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.api.structures.JalviewStructureDisplayI;
  25 import jalview.bin.Cache;
  26 import jalview.bin.Jalview;
  27 import jalview.datamodel.DBRefEntry;
  28 import jalview.datamodel.DBRefSource;
  29 import jalview.datamodel.PDBEntry;
  30 import jalview.datamodel.SequenceI;
  31 import jalview.fts.api.FTSData;
  32 import jalview.fts.api.FTSDataColumnI;
  33 import jalview.fts.api.FTSRestClientI;
  34 import jalview.fts.core.FTSRestRequest;
  35 import jalview.fts.core.FTSRestResponse;
  36 import jalview.fts.service.pdb.PDBFTSRestClient;
  37 import jalview.io.DataSourceType;
  38 import jalview.jbgui.GStructureChooser;
  39 import jalview.structure.StructureMapping;
  40 import jalview.structure.StructureSelectionManager;
  41 import jalview.util.MessageManager;
  42 import jalview.ws.DBRefFetcher;
  43 import jalview.ws.sifts.SiftsSettings;
  44
  45 import java.awt.event.ItemEvent;
  46 import java.util.ArrayList;
  47 import java.util.Collection;
  48 import java.util.HashSet;
  49 import java.util.LinkedHashSet;
  50 import java.util.List;
  51 import java.util.Objects;
  52 import java.util.Set;
  53 import java.util.Vector;
  54
  55 import javax.swing.JCheckBox;
  56 import javax.swing.JComboBox;
  57 import javax.swing.JLabel;
  58 import javax.swing.JTable;
  59 import javax.swing.SwingUtilities;
  60 import javax.swing.table.AbstractTableModel;
  61
  62 /**
  63  * Provides the behaviors for the Structure chooser Panel
  64  *
  65  * @author tcnofoegbu
  66  *
  67  */
  68 @SuppressWarnings("serial")
  69 public class StructureChooser extends GStructureChooser
  70         implements IProgressIndicator
  71 {
  72   private static int MAX_QLENGTH = 7820;
  73
  74   private SequenceI selectedSequence;
  75
  76   private SequenceI[] selectedSequences;
  77
  78   private IProgressIndicator progressIndicator;
  79
  80   private Collection<FTSData> discoveredStructuresSet;
  81
  82   private FTSRestRequest lastPdbRequest;
  83
  84   private FTSRestClientI pdbRestCleint;
  85
  86   private String selectedPdbFileName;
  87
  88   private boolean isValidPBDEntry;
  89
  90   private boolean cachedPDBExists;
  91
  92   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
  93           AlignmentPanel ap)
  94   {
  95     this.ap = ap;
  96     this.selectedSequence = selectedSeq;
  97     this.selectedSequences = selectedSeqs;
  98     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
  99     init();
 100   }
 101
 102   /**
 103    * Initializes parameters used by the Structure Chooser Panel
 104    */
 105   public void init()
 106   {
 107     if (!Jalview.isHeadlessMode())
 108     {
 109       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 110     }
 111
 112     chk_superpose.setSelected(Cache.getDefault("AUTOSUPERIMPOSE", true));
 113
 114     // ensure a filter option is in force for search
 115     populateFilterComboBox(true, cachedPDBExists);
 116     Thread discoverPDBStructuresThread = new Thread(new Runnable()
 117     {
 118       @Override
 119       public void run()
 120       {
 121         long startTime = System.currentTimeMillis();
 122         updateProgressIndicator(MessageManager
 123                 .getString("status.loading_cached_pdb_entries"), startTime);
 124         loadLocalCachedPDBEntries();
 125         updateProgressIndicator(null, startTime);
 126         updateProgressIndicator(MessageManager.getString(
 127                 "status.searching_for_pdb_structures"), startTime);
 128         fetchStructuresMetaData();
 129         // revise filter options if no results were found
 130         populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
 131         discoverStructureViews();
 132         updateProgressIndicator(null, startTime);
 133         mainFrame.setVisible(true);
 134         updateCurrentView();
 135       }
 136     });
 137     discoverPDBStructuresThread.start();
 138   }
 139
 140   private void discoverStructureViews()
 141   {
 142     if (Desktop.instance != null)
 143     {
 144       targetView.removeAllItems();
 145       targetView.addItem(
 146               new StructureViewer(ap.getStructureSelectionManager()));
 147       if (lastTargetedView != null && !lastTargetedView.isVisible())
 148       {
 149         lastTargetedView = null;
 150       }
 151       int linkedViewsAt = 1;
 152       for (StructureViewerBase view : Desktop.instance
 153               .getStructureViewers(null, null))
 154       {
 155         StructureViewer viewHandler = (lastTargetedView != null
 156                 && lastTargetedView.sview == view) ? lastTargetedView
 157                         : StructureViewer.reconfigure(view);
 158
 159         if (view.isLinkedWith(ap))
 160         {
 161           targetView.insertItemAt(viewHandler,
 162                   linkedViewsAt++);
 163         }
 164         else
 165         {
 166           targetView.addItem(viewHandler);
 167         }
 168       }
 169       targetView.setVisible(targetView.getItemCount() > 1);
 170
 171       // finally, restore last targeted view by default.
