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.StructureMapping;
  37 import jalview.structure.StructureSelectionManager;
  38 import jalview.util.MessageManager;
  39 import jalview.ws.DBRefFetcher;
  40 import jalview.ws.sifts.SiftsSettings;
  41
  42 import java.awt.event.ItemEvent;
  43 import java.util.ArrayList;
  44 import java.util.Collection;
  45 import java.util.HashSet;
  46 import java.util.LinkedHashSet;
  47 import java.util.List;
  48 import java.util.Objects;
  49 import java.util.Set;
  50 import java.util.Vector;
  51
  52 import javax.swing.JCheckBox;
  53 import javax.swing.JComboBox;
  54 import javax.swing.JLabel;
  55 import javax.swing.JOptionPane;
  56 import javax.swing.table.AbstractTableModel;
  57
  58 /**
  59  * Provides the behaviors for the Structure chooser Panel
  60  *
  61  * @author tcnofoegbu
  62  *
  63  */
  64 @SuppressWarnings("serial")
  65 public class StructureChooser extends GStructureChooser implements
  66         IProgressIndicator
  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   private boolean cachedPDBExists;
  85
  86   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
  87           AlignmentPanel ap)
  88   {
  89     this.ap = ap;
  90     this.selectedSequence = selectedSeq;
  91     this.selectedSequences = selectedSeqs;
  92     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
  93     init();
  94   }
  95
  96   /**
  97    * Initializes parameters used by the Structure Chooser Panel
  98    */
  99   public void init()
 100   {
 101     if (!Jalview.isHeadlessMode())
 102     {
 103       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 104     }
 105
 106     // ensure a filter option is in force for search
 107     populateFilterComboBox(true, cachedPDBExists);
 108     Thread discoverPDBStructuresThread = new Thread(new Runnable()
 109     {
 110       @Override
 111       public void run()
 112       {
 113         long startTime = System.currentTimeMillis();
 114         updateProgressIndicator(MessageManager
 115                 .getString("status.loading_cached_pdb_entries"), startTime);
 116         loadLocalCachedPDBEntries();
 117         updateProgressIndicator(null, startTime);
 118         updateProgressIndicator(MessageManager
 119                 .getString("status.searching_for_pdb_structures"),
 120                 startTime);
 121         fetchStructuresMetaData();
 122         // revise filter options if no results were found
 123         populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
 124         updateProgressIndicator(null, startTime);
 125         mainFrame.setVisible(true);
 126         updateCurrentView();
 127       }
 128     });
 129     discoverPDBStructuresThread.start();
 130   }
 131
 132   /**
 133    * Updates the progress indicator with the specified message
 134    *
 135    * @param message
 136    *          displayed message for the operation
 137    * @param id
 138    *          unique handle for this indicator
 139    */
 140   public void updateProgressIndicator(String message, long id)
 141   {
 142     if (progressIndicator != null)
 143     {
 144       progressIndicator.setProgressBar(message, id);
 145     }
 146   }
 147
 148   /**
 149    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
 150    * selection group
 151    */
 152   public void fetchStructuresMetaData()
 153   {
 154     long startTime = System.currentTimeMillis();
 155     pdbRestCleint = PDBFTSRestClient.getInstance();
 156     Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
 157             .getStructureSummaryFields();
 158
 159     discoveredStructuresSet = new LinkedHashSet<FTSData>();
 160     HashSet<String> errors = new HashSet<String>();
 161     for (SequenceI seq : selectedSequences)
 162     {
 163       FTSRestRequest pdbRequest = new FTSRestRequest();
 164       pdbRequest.setAllowEmptySeq(false);
 165       pdbRequest.setResponseSize(500);
 166       pdbRequest.setFieldToSearchBy("(");
 167       FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 168               .getSelectedItem());
 169       pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
 170               !chk_invertFilter.isSelected());
 171       pdbRequest.setWantedFields(wantedFields);
 172       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 173       pdbRequest.setAssociatedSequence(seq);
 174       FTSRestResponse resultList;
 175       try
 176       {
 177         resultList = pdbRestCleint.executeRequest(pdbRequest);
 178       } catch (Exception e)
 179       {
 180         e.printStackTrace();
 181         errors.add(e.getMessage());
 182         continue;
 183       }
 184       lastPdbRequest = pdbRequest;
 185       if (resultList.getSearchSummary() != null
 186               && !resultList.getSearchSummary().isEmpty())
