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   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 StructureSelectionManager ssm = ap.getStructureSelectionManager();
 721     new Thread(new Runnable()
 722     {
 723       @Override
 724       public void run()
 725       {
 726     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 727             .getSelectedItem());
 728     String currentView = selectedFilterOpt.getView();
 729     if (currentView == VIEWS_FILTER)
 730     {
 731           int pdbIdColIndex = getResultTable().getColumn("PDB Id")
 732                   .getModelIndex();
 733           int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
 734               .getModelIndex();
 735           int[] selectedRows = getResultTable().getSelectedRows();
 736       PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 737       int count = 0;
 738       ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
 739       for (int row : selectedRows)
 740       {
 741             String pdbIdStr = getResultTable().getValueAt(row,
 742                     pdbIdColIndex)
 743                 .toString();
 744             SequenceI selectedSeq = (SequenceI) getResultTable()
 745                     .getValueAt(row,
 746                 refSeqColIndex);
 747         selectedSeqsToView.add(selectedSeq);
 748             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
 749             if (pdbEntry == null)
 750             {
 751               pdbEntry = getFindEntry(pdbIdStr,
 752                       selectedSeq.getAllPDBEntries());
 753             }
 754         if (pdbEntry == null)
 755         {
 756           pdbEntry = new PDBEntry();
 757           pdbEntry.setId(pdbIdStr);
 758           pdbEntry.setType(PDBEntry.Type.PDB);
 759           selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
 760         }
 761         pdbEntriesToView[count++] = pdbEntry;
 762       }
 763       SequenceI[] selectedSeqs = selectedSeqsToView
 764               .toArray(new SequenceI[selectedSeqsToView.size()]);
 765           launchStructureViewer(ssm, pdbEntriesToView, ap,
 766                   selectedSeqs);
 767     }
 768     else if (currentView == VIEWS_LOCAL_PDB)
 769     {
 770       int[] selectedRows = tbl_local_pdb.getSelectedRows();
 771       PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 772       int count = 0;
 773           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
 774                   .getModelIndex();
 775       int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
 776               .getModelIndex();
 777       ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
 778       for (int row : selectedRows)
 779       {
 780         PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
 781                 pdbIdColIndex);
 782         pdbEntriesToView[count++] = pdbEntry;
 783         SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
 784                 refSeqColIndex);
 785         selectedSeqsToView.add(selectedSeq);
 786       }
 787       SequenceI[] selectedSeqs = selectedSeqsToView
 788               .toArray(new SequenceI[selectedSeqsToView.size()]);
 789           launchStructureViewer(ssm, pdbEntriesToView, ap,
 790                   selectedSeqs);
 791     }
 792     else if (currentView == VIEWS_ENTER_ID)
 793     {
 794       SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
 795               .getCmb_assSeq().getSelectedItem()).getSequence();
 796       if (userSelectedSeq != null)
 797       {
 798         selectedSequence = userSelectedSeq;
 799       }
 800
 801       String pdbIdStr = txt_search.getText();
 802       PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
 803       if (pdbEntry == null)
 804       {
 805         pdbEntry = new PDBEntry();
 806             if (pdbIdStr.split(":").length > 1)
 807             {
 808               pdbEntry.setChainCode(pdbIdStr.split(":")[1]);
 809             }
 810         pdbEntry.setId(pdbIdStr);
 811         pdbEntry.setType(PDBEntry.Type.PDB);
 812         selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
 813       }
 814
 815       PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
 816           launchStructureViewer(ssm, pdbEntriesToView, ap,
 817                   new SequenceI[] { selectedSequence });
 818     }
 819     else if (currentView == VIEWS_FROM_FILE)
 820     {
 821       SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
 822               .getCmb_assSeq().getSelectedItem()).getSequence();
 823       if (userSelectedSeq != null)
 824       {
 825         selectedSequence = userSelectedSeq;
 826       }
 827       PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 828               .associatePdbWithSeq(selectedPdbFileName,
 829                       jalview.io.AppletFormatAdapter.FILE,
 830                       selectedSequence, true, Desktop.instance);
 831
 832           launchStructureViewer(ssm,
 833                   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     long progressId = sequences.hashCode();
 861     setProgressBar(MessageManager
 862             .getString("status.launching_3d_structure_viewer"), progressId);
 863     final StructureViewer sViewer = new StructureViewer(ssm);
 864     setProgressBar(null, progressId);
 865
 866     if (SiftsSettings.isMapWithSifts())
 867     {
 868       // TODO: prompt user if there are lots of sequences without dbrefs.
