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 jalview.api.structures.JalviewStructureDisplayI;
  25 import jalview.bin.Cache;
  26 import jalview.bin.Jalview;
  27 import jalview.datamodel.DBRefEntry;
  28 import jalview.datamodel.DBRefSource;
  29 import jalview.datamodel.PDBEntry;
  30 import jalview.datamodel.SequenceI;
  31 import jalview.fts.api.FTSData;
  32 import jalview.fts.api.FTSDataColumnI;
  33 import jalview.fts.api.FTSRestClientI;
  34 import jalview.fts.core.FTSRestRequest;
  35 import jalview.fts.core.FTSRestResponse;
  36 import jalview.fts.service.pdb.PDBFTSRestClient;
  37 import jalview.io.DataSourceType;
  38 import jalview.jbgui.GStructureChooser;
  39 import jalview.structure.StructureMapping;
  40 import jalview.structure.StructureSelectionManager;
  41 import jalview.util.MessageManager;
  42 import jalview.ws.DBRefFetcher;
  43 import jalview.ws.sifts.SiftsSettings;
  44
  45 import java.awt.event.ItemEvent;
  46 import java.util.ArrayList;
  47 import java.util.Collection;
  48 import java.util.HashSet;
  49 import java.util.LinkedHashSet;
  50 import java.util.List;
  51 import java.util.Objects;
  52 import java.util.Set;
  53 import java.util.Vector;
  54
  55 import javax.swing.JCheckBox;
  56 import javax.swing.JComboBox;
  57 import javax.swing.JLabel;
  58 import javax.swing.JTable;
  59 import javax.swing.SwingUtilities;
  60 import javax.swing.table.AbstractTableModel;
  61
  62 /**
  63  * Provides the behaviors for the Structure chooser Panel
  64  *
  65  * @author tcnofoegbu
  66  *
  67  */
  68 @SuppressWarnings("serial")
  69 public class StructureChooser extends GStructureChooser
  70         implements IProgressIndicator
  71 {
  72   private static int MAX_QLENGTH = 7820;
  73
  74   private SequenceI selectedSequence;
  75
  76   private SequenceI[] selectedSequences;
  77
  78   private IProgressIndicator progressIndicator;
  79
  80   private Collection<FTSData> discoveredStructuresSet;
  81
  82   private FTSRestRequest lastPdbRequest;
  83
  84   private FTSRestClientI pdbRestCleint;
  85
  86   private String selectedPdbFileName;
  87
  88   private boolean isValidPBDEntry;
  89
  90   private boolean cachedPDBExists;
  91
  92   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
  93           AlignmentPanel ap)
  94   {
  95     this.ap = ap;
  96     this.selectedSequence = selectedSeq;
  97     this.selectedSequences = selectedSeqs;
  98     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
  99     init();
 100   }
 101
 102   /**
 103    * Initializes parameters used by the Structure Chooser Panel
 104    */
 105   public void init()
 106   {
 107     if (!Jalview.isHeadlessMode())
 108     {
 109       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 110     }
 111
 112     chk_superpose.setSelected(Cache.getDefault("AUTOSUPERIMPOSE", true));
 113
 114     // ensure a filter option is in force for search
 115     populateFilterComboBox(true, cachedPDBExists);
 116     Thread discoverPDBStructuresThread = new Thread(new Runnable()
 117     {
 118       @Override
 119       public void run()
 120       {
 121         long startTime = System.currentTimeMillis();
 122         updateProgressIndicator(MessageManager
 123                 .getString("status.loading_cached_pdb_entries"), startTime);
 124         loadLocalCachedPDBEntries();
 125         updateProgressIndicator(null, startTime);
 126         updateProgressIndicator(MessageManager.getString(
 127                 "status.searching_for_pdb_structures"), startTime);
 128         fetchStructuresMetaData();
 129         // revise filter options if no results were found
 130         populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
 131         discoverStructureViews();
 132         updateProgressIndicator(null, startTime);
 133         mainFrame.setVisible(true);
 134         updateCurrentView();
 135       }
 136     });
 137     discoverPDBStructuresThread.start();
 138   }
 139
 140   private void discoverStructureViews()
 141   {
 142     if (Desktop.instance != null)
 143     {
 144       targetView.removeAllItems();
 145       if (lastTargetedView != null && !lastTargetedView.isVisible())
 146       {
 147         lastTargetedView = null;
 148       }
 149       int linkedViewsAt = 0;
 150       for (StructureViewerBase view : Desktop.instance
 151               .getStructureViewers(null, null))
 152       {
 153         StructureViewer viewHandler = (lastTargetedView != null
 154                 && lastTargetedView.sview == view) ? lastTargetedView
 155                         : StructureViewer.reconfigure(view);
 156
 157         if (view.isLinkedWith(ap))
 158         {
 159           targetView.insertItemAt(viewHandler,
 160                   linkedViewsAt++);
 161         }
 162         else
 163         {
 164           targetView.addItem(viewHandler);
 165         }
 166       }
 167       targetView.setVisible(targetView.getItemCount() > 0);
 168       btn_view.setVisible(targetView.isVisible());
 169       if (targetView.isVisible()) {
 170         // finally, restore last targeted view by default.
