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.JMenuItem;
  39 import javax.swing.JPopupMenu;
  40 import javax.swing.JTable;
  41 import javax.swing.SwingUtilities;
  42 import javax.swing.table.AbstractTableModel;
  43
  44 import jalview.api.structures.JalviewStructureDisplayI;
  45 import jalview.bin.Cache;
  46 import jalview.bin.Console;
  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   /**
  85    * warn user if need to fetch more than this many uniprot records at once
  86    */
  87   private static final int THRESHOLD_WARN_UNIPROT_FETCH_NEEDED = 20;
  88
  89   private SequenceI selectedSequence;
  90
  91   private SequenceI[] selectedSequences;
  92
  93   private IProgressIndicator progressIndicator;
  94
  95   private Collection<FTSData> discoveredStructuresSet;
  96
  97   private StructureChooserQuerySource data;
  98
  99   @Override
 100   protected FTSDataColumnPreferences getFTSDocFieldPrefs()
 101   {
 102     return data.getDocFieldPrefs();
 103   }
 104
 105   private String selectedPdbFileName;
 106
 107   private boolean isValidPBDEntry;
 108
 109   private boolean cachedPDBExists;
 110
 111   private Collection<FTSData> lastDiscoveredStructuresSet;
 112
 113   private boolean canQueryTDB = false;
 114
 115   private boolean notQueriedTDBYet = true;
 116
 117   List<SequenceI> seqsWithoutSourceDBRef = null;
 118
 119   private static StructureViewer lastTargetedView = null;
 120
 121   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
 122           AlignmentPanel ap)
 123   {
 124     // which FTS engine to use
 125     data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
 126     initDialog();
 127
 128     this.ap = ap;
 129     this.selectedSequence = selectedSeq;
 130     this.selectedSequences = selectedSeqs;
 131     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
 132     init();
 133
 134   }
 135
 136   /**
 137    * sets canQueryTDB if protein sequences without a canonical uniprot ref or at
 138    * least one structure are discovered.
 139    */
 140   private void populateSeqsWithoutSourceDBRef()
 141   {
 142     seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
 143     boolean needCanonical = false;
 144     for (SequenceI seq : selectedSequences)
 145     {
 146       if (seq.isProtein())
 147       {
 148         int dbRef = ThreeDBStructureChooserQuerySource
 149                 .checkUniprotRefs(seq.getDBRefs());
 150         if (dbRef < 0)
 151         {
 152           if (dbRef == -1)
 153           {
 154             // need to retrieve canonicals
 155             needCanonical = true;
 156             seqsWithoutSourceDBRef.add(seq);
 157           }
 158           else
 159           {
 160             // could be a sequence with pdb ref
 161             if (seq.getAllPDBEntries() == null
 162                     || seq.getAllPDBEntries().size() == 0)
 163             {
 164               seqsWithoutSourceDBRef.add(seq);
 165             }
 166           }
 167         }
 168       }
 169     }
 170     // retrieve database refs for protein sequences
 171     if (!seqsWithoutSourceDBRef.isEmpty())
 172     {
 173       canQueryTDB = true;
 174       if (needCanonical)
 175       {
 176         // triggers display of the 'Query TDB' button
 177         notQueriedTDBYet = true;
 178       }
 179     }
 180   };
 181
 182   /**
 183    * Initializes parameters used by the Structure Chooser Panel
 184    */
 185   protected void init()
 186   {
 187     if (!Jalview.isHeadlessMode())
 188     {
 189       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 190     }
 191
 192     chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
 193     btn_queryTDB.addActionListener(new ActionListener()
 194     {
 195
 196       @Override
 197       public void actionPerformed(ActionEvent e)
 198       {
 199         promptForTDBFetch(false);
 200       }
 201     });
 202
 203     Executors.defaultThreadFactory().newThread(new Runnable()
 204     {
 205       @Override
 206       public void run()
 207       {
 208         populateSeqsWithoutSourceDBRef();
 209         initialStructureDiscovery();
 210       }
 211
 212     }).start();
 213
 214   }
 215
 216   // called by init
 217   private void initialStructureDiscovery()
 218   {
 219     // check which FTS engine to use
 220     data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences);
 221
 222     // ensure a filter option is in force for search
 223     populateFilterComboBox(true, cachedPDBExists);
 224
 225     // looks for any existing structures already loaded
 226     // for the sequences (the cached ones)
 227     // then queries the StructureChooserQuerySource to
 228     // discover more structures.
 229     //
 230     // Possible optimisation is to only begin querying
 231     // the structure chooser if there are no cached structures.
 232
 233     long startTime = System.currentTimeMillis();
 234     updateProgressIndicator(
 235             MessageManager.getString("status.loading_cached_pdb_entries"),
 236             startTime);
 237     loadLocalCachedPDBEntries();
 238     updateProgressIndicator(null, startTime);
 239     updateProgressIndicator(
 240             MessageManager.getString("status.searching_for_pdb_structures"),
 241             startTime);
 242     fetchStructuresMetaData();
 243     // revise filter options if no results were found
 244     populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
 245     discoverStructureViews();
 246     updateProgressIndicator(null, startTime);
 247     mainFrame.setVisible(true);
 248     updateCurrentView();
 249   }
 250
 251   /**
 252    * raises dialog for Uniprot fetch followed by 3D beacons search
 253    *
 254    * @param ignoreGui
 255    *          - when true, don't ask, just fetch
 256    */
 257   public void promptForTDBFetch(boolean ignoreGui)
 258   {
 259     final long progressId = System.currentTimeMillis();
 260
 261     // final action after prompting and discovering db refs
 262     final Runnable strucDiscovery = new Runnable()
 263     {
 264       @Override
 265       public void run()
 266       {
 267         mainFrame.setEnabled(false);
 268         cmb_filterOption.setEnabled(false);
 269         progressBar.setProgressBar(
 270                 MessageManager.getString("status.searching_3d_beacons"),
 271                 progressId);
 272         btn_queryTDB.setEnabled(false);
 273         // TODO: warn if no accessions discovered
 274         populateSeqsWithoutSourceDBRef();
 275         // redo initial discovery - this time with 3d beacons
 276         // Executors.
