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.io.File;
  28 import java.io.IOException;
  29 import java.util.ArrayList;
  30 import java.util.Collection;
  31 import java.util.HashSet;
  32 import java.util.LinkedHashSet;
  33 import java.util.List;
  34 import java.util.Locale;
  35 import java.util.concurrent.Callable;
  36 import java.util.concurrent.Executors;
  37
  38 import javax.swing.JCheckBox;
  39 import javax.swing.JComboBox;
  40 import javax.swing.JLabel;
  41 import javax.swing.JMenuItem;
  42 import javax.swing.JPopupMenu;
  43 import javax.swing.JTable;
  44 import javax.swing.SwingUtilities;
  45 import javax.swing.table.AbstractTableModel;
  46
  47 import org.json.simple.parser.ParseException;
  48
  49 import jalview.api.structures.JalviewStructureDisplayI;
  50 import jalview.bin.Cache;
  51 import jalview.bin.Console;
  52 import jalview.bin.Jalview;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.PDBEntry;
  55 import jalview.datamodel.SequenceI;
  56 import jalview.fts.api.FTSData;
  57 import jalview.fts.api.FTSDataColumnI;
  58 import jalview.fts.api.FTSRestClientI;
  59 import jalview.fts.core.FTSDataColumnPreferences;
  60 import jalview.fts.core.FTSRestRequest;
  61 import jalview.fts.core.FTSRestResponse;
  62 import jalview.fts.service.pdb.PDBFTSRestClient;
  63 import jalview.fts.service.threedbeacons.TDB_FTSData;
  64 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
  65 import jalview.gui.structurechooser.StructureChooserQuerySource;
  66 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
  67 import jalview.io.DataSourceType;
  68 import jalview.io.JalviewFileChooser;
  69 import jalview.io.JalviewFileView;
  70 import jalview.io.StructureFile;
  71 import jalview.jbgui.FilterOption;
  72 import jalview.jbgui.GStructureChooser;
  73 import jalview.structure.StructureImportSettings.TFType;
  74 import jalview.structure.StructureMapping;
  75 import jalview.structure.StructureSelectionManager;
  76 import jalview.util.MessageManager;
  77 import jalview.util.Platform;
  78 import jalview.util.StringUtils;
  79 import jalview.ws.DBRefFetcher;
  80 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  81 import jalview.ws.dbsources.EBIAlfaFold;
  82 import jalview.ws.seqfetcher.DbSourceProxy;
  83 import jalview.ws.sifts.SiftsSettings;
  84
  85 /**
  86  * Provides the behaviors for the Structure chooser Panel
  87  *
  88  * @author tcnofoegbu
  89  *
  90  */
  91 @SuppressWarnings("serial")
  92 public class StructureChooser extends GStructureChooser
  93         implements IProgressIndicator
  94 {
  95   private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
  96
  97   /**
  98    * warn user if need to fetch more than this many uniprot records at once
  99    */
 100   private static final int THRESHOLD_WARN_UNIPROT_FETCH_NEEDED = 20;
 101
 102   private SequenceI selectedSequence;
 103
 104   private SequenceI[] selectedSequences;
 105
 106   private IProgressIndicator progressIndicator;
 107
 108   private Collection<FTSData> discoveredStructuresSet;
 109
 110   private StructureChooserQuerySource data;
 111
 112   @Override
 113   protected FTSDataColumnPreferences getFTSDocFieldPrefs()
 114   {
 115     return data.getDocFieldPrefs();
 116   }
 117
 118   private String selectedPdbFileName;
 119
 120   private TFType localPdbTempfacType;
 121
 122   private String localPdbPaeMatrixFileName;
 123
 124   private boolean isValidPBDEntry;
 125
 126   private boolean cachedPDBExists;
 127
 128   private Collection<FTSData> lastDiscoveredStructuresSet;
 129
 130   private boolean canQueryTDB = false;
 131
 132   private boolean notQueriedTDBYet = true;
 133
 134   List<SequenceI> seqsWithoutSourceDBRef = null;
 135
 136   private boolean showChooserGUI = true;
 137
 138   private static StructureViewer lastTargetedView = null;
 139
 140   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
 141           AlignmentPanel ap)
 142   {
 143     this(selectedSeqs, selectedSeq, ap, true);
 144   }
 145
 146   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
 147           AlignmentPanel ap, boolean showGUI)
 148   {
 149     // which FTS engine to use
 150     data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
 151     initDialog();
 152
 153     this.ap = ap;
 154     this.selectedSequence = selectedSeq;
 155     this.selectedSequences = selectedSeqs;
 156     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
 157     this.showChooserGUI = showGUI;
 158     init();
 159
 160   }
 161
 162   /**
 163    * sets canQueryTDB if protein sequences without a canonical uniprot ref or at
 164    * least one structure are discovered.
 165    */
 166   private void populateSeqsWithoutSourceDBRef()
 167   {
 168     seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
 169     boolean needCanonical = false;
 170     for (SequenceI seq : selectedSequences)
 171     {
 172       if (seq.isProtein())
 173       {
 174         int dbRef = ThreeDBStructureChooserQuerySource
 175                 .checkUniprotRefs(seq.getDBRefs());
 176         if (dbRef < 0)
 177         {
 178           if (dbRef == -1)
 179           {
 180             // need to retrieve canonicals
 181             needCanonical = true;
 182             seqsWithoutSourceDBRef.add(seq);
 183           }
 184           else
 185           {
 186             // could be a sequence with pdb ref
 187             if (seq.getAllPDBEntries() == null
 188                     || seq.getAllPDBEntries().size() == 0)
 189             {
 190               seqsWithoutSourceDBRef.add(seq);
 191             }
 192           }
 193         }
 194       }
 195     }
 196     // retrieve database refs for protein sequences
 197     if (!seqsWithoutSourceDBRef.isEmpty())
 198     {
 199       canQueryTDB = true;
 200       if (needCanonical)
 201       {
 202         // triggers display of the 'Query TDB' button
 203         notQueriedTDBYet = true;
 204       }
 205     }
 206   };
 207
 208   /**
 209    * Initializes parameters used by the Structure Chooser Panel
 210    */
 211   protected void init()
 212   {
 213     if (!Jalview.isHeadlessMode())
 214     {
 215       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 216     }
 217
 218     chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
 219     btn_queryTDB.addActionListener(new ActionListener()
 220     {
 221
 222       @Override
 223       public void actionPerformed(ActionEvent e)
 224       {
 225         promptForTDBFetch(false);
 226       }
 227     });
 228
 229     Executors.defaultThreadFactory().newThread(new Runnable()
 230     {
 231       @Override
 232       public void run()
 233       {
 234         populateSeqsWithoutSourceDBRef();
 235         initialStructureDiscovery();
 236       }
 237
 238     }).start();
 239
 240   }
 241
 242   // called by init
 243   private void initialStructureDiscovery()
 244   {
 245     // check which FTS engine to use
 246     data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences);
 247
 248     // ensure a filter option is in force for search
 249     populateFilterComboBox(true, cachedPDBExists);
 250
 251     // looks for any existing structures already loaded
 252     // for the sequences (the cached ones)
 253     // then queries the StructureChooserQuerySource to
 254     // discover more structures.