 187       {
 188         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 189       }
 190     }
 191
 192     int noOfStructuresFound = 0;
 193     String totalTime = (System.currentTimeMillis() - startTime)
 194             + " milli secs";
 195     if (discoveredStructuresSet != null
 196             && !discoveredStructuresSet.isEmpty())
 197     {
 198       getResultTable().setModel(
 199               FTSRestResponse.getTableModel(lastPdbRequest,
 200                       discoveredStructuresSet));
 201       noOfStructuresFound = discoveredStructuresSet.size();
 202       mainFrame.setTitle(MessageManager.formatMessage(
 203               "label.structure_chooser_no_of_structures",
 204               noOfStructuresFound, totalTime));
 205     }
 206     else
 207     {
 208       mainFrame.setTitle(MessageManager
 209               .getString("label.structure_chooser_manual_association"));
 210       if (errors.size() > 0)
 211       {
 212         StringBuilder errorMsg = new StringBuilder();
 213         for (String error : errors)
 214         {
 215           errorMsg.append(error).append("\n");
 216         }
 217         JOptionPane.showMessageDialog(this, errorMsg.toString(),
 218                 MessageManager.getString("label.pdb_web-service_error"),
 219                 JOptionPane.ERROR_MESSAGE);
 220       }
 221     }
 222   }
 223
 224   public void loadLocalCachedPDBEntries()
 225   {
 226     ArrayList<CachedPDB> entries = new ArrayList<CachedPDB>();
 227     for (SequenceI seq : selectedSequences)
 228     {
 229       if (seq.getDatasetSequence() != null
 230               && seq.getDatasetSequence().getAllPDBEntries() != null)
 231       {
 232         for (PDBEntry pdbEntry : seq.getDatasetSequence()
 233                 .getAllPDBEntries())
 234         {
 235           if (pdbEntry.getFile() != null)
 236           {
 237             entries.add(new CachedPDB(seq, pdbEntry));
 238           }
 239         }
 240       }
 241     }
 242     cachedPDBExists = !entries.isEmpty();
 243     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
 244     tbl_local_pdb.setModel(tableModelx);
 245   }
 246
 247   /**
 248    * Builds a query string for a given sequences using its DBRef entries
 249    *
 250    * @param seq
 251    *          the sequences to build a query for
 252    * @return the built query string
 253    */
 254
 255   public static String buildQuery(SequenceI seq)
 256   {
 257     boolean isPDBRefsFound = false;
 258     boolean isUniProtRefsFound = false;
 259     StringBuilder queryBuilder = new StringBuilder();
 260     Set<String> seqRefs = new LinkedHashSet<String>();
 261
 262     if (seq.getAllPDBEntries() != null)
 263     {
 264       for (PDBEntry entry : seq.getAllPDBEntries())
 265       {
 266         if (isValidSeqName(entry.getId()))
 267         {
 268           queryBuilder.append("pdb_id:")
 269                   .append(entry.getId().toLowerCase()).append(" OR ");
 270           isPDBRefsFound = true;
 271           // seqRefs.add(entry.getId());
 272         }
 273       }
 274     }
 275
 276     if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
 277     {
 278       for (DBRefEntry dbRef : seq.getDBRefs())
 279       {
 280         if (isValidSeqName(getDBRefId(dbRef)))
 281         {
 282           if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
 283           {
 284             queryBuilder.append("uniprot_accession:")
 285                     .append(getDBRefId(dbRef)).append(" OR ");
 286             queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
 287                     .append(" OR ");
 288             isUniProtRefsFound = true;
 289           }
 290           else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
 291           {
 292
 293             queryBuilder.append("pdb_id:")
 294                     .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
 295             isPDBRefsFound = true;
 296           }
 297           else
 298           {
 299             seqRefs.add(getDBRefId(dbRef));
 300           }
 301         }
 302       }
 303     }
 304
 305     if (!isPDBRefsFound && !isUniProtRefsFound)
 306     {
 307       String seqName = seq.getName();
 308       seqName = sanitizeSeqName(seqName);
 309       String[] names = seqName.toLowerCase().split("\\|");
 310       for (String name : names)
 311       {
 312         // System.out.println("Found name : " + name);
 313         name.trim();
 314         if (isValidSeqName(name))
 315         {
 316           seqRefs.add(name);
 317         }
 318       }
 319
 320       for (String seqRef : seqRefs)
 321       {
 322         queryBuilder.append("text:").append(seqRef).append(" OR ");
 323       }
 324     }
 325
 326     int endIndex = queryBuilder.lastIndexOf(" OR ");
