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.bin.Jalview;
  25 import jalview.datamodel.DBRefEntry;
  26 import jalview.datamodel.DBRefSource;
  27 import jalview.datamodel.PDBEntry;
  28 import jalview.datamodel.SequenceI;
  29 import jalview.jbgui.GStructureChooser;
  30 import jalview.jbgui.PDBDocFieldPreferences;
  31 import jalview.structure.StructureSelectionManager;
  32 import jalview.util.MessageManager;
  33 import jalview.ws.dbsources.PDBRestClient;
  34 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
  35 import jalview.ws.sifts.SiftsSettings;
  36 import jalview.ws.uimodel.PDBRestRequest;
  37 import jalview.ws.uimodel.PDBRestResponse;
  38 import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
  39
  40 import java.awt.event.ItemEvent;
  41 import java.util.ArrayList;
  42 import java.util.Collection;
  43 import java.util.HashSet;
  44 import java.util.LinkedHashSet;
  45 import java.util.List;
  46 import java.util.Objects;
  47
  48 import javax.swing.JCheckBox;
  49 import javax.swing.JComboBox;
  50 import javax.swing.JLabel;
  51 import javax.swing.JOptionPane;
  52 import javax.swing.table.AbstractTableModel;
  53
  54 /**
  55  * Provides the behaviors for the Structure chooser Panel
  56  *
  57  * @author tcnofoegbu
  58  *
  59  */
  60 @SuppressWarnings("serial")
  61 public class StructureChooser extends GStructureChooser implements
  62         IProgressIndicator
  63 {
  64   private boolean structuresDiscovered = false;
  65
  66   private SequenceI selectedSequence;
  67
  68   private SequenceI[] selectedSequences;
  69
  70   private IProgressIndicator progressIndicator;
  71
  72   private Collection<PDBResponseSummary> discoveredStructuresSet;
  73
  74   private PDBRestRequest lastPdbRequest;
  75
  76   private PDBRestClient pdbRestCleint;
  77
  78   private String selectedPdbFileName;
  79
  80   private boolean isValidPBDEntry;
  81
  82   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
  83           AlignmentPanel ap)
  84   {
  85     this.ap = ap;
  86     this.selectedSequence = selectedSeq;
  87     this.selectedSequences = selectedSeqs;
  88     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
  89     init();
  90   }
  91
  92   /**
  93    * Initializes parameters used by the Structure Chooser Panel
  94    */
  95   public void init()
  96   {
  97     if (!Jalview.isHeadlessMode())
  98     {
  99       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 100     }
 101
 102     Thread discoverPDBStructuresThread = new Thread(new Runnable()
 103     {
 104       @Override
 105       public void run()
 106       {
 107         long startTime = System.currentTimeMillis();
 108         updateProgressIndicator(MessageManager
 109                 .getString("status.loading_cached_pdb_entries"), startTime);
 110         loadLocalCachedPDBEntries();
 111         updateProgressIndicator(null, startTime);
 112         updateProgressIndicator(MessageManager
 113                 .getString("status.searching_for_pdb_structures"),
 114                 startTime);
 115         fetchStructuresMetaData();
 116         populateFilterComboBox();
 117         updateProgressIndicator(null, startTime);
 118         mainFrame.setVisible(true);
 119         updateCurrentView();
 120       }
 121     });
 122     discoverPDBStructuresThread.start();
 123   }
 124
 125   /**
 126    * Updates the progress indicator with the specified message
 127    *
 128    * @param message
 129    *          displayed message for the operation
 130    * @param id
 131    *          unique handle for this indicator
 132    */
 133   public void updateProgressIndicator(String message, long id)
 134   {
 135     if (progressIndicator != null)
 136     {
 137       progressIndicator.setProgressBar(message, id);
 138     }
 139   }
 140
 141   /**
 142    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
 143    * selection group
 144    */
 145   public void fetchStructuresMetaData()
 146   {
 147     long startTime = System.currentTimeMillis();
 148     Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
 149             .getStructureSummaryFields();
 150
 151     discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
 152     HashSet<String> errors = new HashSet<String>();
 153     for (SequenceI seq : selectedSequences)
 154     {
 155       PDBRestRequest pdbRequest = new PDBRestRequest();
 156       pdbRequest.setAllowEmptySeq(false);
 157       pdbRequest.setResponseSize(500);
 158       pdbRequest.setFieldToSearchBy("(");
 159       pdbRequest.setWantedFields(wantedFields);