 171         if (lastTargetedView != null)
 172         {
 173           targetView.setSelectedItem(lastTargetedView);
 174         } else {
 175           targetView.setSelectedIndex(0);
 176         }
 177       }
 178     }
 179   }
 180
 181   private static StructureViewer lastTargetedView = null;
 182
 183   /**
 184    * Updates the progress indicator with the specified message
 185    *
 186    * @param message
 187    *          displayed message for the operation
 188    * @param id
 189    *          unique handle for this indicator
 190    */
 191   public void updateProgressIndicator(String message, long id)
 192   {
 193     if (progressIndicator != null)
 194     {
 195       progressIndicator.setProgressBar(message, id);
 196     }
 197   }
 198
 199   /**
 200    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
 201    * selection group
 202    */
 203   public void fetchStructuresMetaData()
 204   {
 205     long startTime = System.currentTimeMillis();
 206     pdbRestCleint = PDBFTSRestClient.getInstance();
 207     Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
 208             .getStructureSummaryFields();
 209
 210     discoveredStructuresSet = new LinkedHashSet<>();
 211     HashSet<String> errors = new HashSet<>();
 212     for (SequenceI seq : selectedSequences)
 213     {
 214       FTSRestRequest pdbRequest = new FTSRestRequest();
 215       pdbRequest.setAllowEmptySeq(false);
 216       pdbRequest.setResponseSize(500);
 217       pdbRequest.setFieldToSearchBy("(");
 218       FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 219               .getSelectedItem());
 220       pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
 221               !chk_invertFilter.isSelected());
 222       pdbRequest.setWantedFields(wantedFields);
 223       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 224       pdbRequest.setAssociatedSequence(seq);
 225       FTSRestResponse resultList;
 226       try
 227       {
 228         resultList = pdbRestCleint.executeRequest(pdbRequest);
 229       } catch (Exception e)
 230       {
 231         e.printStackTrace();
 232         errors.add(e.getMessage());
 233         continue;
 234       }
 235       lastPdbRequest = pdbRequest;
 236       if (resultList.getSearchSummary() != null
 237               && !resultList.getSearchSummary().isEmpty())
 238       {
 239         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 240       }
 241     }
 242
 243     int noOfStructuresFound = 0;
 244     String totalTime = (System.currentTimeMillis() - startTime)
 245             + " milli secs";
 246     if (discoveredStructuresSet != null
 247             && !discoveredStructuresSet.isEmpty())
 248     {
 249       getResultTable().setModel(FTSRestResponse
 250               .getTableModel(lastPdbRequest, discoveredStructuresSet));
 251       noOfStructuresFound = discoveredStructuresSet.size();
 252       mainFrame.setTitle(MessageManager.formatMessage(
 253               "label.structure_chooser_no_of_structures",
 254               noOfStructuresFound, totalTime));
 255     }
 256     else
 257     {
 258       mainFrame.setTitle(MessageManager
 259               .getString("label.structure_chooser_manual_association"));
 260       if (errors.size() > 0)
 261       {
 262         StringBuilder errorMsg = new StringBuilder();
 263         for (String error : errors)
 264         {
 265           errorMsg.append(error).append("\n");
 266         }
 267         JvOptionPane.showMessageDialog(this, errorMsg.toString(),
 268                 MessageManager.getString("label.pdb_web-service_error"),
 269                 JvOptionPane.ERROR_MESSAGE);
 270       }
 271     }
 272   }
 273
 274   public void loadLocalCachedPDBEntries()
 275   {
 276     ArrayList<CachedPDB> entries = new ArrayList<>();
 277     for (SequenceI seq : selectedSequences)
 278     {
 279       if (seq.getDatasetSequence() != null
 280               && seq.getDatasetSequence().getAllPDBEntries() != null)
 281       {
 282         for (PDBEntry pdbEntry : seq.getDatasetSequence()
 283                 .getAllPDBEntries())
 284         {
 285           if (pdbEntry.getFile() != null)
 286           {
 287             entries.add(new CachedPDB(seq, pdbEntry));
 288           }
 289         }
 290       }
 291     }
 292     cachedPDBExists = !entries.isEmpty();
 293     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
 294     tbl_local_pdb.setModel(tableModelx);
 295   }
 296
 297   /**
 298    * Builds a query string for a given sequences using its DBRef entries
 299    *
 300    * @param seq
 301    *          the sequences to build a query for
 302    * @return the built query string
 303    */
 304
 305   public static String buildQuery(SequenceI seq)
 306   {
 307     boolean isPDBRefsFound = false;
 308     boolean isUniProtRefsFound = false;
 309     StringBuilder queryBuilder = new StringBuilder();
 310     Set<String> seqRefs = new LinkedHashSet<>();
 311
 312     if (seq.getAllPDBEntries() != null
 313             && queryBuilder.length() < MAX_QLENGTH)
 314     {
 315       for (PDBEntry entry : seq.getAllPDBEntries())
 316       {
 317         if (isValidSeqName(entry.getId()))
 318         {
 319           queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase())
 320                   .append(" OR ");
 321           isPDBRefsFound = true;
 322         }
 323       }
 324     }
 325
 326     if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
 327     {
 328       for (DBRefEntry dbRef : seq.getDBRefs())
 329       {
 330         if (isValidSeqName(getDBRefId(dbRef))
 331                 && queryBuilder.length() < MAX_QLENGTH)
 332         {
