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.io.DataSourceType;
  36 import jalview.jbgui.GStructureChooser;
  37 import jalview.structure.StructureMapping;
  38 import jalview.structure.StructureSelectionManager;
  39 import jalview.util.MessageManager;
  40 import jalview.ws.DBRefFetcher;
  41 import jalview.ws.sifts.SiftsSettings;
  42
  43 import java.awt.event.ItemEvent;
  44 import java.util.ArrayList;
  45 import java.util.Collection;
  46 import java.util.HashSet;
  47 import java.util.LinkedHashSet;
  48 import java.util.List;
  49 import java.util.Objects;
  50 import java.util.Set;
  51 import java.util.Vector;
  52
  53 import javax.swing.JCheckBox;
  54 import javax.swing.JComboBox;
  55 import javax.swing.JLabel;
  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
  66         implements IProgressIndicator
  67 {
  68   private static int MAX_QLENGTH = 7820;
  69
  70   private SequenceI selectedSequence;
  71
  72   private SequenceI[] selectedSequences;
  73
  74   private IProgressIndicator progressIndicator;
  75
  76   private Collection<FTSData> discoveredStructuresSet;
  77
  78   private FTSRestRequest lastPdbRequest;
  79
  80   private FTSRestClientI pdbRestCleint;
  81
  82   private String selectedPdbFileName;
  83
  84   private boolean isValidPBDEntry;
  85
  86   private boolean cachedPDBExists;
  87
  88   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
  89           AlignmentPanel ap)
  90   {
  91     this.ap = ap;
  92     this.selectedSequence = selectedSeq;
  93     this.selectedSequences = selectedSeqs;
  94     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
  95     init();
  96   }
  97
  98   /**
  99    * Initializes parameters used by the Structure Chooser Panel
 100    */
 101   public void init()
 102   {
 103     if (!Jalview.isHeadlessMode())
 104     {
 105       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 106     }
 107
 108     // ensure a filter option is in force for search
 109     populateFilterComboBox(true, cachedPDBExists);
 110     Thread discoverPDBStructuresThread = new Thread(new Runnable()
 111     {
 112       @Override
 113       public void run()
 114       {
 115         long startTime = System.currentTimeMillis();
 116         updateProgressIndicator(MessageManager
 117                 .getString("status.loading_cached_pdb_entries"), startTime);
 118         loadLocalCachedPDBEntries();
 119         updateProgressIndicator(null, startTime);
 120         updateProgressIndicator(MessageManager.getString(
 121                 "status.searching_for_pdb_structures"), startTime);
 122         fetchStructuresMetaData();
 123         // revise filter options if no results were found
 124         populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
 125         updateProgressIndicator(null, startTime);
 126         mainFrame.setVisible(true);
 127         updateCurrentView();
 128       }
 129     });
 130     discoverPDBStructuresThread.start();
 131   }
 132
 133   /**
 134    * Updates the progress indicator with the specified message
 135    *
 136    * @param message
 137    *          displayed message for the operation
 138    * @param id
 139    *          unique handle for this indicator
 140    */
 141   public void updateProgressIndicator(String message, long id)
 142   {
 143     if (progressIndicator != null)
 144     {
 145       progressIndicator.setProgressBar(message, id);
 146     }
 147   }
 148
 149   /**
 150    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
 151    * selection group
 152    */
 153   public void fetchStructuresMetaData()
 154   {
 155     long startTime = System.currentTimeMillis();
 156     pdbRestCleint = PDBFTSRestClient.getInstance();
 157     Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
 158             .getStructureSummaryFields();
 159
 160     discoveredStructuresSet = new LinkedHashSet<>();
 161     HashSet<String> errors = new HashSet<>();
 162     for (SequenceI seq : selectedSequences)
 163     {
 164       FTSRestRequest pdbRequest = new FTSRestRequest();
 165       pdbRequest.setAllowEmptySeq(false);
 166       pdbRequest.setResponseSize(500);
 167       pdbRequest.setFieldToSearchBy("(");
 168       FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 169               .getSelectedItem());
 170       pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
 171               !chk_invertFilter.isSelected());
 172       pdbRequest.setWantedFields(wantedFields);
 173       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 174       pdbRequest.setAssociatedSequence(seq);
 175       FTSRestResponse resultList;
 176       try