 277         previousWantedFields = null;
 278         lastSelected = (FilterOption) cmb_filterOption.getSelectedItem();
 279         cmb_filterOption.setSelectedItem(null);
 280         cachedPDBExists = false; // reset to initial
 281         initialStructureDiscovery();
 282         if (!isStructuresDiscovered())
 283         {
 284           progressBar.setProgressBar(MessageManager.getString(
 285                   "status.no_structures_discovered_from_3d_beacons"),
 286                   progressId);
 287           btn_queryTDB.setToolTipText(MessageManager.getString(
 288                   "status.no_structures_discovered_from_3d_beacons"));
 289           btn_queryTDB.setEnabled(false);
 290           pnl_queryTDB.setVisible(false);
 291         }
 292         else
 293         {
 294           cmb_filterOption.setSelectedIndex(0); // select 'best'
 295           btn_queryTDB.setVisible(false);
 296           pnl_queryTDB.setVisible(false);
 297           progressBar.setProgressBar(null, progressId);
 298         }
 299         mainFrame.setEnabled(true);
 300         cmb_filterOption.setEnabled(true);
 301       }
 302     };
 303
 304     final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI()
 305     {
 306
 307       @Override
 308       public void finished()
 309       {
 310         // filter has been selected, so we set flag to remove ourselves
 311         notQueriedTDBYet = false;
 312         // new thread to discover structures - via 3d beacons
 313         Executors.defaultThreadFactory().newThread(strucDiscovery).start();
 314
 315       }
 316     };
 317
 318     // fetch db refs if OK pressed
 319     final Runnable discoverCanonicalDBrefs = new Runnable()
 320     {
 321       @Override
 322       public void run()
 323       {
 324         populateSeqsWithoutSourceDBRef();
 325
 326         final int y = seqsWithoutSourceDBRef.size();
 327         if (y > 0)
 328         {
 329           final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
 330                   .toArray(new SequenceI[y]);
 331           DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
 332                   progressBar, new DbSourceProxy[]
 333                   { new jalview.ws.dbsources.Uniprot() }, null, false);
 334           dbRefFetcher.addListener(afterDbRefFetch);
 335           // ideally this would also gracefully run with callbacks
 336           dbRefFetcher.fetchDBRefs(true);
 337         }
 338         else
 339         {
 340           // call finished action directly
 341           afterDbRefFetch.finished();
 342         }
 343       }
 344
 345     };
 346     final Runnable revertview = new Runnable()
 347     {
 348       @Override
 349       public void run()
 350       {
 351         if (lastSelected != null)
 352         {
 353           cmb_filterOption.setSelectedItem(lastSelected);
 354         }
 355       };
 356     };
 357     int threshold = Cache.getDefault("THRESHOLD_WARN_UNIPROT_FETCH",
 358             THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
 359     Console.debug("Using Uniprot fetch threshold of " + threshold);
 360     if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold)
 361     {
 362       Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs)
 363               .start();
 364       return;
 365     }
 366     // need cancel and no to result in the discoverPDB action - mocked is
 367     // 'cancel' TODO: mock should be OK
 368     JvOptionPane.newOptionDialog(this)
 369             .setResponseHandler(JvOptionPane.OK_OPTION,
 370                     discoverCanonicalDBrefs)
 371             .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
 372             .setResponseHandler(JvOptionPane.NO_OPTION, revertview)
 373             .showDialog(
 374                     MessageManager.formatMessage(
 375                             "label.fetch_references_for_3dbeacons",
 376                             seqsWithoutSourceDBRef.size()),
 377                     MessageManager.getString("label.3dbeacons"),
 378                     JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE,
 379                     null, new Object[]
 380                     { MessageManager.getString("action.ok"),
 381                         MessageManager.getString("action.cancel") },
 382                     MessageManager.getString("action.ok"));
 383   }
 384
 385   /**
 386    * Builds a drop-down choice list of existing structure viewers to which new
 387    * structures may be added. If this list is empty then it, and the 'Add'
 388    * button, are hidden.