 333           if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
 334           {
 335             queryBuilder.append("uniprot_accession:")
 336                     .append(getDBRefId(dbRef)).append(" OR ");
 337             queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
 338                     .append(" OR ");
 339             isUniProtRefsFound = true;
 340           }
 341           else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
 342           {
 343
 344             queryBuilder.append("pdb_id:")
 345                     .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
 346             isPDBRefsFound = true;
 347           }
 348           else
 349           {
 350             seqRefs.add(getDBRefId(dbRef));
 351           }
 352         }
 353       }
 354     }
 355
 356     if (!isPDBRefsFound && !isUniProtRefsFound)
 357     {
 358       String seqName = seq.getName();
 359       seqName = sanitizeSeqName(seqName);
 360       String[] names = seqName.toLowerCase().split("\\|");
 361       for (String name : names)
 362       {
 363         // System.out.println("Found name : " + name);
 364         name.trim();
 365         if (isValidSeqName(name))
 366         {
 367           seqRefs.add(name);
 368         }
 369       }
 370
 371       for (String seqRef : seqRefs)
 372       {
 373         queryBuilder.append("text:").append(seqRef).append(" OR ");
 374       }
 375     }
 376
 377     int endIndex = queryBuilder.lastIndexOf(" OR ");
 378     if (queryBuilder.toString().length() < 6)
 379     {
 380       return null;
 381     }
 382     String query = queryBuilder.toString().substring(0, endIndex);
 383     return query;
 384   }
 385
 386   /**
 387    * Remove the following special characters from input string +, -, &, !, (, ),
 388    * {, }, [, ], ^, ", ~, *, ?, :, \
 389    *
 390    * @param seqName
 391    * @return
 392    */
 393   static String sanitizeSeqName(String seqName)
 394   {
 395     Objects.requireNonNull(seqName);
 396     return seqName.replaceAll("\\[\\d*\\]", "")
 397             .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
 398   }
 399
 400   /**
 401    * Ensures sequence ref names are not less than 3 characters and does not
 402    * contain a database name
 403    *
 404    * @param seqName
 405    * @return
 406    */
 407   public static boolean isValidSeqName(String seqName)
 408   {
 409     // System.out.println("seqName : " + seqName);
 410     String ignoreList = "pdb,uniprot,swiss-prot";
 411     if (seqName.length() < 3)
 412     {
 413       return false;
 414     }
 415     if (seqName.contains(":"))
 416     {
 417       return false;
 418     }
 419     seqName = seqName.toLowerCase();
 420     for (String ignoredEntry : ignoreList.split(","))
 421     {
 422       if (seqName.contains(ignoredEntry))
 423       {
 424         return false;
 425       }
 426     }
 427     return true;
 428   }
 429
 430   public static String getDBRefId(DBRefEntry dbRef)
 431   {
 432     String ref = dbRef.getAccessionId().replaceAll("GO:", "");
 433     return ref;
 434   }
 435
 436   /**
 437    * Filters a given list of discovered structures based on supplied argument
 438    *
 439    * @param fieldToFilterBy
 440    *          the field to filter by
 441    */
 442   public void filterResultSet(final String fieldToFilterBy)
 443   {
 444     Thread filterThread = new Thread(new Runnable()
 445     {
 446       @Override
 447       public void run()
 448       {
 449         long startTime = System.currentTimeMillis();
 450         pdbRestCleint = PDBFTSRestClient.getInstance();
 451         lbl_loading.setVisible(true);
 452         Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
 453                 .getStructureSummaryFields();
 454         Collection<FTSData> filteredResponse = new HashSet<>();
 455         HashSet<String> errors = new HashSet<>();
 456
 457         for (SequenceI seq : selectedSequences)
 458         {
 459           FTSRestRequest pdbRequest = new FTSRestRequest();
 460           if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
 461           {
 462             pdbRequest.setAllowEmptySeq(false);
 463             pdbRequest.setResponseSize(1);
 464             pdbRequest.setFieldToSearchBy("(");
 465             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 466             pdbRequest.setWantedFields(wantedFields);
 467             pdbRequest.setAssociatedSequence(seq);
 468             pdbRequest.setFacet(true);
 469             pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
 470             pdbRequest.setFacetPivotMinCount(1);
 471           }
 472           else
 473           {
 474             pdbRequest.setAllowEmptySeq(false);
 475             pdbRequest.setResponseSize(1);
 476             pdbRequest.setFieldToSearchBy("(");
 477             pdbRequest.setFieldToSortBy(fieldToFilterBy,
 478                     !chk_invertFilter.isSelected());
 479             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 480             pdbRequest.setWantedFields(wantedFields);
 481             pdbRequest.setAssociatedSequence(seq);
 482           }
 483           FTSRestResponse resultList;
 484           try
 485           {
 486             resultList = pdbRestCleint.executeRequest(pdbRequest);
 487           } catch (Exception e)
 488           {
 489             e.printStackTrace();
 490             errors.add(e.getMessage());
 491             continue;
 492           }
 493           lastPdbRequest = pdbRequest;
 494           if (resultList.getSearchSummary() != null
 495                   && !resultList.getSearchSummary().isEmpty())
 496           {
 497             filteredResponse.addAll(resultList.getSearchSummary());