 160       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 161       pdbRequest.setAssociatedSequence(seq);
 162       pdbRestCleint = new PDBRestClient();
 163       PDBRestResponse resultList;
 164       try
 165       {
 166         resultList = pdbRestCleint.executeRequest(pdbRequest);
 167       } catch (Exception e)
 168       {
 169         e.printStackTrace();
 170         errors.add(e.getMessage());
 171         continue;
 172       }
 173       lastPdbRequest = pdbRequest;
 174       if (resultList.getSearchSummary() != null
 175               && !resultList.getSearchSummary().isEmpty())
 176       {
 177         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 178       }
 179     }
 180
 181     int noOfStructuresFound = 0;
 182     String totalTime = (System.currentTimeMillis() - startTime)
 183             + " milli secs";
 184     if (discoveredStructuresSet != null
 185             && !discoveredStructuresSet.isEmpty())
 186     {
 187       tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
 188               discoveredStructuresSet));
 189       structuresDiscovered = true;
 190       noOfStructuresFound = discoveredStructuresSet.size();
 191       mainFrame.setTitle(MessageManager.formatMessage(
 192               "label.structure_chooser_no_of_structures",
 193               noOfStructuresFound, totalTime));
 194     }
 195     else
 196     {
 197       mainFrame.setTitle(MessageManager
 198               .getString("label.structure_chooser_manual_association"));
 199       if (errors.size() > 0)
 200       {
 201         StringBuilder errorMsg = new StringBuilder();
 202         for (String error : errors)
 203         {
 204           errorMsg.append(error).append("\n");
 205         }
 206         JOptionPane.showMessageDialog(this, errorMsg.toString(),
 207                 MessageManager.getString("label.pdb_web-service_error"),
 208                 JOptionPane.ERROR_MESSAGE);
 209       }
 210     }
 211   }
 212
 213   public void loadLocalCachedPDBEntries()
 214   {
 215     ArrayList<CachedPDB> entries = new ArrayList<CachedPDB>();
 216     for (SequenceI seq : selectedSequences)
 217     {
 218       if (seq.getDatasetSequence() != null
 219               && seq.getDatasetSequence().getAllPDBEntries() != null)
 220       {
 221         for (PDBEntry pdbEntry : seq.getDatasetSequence()
 222                 .getAllPDBEntries())
 223         {
 224           if (pdbEntry.getFile() != null)
 225           {
 226             entries.add(new CachedPDB(seq, pdbEntry));
 227           }
 228         }
 229       }
 230     }
 231
 232     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
 233     tbl_local_pdb.setModel(tableModelx);
 234   }
 235
 236   /**
 237    * Builds a query string for a given sequences using its DBRef entries
 238    *
 239    * @param seq
 240    *          the sequences to build a query for
 241    * @return the built query string
 242    */
 243
 244   public static String buildQuery(SequenceI seq)
 245   {
 246     boolean isPDBRefsFound = false;
 247     boolean isUniProtRefsFound = false;
 248     StringBuilder queryBuilder = new StringBuilder();
 249     HashSet<String> seqRefs = new LinkedHashSet<String>();
 250
 251     if (seq.getAllPDBEntries() != null)
 252     {
 253       for (PDBEntry entry : seq.getAllPDBEntries())
 254       {
 255         if (isValidSeqName(entry.getId()))
 256         {
 257           queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode())
 258                   .append(":")
 259 .append(entry.getId().toLowerCase())
 260                   .append(" OR ");
 261           isPDBRefsFound = true;
 262           // seqRefs.add(entry.getId());
 263         }
 264       }
 265     }
 266
 267     if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
 268     {
 269       for (DBRefEntry dbRef : seq.getDBRefs())
 270       {
 271         if (isValidSeqName(getDBRefId(dbRef)))
 272         {
 273           if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
 274           {
 275             queryBuilder
 276                     .append(PDBRestClient.PDBDocField.UNIPROT_ACCESSION
 277                             .getCode()).append(":")
 278                     .append(getDBRefId(dbRef))
 279                     .append(" OR ");
 280             queryBuilder
 281                     .append(PDBRestClient.PDBDocField.UNIPROT_ID.getCode())
 282                     .append(":")
 283                     .append(getDBRefId(dbRef)).append(" OR ");
 284             isUniProtRefsFound = true;
 285           }
 286           else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