 389    */
 390   private void discoverStructureViews()
 391   {
 392     if (Desktop.instance != null)
 393     {
 394       targetView.removeAllItems();
 395       if (lastTargetedView != null && !lastTargetedView.isVisible())
 396       {
 397         lastTargetedView = null;
 398       }
 399       int linkedViewsAt = 0;
 400       for (StructureViewerBase view : Desktop.instance
 401               .getStructureViewers(null, null))
 402       {
 403         StructureViewer viewHandler = (lastTargetedView != null
 404                 && lastTargetedView.sview == view) ? lastTargetedView
 405                         : StructureViewer.reconfigure(view);
 406
 407         if (view.isLinkedWith(ap))
 408         {
 409           targetView.insertItemAt(viewHandler, linkedViewsAt++);
 410         }
 411         else
 412         {
 413           targetView.addItem(viewHandler);
 414         }
 415       }
 416
 417       /*
 418        * show option to Add to viewer if at least 1 viewer found
 419        */
 420       targetView.setVisible(false);
 421       if (targetView.getItemCount() > 0)
 422       {
 423         targetView.setVisible(true);
 424         if (lastTargetedView != null)
 425         {
 426           targetView.setSelectedItem(lastTargetedView);
 427         }
 428         else
 429         {
 430           targetView.setSelectedIndex(0);
 431         }
 432       }
 433       btn_add.setVisible(targetView.isVisible());
 434     }
 435   }
 436
 437   /**
 438    * Updates the progress indicator with the specified message
 439    *
 440    * @param message
 441    *          displayed message for the operation
 442    * @param id
 443    *          unique handle for this indicator
 444    */
 445   protected void updateProgressIndicator(String message, long id)
 446   {
 447     if (progressIndicator != null)
 448     {
 449       progressIndicator.setProgressBar(message, id);
 450     }
 451   }
 452
 453   /**
 454    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
 455    * selection group
 456    */
 457   void fetchStructuresMetaData()
 458   {
 459     long startTime = System.currentTimeMillis();
 460     Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
 461             .getStructureSummaryFields();
 462
 463     discoveredStructuresSet = new LinkedHashSet<>();
 464     HashSet<String> errors = new HashSet<>();
 465
 466     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 467             .getSelectedItem());
 468
 469     for (SequenceI seq : selectedSequences)
 470     {
 471
 472       FTSRestResponse resultList;
 473       try
 474       {
 475         resultList = data.fetchStructuresMetaData(seq, wantedFields,
 476                 selectedFilterOpt, !chk_invertFilter.isSelected());
 477         // null response means the FTSengine didn't yield a query for this
 478         // consider designing a special exception if we really wanted to be
 479         // OOCrazy
 480         if (resultList == null)
 481         {
 482           continue;
 483         }
 484       } catch (Exception e)
 485       {
 486         e.printStackTrace();
 487         errors.add(e.getMessage());
 488         continue;
 489       }
 490       if (resultList.getSearchSummary() != null
 491               && !resultList.getSearchSummary().isEmpty())
 492       {
 493         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 494       }
 495     }
 496
 497     int noOfStructuresFound = 0;
 498     String totalTime = (System.currentTimeMillis() - startTime)
 499             + " milli secs";
 500     if (discoveredStructuresSet != null
 501             && !discoveredStructuresSet.isEmpty())
 502     {
 503       getResultTable()
 504               .setModel(data.getTableModel(discoveredStructuresSet));
 505
 506       noOfStructuresFound = discoveredStructuresSet.size();
 507       lastDiscoveredStructuresSet = discoveredStructuresSet;
 508       mainFrame.setTitle(MessageManager.formatMessage(
 509               "label.structure_chooser_no_of_structures",
 510               noOfStructuresFound, totalTime));
 511     }
 512     else
 513     {
 514       mainFrame.setTitle(MessageManager
 515               .getString("label.structure_chooser_manual_association"));
 516       if (errors.size() > 0)
 517       {
 518         StringBuilder errorMsg = new StringBuilder();
 519         for (String error : errors)
 520         {
 521           errorMsg.append(error).append("\n");
 522         }
 523         JvOptionPane.showMessageDialog(this, errorMsg.toString(),
 524                 MessageManager.getString("label.pdb_web-service_error"),
 525                 JvOptionPane.ERROR_MESSAGE);
 526       }
 527     }
 528   }
 529
 530   protected void loadLocalCachedPDBEntries()
 531   {
 532     ArrayList<CachedPDB> entries = new ArrayList<>();
 533     for (SequenceI seq : selectedSequences)
 534     {
 535       if (seq.getDatasetSequence() != null
 536               && seq.getDatasetSequence().getAllPDBEntries() != null)
 537       {
 538         for (PDBEntry pdbEntry : seq.getDatasetSequence()
 539                 .getAllPDBEntries())
 540         {
 541           if (pdbEntry.getFile() != null)
 542           {
 543             entries.add(new CachedPDB(seq, pdbEntry));
 544           }
 545         }
 546       }
 547     }
 548     cachedPDBExists = !entries.isEmpty();
 549     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
 550     tbl_local_pdb.setModel(tableModelx);
 551   }
 552
 553   /**
 554    * Filters a given list of discovered structures based on supplied argument
 555    *
 556    * @param fieldToFilterBy
 557    *          the field to filter by
 558    */
 559   void filterResultSet(final String fieldToFilterBy)
 560   {
 561     Thread filterThread = new Thread(new Runnable()
 562     {
 563
 564       @Override
 565       public void run()
 566       {
 567         long startTime = System.currentTimeMillis();
 568         lbl_loading.setVisible(true);
 569         Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
 570                 .getStructureSummaryFields();
 571         Collection<FTSData> filteredResponse = new HashSet<>();
 572         HashSet<String> errors = new HashSet<>();
 573
 574         for (SequenceI seq : selectedSequences)
 575         {
 576
 577           FTSRestResponse resultList;
 578           try
 579           {
 580             resultList = data.selectFirstRankedQuery(seq,
 581                     discoveredStructuresSet, wantedFields, fieldToFilterBy,
 582                     !chk_invertFilter.isSelected());
 583
 584           } catch (Exception e)
 585           {
 586             e.printStackTrace();
 587             errors.add(e.getMessage());
 588             continue;
 589           }
 590           if (resultList.getSearchSummary() != null
 591                   && !resultList.getSearchSummary().isEmpty())
 592           {
 593             filteredResponse.addAll(resultList.getSearchSummary());
 594           }
 595         }
 596
 597         String totalTime = (System.currentTimeMillis() - startTime)
 598                 + " milli secs";
 599         if (!filteredResponse.isEmpty())
 600         {
 601           final int filterResponseCount = filteredResponse.size();
 602           Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