 869       // It can take a long time if we need to fetch all dbrefs for all
 870       // sequences!
 871       ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
 872       for (SequenceI seq : sequences)
 873       {
 874         if (seq.getSourceDBRef() == null && seq.getDBRefs() == null)
 875         {
 876             seqsWithoutSourceDBRef.add(seq);
 877             continue;
 878           }
 879       }
 880       if (!seqsWithoutSourceDBRef.isEmpty())
 881       {
 882         int y = seqsWithoutSourceDBRef.size();
 883         setProgressBar(MessageManager.formatMessage(
 884                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
 885                 y,
 886                 progressId);
 887         SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
 888         int x = 0;
 889         for (SequenceI fSeq : seqsWithoutSourceDBRef)
 890         {
 891           seqWithoutSrcDBRef[x++] = fSeq;
 892         }
 893         new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
 894         setProgressBar("Fetch complete.", progressId); // todo i18n
 895       }
 896     }
 897     if (pdbEntriesToView.length > 1)
 898     {
 899       ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
 900       for (SequenceI seq : sequences)
 901       {
 902         seqsMap.add(new SequenceI[] { seq });
 903       }
 904       SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
 905 <<<<<<< Updated upstream
 906       ssm.setProgressBar(null);
 907       ssm.setProgressBar(MessageManager
 908               .getString("status.fetching_3d_structures_for_selected_entries"));
 909 =======
 910       setProgressBar("Fetching structure data", progressId);
 911 >>>>>>> Stashed changes
 912       sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
 913     }
 914     else
 915     {
 916 <<<<<<< Updated upstream
 917       ssm.setProgressBar(null);
 918       ssm.setProgressBar(MessageManager.formatMessage(
 919               "status.fetching_3d_structures_for",
 920               pdbEntriesToView[0].getId()));
 921 =======
 922       setProgressBar(
 923               "Fetching structure for " + pdbEntriesToView[0].getId(),
 924               progressId);
 925 >>>>>>> Stashed changes
 926       sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
 927     }
 928     setProgressBar(null, progressId);
 929   }
 930
 931   /**
 932    * Populates the combo-box used in associating manually fetched structures to
 933    * a unique sequence when more than one sequence selection is made.
 934    */
 935   @Override
 936   public void populateCmbAssociateSeqOptions(
 937           JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
 938   {
 939     cmb_assSeq.removeAllItems();
 940     cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
 941             null));
 942     lbl_associateSeq.setVisible(false);
 943     if (selectedSequences.length > 1)
 944     {
 945       for (SequenceI seq : selectedSequences)
 946       {
 947         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
 948       }
 949     }
 950     else
 951     {
 952       String seqName = selectedSequence.getDisplayId(false);
 953       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
 954       lbl_associateSeq.setText(seqName);
 955       lbl_associateSeq.setVisible(true);
 956       cmb_assSeq.setVisible(false);
 957     }
 958   }
 959
 960   public boolean isStructuresDiscovered()
 961   {
 962     return structuresDiscovered;
 963   }
 964
 965   public void setStructuresDiscovered(boolean structuresDiscovered)
 966   {
 967     this.structuresDiscovered = structuresDiscovered;
 968   }
 969
 970   public Collection<FTSData> getDiscoveredStructuresSet()
 971   {
 972     return discoveredStructuresSet;
 973   }
 974
 975   @Override
 976   protected void txt_search_ActionPerformed()
 977   {
 978     new Thread()
 979     {
 980       @Override
 981       public void run()
 982       {
 983         errorWarning.setLength(0);
 984         isValidPBDEntry = false;
 985         if (txt_search.getText().length() > 0)
 986         {
 987           String searchTerm = txt_search.getText().toLowerCase();
 988           searchTerm = searchTerm.split(":")[0];
 989           // System.out.println(">>>>> search term : " + searchTerm);
 990           List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 991           FTSRestRequest pdbRequest = new FTSRestRequest();
 992           pdbRequest.setAllowEmptySeq(false);
 993           pdbRequest.setResponseSize(1);
