src/jalview/gui/StructureChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21
  22 package jalview.gui;
  23
  24 import jalview.bin.Jalview;
  25 import jalview.datamodel.DBRefEntry;
  26 import jalview.datamodel.DBRefSource;
  27 import jalview.datamodel.PDBEntry;
  28 import jalview.datamodel.SequenceI;
  29 import jalview.fts.api.FTSData;
  30 import jalview.fts.api.FTSDataColumnI;
  31 import jalview.fts.api.FTSRestClientI;
  32 import jalview.fts.core.FTSRestRequest;
  33 import jalview.fts.core.FTSRestResponse;
  34 import jalview.fts.service.pdb.PDBFTSRestClient;
  35 import jalview.jbgui.GStructureChooser;
  36 import jalview.structure.StructureMapping;
  37 import jalview.structure.StructureSelectionManager;
  38 import jalview.util.MessageManager;
  39 import jalview.ws.DBRefFetcher;
  40 import jalview.ws.sifts.SiftsSettings;
  41
  42 import java.awt.event.ItemEvent;
  43 import java.util.ArrayList;
  44 import java.util.Collection;
  45 import java.util.HashSet;
  46 import java.util.LinkedHashSet;
  47 import java.util.List;
  48 import java.util.Objects;
  49 import java.util.Set;
  50 import java.util.Vector;
  51
  52 import javax.swing.JCheckBox;
  53 import javax.swing.JComboBox;
  54 import javax.swing.JLabel;
  55 import javax.swing.JOptionPane;
  56 import javax.swing.table.AbstractTableModel;
  57
  58 /**
  59  * Provides the behaviors for the Structure chooser Panel
  60  *
  61  * @author tcnofoegbu
  62  *
  63  */
  64 @SuppressWarnings("serial")
  65 public class StructureChooser extends GStructureChooser implements
  66         IProgressIndicator
  67 {
  68   private SequenceI selectedSequence;
  69
  70   private SequenceI[] selectedSequences;
  71
  72   private IProgressIndicator progressIndicator;
  73
  74   private Collection<FTSData> discoveredStructuresSet;
  75
  76   private FTSRestRequest lastPdbRequest;
  77
  78   private FTSRestClientI pdbRestCleint;
  79
  80   private String selectedPdbFileName;
  81
  82   private boolean isValidPBDEntry;
  83
  84   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
  85           AlignmentPanel ap)
  86   {
  87     this.ap = ap;
  88     this.selectedSequence = selectedSeq;
  89     this.selectedSequences = selectedSeqs;
  90     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
  91     init();
  92   }
  93
  94   /**
  95    * Initializes parameters used by the Structure Chooser Panel
  96    */
  97   public void init()
  98   {
  99     if (!Jalview.isHeadlessMode())
 100     {
 101       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 102     }
 103
 104     // ensure a filter option is in force for search
 105     populateFilterComboBox(true);
 106     Thread discoverPDBStructuresThread = new Thread(new Runnable()
 107     {
 108       @Override
 109       public void run()
 110       {
 111         long startTime = System.currentTimeMillis();
 112         updateProgressIndicator(MessageManager
 113                 .getString("status.loading_cached_pdb_entries"), startTime);
 114         loadLocalCachedPDBEntries();
 115         updateProgressIndicator(null, startTime);
 116         updateProgressIndicator(MessageManager
 117                 .getString("status.searching_for_pdb_structures"),
 118                 startTime);
 119         fetchStructuresMetaData();
 120         // revise filter options if no results were found
 121         populateFilterComboBox(isStructuresDiscovered());
 122         updateProgressIndicator(null, startTime);
 123         mainFrame.setVisible(true);
 124         updateCurrentView();
 125       }
 126     });
 127     discoverPDBStructuresThread.start();
 128   }
 129
 130   /**
 131    * Updates the progress indicator with the specified message
 132    *
 133    * @param message
 134    *          displayed message for the operation
 135    * @param id
 136    *          unique handle for this indicator
 137    */
 138   public void updateProgressIndicator(String message, long id)
 139   {
 140     if (progressIndicator != null)
 141     {
 142       progressIndicator.setProgressBar(message, id);
 143     }
 144   }
 145
 146   /**
 147    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
 148    * selection group
 149    */
 150   public void fetchStructuresMetaData()
 151   {
 152     long startTime = System.currentTimeMillis();
 153     pdbRestCleint = PDBFTSRestClient.getInstance();
 154     Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
 155             .getStructureSummaryFields();
 156
 157     discoveredStructuresSet = new LinkedHashSet<FTSData>();
 158     HashSet<String> errors = new HashSet<String>();
 159     for (SequenceI seq : selectedSequences)
 160     {
 161       FTSRestRequest pdbRequest = new FTSRestRequest();
 162       pdbRequest.setAllowEmptySeq(false);
 163       pdbRequest.setResponseSize(500);
 164       pdbRequest.setFieldToSearchBy("(");
 165       FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 166               .getSelectedItem());
 167       pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
 168               !chk_invertFilter.isSelected());
 169       pdbRequest.setWantedFields(wantedFields);
 170       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 171       pdbRequest.setAssociatedSequence(seq);
