovery()
 202   {
 203     // check which FTS engine to use
 204     data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences);
 205
 206     // ensure a filter option is in force for search
 207     populateFilterComboBox(true, cachedPDBExists);
 208
 209     // looks for any existing structures already loaded
 210     // for the sequences (the cached ones)
 211     // then queries the StructureChooserQuerySource to
 212     // discover more structures.
 213     //
 214     // Possible optimisation is to only begin querying
 215     // the structure chooser if there are no cached structures.
 216
 217     long startTime = System.currentTimeMillis();
 218     updateProgressIndicator(
 219             MessageManager.getString("status.loading_cached_pdb_entries"),
 220             startTime);
 221     loadLocalCachedPDBEntries();
 222     updateProgressIndicator(null, startTime);
 223     updateProgressIndicator(
 224             MessageManager.getString("status.searching_for_pdb_structures"),
 225             startTime);
 226     fetchStructuresMetaData();
 227     // revise filter options if no results were found
 228     populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
 229     discoverStructureViews();
 230     updateProgressIndicator(null, startTime);
 231     mainFrame.setVisible(true);
 232     updateCurrentView();
 233   }
 234
 235   private void promptForTDBFetch()
 236   {
 237     final long progressId = System.currentTimeMillis();
 238
 239     // final action after prompting and discovering db refs
 240     final Runnable strucDiscovery = new Runnable()
 241     {
 242       @Override
 243       public void run()
 244       {
 245         progressBar.setProgressBar("status.searching_3d_beacons", progressId);
 246         // TODO: warn if no accessions discovered
 247         populateSeqsWithoutSourceDBRef();
 248         // redo initial discovery - this time with 3d beacons
 249         // Executors.
 250         previousWantedFields=null;
 251         initialStructureDiscovery();
 252         if (!isStructuresDiscovered())
 253         {
 254           progressBar.setProgressBar("status.no_structures_discovered_from_3d_beacons", progressId);
 255         } else {
 256           progressBar.setProgressBar(null, progressId);
 257         }
 258       }
 259     };
 260
 261     final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI()
 262     {
 263
 264       @Override
 265       public void finished()
 266       {
 267         // filter has been selected, so we set flag to remove ourselves
 268         notQueriedTDBYet = false;
 269         // new thread to discover structures - via 3d beacons
 270         Executors.defaultThreadFactory().newThread(strucDiscovery).start();
 271
 272       }
 273     };
 274
 275     // fetch db refs if OK pressed
 276     final Runnable discoverCanonicalDBrefs = new Runnable()
 277     {
 278       @Override
 279       public void run()
 280       {
 281         populateSeqsWithoutSourceDBRef();
 282
 283         final int y = seqsWithoutSourceDBRef.size();
 284         if (y > 0)
 285         {
 286           final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
 287                   .toArray(new SequenceI[y]);
 288           DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
 289                   progressBar, new DbSourceProxy[]
 290                   { new jalview.ws.dbsources.Uniprot() }, null, false);
 291           dbRefFetcher.addListener(afterDbRefFetch);
 292           // ideally this would also gracefully run with callbacks
 293           dbRefFetcher.fetchDBRefs(true);
 294         } else {
 295           // call finished action directly
 296           afterDbRefFetch.finished();
 297         }
 298       }
 299
 300     };
 301     final Runnable revertview = new Runnable() {
 302       public void run() {
 303         if (lastSelected!=null) {
 304           cmb_filterOption.setSelectedItem(lastSelected);
 305         }
 306       };
 307     };
 308     // need cancel and no to result in the discoverPDB action - mocked is
 309     // 'cancel'
 310     JvOptionPane.newOptionDialog(this)
 311             .setResponseHandler(JvOptionPane.OK_OPTION,
 312                     discoverCanonicalDBrefs)
 313             .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
 314             .setResponseHandler(JvOptionPane.NO_OPTION, revertview)
 315             .showDialog(
 316                     MessageManager.formatMessage(
 317                             "label.fetch_references_for_3dbeacons",
 318                             seqsWithoutSourceDBRef.size()),
 319                     MessageManager
 320                             .getString("label.3dbeacons"),
 321                     JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE,
 322                     null, new Object[]
 323                     { MessageManager.getString("action.ok"),
 324                         MessageManager.getString("action.cancel") },
 325                     MessageManager.getString("action.ok"));
 326   }
 327
 328   /**
 329    * Builds a drop-down choice list of existing structure viewers to which new
 330    * structures may be added. If this list is empty then it, and the 'Add'
 331    * button, are hidden.