 603           reorderedStructuresSet.addAll(filteredResponse);
 604           reorderedStructuresSet.addAll(discoveredStructuresSet);
 605           getResultTable()
 606                   .setModel(data.getTableModel(reorderedStructuresSet));
 607
 608           FTSRestResponse.configureTableColumn(getResultTable(),
 609                   wantedFields, tempUserPrefs);
 610           getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
 611           getResultTable().getColumn("Ref Sequence").setMinWidth(100);
 612           getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
 613           // Update table selection model here
 614           getResultTable().addRowSelectionInterval(0,
 615                   filterResponseCount - 1);
 616           mainFrame.setTitle(MessageManager.formatMessage(
 617                   "label.structure_chooser_filter_time", totalTime));
 618         }
 619         else
 620         {
 621           mainFrame.setTitle(MessageManager.formatMessage(
 622                   "label.structure_chooser_filter_time", totalTime));
 623           if (errors.size() > 0)
 624           {
 625             StringBuilder errorMsg = new StringBuilder();
 626             for (String error : errors)
 627             {
 628               errorMsg.append(error).append("\n");
 629             }
 630             JvOptionPane.showMessageDialog(null, errorMsg.toString(),
 631                     MessageManager.getString("label.pdb_web-service_error"),
 632                     JvOptionPane.ERROR_MESSAGE);
 633           }
 634         }
 635
 636         lbl_loading.setVisible(false);
 637
 638         validateSelections();
 639       }
 640     });
 641     filterThread.start();
 642   }
 643
 644   /**
 645    * Handles action event for btn_pdbFromFile
 646    */
 647   @Override
 648   protected void pdbFromFile_actionPerformed()
 649   {
 650     // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and
 651     // StructureChooser
 652     // works
 653     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 654             Cache.getProperty("LAST_DIRECTORY"));
 655     chooser.setFileView(new jalview.io.JalviewFileView());
 656     chooser.setDialogTitle(
 657             MessageManager.formatMessage("label.select_pdb_file_for",
 658                     selectedSequence.getDisplayId(false)));
 659     chooser.setToolTipText(MessageManager.formatMessage(
 660             "label.load_pdb_file_associate_with_sequence",
 661             selectedSequence.getDisplayId(false)));
 662
 663     int value = chooser.showOpenDialog(null);
 664     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
 665     {
 666       selectedPdbFileName = chooser.getSelectedFile().getPath();
 667       Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
 668       validateSelections();
 669     }
 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)
 678   {
 679     populateFilterComboBox(haveData, cachedPDBExist, null);
 680   }
 681
 682   /**
 683    * Populates the filter combo-box options dynamically depending on discovered
 684    * structures
 685    */
 686   protected void populateFilterComboBox(boolean haveData,
 687           boolean cachedPDBExist, FilterOption lastSel)
 688   {
 689
 690     /*
 691      * temporarily suspend the change listener behaviour
 692      */
 693     cmb_filterOption.removeItemListener(this);
 694     int selSet = -1;
 695     cmb_filterOption.removeAllItems();
 696     if (haveData)
 697     {
 698       List<FilterOption> filters = data
 699               .getAvailableFilterOptions(VIEWS_FILTER);
 700       data.updateAvailableFilterOptions(VIEWS_FILTER, filters,
 701               lastDiscoveredStructuresSet);
 702       int p = 0;
 703       for (FilterOption filter : filters)
 704       {
 705         if (lastSel != null && filter.equals(lastSel))
 706         {
 707           selSet = p;
 708         }
 709         p++;
 710         cmb_filterOption.addItem(filter);
 711       }
 712     }
 713
 714     cmb_filterOption.addItem(
 715             new FilterOption(MessageManager.getString("label.enter_pdb_id"),
 716                     "-", VIEWS_ENTER_ID, false, null));
 717     cmb_filterOption.addItem(
 718             new FilterOption(MessageManager.getString("label.from_file"),
 719                     "-", VIEWS_FROM_FILE, false, null));
 720     if (canQueryTDB && notQueriedTDBYet)
 721     {
 722       btn_queryTDB.setVisible(true);
 723       pnl_queryTDB.setVisible(true);
 724     }
 725
 726     if (cachedPDBExist)
 727     {
 728       FilterOption cachedOption = new FilterOption(
 729               MessageManager.getString("label.cached_structures"), "-",
 730               VIEWS_LOCAL_PDB, false, null);
 731       cmb_filterOption.addItem(cachedOption);
 732       if (selSet == -1)
 733       {
 734         cmb_filterOption.setSelectedItem(cachedOption);
 735       }
 736     }
 737     if (selSet > -1)
 738     {
 739       cmb_filterOption.setSelectedIndex(selSet);
 740     }
 741     cmb_filterOption.addItemListener(this);
 742   }
 743
 744   /**
 745    * Updates the displayed view based on the selected filter option
 746    */
 747   protected void updateCurrentView()
 748   {
 749     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 750             .getSelectedItem());
 751
 752     if (lastSelected == selectedFilterOpt)
 753     {
 754       // don't need to do anything, probably
 755       return;
 756     }
 757     // otherwise, record selection
 758     // and update the layout and dialog accordingly
 759     lastSelected = selectedFilterOpt;
 760
 761     layout_switchableViews.show(pnl_switchableViews,
 762             selectedFilterOpt.getView());
 763     String filterTitle = mainFrame.getTitle();
 764     mainFrame.setTitle(frameTitle);
 765     chk_invertFilter.setVisible(false);
 766
 767     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 768     {
 769       mainFrame.setTitle(filterTitle);
 770       // TDB Query has no invert as yet
 771       chk_invertFilter.setVisible(selectedFilterOpt
 772               .getQuerySource() instanceof PDBStructureChooserQuerySource);
 773
 774       if (data != selectedFilterOpt.getQuerySource()
 775               || data.needsRefetch(selectedFilterOpt))
 776       {
 777         data = selectedFilterOpt.getQuerySource();
 778         // rebuild the views completely, since prefs will also change
 779         tabRefresh();
 780         return;
 781       }
 782       else
 783       {
 784         filterResultSet(selectedFilterOpt.getValue());
 785       }
 786     }
 787     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 788             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 789     {
 790       mainFrame.setTitle(MessageManager
 791               .getString("label.structure_chooser_manual_association"));
 792       idInputAssSeqPanel.loadCmbAssSeq();
 793       fileChooserAssSeqPanel.loadCmbAssSeq();
 794     }
 795     validateSelections();
 796   }
 797
 798   /**
 799    * Validates user selection and enables the 'Add' and 'New View' buttons if
 800    * all parameters are correct (the Add button will only be visible if there is
 801    * at least one existing structure viewer open). This basically means at least
 802    * one structure selected and no error messages.
