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 cachedPDBExist)
 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(
 539               MessageManager.getString("label.best_quality"),
 540               "overall_quality", VIEWS_FILTER, false));
 541       cmb_filterOption.addItem(new FilterOption(
 542               MessageManager.getString("label.best_resolution"),
 543               "resolution", VIEWS_FILTER, false));
 544       cmb_filterOption.addItem(new FilterOption(
 545               MessageManager.getString("label.most_protein_chain"),
 546               "number_of_protein_chains", VIEWS_FILTER, false));
 547       cmb_filterOption.addItem(new FilterOption(
 548               MessageManager.getString("label.most_bound_molecules"),
 549               "number_of_bound_molecules", VIEWS_FILTER, false));
 550       cmb_filterOption.addItem(new FilterOption(
 551               MessageManager.getString("label.most_polymer_residues"),
 552               "number_of_polymer_residues", VIEWS_FILTER, true));
 553     }
 554     cmb_filterOption.addItem(
 555             new FilterOption(MessageManager.getString("label.enter_pdb_id"),
 556                     "-", VIEWS_ENTER_ID, false));
 557     cmb_filterOption.addItem(
 558             new FilterOption(MessageManager.getString("label.from_file"),
 559                     "-", VIEWS_FROM_FILE, false));
 560
 561     if (cachedPDBExist)
 562     {
 563       FilterOption cachedOption = new FilterOption(
 564               MessageManager.getString("label.cached_structures"),
 565               "-", VIEWS_LOCAL_PDB, false);
 566       cmb_filterOption.addItem(cachedOption);
 567       cmb_filterOption.setSelectedItem(cachedOption);
 568     }
 569
 570     cmb_filterOption.addItemListener(this);
 571   }
 572
 573   /**
 574    * Updates the displayed view based on the selected filter option
 575    */
 576   protected void updateCurrentView()
 577   {
 578     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 579             .getSelectedItem());
 580     layout_switchableViews.show(pnl_switchableViews,
 581             selectedFilterOpt.getView());
 582     String filterTitle = mainFrame.getTitle();
 583     mainFrame.setTitle(frameTitle);
 584     chk_invertFilter.setVisible(false);
 585     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 586     {
 587       mainFrame.setTitle(filterTitle);
 588       chk_invertFilter.setVisible(true);
 589       filterResultSet(selectedFilterOpt.getValue());
 590     }
 591     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 592             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 593     {
 594       mainFrame.setTitle(MessageManager
 595               .getString("label.structure_chooser_manual_association"));
 596       idInputAssSeqPanel.loadCmbAssSeq();
 597       fileChooserAssSeqPanel.loadCmbAssSeq();
 598     }
 599     validateSelections();
 600   }
 601
 602   /**
 603    * Validates user selection and activates the view button if all parameters
 604    * are correct
 605    */
 606   @Override
 607   public void validateSelections()
 608   {
 609     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 610             .getSelectedItem());
 611     btn_view.setEnabled(false);
 612     String currentView = selectedFilterOpt.getView();
 613     if (currentView == VIEWS_FILTER)
 614     {
 615       if (getResultTable().getSelectedRows().length > 0)
 616       {
 617         btn_view.setEnabled(true);
 618       }
 619     }
 620     else if (currentView == VIEWS_LOCAL_PDB)
 621     {
 622       if (tbl_local_pdb.getSelectedRows().length > 0)
 623       {
 624         btn_view.setEnabled(true);
 625       }
 626     }
 627     else if (currentView == VIEWS_ENTER_ID)
 628     {
 629       validateAssociationEnterPdb();
 630     }
 631     else if (currentView == VIEWS_FROM_FILE)
 632     {
 633       validateAssociationFromFile();
 634     }
 635   }
 636
 637   /**
 638    * Validates inputs from the Manual PDB entry panel
 639    */
 640   public void validateAssociationEnterPdb()
 641   {
 642     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 643             .getCmb_assSeq().getSelectedItem();
 644     lbl_pdbManualFetchStatus.setIcon(errorImage);
 645     lbl_pdbManualFetchStatus.setToolTipText("");
 646     if (txt_search.getText().length() > 0)
 647     {
 648       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
 649               MessageManager.formatMessage("info.no_pdb_entry_found_for",
 650                       txt_search.getText())));
 651     }
 652