 177       {
 178         resultList = pdbRestCleint.executeRequest(pdbRequest);
 179       } catch (Exception e)
 180       {
 181         e.printStackTrace();
 182         errors.add(e.getMessage());
 183         continue;
 184       }
 185       lastPdbRequest = pdbRequest;
 186       if (resultList.getSearchSummary() != null
 187               && !resultList.getSearchSummary().isEmpty())
 188       {
 189         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 190       }
 191     }
 192
 193     int noOfStructuresFound = 0;
 194     String totalTime = (System.currentTimeMillis() - startTime)
 195             + " milli secs";
 196     if (discoveredStructuresSet != null
 197             && !discoveredStructuresSet.isEmpty())
 198     {
 199       getResultTable().setModel(FTSRestResponse
 200               .getTableModel(lastPdbRequest, 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         JvOptionPane.showMessageDialog(this, errorMsg.toString(),
 218                 MessageManager.getString("label.pdb_web-service_error"),
 219                 JvOptionPane.ERROR_MESSAGE);
 220       }
 221     }
 222   }
 223
 224   public void loadLocalCachedPDBEntries()
 225   {
 226     ArrayList<CachedPDB> entries = new ArrayList<>();
 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<>();
 261
 262     if (seq.getAllPDBEntries() != null
 263             && queryBuilder.length() < MAX_QLENGTH)
 264     {
 265       for (PDBEntry entry : seq.getAllPDBEntries())
 266       {
 267         if (isValidSeqName(entry.getId()))
 268         {
 269           queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase())
 270                   .append(" OR ");
 271           isPDBRefsFound = true;
 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                 && queryBuilder.length() < MAX_QLENGTH)
 282         {
 283           if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
 284           {
 285             queryBuilder.append("uniprot_accession:")
 286                     .append(getDBRefId(dbRef)).append(" OR ");
 287             queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
 288                     .append(" OR ");
 289             isUniProtRefsFound = true;
 290           }
 291           else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
 292           {
 293
 294             queryBuilder.append("pdb_id:")
 295                     .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
 296             isPDBRefsFound = true;
 297           }
 298           else
 299           {
 300             seqRefs.add(getDBRefId(dbRef));
 301           }
 302         }
 303       }
 304     }
 305
 306     if (!isPDBRefsFound && !isUniProtRefsFound)
 307     {
 308       String seqName = seq.getName();
 309       seqName = sanitizeSeqName(seqName);
 310       String[] names = seqName.toLowerCase().split("\\|");
 311       for (String name : names)
 312       {
 313         // System.out.println("Found name : " + name);
 314         name.trim();
 315         if (isValidSeqName(name))
 316         {
 317           seqRefs.add(name);
 318         }
 319       }
 320
 321       for (String seqRef : seqRefs)
 322       {
 323         queryBuilder.append("text:").append(seqRef).append(" OR ");
 324       }
 325     }
 326
 327     int endIndex = queryBuilder.lastIndexOf(" OR ");
 328     if (queryBuilder.toString().length() < 6)
 329     {
 330       return null;
 331     }
 332     String query = queryBuilder.toString().substring(0, endIndex);
 333     return query;
 334   }
 335
 336   /**
 337    * Remove the following special characters from input string +, -, &, !, (, ),
 338    * {, }, [, ], ^, ", ~, *, ?, :, \
 339    *
 340    * @param seqName
 341    * @return
 342    */
 343   static String sanitizeSeqName(String seqName)
 344   {
 345     Objects.requireNonNull(seqName);
 346     return seqName.replaceAll("\\[\\d*\\]", "")
 347             .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
 348   }
 349
 350   /**
 351    * Ensures sequence ref names are not less than 3 characters and does not
 352    * contain a database name
 353    *
 354    * @param seqName
 355    * @return
 356    */
 357   public static boolean isValidSeqName(String seqName)
 358   {
 359     // System.out.println("seqName : " + seqName);
 360     String ignoreList = "pdb,uniprot,swiss-prot";
 361     if (seqName.length() < 3)
 362     {
 363       return false;
 364     }
 365     if (seqName.contains(":"))
 366     {
 367       return false;
 368     }
 369     seqName = seqName.toLowerCase();
 370     for (String ignoredEntry : ignoreList.split(","))
 371     {
