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