 172       FTSRestResponse resultList;
 173       try
 174       {
 175         resultList = pdbRestCleint.executeRequest(pdbRequest);
 176       } catch (Exception e)
 177       {
 178         e.printStackTrace();
 179         errors.add(e.getMessage());
 180         continue;
 181       }
 182       lastPdbRequest = pdbRequest;
 183       if (resultList.getSearchSummary() != null
 184               && !resultList.getSearchSummary().isEmpty())
 185       {
 186         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 187       }
 188     }
 189
 190     int noOfStructuresFound = 0;
 191     String totalTime = (System.currentTimeMillis() - startTime)
 192             + " milli secs";
 193     if (discoveredStructuresSet != null
 194             && !discoveredStructuresSet.isEmpty())
 195     {
 196       getResultTable().setModel(
 197               FTSRestResponse.getTableModel(lastPdbRequest,
 198                       discoveredStructuresSet));
 199       noOfStructuresFound = discoveredStructuresSet.size();
 200       mainFrame.setTitle(MessageManager.formatMessage(
 201               "label.structure_chooser_no_of_structures",
 202               noOfStructuresFound, totalTime));
 203     }
 204     else
 205     {
 206       mainFrame.setTitle(MessageManager
 207               .getString("label.structure_chooser_manual_association"));
 208       if (errors.size() > 0)
 209       {
 210         StringBuilder errorMsg = new StringBuilder();
 211         for (String error : errors)
 212         {
 213           errorMsg.append(error).append("\n");
 214         }
 215         JOptionPane.showMessageDialog(this, errorMsg.toString(),
 216                 MessageManager.getString("label.pdb_web-service_error"),
 217                 JOptionPane.ERROR_MESSAGE);
 218       }
 219     }
 220   }
 221
 222   public void loadLocalCachedPDBEntries()
 223   {
 224     ArrayList<CachedPDB> entries = new ArrayList<CachedPDB>();
 225     for (SequenceI seq : selectedSequences)
 226     {
 227       if (seq.getDatasetSequence() != null
 228               && seq.getDatasetSequence().getAllPDBEntries() != null)
 229       {
 230         for (PDBEntry pdbEntry : seq.getDatasetSequence()
 231                 .getAllPDBEntries())
 232         {
 233           if (pdbEntry.getFile() != null)
 234           {
 235             entries.add(new CachedPDB(seq, pdbEntry));
 236           }
 237         }
 238       }
 239     }
 240
 241     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
 242     tbl_local_pdb.setModel(tableModelx);
 243   }
 244
 245   /**
 246    * Builds a query string for a given sequences using its DBRef entries
 247    *
 248    * @param seq
 249    *          the sequences to build a query for
 250    * @return the built query string
 251    */
 252
 253   public static String buildQuery(SequenceI seq)
 254   {
 255     boolean isPDBRefsFound = false;
 256     boolean isUniProtRefsFound = false;
 257     StringBuilder queryBuilder = new StringBuilder();
 258     Set<String> seqRefs = new LinkedHashSet<String>();
 259
 260     if (seq.getAllPDBEntries() != null)
 261     {
 262       for (PDBEntry entry : seq.getAllPDBEntries())
 263       {
 264         if (isValidSeqName(entry.getId()))
 265         {
 266           queryBuilder.append("pdb_id:")
 267                   .append(entry.getId().toLowerCase()).append(" OR ");
 268           isPDBRefsFound = true;
 269           // seqRefs.add(entry.getId());
 270         }
 271       }
 272     }
 273
 274     if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
 275     {
 276       for (DBRefEntry dbRef : seq.getDBRefs())
 277       {
 278         if (isValidSeqName(getDBRefId(dbRef)))
 279         {
 280           if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
 281           {
 282             queryBuilder.append("uniprot_accession:")
 283                     .append(getDBRefId(dbRef)).append(" OR ");
 284             queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
 285                     .append(" OR ");
 286             isUniProtRefsFound = true;
 287           }
 288           else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
 289           {
 290
 291             queryBuilder.append("pdb_id:")
 292                     .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
 293             isPDBRefsFound = true;
 294           }
 295           else
 296           {
 297             seqRefs.add(getDBRefId(dbRef));
 298           }
 299         }
 300       }
 301     }
 302
 303     if (!isPDBRefsFound && !isUniProtRefsFound)
 304     {
 305       String seqName = seq.getName();
 306       seqName = sanitizeSeqName(seqName);
 307       String[] names = seqName.toLowerCase().split("\\|");
 308       for (String name : names)
 309       {
 310         // System.out.println("Found name : " + name);
 311         name.trim();
 312         if (isValidSeqName(name))
 313         {
 314           seqRefs.add(name);
 315         }
 316       }
 317
 318       for (String seqRef : seqRefs)
 319       {
 320         queryBuilder.append("text:").append(seqRef).append(" OR ");
 321       }
 322     }
 323