 372       if (seqName.contains(ignoredEntry))
 373       {
 374         return false;
 375       }
 376     }
 377     return true;
 378   }
 379
 380   public static String getDBRefId(DBRefEntry dbRef)
 381   {
 382     String ref = dbRef.getAccessionId().replaceAll("GO:", "");
 383     return ref;
 384   }
 385
 386   /**
 387    * Filters a given list of discovered structures based on supplied argument
 388    *
 389    * @param fieldToFilterBy
 390    *          the field to filter by
 391    */
 392   public void filterResultSet(final String fieldToFilterBy)
 393   {
 394     Thread filterThread = new Thread(new Runnable()
 395     {
 396       @Override
 397       public void run()
 398       {
 399         long startTime = System.currentTimeMillis();
 400         pdbRestCleint = PDBFTSRestClient.getInstance();
 401         lbl_loading.setVisible(true);
 402         Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
 403                 .getStructureSummaryFields();
 404         Collection<FTSData> filteredResponse = new HashSet<>();
 405         HashSet<String> errors = new HashSet<>();
 406
 407         for (SequenceI seq : selectedSequences)
 408         {
 409           FTSRestRequest pdbRequest = new FTSRestRequest();
 410           if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
 411           {
 412             pdbRequest.setAllowEmptySeq(false);
 413             pdbRequest.setResponseSize(1);
 414             pdbRequest.setFieldToSearchBy("(");
 415             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 416             pdbRequest.setWantedFields(wantedFields);
 417             pdbRequest.setAssociatedSequence(seq);
 418             pdbRequest.setFacet(true);
 419             pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
 420             pdbRequest.setFacetPivotMinCount(1);
 421           }
 422           else
 423           {
 424             pdbRequest.setAllowEmptySeq(false);
 425             pdbRequest.setResponseSize(1);
 426             pdbRequest.setFieldToSearchBy("(");
 427             pdbRequest.setFieldToSortBy(fieldToFilterBy,
 428                     !chk_invertFilter.isSelected());
 429             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 430             pdbRequest.setWantedFields(wantedFields);
 431             pdbRequest.setAssociatedSequence(seq);
 432           }
 433           FTSRestResponse resultList;
 434           try
 435           {
 436             resultList = pdbRestCleint.executeRequest(pdbRequest);
 437           } catch (Exception e)
 438           {
 439             e.printStackTrace();
 440             errors.add(e.getMessage());
 441             continue;
 442           }
 443           lastPdbRequest = pdbRequest;
 444           if (resultList.getSearchSummary() != null
 445                   && !resultList.getSearchSummary().isEmpty())
 446           {
 447             filteredResponse.addAll(resultList.getSearchSummary());
 448           }
 449         }
 450
 451         String totalTime = (System.currentTimeMillis() - startTime)
 452                 + " milli secs";
 453         if (!filteredResponse.isEmpty())
 454         {
 455           final int filterResponseCount = filteredResponse.size();
 456           Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
 457           reorderedStructuresSet.addAll(filteredResponse);
 458           reorderedStructuresSet.addAll(discoveredStructuresSet);
 459           getResultTable().setModel(FTSRestResponse
 460                   .getTableModel(lastPdbRequest, 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             JvOptionPane.showMessageDialog(null, errorMsg.toString(),
 485                     MessageManager.getString("label.pdb_web-service_error"),
 486                     JvOptionPane.ERROR_MESSAGE);
 487           }
 488         }
 489
 490         lbl_loading.setVisible(false);
 491
 492         validateSelections();
 493       }
 494     });
 495     filterThread.start();
 496   }
 497
 498   /**
 499    * Handles action event for btn_pdbFromFile
 500    */
 501   @Override
 502   public void pdbFromFile_actionPerformed()
 503   {
 504     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 505             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 506     chooser.setFileView(new jalview.io.JalviewFileView());
 507     chooser.setDialogTitle(
 508             MessageManager.formatMessage("label.select_pdb_file_for",
 509                     selectedSequence.getDisplayId(false)));
 510     chooser.setToolTipText(MessageManager.formatMessage(
 511             "label.load_pdb_file_associate_with_sequence",