 255     //
 256     // Possible optimisation is to only begin querying
 257     // the structure chooser if there are no cached structures.
 258
 259     long startTime = System.currentTimeMillis();
 260     updateProgressIndicator(
 261             MessageManager.getString("status.loading_cached_pdb_entries"),
 262             startTime);
 263     loadLocalCachedPDBEntries();
 264     updateProgressIndicator(null, startTime);
 265     updateProgressIndicator(
 266             MessageManager.getString("status.searching_for_pdb_structures"),
 267             startTime);
 268     fetchStructuresMetaData();
 269     // revise filter options if no results were found
 270     populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
 271     discoverStructureViews();
 272     updateProgressIndicator(null, startTime);
 273     mainFrame.setVisible(showChooserGUI);
 274     updateCurrentView();
 275   }
 276
 277   /**
 278    * raises dialog for Uniprot fetch followed by 3D beacons search
 279    *
 280    * @param ignoreGui
 281    *          - when true, don't ask, just fetch
 282    */
 283   public void promptForTDBFetch(boolean ignoreGui)
 284   {
 285     final long progressId = System.currentTimeMillis();
 286
 287     // final action after prompting and discovering db refs
 288     final Runnable strucDiscovery = new Runnable()
 289     {
 290       @Override
 291       public void run()
 292       {
 293         mainFrame.setEnabled(false);
 294         cmb_filterOption.setEnabled(false);
 295         progressBar.setProgressBar(
 296                 MessageManager.getString("status.searching_3d_beacons"),
 297                 progressId);
 298         btn_queryTDB.setEnabled(false);
 299         // TODO: warn if no accessions discovered
 300         populateSeqsWithoutSourceDBRef();
 301         // redo initial discovery - this time with 3d beacons
 302         // Executors.
 303         previousWantedFields = null;
 304         lastSelected = (FilterOption) cmb_filterOption.getSelectedItem();
 305         cmb_filterOption.setSelectedItem(null);
 306         cachedPDBExists = false; // reset to initial
 307         initialStructureDiscovery();
 308         if (!isStructuresDiscovered())
 309         {
 310           progressBar.setProgressBar(MessageManager.getString(
 311                   "status.no_structures_discovered_from_3d_beacons"),
 312                   progressId);
 313           btn_queryTDB.setToolTipText(MessageManager.getString(
 314                   "status.no_structures_discovered_from_3d_beacons"));
 315           btn_queryTDB.setEnabled(false);
 316           pnl_queryTDB.setVisible(false);
 317         }
 318         else
 319         {
 320           cmb_filterOption.setSelectedIndex(0); // select 'best'
 321           btn_queryTDB.setVisible(false);
 322           pnl_queryTDB.setVisible(false);
 323           progressBar.setProgressBar(null, progressId);
 324         }
 325         mainFrame.setEnabled(true);
 326         cmb_filterOption.setEnabled(true);
 327       }
 328     };
 329
 330     final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI()
 331     {
 332
 333       @Override
 334       public void finished()
 335       {
 336         // filter has been selected, so we set flag to remove ourselves
 337         notQueriedTDBYet = false;
 338         // new thread to discover structures - via 3d beacons
 339         Executors.defaultThreadFactory().newThread(strucDiscovery).start();
 340
 341       }
 342     };
 343
 344     // fetch db refs if OK pressed
 345     final Callable discoverCanonicalDBrefs = () -> {
 346       btn_queryTDB.setEnabled(false);
 347       populateSeqsWithoutSourceDBRef();
 348
 349       final int y = seqsWithoutSourceDBRef.size();
 350       if (y > 0)
 351       {
 352         final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
 353                 .toArray(new SequenceI[y]);
 354         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
 355                 progressBar, new DbSourceProxy[]
 356                 { new jalview.ws.dbsources.Uniprot() }, null, false);
 357         dbRefFetcher.addListener(afterDbRefFetch);
 358         // ideally this would also gracefully run with callbacks
 359
 360         dbRefFetcher.fetchDBRefs(true);
 361       }
 362       else
 363       {
 364         // call finished action directly
 365         afterDbRefFetch.finished();
 366       }
 367       return null;
 368     };
 369     final Callable revertview = () -> {
 370       if (lastSelected != null)
 371       {
 372         cmb_filterOption.setSelectedItem(lastSelected);
 373       }
 374       return null;
 375     };
 376     int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
 377             THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
 378     Console.debug("Using Uniprot fetch threshold of " + threshold);
 379     if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold)
 380     {
 381       Executors.newSingleThreadExecutor().submit(discoverCanonicalDBrefs);
 382       return;
 383     }
 384     // need cancel and no to result in the discoverPDB action - mocked is
 385     // 'cancel' TODO: mock should be OK
 386
 387     StructureChooser thisSC = this;
 388     JvOptionPane.newOptionDialog(thisSC.getFrame())
 389             .setResponseHandler(JvOptionPane.OK_OPTION,
 390                     discoverCanonicalDBrefs)
 391             .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
 392             .setResponseHandler(JvOptionPane.NO_OPTION, revertview)
 393             .showDialog(
 394                     MessageManager.formatMessage(
 395                             "label.fetch_references_for_3dbeacons",
 396                             seqsWithoutSourceDBRef.size()),
 397                     MessageManager.getString("label.3dbeacons"),
 398                     JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE,
 399                     null, new Object[]
 400                     { MessageManager.getString("action.ok"),
 401                         MessageManager.getString("action.cancel") },
 402                     MessageManager.getString("action.ok"), false);
 403   }
 404
 405   /**
 406    * Builds a drop-down choice list of existing structure viewers to which new
 407    * structures may be added. If this list is empty then it, and the 'Add'
 408    * button, are hidden.