 324     int endIndex = queryBuilder.lastIndexOf(" OR ");
 325     if (queryBuilder.toString().length() < 6)
 326     {
 327       return null;
 328     }
 329     String query = queryBuilder.toString().substring(0, endIndex);
 330     return query;
 331   }
 332
 333   /**
 334    * Remove the following special characters from input string +, -, &, !, (, ),
 335    * {, }, [, ], ^, ", ~, *, ?, :, \
 336    *
 337    * @param seqName
 338    * @return
 339    */
 340   static String sanitizeSeqName(String seqName)
 341   {
 342     Objects.requireNonNull(seqName);
 343     return seqName.replaceAll("\\[\\d*\\]", "")
 344             .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
 345   }
 346
 347   /**
 348    * Ensures sequence ref names are not less than 3 characters and does not
 349    * contain a database name
 350    *
 351    * @param seqName
 352    * @return
 353    */
 354   public static boolean isValidSeqName(String seqName)
 355   {
 356     // System.out.println("seqName : " + seqName);
 357     String ignoreList = "pdb,uniprot,swiss-prot";
 358     if (seqName.length() < 3)
 359     {
 360       return false;
 361     }
 362     if (seqName.contains(":"))
 363     {
 364       return false;
 365     }
 366     seqName = seqName.toLowerCase();
 367     for (String ignoredEntry : ignoreList.split(","))
 368     {
 369       if (seqName.contains(ignoredEntry))
 370       {
 371         return false;
 372       }
 373     }
 374     return true;
 375   }
 376
 377   public static String getDBRefId(DBRefEntry dbRef)
 378   {
 379     String ref = dbRef.getAccessionId().replaceAll("GO:", "");
 380     return ref;
 381   }
 382
 383   /**
 384    * Filters a given list of discovered structures based on supplied argument
 385    *
 386    * @param fieldToFilterBy
 387    *          the field to filter by
 388    */
 389   public void filterResultSet(final String fieldToFilterBy)
 390   {
 391     Thread filterThread = new Thread(new Runnable()
 392     {
 393       @Override
 394       public void run()
 395       {
 396         long startTime = System.currentTimeMillis();
 397         pdbRestCleint = PDBFTSRestClient.getInstance();
 398         lbl_loading.setVisible(true);
 399         Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
 400                 .getStructureSummaryFields();
 401         Collection<FTSData> filteredResponse = new HashSet<FTSData>();
 402         HashSet<String> errors = new HashSet<String>();
 403
 404         for (SequenceI seq : selectedSequences)
 405         {
 406           FTSRestRequest pdbRequest = new FTSRestRequest();
 407           if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
 408           {
 409             pdbRequest.setAllowEmptySeq(false);
 410             pdbRequest.setResponseSize(1);
 411             pdbRequest.setFieldToSearchBy("(");
 412             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 413             pdbRequest.setWantedFields(wantedFields);
 414             pdbRequest.setAssociatedSequence(seq);
 415             pdbRequest.setFacet(true);
 416             pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
 417             pdbRequest.setFacetPivotMinCount(1);
 418           }
 419           else
 420           {
 421             pdbRequest.setAllowEmptySeq(false);
 422             pdbRequest.setResponseSize(1);
 423             pdbRequest.setFieldToSearchBy("(");
 424             pdbRequest.setFieldToSortBy(fieldToFilterBy,
 425                     !chk_invertFilter.isSelected());
 426             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 427             pdbRequest.setWantedFields(wantedFields);
 428             pdbRequest.setAssociatedSequence(seq);
 429           }
 430           FTSRestResponse resultList;
 431           try
 432           {
 433             resultList = pdbRestCleint.executeRequest(pdbRequest);
 434           } catch (Exception e)
 435           {
 436             e.printStackTrace();
 437             errors.add(e.getMessage());
 438             continue;
 439           }
 440           lastPdbRequest = pdbRequest;
 441           if (resultList.getSearchSummary() != null
 442                   && !resultList.getSearchSummary().isEmpty())
 443           {
 444             filteredResponse.addAll(resultList.getSearchSummary());
 445           }
 446         }
 447
 448         String totalTime = (System.currentTimeMillis() - startTime)
 449                 + " milli secs";
 450         if (!filteredResponse.isEmpty())
 451         {
 452           final int filterResponseCount = filteredResponse.size();
 453           Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
 454           reorderedStructuresSet.addAll(filteredResponse);
 455           reorderedStructuresSet.addAll(discoveredStructuresSet);
 456           getResultTable().setModel(
 457                   FTSRestResponse.getTableModel(lastPdbRequest,
 458                           reorderedStructuresSet));
 459
 460           FTSRestResponse.configureTableColumn(getResultTable(),
 461                   wantedFields, tempUserPrefs);
 462           getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
 463           getResultTable().getColumn("Ref Sequence").setMinWidth(100);