 498           }
 499         }
 500
 501         String totalTime = (System.currentTimeMillis() - startTime)
 502                 + " milli secs";
 503         if (!filteredResponse.isEmpty())
 504         {
 505           final int filterResponseCount = filteredResponse.size();
 506           Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
 507           reorderedStructuresSet.addAll(filteredResponse);
 508           reorderedStructuresSet.addAll(discoveredStructuresSet);
 509           getResultTable().setModel(FTSRestResponse
 510                   .getTableModel(lastPdbRequest, reorderedStructuresSet));
 511
 512           FTSRestResponse.configureTableColumn(getResultTable(),
 513                   wantedFields, tempUserPrefs);
 514           getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
 515           getResultTable().getColumn("Ref Sequence").setMinWidth(100);
 516           getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
 517           // Update table selection model here
 518           getResultTable().addRowSelectionInterval(0,
 519                   filterResponseCount - 1);
 520           mainFrame.setTitle(MessageManager.formatMessage(
 521                   "label.structure_chooser_filter_time", totalTime));
 522         }
 523         else
 524         {
 525           mainFrame.setTitle(MessageManager.formatMessage(
 526                   "label.structure_chooser_filter_time", totalTime));
 527           if (errors.size() > 0)
 528           {
 529             StringBuilder errorMsg = new StringBuilder();
 530             for (String error : errors)
 531             {
 532               errorMsg.append(error).append("\n");
 533             }
 534             JvOptionPane.showMessageDialog(null, errorMsg.toString(),
 535                     MessageManager.getString("label.pdb_web-service_error"),
 536                     JvOptionPane.ERROR_MESSAGE);
 537           }
 538         }
 539
 540         lbl_loading.setVisible(false);
 541
 542         validateSelections();
 543       }
 544     });
 545     filterThread.start();
 546   }
 547
 548   /**
 549    * Handles action event for btn_pdbFromFile
 550    */
 551   @Override
 552   public void pdbFromFile_actionPerformed()
 553   {
 554     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 555             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 556     chooser.setFileView(new jalview.io.JalviewFileView());
 557     chooser.setDialogTitle(
 558             MessageManager.formatMessage("label.select_pdb_file_for",
 559                     selectedSequence.getDisplayId(false)));
 560     chooser.setToolTipText(MessageManager.formatMessage(
 561             "label.load_pdb_file_associate_with_sequence",
 562             selectedSequence.getDisplayId(false)));
 563
 564     int value = chooser.showOpenDialog(null);
 565     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
 566     {
 567       selectedPdbFileName = chooser.getSelectedFile().getPath();
 568       jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
 569       validateSelections();
 570     }
 571   }
 572
 573   /**
 574    * Populates the filter combo-box options dynamically depending on discovered
 575    * structures
 576    */
 577   protected void populateFilterComboBox(boolean haveData,
 578           boolean cachedPDBExist)
 579   {
 580     /*
 581      * temporarily suspend the change listener behaviour
 582      */
 583     cmb_filterOption.removeItemListener(this);
 584
 585     cmb_filterOption.removeAllItems();
 586     if (haveData)
 587     {
 588       cmb_filterOption.addItem(new FilterOption(
 589               MessageManager.getString("label.best_quality"),
 590               "overall_quality", VIEWS_FILTER, false));
 591       cmb_filterOption.addItem(new FilterOption(
 592               MessageManager.getString("label.best_resolution"),
 593               "resolution", VIEWS_FILTER, false));
 594       cmb_filterOption.addItem(new FilterOption(
 595               MessageManager.getString("label.most_protein_chain"),
 596               "number_of_protein_chains", VIEWS_FILTER, false));
 597       cmb_filterOption.addItem(new FilterOption(
 598               MessageManager.getString("label.most_bound_molecules"),
 599               "number_of_bound_molecules", VIEWS_FILTER, false));
 600       cmb_filterOption.addItem(new FilterOption(
 601               MessageManager.getString("label.most_polymer_residues"),
 602               "number_of_polymer_residues", VIEWS_FILTER, true));
 603     }
 604     cmb_filterOption.addItem(
 605             new FilterOption(MessageManager.getString("label.enter_pdb_id"),
 606                     "-", VIEWS_ENTER_ID, false));
 607     cmb_filterOption.addItem(
 608             new FilterOption(MessageManager.getString("label.from_file"),
 609                     "-", VIEWS_FROM_FILE, false));
 610
 611     if (cachedPDBExist)
 612     {
 613       FilterOption cachedOption = new FilterOption(
 614               MessageManager.getString("label.cached_structures"),
 615               "-", VIEWS_LOCAL_PDB, false);
 616       cmb_filterOption.addItem(cachedOption);
 617       cmb_filterOption.setSelectedItem(cachedOption);
 618     }
 619
 620     cmb_filterOption.addItemListener(this);
 621   }
 622
 623   /**
 624    * Updates the displayed view based on the selected filter option
 625    */
 626   protected void updateCurrentView()
 627   {
 628     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 629             .getSelectedItem());
 630     layout_switchableViews.show(pnl_switchableViews,
 631             selectedFilterOpt.getView());
 632     String filterTitle = mainFrame.getTitle();