 409    */
 410   private void discoverStructureViews()
 411   {
 412     if (Desktop.instance != null)
 413     {
 414       targetView.removeAllItems();
 415       if (lastTargetedView != null && !lastTargetedView.isVisible())
 416       {
 417         lastTargetedView = null;
 418       }
 419       int linkedViewsAt = 0;
 420       for (StructureViewerBase view : Desktop.instance
 421               .getStructureViewers(null, null))
 422       {
 423         StructureViewer viewHandler = (lastTargetedView != null
 424                 && lastTargetedView.sview == view) ? lastTargetedView
 425                         : StructureViewer.reconfigure(view);
 426
 427         if (view.isLinkedWith(ap))
 428         {
 429           targetView.insertItemAt(viewHandler, linkedViewsAt++);
 430         }
 431         else
 432         {
 433           targetView.addItem(viewHandler);
 434         }
 435       }
 436
 437       /*
 438        * show option to Add to viewer if at least 1 viewer found
 439        */
 440       targetView.setVisible(false);
 441       if (targetView.getItemCount() > 0)
 442       {
 443         targetView.setVisible(true);
 444         if (lastTargetedView != null)
 445         {
 446           targetView.setSelectedItem(lastTargetedView);
 447         }
 448         else
 449         {
 450           targetView.setSelectedIndex(0);
 451         }
 452       }
 453       btn_add.setVisible(targetView.isVisible());
 454     }
 455   }
 456
 457   /**
 458    * Updates the progress indicator with the specified message
 459    *
 460    * @param message
 461    *          displayed message for the operation
 462    * @param id
 463    *          unique handle for this indicator
 464    */
 465   protected void updateProgressIndicator(String message, long id)
 466   {
 467     if (progressIndicator != null)
 468     {
 469       progressIndicator.setProgressBar(message, id);
 470     }
 471   }
 472
 473   /**
 474    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
 475    * selection group
 476    */
 477   void fetchStructuresMetaData()
 478   {
 479     long startTime = System.currentTimeMillis();
 480     Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
 481             .getStructureSummaryFields();
 482
 483     discoveredStructuresSet = new LinkedHashSet<>();
 484     HashSet<String> errors = new HashSet<>();
 485
 486     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 487             .getSelectedItem());
 488
 489     for (SequenceI seq : selectedSequences)
 490     {
 491
 492       FTSRestResponse resultList;
 493       try
 494       {
 495         resultList = data.fetchStructuresMetaData(seq, wantedFields,
 496                 selectedFilterOpt, !chk_invertFilter.isSelected());
 497         // null response means the FTSengine didn't yield a query for this
 498         // consider designing a special exception if we really wanted to be
 499         // OOCrazy
 500         if (resultList == null)
 501         {
 502           continue;
 503         }
 504       } catch (Exception e)
 505       {
 506         e.printStackTrace();
 507         errors.add(e.getMessage());
 508         continue;
 509       }
 510       if (resultList.getSearchSummary() != null
 511               && !resultList.getSearchSummary().isEmpty())
 512       {
 513         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 514       }
 515     }
 516
 517     int noOfStructuresFound = 0;
 518     String totalTime = (System.currentTimeMillis() - startTime)
 519             + " milli secs";
 520     if (discoveredStructuresSet != null
 521             && !discoveredStructuresSet.isEmpty())
 522     {
 523       getResultTable()
 524               .setModel(data.getTableModel(discoveredStructuresSet));
 525
 526       noOfStructuresFound = discoveredStructuresSet.size();
 527       lastDiscoveredStructuresSet = discoveredStructuresSet;
 528       mainFrame.setTitle(MessageManager.formatMessage(
 529               "label.structure_chooser_no_of_structures",
 530               noOfStructuresFound, totalTime));
 531     }
 532     else
 533     {
 534       mainFrame.setTitle(MessageManager
 535               .getString("label.structure_chooser_manual_association"));
 536       if (errors.size() > 0)
 537       {
 538         StringBuilder errorMsg = new StringBuilder();
 539         for (String error : errors)
 540         {
 541           errorMsg.append(error).append("\n");
 542         }
 543         JvOptionPane.showMessageDialog(this, errorMsg.toString(),
 544                 MessageManager.getString("label.pdb_web-service_error"),
 545                 JvOptionPane.ERROR_MESSAGE);
 546       }
 547     }
 548   }
 549
 550   protected void loadLocalCachedPDBEntries()
 551   {
 552     ArrayList<CachedPDB> entries = new ArrayList<>();
 553     for (SequenceI seq : selectedSequences)
 554     {
 555       if (seq.getDatasetSequence() != null
 556               && seq.getDatasetSequence().getAllPDBEntries() != null)
 557       {
 558         for (PDBEntry pdbEntry : seq.getDatasetSequence()
 559                 .getAllPDBEntries())
 560         {
 561           if (pdbEntry.getFile() != null)
 562           {
 563             entries.add(new CachedPDB(seq, pdbEntry));
 564           }
 565         }
 566       }
 567     }
 568     cachedPDBExists = !entries.isEmpty();
 569     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
 570     tbl_local_pdb.setModel(tableModelx);
 571   }
 572
 573   /**
 574    * Filters a given list of discovered structures based on supplied argument
 575    *
 576    * @param fieldToFilterBy
 577    *          the field to filter by
 578    */
 579   void filterResultSet(final String fieldToFilterBy)
 580   {
 581     Thread filterThread = new Thread(new Runnable()
 582     {
 583
 584       @Override
 585       public void run()
 586       {
 587         long startTime = System.currentTimeMillis();
 588         lbl_loading.setVisible(true);
 589         Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
 590                 .getStructureSummaryFields();
 591         Collection<FTSData> filteredResponse = new HashSet<>();
 592         HashSet<String> errors = new HashSet<>();
 593
 594         for (SequenceI seq : selectedSequences)
 595         {
 596
 597           FTSRestResponse resultList;
 598           try
 599           {
 600             resultList = data.selectFirstRankedQuery(seq,
 601                     discoveredStructuresSet, wantedFields, fieldToFilterBy,
 602                     !chk_invertFilter.isSelected());
 603
 604           } catch (Exception e)
 605           {
 606             e.printStackTrace();
 607             errors.add(e.getMessage());
 608             continue;
 609           }
 610           if (resultList.getSearchSummary() != null
 611                   && !resultList.getSearchSummary().isEmpty())
 612           {
 613             filteredResponse.addAll(resultList.getSearchSummary());
 614           }
 615         }
 616
 617         String totalTime = (System.currentTimeMillis() - startTime)
 618                 + " milli secs";
 619         if (!filteredResponse.isEmpty())
 620         {
 621           final int filterResponseCount = filteredResponse.size();
 622           Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
 623           reorderedStructuresSet.addAll(filteredResponse);
 624           reorderedStructuresSet.addAll(discoveredStructuresSet);
 625           getResultTable()
 626                   .setModel(data.getTableModel(reorderedStructuresSet));
 627
 628           FTSRestResponse.configureTableColumn(getResultTable(),
 629                   wantedFields, tempUserPrefs);
 630           getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
 631           getResultTable().getColumn("Ref Sequence").setMinWidth(100);
 632           getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
 633           // Update table selection model here
 634           getResultTable().addRowSelectionInterval(0,
 635                   filterResponseCount - 1);
 636           mainFrame.setTitle(MessageManager.formatMessage(
 637                   "label.structure_chooser_filter_time", totalTime));
 638         }
 639         else
 640         {
 641           mainFrame.setTitle(MessageManager.formatMessage(
 642                   "label.structure_chooser_filter_time", totalTime));
 643           if (errors.size() > 0)
 644           {
 645             StringBuilder errorMsg = new StringBuilder();
 646             for (String error : errors)
 647             {
 648               errorMsg.append(error).append("\n");
 649             }
 650             JvOptionPane.showMessageDialog(null, errorMsg.toString(),
 651                     MessageManager.getString("label.pdb_web-service_error"),
 652                     JvOptionPane.ERROR_MESSAGE);
 653           }
 654         }
 655
 656         lbl_loading.setVisible(false);
 657
 658         validateSelections();