 172       if (lastTargetedView != null)
 173       {
 174         targetView.setSelectedItem(lastTargetedView);
 175       }
 176     }
 177   }
 178
 179   private static StructureViewer lastTargetedView = null;
 180
 181   /**
 182    * Updates the progress indicator with the specified message
 183    *
 184    * @param message
 185    *          displayed message for the operation
 186    * @param id
 187    *          unique handle for this indicator
 188    */
 189   public void updateProgressIndicator(String message, long id)
 190   {
 191     if (progressIndicator != null)
 192     {
 193       progressIndicator.setProgressBar(message, id);
 194     }
 195   }
 196
 197   /**
 198    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
 199    * selection group
 200    */
 201   public void fetchStructuresMetaData()
 202   {
 203     long startTime = System.currentTimeMillis();
 204     pdbRestCleint = PDBFTSRestClient.getInstance();
 205     Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
 206             .getStructureSummaryFields();
 207
 208     discoveredStructuresSet = new LinkedHashSet<>();
 209     HashSet<String> errors = new HashSet<>();
 210     for (SequenceI seq : selectedSequences)
 211     {
 212       FTSRestRequest pdbRequest = new FTSRestRequest();
 213       pdbRequest.setAllowEmptySeq(false);
 214       pdbRequest.setResponseSize(500);
 215       pdbRequest.setFieldToSearchBy("(");
 216       FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 217               .getSelectedItem());
 218       pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
 219               !chk_invertFilter.isSelected());
 220       pdbRequest.setWantedFields(wantedFields);
 221       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 222       pdbRequest.setAssociatedSequence(seq);
 223       FTSRestResponse resultList;
 224       try
 225       {
 226         resultList = pdbRestCleint.executeRequest(pdbRequest);
 227       } catch (Exception e)
 228       {
 229         e.printStackTrace();
 230         errors.add(e.getMessage());
 231         continue;
 232       }
 233       lastPdbRequest = pdbRequest;
 234       if (resultList.getSearchSummary() != null
 235               && !resultList.getSearchSummary().isEmpty())
 236       {
 237         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 238       }
 239     }
 240
 241     int noOfStructuresFound = 0;
 242     String totalTime = (System.currentTimeMillis() - startTime)
 243             + " milli secs";
 244     if (discoveredStructuresSet != null
 245             && !discoveredStructuresSet.isEmpty())
 246     {
 247       getResultTable().setModel(FTSRestResponse
 248               .getTableModel(lastPdbRequest, discoveredStructuresSet));
 249       noOfStructuresFound = discoveredStructuresSet.size();
 250       mainFrame.setTitle(MessageManager.formatMessage(
 251               "label.structure_chooser_no_of_structures",
 252               noOfStructuresFound, totalTime));
 253     }
 254     else
 255     {
 256       mainFrame.setTitle(MessageManager
 257               .getString("label.structure_chooser_manual_association"));
 258       if (errors.size() > 0)
 259       {
 260         StringBuilder errorMsg = new StringBuilder();
 261         for (String error : errors)
 262         {
 263           errorMsg.append(error).append("\n");
 264         }
 265         JvOptionPane.showMessageDialog(this, errorMsg.toString(),
 266                 MessageManager.getString("label.pdb_web-service_error"),
 267                 JvOptionPane.ERROR_MESSAGE);
 268       }
 269     }
 270   }
 271
 272   public void loadLocalCachedPDBEntries()
 273   {
 274     ArrayList<CachedPDB> entries = new ArrayList<>();
 275     for (SequenceI seq : selectedSequences)
 276     {
 277       if (seq.getDatasetSequence() != null
 278               && seq.getDatasetSequence().getAllPDBEntries() != null)
 279       {
 280         for (PDBEntry pdbEntry : seq.getDatasetSequence()
 281                 .getAllPDBEntries())
 282         {
 283           if (pdbEntry.getFile() != null)
 284           {
 285             entries.add(new CachedPDB(seq, pdbEntry));
 286           }
 287         }
 288       }
 289     }
 290     cachedPDBExists = !entries.isEmpty();
 291     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
 292     tbl_local_pdb.setModel(tableModelx);
 293   }
 294
 295   /**
 296    * Builds a query string for a given sequences using its DBRef entries
 297    *
 298    * @param seq
 299    *          the sequences to build a query for
 300    * @return the built query string
 301    */
 302
 303   public static String buildQuery(SequenceI seq)
 304   {
 305     boolean isPDBRefsFound = false;
 306     boolean isUniProtRefsFound = false;
 307     StringBuilder queryBuilder = new StringBuilder();
 308     Set<String> seqRefs = new LinkedHashSet<>();
 309
 310     if (seq.getAllPDBEntries() != null
 311             && queryBuilder.length() < MAX_QLENGTH)
 312     {
 313       for (PDBEntry entry : seq.getAllPDBEntries())
 314       {
 315         if (isValidSeqName(entry.getId()))
 316         {
 317           queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase())
 318                   .append(" OR ");
 319           isPDBRefsFound = true;
 320         }
 321       }
 322     }
 323
 324     if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
 325     {
 326       for (DBRefEntry dbRef : seq.getDBRefs())
 327       {
 328         if (isValidSeqName(getDBRefId(dbRef))
 329                 && queryBuilder.length() < MAX_QLENGTH)
 330         {
 331           if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