 332    */
 333   private void discoverStructureViews()
 334   {
 335     if (Desktop.instance != null)
 336     {
 337       targetView.removeAllItems();
 338       if (lastTargetedView != null && !lastTargetedView.isVisible())
 339       {
 340         lastTargetedView = null;
 341       }
 342       int linkedViewsAt = 0;
 343       for (StructureViewerBase view : Desktop.instance
 344               .getStructureViewers(null, null))
 345       {
 346         StructureViewer viewHandler = (lastTargetedView != null
 347                 && lastTargetedView.sview == view) ? lastTargetedView
 348                         : StructureViewer.reconfigure(view);
 349
 350         if (view.isLinkedWith(ap))
 351         {
 352           targetView.insertItemAt(viewHandler, linkedViewsAt++);
 353         }
 354         else
 355         {
 356           targetView.addItem(viewHandler);
 357         }
 358       }
 359
 360       /*
 361        * show option to Add to viewer if at least 1 viewer found
 362        */
 363       targetView.setVisible(false);
 364       if (targetView.getItemCount() > 0)
 365       {
 366         targetView.setVisible(true);
 367         if (lastTargetedView != null)
 368         {
 369           targetView.setSelectedItem(lastTargetedView);
 370         }
 371         else
 372         {
 373           targetView.setSelectedIndex(0);
 374         }
 375       }
 376       btn_add.setVisible(targetView.isVisible());
 377     }
 378   }
 379
 380   /**
 381    * Updates the progress indicator with the specified message
 382    *
 383    * @param message
 384    *          displayed message for the operation
 385    * @param id
 386    *          unique handle for this indicator
 387    */
 388   protected void updateProgressIndicator(String message, long id)
 389   {
 390     if (progressIndicator != null)
 391     {
 392       progressIndicator.setProgressBar(message, id);
 393     }
 394   }
 395
 396   /**
 397    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
 398    * selection group
 399    */
 400   void fetchStructuresMetaData()
 401   {
 402     long startTime = System.currentTimeMillis();
 403     Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
 404             .getStructureSummaryFields();
 405
 406     discoveredStructuresSet = new LinkedHashSet<>();
 407     HashSet<String> errors = new HashSet<>();
 408
 409     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 410             .getSelectedItem());
 411
 412     for (SequenceI seq : selectedSequences)
 413     {
 414
 415       FTSRestResponse resultList;
 416       try
 417       {
 418         resultList = data.fetchStructuresMetaData(seq, wantedFields,
 419                 selectedFilterOpt, !chk_invertFilter.isSelected());
 420         // null response means the FTSengine didn't yield a query for this
 421         // consider designing a special exception if we really wanted to be
 422         // OOCrazy
 423         if (resultList == null)
 424         {
 425           continue;
 426         }
 427       } catch (Exception e)
 428       {
 429         e.printStackTrace();
 430         errors.add(e.getMessage());
 431         continue;
 432       }
 433       if (resultList.getSearchSummary() != null
 434               && !resultList.getSearchSummary().isEmpty())
 435       {
 436         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 437       }
 438     }
 439
 440     int noOfStructuresFound = 0;
 441     String totalTime = (System.currentTimeMillis() - startTime)
 442             + " milli secs";
 443     if (discoveredStructuresSet != null
 444             && !discoveredStructuresSet.isEmpty())
 445     {
 446       getResultTable()
 447               .setModel(data.getTableModel(discoveredStructuresSet));
 448
 449       noOfStructuresFound = discoveredStructuresSet.size();
 450       lastDiscoveredStructuresSet = discoveredStructuresSet;
 451       mainFrame.setTitle(MessageManager.formatMessage(
 452               "label.structure_chooser_no_of_structures",
 453               noOfStructuresFound, totalTime));
 454     }
 455     else
 456     {
 457       mainFrame.setTitle(MessageManager
 458               .getString("label.structure_chooser_manual_association"));
 459       if (errors.size() > 0)
 460       {
 461         StringBuilder errorMsg = new StringBuilder();
 462         for (String error : errors)
 463         {
 464           errorMsg.append(error).append("\n");
 465         }
 466         JvOptionPane.showMessageDialog(this, errorMsg.toString(),
 467                 MessageManager.getString("label.pdb_web-service_error"),
 468                 JvOptionPane.ERROR_MESSAGE);
 469       }
 470     }
 471   }
 472
 473   protected void loadLocalCachedPDBEntries()
 474   {
 475     ArrayList<CachedPDB> entries = new ArrayList<>();
 476     for (SequenceI seq : selectedSequences)
 477     {
 478       if (seq.getDatasetSequence() != null
 479               && seq.getDatasetSequence().getAllPDBEntries() != null)
 480       {
 481         for (PDBEntry pdbEntry : seq.getDatasetSequence()
 482                 .getAllPDBEntries())
 483         {
