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.awt.event.ActionEvent;
  25 import java.awt.event.ActionListener;
  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.Locale;
  33 import java.util.concurrent.Executors;
  34
  35 import javax.swing.JCheckBox;
  36 import javax.swing.JComboBox;
  37 import javax.swing.JLabel;
  38 import javax.swing.JMenu;
  39 import javax.swing.JMenuItem;
  40 import javax.swing.JPopupMenu;
  41 import javax.swing.JTable;
  42 import javax.swing.SwingUtilities;
  43 import javax.swing.table.AbstractTableModel;
  44
  45 import jalview.api.structures.JalviewStructureDisplayI;
  46 import jalview.bin.Cache;
  47 import jalview.bin.Jalview;
  48 import jalview.datamodel.PDBEntry;
  49 import jalview.datamodel.SequenceI;
  50 import jalview.fts.api.FTSData;
  51 import jalview.fts.api.FTSDataColumnI;
  52 import jalview.fts.api.FTSRestClientI;
  53 import jalview.fts.core.FTSDataColumnPreferences;
  54 import jalview.fts.core.FTSRestRequest;
  55 import jalview.fts.core.FTSRestResponse;
  56 import jalview.fts.service.pdb.PDBFTSRestClient;
  57 import jalview.fts.service.threedbeacons.TDB_FTSData;
  58 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
  59 import jalview.gui.structurechooser.StructureChooserQuerySource;
  60 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
  61 import jalview.io.DataSourceType;
  62 import jalview.jbgui.FilterOption;
  63 import jalview.jbgui.GStructureChooser;
  64 import jalview.structure.StructureMapping;
  65 import jalview.structure.StructureSelectionManager;
  66 import jalview.util.MessageManager;
  67 import jalview.ws.DBRefFetcher;
  68 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  69 import jalview.ws.seqfetcher.DbSourceProxy;
  70 import jalview.ws.sifts.SiftsSettings;
  71
  72 /**
  73  * Provides the behaviors for the Structure chooser Panel
  74  *
  75  * @author tcnofoegbu
  76  *
  77  */
  78 @SuppressWarnings("serial")
  79 public class StructureChooser extends GStructureChooser
  80         implements IProgressIndicator
  81 {
  82   private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
  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         // triggers display of the 'Query TDB' button
 172         notQueriedTDBYet = true;
 173       }
 174     }
 175   };
 176
 177   /**
 178    * Initializes parameters used by the Structure Chooser Panel
 179    */
 180   protected void init()
 181   {
 182     if (!Jalview.isHeadlessMode())
 183     {
 184       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 185     }
 186
 187     chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
 188     btn_queryTDB.addActionListener(new ActionListener()
 189     {
 190
 191       @Override
 192       public void actionPerformed(ActionEvent e)
 193       {
 194         promptForTDBFetch(false);
 195       }
 196     });
 197
 198     Executors.defaultThreadFactory().newThread(new Runnable()
 199     {
 200       public void run()
 201       {
 202         populateSeqsWithoutSourceDBRef();
 203         initialStructureDiscovery();
 204       }
 205
 206     }).start();
 207
 208   }
 209
 210   // called by init
 211   private void initialStructureDiscovery()
 212   {
 213     // check which FTS engine to use
 214     data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences);
 215
 216     // ensure a filter option is in force for search
 217     populateFilterComboBox(true, cachedPDBExists);
 218
 219     // looks for any existing structures already loaded
 220     // for the sequences (the cached ones)
 221     // then queries the StructureChooserQuerySource to
 222     // discover more structures.
 223     //
 224     // Possible optimisation is to only begin querying
 225     // the structure chooser if there are no cached structures.
 226
 227     long startTime = System.currentTimeMillis();
 228     updateProgressIndicator(
 229             MessageManager.getString("status.loading_cached_pdb_entries"),
 230             startTime);
 231     loadLocalCachedPDBEntries();
 232     updateProgressIndicator(null, startTime);
 233     updateProgressIndicator(
 234             MessageManager.getString("status.searching_for_pdb_structures"),
 235             startTime);
 236     fetchStructuresMetaData();
 237     // revise filter options if no results were found
 238     populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
 239     discoverStructureViews();
 240     updateProgressIndicator(null, startTime);
 241     mainFrame.setVisible(true);
 242     updateCurrentView();
 243   }
 244
 245   /**
 246    * raises dialog for Uniprot fetch followed by 3D beacons search
 247    *
 248    * @param ignoreGui
 249    *          - when true, don't ask, just fetch
 250    */
 251   public void promptForTDBFetch(boolean ignoreGui)
 252   {
 253     final long progressId = System.currentTimeMillis();
 254
 255     // final action after prompting and discovering db refs
 256     final Runnable strucDiscovery = new Runnable()
 257     {
 258       @Override
 259       public void run()
 260       {
 261         mainFrame.setEnabled(false);
 262         cmb_filterOption.setEnabled(false);
 263         progressBar.setProgressBar(
 264                 MessageManager.getString("status.searching_3d_beacons"),
 265                 progressId);
 266         btn_queryTDB.setEnabled(false);
 267         // TODO: warn if no accessions discovered
 268         populateSeqsWithoutSourceDBRef();
 269         // redo initial discovery - this time with 3d beacons
 270         // Executors.