 332           {
 333             queryBuilder.append("uniprot_accession:")
 334                     .append(getDBRefId(dbRef)).append(" OR ");
 335             queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
 336                     .append(" OR ");
 337             isUniProtRefsFound = true;
 338           }
 339           else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
 340           {
 341
 342             queryBuilder.append("pdb_id:")
 343                     .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
 344             isPDBRefsFound = true;
 345           }
 346           else
 347           {
 348             seqRefs.add(getDBRefId(dbRef));
 349           }
 350         }
 351       }
 352     }
 353
 354     if (!isPDBRefsFound && !isUniProtRefsFound)
 355     {
 356       String seqName = seq.getName();
 357       seqName = sanitizeSeqName(seqName);
 358       String[] names = seqName.toLowerCase().split("\\|");
 359       for (String name : names)
 360       {
 361         // System.out.println("Found name : " + name);
 362         name.trim();
 363         if (isValidSeqName(name))
 364         {
 365           seqRefs.add(name);
 366         }
 367       }
 368
 369       for (String seqRef : seqRefs)
 370       {
 371         queryBuilder.append("text:").append(seqRef).append(" OR ");
 372       }
 373     }
 374
 375     int endIndex = queryBuilder.lastIndexOf(" OR ");
 376     if (queryBuilder.toString().length() < 6)
 377     {
 378       return null;
 379     }
 380     String query = queryBuilder.toString().substring(0, endIndex);
 381     return query;
 382   }
 383
 384   /**
 385    * Remove the following special characters from input string +, -, &, !, (, ),
 386    * {, }, [, ], ^, ", ~, *, ?, :, \
 387    *
 388    * @param seqName
 389    * @return
 390    */
 391   static String sanitizeSeqName(String seqName)
 392   {
 393     Objects.requireNonNull(seqName);
 394     return seqName.replaceAll("\\[\\d*\\]", "")
 395             .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
 396   }
 397
 398   /**
 399    * Ensures sequence ref names are not less than 3 characters and does not
 400    * contain a database name
 401    *
 402    * @param seqName
 403    * @return
 404    */
 405   public static boolean isValidSeqName(String seqName)
 406   {
 407     // System.out.println("seqName : " + seqName);
 408     String ignoreList = "pdb,uniprot,swiss-prot";
 409     if (seqName.length() < 3)
 410     {
 411       return false;
 412     }
 413     if (seqName.contains(":"))
 414     {
 415       return false;
 416     }
 417     seqName = seqName.toLowerCase();
 418     for (String ignoredEntry : ignoreList.split(","))
 419     {
 420       if (seqName.contains(ignoredEntry))
 421       {
 422         return false;
 423       }
 424     }
 425     return true;
 426   }
 427
 428   public static String getDBRefId(DBRefEntry dbRef)
 429   {
 430     String ref = dbRef.getAccessionId().replaceAll("GO:", "");
 431     return ref;
 432   }
 433
 434   /**
 435    * Filters a given list of discovered structures based on supplied argument
 436    *
 437    * @param fieldToFilterBy
 438    *          the field to filter by
 439    */
 440   public void filterResultSet(final String fieldToFilterBy)
 441   {
 442     Thread filterThread = new Thread(new Runnable()
 443     {
 444       @Override
 445       public void run()
 446       {
 447         long startTime = System.currentTimeMillis();
 448         pdbRestCleint = PDBFTSRestClient.getInstance();
 449         lbl_loading.setVisible(true);
 450         Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
 451                 .getStructureSummaryFields();
 452         Collection<FTSData> filteredResponse = new HashSet<>();
 453         HashSet<String> errors = new HashSet<>();
 454
 455         for (SequenceI seq : selectedSequences)
 456         {
 457           FTSRestRequest pdbRequest = new FTSRestRequest();
 458           if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
 459           {
 460             pdbRequest.setAllowEmptySeq(false);
 461             pdbRequest.setResponseSize(1);
 462             pdbRequest.setFieldToSearchBy("(");
 463             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 464             pdbRequest.setWantedFields(wantedFields);
 465             pdbRequest.setAssociatedSequence(seq);
 466             pdbRequest.setFacet(true);
 467             pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
 468             pdbRequest.setFacetPivotMinCount(1);
 469           }
 470           else
 471           {
 472             pdbRequest.setAllowEmptySeq(false);
 473             pdbRequest.setResponseSize(1);
 474             pdbRequest.setFieldToSearchBy("(");
 475             pdbRequest.setFieldToSortBy(fieldToFilterBy,
 476                     !chk_invertFilter.isSelected());
 477             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 478             pdbRequest.setWantedFields(wantedFields);
 479             pdbRequest.setAssociatedSequence(seq);
 480           }
 481           FTSRestResponse resultList;
 482           try
 483           {
 484             resultList = pdbRestCleint.executeRequest(pdbRequest);
 485           } catch (Exception e)
 486           {
 487             e.printStackTrace();
 488             errors.add(e.getMessage());
 489             continue;
 490           }
 491           lastPdbRequest = pdbRequest;
 492           if (resultList.getSearchSummary() != null
 493                   && !resultList.getSearchSummary().isEmpty())
 494           {
 495             filteredResponse.addAll(resultList.getSearchSummary());