 659       }
 660     });
 661     filterThread.start();
 662   }
 663
 664   /**
 665    * Handles action event for btn_pdbFromFile
 666    */
 667   @Override
 668   protected void pdbFromFile_actionPerformed()
 669   {
 670     // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and
 671     // StructureChooser
 672     // works
 673     JalviewFileChooser chooser = new JalviewFileChooser(
 674             Cache.getProperty("LAST_DIRECTORY"));
 675     chooser.setFileView(new JalviewFileView());
 676     chooser.setDialogTitle(
 677             MessageManager.formatMessage("label.select_pdb_file_for",
 678                     selectedSequence.getDisplayId(false)));
 679     chooser.setToolTipText(MessageManager.formatMessage(
 680             "label.load_pdb_file_associate_with_sequence",
 681             selectedSequence.getDisplayId(false)));
 682
 683     int value = chooser.showOpenDialog(null);
 684     if (value == JalviewFileChooser.APPROVE_OPTION)
 685     {
 686       selectedPdbFileName = chooser.getSelectedFile().getPath();
 687       Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
 688       boolean guessTFType = localPdbPaeMatrixFileName == null;
 689       localPdbPaeMatrixFileName = guessPAEFilename();
 690       guessTFType |= localPdbPaeMatrixFileName != null;
 691       if (guessTFType
 692               && new File(selectedPdbFileName).getName().startsWith("AF-")
 693               && !tempFacAsChanged)
 694       {
 695         // localPdbPaeMatrixFileName was null and now isn't and filename could
 696         // well be AlphaFold and user hasn't adjusted the tempFacType
 697         combo_tempFacAs.setSelectedItem(TFType.PLDDT);
 698       }
 699       validateSelections();
 700     }
 701   }
 702
 703   /**
 704    * Handles action event for btn_pdbFromFile
 705    */
 706   @Override
 707   protected void paeMatrixFile_actionPerformed()
 708   {
 709     File pdbFile = new File(selectedPdbFileName);
 710     String setFile = Cache.getProperty("LAST_DIRECTORY");
 711     if (localPdbPaeMatrixFileName != null)
 712     {
 713       File paeFile = new File(localPdbPaeMatrixFileName);
 714       if (paeFile.exists())
 715         setFile = paeFile.getAbsolutePath();
 716       else if (paeFile.getParentFile().exists())
 717         setFile = paeFile.getParentFile().getAbsolutePath();
 718     }
 719     else
 720     {
 721       String guess = guessPAEFilename();
 722       if (guess != null)
 723         setFile = guess;
 724     }
 725     JalviewFileChooser chooser = new JalviewFileChooser(setFile);
 726     chooser.setFileView(new JalviewFileView());
 727     chooser.setDialogTitle(MessageManager.formatMessage(
 728             "label.select_pae_matrix_file_for", pdbFile.getName()));
 729     chooser.setToolTipText(MessageManager.formatMessage(
 730             "label.load_pae_matrix_file_associate_with_structure",
 731             pdbFile.getName()));
 732
 733     int value = chooser.showOpenDialog(null);
 734     if (value == JalviewFileChooser.APPROVE_OPTION)
 735     {
 736       localPdbPaeMatrixFileName = chooser.getSelectedFile().getPath();
 737       Cache.setProperty("LAST_DIRECTORY", localPdbPaeMatrixFileName);
 738     }
 739     validateAssociationFromFile();
 740   }
 741
 742   private String guessPAEFilename()
 743   {
 744     if (selectedPdbFileName.toLowerCase(Locale.ROOT).endsWith(".pdb")
 745             || selectedPdbFileName.toLowerCase(Locale.ROOT)
 746                     .endsWith(".cif"))
 747     {
 748       String jsonExt = selectedPdbFileName.substring(0,
 749               selectedPdbFileName.length() - 4) + ".json";
 750       // AlphaFold naming scheme
 751       String guessFile1 = StringUtils.replaceLast(jsonExt, "model",
 752               "predicted_aligned_error");
 753       // nf-core mode naming scheme
 754       String guessFile2 = StringUtils.replaceLast(jsonExt, ".json",
 755               "_scores.json");
 756       if (new File(guessFile1).exists())
 757       {
 758         return guessFile1;
 759       }
 760       else if (new File(jsonExt).exists())
 761       {
 762         return jsonExt;
 763       }
 764       else if (new File(guessFile2).exists())
 765       {
 766         return guessFile2;
 767       }
 768     }
 769     return null;
 770   }
 771
 772   /**
 773    * Populates the filter combo-box options dynamically depending on discovered
 774    * structures
 775    */
 776   protected void populateFilterComboBox(boolean haveData,
 777           boolean cachedPDBExist)
 778   {
 779     populateFilterComboBox(haveData, cachedPDBExist, null);
 780   }
 781
 782   /**
 783    * Populates the filter combo-box options dynamically depending on discovered
 784    * structures
 785    */
 786   protected void populateFilterComboBox(boolean haveData,
 787           boolean cachedPDBExist, FilterOption lastSel)
 788   {
 789
 790     /*
 791      * temporarily suspend the change listener behaviour
 792      */
 793     cmb_filterOption.removeItemListener(this);
 794     int selSet = -1;
 795     cmb_filterOption.removeAllItems();
 796     if (haveData)
 797     {
 798       List<FilterOption> filters = data
 799               .getAvailableFilterOptions(VIEWS_FILTER);
 800       data.updateAvailableFilterOptions(VIEWS_FILTER, filters,
 801               lastDiscoveredStructuresSet);
 802       int p = 0;
 803       for (FilterOption filter : filters)
 804       {
 805         if (lastSel != null && filter.equals(lastSel))
 806         {
 807           selSet = p;
 808         }
 809         p++;
 810         cmb_filterOption.addItem(filter);
 811       }
 812     }
 813
 814     cmb_filterOption.addItem(
 815             new FilterOption(MessageManager.getString("label.enter_pdb_id"),
 816                     "-", VIEWS_ENTER_ID, false, null));
 817     cmb_filterOption.addItem(
 818             new FilterOption(MessageManager.getString("label.from_file"),
 819                     "-", VIEWS_FROM_FILE, false, null));
 820     if (canQueryTDB && notQueriedTDBYet)
 821     {
 822       btn_queryTDB.setVisible(true);
 823       pnl_queryTDB.setVisible(true);
 824     }
 825
 826     if (cachedPDBExist)
 827     {
 828       FilterOption cachedOption = new FilterOption(
 829               MessageManager.getString("label.cached_structures"), "-",
 830               VIEWS_LOCAL_PDB, false, null);
 831       cmb_filterOption.addItem(cachedOption);
 832       if (selSet == -1)
 833       {
 834         cmb_filterOption.setSelectedItem(cachedOption);
 835       }
 836     }
 837     if (selSet > -1)
 838     {
 839       cmb_filterOption.setSelectedIndex(selSet);
 840     }
 841     cmb_filterOption.addItemListener(this);
 842   }
 843
 844   /**
 845    * Updates the displayed view based on the selected filter option
 846    */
 847   protected void updateCurrentView()
 848   {
 849     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 850             .getSelectedItem());
 851
 852     if (lastSelected == selectedFilterOpt)
 853     {
 854       // don't need to do anything, probably
 855       return;
 856     }
 857     // otherwise, record selection
 858     // and update the layout and dialog accordingly
 859     lastSelected = selectedFilterOpt;
 860
 861     layout_switchableViews.show(pnl_switchableViews,
 862             selectedFilterOpt.getView());
 863     String filterTitle = mainFrame.getTitle();
 864     mainFrame.setTitle(frameTitle);
 865     chk_invertFilter.setVisible(false);
 866
 867     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 868     {
 869       mainFrame.setTitle(filterTitle);
 870       // TDB Query has no invert as yet
 871       chk_invertFilter.setVisible(selectedFilterOpt
 872               .getQuerySource() instanceof PDBStructureChooserQuerySource);
 873
 874       if (data != selectedFilterOpt.getQuerySource()
 875               || data.needsRefetch(selectedFilterOpt))
 876       {
 877         data = selectedFilterOpt.getQuerySource();
 878         // rebuild the views completely, since prefs will also change
 879         tabRefresh();
 880         return;
 881       }
 882       else
 883       {
 884         filterResultSet(selectedFilterOpt.getValue());
 885       }
 886     }
 887     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 888             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 889     {
 890       mainFrame.setTitle(MessageManager
 891               .getString("label.structure_chooser_manual_association"));
 892       idInputAssSeqPanel.loadCmbAssSeq();
 893       fileChooserAssSeqPanel.loadCmbAssSeq();
 894     }
 895     validateSelections();
 896   }
 897
 898   /**
 899    * Validates user selection and enables the 'Add' and 'New View' buttons if
 900    * all parameters are correct (the Add button will only be visible if there is
 901    * at least one existing structure viewer open). This basically means at least
 902    * one structure selected and no error messages.