 271         previousWantedFields = null;
 272         lastSelected = (FilterOption) cmb_filterOption.getSelectedItem();
 273         cmb_filterOption.setSelectedItem(null);
 274         cachedPDBExists = false; // reset to initial
 275         initialStructureDiscovery();
 276         if (!isStructuresDiscovered())
 277         {
 278           progressBar.setProgressBar(MessageManager.getString(
 279                   "status.no_structures_discovered_from_3d_beacons"),
 280                   progressId);
 281           btn_queryTDB.setToolTipText(MessageManager.getString(
 282                   "status.no_structures_discovered_from_3d_beacons"));
 283           btn_queryTDB.setEnabled(false);
 284           pnl_queryTDB.setVisible(false);
 285         }
 286         else
 287         {
 288           cmb_filterOption.setSelectedIndex(0); // select 'best'
 289           btn_queryTDB.setVisible(false);
 290           pnl_queryTDB.setVisible(false);
 291           progressBar.setProgressBar(null, progressId);
 292         }
 293         mainFrame.setEnabled(true);
 294         cmb_filterOption.setEnabled(true);
 295       }
 296     };
 297
 298     final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI()
 299     {
 300
 301       @Override
 302       public void finished()
 303       {
 304         // filter has been selected, so we set flag to remove ourselves
 305         notQueriedTDBYet = false;
 306         // new thread to discover structures - via 3d beacons
 307         Executors.defaultThreadFactory().newThread(strucDiscovery).start();
 308
 309       }
 310     };
 311
 312     // fetch db refs if OK pressed
 313     final Runnable discoverCanonicalDBrefs = new Runnable()
 314     {
 315       @Override
 316       public void run()
 317       {
 318         populateSeqsWithoutSourceDBRef();
 319
 320         final int y = seqsWithoutSourceDBRef.size();
 321         if (y > 0)
 322         {
 323           final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
 324                   .toArray(new SequenceI[y]);
 325           DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
 326                   progressBar, new DbSourceProxy[]
 327                   { new jalview.ws.dbsources.Uniprot() }, null, false);
 328           dbRefFetcher.addListener(afterDbRefFetch);
 329           // ideally this would also gracefully run with callbacks
 330           dbRefFetcher.fetchDBRefs(true);
 331         }
 332         else
 333         {
 334           // call finished action directly
 335           afterDbRefFetch.finished();
 336         }
 337       }
 338
 339     };
 340     final Runnable revertview = new Runnable()
 341     {
 342       public void run()
 343       {
 344         if (lastSelected != null)
 345         {
 346           cmb_filterOption.setSelectedItem(lastSelected);
 347         }
 348       };
 349     };
 350     if (ignoreGui)
 351     {
 352       Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs)
 353               .start();
 354       return;
 355     }
 356     // need cancel and no to result in the discoverPDB action - mocked is
 357     // 'cancel' TODO: mock should be OK
 358     JvOptionPane.newOptionDialog(this)
 359             .setResponseHandler(JvOptionPane.OK_OPTION,
 360                     discoverCanonicalDBrefs)
 361             .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
 362             .setResponseHandler(JvOptionPane.NO_OPTION, revertview)
 363             .showDialog(
 364                     MessageManager.formatMessage(
 365                             "label.fetch_references_for_3dbeacons",
 366                             seqsWithoutSourceDBRef.size()),
 367                     MessageManager.getString("label.3dbeacons"),
 368                     JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE,
 369                     null, new Object[]
 370                     { MessageManager.getString("action.ok"),
 371                         MessageManager.getString("action.cancel") },
 372                     MessageManager.getString("action.ok"));
 373   }
 374
 375   /**
 376    * Builds a drop-down choice list of existing structure viewers to which new
 377    * structures may be added. If this list is empty then it, and the 'Add'
 378    * button, are hidden.
 379    */
 380   private void discoverStructureViews()
 381   {
 382     if (Desktop.instance != null)
 383     {
 384       targetView.removeAllItems();
 385       if (lastTargetedView != null && !lastTargetedView.isVisible())
 386       {
 387         lastTargetedView = null;
 388       }
 389       int linkedViewsAt = 0;
 390       for (StructureViewerBase view : Desktop.instance
 391               .getStructureViewers(null, null))
 392       {
 393         StructureViewer viewHandler = (lastTargetedView != null
 394                 && lastTargetedView.sview == view) ? lastTargetedView
 395                         : StructureViewer.reconfigure(view);
 396
 397         if (view.isLinkedWith(ap))
 398         {
 399           targetView.insertItemAt(viewHandler, linkedViewsAt++);
 400         }
 401         else
 402         {
 403           targetView.addItem(viewHandler);
 404         }
 405       }
 406
 407       /*
 408        * show option to Add to viewer if at least 1 viewer found
 409        */
 410       targetView.setVisible(false);
 411       if (targetView.getItemCount() > 0)
 412       {
 413         targetView.setVisible(true);
 414         if (lastTargetedView != null)
 415         {
 416           targetView.setSelectedItem(lastTargetedView);
 417         }
 418         else
 419         {
 420           targetView.setSelectedIndex(0);
 421         }
 422       }
 423       btn_add.setVisible(targetView.isVisible());
 424     }
 425   }
 426
 427   /**
 428    * Updates the progress indicator with the specified message
 429    *
 430    * @param message
 431    *          displayed message for the operation
 432    * @param id
 433    *          unique handle for this indicator
 434    */
 435   protected void updateProgressIndicator(String message, long id)
 436   {
 437     if (progressIndicator != null)
 438     {
 439       progressIndicator.setProgressBar(message, id);
 440     }
 441   }
 442
 443   /**
 444    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
 445    * selection group
 446    */
 447   void fetchStructuresMetaData()