 512             selectedSequence.getDisplayId(false)));
 513
 514     int value = chooser.showOpenDialog(null);
 515     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
 516     {
 517       selectedPdbFileName = chooser.getSelectedFile().getPath();
 518       jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
 519       validateSelections();
 520     }
 521   }
 522
 523   /**
 524    * Populates the filter combo-box options dynamically depending on discovered
 525    * structures
 526    */
 527   protected void populateFilterComboBox(boolean haveData,
 528           boolean cachedPDBExists)
 529   {
 530     /*
 531      * temporarily suspend the change listener behaviour
 532      */
 533     cmb_filterOption.removeItemListener(this);
 534
 535     cmb_filterOption.removeAllItems();
 536     if (haveData)
 537     {
 538       cmb_filterOption.addItem(new FilterOption("Best Quality",
 539               "overall_quality", VIEWS_FILTER, false));
 540       cmb_filterOption.addItem(new FilterOption("Best Resolution",
 541               "resolution", VIEWS_FILTER, false));
 542       cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
 543               "number_of_protein_chains", VIEWS_FILTER, false));
 544       cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
 545               "number_of_bound_molecules", VIEWS_FILTER, false));
 546       cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
 547               "number_of_polymer_residues", VIEWS_FILTER, true));
 548     }
 549     cmb_filterOption.addItem(
 550             new FilterOption("Enter PDB Id", "-", VIEWS_ENTER_ID, false));
 551     cmb_filterOption.addItem(
 552             new FilterOption("From File", "-", VIEWS_FROM_FILE, false));
 553
 554     if (cachedPDBExists)
 555     {
 556       FilterOption cachedOption = new FilterOption("Cached Structures",
 557               "-", VIEWS_LOCAL_PDB, false);
 558       cmb_filterOption.addItem(cachedOption);
 559       cmb_filterOption.setSelectedItem(cachedOption);
 560     }
 561
 562     cmb_filterOption.addItemListener(this);
 563   }
 564
 565   /**
 566    * Updates the displayed view based on the selected filter option
 567    */
 568   protected void updateCurrentView()
 569   {
 570     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 571             .getSelectedItem());
 572     layout_switchableViews.show(pnl_switchableViews,
 573             selectedFilterOpt.getView());
 574     String filterTitle = mainFrame.getTitle();
 575     mainFrame.setTitle(frameTitle);
 576     chk_invertFilter.setVisible(false);
 577     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 578     {
 579       mainFrame.setTitle(filterTitle);
 580       chk_invertFilter.setVisible(true);
 581       filterResultSet(selectedFilterOpt.getValue());
 582     }
 583     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 584             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 585     {
 586       mainFrame.setTitle(MessageManager
 587               .getString("label.structure_chooser_manual_association"));
 588       idInputAssSeqPanel.loadCmbAssSeq();
 589       fileChooserAssSeqPanel.loadCmbAssSeq();
 590     }
 591     validateSelections();
 592   }
 593
 594   /**
 595    * Validates user selection and activates the view button if all parameters
 596    * are correct
 597    */
 598   @Override
 599   public void validateSelections()
 600   {
 601     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 602             .getSelectedItem());
 603     btn_view.setEnabled(false);
 604     String currentView = selectedFilterOpt.getView();
 605     if (currentView == VIEWS_FILTER)
 606     {
 607       if (getResultTable().getSelectedRows().length > 0)
 608       {
 609         btn_view.setEnabled(true);
 610       }
 611     }
 612     else if (currentView == VIEWS_LOCAL_PDB)
 613     {
 614       if (tbl_local_pdb.getSelectedRows().length > 0)
 615       {
 616         btn_view.setEnabled(true);
 617       }
 618     }
 619     else if (currentView == VIEWS_ENTER_ID)
 620     {
 621       validateAssociationEnterPdb();
 622     }
 623     else if (currentView == VIEWS_FROM_FILE)
 624     {
 625       validateAssociationFromFile();
 626     }
 627   }
 628
 629   /**
 630    * Validates inputs from the Manual PDB entry panel
 631    */
 632   public void validateAssociationEnterPdb()
 633   {
 634     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 635             .getCmb_assSeq().getSelectedItem();
 636     lbl_pdbManualFetchStatus.setIcon(errorImage);
 637     lbl_pdbManualFetchStatus.setToolTipText("");
 638     if (txt_search.getText().length() > 0)
 639     {