 464           getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
 465           // Update table selection model here
 466           getResultTable().addRowSelectionInterval(0,
 467                   filterResponseCount - 1);
 468           mainFrame.setTitle(MessageManager.formatMessage(
 469                   "label.structure_chooser_filter_time", totalTime));
 470         }
 471         else
 472         {
 473           mainFrame.setTitle(MessageManager.formatMessage(
 474                   "label.structure_chooser_filter_time", totalTime));
 475           if (errors.size() > 0)
 476           {
 477             StringBuilder errorMsg = new StringBuilder();
 478             for (String error : errors)
 479             {
 480               errorMsg.append(error).append("\n");
 481             }
 482             JOptionPane.showMessageDialog(
 483                     null,
 484                     errorMsg.toString(),
 485                     MessageManager.getString("label.pdb_web-service_error"),
 486                     JOptionPane.ERROR_MESSAGE);
 487           }
 488         }
 489
 490         lbl_loading.setVisible(false);
 491
 492         validateSelections();
 493       }
 494     });
 495     filterThread.start();
 496   }
 497
 498   /**
 499    * Handles action event for btn_pdbFromFile
 500    */
 501   @Override
 502   public void pdbFromFile_actionPerformed()
 503   {
 504     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 505             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 506     chooser.setFileView(new jalview.io.JalviewFileView());
 507     chooser.setDialogTitle(MessageManager.formatMessage(
 508             "label.select_pdb_file_for",
 509             selectedSequence.getDisplayId(false)));
 510     chooser.setToolTipText(MessageManager.formatMessage(
 511             "label.load_pdb_file_associate_with_sequence",
 512             selectedSequence.getDisplayId(false)));
 513
 514     int value = chooser.showOpenDialog(null);
 515     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
 516     {
 517       selectedPdbFileName = chooser.getSelectedFile().getPath();
 518       jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
 519       validateSelections();
 520     }
 521   }
 522
 523   /**
 524    * Populates the filter combo-box options dynamically depending on discovered
 525    * structures
 526    */
 527   protected void populateFilterComboBox(boolean haveData)
 528   {
 529     /*
 530      * temporarily suspend the change listener behaviour
 531      */
 532     cmb_filterOption.removeItemListener(this);
 533
 534     cmb_filterOption.removeAllItems();
 535     if (haveData)
 536     {
 537       cmb_filterOption.addItem(new FilterOption("Best Quality",
 538               "overall_quality", VIEWS_FILTER));
 539       cmb_filterOption.addItem(new FilterOption("Best Resolution",
 540               "resolution", VIEWS_FILTER));
 541       cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
 542               "number_of_protein_chains", VIEWS_FILTER));
 543       cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
 544               "number_of_bound_molecules", VIEWS_FILTER));
 545       cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
 546               "number_of_polymer_residues", VIEWS_FILTER));
 547     }
 548     cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
 549             VIEWS_ENTER_ID));
 550     cmb_filterOption.addItem(new FilterOption("From File", "-",
 551             VIEWS_FROM_FILE));
 552     cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
 553             VIEWS_LOCAL_PDB));
 554
 555     cmb_filterOption.addItemListener(this);
 556   }
 557
 558   /**
 559    * Updates the displayed view based on the selected filter option
 560    */
 561   protected void updateCurrentView()
 562   {
 563     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 564             .getSelectedItem());
 565     layout_switchableViews.show(pnl_switchableViews,
 566             selectedFilterOpt.getView());
 567     String filterTitle = mainFrame.getTitle();
 568     mainFrame.setTitle(frameTitle);
 569     chk_invertFilter.setVisible(false);
 570     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 571     {
 572       mainFrame.setTitle(filterTitle);
 573       chk_invertFilter.setVisible(true);
 574       filterResultSet(selectedFilterOpt.getValue());
 575     }
 576     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 577             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 578     {
 579       mainFrame.setTitle(MessageManager
 580               .getString("label.structure_chooser_manual_association"));
 581       idInputAssSeqPanel.loadCmbAssSeq();
 582       fileChooserAssSeqPanel.loadCmbAssSeq();
 583     }
 584     validateSelections();
 585   }
 586
 587   /**
 588    * Validates user selection and activates the view button if all parameters
 589    * are correct
 590    */
 591   @Override
 592   public void validateSelections()
 593   {
 594     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 595             .getSelectedItem());
 596     btn_view.setEnabled(false);
 597     String currentView = selectedFilterOpt.getView();