 903    * <p>
 904    * The 'Superpose Structures' option is enabled if either more than one
 905    * structure is selected, or the 'Add' to existing view option is enabled, and
 906    * disabled if the only option is to open a new view of a single structure.
 907    */
 908   @Override
 909   protected void validateSelections()
 910   {
 911     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 912             .getSelectedItem());
 913     btn_add.setEnabled(false);
 914     String currentView = selectedFilterOpt.getView();
 915     int selectedCount = 0;
 916     if (currentView == VIEWS_FILTER)
 917     {
 918       selectedCount = getResultTable().getSelectedRows().length;
 919       if (selectedCount > 0)
 920       {
 921         btn_add.setEnabled(true);
 922       }
 923     }
 924     else if (currentView == VIEWS_LOCAL_PDB)
 925     {
 926       selectedCount = tbl_local_pdb.getSelectedRows().length;
 927       if (selectedCount > 0)
 928       {
 929         btn_add.setEnabled(true);
 930       }
 931     }
 932     else if (currentView == VIEWS_ENTER_ID)
 933     {
 934       validateAssociationEnterPdb();
 935     }
 936     else if (currentView == VIEWS_FROM_FILE)
 937     {
 938       validateAssociationFromFile();
 939     }
 940
 941     btn_newView.setEnabled(btn_add.isEnabled());
 942
 943     /*
 944      * enable 'Superpose' option if more than one structure is selected,
 945      * or there are view(s) available to add structure(s) to
 946      */
 947     chk_superpose
 948             .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
 949   }
 950
 951   @Override
 952   protected boolean showPopupFor(int selectedRow, int x, int y)
 953   {
 954     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 955             .getSelectedItem());
 956     String currentView = selectedFilterOpt.getView();
 957
 958     if (currentView == VIEWS_FILTER
 959             && data instanceof ThreeDBStructureChooserQuerySource)
 960     {
 961
 962       TDB_FTSData row = ((ThreeDBStructureChooserQuerySource) data)
 963               .getFTSDataFor(getResultTable(), selectedRow,
 964                       discoveredStructuresSet);
 965       String pageUrl = row.getModelViewUrl();
 966       JPopupMenu popup = new JPopupMenu("3D Beacons");
 967       JMenuItem viewUrl = new JMenuItem("View model web page");
 968       viewUrl.addActionListener(new ActionListener()
 969       {
 970         @Override
 971         public void actionPerformed(ActionEvent e)
 972         {
 973           Desktop.showUrl(pageUrl);
 974         }
 975       });
 976       popup.add(viewUrl);
 977       SwingUtilities.invokeLater(new Runnable()
 978       {
 979         @Override
 980         public void run()
 981         {
 982           popup.show(getResultTable(), x, y);
 983         }
 984       });
 985       return true;
 986     }
 987     // event not handled by us
 988     return false;
 989   }
 990
 991   /**
 992    * Validates inputs from the Manual PDB entry panel
 993    */
 994   protected void validateAssociationEnterPdb()
 995   {
 996     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 997             .getCmb_assSeq().getSelectedItem();
 998     lbl_pdbManualFetchStatus.setIcon(errorImage);
 999     lbl_pdbManualFetchStatus.setToolTipText("");
1000     if (txt_search.getText().length() > 0)
1001     {
1002       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
1003               MessageManager.formatMessage("info.no_pdb_entry_found_for",
1004                       txt_search.getText())));
1005     }
1006
1007     if (errorWarning.length() > 0)
1008     {
1009       lbl_pdbManualFetchStatus.setIcon(warningImage);
1010       lbl_pdbManualFetchStatus.setToolTipText(
1011               JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
1012     }
1013
1014     if (selectedSequences.length == 1 || !assSeqOpt.getName()
1015             .equalsIgnoreCase("-Select Associated Seq-"))
1016     {
1017       txt_search.setEnabled(true);
1018       if (isValidPBDEntry)
1019       {
1020         btn_add.setEnabled(true);
1021         lbl_pdbManualFetchStatus.setToolTipText("");
1022         lbl_pdbManualFetchStatus.setIcon(goodImage);
1023       }
1024     }
1025     else
1026     {
1027       txt_search.setEnabled(false);
1028       lbl_pdbManualFetchStatus.setIcon(errorImage);
1029     }
1030   }
1031
1032   /**
1033    * Validates inputs for the manual PDB file selection options
1034    */
1035   protected void validateAssociationFromFile()
1036   {
1037     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
1038             .getCmb_assSeq().getSelectedItem();
1039     // lbl_fromFileStatus.setIcon(errorImage);
1040     String pdbFileString = "";
1041     String pdbFileTooltip = "";
1042     if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
1043             .getName().equalsIgnoreCase("-Select Associated Seq-")))
1044     {
1045       btn_pdbFromFile.setEnabled(true);
1046       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
1047       {
1048         btn_add.setEnabled(true);
1049         // lbl_fromFileStatus.setIcon(goodImage);
1050         pdbFileString = new File(selectedPdbFileName).getName();
1051         pdbFileTooltip = new File(selectedPdbFileName).getAbsolutePath();
1052         setPdbOptionsEnabled(true);
1053       }
1054       else
1055       {
1056         pdbFileString = MessageManager.getString("label.none");
1057         pdbFileTooltip = MessageManager.getString("label.nothing_selected");
1058       }
1059     }
1060     else
1061     {
1062       btn_pdbFromFile.setEnabled(false);
1063       // lbl_fromFileStatus.setIcon(errorImage);
1064       pdbFileString = MessageManager.getString("label.none");
1065       pdbFileTooltip = MessageManager.getString("label.nothing_selected");
1066     }
1067     lbl_pdbFile.setText(pdbFileString);
1068     lbl_pdbFile.setToolTipText(pdbFileTooltip);
1069
1070     // PAE file choice
1071     String paeFileString = "";
1072     String paeFileTooltip = "";
1073     if (localPdbPaeMatrixFileName != null
1074             && localPdbPaeMatrixFileName.length() > 0)
1075     {
1076       paeFileString = new File(localPdbPaeMatrixFileName).getName();
1077       paeFileTooltip = new File(localPdbPaeMatrixFileName)
1078               .getAbsolutePath();
1079     }
1080     else
1081     {
1082       paeFileString = MessageManager.getString("label.none");
1083       paeFileTooltip = MessageManager.getString("label.nothing_selected");
1084     }
1085     lbl_paeFile.setText(paeFileString);
1086     lbl_paeFile.setToolTipText(paeFileTooltip);
1087   }
1088
1089   @Override
1090   protected void cmbAssSeqStateChanged()
1091   {
1092     validateSelections();
1093   }
1094
1095   private FilterOption lastSelected = null;
1096
1097   /**
1098    * Handles the state change event for the 'filter' combo-box and 'invert'
1099    * check-box
1100    */
1101   @Override
1102   protected void stateChanged(ItemEvent e)
1103   {
1104     if (e.getSource() instanceof JCheckBox)
1105     {
1106       updateCurrentView();
1107     }
1108     else
1109     {
1110       if (e.getStateChange() == ItemEvent.SELECTED)