 484           if (pdbEntry.getFile() != null)
 485           {
 486             entries.add(new CachedPDB(seq, pdbEntry));
 487           }
 488         }
 489       }
 490     }
 491     cachedPDBExists = !entries.isEmpty();
 492     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
 493     tbl_local_pdb.setModel(tableModelx);
 494   }
 495
 496   /**
 497    * Filters a given list of discovered structures based on supplied argument
 498    *
 499    * @param fieldToFilterBy
 500    *          the field to filter by
 501    */
 502   void filterResultSet(final String fieldToFilterBy)
 503   {
 504     Thread filterThread = new Thread(new Runnable()
 505     {
 506
 507       @Override
 508       public void run()
 509       {
 510         long startTime = System.currentTimeMillis();
 511         lbl_loading.setVisible(true);
 512         Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
 513                 .getStructureSummaryFields();
 514         Collection<FTSData> filteredResponse = new HashSet<>();
 515         HashSet<String> errors = new HashSet<>();
 516
 517         for (SequenceI seq : selectedSequences)
 518         {
 519
 520           FTSRestResponse resultList;
 521           try
 522           {
 523             resultList = data.selectFirstRankedQuery(seq,
 524                     discoveredStructuresSet, wantedFields, fieldToFilterBy,
 525                     !chk_invertFilter.isSelected());
 526
 527           } catch (Exception e)
 528           {
 529             e.printStackTrace();
 530             errors.add(e.getMessage());
 531             continue;
 532           }
 533           if (resultList.getSearchSummary() != null
 534                   && !resultList.getSearchSummary().isEmpty())
 535           {
 536             filteredResponse.addAll(resultList.getSearchSummary());
 537           }
 538         }
 539
 540         String totalTime = (System.currentTimeMillis() - startTime)
 541                 + " milli secs";
 542         if (!filteredResponse.isEmpty())
 543         {
 544           final int filterResponseCount = filteredResponse.size();
 545           Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
 546           reorderedStructuresSet.addAll(filteredResponse);
 547           reorderedStructuresSet.addAll(discoveredStructuresSet);
 548           getResultTable()
 549                   .setModel(data.getTableModel(reorderedStructuresSet));
 550
 551           FTSRestResponse.configureTableColumn(getResultTable(),
 552                   wantedFields, tempUserPrefs);
 553           getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
 554           getResultTable().getColumn("Ref Sequence").setMinWidth(100);
 555           getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
 556           // Update table selection model here
 557           getResultTable().addRowSelectionInterval(0,
 558                   filterResponseCount - 1);
 559           mainFrame.setTitle(MessageManager.formatMessage(
 560                   "label.structure_chooser_filter_time", totalTime));
 561         }
 562         else
 563         {
 564           mainFrame.setTitle(MessageManager.formatMessage(
 565                   "label.structure_chooser_filter_time", totalTime));
 566           if (errors.size() > 0)
 567           {
 568             StringBuilder errorMsg = new StringBuilder();
 569             for (String error : errors)
 570             {
 571               errorMsg.append(error).append("\n");
 572             }
 573             JvOptionPane.showMessageDialog(null, errorMsg.toString(),
 574                     MessageManager.getString("label.pdb_web-service_error"),
 575                     JvOptionPane.ERROR_MESSAGE);
 576           }
 577         }
 578
 579         lbl_loading.setVisible(false);
 580
 581         validateSelections();
 582       }
 583     });
 584     filterThread.start();
 585   }
 586
 587   /**
 588    * Handles action event for btn_pdbFromFile
 589    */
 590   @Override
 591   protected void pdbFromFile_actionPerformed()
 592   {
 593     // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and
 594     // StructureChooser
 595     // works
 596     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 597             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 598     chooser.setFileView(new jalview.io.JalviewFileView());
 599     chooser.setDialogTitle(
 600             MessageManager.formatMessage("label.select_pdb_file_for",
 601                     selectedSequence.getDisplayId(false)));
 602     chooser.setToolTipText(MessageManager.formatMessage(
 603             "label.load_pdb_file_associate_with_sequence",
 604             selectedSequence.getDisplayId(false)));
 605
 606     int value = chooser.showOpenDialog(null);
 607     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
 608     {
 609       selectedPdbFileName = chooser.getSelectedFile().getPath();
 610       jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
 611       validateSelections();
 612     }
 613   }
 614
 615   /**
 616    * Populates the filter combo-box options dynamically depending on discovered
 617    * structures