 496           }
 497         }
 498
 499         String totalTime = (System.currentTimeMillis() - startTime)
 500                 + " milli secs";
 501         if (!filteredResponse.isEmpty())
 502         {
 503           final int filterResponseCount = filteredResponse.size();
 504           Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
 505           reorderedStructuresSet.addAll(filteredResponse);
 506           reorderedStructuresSet.addAll(discoveredStructuresSet);
 507           getResultTable().setModel(FTSRestResponse
 508                   .getTableModel(lastPdbRequest, reorderedStructuresSet));
 509
 510           FTSRestResponse.configureTableColumn(getResultTable(),
 511                   wantedFields, tempUserPrefs);
 512           getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
 513           getResultTable().getColumn("Ref Sequence").setMinWidth(100);
 514           getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
 515           // Update table selection model here
 516           getResultTable().addRowSelectionInterval(0,
 517                   filterResponseCount - 1);
 518           mainFrame.setTitle(MessageManager.formatMessage(
 519                   "label.structure_chooser_filter_time", totalTime));
 520         }
 521         else
 522         {
 523           mainFrame.setTitle(MessageManager.formatMessage(
 524                   "label.structure_chooser_filter_time", totalTime));
 525           if (errors.size() > 0)
 526           {
 527             StringBuilder errorMsg = new StringBuilder();
 528             for (String error : errors)
 529             {
 530               errorMsg.append(error).append("\n");
 531             }
 532             JvOptionPane.showMessageDialog(null, errorMsg.toString(),
 533                     MessageManager.getString("label.pdb_web-service_error"),
 534                     JvOptionPane.ERROR_MESSAGE);
 535           }
 536         }
 537
 538         lbl_loading.setVisible(false);
 539
 540         validateSelections();
 541       }
 542     });
 543     filterThread.start();
 544   }
 545
 546   /**
 547    * Handles action event for btn_pdbFromFile
 548    */
 549   @Override
 550   public void pdbFromFile_actionPerformed()
 551   {
 552     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 553             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 554     chooser.setFileView(new jalview.io.JalviewFileView());
 555     chooser.setDialogTitle(
 556             MessageManager.formatMessage("label.select_pdb_file_for",
 557                     selectedSequence.getDisplayId(false)));
 558     chooser.setToolTipText(MessageManager.formatMessage(
 559             "label.load_pdb_file_associate_with_sequence",
 560             selectedSequence.getDisplayId(false)));
 561
 562     int value = chooser.showOpenDialog(null);
 563     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
 564     {
 565       selectedPdbFileName = chooser.getSelectedFile().getPath();
 566       jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
 567       validateSelections();
 568     }
 569   }
 570
 571   /**
 572    * Populates the filter combo-box options dynamically depending on discovered
 573    * structures
 574    */
 575   protected void populateFilterComboBox(boolean haveData,
 576           boolean cachedPDBExist)
 577   {
 578     /*
 579      * temporarily suspend the change listener behaviour
 580      */
 581     cmb_filterOption.removeItemListener(this);
 582
 583     cmb_filterOption.removeAllItems();
 584     if (haveData)
 585     {
 586       cmb_filterOption.addItem(new FilterOption(
 587               MessageManager.getString("label.best_quality"),
 588               "overall_quality", VIEWS_FILTER, false));
 589       cmb_filterOption.addItem(new FilterOption(
 590               MessageManager.getString("label.best_resolution"),
 591               "resolution", VIEWS_FILTER, false));
 592       cmb_filterOption.addItem(new FilterOption(
 593               MessageManager.getString("label.most_protein_chain"),
 594               "number_of_protein_chains", VIEWS_FILTER, false));
 595       cmb_filterOption.addItem(new FilterOption(
 596               MessageManager.getString("label.most_bound_molecules"),
 597               "number_of_bound_molecules", VIEWS_FILTER, false));
 598       cmb_filterOption.addItem(new FilterOption(
 599               MessageManager.getString("label.most_polymer_residues"),
 600               "number_of_polymer_residues", VIEWS_FILTER, true));
 601     }
 602     cmb_filterOption.addItem(
 603             new FilterOption(MessageManager.getString("label.enter_pdb_id"),
 604                     "-", VIEWS_ENTER_ID, false));
 605     cmb_filterOption.addItem(
 606             new FilterOption(MessageManager.getString("label.from_file"),
 607                     "-", VIEWS_FROM_FILE, false));
 608
 609     if (cachedPDBExist)
 610     {
 611       FilterOption cachedOption = new FilterOption(
 612               MessageManager.getString("label.cached_structures"),
 613               "-", VIEWS_LOCAL_PDB, false);
 614       cmb_filterOption.addItem(cachedOption);
 615       cmb_filterOption.setSelectedItem(cachedOption);
 616     }
 617
 618     cmb_filterOption.addItemListener(this);
 619   }
 620
 621   /**
 622    * Updates the displayed view based on the selected filter option
 623    */
 624   protected void updateCurrentView()
 625   {
 626     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 627             .getSelectedItem());
 628     layout_switchableViews.show(pnl_switchableViews,