 653     if (errorWarning.length() > 0)
 654     {
 655       lbl_pdbManualFetchStatus.setIcon(warningImage);
 656       lbl_pdbManualFetchStatus.setToolTipText(
 657               JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
 658     }
 659
 660     if (selectedSequences.length == 1 || !assSeqOpt.getName()
 661             .equalsIgnoreCase("-Select Associated Seq-"))
 662     {
 663       txt_search.setEnabled(true);
 664       if (isValidPBDEntry)
 665       {
 666         btn_view.setEnabled(true);
 667         lbl_pdbManualFetchStatus.setToolTipText("");
 668         lbl_pdbManualFetchStatus.setIcon(goodImage);
 669       }
 670     }
 671     else
 672     {
 673       txt_search.setEnabled(false);
 674       lbl_pdbManualFetchStatus.setIcon(errorImage);
 675     }
 676   }
 677
 678   /**
 679    * Validates inputs for the manual PDB file selection options
 680    */
 681   public void validateAssociationFromFile()
 682   {
 683     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
 684             .getCmb_assSeq().getSelectedItem();
 685     lbl_fromFileStatus.setIcon(errorImage);
 686     if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
 687             .getName().equalsIgnoreCase("-Select Associated Seq-")))
 688     {
 689       btn_pdbFromFile.setEnabled(true);
 690       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
 691       {
 692         btn_view.setEnabled(true);
 693         lbl_fromFileStatus.setIcon(goodImage);
 694       }
 695     }
 696     else
 697     {
 698       btn_pdbFromFile.setEnabled(false);
 699       lbl_fromFileStatus.setIcon(errorImage);
 700     }
 701   }
 702
 703   @Override
 704   public void cmbAssSeqStateChanged()
 705   {
 706     validateSelections();
 707   }
 708
 709   /**
 710    * Handles the state change event for the 'filter' combo-box and 'invert'
 711    * check-box
 712    */
 713   @Override
 714   protected void stateChanged(ItemEvent e)
 715   {
 716     if (e.getSource() instanceof JCheckBox)
 717     {
 718       updateCurrentView();
 719     }
 720     else
 721     {
 722       if (e.getStateChange() == ItemEvent.SELECTED)
 723       {
 724         updateCurrentView();
 725       }
 726     }
 727
 728   }
 729
 730   /**
 731    * Handles action event for btn_ok
 732    */
 733   @Override
 734   public void ok_ActionPerformed()
 735   {
 736     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 737
 738     final int preferredHeight = pnl_filter.getHeight();
 739
 740     new Thread(new Runnable()
 741     {
 742       @Override
 743       public void run()
 744       {
 745         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 746                 .getSelectedItem());
 747         String currentView = selectedFilterOpt.getView();
 748         JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
 749                 : tbl_local_pdb;
 750
 751         if (currentView == VIEWS_FILTER)
 752         {
 753           int pdbIdColIndex = restable.getColumn("PDB Id")
 754                   .getModelIndex();
 755           int refSeqColIndex = restable.getColumn("Ref Sequence")
 756                   .getModelIndex();
 757           int[] selectedRows = restable.getSelectedRows();
 758           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 759           int count = 0;
 760           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 761           for (int row : selectedRows)
 762           {
 763             String pdbIdStr = restable
 764                     .getValueAt(row, pdbIdColIndex).toString();
 765             SequenceI selectedSeq = (SequenceI) restable
 766                     .getValueAt(row, refSeqColIndex);
 767             selectedSeqsToView.add(selectedSeq);
 768             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
 769             if (pdbEntry == null)
 770             {
 771               pdbEntry = getFindEntry(pdbIdStr,
 772                       selectedSeq.getAllPDBEntries());
 773             }
 774
 775             if (pdbEntry == null)
 776             {
 777               pdbEntry = new PDBEntry();
 778               pdbEntry.setId(pdbIdStr);
 779               pdbEntry.setType(PDBEntry.Type.PDB);
 780               selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
 781             }
 782             pdbEntriesToView[count++] = pdbEntry;
 783           }
 784           SequenceI[] selectedSeqs = selectedSeqsToView
 785                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 786           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
 787         }