 448   {
 449     long startTime = System.currentTimeMillis();
 450     Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
 451             .getStructureSummaryFields();
 452
 453     discoveredStructuresSet = new LinkedHashSet<>();
 454     HashSet<String> errors = new HashSet<>();
 455
 456     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 457             .getSelectedItem());
 458
 459     for (SequenceI seq : selectedSequences)
 460     {
 461
 462       FTSRestResponse resultList;
 463       try
 464       {
 465         resultList = data.fetchStructuresMetaData(seq, wantedFields,
 466                 selectedFilterOpt, !chk_invertFilter.isSelected());
 467         // null response means the FTSengine didn't yield a query for this
 468         // consider designing a special exception if we really wanted to be
 469         // OOCrazy
 470         if (resultList == null)
 471         {
 472           continue;
 473         }
 474       } catch (Exception e)
 475       {
 476         e.printStackTrace();
 477         errors.add(e.getMessage());
 478         continue;
 479       }
 480       if (resultList.getSearchSummary() != null
 481               && !resultList.getSearchSummary().isEmpty())
 482       {
 483         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 484       }
 485     }
 486
 487     int noOfStructuresFound = 0;
 488     String totalTime = (System.currentTimeMillis() - startTime)
 489             + " milli secs";
 490     if (discoveredStructuresSet != null
 491             && !discoveredStructuresSet.isEmpty())
 492     {
 493       getResultTable()
 494               .setModel(data.getTableModel(discoveredStructuresSet));
 495
 496       noOfStructuresFound = discoveredStructuresSet.size();
 497       lastDiscoveredStructuresSet = discoveredStructuresSet;
 498       mainFrame.setTitle(MessageManager.formatMessage(
 499               "label.structure_chooser_no_of_structures",
 500               noOfStructuresFound, totalTime));
 501     }
 502     else
 503     {
 504       mainFrame.setTitle(MessageManager
 505               .getString("label.structure_chooser_manual_association"));
 506       if (errors.size() > 0)
 507       {
 508         StringBuilder errorMsg = new StringBuilder();
 509         for (String error : errors)
 510         {
 511           errorMsg.append(error).append("\n");
 512         }
 513         JvOptionPane.showMessageDialog(this, errorMsg.toString(),
 514                 MessageManager.getString("label.pdb_web-service_error"),
 515                 JvOptionPane.ERROR_MESSAGE);
 516       }
 517     }
 518   }
 519
 520   protected void loadLocalCachedPDBEntries()
 521   {
 522     ArrayList<CachedPDB> entries = new ArrayList<>();
 523     for (SequenceI seq : selectedSequences)
 524     {
 525       if (seq.getDatasetSequence() != null
 526               && seq.getDatasetSequence().getAllPDBEntries() != null)
 527       {
 528         for (PDBEntry pdbEntry : seq.getDatasetSequence()
 529                 .getAllPDBEntries())
 530         {
 531           if (pdbEntry.getFile() != null)
 532           {
 533             entries.add(new CachedPDB(seq, pdbEntry));
 534           }
 535         }
 536       }
 537     }
 538     cachedPDBExists = !entries.isEmpty();
 539     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
 540     tbl_local_pdb.setModel(tableModelx);
 541   }
 542
 543   /**
 544    * Filters a given list of discovered structures based on supplied argument
 545    *
 546    * @param fieldToFilterBy
 547    *          the field to filter by
 548    */
 549   void filterResultSet(final String fieldToFilterBy)
 550   {
 551     Thread filterThread = new Thread(new Runnable()
 552     {
 553
 554       @Override
 555       public void run()
 556       {
 557         long startTime = System.currentTimeMillis();
 558         lbl_loading.setVisible(true);
 559         Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
 560                 .getStructureSummaryFields();
 561         Collection<FTSData> filteredResponse = new HashSet<>();
 562         HashSet<String> errors = new HashSet<>();
 563
 564         for (SequenceI seq : selectedSequences)
 565         {
 566
 567           FTSRestResponse resultList;
 568           try
 569           {
 570             resultList = data.selectFirstRankedQuery(seq,
 571                     discoveredStructuresSet, wantedFields, fieldToFilterBy,
 572                     !chk_invertFilter.isSelected());
 573
 574           } catch (Exception e)
 575           {
 576             e.printStackTrace();
 577             errors.add(e.getMessage());
 578             continue;
 579           }
 580           if (resultList.getSearchSummary() != null
 581                   && !resultList.getSearchSummary().isEmpty())
 582           {
 583             filteredResponse.addAll(resultList.getSearchSummary());
 584           }
 585         }
 586
 587         String totalTime = (System.currentTimeMillis() - startTime)
 588                 + " milli secs";
 589         if (!filteredResponse.isEmpty())
 590         {
 591           final int filterResponseCount = filteredResponse.size();
 592           Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
 593           reorderedStructuresSet.addAll(filteredResponse);
 594           reorderedStructuresSet.addAll(discoveredStructuresSet);
 595           getResultTable()
 596                   .setModel(data.getTableModel(reorderedStructuresSet));
 597
 598           FTSRestResponse.configureTableColumn(getResultTable(),
 599                   wantedFields, tempUserPrefs);
 600           getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
 601           getResultTable().getColumn("Ref Sequence").setMinWidth(100);
 602           getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
 603           // Update table selection model here
 604           getResultTable().addRowSelectionInterval(0,
 605                   filterResponseCount - 1);
 606           mainFrame.setTitle(MessageManager.formatMessage(
 607                   "label.structure_chooser_filter_time", totalTime));
 608         }
 609         else
 610         {
 611           mainFrame.setTitle(MessageManager.formatMessage(
 612                   "label.structure_chooser_filter_time", totalTime));
 613           if (errors.size() > 0)
 614           {