 633     mainFrame.setTitle(frameTitle);
 634     chk_invertFilter.setVisible(false);
 635     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 636     {
 637       mainFrame.setTitle(filterTitle);
 638       chk_invertFilter.setVisible(true);
 639       filterResultSet(selectedFilterOpt.getValue());
 640     }
 641     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 642             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 643     {
 644       mainFrame.setTitle(MessageManager
 645               .getString("label.structure_chooser_manual_association"));
 646       idInputAssSeqPanel.loadCmbAssSeq();
 647       fileChooserAssSeqPanel.loadCmbAssSeq();
 648     }
 649     validateSelections();
 650   }
 651
 652   /**
 653    * Validates user selection and activates the view button if all parameters
 654    * are correct
 655    */
 656   @Override
 657   public void validateSelections()
 658   {
 659     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 660             .getSelectedItem());
 661     btn_view.setEnabled(false);
 662     String currentView = selectedFilterOpt.getView();
 663     if (currentView == VIEWS_FILTER)
 664     {
 665       if (getResultTable().getSelectedRows().length > 0)
 666       {
 667         btn_view.setEnabled(true);
 668       }
 669     }
 670     else if (currentView == VIEWS_LOCAL_PDB)
 671     {
 672       if (tbl_local_pdb.getSelectedRows().length > 0)
 673       {
 674         btn_view.setEnabled(true);
 675       }
 676     }
 677     else if (currentView == VIEWS_ENTER_ID)
 678     {
 679       validateAssociationEnterPdb();
 680     }
 681     else if (currentView == VIEWS_FROM_FILE)
 682     {
 683       validateAssociationFromFile();
 684     }
 685   }
 686
 687   /**
 688    * Validates inputs from the Manual PDB entry panel
 689    */
 690   public void validateAssociationEnterPdb()
 691   {
 692     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 693             .getCmb_assSeq().getSelectedItem();
 694     lbl_pdbManualFetchStatus.setIcon(errorImage);
 695     lbl_pdbManualFetchStatus.setToolTipText("");
 696     if (txt_search.getText().length() > 0)
 697     {
 698       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
 699               MessageManager.formatMessage("info.no_pdb_entry_found_for",
 700                       txt_search.getText())));
 701     }
 702
 703     if (errorWarning.length() > 0)
 704     {
 705       lbl_pdbManualFetchStatus.setIcon(warningImage);
 706       lbl_pdbManualFetchStatus.setToolTipText(
 707               JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
 708     }
 709
 710     if (selectedSequences.length == 1 || !assSeqOpt.getName()
 711             .equalsIgnoreCase("-Select Associated Seq-"))
 712     {
 713       txt_search.setEnabled(true);
 714       if (isValidPBDEntry)
 715       {
 716         btn_view.setEnabled(true);
 717         lbl_pdbManualFetchStatus.setToolTipText("");
 718         lbl_pdbManualFetchStatus.setIcon(goodImage);
 719       }
 720     }
 721     else
 722     {
 723       txt_search.setEnabled(false);
 724       lbl_pdbManualFetchStatus.setIcon(errorImage);
 725     }
 726   }
 727
 728   /**
 729    * Validates inputs for the manual PDB file selection options
 730    */
 731   public void validateAssociationFromFile()
 732   {
 733     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
 734             .getCmb_assSeq().getSelectedItem();
 735     lbl_fromFileStatus.setIcon(errorImage);
 736     if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
 737             .getName().equalsIgnoreCase("-Select Associated Seq-")))
 738     {
 739       btn_pdbFromFile.setEnabled(true);
 740       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
 741       {
 742         btn_view.setEnabled(true);
 743         lbl_fromFileStatus.setIcon(goodImage);
 744       }
 745     }
 746     else
 747     {
 748       btn_pdbFromFile.setEnabled(false);
 749       lbl_fromFileStatus.setIcon(errorImage);
 750     }
 751   }
 752
 753   @Override
 754   public void cmbAssSeqStateChanged()
 755   {
 756     validateSelections();
 757   }
 758
 759   /**
 760    * Handles the state change event for the 'filter' combo-box and 'invert'
 761    * check-box
 762    */
 763   @Override
 764   protected void stateChanged(ItemEvent e)
 765   {
 766     if (e.getSource() instanceof JCheckBox)
 767     {
 768       updateCurrentView();
 769     }
 770     else
 771     {
 772       if (e.getStateChange() == ItemEvent.SELECTED)
 773       {
 774         updateCurrentView();
 775       }
 776     }
 777
 778   }
 779
 780   /**
 781    * select structures for viewing by their PDB IDs
 782    *
 783    * @param pdbids
 784    * @return true if structures were found and marked as selected
 785    */
 786   public boolean selectStructure(String... pdbids)
 787   {
 788     boolean found = false;
 789
 790     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 791             .getSelectedItem());
 792     String currentView = selectedFilterOpt.getView();
 793     JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
 794             : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
 795
 796     if (restable == null)
 797     {
 798       // can't select (enter PDB ID, or load file - need to also select which
 799       // sequence to associate with)
 800       return false;
 801     }
 802
 803     int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
 804     for (int r = 0; r < restable.getRowCount(); r++)
 805     {
 806       for (int p = 0; p < pdbids.length; p++)
 807       {
 808         if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
 809                 .equalsIgnoreCase(pdbids[p]))