 287           {
 288
 289             queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode())
 290                     .append(":").append(getDBRefId(dbRef).toLowerCase())
 291                     .append(" OR ");
 292             isPDBRefsFound = true;
 293           }
 294           else
 295           {
 296             seqRefs.add(getDBRefId(dbRef));
 297           }
 298         }
 299       }
 300     }
 301
 302     if (!isPDBRefsFound && !isUniProtRefsFound)
 303     {
 304       String seqName = seq.getName();
 305       seqName = sanitizeSeqName(seqName);
 306       String[] names = seqName.toLowerCase().split("\\|");
 307       for (String name : names)
 308       {
 309         // System.out.println("Found name : " + name);
 310         name.trim();
 311         if (isValidSeqName(name))
 312         {
 313           seqRefs.add(name);
 314         }
 315       }
 316
 317       for (String seqRef : seqRefs)
 318       {
 319         queryBuilder.append("text:").append(seqRef).append(" OR ");
 320       }
 321     }
 322
 323     int endIndex = queryBuilder.lastIndexOf(" OR ");
 324     if (queryBuilder.toString().length() < 6)
 325     {
 326       return null;
 327     }
 328     String query = queryBuilder.toString().substring(0, endIndex);
 329     return query;
 330   }
 331
 332   /**
 333    * Remove the following special characters from input string +, -, &, |, !, (,
 334    * ), {, }, [, ], ^, ", ~, *, ?, :, \
 335    *
 336    * @param seqName
 337    * @return
 338    */
 339   private static String sanitizeSeqName(String seqName)
 340   {
 341     Objects.requireNonNull(seqName);
 342     return seqName.replaceAll("\\[\\d*\\]", "")
 343             .replaceAll("[^\\dA-Za-z ]", "").replaceAll("\\s+", "+");
 344   }
 345
 346
 347   /**
 348    * Ensures sequence ref names are not less than 3 characters and does not
 349    * contain a database name
 350    *
 351    * @param seqName
 352    * @return
 353    */
 354   public static boolean isValidSeqName(String seqName)
 355   {
 356     // System.out.println("seqName : " + seqName);
 357     String ignoreList = "pdb,uniprot,swiss-prot";
 358     if (seqName.length() < 3)
 359     {
 360       return false;
 361     }
 362     if (seqName.contains(":"))
 363     {
 364       return false;
 365     }
 366     seqName = seqName.toLowerCase();
 367     for (String ignoredEntry : ignoreList.split(","))
 368     {
 369       if (seqName.contains(ignoredEntry))
 370       {
 371         return false;
 372       }
 373     }
 374     return true;
 375   }
 376
 377   public static String getDBRefId(DBRefEntry dbRef)
 378   {
 379     String ref = dbRef.getAccessionId().replaceAll("GO:", "");
 380     return ref;
 381   }
 382
 383   /**
 384    * Filters a given list of discovered structures based on supplied argument
 385    *
 386    * @param fieldToFilterBy
 387    *          the field to filter by
 388    */
 389   public void filterResultSet(final String fieldToFilterBy)
 390   {
 391     Thread filterThread = new Thread(new Runnable()
 392     {
 393       @Override
 394       public void run()
 395       {
 396         long startTime = System.currentTimeMillis();
 397         lbl_loading.setVisible(true);
 398         Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
 399                 .getStructureSummaryFields();
 400         Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
 401         HashSet<String> errors = new HashSet<String>();
 402
 403         for (SequenceI seq : selectedSequences)
 404         {
 405           PDBRestRequest pdbRequest = new PDBRestRequest();
 406           if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
 407           {
 408             System.out.println(">>>>>> Filtering with uniprot coverate");
 409             pdbRequest.setAllowEmptySeq(false);
 410             pdbRequest.setResponseSize(1);
 411             pdbRequest.setFieldToSearchBy("(");
 412             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 413             pdbRequest.setWantedFields(wantedFields);
 414             pdbRequest.setAssociatedSequence(seq);
 415             pdbRequest.setFacet(true);
 416             pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
 417             pdbRequest.setFacetPivotMinCount(1);
 418           }
 419           else
 420           {
 421             pdbRequest.setAllowEmptySeq(false);
 422             pdbRequest.setResponseSize(1);
 423             pdbRequest.setFieldToSearchBy("(");
 424             pdbRequest.setFieldToSortBy(fieldToFilterBy,
 425                     !chk_invertFilter.isSelected());