 618    */
 619   protected void populateFilterComboBox(boolean haveData,
 620           boolean cachedPDBExist)
 621   {
 622     populateFilterComboBox(haveData, cachedPDBExist, null);
 623   }
 624
 625   /**
 626    * Populates the filter combo-box options dynamically depending on discovered
 627    * structures
 628    */
 629   protected void populateFilterComboBox(boolean haveData,
 630           boolean cachedPDBExist, FilterOption lastSel)
 631   {
 632
 633     /*
 634      * temporarily suspend the change listener behaviour
 635      */
 636     cmb_filterOption.removeItemListener(this);
 637     int selSet = -1;
 638     cmb_filterOption.removeAllItems();
 639     if (haveData)
 640     {
 641       List<FilterOption> filters = data
 642               .getAvailableFilterOptions(VIEWS_FILTER);
 643       data.updateAvailableFilterOptions(VIEWS_FILTER, filters,
 644               lastDiscoveredStructuresSet);
 645       int p = 0;
 646       for (FilterOption filter : filters)
 647       {
 648         if (lastSel != null && filter.equals(lastSel))
 649         {
 650           selSet = p;
 651         }
 652         p++;
 653         cmb_filterOption.addItem(filter);
 654       }
 655     }
 656
 657     cmb_filterOption.addItem(
 658             new FilterOption(MessageManager.getString("label.enter_pdb_id"),
 659                     "-", VIEWS_ENTER_ID, false, null));
 660     cmb_filterOption.addItem(
 661             new FilterOption(MessageManager.getString("label.from_file"),
 662                     "-", VIEWS_FROM_FILE, false, null));
 663     if (canQueryTDB && notQueriedTDBYet)
 664     {
 665       FilterOption queryTDBOption = new FilterOption(
 666               MessageManager.getString("label.search_3dbeacons"), "-",
 667               VIEWS_QUERYING_TDB, false, null);
 668       cmb_filterOption.addItem(queryTDBOption);
 669     }
 670
 671     if (cachedPDBExist)
 672     {
 673       FilterOption cachedOption = new FilterOption(
 674               MessageManager.getString("label.cached_structures"), "-",
 675               VIEWS_LOCAL_PDB, false, null);
 676       cmb_filterOption.addItem(cachedOption);
 677       if (selSet == -1)
 678       {
 679         cmb_filterOption.setSelectedItem(cachedOption);
 680       }
 681     }
 682     if (selSet > -1)
 683     {
 684       cmb_filterOption.setSelectedIndex(selSet);
 685     }
 686     cmb_filterOption.addItemListener(this);
 687   }
 688
 689   /**
 690    * Updates the displayed view based on the selected filter option
 691    */
 692   protected void updateCurrentView()
 693   {
 694     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 695             .getSelectedItem());
 696
 697     // first check if we need to rebuild dialog
 698     if (selectedFilterOpt.getView() == VIEWS_QUERYING_TDB)
 699     {
 700       promptForTDBFetch();
 701       return;
 702     }
 703     if (lastSelected == selectedFilterOpt)
 704     {
 705       // don't need to do anything, probably
 706       return;
 707     }
 708     // otherwise, record selection
 709     // and update the layout and dialog accordingly
 710     lastSelected = selectedFilterOpt;
 711
 712     layout_switchableViews.show(pnl_switchableViews,
 713             selectedFilterOpt.getView());
 714     String filterTitle = mainFrame.getTitle();
 715     mainFrame.setTitle(frameTitle);
 716     chk_invertFilter.setVisible(false);
 717
 718     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 719     {
 720       mainFrame.setTitle(filterTitle);
 721       // TDB Query has no invert as yet
 722       chk_invertFilter.setVisible(selectedFilterOpt
 723               .getQuerySource() instanceof PDBStructureChooserQuerySource);
 724
 725       if (data != selectedFilterOpt.getQuerySource()
 726               || data.needsRefetch(selectedFilterOpt))
 727       {
 728         data = selectedFilterOpt.getQuerySource();
 729         // rebuild the views completely, since prefs will also change
 730         tabRefresh();
 731         return;
 732       }
 733       else
 734       {
 735         filterResultSet(selectedFilterOpt.getValue());
 736       }
 737     }
 738     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 739             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 740     {
 741       mainFrame.setTitle(MessageManager
 742               .getString("label.structure_chooser_manual_association"));
 743       idInputAssSeqPanel.loadCmbAssSeq();
 744       fileChooserAssSeqPanel.loadCmbAssSeq();
 745     }
 746     validateSelections();
 747   }
 748
 749   /**
 750    * Validates user selection and enables the 'Add' and 'New View' buttons if
 751    * all parameters are correct (the Add button will only be visible if there is
 752    * at least one existing structure viewer open). This basically means at least
 753    * one structure selected and no error messages.
 754    * <p>
 755    * The 'Superpose Structures' option is enabled if either more than one
 756    * structure is selected, or the 'Add' to existing view option is enabled, and
 757    * disabled if the only option is to open a new view of a single structure.