 615             StringBuilder errorMsg = new StringBuilder();
 616             for (String error : errors)
 617             {
 618               errorMsg.append(error).append("\n");
 619             }
 620             JvOptionPane.showMessageDialog(null, errorMsg.toString(),
 621                     MessageManager.getString("label.pdb_web-service_error"),
 622                     JvOptionPane.ERROR_MESSAGE);
 623           }
 624         }
 625
 626         lbl_loading.setVisible(false);
 627
 628         validateSelections();
 629       }
 630     });
 631     filterThread.start();
 632   }
 633
 634   /**
 635    * Handles action event for btn_pdbFromFile
 636    */
 637   @Override
 638   protected void pdbFromFile_actionPerformed()
 639   {
 640     // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and
 641     // StructureChooser
 642     // works
 643     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 644             Cache.getProperty("LAST_DIRECTORY"));
 645     chooser.setFileView(new jalview.io.JalviewFileView());
 646     chooser.setDialogTitle(
 647             MessageManager.formatMessage("label.select_pdb_file_for",
 648                     selectedSequence.getDisplayId(false)));
 649     chooser.setToolTipText(MessageManager.formatMessage(
 650             "label.load_pdb_file_associate_with_sequence",
 651             selectedSequence.getDisplayId(false)));
 652
 653     int value = chooser.showOpenDialog(null);
 654     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
 655     {
 656       selectedPdbFileName = chooser.getSelectedFile().getPath();
 657       Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
 658       validateSelections();
 659     }
 660   }
 661
 662   /**
 663    * Populates the filter combo-box options dynamically depending on discovered
 664    * structures
 665    */
 666   protected void populateFilterComboBox(boolean haveData,
 667           boolean cachedPDBExist)
 668   {
 669     populateFilterComboBox(haveData, cachedPDBExist, null);
 670   }
 671
 672   /**
 673    * Populates the filter combo-box options dynamically depending on discovered
 674    * structures
 675    */
 676   protected void populateFilterComboBox(boolean haveData,
 677           boolean cachedPDBExist, FilterOption lastSel)
 678   {
 679
 680     /*
 681      * temporarily suspend the change listener behaviour
 682      */
 683     cmb_filterOption.removeItemListener(this);
 684     int selSet = -1;
 685     cmb_filterOption.removeAllItems();
 686     if (haveData)
 687     {
 688       List<FilterOption> filters = data
 689               .getAvailableFilterOptions(VIEWS_FILTER);
 690       data.updateAvailableFilterOptions(VIEWS_FILTER, filters,
 691               lastDiscoveredStructuresSet);
 692       int p = 0;
 693       for (FilterOption filter : filters)
 694       {
 695         if (lastSel != null && filter.equals(lastSel))
 696         {
 697           selSet = p;
 698         }
 699         p++;
 700         cmb_filterOption.addItem(filter);
 701       }
 702     }
 703
 704     cmb_filterOption.addItem(
 705             new FilterOption(MessageManager.getString("label.enter_pdb_id"),
 706                     "-", VIEWS_ENTER_ID, false, null));
 707     cmb_filterOption.addItem(
 708             new FilterOption(MessageManager.getString("label.from_file"),
 709                     "-", VIEWS_FROM_FILE, false, null));
 710     if (canQueryTDB && notQueriedTDBYet)
 711     {
 712       btn_queryTDB.setVisible(true);
 713       pnl_queryTDB.setVisible(true);
 714     }
 715
 716     if (cachedPDBExist)
 717     {
 718       FilterOption cachedOption = new FilterOption(
 719               MessageManager.getString("label.cached_structures"), "-",
 720               VIEWS_LOCAL_PDB, false, null);
 721       cmb_filterOption.addItem(cachedOption);
 722       if (selSet == -1)
 723       {
 724         cmb_filterOption.setSelectedItem(cachedOption);
 725       }
 726     }
 727     if (selSet > -1)
 728     {
 729       cmb_filterOption.setSelectedIndex(selSet);
 730     }
 731     cmb_filterOption.addItemListener(this);
 732   }
 733
 734   /**
 735    * Updates the displayed view based on the selected filter option
 736    */
 737   protected void updateCurrentView()
 738   {
 739     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 740             .getSelectedItem());
 741
 742     if (lastSelected == selectedFilterOpt)
 743     {
 744       // don't need to do anything, probably
 745       return;
 746     }
 747     // otherwise, record selection
 748     // and update the layout and dialog accordingly
 749     lastSelected = selectedFilterOpt;
 750
 751     layout_switchableViews.show(pnl_switchableViews,
 752             selectedFilterOpt.getView());
 753     String filterTitle = mainFrame.getTitle();
 754     mainFrame.setTitle(frameTitle);
 755     chk_invertFilter.setVisible(false);
 756
 757     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 758     {
 759       mainFrame.setTitle(filterTitle);
 760       // TDB Query has no invert as yet
 761       chk_invertFilter.setVisible(selectedFilterOpt
 762               .getQuerySource() instanceof PDBStructureChooserQuerySource);
 763
 764       if (data != selectedFilterOpt.getQuerySource()
 765               || data.needsRefetch(selectedFilterOpt))
 766       {
 767         data = selectedFilterOpt.getQuerySource();
 768         // rebuild the views completely, since prefs will also change
 769         tabRefresh();
 770         return;
 771       }
 772       else
 773       {
 774         filterResultSet(selectedFilterOpt.getValue());
 775       }
 776     }
 777     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 778             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 779     {
 780       mainFrame.setTitle(MessageManager
 781               .getString("label.structure_chooser_manual_association"));
 782       idInputAssSeqPanel.loadCmbAssSeq();
 783       fileChooserAssSeqPanel.loadCmbAssSeq();
 784     }
 785     validateSelections();
 786   }
 787
 788   /**
 789    * Validates user selection and enables the 'Add' and 'New View' buttons if
 790    * all parameters are correct (the Add button will only be visible if there is
 791    * at least one existing structure viewer open). This basically means at least
 792    * one structure selected and no error messages.