 640       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
 641               MessageManager.formatMessage("info.no_pdb_entry_found_for",
 642                       txt_search.getText())));
 643     }
 644
 645     if (errorWarning.length() > 0)
 646     {
 647       lbl_pdbManualFetchStatus.setIcon(warningImage);
 648       lbl_pdbManualFetchStatus.setToolTipText(
 649               JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
 650     }
 651
 652     if (selectedSequences.length == 1 || !assSeqOpt.getName()
 653             .equalsIgnoreCase("-Select Associated Seq-"))
 654     {
 655       txt_search.setEnabled(true);
 656       if (isValidPBDEntry)
 657       {
 658         btn_view.setEnabled(true);
 659         lbl_pdbManualFetchStatus.setToolTipText("");
 660         lbl_pdbManualFetchStatus.setIcon(goodImage);
 661       }
 662     }
 663     else
 664     {
 665       txt_search.setEnabled(false);
 666       lbl_pdbManualFetchStatus.setIcon(errorImage);
 667     }
 668   }
 669
 670   /**
 671    * Validates inputs for the manual PDB file selection options
 672    */
 673   public void validateAssociationFromFile()
 674   {
 675     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
 676             .getCmb_assSeq().getSelectedItem();
 677     lbl_fromFileStatus.setIcon(errorImage);
 678     if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
 679             .getName().equalsIgnoreCase("-Select Associated Seq-")))
 680     {
 681       btn_pdbFromFile.setEnabled(true);
 682       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
 683       {
 684         btn_view.setEnabled(true);
 685         lbl_fromFileStatus.setIcon(goodImage);
 686       }
 687     }
 688     else
 689     {
 690       btn_pdbFromFile.setEnabled(false);
 691       lbl_fromFileStatus.setIcon(errorImage);
 692     }
 693   }
 694
 695   @Override
 696   public void cmbAssSeqStateChanged()
 697   {
 698     validateSelections();
 699   }
 700
 701   /**
 702    * Handles the state change event for the 'filter' combo-box and 'invert'
 703    * check-box
 704    */
 705   @Override
 706   protected void stateChanged(ItemEvent e)
 707   {
 708     if (e.getSource() instanceof JCheckBox)
 709     {
 710       updateCurrentView();
 711     }
 712     else
 713     {
 714       if (e.getStateChange() == ItemEvent.SELECTED)
 715       {
 716         updateCurrentView();
 717       }
 718     }
 719
 720   }
 721
 722   /**
 723    * Handles action event for btn_ok
 724    */
 725   @Override
 726   public void ok_ActionPerformed()
 727   {
 728     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 729
 730     final int preferredHeight = pnl_filter.getHeight();
 731
 732     new Thread(new Runnable()
 733     {
 734       @Override
 735       public void run()
 736       {
 737         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 738                 .getSelectedItem());
 739         String currentView = selectedFilterOpt.getView();
 740         if (currentView == VIEWS_FILTER)
 741         {
 742           int pdbIdColIndex = getResultTable().getColumn("PDB Id")
 743                   .getModelIndex();
 744           int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
 745                   .getModelIndex();
 746           int[] selectedRows = getResultTable().getSelectedRows();
 747           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 748           int count = 0;
 749           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 750           for (int row : selectedRows)
 751           {
 752             String pdbIdStr = getResultTable()
 753                     .getValueAt(row, pdbIdColIndex).toString();
 754             SequenceI selectedSeq = (SequenceI) getResultTable()
 755                     .getValueAt(row, refSeqColIndex);
 756             selectedSeqsToView.add(selectedSeq);
 757             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
 758             if (pdbEntry == null)
 759             {
 760               pdbEntry = getFindEntry(pdbIdStr,
 761                       selectedSeq.getAllPDBEntries());
 762             }
 763
 764             if (pdbEntry == null)
 765             {
 766               pdbEntry = new PDBEntry();
 767               pdbEntry.setId(pdbIdStr);
 768               pdbEntry.setType(PDBEntry.Type.PDB);
 769               selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
 770             }
 771             pdbEntriesToView[count++] = pdbEntry;
 772           }
 773           SequenceI[] selectedSeqs = selectedSeqsToView
 774                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 775           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