 758    */
 759   @Override
 760   protected void validateSelections()
 761   {
 762     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 763             .getSelectedItem());
 764     btn_add.setEnabled(false);
 765     String currentView = selectedFilterOpt.getView();
 766     int selectedCount = 0;
 767     if (currentView == VIEWS_FILTER)
 768     {
 769       selectedCount = getResultTable().getSelectedRows().length;
 770       if (selectedCount > 0)
 771       {
 772         btn_add.setEnabled(true);
 773       }
 774     }
 775     else if (currentView == VIEWS_LOCAL_PDB)
 776     {
 777       selectedCount = tbl_local_pdb.getSelectedRows().length;
 778       if (selectedCount > 0)
 779       {
 780         btn_add.setEnabled(true);
 781       }
 782     }
 783     else if (currentView == VIEWS_ENTER_ID)
 784     {
 785       validateAssociationEnterPdb();
 786     }
 787     else if (currentView == VIEWS_FROM_FILE)
 788     {
 789       validateAssociationFromFile();
 790     }
 791
 792     btn_newView.setEnabled(btn_add.isEnabled());
 793
 794     /*
 795      * enable 'Superpose' option if more than one structure is selected,
 796      * or there are view(s) available to add structure(s) to
 797      */
 798     chk_superpose
 799             .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
 800   }
 801
 802   /**
 803    * Validates inputs from the Manual PDB entry panel
 804    */
 805   protected void validateAssociationEnterPdb()
 806   {
 807     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 808             .getCmb_assSeq().getSelectedItem();
 809     lbl_pdbManualFetchStatus.setIcon(errorImage);
 810     lbl_pdbManualFetchStatus.setToolTipText("");
 811     if (txt_search.getText().length() > 0)
 812     {
 813       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
 814               MessageManager.formatMessage("info.no_pdb_entry_found_for",
 815                       txt_search.getText())));
 816     }
 817
 818     if (errorWarning.length() > 0)
 819     {
 820       lbl_pdbManualFetchStatus.setIcon(warningImage);
 821       lbl_pdbManualFetchStatus.setToolTipText(
 822               JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
 823     }
 824
 825     if (selectedSequences.length == 1 || !assSeqOpt.getName()
 826             .equalsIgnoreCase("-Select Associated Seq-"))
 827     {
 828       txt_search.setEnabled(true);
 829       if (isValidPBDEntry)
 830       {
 831         btn_add.setEnabled(true);
 832         lbl_pdbManualFetchStatus.setToolTipText("");
 833         lbl_pdbManualFetchStatus.setIcon(goodImage);
 834       }
 835     }
 836     else
 837     {
 838       txt_search.setEnabled(false);
 839       lbl_pdbManualFetchStatus.setIcon(errorImage);
 840     }
 841   }
 842
 843   /**
 844    * Validates inputs for the manual PDB file selection options
 845    */
 846   protected void validateAssociationFromFile()
 847   {
 848     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
 849             .getCmb_assSeq().getSelectedItem();
 850     lbl_fromFileStatus.setIcon(errorImage);
 851     if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
 852             .getName().equalsIgnoreCase("-Select Associated Seq-")))
 853     {
 854       btn_pdbFromFile.setEnabled(true);
 855       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
 856       {
 857         btn_add.setEnabled(true);
 858         lbl_fromFileStatus.setIcon(goodImage);
 859       }
 860     }
 861     else
 862     {
 863       btn_pdbFromFile.setEnabled(false);
 864       lbl_fromFileStatus.setIcon(errorImage);
 865     }
 866   }
 867
 868   @Override
 869   protected void cmbAssSeqStateChanged()
 870   {
 871     validateSelections();
 872   }
 873   private FilterOption lastSelected=null;
 874   /**
 875    * Handles the state change event for the 'filter' combo-box and 'invert'
 876    * check-box
 877    */
 878   @Override
 879   protected void stateChanged(ItemEvent e)
 880   {
 881     if (e.getSource() instanceof JCheckBox)
 882     {
 883       updateCurrentView();
 884     }
 885     else
 886     {
 887       if (e.getStateChange() == ItemEvent.SELECTED)
 888       {
 889         updateCurrentView();
 890       }
 891     }
 892
 893   }
 894
 895   /**
 896    * select structures for viewing by their PDB IDs
 897    *
 898    * @param pdbids
 899    * @return true if structures were found and marked as selected
 900    */
 901   public boolean selectStructure(String... pdbids)
 902   {
 903     boolean found = false;
 904
 905     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 906             .getSelectedItem());
 907     String currentView = selectedFilterOpt.getView();
 908     JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
 909             : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
 910
 911     if (restable == null)
 912     {
 913       // can't select (enter PDB ID, or load file - need to also select which
 914       // sequence to associate with)
 915       return false;
 916     }
 917
 918     int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
 919     for (int r = 0; r < restable.getRowCount(); r++)
 920     {
 921       for (int p = 0; p < pdbids.length; p++)
 922       {
 923         if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
 924                 .equalsIgnoreCase(pdbids[p]))
 925         {
 926           restable.setRowSelectionInterval(r, r);
 927           found = true;
 928         }
 929       }
 930     }
 931     return found;
 932   }
 933
 934   /**
 935    * Handles the 'New View' action
 936    */
 937   @Override
 938   protected void newView_ActionPerformed()
 939   {
 940     targetView.setSelectedItem(null);
 941     showStructures(false);
 942   }
 943
 944   /**
 945    * Handles the 'Add to existing viewer' action
 946    */
 947   @Override
 948   protected void add_ActionPerformed()
 949   {
 950     showStructures(false);
 951   }
 952
 953   /**
 954    * structure viewer opened by this dialog, or null
 955    */
 956   private StructureViewer sViewer = null;
 957
 958   public void showStructures(boolean waitUntilFinished)
 959   {
 960
 961     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 962
 963     final int preferredHeight = pnl_filter.getHeight();
 964
 965     Runnable viewStruc = new Runnable()
 966     {
 967       @Override
 968       public void run()
 969       {
 970         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 971                 .getSelectedItem());
 972         String currentView = selectedFilterOpt.getView();
