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