 598     if (currentView == VIEWS_FILTER)
 599     {
 600       if (getResultTable().getSelectedRows().length > 0)
 601       {
 602         btn_view.setEnabled(true);
 603       }
 604     }
 605     else if (currentView == VIEWS_LOCAL_PDB)
 606     {
 607       if (tbl_local_pdb.getSelectedRows().length > 0)
 608       {
 609         btn_view.setEnabled(true);
 610       }
 611     }
 612     else if (currentView == VIEWS_ENTER_ID)
 613     {
 614       validateAssociationEnterPdb();
 615     }
 616     else if (currentView == VIEWS_FROM_FILE)
 617     {
 618       validateAssociationFromFile();
 619     }
 620   }
 621
 622   /**
 623    * Validates inputs from the Manual PDB entry panel
 624    */
 625   public void validateAssociationEnterPdb()
 626   {
 627     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 628             .getCmb_assSeq().getSelectedItem();
 629     lbl_pdbManualFetchStatus.setIcon(errorImage);
 630     lbl_pdbManualFetchStatus.setToolTipText("");
 631     if (txt_search.getText().length() > 0)
 632     {
 633       lbl_pdbManualFetchStatus
 634               .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 635                       .formatMessage("info.no_pdb_entry_found_for",
 636                               txt_search.getText())));
 637     }
 638
 639     if (errorWarning.length() > 0)
 640     {
 641       lbl_pdbManualFetchStatus.setIcon(warningImage);
 642       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
 643               true, errorWarning.toString()));
 644     }
 645
 646     if (selectedSequences.length == 1
 647             || !assSeqOpt.getName().equalsIgnoreCase(
 648                     "-Select Associated Seq-"))
 649     {
 650       txt_search.setEnabled(true);
 651       if (isValidPBDEntry)
 652       {
 653         btn_view.setEnabled(true);
 654         lbl_pdbManualFetchStatus.setToolTipText("");
 655         lbl_pdbManualFetchStatus.setIcon(goodImage);
 656       }
 657     }
 658     else
 659     {
 660       txt_search.setEnabled(false);
 661       lbl_pdbManualFetchStatus.setIcon(errorImage);
 662     }
 663   }
 664
 665   /**
 666    * Validates inputs for the manual PDB file selection options
 667    */
 668   public void validateAssociationFromFile()
 669   {
 670     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
 671             .getCmb_assSeq().getSelectedItem();
 672     lbl_fromFileStatus.setIcon(errorImage);
 673     if (selectedSequences.length == 1
 674             || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
 675                     "-Select Associated Seq-")))
 676     {
 677       btn_pdbFromFile.setEnabled(true);
 678       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
 679       {
 680         btn_view.setEnabled(true);
 681         lbl_fromFileStatus.setIcon(goodImage);
 682       }
 683     }
 684     else
 685     {
 686       btn_pdbFromFile.setEnabled(false);
 687       lbl_fromFileStatus.setIcon(errorImage);
 688     }
 689   }
 690
 691   @Override
 692   public void cmbAssSeqStateChanged()
 693   {
 694     validateSelections();
 695   }
 696
 697   /**
 698    * Handles the state change event for the 'filter' combo-box and 'invert'
 699    * check-box
 700    */
 701   @Override
 702   protected void stateChanged(ItemEvent e)
 703   {
 704     if (e.getSource() instanceof JCheckBox)
 705     {
 706       updateCurrentView();
 707     }
 708     else
 709     {
 710       if (e.getStateChange() == ItemEvent.SELECTED)
 711       {
 712         updateCurrentView();
 713       }
 714     }
 715
 716   }
 717
 718   /**
 719    * Handles action event for btn_ok
 720    */
 721   @Override
 722   public void ok_ActionPerformed()
 723   {
 724     final long progressSessionId = System.currentTimeMillis();
 725     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 726     final int preferredHeight = pnl_filter.getHeight();
 727     ssm.setProgressIndicator(this);
 728     ssm.setProgressSessionId(progressSessionId);
 729     new Thread(new Runnable()
 730     {
 731       @Override
 732       public void run()
 733       {
 734         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 735                 .getSelectedItem());
 736         String currentView = selectedFilterOpt.getView();
 737         if (currentView == VIEWS_FILTER)
 738         {
 739           int pdbIdColIndex = getResultTable().getColumn("PDB Id")
 740                   .getModelIndex();
 741           int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
 742                   .getModelIndex();
 743           int[] selectedRows = getResultTable().getSelectedRows();
 744           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 745           int count = 0;
 746           ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
 747           for (int row : selectedRows)
 748           {
 749             String pdbIdStr = getResultTable().getValueAt(row,
 750                     pdbIdColIndex).toString();
 751             SequenceI selectedSeq = (SequenceI) getResultTable()
 752                     .getValueAt(row, refSeqColIndex);
 753             selectedSeqsToView.add(selectedSeq);
 754             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