 327     if (queryBuilder.toString().length() < 6)
 328     {
 329       return null;
 330     }
 331     String query = queryBuilder.toString().substring(0, endIndex);
 332     return query;
 333   }
 334
 335   /**
 336    * Remove the following special characters from input string +, -, &, !, (, ),
 337    * {, }, [, ], ^, ", ~, *, ?, :, \
 338    *
 339    * @param seqName
 340    * @return
 341    */
 342   static String sanitizeSeqName(String seqName)
 343   {
 344     Objects.requireNonNull(seqName);
 345     return seqName.replaceAll("\\[\\d*\\]", "")
 346             .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
 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(lastPdbRequest,
 460                           reorderedStructuresSet));
 461
 462           FTSRestResponse.configureTableColumn(getResultTable(),
 463                   wantedFields, tempUserPrefs);
 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   protected void populateFilterComboBox(boolean haveData,
 530           boolean cachedPDBExists)
 531   {
 532     /*
 533      * temporarily suspend the change listener behaviour
 534      */
 535     cmb_filterOption.removeItemListener(this);
 536
 537     cmb_filterOption.removeAllItems();
 538     if (haveData)
 539     {
 540       cmb_filterOption.addItem(new FilterOption("Best Quality",
 541               "overall_quality", VIEWS_FILTER));
 542       cmb_filterOption.addItem(new FilterOption("Best Resolution",
 543               "resolution", VIEWS_FILTER));
 544       cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
 545               "number_of_protein_chains", VIEWS_FILTER));
 546       cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
 547               "number_of_bound_molecules", VIEWS_FILTER));
 548       cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
 549               "number_of_polymer_residues", VIEWS_FILTER));
 550     }
 551     cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
 552             VIEWS_ENTER_ID));
 553     cmb_filterOption.addItem(new FilterOption("From File", "-",
 554             VIEWS_FROM_FILE));
 555     FilterOption cachedOption = new FilterOption("Cached PDB Entries", "-",
 556             VIEWS_LOCAL_PDB);
 557     cmb_filterOption.addItem(cachedOption);
 558
 559     if (/*!haveData &&*/cachedPDBExists)
 560     {
 561       cmb_filterOption.setSelectedItem(cachedOption);
 562     }
 563
 564     cmb_filterOption.addItemListener(this);
 565   }
 566
 567   /**
 568    * Updates the displayed view based on the selected filter option
 569    */
 570   protected void updateCurrentView()
 571   {
 572     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 573             .getSelectedItem());
 574     layout_switchableViews.show(pnl_switchableViews,
 575             selectedFilterOpt.getView());
 576     String filterTitle = mainFrame.getTitle();
 577     mainFrame.setTitle(frameTitle);
 578     chk_invertFilter.setVisible(false);
 579     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 580     {
 581       mainFrame.setTitle(filterTitle);
 582       chk_invertFilter.setVisible(true);
 583       filterResultSet(selectedFilterOpt.getValue());
 584     }
 585     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 586             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 587     {
 588       mainFrame.setTitle(MessageManager
 589               .getString("label.structure_chooser_manual_association"));
 590       idInputAssSeqPanel.loadCmbAssSeq();
 591       fileChooserAssSeqPanel.loadCmbAssSeq();
 592     }
 593     validateSelections();
 594   }
 595
 596   /**
 597    * Validates user selection and activates the view button if all parameters
 598    * are correct
 599    */
 600   @Override
 601   public void validateSelections()
 602   {
 603     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 604             .getSelectedItem());
 605     btn_view.setEnabled(false);
 606     String currentView = selectedFilterOpt.getView();
 607     if (currentView == VIEWS_FILTER)
 608     {
 609       if (getResultTable().getSelectedRows().length > 0)
 610       {
 611         btn_view.setEnabled(true);
 612       }
 613     }
 614     else if (currentView == VIEWS_LOCAL_PDB)
 615     {
 616       if (tbl_local_pdb.getSelectedRows().length > 0)
 617       {
 618         btn_view.setEnabled(true);
 619       }
 620     }
 621     else if (currentView == VIEWS_ENTER_ID)
 622     {
 623       validateAssociationEnterPdb();
 624     }
 625     else if (currentView == VIEWS_FROM_FILE)
 626     {
 627       validateAssociationFromFile();
 628     }
 629   }
 630
 631   /**
 632    * Validates inputs from the Manual PDB entry panel
 633    */
 634   public void validateAssociationEnterPdb()
 635   {