 803    * <p>
 804    * The 'Superpose Structures' option is enabled if either more than one
 805    * structure is selected, or the 'Add' to existing view option is enabled, and
 806    * disabled if the only option is to open a new view of a single structure.
 807    */
 808   @Override
 809   protected void validateSelections()
 810   {
 811     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 812             .getSelectedItem());
 813     btn_add.setEnabled(false);
 814     String currentView = selectedFilterOpt.getView();
 815     int selectedCount = 0;
 816     if (currentView == VIEWS_FILTER)
 817     {
 818       selectedCount = getResultTable().getSelectedRows().length;
 819       if (selectedCount > 0)
 820       {
 821         btn_add.setEnabled(true);
 822       }
 823     }
 824     else if (currentView == VIEWS_LOCAL_PDB)
 825     {
 826       selectedCount = tbl_local_pdb.getSelectedRows().length;
 827       if (selectedCount > 0)
 828       {
 829         btn_add.setEnabled(true);
 830       }
 831     }
 832     else if (currentView == VIEWS_ENTER_ID)
 833     {
 834       validateAssociationEnterPdb();
 835     }
 836     else if (currentView == VIEWS_FROM_FILE)
 837     {
 838       validateAssociationFromFile();
 839     }
 840
 841     btn_newView.setEnabled(btn_add.isEnabled());
 842
 843     /*
 844      * enable 'Superpose' option if more than one structure is selected,
 845      * or there are view(s) available to add structure(s) to
 846      */
 847     chk_superpose
 848             .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
 849   }
 850
 851   @Override
 852   protected boolean showPopupFor(int selectedRow, int x, int y)
 853   {
 854     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 855             .getSelectedItem());
 856     String currentView = selectedFilterOpt.getView();
 857
 858     if (currentView == VIEWS_FILTER
 859             && data instanceof ThreeDBStructureChooserQuerySource)
 860     {
 861
 862       TDB_FTSData row = ((ThreeDBStructureChooserQuerySource) data)
 863               .getFTSDataFor(getResultTable(), selectedRow,
 864                       discoveredStructuresSet);
 865       String pageUrl = row.getModelViewUrl();
 866       JPopupMenu popup = new JPopupMenu("3D Beacons");
 867       JMenuItem viewUrl = new JMenuItem("View model web page");
 868       viewUrl.addActionListener(new ActionListener()
 869       {
 870         @Override
 871         public void actionPerformed(ActionEvent e)
 872         {
 873           Desktop.showUrl(pageUrl);
 874         }
 875       });
 876       popup.add(viewUrl);
 877       SwingUtilities.invokeLater(new Runnable()
 878       {
 879         @Override
 880         public void run()
 881         {
 882           popup.show(getResultTable(), x, y);
 883         }
 884       });
 885       return true;
 886     }
 887     // event not handled by us
 888     return false;
 889   }
 890
 891   /**
 892    * Validates inputs from the Manual PDB entry panel
 893    */
 894   protected void validateAssociationEnterPdb()
 895   {
 896     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 897             .getCmb_assSeq().getSelectedItem();
 898     lbl_pdbManualFetchStatus.setIcon(errorImage);
 899     lbl_pdbManualFetchStatus.setToolTipText("");
 900     if (txt_search.getText().length() > 0)
 901     {
 902       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
 903               MessageManager.formatMessage("info.no_pdb_entry_found_for",
 904                       txt_search.getText())));
 905     }
 906
 907     if (errorWarning.length() > 0)
 908     {
 909       lbl_pdbManualFetchStatus.setIcon(warningImage);
 910       lbl_pdbManualFetchStatus.setToolTipText(
 911               JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
 912     }
 913
 914     if (selectedSequences.length == 1 || !assSeqOpt.getName()
 915             .equalsIgnoreCase("-Select Associated Seq-"))
 916     {
 917       txt_search.setEnabled(true);
 918       if (isValidPBDEntry)
 919       {
 920         btn_add.setEnabled(true);
 921         lbl_pdbManualFetchStatus.setToolTipText("");
 922         lbl_pdbManualFetchStatus.setIcon(goodImage);
 923       }
 924     }
 925     else
 926     {
 927       txt_search.setEnabled(false);
 928       lbl_pdbManualFetchStatus.setIcon(errorImage);
 929     }
 930   }
 931
 932   /**
 933    * Validates inputs for the manual PDB file selection options
 934    */
 935   protected void validateAssociationFromFile()
 936   {
 937     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
 938             .getCmb_assSeq().getSelectedItem();
 939     lbl_fromFileStatus.setIcon(errorImage);
 940     if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
 941             .getName().equalsIgnoreCase("-Select Associated Seq-")))
 942     {
 943       btn_pdbFromFile.setEnabled(true);
 944       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
 945       {
 946         btn_add.setEnabled(true);
 947         lbl_fromFileStatus.setIcon(goodImage);
 948       }
 949     }
 950     else
 951     {
 952       btn_pdbFromFile.setEnabled(false);
 953       lbl_fromFileStatus.setIcon(errorImage);
 954     }
 955   }
 956
 957   @Override
 958   protected void cmbAssSeqStateChanged()
 959   {
 960     validateSelections();
 961   }
 962
 963   private FilterOption lastSelected = null;
 964
 965   /**
 966    * Handles the state change event for the 'filter' combo-box and 'invert'
 967    * check-box
 968    */
 969   @Override
 970   protected void stateChanged(ItemEvent e)
 971   {
 972     if (e.getSource() instanceof JCheckBox)
 973     {
 974       updateCurrentView();
 975     }
 976     else
 977     {
 978       if (e.getStateChange() == ItemEvent.SELECTED)
 979       {
 980         updateCurrentView();
 981       }
 982     }
 983
 984   }
 985
 986   /**
 987    * select structures for viewing by their PDB IDs
 988    *
 989    * @param pdbids
 990    * @return true if structures were found and marked as selected
 991    */
 992   public boolean selectStructure(String... pdbids)
 993   {
 994     boolean found = false;