 810         {
 811           restable.setRowSelectionInterval(r, r);
 812           found = true;
 813         }
 814       }
 815     }
 816     return found;
 817   }
 818   /**
 819    * Handles action event for btn_ok
 820    */
 821   @Override
 822   public void newview_ActionPerformed()
 823   {
 824     targetView.setSelectedItem(null);
 825     showStructures(false);
 826   }
 827
 828   /**
 829    * Handles action event for btn_ok
 830    */
 831   @Override
 832   public void view_ActionPerformed()
 833   {
 834     showStructures(false);
 835   }
 836
 837   /**
 838    * structure viewer opened by this dialog, or null
 839    */
 840   private StructureViewer sViewer = null;
 841
 842   public void showStructures(boolean waitUntilFinished)
 843   {
 844
 845     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 846
 847     final int preferredHeight = pnl_filter.getHeight();
 848
 849     Runnable viewStruc = new Runnable()
 850     {
 851       @Override
 852       public void run()
 853       {
 854         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 855                 .getSelectedItem());
 856         String currentView = selectedFilterOpt.getView();
 857         JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
 858                 : tbl_local_pdb;
 859
 860         if (currentView == VIEWS_FILTER)
 861         {
 862           int pdbIdColIndex = restable.getColumn("PDB Id")
 863                   .getModelIndex();
 864           int refSeqColIndex = restable.getColumn("Ref Sequence")
 865                   .getModelIndex();
 866           int[] selectedRows = restable.getSelectedRows();
 867           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 868           int count = 0;
 869           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 870           for (int row : selectedRows)
 871           {
 872             String pdbIdStr = restable
 873                     .getValueAt(row, pdbIdColIndex).toString();
 874             SequenceI selectedSeq = (SequenceI) restable
 875                     .getValueAt(row, refSeqColIndex);
 876             selectedSeqsToView.add(selectedSeq);
 877             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
 878             if (pdbEntry == null)
 879             {
 880               pdbEntry = getFindEntry(pdbIdStr,
 881                       selectedSeq.getAllPDBEntries());
 882             }
 883
 884             if (pdbEntry == null)
 885             {
 886               pdbEntry = new PDBEntry();
 887               pdbEntry.setId(pdbIdStr);
 888               pdbEntry.setType(PDBEntry.Type.PDB);
 889               selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
 890             }
 891             pdbEntriesToView[count++] = pdbEntry;
 892           }
 893           SequenceI[] selectedSeqs = selectedSeqsToView
 894                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 895           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 896                   selectedSeqs);
 897         }
 898         else if (currentView == VIEWS_LOCAL_PDB)
 899         {
 900           int[] selectedRows = tbl_local_pdb.getSelectedRows();
 901           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 902           int count = 0;
 903           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
 904                   .getModelIndex();
 905           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
 906                   .getModelIndex();
 907           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 908           for (int row : selectedRows)
 909           {
 910             PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
 911                     pdbIdColIndex);
 912             pdbEntriesToView[count++] = pdbEntry;
 913             SequenceI selectedSeq = (SequenceI) tbl_local_pdb
 914                     .getValueAt(row, refSeqColIndex);
 915             selectedSeqsToView.add(selectedSeq);
 916           }
 917           SequenceI[] selectedSeqs = selectedSeqsToView
 918                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 919           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 920                   selectedSeqs);
 921         }
 922         else if (currentView == VIEWS_ENTER_ID)
 923         {
 924           SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
 925                   .getCmb_assSeq().getSelectedItem()).getSequence();
 926           if (userSelectedSeq != null)
 927           {
 928             selectedSequence = userSelectedSeq;
 929           }
 930           String pdbIdStr = txt_search.getText();
 931           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
 932           if (pdbEntry == null)
 933           {
 934             pdbEntry = new PDBEntry();
 935             if (pdbIdStr.split(":").length > 1)
 936             {
 937               pdbEntry.setId(pdbIdStr.split(":")[0]);
 938               pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
 939             }
 940             else
 941             {
 942               pdbEntry.setId(pdbIdStr);
 943             }
 944             pdbEntry.setType(PDBEntry.Type.PDB);
 945             selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
 946           }
 947
 948           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
 949           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 950                   new SequenceI[]
 951                   { selectedSequence });
 952         }
 953         else if (currentView == VIEWS_FROM_FILE)
 954         {
 955           SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