 755             if (pdbEntry == null)
 756             {
 757               pdbEntry = getFindEntry(pdbIdStr,
 758                       selectedSeq.getAllPDBEntries());
 759             }
 760             if (pdbEntry == null)
 761             {
 762               pdbEntry = new PDBEntry();
 763               pdbEntry.setId(pdbIdStr);
 764               pdbEntry.setType(PDBEntry.Type.PDB);
 765               selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
 766             }
 767             pdbEntriesToView[count++] = pdbEntry;
 768           }
 769           SequenceI[] selectedSeqs = selectedSeqsToView
 770                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 771           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
 772         }
 773         else if (currentView == VIEWS_LOCAL_PDB)
 774         {
 775           int[] selectedRows = tbl_local_pdb.getSelectedRows();
 776           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 777           int count = 0;
 778           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
 779                   .getModelIndex();
 780           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
 781                   .getModelIndex();
 782           ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
 783           for (int row : selectedRows)
 784           {
 785             PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
 786                     pdbIdColIndex);
 787             pdbEntriesToView[count++] = pdbEntry;
 788             SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(
 789                     row, refSeqColIndex);
 790             selectedSeqsToView.add(selectedSeq);
 791           }
 792           SequenceI[] selectedSeqs = selectedSeqsToView
 793                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 794           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
 795         }
 796         else if (currentView == VIEWS_ENTER_ID)
 797         {
 798           SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
 799                   .getCmb_assSeq().getSelectedItem()).getSequence();
 800           if (userSelectedSeq != null)
 801           {
 802             selectedSequence = userSelectedSeq;
 803           }
 804
 805           String pdbIdStr = txt_search.getText();
 806           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
 807           if (pdbEntry == null)
 808           {
 809             pdbEntry = new PDBEntry();
 810             if (pdbIdStr.split(":").length > 1)
 811             {
 812               pdbEntry.setId(pdbIdStr.split(":")[0]);
 813               pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
 814             }
 815             else
 816             {
 817               pdbEntry.setId(pdbIdStr);
 818             }
 819             pdbEntry.setType(PDBEntry.Type.PDB);
 820             selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
 821           }
 822
 823           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
 824           launchStructureViewer(ssm, pdbEntriesToView, ap,
 825                   new SequenceI[] { selectedSequence });
 826         }
 827         else if (currentView == VIEWS_FROM_FILE)
 828         {
 829           SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
 830                   .getCmb_assSeq().getSelectedItem()).getSequence();
 831           if (userSelectedSeq != null)
 832           {
 833             selectedSequence = userSelectedSeq;
 834           }
 835           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 836                   .associatePdbWithSeq(selectedPdbFileName,
 837                           jalview.io.AppletFormatAdapter.FILE,
 838                           selectedSequence, true, Desktop.instance);
 839
 840           launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
 841                   new SequenceI[] { selectedSequence });
 842         }
 843         closeAction(preferredHeight);
 844       }
 845     }).start();
 846   }
 847
 848   private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
 849   {
 850     Objects.requireNonNull(id);
 851     Objects.requireNonNull(pdbEntries);
 852     PDBEntry foundEntry = null;
 853     for (PDBEntry entry : pdbEntries)
 854     {
 855       if (entry.getId().equalsIgnoreCase(id))
 856       {
 857         return entry;
 858       }
 859     }
 860     return foundEntry;
 861   }
 862
 863   private void launchStructureViewer(StructureSelectionManager ssm,
 864           final PDBEntry[] pdbEntriesToView,
 865           final AlignmentPanel alignPanel, SequenceI[] sequences)
 866   {
 867     ssm.setProgressBar(MessageManager
 868             .getString("status.launching_3d_structure_viewer"));
 869     final StructureViewer sViewer = new StructureViewer(ssm);
 870
 871     if (SiftsSettings.isMapWithSifts())
 872     {
 873       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
 874       int p = 0;
 875       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
 876       // real PDB ID. For moment, we can also safely do this if there is already
 877       // a known mapping between the PDBEntry and the sequence.