1111       {
1112         updateCurrentView();
1113       }
1114     }
1115
1116   }
1117
1118   /**
1119    * select structures for viewing by their PDB IDs
1120    *
1121    * @param pdbids
1122    * @return true if structures were found and marked as selected
1123    */
1124   public boolean selectStructure(String... pdbids)
1125   {
1126     boolean found = false;
1127
1128     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
1129             .getSelectedItem());
1130     String currentView = selectedFilterOpt.getView();
1131     JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
1132             : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
1133
1134     if (restable == null)
1135     {
1136       // can't select (enter PDB ID, or load file - need to also select which
1137       // sequence to associate with)
1138       return false;
1139     }
1140
1141     int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
1142     for (int r = 0; r < restable.getRowCount(); r++)
1143     {
1144       for (int p = 0; p < pdbids.length; p++)
1145       {
1146         if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
1147                 .equalsIgnoreCase(pdbids[p]))
1148         {
1149           restable.setRowSelectionInterval(r, r);
1150           found = true;
1151         }
1152       }
1153     }
1154     return found;
1155   }
1156
1157   /**
1158    * Handles the 'New View' action
1159    */
1160   @Override
1161   protected void newView_ActionPerformed()
1162   {
1163     targetView.setSelectedItem(null);
1164     showStructures(false);
1165   }
1166
1167   /**
1168    * Handles the 'Add to existing viewer' action
1169    */
1170   @Override
1171   protected void add_ActionPerformed()
1172   {
1173     showStructures(false);
1174   }
1175
1176   /**
1177    * structure viewer opened by this dialog, or null
1178    */
1179   private StructureViewer sViewer = null;
1180
1181   public void showStructures(boolean waitUntilFinished)
1182   {
1183
1184     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
1185
1186     final int preferredHeight = pnl_filter.getHeight();
1187
1188     Runnable viewStruc = new Runnable()
1189     {
1190       @Override
1191       public void run()
1192       {
1193         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
1194                 .getSelectedItem());
1195         String currentView = selectedFilterOpt.getView();
1196         JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
1197                 : tbl_local_pdb;
1198
1199         if (currentView == VIEWS_FILTER)
1200         {
1201           int[] selectedRows = restable.getSelectedRows();
1202           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
1203           List<SequenceI> selectedSeqsToView = new ArrayList<>();
1204           pdbEntriesToView = data.collectSelectedRows(restable,
1205                   selectedRows, selectedSeqsToView);
1206
1207           SequenceI[] selectedSeqs = selectedSeqsToView
1208                   .toArray(new SequenceI[selectedSeqsToView.size()]);
1209           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1210                   selectedSeqs);
1211         }
1212         else if (currentView == VIEWS_LOCAL_PDB)
1213         {
1214           int[] selectedRows = tbl_local_pdb.getSelectedRows();
1215           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
1216           int count = 0;
1217           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
1218                   .getModelIndex();
1219           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
1220                   .getModelIndex();
1221           List<SequenceI> selectedSeqsToView = new ArrayList<>();
1222           for (int row : selectedRows)
1223           {
1224             PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb
1225                     .getModel()).getPDBEntryAt(row).getPdbEntry();
1226
1227             pdbEntriesToView[count++] = pdbEntry;
1228             SequenceI selectedSeq = (SequenceI) tbl_local_pdb
1229                     .getValueAt(row, refSeqColIndex);
1230             selectedSeqsToView.add(selectedSeq);
1231           }
1232           SequenceI[] selectedSeqs = selectedSeqsToView
1233                   .toArray(new SequenceI[selectedSeqsToView.size()]);
1234           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1235                   selectedSeqs);
1236         }
1237         else if (currentView == VIEWS_ENTER_ID)
1238         {
1239           SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
1240                   .getCmb_assSeq().getSelectedItem()).getSequence();
1241           if (userSelectedSeq != null)
1242           {
1243             selectedSequence = userSelectedSeq;
1244           }
1245           String pdbIdStr = txt_search.getText();
1246           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
1247           if (pdbEntry == null)
1248           {
1249             pdbEntry = new PDBEntry();
1250             if (pdbIdStr.split(":").length > 1)
1251             {
1252               pdbEntry.setId(pdbIdStr.split(":")[0]);
1253               pdbEntry.setChainCode(
1254                       pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
1255             }
1256             else
1257             {
1258               pdbEntry.setId(pdbIdStr);
1259             }
1260             pdbEntry.setType(PDBEntry.Type.PDB);
1261             selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
1262           }
1263
1264           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
1265           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
1266                   new SequenceI[]
1267                   { selectedSequence });
1268         }
1269         else if (currentView == VIEWS_FROM_FILE)
1270         {
1271
1272           // TEMPFAC NOT WORKING
1273           TFType tft = (TFType) StructureChooser.this.combo_tempFacAs
1274                   .getSelectedItem();
1275           if (tft != null && tft != TFType.DEFAULT)
1276           {
1277             ssm.setAddTempFacAnnot(true);
1278           }
1279
1280           AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
1281                   .getCmb_assSeq().getSelectedItem();
1282
1283           SequenceI userSelectedSeq = assSeqOpt.getSequence();
1284           if (userSelectedSeq != null)
1285           {
1286             selectedSequence = userSelectedSeq;
1287           }
1288           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
1289                   .associatePdbWithSeq(selectedPdbFileName,
1290                           DataSourceType.FILE, selectedSequence, true,
1291                           Desktop.instance);
1292
1293           List<SequenceI> seqList = new ArrayList<>();
1294           seqList.add(selectedSequence);
1295           SequenceI[] seqArray = new SequenceI[] { selectedSequence };
1296           StructureFile sf = ssm.computeMapping(true, seqArray, null,
1297                   selectedPdbFileName, DataSourceType.FILE, null);
1298           // EBIAlfaFold.addAlphaFoldPAEToStructure(pdbAlignment, pae, index,