 793    * <p>
 794    * The 'Superpose Structures' option is enabled if either more than one
 795    * structure is selected, or the 'Add' to existing view option is enabled, and
 796    * disabled if the only option is to open a new view of a single structure.
 797    */
 798   @Override
 799   protected void validateSelections()
 800   {
 801     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 802             .getSelectedItem());
 803     btn_add.setEnabled(false);
 804     String currentView = selectedFilterOpt.getView();
 805     int selectedCount = 0;
 806     if (currentView == VIEWS_FILTER)
 807     {
 808       selectedCount = getResultTable().getSelectedRows().length;
 809       if (selectedCount > 0)
 810       {
 811         btn_add.setEnabled(true);
 812       }
 813     }
 814     else if (currentView == VIEWS_LOCAL_PDB)
 815     {
 816       selectedCount = tbl_local_pdb.getSelectedRows().length;
 817       if (selectedCount > 0)
 818       {
 819         btn_add.setEnabled(true);
 820       }
 821     }
 822     else if (currentView == VIEWS_ENTER_ID)
 823     {
 824       validateAssociationEnterPdb();
 825     }
 826     else if (currentView == VIEWS_FROM_FILE)
 827     {
 828       validateAssociationFromFile();
 829     }
 830
 831     btn_newView.setEnabled(btn_add.isEnabled());
 832
 833     /*
 834      * enable 'Superpose' option if more than one structure is selected,
 835      * or there are view(s) available to add structure(s) to
 836      */
 837     chk_superpose
 838             .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
 839   }
 840
 841   @Override
 842   protected boolean showPopupFor(int selectedRow, int x, int y)
 843   {
 844     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 845             .getSelectedItem());
 846     String currentView = selectedFilterOpt.getView();
 847
 848     if (currentView == VIEWS_FILTER
 849             && data instanceof ThreeDBStructureChooserQuerySource)
 850     {
 851
 852       TDB_FTSData row = ((ThreeDBStructureChooserQuerySource) data)
 853               .getFTSDataFor(getResultTable(), selectedRow,
 854                       discoveredStructuresSet);
 855       String pageUrl = row.getModelViewUrl();
 856       JPopupMenu popup = new JPopupMenu("3D Beacons");
 857       JMenuItem viewUrl = new JMenuItem("View model web page");
 858       viewUrl.addActionListener(new ActionListener()
 859       {
 860         @Override
 861         public void actionPerformed(ActionEvent e)
 862         {
 863           Desktop.showUrl(pageUrl);
 864         }
 865       });
 866       popup.add(viewUrl);
 867       SwingUtilities.invokeLater(new Runnable()
 868       {
 869         public void run()
 870         {
 871           popup.show(getResultTable(), x, y);
 872         }
 873       });
 874       return true;
 875     }
 876     // event not handled by us
 877     return false;
 878   }
 879
 880   /**
 881    * Validates inputs from the Manual PDB entry panel
 882    */
 883   protected void validateAssociationEnterPdb()
 884   {
 885     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 886             .getCmb_assSeq().getSelectedItem();
 887     lbl_pdbManualFetchStatus.setIcon(errorImage);
 888     lbl_pdbManualFetchStatus.setToolTipText("");
 889     if (txt_search.getText().length() > 0)
 890     {
 891       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
 892               MessageManager.formatMessage("info.no_pdb_entry_found_for",
 893                       txt_search.getText())));
 894     }
 895
 896     if (errorWarning.length() > 0)
 897     {
 898       lbl_pdbManualFetchStatus.setIcon(warningImage);
 899       lbl_pdbManualFetchStatus.setToolTipText(
 900               JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
 901     }
 902
 903     if (selectedSequences.length == 1 || !assSeqOpt.getName()
 904             .equalsIgnoreCase("-Select Associated Seq-"))
 905     {
 906       txt_search.setEnabled(true);
 907       if (isValidPBDEntry)
 908       {
 909         btn_add.setEnabled(true);
 910         lbl_pdbManualFetchStatus.setToolTipText("");
 911         lbl_pdbManualFetchStatus.setIcon(goodImage);
 912       }
 913     }
 914     else
 915     {
 916       txt_search.setEnabled(false);
 917       lbl_pdbManualFetchStatus.setIcon(errorImage);
 918     }
 919   }
 920
 921   /**
 922    * Validates inputs for the manual PDB file selection options
 923    */
 924   protected void validateAssociationFromFile()
 925   {
 926     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
 927             .getCmb_assSeq().getSelectedItem();
 928     lbl_fromFileStatus.setIcon(errorImage);
 929     if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
 930             .getName().equalsIgnoreCase("-Select Associated Seq-")))
 931     {
 932       btn_pdbFromFile.setEnabled(true);
 933       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
 934       {
 935         btn_add.setEnabled(true);
 936         lbl_fromFileStatus.setIcon(goodImage);
 937       }
 938     }
 939     else
 940     {
 941       btn_pdbFromFile.setEnabled(false);
 942       lbl_fromFileStatus.setIcon(errorImage);
 943     }
 944   }
 945
 946   @Override
 947   protected void cmbAssSeqStateChanged()
 948   {
 949     validateSelections();
 950   }
 951
 952   private FilterOption lastSelected = null;
 953
 954   /**
 955    * Handles the state change event for the 'filter' combo-box and 'invert'
 956    * check-box
 957    */
 958   @Override
 959   protected void stateChanged(ItemEvent e)
 960   {
 961     if (e.getSource() instanceof JCheckBox)
 962     {
 963       updateCurrentView();
 964     }
 965     else
 966     {
 967       if (e.getStateChange() == ItemEvent.SELECTED)
 968       {
 969         updateCurrentView();
 970       }
 971     }
 972
 973   }
 974
 975   /**
 976    * select structures for viewing by their PDB IDs
 977    *
 978    * @param pdbids
 979    * @return true if structures were found and marked as selected
 980    */
 981   public boolean selectStructure(String... pdbids)
 982   {
 983     boolean found = false;
 984