 956                   .getCmb_assSeq().getSelectedItem()).getSequence();
 957           if (userSelectedSeq != null)
 958           {
 959             selectedSequence = userSelectedSeq;
 960           }
 961           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 962                   .associatePdbWithSeq(selectedPdbFileName,
 963                           DataSourceType.FILE, selectedSequence, true,
 964                           Desktop.instance);
 965
 966           sViewer = launchStructureViewer(
 967                   ssm, new PDBEntry[]
 968                   { fileEntry }, ap,
 969                   new SequenceI[]
 970                   { selectedSequence });
 971         }
 972         SwingUtilities.invokeLater(new Runnable()
 973         {
 974           @Override
 975           public void run()
 976           {
 977             closeAction(preferredHeight);
 978             mainFrame.dispose();
 979           }
 980         });
 981       }
 982     };
 983     Thread runner = new Thread(viewStruc);
 984     runner.start();
 985     if (waitUntilFinished)
 986     {
 987       while (sViewer == null ? runner.isAlive()
 988               : (sViewer.sview == null ? true
 989                       : !sViewer.sview.hasMapping()))
 990       {
 991         try
 992         {
 993           Thread.sleep(300);
 994         } catch (InterruptedException ie)
 995         {
 996
 997         }
 998       }
 999     }
1000   }
1001
1002   private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
1003   {
1004     Objects.requireNonNull(id);
1005     Objects.requireNonNull(pdbEntries);
1006     PDBEntry foundEntry = null;
1007     for (PDBEntry entry : pdbEntries)
1008     {
1009       if (entry.getId().equalsIgnoreCase(id))
1010       {
1011         return entry;
1012       }
1013     }
1014     return foundEntry;
1015   }
1016
1017   /**
1018    * @param ssm
1019    * @return targetted structure view (new or existing) configured according to
1020    *         superpose checkbox
1021    */
1022   public StructureViewer getTargetedStructureViewer(
1023           StructureSelectionManager ssm)
1024   {
1025     Object _sv = targetView.getSelectedItem();
1026     StructureViewer sv;
1027     if (_sv == null)
1028     {
1029       sv = new StructureViewer(ssm);
1030     } else {
1031       sv = (StructureViewer) _sv;
1032     }
1033     sv.setSuperpose(chk_superpose.isSelected());
1034     return sv;
1035   }
1036   private StructureViewer launchStructureViewer(
1037           StructureSelectionManager ssm,
1038           final PDBEntry[] pdbEntriesToView,
1039           final AlignmentPanel alignPanel, SequenceI[] sequences)
1040   {
1041     long progressId = sequences.hashCode();
1042     setProgressBar(MessageManager
1043             .getString("status.launching_3d_structure_viewer"), progressId);
1044     final StructureViewer sViewer = getTargetedStructureViewer(ssm);
1045     sViewer.setSuperpose(chk_superpose.isSelected());
1046
1047     setProgressBar(null, progressId);
1048     if (SiftsSettings.isMapWithSifts())
1049     {
1050       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
1051       int p = 0;
1052       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
1053       // real PDB ID. For moment, we can also safely do this if there is already
1054       // a known mapping between the PDBEntry and the sequence.
1055       for (SequenceI seq : sequences)
1056       {
1057         PDBEntry pdbe = pdbEntriesToView[p++];
1058         if (pdbe != null && pdbe.getFile() != null)
1059         {
1060           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
1061           if (smm != null && smm.length > 0)
1062           {
1063             for (StructureMapping sm : smm)
1064             {
1065               if (sm.getSequence() == seq)
1066               {
1067                 continue;
1068               }
1069             }
1070           }
1071         }
1072         if (seq.getPrimaryDBRefs().size() == 0)
1073         {
1074           seqsWithoutSourceDBRef.add(seq);
1075           continue;
1076         }
1077       }
1078       if (!seqsWithoutSourceDBRef.isEmpty())
1079       {
1080         int y = seqsWithoutSourceDBRef.size();
1081         setProgressBar(MessageManager.formatMessage(
1082                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
1083                 y), progressId);
1084         SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
1085         int x = 0;
1086         for (SequenceI fSeq : seqsWithoutSourceDBRef)
1087         {
1088           seqWithoutSrcDBRef[x++] = fSeq;
1089         }
1090
1091         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
1092         dbRefFetcher.fetchDBRefs(true);
1093
1094         setProgressBar("Fetch complete.", progressId); // todo i18n
1095       }
1096     }
1097     if (pdbEntriesToView.length > 1)
1098     {
1099       setProgressBar(MessageManager.getString(
1100               "status.fetching_3d_structures_for_selected_entries"),
1101               progressId);
1102       sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
1103     }
1104     else
1105     {
1106       setProgressBar(MessageManager.formatMessage(
1107               "status.fetching_3d_structures_for",
1108               pdbEntriesToView[0].getId()),progressId);
1109       sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
1110     }
1111     setProgressBar(null, progressId);
1112     // remember the last viewer we used...
1113     lastTargetedView = sViewer;
1114     return sViewer;
1115   }
1116
1117   /**
1118    * Populates the combo-box used in associating manually fetched structures to
1119    * a unique sequence when more than one sequence selection is made.