 994           pdbRequest.setFieldToSearchBy("(pdb_id:");
 995           pdbRequest.setWantedFields(wantedFields);
 996           pdbRequest
 997 .setSearchTerm(searchTerm + ")");
 998           pdbRequest.setAssociatedSequence(selectedSequence);
 999           pdbRestCleint = PDBFTSRestClient.getInstance();
1000           wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
1001           FTSRestResponse resultList;
1002           try
1003           {
1004             resultList = pdbRestCleint.executeRequest(pdbRequest);
1005           } catch (Exception e)
1006           {
1007             errorWarning.append(e.getMessage());
1008             return;
1009           } finally
1010           {
1011             validateSelections();
1012           }
1013           if (resultList.getSearchSummary() != null
1014                   && resultList.getSearchSummary().size() > 0)
1015           {
1016             isValidPBDEntry = true;
1017           }
1018         }
1019         validateSelections();
1020       }
1021     }.start();
1022   }
1023
1024   @Override
1025   public void tabRefresh()
1026   {
1027     if (selectedSequences != null)
1028     {
1029       Thread refreshThread = new Thread(new Runnable()
1030       {
1031         @Override
1032         public void run()
1033         {
1034           fetchStructuresMetaData();
1035           filterResultSet(((FilterOption) cmb_filterOption
1036                   .getSelectedItem()).getValue());
1037         }
1038       });
1039       refreshThread.start();
1040     }
1041   }
1042
1043   public class PDBEntryTableModel extends AbstractTableModel
1044   {
1045     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
1046
1047     private List<CachedPDB> pdbEntries;
1048
1049     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1050     {
1051       this.pdbEntries = new ArrayList<CachedPDB>(pdbEntries);
1052     }
1053
1054     @Override
1055     public String getColumnName(int columnIndex)
1056     {
1057       return columns[columnIndex];
1058     }
1059
1060     @Override
1061     public int getRowCount()
1062     {
1063       return pdbEntries.size();
1064     }
1065
1066     @Override
1067     public int getColumnCount()
1068     {
1069       return columns.length;
1070     }
1071
1072     @Override
1073     public boolean isCellEditable(int row, int column)
1074     {
1075       return false;
1076     }
1077
1078     @Override
1079     public Object getValueAt(int rowIndex, int columnIndex)
1080     {
1081       Object value = "??";
1082       CachedPDB entry = pdbEntries.get(rowIndex);
1083       switch (columnIndex)
1084       {
1085       case 0:
1086         value = entry.getSequence();
1087         break;
1088       case 1:
1089         value = entry.getPdbEntry();
1090         break;
1091       case 2:
1092         value = entry.getPdbEntry().getChainCode() == null ? "_" : entry
1093                 .getPdbEntry().getChainCode();
1094         break;
1095       case 3:
1096         value = entry.getPdbEntry().getType();
1097         break;
1098       case 4:
1099         value = entry.getPdbEntry().getFile();
1100         break;
1101       }
1102       return value;
1103     }
1104
1105     @Override
1106     public Class<?> getColumnClass(int columnIndex)
1107     {
1108       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1109     }
1110
1111     public CachedPDB getPDBEntryAt(int row)
1112     {
1113       return pdbEntries.get(row);
1114     }
1115
1116   }
1117
1118   private class CachedPDB
1119   {
1120     private SequenceI sequence;
1121
1122     private PDBEntry pdbEntry;
1123
1124     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1125     {
1126       this.sequence = sequence;
1127       this.pdbEntry = pdbEntry;
1128     }
1129
1130     public SequenceI getSequence()
1131     {
1132       return sequence;
1133     }
1134
1135     public PDBEntry getPdbEntry()
1136     {
1137       return pdbEntry;
1138     }
1139
1140   }
1141
1142   private IProgressIndicator progressBar;
1143
1144   @Override
1145   public void setProgressBar(String message, long id)
1146   {
1147     progressBar.setProgressBar(message, id);
1148   }
1149
1150   @Override
1151   public void registerHandler(long id, IProgressIndicatorHandler handler)
1152   {
1153     progressBar.registerHandler(id, handler);
1154   }
1155
1156   @Override
1157   public boolean operationInProgress()
1158   {
1159     return progressBar.operationInProgress();
1160   }
1161 }