 985     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 986             .getSelectedItem());
 987     String currentView = selectedFilterOpt.getView();
 988     JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
 989             : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
 990
 991     if (restable == null)
 992     {
 993       // can't select (enter PDB ID, or load file - need to also select which
 994       // sequence to associate with)
 995       return false;
 996     }
 997
 998     int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
 999     for (int r = 0; r < restable.getRowCount(); r++)
1000     {
1001       for (int p = 0; p < pdbids.length; p++)
1002       {
1003         if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
1004                 .equalsIgnoreCase(pdbids[p]))
1005         {
1006           restable.setRowSelectionInterval(r, r);
1007           found = true;
1008         }
1009       }
1010     }
1011     return found;
1012   }
1013
1014   /**
1015    * Handles the 'New View' action
1016    */
1017   @Override
1018   protected void newView_ActionPerformed()
1019   {
1020     targetView.setSelectedItem(null);
1021     showStructures(false);
1022   }
1023
1024   /**
1025    * Handles the 'Add to existing viewer' action
1026    */
1027   @Override
1028   protected void add_ActionPerformed()
1029   {
1030     showStructures(false);
1031   }
1032
1033   /**
1034    * structure viewer opened by this dialog, or null
1035    */
1036   private StructureViewer sViewer = null;
1037
1038   public void showStructures(boolean waitUntilFinished)
1039   {
1040
1041     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
1042
1043     final int preferredHeight = pnl_filter.getHeight();
1044
1045     Runnable viewStruc = new Runnable()
1046     {
1047       @Override
1048       public void run()
1049       {
1050         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
1051                 .getSelectedItem());
1052         String currentView = selectedFilterOpt.getView();
1053         JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
1054                 : tbl_local_pdb;
1055
1056         if (currentView == VIEWS_FILTER)
1057         {
1058           int[] selectedRows = restable.getSelectedRows();
1059           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
1060           List<SequenceI> selectedSeqsToView = new ArrayList<>();
1061           pdbEntriesToView = data.collectSelectedRows(restable,
1062                   selectedRows, selectedSeqsToView);
1063
1064           SequenceI[] selectedSeqs = selectedSeqsToView
1065                   .toArray(new SequenceI[selectedSeqsToView.size()]);
1066           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1067                   selectedSeqs);
1068         }
1069         else if (currentView == VIEWS_LOCAL_PDB)
1070         {
1071           int[] selectedRows = tbl_local_pdb.getSelectedRows();
1072           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
1073           int count = 0;
1074           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
1075                   .getModelIndex();
1076           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
1077                   .getModelIndex();
1078           List<SequenceI> selectedSeqsToView = new ArrayList<>();
1079           for (int row : selectedRows)
1080           {
1081             PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb
1082                     .getModel()).getPDBEntryAt(row).getPdbEntry();
1083
1084             pdbEntriesToView[count++] = pdbEntry;
1085             SequenceI selectedSeq = (SequenceI) tbl_local_pdb
1086                     .getValueAt(row, refSeqColIndex);
1087             selectedSeqsToView.add(selectedSeq);
1088           }
1089           SequenceI[] selectedSeqs = selectedSeqsToView
1090                   .toArray(new SequenceI[selectedSeqsToView.size()]);
1091           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1092                   selectedSeqs);
1093         }
1094         else if (currentView == VIEWS_ENTER_ID)
1095         {
1096           SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
1097                   .getCmb_assSeq().getSelectedItem()).getSequence();
1098           if (userSelectedSeq != null)
1099           {
1100             selectedSequence = userSelectedSeq;
1101           }
1102           String pdbIdStr = txt_search.getText();
1103           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
1104           if (pdbEntry == null)
1105           {
1106             pdbEntry = new PDBEntry();
1107             if (pdbIdStr.split(":").length > 1)
1108             {
1109               pdbEntry.setId(pdbIdStr.split(":")[0]);
1110               pdbEntry.setChainCode(
1111                       pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
1112             }
1113             else
1114             {
1115               pdbEntry.setId(pdbIdStr);
1116             }
1117             pdbEntry.setType(PDBEntry.Type.PDB);
1118             selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
1119           }
1120
1121           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
1122           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1123                   new SequenceI[]
1124                   { selectedSequence });
1125         }
1126         else if (currentView == VIEWS_FROM_FILE)
1127         {
1128           SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
1129                   .getCmb_assSeq().getSelectedItem()).getSequence();
1130           if (userSelectedSeq != null)
1131           {
1132             selectedSequence = userSelectedSeq;
1133           }
1134           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
1135                   .associatePdbWithSeq(selectedPdbFileName,
1136                           DataSourceType.FILE, selectedSequence, true,
1137                           Desktop.instance);
1138
1139           sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
1140                   ap, new SequenceI[]
1141                   { selectedSequence });