 629             selectedFilterOpt.getView());
 630     String filterTitle = mainFrame.getTitle();
 631     mainFrame.setTitle(frameTitle);
 632     chk_invertFilter.setVisible(false);
 633     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 634     {
 635       mainFrame.setTitle(filterTitle);
 636       chk_invertFilter.setVisible(true);
 637       filterResultSet(selectedFilterOpt.getValue());
 638     }
 639     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 640             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 641     {
 642       mainFrame.setTitle(MessageManager
 643               .getString("label.structure_chooser_manual_association"));
 644       idInputAssSeqPanel.loadCmbAssSeq();
 645       fileChooserAssSeqPanel.loadCmbAssSeq();
 646     }
 647     validateSelections();
 648   }
 649
 650   /**
 651    * Validates user selection and activates the view button if all parameters
 652    * are correct
 653    */
 654   @Override
 655   public void validateSelections()
 656   {
 657     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 658             .getSelectedItem());
 659     btn_view.setEnabled(false);
 660     String currentView = selectedFilterOpt.getView();
 661     if (currentView == VIEWS_FILTER)
 662     {
 663       if (getResultTable().getSelectedRows().length > 0)
 664       {
 665         btn_view.setEnabled(true);
 666       }
 667     }
 668     else if (currentView == VIEWS_LOCAL_PDB)
 669     {
 670       if (tbl_local_pdb.getSelectedRows().length > 0)
 671       {
 672         btn_view.setEnabled(true);
 673       }
 674     }
 675     else if (currentView == VIEWS_ENTER_ID)
 676     {
 677       validateAssociationEnterPdb();
 678     }
 679     else if (currentView == VIEWS_FROM_FILE)
 680     {
 681       validateAssociationFromFile();
 682     }
 683   }
 684
 685   /**
 686    * Validates inputs from the Manual PDB entry panel
 687    */
 688   public void validateAssociationEnterPdb()
 689   {
 690     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 691             .getCmb_assSeq().getSelectedItem();
 692     lbl_pdbManualFetchStatus.setIcon(errorImage);
 693     lbl_pdbManualFetchStatus.setToolTipText("");
 694     if (txt_search.getText().length() > 0)
 695     {
 696       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
 697               MessageManager.formatMessage("info.no_pdb_entry_found_for",
 698                       txt_search.getText())));
 699     }
 700
 701     if (errorWarning.length() > 0)
 702     {
 703       lbl_pdbManualFetchStatus.setIcon(warningImage);
 704       lbl_pdbManualFetchStatus.setToolTipText(
 705               JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
 706     }
 707
 708     if (selectedSequences.length == 1 || !assSeqOpt.getName()
 709             .equalsIgnoreCase("-Select Associated Seq-"))
 710     {
 711       txt_search.setEnabled(true);
 712       if (isValidPBDEntry)
 713       {
 714         btn_view.setEnabled(true);
 715         lbl_pdbManualFetchStatus.setToolTipText("");
 716         lbl_pdbManualFetchStatus.setIcon(goodImage);
 717       }
 718     }
 719     else
 720     {
 721       txt_search.setEnabled(false);
 722       lbl_pdbManualFetchStatus.setIcon(errorImage);
 723     }
 724   }
 725
 726   /**
 727    * Validates inputs for the manual PDB file selection options
 728    */
 729   public void validateAssociationFromFile()
 730   {
 731     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
 732             .getCmb_assSeq().getSelectedItem();
 733     lbl_fromFileStatus.setIcon(errorImage);
 734     if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
 735             .getName().equalsIgnoreCase("-Select Associated Seq-")))
 736     {
 737       btn_pdbFromFile.setEnabled(true);
 738       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
 739       {
 740         btn_view.setEnabled(true);
 741         lbl_fromFileStatus.setIcon(goodImage);
 742       }
 743     }
 744     else
 745     {
 746       btn_pdbFromFile.setEnabled(false);
 747       lbl_fromFileStatus.setIcon(errorImage);
 748     }
 749   }
 750
 751   @Override
 752   public void cmbAssSeqStateChanged()
 753   {
 754     validateSelections();
 755   }
 756
 757   /**
 758    * Handles the state change event for the 'filter' combo-box and 'invert'
 759    * check-box
 760    */
 761   @Override
 762   protected void stateChanged(ItemEvent e)
 763   {
 764     if (e.getSource() instanceof JCheckBox)
 765     {
 766       updateCurrentView();
 767     }
 768     else
 769     {
 770       if (e.getStateChange() == ItemEvent.SELECTED)
 771       {
 772         updateCurrentView();
 773       }
 774     }
 775
 776   }
 777
 778   /**
 779    * select structures for viewing by their PDB IDs
 780    *
 781    * @param pdbids
 782    * @return true if structures were found and marked as selected
 783    */
 784   public boolean selectStructure(String... pdbids)
 785   {
 786     boolean found = false;
 787
 788     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 789             .getSelectedItem());
 790     String currentView = selectedFilterOpt.getView();
 791     JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
 792             : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
 793
 794     if (restable == null)
 795     {
 796       // can't select (enter PDB ID, or load file - need to also select which
 797       // sequence to associate with)
 798       return false;
 799     }
 800
 801     int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
 802     for (int r = 0; r < restable.getRowCount(); r++)
 803     {
 804       for (int p = 0; p < pdbids.length; p++)