1120    */
1121   @Override
1122   public void populateCmbAssociateSeqOptions(
1123           JComboBox<AssociateSeqOptions> cmb_assSeq,
1124           JLabel lbl_associateSeq)
1125   {
1126     cmb_assSeq.removeAllItems();
1127     cmb_assSeq.addItem(
1128             new AssociateSeqOptions("-Select Associated Seq-", null));
1129     lbl_associateSeq.setVisible(false);
1130     if (selectedSequences.length > 1)
1131     {
1132       for (SequenceI seq : selectedSequences)
1133       {
1134         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
1135       }
1136     }
1137     else
1138     {
1139       String seqName = selectedSequence.getDisplayId(false);
1140       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
1141       lbl_associateSeq.setText(seqName);
1142       lbl_associateSeq.setVisible(true);
1143       cmb_assSeq.setVisible(false);
1144     }
1145   }
1146
1147   public boolean isStructuresDiscovered()
1148   {
1149     return discoveredStructuresSet != null
1150             && !discoveredStructuresSet.isEmpty();
1151   }
1152
1153   public Collection<FTSData> getDiscoveredStructuresSet()
1154   {
1155     return discoveredStructuresSet;
1156   }
1157
1158   @Override
1159   protected void txt_search_ActionPerformed()
1160   {
1161     new Thread()
1162     {
1163       @Override
1164       public void run()
1165       {
1166         errorWarning.setLength(0);
1167         isValidPBDEntry = false;
1168         if (txt_search.getText().length() > 0)
1169         {
1170           String searchTerm = txt_search.getText().toLowerCase();
1171           searchTerm = searchTerm.split(":")[0];
1172           // System.out.println(">>>>> search term : " + searchTerm);
1173           List<FTSDataColumnI> wantedFields = new ArrayList<>();
1174           FTSRestRequest pdbRequest = new FTSRestRequest();
1175           pdbRequest.setAllowEmptySeq(false);
1176           pdbRequest.setResponseSize(1);
1177           pdbRequest.setFieldToSearchBy("(pdb_id:");
1178           pdbRequest.setWantedFields(wantedFields);
1179           pdbRequest.setSearchTerm(searchTerm + ")");
1180           pdbRequest.setAssociatedSequence(selectedSequence);
1181           pdbRestCleint = PDBFTSRestClient.getInstance();
1182           wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
1183           FTSRestResponse resultList;
1184           try
1185           {
1186             resultList = pdbRestCleint.executeRequest(pdbRequest);
1187           } catch (Exception e)
1188           {
1189             errorWarning.append(e.getMessage());
1190             return;
1191           } finally
1192           {
1193             validateSelections();
1194           }
1195           if (resultList.getSearchSummary() != null
1196                   && resultList.getSearchSummary().size() > 0)
1197           {
1198             isValidPBDEntry = true;
1199           }
1200         }
1201         validateSelections();
1202       }
1203     }.start();
1204   }
1205
1206   @Override
1207   public void tabRefresh()
1208   {
1209     if (selectedSequences != null)
1210     {
1211       Thread refreshThread = new Thread(new Runnable()
1212       {
1213         @Override
1214         public void run()
1215         {
1216           fetchStructuresMetaData();
1217           filterResultSet(
1218                   ((FilterOption) cmb_filterOption.getSelectedItem())
1219                           .getValue());
1220         }
1221       });
1222       refreshThread.start();
1223     }
1224   }
1225
1226   public class PDBEntryTableModel extends AbstractTableModel
1227   {
1228     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1229         "File" };
1230
1231     private List<CachedPDB> pdbEntries;
1232
1233     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1234     {
1235       this.pdbEntries = new ArrayList<>(pdbEntries);
1236     }
1237
1238     @Override
1239     public String getColumnName(int columnIndex)
1240     {
1241       return columns[columnIndex];
1242     }
1243
1244     @Override
1245     public int getRowCount()
1246     {
1247       return pdbEntries.size();
1248     }
1249
1250     @Override
1251     public int getColumnCount()
1252     {
1253       return columns.length;
1254     }
1255
1256     @Override
1257     public boolean isCellEditable(int row, int column)
1258     {
1259       return false;
1260     }
1261
1262     @Override
1263     public Object getValueAt(int rowIndex, int columnIndex)
1264     {
1265       Object value = "??";
1266       CachedPDB entry = pdbEntries.get(rowIndex);
1267       switch (columnIndex)
1268       {
1269       case 0:
1270         value = entry.getSequence();
1271         break;
1272       case 1:
1273         value = entry.getPdbEntry();
1274         break;
1275       case 2:
1276         value = entry.getPdbEntry().getChainCode() == null ? "_"
1277                 : entry.getPdbEntry().getChainCode();
1278         break;
1279       case 3:
1280         value = entry.getPdbEntry().getType();
1281         break;
1282       case 4:
1283         value = entry.getPdbEntry().getFile();
1284         break;
1285       }
1286       return value;
1287     }
1288
1289     @Override
1290     public Class<?> getColumnClass(int columnIndex)
1291     {
1292       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1293     }
1294
1295     public CachedPDB getPDBEntryAt(int row)
1296     {
1297       return pdbEntries.get(row);
1298     }
1299
1300   }
1301
1302   private class CachedPDB
1303   {
1304     private SequenceI sequence;
1305
1306     private PDBEntry pdbEntry;
1307
1308     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1309     {
1310       this.sequence = sequence;
1311       this.pdbEntry = pdbEntry;
1312     }
1313
1314     public SequenceI getSequence()
1315     {
1316       return sequence;
1317     }
1318
1319     public PDBEntry getPdbEntry()
1320     {
1321       return pdbEntry;
1322     }
1323
1324   }
1325
1326   private IProgressIndicator progressBar;
1327
1328   @Override
1329   public void setProgressBar(String message, long id)
1330   {
1331     progressBar.setProgressBar(message, id);
1332   }
1333
1334   @Override
1335   public void registerHandler(long id, IProgressIndicatorHandler handler)
1336   {
1337     progressBar.registerHandler(id, handler);
1338   }
1339
1340   @Override
1341   public boolean operationInProgress()
1342   {
1343     return progressBar.operationInProgress();
1344   }
1345
1346   public JalviewStructureDisplayI getOpenedStructureViewer()
1347   {
1348     return sViewer == null ? null : sViewer.sview;
1349   }
1350 }