1142         }
1143         SwingUtilities.invokeLater(new Runnable()
1144         {
1145           @Override
1146           public void run()
1147           {
1148             closeAction(preferredHeight);
1149             mainFrame.dispose();
1150           }
1151         });
1152       }
1153     };
1154     Thread runner = new Thread(viewStruc);
1155     runner.start();
1156     if (waitUntilFinished)
1157     {
1158       while (sViewer == null ? runner.isAlive()
1159               : (sViewer.sview == null ? true
1160                       : !sViewer.sview.hasMapping()))
1161       {
1162         try
1163         {
1164           Thread.sleep(300);
1165         } catch (InterruptedException ie)
1166         {
1167
1168         }
1169       }
1170     }
1171   }
1172
1173   /**
1174    * Answers a structure viewer (new or existing) configured to superimpose
1175    * added structures or not according to the user's choice
1176    *
1177    * @param ssm
1178    * @return
1179    */
1180   StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm)
1181   {
1182     Object sv = targetView.getSelectedItem();
1183
1184     return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
1185   }
1186
1187   /**
1188    * Adds PDB structures to a new or existing structure viewer
1189    *
1190    * @param ssm
1191    * @param pdbEntriesToView
1192    * @param alignPanel
1193    * @param sequences
1194    * @return
1195    */
1196   private StructureViewer launchStructureViewer(
1197           StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
1198           final AlignmentPanel alignPanel, SequenceI[] sequences)
1199   {
1200     long progressId = sequences.hashCode();
1201     setProgressBar(MessageManager
1202             .getString("status.launching_3d_structure_viewer"), progressId);
1203     final StructureViewer theViewer = getTargetedStructureViewer(ssm);
1204     boolean superimpose = chk_superpose.isSelected();
1205     theViewer.setSuperpose(superimpose);
1206
1207     /*
1208      * remember user's choice of superimpose or not
1209      */
1210     Cache.setProperty(AUTOSUPERIMPOSE,
1211             Boolean.valueOf(superimpose).toString());
1212
1213     setProgressBar(null, progressId);
1214     if (SiftsSettings.isMapWithSifts())
1215     {
1216       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
1217       int p = 0;
1218       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
1219       // real PDB ID. For moment, we can also safely do this if there is already
1220       // a known mapping between the PDBEntry and the sequence.
1221       for (SequenceI seq : sequences)
1222       {
1223         PDBEntry pdbe = pdbEntriesToView[p++];
1224         if (pdbe != null && pdbe.getFile() != null)
1225         {
1226           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
1227           if (smm != null && smm.length > 0)
1228           {
1229             for (StructureMapping sm : smm)
1230             {
1231               if (sm.getSequence() == seq)
1232               {
1233                 continue;
1234               }
1235             }
1236           }
1237         }
1238         if (seq.getPrimaryDBRefs().isEmpty())
1239         {
1240           seqsWithoutSourceDBRef.add(seq);
1241           continue;
1242         }
1243       }
1244       if (!seqsWithoutSourceDBRef.isEmpty())
1245       {
1246         int y = seqsWithoutSourceDBRef.size();
1247         setProgressBar(MessageManager.formatMessage(
1248                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
1249                 y), progressId);
1250         SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
1251                 .toArray(new SequenceI[y]);
1252         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
1253         dbRefFetcher.fetchDBRefs(true);
1254
1255         setProgressBar("Fetch complete.", progressId); // todo i18n
1256       }
1257     }
1258     if (pdbEntriesToView.length > 1)
1259     {
1260       setProgressBar(
1261               MessageManager.getString(
1262                       "status.fetching_3d_structures_for_selected_entries"),
1263               progressId);
1264       theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
1265     }
1266     else
1267     {
1268       setProgressBar(MessageManager.formatMessage(
1269               "status.fetching_3d_structures_for",
1270               pdbEntriesToView[0].getId()), progressId);
1271       theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
1272     }
1273     setProgressBar(null, progressId);
1274     // remember the last viewer we used...
1275     lastTargetedView = theViewer;
1276     return theViewer;
1277   }
1278
1279   /**
1280    * Populates the combo-box used in associating manually fetched structures to
1281    * a unique sequence when more than one sequence selection is made.
1282    */
1283   @Override
1284   protected void populateCmbAssociateSeqOptions(
1285           JComboBox<AssociateSeqOptions> cmb_assSeq,
1286           JLabel lbl_associateSeq)
1287   {
1288     cmb_assSeq.removeAllItems();
1289     cmb_assSeq.addItem(
1290             new AssociateSeqOptions("-Select Associated Seq-", null));
1291     lbl_associateSeq.setVisible(false);
1292     if (selectedSequences.length > 1)
1293     {
1294       for (SequenceI seq : selectedSequences)
1295       {
1296         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
1297       }
1298     }
1299     else
1300     {
1301       String seqName = selectedSequence.getDisplayId(false);
1302       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
1303       lbl_associateSeq.setText(seqName);
1304       lbl_associateSeq.setVisible(true);
1305       cmb_assSeq.setVisible(false);
1306     }
1307   }
1308
1309   protected boolean isStructuresDiscovered()
1310   {
1311     return discoveredStructuresSet != null
1312             && !discoveredStructuresSet.isEmpty();
1313   }
1314
1315   protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes
1316                                // this.
1317   // Doing a search for "1" or "1c" is valuable?
1318   // Those work but are enormously slow.