 776         }
 777         else if (currentView == VIEWS_LOCAL_PDB)
 778         {
 779           int[] selectedRows = tbl_local_pdb.getSelectedRows();
 780           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 781           int count = 0;
 782           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
 783                   .getModelIndex();
 784           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
 785                   .getModelIndex();
 786           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 787           for (int row : selectedRows)
 788           {
 789             PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
 790                     pdbIdColIndex);
 791             pdbEntriesToView[count++] = pdbEntry;
 792             SequenceI selectedSeq = (SequenceI) tbl_local_pdb
 793                     .getValueAt(row, refSeqColIndex);
 794             selectedSeqsToView.add(selectedSeq);
 795           }
 796           SequenceI[] selectedSeqs = selectedSeqsToView
 797                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 798           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
 799         }
 800         else if (currentView == VIEWS_ENTER_ID)
 801         {
 802           SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
 803                   .getCmb_assSeq().getSelectedItem()).getSequence();
 804           if (userSelectedSeq != null)
 805           {
 806             selectedSequence = userSelectedSeq;
 807           }
 808           String pdbIdStr = txt_search.getText();
 809           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
 810           if (pdbEntry == null)
 811           {
 812             pdbEntry = new PDBEntry();
 813             if (pdbIdStr.split(":").length > 1)
 814             {
 815               pdbEntry.setId(pdbIdStr.split(":")[0]);
 816               pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
 817             }
 818             else
 819             {
 820               pdbEntry.setId(pdbIdStr);
 821             }
 822             pdbEntry.setType(PDBEntry.Type.PDB);
 823             selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
 824           }
 825
 826           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
 827           launchStructureViewer(ssm, pdbEntriesToView, ap,
 828                   new SequenceI[]
 829                   { selectedSequence });
 830         }
 831         else if (currentView == VIEWS_FROM_FILE)
 832         {
 833           SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
 834                   .getCmb_assSeq().getSelectedItem()).getSequence();
 835           if (userSelectedSeq != null)
 836           {
 837             selectedSequence = userSelectedSeq;
 838           }
 839           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 840                   .associatePdbWithSeq(selectedPdbFileName,
 841                           DataSourceType.FILE, selectedSequence, true,
 842                           Desktop.instance);
 843
 844           launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
 845                   new SequenceI[]
 846                   { selectedSequence });
 847         }
 848         closeAction(preferredHeight);
 849         mainFrame.dispose();
 850       }
 851     }).start();
 852   }
 853
 854   private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
 855   {
 856     Objects.requireNonNull(id);
 857     Objects.requireNonNull(pdbEntries);
 858     PDBEntry foundEntry = null;
 859     for (PDBEntry entry : pdbEntries)
 860     {
 861       if (entry.getId().equalsIgnoreCase(id))
 862       {
 863         return entry;
 864       }
 865     }
 866     return foundEntry;
 867   }
 868
 869   private void launchStructureViewer(StructureSelectionManager ssm,
 870           final PDBEntry[] pdbEntriesToView,
 871           final AlignmentPanel alignPanel, SequenceI[] sequences)
 872   {
 873     long progressId = sequences.hashCode();
 874     setProgressBar(MessageManager
 875             .getString("status.launching_3d_structure_viewer"), progressId);
 876     final StructureViewer sViewer = new StructureViewer(ssm);
 877     setProgressBar(null, progressId);
 878
 879     if (SiftsSettings.isMapWithSifts())
 880     {
 881       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
 882       int p = 0;
 883       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
 884       // real PDB ID. For moment, we can also safely do this if there is already
 885       // a known mapping between the PDBEntry and the sequence.