 805       {
 806         if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
 807                 .equalsIgnoreCase(pdbids[p]))
 808         {
 809           restable.setRowSelectionInterval(r, r);
 810           found = true;
 811         }
 812       }
 813     }
 814     return found;
 815   }
 816   /**
 817    * Handles action event for btn_ok
 818    */
 819   @Override
 820   public void ok_ActionPerformed()
 821   {
 822     showStructures(false);
 823   }
 824
 825   /**
 826    * structure viewer opened by this dialog, or null
 827    */
 828   private StructureViewer sViewer = null;
 829
 830   public void showStructures(boolean waitUntilFinished)
 831   {
 832
 833     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 834
 835     final int preferredHeight = pnl_filter.getHeight();
 836
 837     Runnable viewStruc = new Runnable()
 838     {
 839       @Override
 840       public void run()
 841       {
 842         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 843                 .getSelectedItem());
 844         String currentView = selectedFilterOpt.getView();
 845         JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
 846                 : tbl_local_pdb;
 847
 848         if (currentView == VIEWS_FILTER)
 849         {
 850           int pdbIdColIndex = restable.getColumn("PDB Id")
 851                   .getModelIndex();
 852           int refSeqColIndex = restable.getColumn("Ref Sequence")
 853                   .getModelIndex();
 854           int[] selectedRows = restable.getSelectedRows();
 855           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 856           int count = 0;
 857           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 858           for (int row : selectedRows)
 859           {
 860             String pdbIdStr = restable
 861                     .getValueAt(row, pdbIdColIndex).toString();
 862             SequenceI selectedSeq = (SequenceI) restable
 863                     .getValueAt(row, refSeqColIndex);
 864             selectedSeqsToView.add(selectedSeq);
 865             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
 866             if (pdbEntry == null)
 867             {
 868               pdbEntry = getFindEntry(pdbIdStr,
 869                       selectedSeq.getAllPDBEntries());
 870             }
 871
 872             if (pdbEntry == null)
 873             {
 874               pdbEntry = new PDBEntry();
 875               pdbEntry.setId(pdbIdStr);
 876               pdbEntry.setType(PDBEntry.Type.PDB);
 877               selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
 878             }
 879             pdbEntriesToView[count++] = pdbEntry;
 880           }
 881           SequenceI[] selectedSeqs = selectedSeqsToView
 882                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 883           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 884                   selectedSeqs);
 885         }
 886         else if (currentView == VIEWS_LOCAL_PDB)
 887         {
 888           int[] selectedRows = tbl_local_pdb.getSelectedRows();
 889           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 890           int count = 0;
 891           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
 892                   .getModelIndex();
 893           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
 894                   .getModelIndex();
 895           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 896           for (int row : selectedRows)
 897           {
 898             PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
 899                     pdbIdColIndex);
 900             pdbEntriesToView[count++] = pdbEntry;
 901             SequenceI selectedSeq = (SequenceI) tbl_local_pdb
 902                     .getValueAt(row, refSeqColIndex);
 903             selectedSeqsToView.add(selectedSeq);
 904           }
 905           SequenceI[] selectedSeqs = selectedSeqsToView
 906                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 907           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 908                   selectedSeqs);
 909         }
 910         else if (currentView == VIEWS_ENTER_ID)
 911         {
 912           SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
 913                   .getCmb_assSeq().getSelectedItem()).getSequence();
 914           if (userSelectedSeq != null)
 915           {
 916             selectedSequence = userSelectedSeq;
 917           }
 918           String pdbIdStr = txt_search.getText();
 919           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
 920           if (pdbEntry == null)
 921           {
 922             pdbEntry = new PDBEntry();
 923             if (pdbIdStr.split(":").length > 1)
 924             {
 925               pdbEntry.setId(pdbIdStr.split(":")[0]);
 926               pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
 927             }
 928             else
 929             {
 930               pdbEntry.setId(pdbIdStr);
 931             }
 932             pdbEntry.setType(PDBEntry.Type.PDB);
 933             selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
 934           }
 935
 936           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
 937           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 938                   new SequenceI[]
 939                   { selectedSequence });
 940         }
 941         else if (currentView == VIEWS_FROM_FILE)
 942         {
 943           SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
 944                   .getCmb_assSeq().getSelectedItem()).getSequence();