 995
 996     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 997             .getSelectedItem());
 998     String currentView = selectedFilterOpt.getView();
 999     JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
1000             : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
1001
1002     if (restable == null)
1003     {
1004       // can't select (enter PDB ID, or load file - need to also select which
1005       // sequence to associate with)
1006       return false;
1007     }
1008
1009     int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
1010     for (int r = 0; r < restable.getRowCount(); r++)
1011     {
1012       for (int p = 0; p < pdbids.length; p++)
1013       {
1014         if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
1015                 .equalsIgnoreCase(pdbids[p]))
1016         {
1017           restable.setRowSelectionInterval(r, r);
1018           found = true;
1019         }
1020       }
1021     }
1022     return found;
1023   }
1024
1025   /**
1026    * Handles the 'New View' action
1027    */
1028   @Override
1029   protected void newView_ActionPerformed()
1030   {
1031     targetView.setSelectedItem(null);
1032     showStructures(false);
1033   }
1034
1035   /**
1036    * Handles the 'Add to existing viewer' action
1037    */
1038   @Override
1039   protected void add_ActionPerformed()
1040   {
1041     showStructures(false);
1042   }
1043
1044   /**
1045    * structure viewer opened by this dialog, or null
1046    */
1047   private StructureViewer sViewer = null;
1048
1049   public void showStructures(boolean waitUntilFinished)
1050   {
1051
1052     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
1053
1054     final int preferredHeight = pnl_filter.getHeight();
1055
1056     Runnable viewStruc = new Runnable()
1057     {
1058       @Override
1059       public void run()
1060       {
1061         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
1062                 .getSelectedItem());
1063         String currentView = selectedFilterOpt.getView();
1064         JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
1065                 : tbl_local_pdb;
1066
1067         if (currentView == VIEWS_FILTER)
1068         {
1069           int[] selectedRows = restable.getSelectedRows();
1070           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
1071           List<SequenceI> selectedSeqsToView = new ArrayList<>();
1072           pdbEntriesToView = data.collectSelectedRows(restable,
1073                   selectedRows, selectedSeqsToView);
1074
1075           SequenceI[] selectedSeqs = selectedSeqsToView
1076                   .toArray(new SequenceI[selectedSeqsToView.size()]);
1077           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1078                   selectedSeqs);
1079         }
1080         else if (currentView == VIEWS_LOCAL_PDB)
1081         {
1082           int[] selectedRows = tbl_local_pdb.getSelectedRows();
1083           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
1084           int count = 0;
1085           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
1086                   .getModelIndex();
1087           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
1088                   .getModelIndex();
1089           List<SequenceI> selectedSeqsToView = new ArrayList<>();
1090           for (int row : selectedRows)
1091           {
1092             PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb
1093                     .getModel()).getPDBEntryAt(row).getPdbEntry();
1094
1095             pdbEntriesToView[count++] = pdbEntry;
1096             SequenceI selectedSeq = (SequenceI) tbl_local_pdb
1097                     .getValueAt(row, refSeqColIndex);
1098             selectedSeqsToView.add(selectedSeq);
1099           }
1100           SequenceI[] selectedSeqs = selectedSeqsToView
1101                   .toArray(new SequenceI[selectedSeqsToView.size()]);
1102           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1103                   selectedSeqs);
1104         }
1105         else if (currentView == VIEWS_ENTER_ID)
1106         {
1107           SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
1108                   .getCmb_assSeq().getSelectedItem()).getSequence();
1109           if (userSelectedSeq != null)
1110           {
1111             selectedSequence = userSelectedSeq;
1112           }
1113           String pdbIdStr = txt_search.getText();
1114           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
1115           if (pdbEntry == null)
1116           {
1117             pdbEntry = new PDBEntry();
1118             if (pdbIdStr.split(":").length > 1)
1119             {
1120               pdbEntry.setId(pdbIdStr.split(":")[0]);
1121               pdbEntry.setChainCode(
1122                       pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
1123             }
1124             else
1125             {
1126               pdbEntry.setId(pdbIdStr);
1127             }
1128             pdbEntry.setType(PDBEntry.Type.PDB);
1129             selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
1130           }
1131
1132           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
1133           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1134                   new SequenceI[]
1135                   { selectedSequence });
1136         }
1137         else if (currentView == VIEWS_FROM_FILE)
1138         {
1139           SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
1140                   .getCmb_assSeq().getSelectedItem()).getSequence();
1141           if (userSelectedSeq != null)
1142           {
1143             selectedSequence = userSelectedSeq;
1144           }
1145           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
1146                   .associatePdbWithSeq(selectedPdbFileName,
1147                           DataSourceType.FILE, selectedSequence, true,
1148                           Desktop.instance);
1149
1150           sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
1151                   ap, new SequenceI[]
1152                   { selectedSequence });