 878       for (SequenceI seq : sequences)
 879       {
 880         PDBEntry pdbe = pdbEntriesToView[p++];
 881         if (pdbe != null && pdbe.getFile() != null)
 882         {
 883           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
 884           if (smm != null && smm.length > 0)
 885           {
 886             for (StructureMapping sm : smm)
 887             {
 888               if (sm.getSequence() == seq)
 889               {
 890                 continue;
 891               }
 892             }
 893           }
 894         }
 895         if (seq.getPrimaryDBRefs().size() == 0)
 896         {
 897           seqsWithoutSourceDBRef.add(seq);
 898           continue;
 899         }
 900       }
 901       if (!seqsWithoutSourceDBRef.isEmpty())
 902       {
 903         int y = seqsWithoutSourceDBRef.size();
 904         ssm.setProgressBar(null);
 905         ssm.setProgressBar(MessageManager.formatMessage(
 906                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
 907                 y));
 908         SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
 909         int x = 0;
 910         for (SequenceI fSeq : seqsWithoutSourceDBRef)
 911         {
 912           seqWithoutSrcDBRef[x++] = fSeq;
 913         }
 914         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
 915         dbRefFetcher.fetchDBRefs(true);
 916       }
 917     }
 918     if (pdbEntriesToView.length > 1)
 919     {
 920       ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
 921       for (SequenceI seq : sequences)
 922       {
 923         seqsMap.add(new SequenceI[] { seq });
 924       }
 925       SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
 926       ssm.setProgressBar(null);
 927       ssm.setProgressBar(MessageManager
 928               .getString("status.fetching_3d_structures_for_selected_entries"));
 929       sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
 930     }
 931     else
 932     {
 933       ssm.setProgressBar(null);
 934       ssm.setProgressBar(MessageManager.formatMessage(
 935               "status.fetching_3d_structures_for",
 936               pdbEntriesToView[0].getId()));
 937       sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
 938     }
 939   }
 940
 941   /**
 942    * Populates the combo-box used in associating manually fetched structures to
 943    * a unique sequence when more than one sequence selection is made.
 944    */
 945   @Override
 946   public void populateCmbAssociateSeqOptions(
 947           JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
 948   {
 949     cmb_assSeq.removeAllItems();
 950     cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
 951             null));
 952     lbl_associateSeq.setVisible(false);
 953     if (selectedSequences.length > 1)
 954     {
 955       for (SequenceI seq : selectedSequences)
 956       {
 957         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
 958       }
 959     }
 960     else
 961     {
 962       String seqName = selectedSequence.getDisplayId(false);
 963       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
 964       lbl_associateSeq.setText(seqName);
 965       lbl_associateSeq.setVisible(true);
 966       cmb_assSeq.setVisible(false);
 967     }
 968   }
 969
 970   public boolean isStructuresDiscovered()
 971   {
 972     return discoveredStructuresSet != null
 973             && !discoveredStructuresSet.isEmpty();
 974   }
 975
 976   public Collection<FTSData> getDiscoveredStructuresSet()
 977   {
 978     return discoveredStructuresSet;
 979   }
 980
 981   @Override
 982   protected void txt_search_ActionPerformed()
 983   {
 984     new Thread()
 985     {
 986       @Override
 987       public void run()
 988       {
 989         errorWarning.setLength(0);
 990         isValidPBDEntry = false;
 991         if (txt_search.getText().length() > 0)
 992         {
 993           String searchTerm = txt_search.getText().toLowerCase();
 994           searchTerm = searchTerm.split(":")[0];
 995           // System.out.println(">>>>> search term : " + searchTerm);
 996           List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 997           FTSRestRequest pdbRequest = new FTSRestRequest();
 998           pdbRequest.setAllowEmptySeq(false);
 999           pdbRequest.setResponseSize(1);
1000           pdbRequest.setFieldToSearchBy("(pdb_id:");