 973         JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
 974                 : tbl_local_pdb;
 975
 976         if (currentView == VIEWS_FILTER)
 977         {
 978           int[] selectedRows = restable.getSelectedRows();
 979           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 980           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 981           pdbEntriesToView = data.collectSelectedRows(restable,
 982                   selectedRows, selectedSeqsToView);
 983
 984           SequenceI[] selectedSeqs = selectedSeqsToView
 985                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 986           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 987                   selectedSeqs);
 988         }
 989         else if (currentView == VIEWS_LOCAL_PDB)
 990         {
 991           int[] selectedRows = tbl_local_pdb.getSelectedRows();
 992           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 993           int count = 0;
 994           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
 995                   .getModelIndex();
 996           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
 997                   .getModelIndex();
 998           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 999           for (int row : selectedRows)
1000           {
1001             PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb
1002                     .getModel()).getPDBEntryAt(row).getPdbEntry();
1003
1004             pdbEntriesToView[count++] = pdbEntry;
1005             SequenceI selectedSeq = (SequenceI) tbl_local_pdb
1006                     .getValueAt(row, refSeqColIndex);
1007             selectedSeqsToView.add(selectedSeq);
1008           }
1009           SequenceI[] selectedSeqs = selectedSeqsToView
1010                   .toArray(new SequenceI[selectedSeqsToView.size()]);
1011           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1012                   selectedSeqs);
1013         }
1014         else if (currentView == VIEWS_ENTER_ID)
1015         {
1016           SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
1017                   .getCmb_assSeq().getSelectedItem()).getSequence();
1018           if (userSelectedSeq != null)
1019           {
1020             selectedSequence = userSelectedSeq;
1021           }
1022           String pdbIdStr = txt_search.getText();
1023           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
1024           if (pdbEntry == null)
1025           {
1026             pdbEntry = new PDBEntry();
1027             if (pdbIdStr.split(":").length > 1)
1028             {
1029               pdbEntry.setId(pdbIdStr.split(":")[0]);
1030               pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
1031             }
1032             else
1033             {
1034               pdbEntry.setId(pdbIdStr);
1035             }
1036             pdbEntry.setType(PDBEntry.Type.PDB);
1037             selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
1038           }
1039
1040           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
1041           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1042                   new SequenceI[]
1043                   { selectedSequence });
1044         }
1045         else if (currentView == VIEWS_FROM_FILE)
1046         {
1047           SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
1048                   .getCmb_assSeq().getSelectedItem()).getSequence();
1049           if (userSelectedSeq != null)
1050           {
1051             selectedSequence = userSelectedSeq;
1052           }
1053           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
1054                   .associatePdbWithSeq(selectedPdbFileName,
1055                           DataSourceType.FILE, selectedSequence, true,
1056                           Desktop.instance);
1057
1058           sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
1059                   ap, new SequenceI[]
1060                   { selectedSequence });
1061         }
1062         SwingUtilities.invokeLater(new Runnable()
1063         {
1064           @Override
1065           public void run()
1066           {
1067             closeAction(preferredHeight);
1068             mainFrame.dispose();
1069           }
1070         });
1071       }
1072     };
1073     Thread runner = new Thread(viewStruc);
1074     runner.start();
1075     if (waitUntilFinished)
1076     {
1077       while (sViewer == null ? runner.isAlive()
1078               : (sViewer.sview == null ? true
1079                       : !sViewer.sview.hasMapping()))
1080       {
1081         try
1082         {
1083           Thread.sleep(300);
1084         } catch (InterruptedException ie)
1085         {
1086
1087         }
1088       }
1089     }
1090   }
1091
1092   /**
1093    * Answers a structure viewer (new or existing) configured to superimpose
1094    * added structures or not according to the user's choice
1095    *
1096    * @param ssm
1097    * @return
1098    */
1099   StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm)
1100   {
1101     Object sv = targetView.getSelectedItem();
1102
1103     return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
1104   }
1105
1106   /**
1107    * Adds PDB structures to a new or existing structure viewer
1108    *
1109    * @param ssm
1110    * @param pdbEntriesToView
1111    * @param alignPanel
1112    * @param sequences
1113    * @return
1114    */
1115   private StructureViewer launchStructureViewer(
1116           StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
1117           final AlignmentPanel alignPanel, SequenceI[] sequences)
1118   {
1119     long progressId = sequences.hashCode();
1120     setProgressBar(MessageManager
1121             .getString("status.launching_3d_structure_viewer"), progressId);
1122     final StructureViewer theViewer = getTargetedStructureViewer(ssm);
1123     boolean superimpose = chk_superpose.isSelected();
1124     theViewer.setSuperpose(superimpose);
1125
1126     /*
1127      * remember user's choice of superimpose or not
1128      */
1129     Cache.setProperty(AUTOSUPERIMPOSE,
1130             Boolean.valueOf(superimpose).toString());
1131
1132     setProgressBar(null, progressId);
1133     if (SiftsSettings.isMapWithSifts())
1134     {
1135       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
1136       int p = 0;
1137       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
1138       // real PDB ID. For moment, we can also safely do this if there is already
1139       // a known mapping between the PDBEntry and the sequence.