 636     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 637             .getCmb_assSeq().getSelectedItem();
 638     lbl_pdbManualFetchStatus.setIcon(errorImage);
 639     lbl_pdbManualFetchStatus.setToolTipText("");
 640     if (txt_search.getText().length() > 0)
 641     {
 642       lbl_pdbManualFetchStatus
 643               .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 644                       .formatMessage("info.no_pdb_entry_found_for",
 645                               txt_search.getText())));
 646     }
 647
 648     if (errorWarning.length() > 0)
 649     {
 650       lbl_pdbManualFetchStatus.setIcon(warningImage);
 651       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
 652               true, errorWarning.toString()));
 653     }
 654
 655     if (selectedSequences.length == 1
 656             || !assSeqOpt.getName().equalsIgnoreCase(
 657                     "-Select Associated Seq-"))
 658     {
 659       txt_search.setEnabled(true);
 660       if (isValidPBDEntry)
 661       {
 662         btn_view.setEnabled(true);
 663         lbl_pdbManualFetchStatus.setToolTipText("");
 664         lbl_pdbManualFetchStatus.setIcon(goodImage);
 665       }
 666     }
 667     else
 668     {
 669       txt_search.setEnabled(false);
 670       lbl_pdbManualFetchStatus.setIcon(errorImage);
 671     }
 672   }
 673
 674   /**
 675    * Validates inputs for the manual PDB file selection options
 676    */
 677   public void validateAssociationFromFile()
 678   {
 679     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
 680             .getCmb_assSeq().getSelectedItem();
 681     lbl_fromFileStatus.setIcon(errorImage);
 682     if (selectedSequences.length == 1
 683             || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
 684                     "-Select Associated Seq-")))
 685     {
 686       btn_pdbFromFile.setEnabled(true);
 687       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
 688       {
 689         btn_view.setEnabled(true);
 690         lbl_fromFileStatus.setIcon(goodImage);
 691       }
 692     }
 693     else
 694     {
 695       btn_pdbFromFile.setEnabled(false);
 696       lbl_fromFileStatus.setIcon(errorImage);
 697     }
 698   }
 699
 700   @Override
 701   public void cmbAssSeqStateChanged()
 702   {
 703     validateSelections();
 704   }
 705
 706   /**
 707    * Handles the state change event for the 'filter' combo-box and 'invert'
 708    * check-box
 709    */
 710   @Override
 711   protected void stateChanged(ItemEvent e)
 712   {
 713     if (e.getSource() instanceof JCheckBox)
 714     {
 715       updateCurrentView();
 716     }
 717     else
 718     {
 719       if (e.getStateChange() == ItemEvent.SELECTED)
 720       {
 721         updateCurrentView();
 722       }
 723     }
 724
 725   }
 726
 727   /**
 728    * Handles action event for btn_ok
 729    */
 730   @Override
 731   public void ok_ActionPerformed()
 732   {
 733     final long progressSessionId = System.currentTimeMillis();
 734     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 735     final int preferredHeight = pnl_filter.getHeight();
 736     ssm.setProgressIndicator(this);
 737     ssm.setProgressSessionId(progressSessionId);
 738     new Thread(new Runnable()
 739     {
 740       @Override
 741       public void run()
 742       {
 743         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 744                 .getSelectedItem());
 745         String currentView = selectedFilterOpt.getView();
 746         if (currentView == VIEWS_FILTER)
 747         {
 748           int pdbIdColIndex = getResultTable().getColumn("PDB Id")
 749                   .getModelIndex();
 750           int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
 751                   .getModelIndex();
 752           int[] selectedRows = getResultTable().getSelectedRows();
 753           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 754           int count = 0;
 755           ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
 756           for (int row : selectedRows)
 757           {
 758             String pdbIdStr = getResultTable().getValueAt(row,
 759                     pdbIdColIndex).toString();
 760             SequenceI selectedSeq = (SequenceI) getResultTable()
 761                     .getValueAt(row, refSeqColIndex);
 762             selectedSeqsToView.add(selectedSeq);
 763             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
 764             if (pdbEntry == null)
 765             {
 766               pdbEntry = getFindEntry(pdbIdStr,
 767                       selectedSeq.getAllPDBEntries());
 768             }
 769             if (pdbEntry == null)
 770             {
 771               pdbEntry = new PDBEntry();
 772               pdbEntry.setId(pdbIdStr);
 773               pdbEntry.setType(PDBEntry.Type.PDB);