1001           pdbRequest.setWantedFields(wantedFields);
1002           pdbRequest.setSearchTerm(searchTerm + ")");
1003           pdbRequest.setAssociatedSequence(selectedSequence);
1004           pdbRestCleint = PDBFTSRestClient.getInstance();
1005           wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
1006           FTSRestResponse resultList;
1007           try
1008           {
1009             resultList = pdbRestCleint.executeRequest(pdbRequest);
1010           } catch (Exception e)
1011           {
1012             errorWarning.append(e.getMessage());
1013             return;
1014           } finally
1015           {
1016             validateSelections();
1017           }
1018           if (resultList.getSearchSummary() != null
1019                   && resultList.getSearchSummary().size() > 0)
1020           {
1021             isValidPBDEntry = true;
1022           }
1023         }
1024         validateSelections();
1025       }
1026     }.start();
1027   }
1028
1029   @Override
1030   public void tabRefresh()
1031   {
1032     if (selectedSequences != null)
1033     {
1034       Thread refreshThread = new Thread(new Runnable()
1035       {
1036         @Override
1037         public void run()
1038         {
1039           fetchStructuresMetaData();
1040           filterResultSet(((FilterOption) cmb_filterOption
1041                   .getSelectedItem()).getValue());
1042         }
1043       });
1044       refreshThread.start();
1045     }
1046   }
1047
1048   public class PDBEntryTableModel extends AbstractTableModel
1049   {
1050     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
1051
1052     private List<CachedPDB> pdbEntries;
1053
1054     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1055     {
1056       this.pdbEntries = new ArrayList<CachedPDB>(pdbEntries);
1057     }
1058
1059     @Override
1060     public String getColumnName(int columnIndex)
1061     {
1062       return columns[columnIndex];
1063     }
1064
1065     @Override
1066     public int getRowCount()
1067     {
1068       return pdbEntries.size();
1069     }
1070
1071     @Override
1072     public int getColumnCount()
1073     {
1074       return columns.length;
1075     }
1076
1077     @Override
1078     public boolean isCellEditable(int row, int column)
1079     {
1080       return false;
1081     }
1082
1083     @Override
1084     public Object getValueAt(int rowIndex, int columnIndex)
1085     {
1086       Object value = "??";
1087       CachedPDB entry = pdbEntries.get(rowIndex);
1088       switch (columnIndex)
1089       {
1090       case 0:
1091         value = entry.getSequence();
1092         break;
1093       case 1:
1094         value = entry.getPdbEntry();
1095         break;
1096       case 2:
1097         value = entry.getPdbEntry().getChainCode() == null ? "_" : entry
1098                 .getPdbEntry().getChainCode();
1099         break;
1100       case 3:
1101         value = entry.getPdbEntry().getType();
1102         break;
1103       case 4:
1104         value = entry.getPdbEntry().getFile();
1105         break;
1106       }
1107       return value;
1108     }
1109
1110     @Override
1111     public Class<?> getColumnClass(int columnIndex)
1112     {
1113       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1114     }
1115
1116     public CachedPDB getPDBEntryAt(int row)
1117     {
1118       return pdbEntries.get(row);
1119     }
1120
1121   }
1122
1123   private class CachedPDB
1124   {
1125     private SequenceI sequence;
1126
1127     private PDBEntry pdbEntry;
1128
1129     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1130     {
1131       this.sequence = sequence;
1132       this.pdbEntry = pdbEntry;
1133     }
1134
1135     public SequenceI getSequence()
1136     {
1137       return sequence;
1138     }
1139
1140     public PDBEntry getPdbEntry()
1141     {
1142       return pdbEntry;
1143     }
1144
1145   }
1146
1147   private IProgressIndicator progressBar;
1148
1149   @Override
1150   public void setProgressBar(String message, long id)
1151   {
1152     progressBar.setProgressBar(message, id);
1153   }
1154
1155   @Override
1156   public void registerHandler(long id, IProgressIndicatorHandler handler)
1157   {
1158     progressBar.registerHandler(id, handler);
1159   }
1160
1161   @Override
1162   public boolean operationInProgress()
1163   {
1164     return progressBar.operationInProgress();
1165   }
1166 }