1319
1320   @Override
1321   protected void txt_search_ActionPerformed()
1322   {
1323     String text = txt_search.getText().trim();
1324     if (text.length() >= PDB_ID_MIN)
1325       new Thread()
1326       {
1327
1328         @Override
1329         public void run()
1330         {
1331           errorWarning.setLength(0);
1332           isValidPBDEntry = false;
1333           if (text.length() > 0)
1334           {
1335             // TODO move this pdb id search into the PDB specific
1336             // FTSSearchEngine
1337             // for moment, it will work fine as is because it is self-contained
1338             String searchTerm = text.toLowerCase(Locale.ROOT);
1339             searchTerm = searchTerm.split(":")[0];
1340             // System.out.println(">>>>> search term : " + searchTerm);
1341             List<FTSDataColumnI> wantedFields = new ArrayList<>();
1342             FTSRestRequest pdbRequest = new FTSRestRequest();
1343             pdbRequest.setAllowEmptySeq(false);
1344             pdbRequest.setResponseSize(1);
1345             pdbRequest.setFieldToSearchBy("(pdb_id:");
1346             pdbRequest.setWantedFields(wantedFields);
1347             pdbRequest.setSearchTerm(searchTerm + ")");
1348             pdbRequest.setAssociatedSequence(selectedSequence);
1349             FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
1350             wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
1351             FTSRestResponse resultList;
1352             try
1353             {
1354               resultList = pdbRestClient.executeRequest(pdbRequest);
1355             } catch (Exception e)
1356             {
1357               errorWarning.append(e.getMessage());
1358               return;
1359             } finally
1360             {
1361               validateSelections();
1362             }
1363             if (resultList.getSearchSummary() != null
1364                     && resultList.getSearchSummary().size() > 0)
1365             {
1366               isValidPBDEntry = true;
1367             }
1368           }
1369           validateSelections();
1370         }
1371       }.start();
1372   }
1373
1374   @Override
1375   protected void tabRefresh()
1376   {
1377     if (selectedSequences != null)
1378     {
1379       Thread refreshThread = new Thread(new Runnable()
1380       {
1381         @Override
1382         public void run()
1383         {
1384           fetchStructuresMetaData();
1385           // populateFilterComboBox(true, cachedPDBExists);
1386
1387           filterResultSet(
1388                   ((FilterOption) cmb_filterOption.getSelectedItem())
1389                           .getValue());
1390         }
1391       });
1392       refreshThread.start();
1393     }
1394   }
1395
1396   public class PDBEntryTableModel extends AbstractTableModel
1397   {
1398     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1399         "File" };
1400
1401     private List<CachedPDB> pdbEntries;
1402
1403     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1404     {
1405       this.pdbEntries = new ArrayList<>(pdbEntries);
1406     }
1407
1408     @Override
1409     public String getColumnName(int columnIndex)
1410     {
1411       return columns[columnIndex];
1412     }
1413
1414     @Override
1415     public int getRowCount()
1416     {
1417       return pdbEntries.size();
1418     }
1419
1420     @Override
1421     public int getColumnCount()
1422     {
1423       return columns.length;
1424     }
1425
1426     @Override
1427     public boolean isCellEditable(int row, int column)
1428     {
1429       return false;
1430     }
1431
1432     @Override
1433     public Object getValueAt(int rowIndex, int columnIndex)
1434     {
1435       Object value = "??";
1436       CachedPDB entry = pdbEntries.get(rowIndex);
1437       switch (columnIndex)
1438       {
1439       case 0:
1440         value = entry.getSequence();
1441         break;
1442       case 1:
1443         value = entry.getQualifiedId();
1444         break;
1445       case 2:
1446         value = entry.getPdbEntry().getChainCode() == null ? "_"
1447                 : entry.getPdbEntry().getChainCode();
1448         break;
1449       case 3:
1450         value = entry.getPdbEntry().getType();
1451         break;
1452       case 4:
1453         value = entry.getPdbEntry().getFile();
1454         break;
1455       }
1456       return value;
1457     }
1458
1459     @Override
1460     public Class<?> getColumnClass(int columnIndex)
1461     {
1462       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1463     }
1464
1465     public CachedPDB getPDBEntryAt(int row)
1466     {
1467       return pdbEntries.get(row);
1468     }
1469
1470   }
1471
1472   private class CachedPDB
1473   {
1474     private SequenceI sequence;
1475
1476     private PDBEntry pdbEntry;
1477
1478     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1479     {
1480       this.sequence = sequence;
1481       this.pdbEntry = pdbEntry;
1482     }
1483
1484     public String getQualifiedId()
1485     {
1486       if (pdbEntry.hasProvider())
1487       {
1488         return pdbEntry.getProvider() + ":" + pdbEntry.getId();
1489       }
1490       return pdbEntry.toString();
1491     }
1492
1493     public SequenceI getSequence()
1494     {
1495       return sequence;
1496     }
1497
1498     public PDBEntry getPdbEntry()
1499     {
1500       return pdbEntry;
1501     }
1502
1503   }
1504
1505   private IProgressIndicator progressBar;
1506
1507   @Override
1508   public void setProgressBar(String message, long id)
1509   {
1510     progressBar.setProgressBar(message, id);
1511   }
1512
1513   @Override
1514   public void registerHandler(long id, IProgressIndicatorHandler handler)
1515   {
1516     progressBar.registerHandler(id, handler);
1517   }
1518
1519   @Override
1520   public boolean operationInProgress()
1521   {
1522     return progressBar.operationInProgress();
1523   }
1524
1525   public JalviewStructureDisplayI getOpenedStructureViewer()
1526   {
1527     return sViewer == null ? null : sViewer.sview;
1528   }
1529
1530   @Override
1531   protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs)
1532   {
1533     data.setDocFieldPrefs(newPrefs);
1534
1535   }
1536
1537   /**
1538    *
1539    * @return true when all initialisation threads have finished and dialog is
1540    *         visible
1541    */
1542   public boolean isDialogVisible()
1543   {
1544     return mainFrame != null && data != null && cmb_filterOption != null
1545             && mainFrame.isVisible()
1546             && cmb_filterOption.getSelectedItem() != null;
1547   }
1548
1549   /**
1550    *
1551    * @return true if the 3D-Beacons query button will/has been displayed
1552    */
1553   public boolean isCanQueryTDB()
1554   {
1555     return canQueryTDB;
1556   }
1557
1558   public boolean isNotQueriedTDBYet()
1559   {
1560     return notQueriedTDBYet;
1561   }
1562 }