1299           // structIdOrFile, isStructId);
1300           StructureMapping[] sm = ssm.getMapping(fileEntry.getFile());
1301           // DO SOMETHING WITH
1302           String paeFilename = StructureChooser.this.localPdbPaeMatrixFileName;
1303           File paeFile = paeFilename == null ? null : new File(paeFilename);
1304           if (paeFilename != null && paeFile.exists())
1305           {
1306             AlignmentI al = StructureChooser.this.ap.getAlignment();
1307             try
1308             {
1309               EBIAlfaFold.importPaeJSONAsContactMatrixToSequence(al,
1310                       paeFile, -1, selectedSequence.getName());
1311             } catch (IOException | ParseException e)
1312             {
1313               // TODO Auto-generated catch block
1314               e.printStackTrace();
1315             }
1316           }
1317
1318           sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
1319                   ap, new SequenceI[]
1320                   { selectedSequence });
1321         }
1322         SwingUtilities.invokeLater(new Runnable()
1323         {
1324           @Override
1325           public void run()
1326           {
1327             closeAction(preferredHeight);
1328             mainFrame.dispose();
1329           }
1330         });
1331       }
1332     };
1333     Thread runner = new Thread(viewStruc);
1334     runner.start();
1335     if (waitUntilFinished)
1336     {
1337       while (sViewer == null ? runner.isAlive()
1338               : (sViewer.sview == null ? true
1339                       : !sViewer.sview.hasMapping()))
1340       {
1341         try
1342         {
1343           Thread.sleep(300);
1344         } catch (InterruptedException ie)
1345         {
1346
1347         }
1348       }
1349     }
1350   }
1351
1352   /**
1353    * Answers a structure viewer (new or existing) configured to superimpose
1354    * added structures or not according to the user's choice
1355    *
1356    * @param ssm
1357    * @return
1358    */
1359   StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm)
1360   {
1361     Object sv = targetView.getSelectedItem();
1362
1363     return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
1364   }
1365
1366   /**
1367    * Adds PDB structures to a new or existing structure viewer
1368    *
1369    * @param ssm
1370    * @param pdbEntriesToView
1371    * @param alignPanel
1372    * @param sequences
1373    * @return
1374    */
1375   private StructureViewer launchStructureViewer(
1376           StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
1377           final AlignmentPanel alignPanel, SequenceI[] sequences)
1378   {
1379     long progressId = sequences.hashCode();
1380     setProgressBar(MessageManager
1381             .getString("status.launching_3d_structure_viewer"), progressId);
1382     final StructureViewer theViewer = getTargetedStructureViewer(ssm);
1383     boolean superimpose = chk_superpose.isSelected();
1384     theViewer.setSuperpose(superimpose);
1385
1386     /*
1387      * remember user's choice of superimpose or not
1388      */
1389     Cache.setProperty(AUTOSUPERIMPOSE,
1390             Boolean.valueOf(superimpose).toString());
1391
1392     setProgressBar(null, progressId);
1393     if (SiftsSettings.isMapWithSifts())
1394     {
1395       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
1396       int p = 0;
1397       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
1398       // real PDB ID. For moment, we can also safely do this if there is already
1399       // a known mapping between the PDBEntry and the sequence.
1400       for (SequenceI seq : sequences)
1401       {
1402         PDBEntry pdbe = pdbEntriesToView[p++];
1403         if (pdbe != null && pdbe.getFile() != null)
1404         {
1405           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
1406           if (smm != null && smm.length > 0)
1407           {
1408             for (StructureMapping sm : smm)
1409             {
1410               if (sm.getSequence() == seq)
1411               {
1412                 continue;
1413               }
1414             }
1415           }
1416         }
1417         if (seq.getPrimaryDBRefs().isEmpty())
1418         {
1419           seqsWithoutSourceDBRef.add(seq);
1420           continue;
1421         }
1422       }
1423       if (!seqsWithoutSourceDBRef.isEmpty())
1424       {
1425         int y = seqsWithoutSourceDBRef.size();
1426         setProgressBar(MessageManager.formatMessage(
1427                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
1428                 y), progressId);
1429         SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
1430                 .toArray(new SequenceI[y]);
1431         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
1432         dbRefFetcher.fetchDBRefs(true);
1433
1434         setProgressBar("Fetch complete.", progressId); // todo i18n
1435       }
1436     }
1437     if (pdbEntriesToView.length > 1)
1438     {
1439       setProgressBar(
1440               MessageManager.getString(
1441                       "status.fetching_3d_structures_for_selected_entries"),
1442               progressId);
1443       theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
1444     }
1445     else
1446     {
1447       setProgressBar(MessageManager.formatMessage(
1448               "status.fetching_3d_structures_for",
1449               pdbEntriesToView[0].getId()), progressId);
1450       theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
1451     }
1452     setProgressBar(null, progressId);
1453     // remember the last viewer we used...
1454     lastTargetedView = theViewer;
1455     return theViewer;
1456   }
1457
1458   /**
1459    * Populates the combo-box used in associating manually fetched structures to
1460    * a unique sequence when more than one sequence selection is made.
1461    */
1462   @Override
1463   protected void populateCmbAssociateSeqOptions(
1464           JComboBox<AssociateSeqOptions> cmb_assSeq,
1465           JLabel lbl_associateSeq)
1466   {
1467     cmb_assSeq.removeAllItems();
1468     cmb_assSeq.addItem(
1469             new AssociateSeqOptions("-Select Associated Seq-", null));
1470     lbl_associateSeq.setVisible(false);
1471     if (selectedSequences.length > 1)
1472     {
1473       for (SequenceI seq : selectedSequences)
1474       {
1475         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
1476       }
1477     }
1478     else
1479     {
1480       String seqName = selectedSequence.getDisplayId(false);
1481       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
1482       lbl_associateSeq.setText(seqName);
1483       lbl_associateSeq.setVisible(true);
1484       cmb_assSeq.setVisible(false);
1485     }
1486   }
1487
1488   protected boolean isStructuresDiscovered()
1489   {
1490     return discoveredStructuresSet != null
1491             && !discoveredStructuresSet.isEmpty();
1492   }
1493
1494   protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes
1495                                // this.
1496   // Doing a search for "1" or "1c" is valuable?
1497   // Those work but are enormously slow.