1153         }
1154         SwingUtilities.invokeLater(new Runnable()
1155         {
1156           @Override
1157           public void run()
1158           {
1159             closeAction(preferredHeight);
1160             mainFrame.dispose();
1161           }
1162         });
1163       }
1164     };
1165     Thread runner = new Thread(viewStruc);
1166     runner.start();
1167     if (waitUntilFinished)
1168     {
1169       while (sViewer == null ? runner.isAlive()
1170               : (sViewer.sview == null ? true
1171                       : !sViewer.sview.hasMapping()))
1172       {
1173         try
1174         {
1175           Thread.sleep(300);
1176         } catch (InterruptedException ie)
1177         {
1178
1179         }
1180       }
1181     }
1182   }
1183
1184   /**
1185    * Answers a structure viewer (new or existing) configured to superimpose
1186    * added structures or not according to the user's choice
1187    *
1188    * @param ssm
1189    * @return
1190    */
1191   StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm)
1192   {
1193     Object sv = targetView.getSelectedItem();
1194
1195     return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
1196   }
1197
1198   /**
1199    * Adds PDB structures to a new or existing structure viewer
1200    *
1201    * @param ssm
1202    * @param pdbEntriesToView
1203    * @param alignPanel
1204    * @param sequences
1205    * @return
1206    */
1207   private StructureViewer launchStructureViewer(
1208           StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
1209           final AlignmentPanel alignPanel, SequenceI[] sequences)
1210   {
1211     long progressId = sequences.hashCode();
1212     setProgressBar(MessageManager
1213             .getString("status.launching_3d_structure_viewer"), progressId);
1214     final StructureViewer theViewer = getTargetedStructureViewer(ssm);
1215     boolean superimpose = chk_superpose.isSelected();
1216     theViewer.setSuperpose(superimpose);
1217
1218     /*
1219      * remember user's choice of superimpose or not
1220      */
1221     Cache.setProperty(AUTOSUPERIMPOSE,
1222             Boolean.valueOf(superimpose).toString());
1223
1224     setProgressBar(null, progressId);
1225     if (SiftsSettings.isMapWithSifts())
1226     {
1227       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
1228       int p = 0;
1229       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
1230       // real PDB ID. For moment, we can also safely do this if there is already
1231       // a known mapping between the PDBEntry and the sequence.
1232       for (SequenceI seq : sequences)
1233       {
1234         PDBEntry pdbe = pdbEntriesToView[p++];
1235         if (pdbe != null && pdbe.getFile() != null)
1236         {
1237           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
1238           if (smm != null && smm.length > 0)
1239           {
1240             for (StructureMapping sm : smm)
1241             {
1242               if (sm.getSequence() == seq)
1243               {
1244                 continue;
1245               }
1246             }
1247           }
1248         }
1249         if (seq.getPrimaryDBRefs().isEmpty())
1250         {
1251           seqsWithoutSourceDBRef.add(seq);
1252           continue;
1253         }
1254       }
1255       if (!seqsWithoutSourceDBRef.isEmpty())
1256       {
1257         int y = seqsWithoutSourceDBRef.size();
1258         setProgressBar(MessageManager.formatMessage(
1259                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
1260                 y), progressId);
1261         SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
1262                 .toArray(new SequenceI[y]);
1263         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
1264         dbRefFetcher.fetchDBRefs(true);
1265
1266         setProgressBar("Fetch complete.", progressId); // todo i18n
1267       }
1268     }
1269     if (pdbEntriesToView.length > 1)
1270     {
1271       setProgressBar(
1272               MessageManager.getString(
1273                       "status.fetching_3d_structures_for_selected_entries"),
1274               progressId);
1275       theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
1276     }
1277     else
1278     {
1279       setProgressBar(MessageManager.formatMessage(
1280               "status.fetching_3d_structures_for",
1281               pdbEntriesToView[0].getId()), progressId);
1282       theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
1283     }
1284     setProgressBar(null, progressId);
1285     // remember the last viewer we used...
1286     lastTargetedView = theViewer;
1287     return theViewer;
1288   }
1289
1290   /**
1291    * Populates the combo-box used in associating manually fetched structures to
1292    * a unique sequence when more than one sequence selection is made.
1293    */
1294   @Override
1295   protected void populateCmbAssociateSeqOptions(
1296           JComboBox<AssociateSeqOptions> cmb_assSeq,
1297           JLabel lbl_associateSeq)
1298   {
1299     cmb_assSeq.removeAllItems();
1300     cmb_assSeq.addItem(
1301             new AssociateSeqOptions("-Select Associated Seq-", null));
1302     lbl_associateSeq.setVisible(false);
1303     if (selectedSequences.length > 1)
1304     {
1305       for (SequenceI seq : selectedSequences)
1306       {
1307         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
1308       }
1309     }
1310     else
1311     {
1312       String seqName = selectedSequence.getDisplayId(false);
1313       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
1314       lbl_associateSeq.setText(seqName);
1315       lbl_associateSeq.setVisible(true);
1316       cmb_assSeq.setVisible(false);
1317     }
1318   }
1319
1320   protected boolean isStructuresDiscovered()
1321   {
1322     return discoveredStructuresSet != null
1323             && !discoveredStructuresSet.isEmpty();
1324   }
1325
1326   protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes
1327                                // this.
1328   // Doing a search for "1" or "1c" is valuable?
1329   // Those work but are enormously slow.