 945           if (userSelectedSeq != null)
 946           {
 947             selectedSequence = userSelectedSeq;
 948           }
 949           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 950                   .associatePdbWithSeq(selectedPdbFileName,
 951                           DataSourceType.FILE, selectedSequence, true,
 952                           Desktop.instance);
 953
 954           sViewer = launchStructureViewer(
 955                   ssm, new PDBEntry[]
 956                   { fileEntry }, ap,
 957                   new SequenceI[]
 958                   { selectedSequence });
 959         }
 960         SwingUtilities.invokeLater(new Runnable()
 961         {
 962           @Override
 963           public void run()
 964           {
 965             closeAction(preferredHeight);
 966             mainFrame.dispose();
 967           }
 968         });
 969       }
 970     };
 971     Thread runner = new Thread(viewStruc);
 972     runner.start();
 973     if (waitUntilFinished)
 974     {
 975       while (sViewer == null ? runner.isAlive()
 976               : (sViewer.sview == null ? true
 977                       : !sViewer.sview.hasMapping()))
 978       {
 979         try
 980         {
 981           Thread.sleep(300);
 982         } catch (InterruptedException ie)
 983         {
 984
 985         }
 986       }
 987     }
 988   }
 989
 990   private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
 991   {
 992     Objects.requireNonNull(id);
 993     Objects.requireNonNull(pdbEntries);
 994     PDBEntry foundEntry = null;
 995     for (PDBEntry entry : pdbEntries)
 996     {
 997       if (entry.getId().equalsIgnoreCase(id))
 998       {
 999         return entry;
1000       }
1001     }
1002     return foundEntry;
1003   }
1004
1005   /**
1006    * @param ssm
1007    * @return targetted structure view (new or existing) configured according to
1008    *         superpose checkbox
1009    */
1010   public StructureViewer getTargetedStructureViewer(
1011           StructureSelectionManager ssm)
1012   {
1013     Object _sv = targetView.getSelectedItem();
1014     StructureViewer sv;
1015     if (_sv == null)
1016     {
1017       sv = new StructureViewer(ssm);
1018     } else {
1019       sv = (StructureViewer) _sv;
1020     }
1021     sv.setSuperpose(chk_superpose.isSelected());
1022     return sv;
1023   }
1024   private StructureViewer launchStructureViewer(
1025           StructureSelectionManager ssm,
1026           final PDBEntry[] pdbEntriesToView,
1027           final AlignmentPanel alignPanel, SequenceI[] sequences)
1028   {
1029     long progressId = sequences.hashCode();
1030     setProgressBar(MessageManager
1031             .getString("status.launching_3d_structure_viewer"), progressId);
1032     final StructureViewer sViewer = getTargetedStructureViewer(ssm);
1033     sViewer.setSuperpose(chk_superpose.isSelected());
1034
1035     setProgressBar(null, progressId);
1036     if (SiftsSettings.isMapWithSifts())
1037     {
1038       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
1039       int p = 0;
1040       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
1041       // real PDB ID. For moment, we can also safely do this if there is already
1042       // a known mapping between the PDBEntry and the sequence.
1043       for (SequenceI seq : sequences)
1044       {
1045         PDBEntry pdbe = pdbEntriesToView[p++];
1046         if (pdbe != null && pdbe.getFile() != null)
1047         {
1048           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
1049           if (smm != null && smm.length > 0)
1050           {
1051             for (StructureMapping sm : smm)
1052             {
1053               if (sm.getSequence() == seq)
1054               {
1055                 continue;
1056               }
1057             }
1058           }
1059         }
1060         if (seq.getPrimaryDBRefs().size() == 0)
1061         {
1062           seqsWithoutSourceDBRef.add(seq);
1063           continue;
1064         }
1065       }
1066       if (!seqsWithoutSourceDBRef.isEmpty())
1067       {
1068         int y = seqsWithoutSourceDBRef.size();
1069         setProgressBar(MessageManager.formatMessage(
1070                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
1071                 y), progressId);
1072         SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
1073         int x = 0;
1074         for (SequenceI fSeq : seqsWithoutSourceDBRef)
1075         {
1076           seqWithoutSrcDBRef[x++] = fSeq;
1077         }
1078
1079         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
1080         dbRefFetcher.fetchDBRefs(true);
1081
1082         setProgressBar("Fetch complete.", progressId); // todo i18n
1083       }
1084     }
1085     if (pdbEntriesToView.length > 1)
1086     {
1087       setProgressBar(MessageManager.getString(
1088               "status.fetching_3d_structures_for_selected_entries"),
1089               progressId);
1090       sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
1091     }
1092     else
1093     {
1094       setProgressBar(MessageManager.formatMessage(
1095               "status.fetching_3d_structures_for",
1096               pdbEntriesToView[0].getId()),progressId);
1097       sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
1098     }
1099     setProgressBar(null, progressId);
1100     // remember the last viewer we used...
1101     lastTargetedView = sViewer;
1102     return sViewer;
1103   }
1104
1105   /**
1106    * Populates the combo-box used in associating manually fetched structures to
1107    * a unique sequence when more than one sequence selection is made.