1498
1499   @Override
1500   protected void txt_search_ActionPerformed()
1501   {
1502     String text = txt_search.getText().trim();
1503     if (text.length() >= PDB_ID_MIN)
1504       new Thread()
1505       {
1506
1507         @Override
1508         public void run()
1509         {
1510           errorWarning.setLength(0);
1511           isValidPBDEntry = false;
1512           if (text.length() > 0)
1513           {
1514             // TODO move this pdb id search into the PDB specific
1515             // FTSSearchEngine
1516             // for moment, it will work fine as is because it is self-contained
1517             String searchTerm = text.toLowerCase(Locale.ROOT);
1518             searchTerm = searchTerm.split(":")[0];
1519             // System.out.println(">>>>> search term : " + searchTerm);
1520             List<FTSDataColumnI> wantedFields = new ArrayList<>();
1521             FTSRestRequest pdbRequest = new FTSRestRequest();
1522             pdbRequest.setAllowEmptySeq(false);
1523             pdbRequest.setResponseSize(1);
1524             pdbRequest.setFieldToSearchBy("(pdb_id:");
1525             pdbRequest.setWantedFields(wantedFields);
1526             pdbRequest.setSearchTerm(searchTerm + ")");
1527             pdbRequest.setAssociatedSequence(selectedSequence);
1528             FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
1529             wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
1530             FTSRestResponse resultList;
1531             try
1532             {
1533               resultList = pdbRestClient.executeRequest(pdbRequest);
1534             } catch (Exception e)
1535             {
1536               errorWarning.append(e.getMessage());
1537               return;
1538             } finally
1539             {
1540               validateSelections();
1541             }
1542             if (resultList.getSearchSummary() != null
1543                     && resultList.getSearchSummary().size() > 0)
1544             {
1545               isValidPBDEntry = true;
1546             }
1547           }
1548           validateSelections();
1549         }
1550       }.start();
1551   }
1552
1553   @Override
1554   protected void tabRefresh()
1555   {
1556     if (selectedSequences != null)
1557     {
1558       lbl_loading.setVisible(true);
1559       Thread refreshThread = new Thread(new Runnable()
1560       {
1561         @Override
1562         public void run()
1563         {
1564           fetchStructuresMetaData();
1565           // populateFilterComboBox(true, cachedPDBExists);
1566
1567           filterResultSet(
1568                   ((FilterOption) cmb_filterOption.getSelectedItem())
1569                           .getValue());
1570           lbl_loading.setVisible(false);
1571         }
1572       });
1573       refreshThread.start();
1574     }
1575   }
1576
1577   public class PDBEntryTableModel extends AbstractTableModel
1578   {
1579     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1580         "File" };
1581
1582     private List<CachedPDB> pdbEntries;
1583
1584     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1585     {
1586       this.pdbEntries = new ArrayList<>(pdbEntries);
1587     }
1588
1589     @Override
1590     public String getColumnName(int columnIndex)
1591     {
1592       return columns[columnIndex];
1593     }
1594
1595     @Override
1596     public int getRowCount()
1597     {
1598       return pdbEntries.size();
1599     }
1600
1601     @Override
1602     public int getColumnCount()
1603     {
1604       return columns.length;
1605     }
1606
1607     @Override
1608     public boolean isCellEditable(int row, int column)
1609     {
1610       return false;
1611     }
1612
1613     @Override
1614     public Object getValueAt(int rowIndex, int columnIndex)
1615     {
1616       Object value = "??";
1617       CachedPDB entry = pdbEntries.get(rowIndex);
1618       switch (columnIndex)
1619       {
1620       case 0:
1621         value = entry.getSequence();
1622         break;
1623       case 1:
1624         value = entry.getQualifiedId();
1625         break;
1626       case 2:
1627         value = entry.getPdbEntry().getChainCode() == null ? "_"
1628                 : entry.getPdbEntry().getChainCode();
1629         break;
1630       case 3:
1631         value = entry.getPdbEntry().getType();
1632         break;
1633       case 4:
1634         value = entry.getPdbEntry().getFile();
1635         break;
1636       }
1637       return value;
1638     }
1639
1640     @Override
1641     public Class<?> getColumnClass(int columnIndex)
1642     {
1643       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1644     }
1645
1646     public CachedPDB getPDBEntryAt(int row)
1647     {
1648       return pdbEntries.get(row);
1649     }
1650
1651   }
1652
1653   private class CachedPDB
1654   {
1655     private SequenceI sequence;
1656
1657     private PDBEntry pdbEntry;
1658
1659     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1660     {
1661       this.sequence = sequence;
1662       this.pdbEntry = pdbEntry;
1663     }
1664
1665     public String getQualifiedId()
1666     {
1667       if (pdbEntry.hasProvider())
1668       {
1669         return pdbEntry.getProvider() + ":" + pdbEntry.getId();
1670       }
1671       return pdbEntry.toString();
1672     }
1673
1674     public SequenceI getSequence()
1675     {
1676       return sequence;
1677     }
1678
1679     public PDBEntry getPdbEntry()
1680     {
1681       return pdbEntry;
1682     }
1683
1684   }
1685
1686   private IProgressIndicator progressBar;
1687
1688   @Override
1689   public void setProgressBar(String message, long id)
1690   {
1691     if (!Platform.isHeadless())
1692       progressBar.setProgressBar(message, id);
1693   }
1694
1695   @Override
1696   public void registerHandler(long id, IProgressIndicatorHandler handler)
1697   {
1698     progressBar.registerHandler(id, handler);
1699   }
1700
1701   @Override
1702   public boolean operationInProgress()
1703   {
1704     return progressBar.operationInProgress();
1705   }
1706
1707   public JalviewStructureDisplayI getOpenedStructureViewer()
1708   {
1709     return sViewer == null ? null : sViewer.sview;
1710   }
1711
1712   @Override
1713   protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs)
1714   {
1715     data.setDocFieldPrefs(newPrefs);
1716
1717   }
1718
1719   /**
1720    *
1721    * @return true when all initialisation threads have finished and dialog is
1722    *         visible
1723    */
1724   public boolean isDialogVisible()
1725   {
1726     return mainFrame != null && data != null && cmb_filterOption != null
1727             && mainFrame.isVisible()
1728             && cmb_filterOption.getSelectedItem() != null;
1729   }
1730
1731   /**
1732    *
1733    * @return true if the 3D-Beacons query button will/has been displayed
1734    */
1735   public boolean isCanQueryTDB()
1736   {
1737     return canQueryTDB;
1738   }
1739
1740   public boolean isNotQueriedTDBYet()
1741   {
1742     return notQueriedTDBYet;
1743   }
1744
1745   /**
1746    * Open a single structure file for a given sequence
1747    */
1748   public static void openStructureFileForSequence(AlignmentPanel ap,
1749           SequenceI seq, File sFile)
1750   {
1751     // Open the chooser headlessly. Not sure this is actually needed ?
1752     StructureChooser sc = new StructureChooser(new SequenceI[] { seq }, seq,
1753             ap, false);
1754     StructureSelectionManager ssm = ap.getStructureSelectionManager();
1755     PDBEntry fileEntry = null;
1756     try
1757     {
1758       fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
1759               sFile.getAbsolutePath(), DataSourceType.FILE, seq, true,
1760               Desktop.instance);
1761     } catch (Exception e)
1762     {
1763       Console.error("Could not open structure file '"
1764               + sFile.getAbsolutePath() + "'");
1765       return;
1766     }
1767
1768     StructureViewer sViewer = sc.launchStructureViewer(ssm,
1769             new PDBEntry[]
1770             { fileEntry }, ap, new SequenceI[] { seq });
1771
1772     sc.mainFrame.dispose();
1773   }
1774 }