 788         else if (currentView == VIEWS_LOCAL_PDB)
 789         {
 790           int[] selectedRows = tbl_local_pdb.getSelectedRows();
 791           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 792           int count = 0;
 793           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
 794                   .getModelIndex();
 795           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
 796                   .getModelIndex();
 797           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 798           for (int row : selectedRows)
 799           {
 800             PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
 801                     pdbIdColIndex);
 802             pdbEntriesToView[count++] = pdbEntry;
 803             SequenceI selectedSeq = (SequenceI) tbl_local_pdb
 804                     .getValueAt(row, refSeqColIndex);
 805             selectedSeqsToView.add(selectedSeq);
 806           }
 807           SequenceI[] selectedSeqs = selectedSeqsToView
 808                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 809           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
 810         }
 811         else if (currentView == VIEWS_ENTER_ID)
 812         {
 813           SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
 814                   .getCmb_assSeq().getSelectedItem()).getSequence();
 815           if (userSelectedSeq != null)
 816           {
 817             selectedSequence = userSelectedSeq;
 818           }
 819           String pdbIdStr = txt_search.getText();
 820           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
 821           if (pdbEntry == null)
 822           {
 823             pdbEntry = new PDBEntry();
 824             if (pdbIdStr.split(":").length > 1)
 825             {
 826               pdbEntry.setId(pdbIdStr.split(":")[0]);
 827               pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
 828             }
 829             else
 830             {
 831               pdbEntry.setId(pdbIdStr);
 832             }
 833             pdbEntry.setType(PDBEntry.Type.PDB);
 834             selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
 835           }
 836
 837           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
 838           launchStructureViewer(ssm, pdbEntriesToView, ap,
 839                   new SequenceI[]
 840                   { selectedSequence });
 841         }
 842         else if (currentView == VIEWS_FROM_FILE)
 843         {
 844           SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
 845                   .getCmb_assSeq().getSelectedItem()).getSequence();
 846           if (userSelectedSeq != null)
 847           {
 848             selectedSequence = userSelectedSeq;
 849           }
 850           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 851                   .associatePdbWithSeq(selectedPdbFileName,
 852                           DataSourceType.FILE, selectedSequence, true,
 853                           Desktop.instance);
 854
 855           launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
 856                   new SequenceI[]
 857                   { selectedSequence });
 858         }
 859         closeAction(preferredHeight);
 860         mainFrame.dispose();
 861       }
 862     }).start();
 863   }
 864
 865   private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
 866   {
 867     Objects.requireNonNull(id);
 868     Objects.requireNonNull(pdbEntries);
 869     PDBEntry foundEntry = null;
 870     for (PDBEntry entry : pdbEntries)
 871     {
 872       if (entry.getId().equalsIgnoreCase(id))
 873       {
 874         return entry;
 875       }
 876     }
 877     return foundEntry;
 878   }
 879
 880   private void launchStructureViewer(StructureSelectionManager ssm,
 881           final PDBEntry[] pdbEntriesToView,
 882           final AlignmentPanel alignPanel, SequenceI[] sequences)
 883   {
 884     long progressId = sequences.hashCode();
 885     setProgressBar(MessageManager
 886             .getString("status.launching_3d_structure_viewer"), progressId);
 887     final StructureViewer sViewer = new StructureViewer(ssm);
 888     setProgressBar(null, progressId);
 889
 890     if (SiftsSettings.isMapWithSifts())
 891     {
 892       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
 893       int p = 0;
 894       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
 895       // real PDB ID. For moment, we can also safely do this if there is already
 896       // a known mapping between the PDBEntry and the sequence.