1140       for (SequenceI seq : sequences)
1141       {
1142         PDBEntry pdbe = pdbEntriesToView[p++];
1143         if (pdbe != null && pdbe.getFile() != null)
1144         {
1145           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
1146           if (smm != null && smm.length > 0)
1147           {
1148             for (StructureMapping sm : smm)
1149             {
1150               if (sm.getSequence() == seq)
1151               {
1152                 continue;
1153               }
1154             }
1155           }
1156         }
1157         if (seq.getPrimaryDBRefs().isEmpty())
1158         {
1159           seqsWithoutSourceDBRef.add(seq);
1160           continue;
1161         }
1162       }
1163       if (!seqsWithoutSourceDBRef.isEmpty())
1164       {
1165         int y = seqsWithoutSourceDBRef.size();
1166         setProgressBar(MessageManager.formatMessage(
1167                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
1168                 y), progressId);
1169         SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
1170                 .toArray(new SequenceI[y]);
1171         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
1172         dbRefFetcher.fetchDBRefs(true);
1173
1174         setProgressBar("Fetch complete.", progressId); // todo i18n
1175       }
1176     }
1177     if (pdbEntriesToView.length > 1)
1178     {
1179       setProgressBar(
1180               MessageManager.getString(
1181                       "status.fetching_3d_structures_for_selected_entries"),
1182               progressId);
1183       theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
1184     }
1185     else
1186     {
1187       setProgressBar(MessageManager.formatMessage(
1188               "status.fetching_3d_structures_for",
1189               pdbEntriesToView[0].getId()), progressId);
1190       theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
1191     }
1192     setProgressBar(null, progressId);
1193     // remember the last viewer we used...
1194     lastTargetedView = theViewer;
1195     return theViewer;
1196   }
1197
1198   /**
1199    * Populates the combo-box used in associating manually fetched structures to
1200    * a unique sequence when more than one sequence selection is made.
1201    */
1202   @Override
1203   protected void populateCmbAssociateSeqOptions(
1204           JComboBox<AssociateSeqOptions> cmb_assSeq,
1205           JLabel lbl_associateSeq)
1206   {
1207     cmb_assSeq.removeAllItems();
1208     cmb_assSeq.addItem(
1209             new AssociateSeqOptions("-Select Associated Seq-", null));
1210     lbl_associateSeq.setVisible(false);
1211     if (selectedSequences.length > 1)
1212     {
1213       for (SequenceI seq : selectedSequences)
1214       {
1215         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
1216       }
1217     }
1218     else
1219     {
1220       String seqName = selectedSequence.getDisplayId(false);
1221       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
1222       lbl_associateSeq.setText(seqName);
1223       lbl_associateSeq.setVisible(true);
1224       cmb_assSeq.setVisible(false);
1225     }
1226   }
1227
1228   protected boolean isStructuresDiscovered()
1229   {
1230     return discoveredStructuresSet != null
1231             && !discoveredStructuresSet.isEmpty();
1232   }
1233
1234   protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes
1235                                // this.
1236   // Doing a search for "1" or "1c" is valuable?
1237   // Those work but are enormously slow.
