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