 897       for (SequenceI seq : sequences)
 898       {
 899         PDBEntry pdbe = pdbEntriesToView[p++];
 900         if (pdbe != null && pdbe.getFile() != null)
 901         {
 902           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
 903           if (smm != null && smm.length > 0)
 904           {
 905             for (StructureMapping sm : smm)
 906             {
 907               if (sm.getSequence() == seq)
 908               {
 909                 continue;
 910               }
 911             }
 912           }
 913         }
 914         if (seq.getPrimaryDBRefs().size() == 0)
 915         {
 916           seqsWithoutSourceDBRef.add(seq);
 917           continue;
 918         }
 919       }
 920       if (!seqsWithoutSourceDBRef.isEmpty())
 921       {
 922         int y = seqsWithoutSourceDBRef.size();
 923         setProgressBar(MessageManager.formatMessage(
 924                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
 925                 y), progressId);
 926         SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
 927         int x = 0;
 928         for (SequenceI fSeq : seqsWithoutSourceDBRef)
 929         {
 930           seqWithoutSrcDBRef[x++] = fSeq;
 931         }
 932
 933         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
 934         dbRefFetcher.fetchDBRefs(true);
 935
 936         setProgressBar("Fetch complete.", progressId); // todo i18n
 937       }
 938     }
 939     if (pdbEntriesToView.length > 1)
 940     {
 941       setProgressBar(MessageManager.getString(
 942               "status.fetching_3d_structures_for_selected_entries"),
 943               progressId);
 944       sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
 945     }
 946     else
 947     {
 948       setProgressBar(MessageManager.formatMessage(
 949               "status.fetching_3d_structures_for",
 950               pdbEntriesToView[0].getId()),progressId);
 951       sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
 952     }
 953     setProgressBar(null, progressId);
 954   }
 955
 956   /**
 957    * Populates the combo-box used in associating manually fetched structures to
 958    * a unique sequence when more than one sequence selection is made.
 959    */
 960   @Override
 961   public void populateCmbAssociateSeqOptions(
 962           JComboBox<AssociateSeqOptions> cmb_assSeq,
 963           JLabel lbl_associateSeq)
 964   {
 965     cmb_assSeq.removeAllItems();
 966     cmb_assSeq.addItem(
 967             new AssociateSeqOptions("-Select Associated Seq-", null));
 968     lbl_associateSeq.setVisible(false);
 969     if (selectedSequences.length > 1)
 970     {
 971       for (SequenceI seq : selectedSequences)
 972       {
 973         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
 974       }
 975     }
 976     else
 977     {
 978       String seqName = selectedSequence.getDisplayId(false);
 979       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
 980       lbl_associateSeq.setText(seqName);
 981       lbl_associateSeq.setVisible(true);
 982       cmb_assSeq.setVisible(false);
 983     }
 984   }
 985
 986   public boolean isStructuresDiscovered()
 987   {
 988     return discoveredStructuresSet != null
 989             && !discoveredStructuresSet.isEmpty();
 990   }
 991
 992   public Collection<FTSData> getDiscoveredStructuresSet()
 993   {
 994     return discoveredStructuresSet;
 995   }
 996
 997   @Override
 998   protected void txt_search_ActionPerformed()
 999   {
1000     new Thread()
1001     {
1002       @Override
1003       public void run()
1004       {
1005         errorWarning.setLength(0);
1006         isValidPBDEntry = false;
1007         if (txt_search.getText().length() > 0)
1008         {
1009           String searchTerm = txt_search.getText().toLowerCase();
1010           searchTerm = searchTerm.split(":")[0];
1011           // System.out.println(">>>>> search term : " + searchTerm);
1012           List<FTSDataColumnI> wantedFields = new ArrayList<>();
1013           FTSRestRequest pdbRequest = new FTSRestRequest();
1014           pdbRequest.setAllowEmptySeq(false);
1015           pdbRequest.setResponseSize(1);
1016           pdbRequest.setFieldToSearchBy("(pdb_id:");
1017           pdbRequest.setWantedFields(wantedFields);
1018           pdbRequest.setSearchTerm(searchTerm + ")");