1108    */
1109   @Override
1110   public void populateCmbAssociateSeqOptions(
1111           JComboBox<AssociateSeqOptions> cmb_assSeq,
1112           JLabel lbl_associateSeq)
1113   {
1114     cmb_assSeq.removeAllItems();
1115     cmb_assSeq.addItem(
1116             new AssociateSeqOptions("-Select Associated Seq-", null));
1117     lbl_associateSeq.setVisible(false);
1118     if (selectedSequences.length > 1)
1119     {
1120       for (SequenceI seq : selectedSequences)
1121       {
1122         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
1123       }
1124     }
1125     else
1126     {
1127       String seqName = selectedSequence.getDisplayId(false);
1128       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
1129       lbl_associateSeq.setText(seqName);
1130       lbl_associateSeq.setVisible(true);
1131       cmb_assSeq.setVisible(false);
1132     }
1133   }
1134
1135   public boolean isStructuresDiscovered()
1136   {
1137     return discoveredStructuresSet != null
1138             && !discoveredStructuresSet.isEmpty();
1139   }
1140
1141   public Collection<FTSData> getDiscoveredStructuresSet()
1142   {
1143     return discoveredStructuresSet;
1144   }
1145
1146   @Override
1147   protected void txt_search_ActionPerformed()
1148   {
1149     new Thread()
1150     {
1151       @Override
1152       public void run()
1153       {
1154         errorWarning.setLength(0);
1155         isValidPBDEntry = false;
1156         if (txt_search.getText().length() > 0)
1157         {
1158           String searchTerm = txt_search.getText().toLowerCase();
1159           searchTerm = searchTerm.split(":")[0];
1160           // System.out.println(">>>>> search term : " + searchTerm);
1161           List<FTSDataColumnI> wantedFields = new ArrayList<>();
1162           FTSRestRequest pdbRequest = new FTSRestRequest();
1163           pdbRequest.setAllowEmptySeq(false);
1164           pdbRequest.setResponseSize(1);
1165           pdbRequest.setFieldToSearchBy("(pdb_id:");
1166           pdbRequest.setWantedFields(wantedFields);
1167           pdbRequest.setSearchTerm(searchTerm + ")");
1168           pdbRequest.setAssociatedSequence(selectedSequence);
1169           pdbRestCleint = PDBFTSRestClient.getInstance();
1170           wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
1171           FTSRestResponse resultList;
1172           try
1173           {
1174             resultList = pdbRestCleint.executeRequest(pdbRequest);
1175           } catch (Exception e)
1176           {
1177             errorWarning.append(e.getMessage());
1178             return;
1179           } finally
1180           {
1181             validateSelections();
1182           }
1183           if (resultList.getSearchSummary() != null
1184                   && resultList.getSearchSummary().size() > 0)
1185           {
1186             isValidPBDEntry = true;
1187           }
1188         }
1189         validateSelections();
1190       }
1191     }.start();
1192   }
1193
1194   @Override
1195   public void tabRefresh()
1196   {
1197     if (selectedSequences != null)
1198     {
1199       Thread refreshThread = new Thread(new Runnable()
1200       {
1201         @Override
1202         public void run()
1203         {
1204           fetchStructuresMetaData();
1205           filterResultSet(
1206                   ((FilterOption) cmb_filterOption.getSelectedItem())
1207                           .getValue());
1208         }
1209       });
1210       refreshThread.start();
1211     }
1212   }
1213
1214   public class PDBEntryTableModel extends AbstractTableModel
1215   {
1216     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1217         "File" };
1218
1219     private List<CachedPDB> pdbEntries;
1220
1221     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1222     {
1223       this.pdbEntries = new ArrayList<>(pdbEntries);
1224     }
1225
1226     @Override
1227     public String getColumnName(int columnIndex)
1228     {
1229       return columns[columnIndex];
1230     }
1231
1232     @Override
1233     public int getRowCount()
1234     {
1235       return pdbEntries.size();
1236     }
1237
1238     @Override
1239     public int getColumnCount()
1240     {
1241       return columns.length;
1242     }
1243
1244     @Override
1245     public boolean isCellEditable(int row, int column)
1246     {
1247       return false;
1248     }
1249
1250     @Override
1251     public Object getValueAt(int rowIndex, int columnIndex)
1252     {
1253       Object value = "??";
1254       CachedPDB entry = pdbEntries.get(rowIndex);
1255       switch (columnIndex)
1256       {
1257       case 0:
1258         value = entry.getSequence();
1259         break;
1260       case 1:
1261         value = entry.getPdbEntry();
1262         break;
1263       case 2:
1264         value = entry.getPdbEntry().getChainCode() == null ? "_"
1265                 : entry.getPdbEntry().getChainCode();
1266         break;
1267       case 3:
1268         value = entry.getPdbEntry().getType();
1269         break;
1270       case 4:
1271         value = entry.getPdbEntry().getFile();
1272         break;
1273       }
1274       return value;
1275     }
1276
1277     @Override
1278     public Class<?> getColumnClass(int columnIndex)
1279     {
1280       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1281     }
1282
1283     public CachedPDB getPDBEntryAt(int row)
1284     {
1285       return pdbEntries.get(row);
1286     }
1287
1288   }
1289
1290   private class CachedPDB
1291   {
1292     private SequenceI sequence;
1293
1294     private PDBEntry pdbEntry;
1295
1296     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1297     {
1298       this.sequence = sequence;
1299       this.pdbEntry = pdbEntry;
1300     }
1301
1302     public SequenceI getSequence()
1303     {
1304       return sequence;
1305     }
1306
1307     public PDBEntry getPdbEntry()
1308     {
1309       return pdbEntry;
1310     }
1311
1312   }
1313
1314   private IProgressIndicator progressBar;
1315
1316   @Override
1317   public void setProgressBar(String message, long id)
1318   {
1319     progressBar.setProgressBar(message, id);
1320   }
1321
1322   @Override
1323   public void registerHandler(long id, IProgressIndicatorHandler handler)
1324   {
1325     progressBar.registerHandler(id, handler);
1326   }
1327
1328   @Override
1329   public boolean operationInProgress()
1330   {
1331     return progressBar.operationInProgress();
1332   }
1333
1334   public JalviewStructureDisplayI getOpenedStructureViewer()
1335   {
1336     return sViewer == null ? null : sViewer.sview;
1337   }
1338 }