 774               selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
 775             }
 776             pdbEntriesToView[count++] = pdbEntry;
 777           }
 778           SequenceI[] selectedSeqs = selectedSeqsToView
 779                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 780           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
 781         }
 782         else if (currentView == VIEWS_LOCAL_PDB)
 783         {
 784           int[] selectedRows = tbl_local_pdb.getSelectedRows();
 785           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 786           int count = 0;
 787           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
 788                   .getModelIndex();
 789           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
 790                   .getModelIndex();
 791           ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
 792           for (int row : selectedRows)
 793           {
 794             PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
 795                     pdbIdColIndex);
 796             pdbEntriesToView[count++] = pdbEntry;
 797             SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(
 798                     row, refSeqColIndex);
 799             selectedSeqsToView.add(selectedSeq);
 800           }
 801           SequenceI[] selectedSeqs = selectedSeqsToView
 802                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 803           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
 804         }
 805         else if (currentView == VIEWS_ENTER_ID)
 806         {
 807           SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
 808                   .getCmb_assSeq().getSelectedItem()).getSequence();
 809           if (userSelectedSeq != null)
 810           {
 811             selectedSequence = userSelectedSeq;
 812           }
 813
 814           String pdbIdStr = txt_search.getText();
 815           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
 816           if (pdbEntry == null)
 817           {
 818             pdbEntry = new PDBEntry();
 819             if (pdbIdStr.split(":").length > 1)
 820             {
 821               pdbEntry.setId(pdbIdStr.split(":")[0]);
 822               pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
 823             }
 824             else
 825             {
 826               pdbEntry.setId(pdbIdStr);
 827             }
 828             pdbEntry.setType(PDBEntry.Type.PDB);
 829             selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
 830           }
 831
 832           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
 833           launchStructureViewer(ssm, pdbEntriesToView, ap,
 834                   new SequenceI[] { selectedSequence });
 835         }
 836         else if (currentView == VIEWS_FROM_FILE)
 837         {
 838           SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
 839                   .getCmb_assSeq().getSelectedItem()).getSequence();
 840           if (userSelectedSeq != null)
 841           {
 842             selectedSequence = userSelectedSeq;
 843           }
 844           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 845                   .associatePdbWithSeq(selectedPdbFileName,
 846                           jalview.io.AppletFormatAdapter.FILE,
 847                           selectedSequence, true, Desktop.instance);
 848
 849           launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
 850                   new SequenceI[] { selectedSequence });
 851         }
 852         closeAction(preferredHeight);
 853       }
 854     }).start();
 855   }
 856
 857   private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
 858   {
 859     Objects.requireNonNull(id);
 860     Objects.requireNonNull(pdbEntries);
 861     PDBEntry foundEntry = null;
 862     for (PDBEntry entry : pdbEntries)
 863     {
 864       if (entry.getId().equalsIgnoreCase(id))
 865       {
 866         return entry;
 867       }
 868     }
 869     return foundEntry;
 870   }
 871
 872   private void launchStructureViewer(StructureSelectionManager ssm,
 873           final PDBEntry[] pdbEntriesToView,
 874           final AlignmentPanel alignPanel, SequenceI[] sequences)
 875   {
 876     ssm.setProgressBar(MessageManager
 877             .getString("status.launching_3d_structure_viewer"));
 878     final StructureViewer sViewer = new StructureViewer(ssm);
 879
 880     if (SiftsSettings.isMapWithSifts())
 881     {
 882       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
 883       int p = 0;
 884       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
 885       // real PDB ID. For moment, we can also safely do this if there is already
 886       // a known mapping between the PDBEntry and the sequence.