 426             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 427             pdbRequest.setWantedFields(wantedFields);
 428             pdbRequest.setAssociatedSequence(seq);
 429           }
 430           pdbRestCleint = new PDBRestClient();
 431           PDBRestResponse resultList;
 432           try
 433           {
 434             resultList = pdbRestCleint.executeRequest(pdbRequest);
 435           } catch (Exception e)
 436           {
 437             e.printStackTrace();
 438             errors.add(e.getMessage());
 439             continue;
 440           }
 441           lastPdbRequest = pdbRequest;
 442           if (resultList.getSearchSummary() != null
 443                   && !resultList.getSearchSummary().isEmpty())
 444           {
 445             filteredResponse.addAll(resultList.getSearchSummary());
 446           }
 447         }
 448
 449         String totalTime = (System.currentTimeMillis() - startTime)
 450                 + " milli secs";
 451         if (!filteredResponse.isEmpty())
 452         {
 453           final int filterResponseCount = filteredResponse.size();
 454           Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
 455           reorderedStructuresSet.addAll(filteredResponse);
 456           reorderedStructuresSet.addAll(discoveredStructuresSet);
 457           tbl_summary.setModel(PDBRestResponse.getTableModel(
 458                   lastPdbRequest, reorderedStructuresSet));
 459
 460           // Update table selection model here
 461           tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
 462           mainFrame.setTitle(MessageManager.formatMessage(
 463                   "label.structure_chooser_filter_time", totalTime));
 464         }
 465         else
 466         {
 467           mainFrame.setTitle(MessageManager.formatMessage(
 468                   "label.structure_chooser_filter_time", totalTime));
 469           if (errors.size() > 0)
 470           {
 471             StringBuilder errorMsg = new StringBuilder();
 472             for (String error : errors)
 473             {
 474               errorMsg.append(error).append("\n");
 475             }
 476             JOptionPane.showMessageDialog(
 477                     null,
 478                     errorMsg.toString(),
 479                     MessageManager.getString("label.pdb_web-service_error"),
 480                     JOptionPane.ERROR_MESSAGE);
 481           }
 482         }
 483
 484         lbl_loading.setVisible(false);
 485
 486         validateSelections();
 487       }
 488     });
 489     filterThread.start();
 490   }
 491
 492   /**
 493    * Handles action event for btn_pdbFromFile
 494    */
 495   @Override
 496   public void pdbFromFile_actionPerformed()
 497   {
 498     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 499             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 500     chooser.setFileView(new jalview.io.JalviewFileView());
 501     chooser.setDialogTitle(MessageManager.formatMessage(
 502             "label.select_pdb_file_for",
 503             selectedSequence.getDisplayId(false)));
 504     chooser.setToolTipText(MessageManager.formatMessage(
 505             "label.load_pdb_file_associate_with_sequence",
 506             selectedSequence.getDisplayId(false)));
 507
 508     int value = chooser.showOpenDialog(null);
 509     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
 510     {
 511       selectedPdbFileName = chooser.getSelectedFile().getPath();
 512       jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
 513       validateSelections();
 514     }
 515   }
 516
 517   /**
 518    * Populates the filter combo-box options dynamically depending on discovered
 519    * structures
 520    */
 521   @Override
 522   protected void populateFilterComboBox()
 523   {
 524     if (isStructuresDiscovered())
 525     {
 526       cmb_filterOption.addItem(new FilterOption("Best Quality",
 527               PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
 528       cmb_filterOption.addItem(new FilterOption("Most UniProt Coverage",
 529               PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER));
 530       cmb_filterOption.addItem(new FilterOption("Best Resolution",
 531               PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
 532       cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
 533               PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER));
 534       cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
 535               PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER));