1019           pdbRequest.setAssociatedSequence(selectedSequence);
1020           pdbRestCleint = PDBFTSRestClient.getInstance();
1021           wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
1022           FTSRestResponse resultList;
1023           try
1024           {
1025             resultList = pdbRestCleint.executeRequest(pdbRequest);
1026           } catch (Exception e)
1027           {
1028             errorWarning.append(e.getMessage());
1029             return;
1030           } finally
1031           {
1032             validateSelections();
1033           }
1034           if (resultList.getSearchSummary() != null
1035                   && resultList.getSearchSummary().size() > 0)
1036           {
1037             isValidPBDEntry = true;
1038           }
1039         }
1040         validateSelections();
1041       }
1042     }.start();
1043   }
1044
1045   @Override
1046   public void tabRefresh()
1047   {
1048     if (selectedSequences != null)
1049     {
1050       Thread refreshThread = new Thread(new Runnable()
1051       {
1052         @Override
1053         public void run()
1054         {
1055           fetchStructuresMetaData();
1056           filterResultSet(
1057                   ((FilterOption) cmb_filterOption.getSelectedItem())
1058                           .getValue());
1059         }
1060       });
1061       refreshThread.start();
1062     }
1063   }
1064
1065   public class PDBEntryTableModel extends AbstractTableModel
1066   {
1067     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1068         "File" };
1069
1070     private List<CachedPDB> pdbEntries;
1071
1072     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1073     {
1074       this.pdbEntries = new ArrayList<>(pdbEntries);
1075     }
1076
1077     @Override
1078     public String getColumnName(int columnIndex)
1079     {
1080       return columns[columnIndex];
1081     }
1082
1083     @Override
1084     public int getRowCount()
1085     {
1086       return pdbEntries.size();
1087     }
1088
1089     @Override
1090     public int getColumnCount()
1091     {
1092       return columns.length;
1093     }
1094
1095     @Override
1096     public boolean isCellEditable(int row, int column)
1097     {
1098       return false;
1099     }
1100
1101     @Override
1102     public Object getValueAt(int rowIndex, int columnIndex)
1103     {
1104       Object value = "??";
1105       CachedPDB entry = pdbEntries.get(rowIndex);
1106       switch (columnIndex)
1107       {
1108       case 0:
1109         value = entry.getSequence();
1110         break;
1111       case 1:
1112         value = entry.getPdbEntry();
1113         break;
1114       case 2:
1115         value = entry.getPdbEntry().getChainCode() == null ? "_"
1116                 : entry.getPdbEntry().getChainCode();
1117         break;
1118       case 3:
1119         value = entry.getPdbEntry().getType();
1120         break;
1121       case 4:
1122         value = entry.getPdbEntry().getFile();
1123         break;
1124       }
1125       return value;
1126     }
1127
1128     @Override
1129     public Class<?> getColumnClass(int columnIndex)
1130     {
1131       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1132     }
1133
1134     public CachedPDB getPDBEntryAt(int row)
1135     {
1136       return pdbEntries.get(row);
1137     }
1138
1139   }
1140
1141   private class CachedPDB
1142   {
1143     private SequenceI sequence;
1144
1145     private PDBEntry pdbEntry;
1146
1147     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1148     {
1149       this.sequence = sequence;
1150       this.pdbEntry = pdbEntry;
1151     }
1152
1153     public SequenceI getSequence()
1154     {
1155       return sequence;
1156     }
1157
1158     public PDBEntry getPdbEntry()
1159     {
1160       return pdbEntry;
1161     }
1162
1163   }
1164
1165   private IProgressIndicator progressBar;
1166
1167   @Override
1168   public void setProgressBar(String message, long id)
1169   {
1170     progressBar.setProgressBar(message, id);
1171   }
1172
1173   @Override
1174   public void registerHandler(long id, IProgressIndicatorHandler handler)
1175   {
1176     progressBar.registerHandler(id, handler);
1177   }
1178
1179   @Override
1180   public boolean operationInProgress()
1181   {
1182     return progressBar.operationInProgress();
1183   }
1184 }