 887       for (SequenceI seq : sequences)
 888       {
 889         PDBEntry pdbe = pdbEntriesToView[p++];
 890         if (pdbe != null && pdbe.getFile() != null)
 891         {
 892           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
 893           if (smm != null && smm.length > 0)
 894           {
 895             for (StructureMapping sm : smm)
 896             {
 897               if (sm.getSequence() == seq)
 898               {
 899                 continue;
 900               }
 901             }
 902           }
 903         }
 904         if (seq.getPrimaryDBRefs().size() == 0)
 905         {
 906           seqsWithoutSourceDBRef.add(seq);
 907           continue;
 908         }
 909       }
 910       if (!seqsWithoutSourceDBRef.isEmpty())
 911       {
 912         int y = seqsWithoutSourceDBRef.size();
 913         ssm.setProgressBar(null);
 914         ssm.setProgressBar(MessageManager.formatMessage(
 915                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
 916                 y));
 917         SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
 918         int x = 0;
 919         for (SequenceI fSeq : seqsWithoutSourceDBRef)
 920         {
 921           seqWithoutSrcDBRef[x++] = fSeq;
 922         }
 923         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
 924         dbRefFetcher.fetchDBRefs(true);
 925       }
 926     }
 927     if (pdbEntriesToView.length > 1)
 928     {
 929       ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
 930       for (SequenceI seq : sequences)
 931       {
 932         seqsMap.add(new SequenceI[] { seq });
 933       }
 934       SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
 935       ssm.setProgressBar(null);
 936       ssm.setProgressBar(MessageManager
 937               .getString("status.fetching_3d_structures_for_selected_entries"));
 938       sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
 939     }
 940     else
 941     {
 942       ssm.setProgressBar(null);
 943       ssm.setProgressBar(MessageManager.formatMessage(
 944               "status.fetching_3d_structures_for",
 945               pdbEntriesToView[0].getId()));
 946       sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
 947     }
 948   }
 949
 950   /**
 951    * Populates the combo-box used in associating manually fetched structures to
 952    * a unique sequence when more than one sequence selection is made.
 953    */
 954   @Override
 955   public void populateCmbAssociateSeqOptions(
 956           JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
 957   {
 958     cmb_assSeq.removeAllItems();
 959     cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
 960             null));
 961     lbl_associateSeq.setVisible(false);
 962     if (selectedSequences.length > 1)
 963     {
 964       for (SequenceI seq : selectedSequences)
 965       {
 966         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
 967       }
 968     }
 969     else
 970     {
 971       String seqName = selectedSequence.getDisplayId(false);
 972       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
 973       lbl_associateSeq.setText(seqName);
 974       lbl_associateSeq.setVisible(true);
 975       cmb_assSeq.setVisible(false);
 976     }
 977   }
 978
 979   public boolean isStructuresDiscovered()
 980   {
 981     return discoveredStructuresSet != null
 982             && !discoveredStructuresSet.isEmpty();
 983   }
 984
 985   public Collection<FTSData> getDiscoveredStructuresSet()
 986   {
 987     return discoveredStructuresSet;
 988   }
 989
 990   @Override
 991   protected void txt_search_ActionPerformed()
 992   {
 993     new Thread()
 994     {
 995       @Override
 996       public void run()
 997       {
 998         errorWarning.setLength(0);
 999         isValidPBDEntry = false;
1000         if (txt_search.getText().length() > 0)
1001         {
1002           String searchTerm = txt_search.getText().toLowerCase();
1003           searchTerm = searchTerm.split(":")[0];
1004           // System.out.println(">>>>> search term : " + searchTerm);
1005           List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
1006           FTSRestRequest pdbRequest = new FTSRestRequest();
1007           pdbRequest.setAllowEmptySeq(false);
1008           pdbRequest.setResponseSize(1);
1009           pdbRequest.setFieldToSearchBy("(pdb_id:");