 536       cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
 537               PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER));
 538     }
 539     cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
 540             VIEWS_ENTER_ID));
 541     cmb_filterOption.addItem(new FilterOption("From File", "-",
 542             VIEWS_FROM_FILE));
 543     cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
 544             VIEWS_LOCAL_PDB));
 545   }
 546
 547   /**
 548    * Updates the displayed view based on the selected filter option
 549    */
 550   @Override
 551   protected void updateCurrentView()
 552   {
 553     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 554             .getSelectedItem());
 555     layout_switchableViews.show(pnl_switchableViews,
 556             selectedFilterOpt.getView());
 557     String filterTitle = mainFrame.getTitle();
 558     mainFrame.setTitle(frameTitle);
 559     chk_invertFilter.setVisible(false);
 560     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 561     {
 562       mainFrame.setTitle(filterTitle);
 563       chk_invertFilter.setVisible(true);
 564       filterResultSet(selectedFilterOpt.getValue());
 565     }
 566     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 567             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 568     {
 569       mainFrame.setTitle(MessageManager
 570               .getString("label.structure_chooser_manual_association"));
 571       idInputAssSeqPanel.loadCmbAssSeq();
 572       fileChooserAssSeqPanel.loadCmbAssSeq();
 573     }
 574     validateSelections();
 575   }
 576
 577   /**
 578    * Validates user selection and activates the view button if all parameters
 579    * are correct
 580    */
 581   @Override
 582   public void validateSelections()
 583   {
 584     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 585             .getSelectedItem());
 586     btn_view.setEnabled(false);
 587     String currentView = selectedFilterOpt.getView();
 588     if (currentView == VIEWS_FILTER)
 589     {
 590       if (tbl_summary.getSelectedRows().length > 0)
 591       {
 592         btn_view.setEnabled(true);
 593       }
 594     }
 595     else if (currentView == VIEWS_LOCAL_PDB)
 596     {
 597       if (tbl_local_pdb.getSelectedRows().length > 0)
 598       {
 599         btn_view.setEnabled(true);
 600       }
 601     }
 602     else if (currentView == VIEWS_ENTER_ID)
 603     {
 604       validateAssociationEnterPdb();
 605     }
 606     else if (currentView == VIEWS_FROM_FILE)
 607     {
 608       validateAssociationFromFile();
 609     }
 610   }
 611
 612   /**
 613    * Validates inputs from the Manual PDB entry panel
 614    */
 615   public void validateAssociationEnterPdb()
 616   {
 617     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 618             .getCmb_assSeq().getSelectedItem();
 619     lbl_pdbManualFetchStatus.setIcon(errorImage);
 620     lbl_pdbManualFetchStatus.setToolTipText("");
 621     if (txt_search.getText().length() > 0)
 622     {
 623       lbl_pdbManualFetchStatus
 624               .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 625                       .formatMessage("info.no_pdb_entry_found_for",
 626                               txt_search.getText())));
 627     }
 628
 629     if (errorWarning.length() > 0)
 630     {
 631       lbl_pdbManualFetchStatus.setIcon(warningImage);
 632       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
 633               true, errorWarning.toString()));
 634     }
 635
 636     if (selectedSequences.length == 1
 637             || !assSeqOpt.getName().equalsIgnoreCase(
 638                     "-Select Associated Seq-"))
 639     {
 640       txt_search.setEnabled(true);
 641       if (isValidPBDEntry)
 642       {
 643         btn_view.setEnabled(true);
 644         lbl_pdbManualFetchStatus.setToolTipText("");
 645         lbl_pdbManualFetchStatus.setIcon(goodImage);
 646       }
 647     }
 648     else
 649     {
 650       txt_search.setEnabled(false);
 651       lbl_pdbManualFetchStatus.setIcon(errorImage);
 652     }
 653   }
 654
 655   /**
 656    * Validates inputs for the manual PDB file selection options
 657    */
 658   public void validateAssociationFromFile()
 659   {
 660     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
 661             .getCmb_assSeq().getSelectedItem();
 662     lbl_fromFileStatus.setIcon(errorImage);
 663     if (selectedSequences.length == 1
 664             || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
 665                     "-Select Associated Seq-")))
 666     {
 667       btn_pdbFromFile.setEnabled(true);