1238
1239   @Override
1240   protected void txt_search_ActionPerformed()
1241   {
1242     String text = txt_search.getText().trim();
1243     if (text.length() >= PDB_ID_MIN)
1244       new Thread()
1245       {
1246
1247         @Override
1248         public void run()
1249         {
1250           errorWarning.setLength(0);
1251           isValidPBDEntry = false;
1252           if (text.length() > 0)
1253           {
1254             // TODO move this pdb id search into the PDB specific
1255             // FTSSearchEngine
1256             // for moment, it will work fine as is because it is self-contained
1257             String searchTerm = text.toLowerCase(Locale.ROOT);
1258             searchTerm = searchTerm.split(":")[0];
1259             // System.out.println(">>>>> search term : " + searchTerm);
1260             List<FTSDataColumnI> wantedFields = new ArrayList<>();
1261             FTSRestRequest pdbRequest = new FTSRestRequest();
1262             pdbRequest.setAllowEmptySeq(false);
1263             pdbRequest.setResponseSize(1);
1264             pdbRequest.setFieldToSearchBy("(pdb_id:");
1265             pdbRequest.setWantedFields(wantedFields);
1266             pdbRequest.setSearchTerm(searchTerm + ")");
1267             pdbRequest.setAssociatedSequence(selectedSequence);
1268             FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
1269             wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
1270             FTSRestResponse resultList;
1271             try
1272             {
1273               resultList = pdbRestClient.executeRequest(pdbRequest);
1274             } catch (Exception e)
1275             {
1276               errorWarning.append(e.getMessage());
1277               return;
1278             } finally
1279             {
1280               validateSelections();
1281             }
1282             if (resultList.getSearchSummary() != null
1283                     && resultList.getSearchSummary().size() > 0)
1284             {
1285               isValidPBDEntry = true;
1286             }
1287           }
1288           validateSelections();
1289         }
1290       }.start();
1291   }
1292
1293   @Override
1294   protected void tabRefresh()
1295   {
1296     if (selectedSequences != null)
1297     {
1298       Thread refreshThread = new Thread(new Runnable()
1299       {
1300         @Override
1301         public void run()
1302         {
1303           fetchStructuresMetaData();
1304           // populateFilterComboBox(true, cachedPDBExists);
1305
1306           filterResultSet(
1307                   ((FilterOption) cmb_filterOption.getSelectedItem())
1308                           .getValue());
1309         }
1310       });
1311       refreshThread.start();
1312     }
1313   }
1314
1315   public class PDBEntryTableModel extends AbstractTableModel
1316   {
1317     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1318         "File" };
1319
1320     private List<CachedPDB> pdbEntries;
1321
1322     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1323     {
1324       this.pdbEntries = new ArrayList<>(pdbEntries);
1325     }
1326
1327     @Override
1328     public String getColumnName(int columnIndex)
1329     {
1330       return columns[columnIndex];
1331     }
1332
1333     @Override
1334     public int getRowCount()
1335     {
1336       return pdbEntries.size();
1337     }
1338
1339     @Override
1340     public int getColumnCount()
1341     {
1342       return columns.length;
1343     }
1344
1345     @Override
1346     public boolean isCellEditable(int row, int column)
1347     {
1348       return false;
1349     }
1350
1351     @Override
1352     public Object getValueAt(int rowIndex, int columnIndex)
1353     {
1354       Object value = "??";
1355       CachedPDB entry = pdbEntries.get(rowIndex);
1356       switch (columnIndex)
1357       {
1358       case 0:
1359         value = entry.getSequence();
1360         break;
1361       case 1:
1362         value = entry.getQualifiedId();
1363         break;
1364       case 2:
1365         value = entry.getPdbEntry().getChainCode() == null ? "_"
1366                 : entry.getPdbEntry().getChainCode();
1367         break;
1368       case 3:
1369         value = entry.getPdbEntry().getType();
1370         break;
1371       case 4:
1372         value = entry.getPdbEntry().getFile();
1373         break;
1374       }
1375       return value;
1376     }
1377
1378     @Override
1379     public Class<?> getColumnClass(int columnIndex)
1380     {
1381       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1382     }
1383
1384     public CachedPDB getPDBEntryAt(int row)
1385     {
1386       return pdbEntries.get(row);
1387     }
1388
1389   }
1390
1391   private class CachedPDB
1392   {
1393     private SequenceI sequence;
1394
1395     private PDBEntry pdbEntry;
1396
1397     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1398     {
1399       this.sequence = sequence;
1400       this.pdbEntry = pdbEntry;
1401     }
1402
1403     public String getQualifiedId()
1404     {
1405       if (pdbEntry.hasProvider())
1406       {
1407         return pdbEntry.getProvider() + ":" + pdbEntry.getId();
1408       }
1409       return pdbEntry.toString();
1410     }
1411
1412     public SequenceI getSequence()
1413     {
1414       return sequence;
1415     }
1416
1417     public PDBEntry getPdbEntry()
1418     {
1419       return pdbEntry;
1420     }
1421
1422   }
1423
1424   private IProgressIndicator progressBar;
1425
1426   @Override
1427   public void setProgressBar(String message, long id)
1428   {
1429     progressBar.setProgressBar(message, id);
1430   }
1431
1432   @Override
1433   public void registerHandler(long id, IProgressIndicatorHandler handler)
1434   {
1435     progressBar.registerHandler(id, handler);
1436   }
1437
1438   @Override
1439   public boolean operationInProgress()
1440   {
1441     return progressBar.operationInProgress();
1442   }
1443
1444   public JalviewStructureDisplayI getOpenedStructureViewer()
1445   {
1446     return sViewer == null ? null : sViewer.sview;
1447   }
1448
1449   @Override
1450   protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs)
1451   {
1452     data.setDocFieldPrefs(newPrefs);
1453
1454   }
1455
1456   /**
1457    *
1458    * @return true when all initialisation threads have finished and dialog is
1459    *         visible
1460    */
1461   public boolean isDialogVisible()
1462   {
1463     return mainFrame != null && data != null && cmb_filterOption != null
1464             && mainFrame.isVisible()
1465             && cmb_filterOption.getSelectedItem() != null;
1466   }
1467 }