1010           pdbRequest.setWantedFields(wantedFields);
1011           pdbRequest.setSearchTerm(searchTerm + ")");
1012           pdbRequest.setAssociatedSequence(selectedSequence);
1013           pdbRestCleint = PDBFTSRestClient.getInstance();
1014           wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
1015           FTSRestResponse resultList;
1016           try
1017           {
1018             resultList = pdbRestCleint.executeRequest(pdbRequest);
1019           } catch (Exception e)
1020           {
1021             errorWarning.append(e.getMessage());
1022             return;
1023           } finally
1024           {
1025             validateSelections();
1026           }
1027           if (resultList.getSearchSummary() != null
1028                   && resultList.getSearchSummary().size() > 0)
1029           {
1030             isValidPBDEntry = true;
1031           }
1032         }
1033         validateSelections();
1034       }
1035     }.start();
1036   }
1037
1038   @Override
1039   public void tabRefresh()
1040   {
1041     if (selectedSequences != null)
1042     {
1043       Thread refreshThread = new Thread(new Runnable()
1044       {
1045         @Override
1046         public void run()
1047         {
1048           fetchStructuresMetaData();
1049           filterResultSet(((FilterOption) cmb_filterOption
1050                   .getSelectedItem()).getValue());
1051         }
1052       });
1053       refreshThread.start();
1054     }
1055   }
1056
1057   public class PDBEntryTableModel extends AbstractTableModel
1058   {
1059     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
1060
1061     private List<CachedPDB> pdbEntries;
1062
1063     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1064     {
1065       this.pdbEntries = new ArrayList<CachedPDB>(pdbEntries);
1066     }
1067
1068     @Override
1069     public String getColumnName(int columnIndex)
1070     {
1071       return columns[columnIndex];
1072     }
1073
1074     @Override
1075     public int getRowCount()
1076     {
1077       return pdbEntries.size();
1078     }
1079
1080     @Override
1081     public int getColumnCount()
1082     {
1083       return columns.length;
1084     }
1085
1086     @Override
1087     public boolean isCellEditable(int row, int column)
1088     {
1089       return false;
1090     }
1091
1092     @Override
1093     public Object getValueAt(int rowIndex, int columnIndex)
1094     {
1095       Object value = "??";
1096       CachedPDB entry = pdbEntries.get(rowIndex);
1097       switch (columnIndex)
1098       {
1099       case 0:
1100         value = entry.getSequence();
1101         break;
1102       case 1:
1103         value = entry.getPdbEntry();
1104         break;
1105       case 2:
1106         value = entry.getPdbEntry().getChainCode() == null ? "_" : entry
1107                 .getPdbEntry().getChainCode();
1108         break;
1109       case 3:
1110         value = entry.getPdbEntry().getType();
1111         break;
1112       case 4:
1113         value = entry.getPdbEntry().getFile();
1114         break;
1115       }
1116       return value;
1117     }
1118
1119     @Override
1120     public Class<?> getColumnClass(int columnIndex)
1121     {
1122       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1123     }
1124
1125     public CachedPDB getPDBEntryAt(int row)
1126     {
1127       return pdbEntries.get(row);
1128     }
1129
1130   }
1131
1132   private class CachedPDB
1133   {
1134     private SequenceI sequence;
1135
1136     private PDBEntry pdbEntry;
1137
1138     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1139     {
1140       this.sequence = sequence;
1141       this.pdbEntry = pdbEntry;
1142     }
1143
1144     public SequenceI getSequence()
1145     {
1146       return sequence;
1147     }
1148
1149     public PDBEntry getPdbEntry()
1150     {
1151       return pdbEntry;
1152     }
1153
1154   }
1155
1156   private IProgressIndicator progressBar;
1157
1158   @Override
1159   public void setProgressBar(String message, long id)
1160   {
1161     progressBar.setProgressBar(message, id);
1162   }
1163
1164   @Override
1165   public void registerHandler(long id, IProgressIndicatorHandler handler)
1166   {
1167     progressBar.registerHandler(id, handler);
1168   }
1169
1170   @Override
1171   public boolean operationInProgress()
1172   {
1173     return progressBar.operationInProgress();
1174   }
1175 }