 668       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
 669       {
 670         btn_view.setEnabled(true);
 671         lbl_fromFileStatus.setIcon(goodImage);
 672       }
 673     }
 674     else
 675     {
 676       btn_pdbFromFile.setEnabled(false);
 677       lbl_fromFileStatus.setIcon(errorImage);
 678     }
 679   }
 680
 681   @Override
 682   public void cmbAssSeqStateChanged()
 683   {
 684     validateSelections();
 685   }
 686
 687   /**
 688    * Handles the state change event for the 'filter' combo-box and 'invert'
 689    * check-box
 690    */
 691   @Override
 692   protected void stateChanged(ItemEvent e)
 693   {
 694     if (e.getSource() instanceof JCheckBox)
 695     {
 696       updateCurrentView();
 697     }
 698     else
 699     {
 700       if (e.getStateChange() == ItemEvent.SELECTED)
 701       {
 702         updateCurrentView();
 703       }
 704     }
 705
 706   }
 707
 708   /**
 709    * Handles action event for btn_ok
 710    */
 711   @Override
 712   public void ok_ActionPerformed()
 713   {
 714     final long progressSessionId = System.currentTimeMillis();
 715     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 716     ssm.setProgressIndicator(this);
 717     ssm.setProgressSessionId(progressSessionId);
 718     new Thread(new Runnable()
 719     {
 720       @Override
 721       public void run()
 722       {
 723     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 724             .getSelectedItem());
 725     String currentView = selectedFilterOpt.getView();
 726     if (currentView == VIEWS_FILTER)
 727     {
 728       int pdbIdColIndex = tbl_summary.getColumn(
 729               PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
 730       int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
 731               .getModelIndex();
 732       int[] selectedRows = tbl_summary.getSelectedRows();
 733       PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 734       int count = 0;
 735       ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
 736       for (int row : selectedRows)
 737       {
 738         String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex)
 739                 .toString();
 740         SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
 741                 refSeqColIndex);
 742         selectedSeqsToView.add(selectedSeq);
 743         PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
 744         if (pdbEntry == null)
 745         {
 746           pdbEntry = new PDBEntry();
 747           pdbEntry.setId(pdbIdStr);
 748           pdbEntry.setType(PDBEntry.Type.PDB);
 749           selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
 750         }
 751         pdbEntriesToView[count++] = pdbEntry;
 752       }
 753       SequenceI[] selectedSeqs = selectedSeqsToView
 754               .toArray(new SequenceI[selectedSeqsToView.size()]);
 755           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
 756     }
 757     else if (currentView == VIEWS_LOCAL_PDB)
 758     {
 759       int[] selectedRows = tbl_local_pdb.getSelectedRows();
 760       PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 761       int count = 0;
 762       int pdbIdColIndex = tbl_local_pdb.getColumn(
 763               PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
 764       int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
 765               .getModelIndex();
 766       ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
 767       for (int row : selectedRows)
 768       {
 769         PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
 770                 pdbIdColIndex);
 771         pdbEntriesToView[count++] = pdbEntry;
 772         SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
 773                 refSeqColIndex);
 774         selectedSeqsToView.add(selectedSeq);
 775       }
 776       SequenceI[] selectedSeqs = selectedSeqsToView
 777               .toArray(new SequenceI[selectedSeqsToView.size()]);
 778           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
 779     }
 780     else if (currentView == VIEWS_ENTER_ID)
 781     {
 782       SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
 783               .getCmb_assSeq().getSelectedItem()).getSequence();
 784       if (userSelectedSeq != null)
 785       {
 786         selectedSequence = userSelectedSeq;
 787       }
 788
 789       String pdbIdStr = txt_search.getText();
 790       PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
 791       if (pdbEntry == null)
 792       {
 793         pdbEntry = new PDBEntry();