 886       for (SequenceI seq : sequences)
 887       {
 888         PDBEntry pdbe = pdbEntriesToView[p++];
 889         if (pdbe != null && pdbe.getFile() != null)
 890         {
 891           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
 892           if (smm != null && smm.length > 0)
 893           {
 894             for (StructureMapping sm : smm)
 895             {
 896               if (sm.getSequence() == seq)
 897               {
 898                 continue;
 899               }
 900             }
 901           }
 902         }
 903         if (seq.getPrimaryDBRefs().size() == 0)
 904         {
 905           seqsWithoutSourceDBRef.add(seq);
 906           continue;
 907         }
 908       }
 909       if (!seqsWithoutSourceDBRef.isEmpty())
 910       {
 911         int y = seqsWithoutSourceDBRef.size();
 912         setProgressBar(MessageManager.formatMessage(
 913                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
 914                 y), progressId);
 915         SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
 916         int x = 0;
 917         for (SequenceI fSeq : seqsWithoutSourceDBRef)
 918         {
 919           seqWithoutSrcDBRef[x++] = fSeq;
 920         }
 921
 922         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
 923         dbRefFetcher.fetchDBRefs(true);
 924
 925         setProgressBar("Fetch complete.", progressId); // todo i18n
 926       }
 927     }
 928     if (pdbEntriesToView.length > 1)
 929     {
 930       setProgressBar(MessageManager.getString(
 931               "status.fetching_3d_structures_for_selected_entries"),
 932               progressId);
 933       sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
 934     }
 935     else
 936     {
 937       setProgressBar(MessageManager.formatMessage(
 938               "status.fetching_3d_structures_for",
 939               pdbEntriesToView[0].getId()),progressId);
 940       sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
 941     }
 942     setProgressBar(null, progressId);
 943   }
 944
 945   /**
 946    * Populates the combo-box used in associating manually fetched structures to
 947    * a unique sequence when more than one sequence selection is made.
 948    */
 949   @Override
 950   public void populateCmbAssociateSeqOptions(
 951           JComboBox<AssociateSeqOptions> cmb_assSeq,
 952           JLabel lbl_associateSeq)
 953   {
 954     cmb_assSeq.removeAllItems();
 955     cmb_assSeq.addItem(
 956             new AssociateSeqOptions("-Select Associated Seq-", null));
 957     lbl_associateSeq.setVisible(false);
 958     if (selectedSequences.length > 1)
 959     {
 960       for (SequenceI seq : selectedSequences)
 961       {
 962         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
 963       }
 964     }
 965     else
 966     {
 967       String seqName = selectedSequence.getDisplayId(false);
 968       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
 969       lbl_associateSeq.setText(seqName);
 970       lbl_associateSeq.setVisible(true);
 971       cmb_assSeq.setVisible(false);
 972     }
 973   }
 974
 975   public boolean isStructuresDiscovered()
 976   {
 977     return discoveredStructuresSet != null
 978             && !discoveredStructuresSet.isEmpty();
 979   }
 980
 981   public Collection<FTSData> getDiscoveredStructuresSet()
 982   {
 983     return discoveredStructuresSet;
 984   }
 985
 986   @Override
 987   protected void txt_search_ActionPerformed()
 988   {
 989     new Thread()
 990     {
 991       @Override
 992       public void run()
 993       {
 994         errorWarning.setLength(0);
 995         isValidPBDEntry = false;
 996         if (txt_search.getText().length() > 0)
 997         {
 998           String searchTerm = txt_search.getText().toLowerCase();
 999           searchTerm = searchTerm.split(":")[0];
1000           // System.out.println(">>>>> search term : " + searchTerm);
1001           List<FTSDataColumnI> wantedFields = new ArrayList<>();
1002           FTSRestRequest pdbRequest = new FTSRestRequest();
1003           pdbRequest.setAllowEmptySeq(false);
1004           pdbRequest.setResponseSize(1);
1005           pdbRequest.setFieldToSearchBy("(pdb_id:");
1006           pdbRequest.setWantedFields(wantedFields);
1007           pdbRequest.setSearchTerm(searchTerm + ")");
