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