 794         pdbEntry.setId(pdbIdStr);
 795         pdbEntry.setType(PDBEntry.Type.PDB);
 796         selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
 797       }
 798
 799       PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
 800           launchStructureViewer(ssm, pdbEntriesToView, ap,
 801                   new SequenceI[] { selectedSequence });
 802     }
 803     else if (currentView == VIEWS_FROM_FILE)
 804     {
 805       SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
 806               .getCmb_assSeq().getSelectedItem()).getSequence();
 807       if (userSelectedSeq != null)
 808       {
 809         selectedSequence = userSelectedSeq;
 810       }
 811       PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 812               .associatePdbWithSeq(selectedPdbFileName,
 813                       jalview.io.AppletFormatAdapter.FILE,
 814                       selectedSequence, true, Desktop.instance);
 815
 816           launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
 817                   new SequenceI[] { selectedSequence });
 818     }
 819     mainFrame.dispose();
 820       }
 821     }).start();
 822   }
 823
 824   private void launchStructureViewer(StructureSelectionManager ssm,
 825           final PDBEntry[] pdbEntriesToView,
 826           final AlignmentPanel alignPanel, SequenceI[] sequences)
 827   {
 828     ssm.setProgressBar("Launching PDB structure viewer..");
 829     final StructureViewer sViewer = new StructureViewer(ssm);
 830
 831     if (SiftsSettings.isMapWithSifts())
 832     {
 833       for (SequenceI seq : sequences)
 834       {
 835         if (seq.getSourceDBRef() == null)
 836         {
 837           ssm.setProgressBar(null);
 838           ssm.setProgressBar("Fetching Database refs..");
 839           new jalview.ws.DBRefFetcher(sequences, null, null, null, false)
 840                   .fetchDBRefs(true);
 841           break;
 842         }
 843       }
 844     }
 845         if (pdbEntriesToView.length > 1)
 846         {
 847           ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
 848           for (SequenceI seq : sequences)
 849           {
 850             seqsMap.add(new SequenceI[] { seq });
 851           }
 852           SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
 853       ssm.setProgressBar(null);
 854       ssm.setProgressBar("Fetching PDB Structures for selected entries..");
 855           sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
 856         }
 857         else
 858         {
 859       ssm.setProgressBar(null);
 860       ssm.setProgressBar("Fetching PDB Structure for "
 861               + pdbEntriesToView[0].getId());
 862           sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
 863         }
 864   }
 865
 866   /**
 867    * Populates the combo-box used in associating manually fetched structures to
 868    * a unique sequence when more than one sequence selection is made.
 869    */
 870   @Override
 871   public void populateCmbAssociateSeqOptions(
 872           JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
 873   {
 874     cmb_assSeq.removeAllItems();
 875     cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
 876             null));
 877     lbl_associateSeq.setVisible(false);
 878     if (selectedSequences.length > 1)
 879     {
 880       for (SequenceI seq : selectedSequences)
 881       {
 882         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
 883       }
 884     }
 885     else
 886     {
 887       String seqName = selectedSequence.getDisplayId(false);
 888       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
 889       lbl_associateSeq.setText(seqName);
 890       lbl_associateSeq.setVisible(true);
 891       cmb_assSeq.setVisible(false);
 892     }
 893   }
 894
 895   public boolean isStructuresDiscovered()
 896   {
 897     return structuresDiscovered;
 898   }
 899
 900   public void setStructuresDiscovered(boolean structuresDiscovered)
 901   {
 902     this.structuresDiscovered = structuresDiscovered;
 903   }
 904
 905   public Collection<PDBResponseSummary> getDiscoveredStructuresSet()
 906   {
 907     return discoveredStructuresSet;
 908   }
 909
 910   @Override
 911   protected void txt_search_ActionPerformed()
 912   {
 913     new Thread()
 914     {
 915       @Override
 916       public void run()
 917       {
 918         errorWarning.setLength(0);
 919         isValidPBDEntry = false;
 920         if (txt_search.getText().length() > 0)
 921         {
 922           List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
 923           wantedFields.add(PDBDocField.PDB_ID);