1008           pdbRequest.setAssociatedSequence(selectedSequence);
1009           pdbRestCleint = PDBFTSRestClient.getInstance();
1010           wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
1011           FTSRestResponse resultList;
1012           try
1013           {
1014             resultList = pdbRestCleint.executeRequest(pdbRequest);
1015           } catch (Exception e)
1016           {
1017             errorWarning.append(e.getMessage());
1018             return;
1019           } finally
1020           {
1021             validateSelections();
1022           }
1023           if (resultList.getSearchSummary() != null
1024                   && resultList.getSearchSummary().size() > 0)
1025           {
1026             isValidPBDEntry = true;
1027           }
1028         }
1029         validateSelections();
1030       }
1031     }.start();
1032   }
1033
1034   @Override
1035   public void tabRefresh()
1036   {
1037     if (selectedSequences != null)
1038     {
1039       Thread refreshThread = new Thread(new Runnable()
1040       {
1041         @Override
1042         public void run()
1043         {
1044           fetchStructuresMetaData();
1045           filterResultSet(
1046                   ((FilterOption) cmb_filterOption.getSelectedItem())
1047                           .getValue());
1048         }
1049       });
1050       refreshThread.start();
1051     }
1052   }
1053
1054   public class PDBEntryTableModel extends AbstractTableModel
1055   {
1056     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1057         "File" };
1058
1059     private List<CachedPDB> pdbEntries;
1060
1061     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1062     {
1063       this.pdbEntries = new ArrayList<>(pdbEntries);
1064     }
1065
1066     @Override
1067     public String getColumnName(int columnIndex)
1068     {
1069       return columns[columnIndex];
1070     }
1071
1072     @Override
1073     public int getRowCount()
1074     {
1075       return pdbEntries.size();
1076     }
1077
1078     @Override
1079     public int getColumnCount()
1080     {
1081       return columns.length;
1082     }
1083
1084     @Override
1085     public boolean isCellEditable(int row, int column)
1086     {
1087       return false;
1088     }
1089
1090     @Override
1091     public Object getValueAt(int rowIndex, int columnIndex)
1092     {
1093       Object value = "??";
1094       CachedPDB entry = pdbEntries.get(rowIndex);
1095       switch (columnIndex)
1096       {
1097       case 0:
1098         value = entry.getSequence();
1099         break;
1100       case 1:
1101         value = entry.getPdbEntry();
1102         break;
1103       case 2:
1104         value = entry.getPdbEntry().getChainCode() == null ? "_"
1105                 : entry.getPdbEntry().getChainCode();
1106         break;
1107       case 3:
1108         value = entry.getPdbEntry().getType();
1109         break;
1110       case 4:
1111         value = entry.getPdbEntry().getFile();
1112         break;
1113       }
1114       return value;
1115     }
1116
1117     @Override
1118     public Class<?> getColumnClass(int columnIndex)
1119     {
1120       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1121     }
1122
1123     public CachedPDB getPDBEntryAt(int row)
1124     {
1125       return pdbEntries.get(row);
1126     }
1127
1128   }
1129
1130   private class CachedPDB
1131   {
1132     private SequenceI sequence;
1133
1134     private PDBEntry pdbEntry;
1135
1136     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1137     {
1138       this.sequence = sequence;
1139       this.pdbEntry = pdbEntry;
1140     }
1141
1142     public SequenceI getSequence()
1143     {
1144       return sequence;
1145     }
1146
1147     public PDBEntry getPdbEntry()
1148     {
1149       return pdbEntry;
1150     }
1151
1152   }
1153
1154   private IProgressIndicator progressBar;
1155
1156   @Override
1157   public void setProgressBar(String message, long id)
1158   {
1159     progressBar.setProgressBar(message, id);
1160   }
1161
1162   @Override
1163   public void registerHandler(long id, IProgressIndicatorHandler handler)
1164   {
1165     progressBar.registerHandler(id, handler);
1166   }
1167
1168   @Override
1169   public boolean operationInProgress()
1170   {
1171     return progressBar.operationInProgress();
1172   }
1173 }