1330
1331   @Override
1332   protected void txt_search_ActionPerformed()
1333   {
1334     String text = txt_search.getText().trim();
1335     if (text.length() >= PDB_ID_MIN)
1336       new Thread()
1337       {
1338
1339         @Override
1340         public void run()
1341         {
1342           errorWarning.setLength(0);
1343           isValidPBDEntry = false;
1344           if (text.length() > 0)
1345           {
1346             // TODO move this pdb id search into the PDB specific
1347             // FTSSearchEngine
1348             // for moment, it will work fine as is because it is self-contained
1349             String searchTerm = text.toLowerCase(Locale.ROOT);
1350             searchTerm = searchTerm.split(":")[0];
1351             // System.out.println(">>>>> search term : " + searchTerm);
1352             List<FTSDataColumnI> wantedFields = new ArrayList<>();
1353             FTSRestRequest pdbRequest = new FTSRestRequest();
1354             pdbRequest.setAllowEmptySeq(false);
1355             pdbRequest.setResponseSize(1);
1356             pdbRequest.setFieldToSearchBy("(pdb_id:");
1357             pdbRequest.setWantedFields(wantedFields);
1358             pdbRequest.setSearchTerm(searchTerm + ")");
1359             pdbRequest.setAssociatedSequence(selectedSequence);
1360             FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
1361             wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
1362             FTSRestResponse resultList;
1363             try
1364             {
1365               resultList = pdbRestClient.executeRequest(pdbRequest);
1366             } catch (Exception e)
1367             {
1368               errorWarning.append(e.getMessage());
1369               return;
1370             } finally
1371             {
1372               validateSelections();
1373             }
1374             if (resultList.getSearchSummary() != null
1375                     && resultList.getSearchSummary().size() > 0)
1376             {
1377               isValidPBDEntry = true;
1378             }
1379           }
1380           validateSelections();
1381         }
1382       }.start();
1383   }
1384
1385   @Override
1386   protected void tabRefresh()
1387   {
1388     if (selectedSequences != null)
1389     {
1390       Thread refreshThread = new Thread(new Runnable()
1391       {
1392         @Override
1393         public void run()
1394         {
1395           fetchStructuresMetaData();
1396           // populateFilterComboBox(true, cachedPDBExists);
1397
1398           filterResultSet(
1399                   ((FilterOption) cmb_filterOption.getSelectedItem())
1400                           .getValue());
1401         }
1402       });
1403       refreshThread.start();
1404     }
1405   }
1406
1407   public class PDBEntryTableModel extends AbstractTableModel
1408   {
1409     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1410         "File" };
1411
1412     private List<CachedPDB> pdbEntries;
1413
1414     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1415     {
1416       this.pdbEntries = new ArrayList<>(pdbEntries);
1417     }
1418
1419     @Override
1420     public String getColumnName(int columnIndex)
1421     {
1422       return columns[columnIndex];
1423     }
1424
1425     @Override
1426     public int getRowCount()
1427     {
1428       return pdbEntries.size();
1429     }
1430
1431     @Override
1432     public int getColumnCount()
1433     {
1434       return columns.length;
1435     }
1436
1437     @Override
1438     public boolean isCellEditable(int row, int column)
1439     {
1440       return false;
1441     }
1442
1443     @Override
1444     public Object getValueAt(int rowIndex, int columnIndex)
1445     {
1446       Object value = "??";
1447       CachedPDB entry = pdbEntries.get(rowIndex);
1448       switch (columnIndex)
1449       {
1450       case 0:
1451         value = entry.getSequence();
1452         break;
1453       case 1:
1454         value = entry.getQualifiedId();
1455         break;
1456       case 2:
1457         value = entry.getPdbEntry().getChainCode() == null ? "_"
1458                 : entry.getPdbEntry().getChainCode();
1459         break;
1460       case 3:
1461         value = entry.getPdbEntry().getType();
1462         break;
1463       case 4:
1464         value = entry.getPdbEntry().getFile();
1465         break;
1466       }
1467       return value;
1468     }
1469
1470     @Override
1471     public Class<?> getColumnClass(int columnIndex)
1472     {
1473       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1474     }
1475
1476     public CachedPDB getPDBEntryAt(int row)
1477     {
1478       return pdbEntries.get(row);
1479     }
1480
1481   }
1482
1483   private class CachedPDB
1484   {
1485     private SequenceI sequence;
1486
1487     private PDBEntry pdbEntry;
1488
1489     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1490     {
1491       this.sequence = sequence;
1492       this.pdbEntry = pdbEntry;
1493     }
1494
1495     public String getQualifiedId()
1496     {
1497       if (pdbEntry.hasProvider())
1498       {
1499         return pdbEntry.getProvider() + ":" + pdbEntry.getId();
1500       }
1501       return pdbEntry.toString();
1502     }
1503
1504     public SequenceI getSequence()
1505     {
1506       return sequence;
1507     }
1508
1509     public PDBEntry getPdbEntry()
1510     {
1511       return pdbEntry;
1512     }
1513
1514   }
1515
1516   private IProgressIndicator progressBar;
1517
1518   @Override
1519   public void setProgressBar(String message, long id)
1520   {
1521     progressBar.setProgressBar(message, id);
1522   }
1523
1524   @Override
1525   public void registerHandler(long id, IProgressIndicatorHandler handler)
1526   {
1527     progressBar.registerHandler(id, handler);
1528   }
1529
1530   @Override
1531   public boolean operationInProgress()
1532   {
1533     return progressBar.operationInProgress();
1534   }
1535
1536   public JalviewStructureDisplayI getOpenedStructureViewer()
1537   {
1538     return sViewer == null ? null : sViewer.sview;
1539   }
1540
1541   @Override
1542   protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs)
1543   {
1544     data.setDocFieldPrefs(newPrefs);
1545
1546   }
1547
1548   /**
1549    *
1550    * @return true when all initialisation threads have finished and dialog is
1551    *         visible
1552    */
1553   public boolean isDialogVisible()
1554   {
1555     return mainFrame != null && data != null && cmb_filterOption != null
1556             && mainFrame.isVisible()
1557             && cmb_filterOption.getSelectedItem() != null;
1558   }
1559
1560   /**
1561    *
1562    * @return true if the 3D-Beacons query button will/has been displayed
1563    */
1564   public boolean isCanQueryTDB()
1565   {
1566     return canQueryTDB;
1567   }
1568
1569   public boolean isNotQueriedTDBYet()
1570   {
1571     return notQueriedTDBYet;
1572   }
1573 }