 924           PDBRestRequest pdbRequest = new PDBRestRequest();
 925           pdbRequest.setAllowEmptySeq(false);
 926           pdbRequest.setResponseSize(1);
 927           pdbRequest.setFieldToSearchBy("(pdb_id:");
 928           pdbRequest.setWantedFields(wantedFields);
 929           pdbRequest
 930                   .setSearchTerm(txt_search.getText().toLowerCase() + ")");
 931           pdbRequest.setAssociatedSequence(selectedSequence);
 932           pdbRestCleint = new PDBRestClient();
 933           PDBRestResponse resultList;
 934           try
 935           {
 936             resultList = pdbRestCleint.executeRequest(pdbRequest);
 937           } catch (Exception e)
 938           {
 939             errorWarning.append(e.getMessage());
 940             return;
 941           } finally
 942           {
 943             validateSelections();
 944           }
 945           if (resultList.getSearchSummary() != null
 946                   && resultList.getSearchSummary().size() > 0)
 947           {
 948             isValidPBDEntry = true;
 949           }
 950         }
 951         validateSelections();
 952       }
 953     }.start();
 954   }
 955
 956   @Override
 957   public void tabRefresh()
 958   {
 959     if (selectedSequences != null)
 960     {
 961       Thread refreshThread = new Thread(new Runnable()
 962       {
 963         @Override
 964         public void run()
 965         {
 966           fetchStructuresMetaData();
 967           filterResultSet(((FilterOption) cmb_filterOption
 968                   .getSelectedItem()).getValue());
 969         }
 970       });
 971       refreshThread.start();
 972     }
 973   }
 974
 975   public class PDBEntryTableModel extends AbstractTableModel
 976   {
 977     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
 978
 979     private List<CachedPDB> pdbEntries;
 980
 981     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
 982     {
 983       this.pdbEntries = new ArrayList<CachedPDB>(pdbEntries);
 984     }
 985
 986     @Override
 987     public String getColumnName(int columnIndex)
 988     {
 989       return columns[columnIndex];
 990     }
 991
 992     @Override
 993     public int getRowCount()
 994     {
 995       return pdbEntries.size();
 996     }
 997
 998     @Override
 999     public int getColumnCount()
1000     {
1001       return columns.length;
1002     }
1003
1004     @Override
1005     public boolean isCellEditable(int row, int column)
1006     {
1007       return false;
1008     }
1009
1010     @Override
1011     public Object getValueAt(int rowIndex, int columnIndex)
1012     {
1013       Object value = "??";
1014       CachedPDB entry = pdbEntries.get(rowIndex);
1015       switch (columnIndex)
1016       {
1017       case 0:
1018         value = entry.getSequence();
1019         break;
1020       case 1:
1021         value = entry.getPdbEntry();
1022         break;
1023       case 2:
1024         value = entry.getPdbEntry().getChainCode() == null ? "_" : entry
1025                 .getPdbEntry().getChainCode();
1026         break;
1027       case 3:
1028         value = entry.getPdbEntry().getType();
1029         break;
1030       case 4:
1031         value = entry.getPdbEntry().getFile();
1032         break;
1033       }
1034       return value;
1035     }
1036
1037     @Override
1038     public Class<?> getColumnClass(int columnIndex)
1039     {
1040       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1041     }
1042
1043     public CachedPDB getPDBEntryAt(int row)
1044     {
1045       return pdbEntries.get(row);
1046     }
1047
1048   }
1049
1050   private class CachedPDB
1051   {
1052     private SequenceI sequence;
1053
1054     private PDBEntry pdbEntry;
1055
1056     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1057     {
1058       this.sequence = sequence;
1059       this.pdbEntry = pdbEntry;
1060     }
1061
1062     public SequenceI getSequence()
1063     {
1064       return sequence;
1065     }
1066
1067     public PDBEntry getPdbEntry()
1068     {
1069       return pdbEntry;
1070     }
1071
1072   }
1073
1074   private IProgressIndicator progressBar;
1075
1076   @Override
1077   public void setProgressBar(String message, long id)
1078   {
1079     progressBar.setProgressBar(message, id);
1080   }
1081
1082   @Override
1083   public void registerHandler(long id, IProgressIndicatorHandler handler)
1084   {
1085     progressBar.registerHandler(id, handler);
1086   }
1087
1088   @Override
1089   public boolean operationInProgress()
1090   {
1091     return progressBar.operationInProgress();
1092   }
1093 }