src/jalview/gui/StructureChooser.java

   1 /*
   2
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   4  * Copyright (C) 2014 The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3
  11  * of the License, or (at your option) any later version.
  12  *
  13  * Jalview is distributed in the hope that it will be useful, but
  14  * WITHOUT ANY WARRANTY; without even the implied warranty
  15  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  16  * PURPOSE.  See the GNU General Public License for more details.
  17  *
  18  * You should have received a copy of the GNU General Public License
  19  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  20  * The Jalview Authors are detailed in the 'AUTHORS' file.
  21  */
  22
  23 package jalview.gui;
  24
  25 import jalview.datamodel.DBRefEntry;
  26 import jalview.datamodel.PDBEntry;
  27 import jalview.datamodel.SequenceI;
  28 import jalview.jbgui.GStructureChooser;
  29 import jalview.jbgui.PDBDocFieldPreferences;
  30 import jalview.structure.StructureSelectionManager;
  31 import jalview.util.MessageManager;
  32 import jalview.ws.dbsources.PDBRestClient;
  33 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
  34 import jalview.ws.uimodel.PDBRestRequest;
  35 import jalview.ws.uimodel.PDBRestResponse;
  36 import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
  37
  38 import java.awt.event.ItemEvent;
  39 import java.util.ArrayList;
  40 import java.util.Collection;
  41 import java.util.HashSet;
  42 import java.util.Hashtable;
  43 import java.util.LinkedHashSet;
  44 import java.util.List;
  45
  46 import javax.swing.JCheckBox;
  47 import javax.swing.JComboBox;
  48 import javax.swing.JLabel;
  49 import javax.swing.JOptionPane;
  50 import javax.swing.table.DefaultTableModel;
  51
  52
  53 /**
  54  * Provides the behaviors for the Structure chooser Panel
  55  *
  56  * @author tcnofoegbu
  57  *
  58  */
  59 @SuppressWarnings("serial")
  60 public class StructureChooser extends GStructureChooser
  61 {
  62   private boolean structuresDiscovered = false;
  63
  64   private SequenceI selectedSequence;
  65
  66   private SequenceI[] selectedSequences;
  67
  68   private IProgressIndicator progressIndicator;
  69
  70   private Collection<PDBResponseSummary> discoveredStructuresSet;
  71
  72   private PDBRestRequest lastPdbRequest;
  73
  74   private PDBRestClient pdbRestCleint;
  75
  76   private String selectedPdbFileName;
  77
  78   private boolean isValidPBDEntry;
  79
  80   private static Hashtable<String, PDBEntry> cachedEntryMap;
  81
  82   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
  83           AlignmentPanel ap)
  84   {
  85     this.ap = ap;
  86     this.selectedSequence = selectedSeq;
  87     this.selectedSequences = selectedSeqs;
  88     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
  89     init();
  90   }
  91
  92   /**
  93    * Initializes parameters used by the Structure Chooser Panel
  94    */
  95   public void init()
  96   {
  97     Thread discoverPDBStructuresThread = new Thread(new Runnable()
  98     {
  99       @Override
 100       public void run()
 101       {
 102         long startTime = System.currentTimeMillis();
 103         updateProgressIndicator(MessageManager
 104                 .getString("status.loading_cached_pdb_entries"), startTime);
 105         loadLocalCachedPDBEntries();
 106         updateProgressIndicator(null, startTime);
 107         updateProgressIndicator(MessageManager
 108                 .getString("status.searching_for_pdb_structures"),
 109                 startTime);
 110         fetchStructuresMetaData();
 111         populateFilterComboBox();
 112         updateProgressIndicator(null, startTime);
 113         mainFrame.setVisible(true);
 114         updateCurrentView();
 115       }
 116     });
 117     discoverPDBStructuresThread.start();
 118   }
 119
 120   /**
 121    * Updates the progress indicator with the specified message
 122    *
 123    * @param message
 124    *          displayed message for the operation
 125    * @param id
 126    *          unique handle for this indicator
 127    */
 128   public void updateProgressIndicator(String message, long id)
 129   {
 130     if (progressIndicator != null)
 131     {
 132       progressIndicator.setProgressBar(message, id);
 133     }
 134   }
 135
 136   /**
 137    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
 138    * selection group
 139    */
 140   public void fetchStructuresMetaData()
 141   {
 142     long startTime = System.currentTimeMillis();
 143     Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
 144             .getStructureSummaryFields();
 145
 146     discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
 147     HashSet<String> errors = new HashSet<String>();
 148     for (SequenceI seq : selectedSequences)
 149     {
 150       PDBRestRequest pdbRequest = new PDBRestRequest();
 151       pdbRequest.setAllowEmptySeq(false);
 152       pdbRequest.setResponseSize(500);
 153       pdbRequest.setFieldToSearchBy("(text:");
 154       pdbRequest.setWantedFields(wantedFields);
 155       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 156       pdbRequest.setAssociatedSequence(seq);
 157       pdbRestCleint = new PDBRestClient();
 158       PDBRestResponse resultList;
 159       try
 160       {
 161         resultList = pdbRestCleint.executeRequest(pdbRequest);
 162       } catch (Exception e)
 163       {
 164         e.printStackTrace();
 165         errors.add(e.getMessage());
 166         continue;
 167       }
 168       lastPdbRequest = pdbRequest;
 169       if (resultList.getSearchSummary() != null
 170               && !resultList.getSearchSummary().isEmpty())
 171       {
 172         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 173         updateSequencePDBEntries(seq, resultList.getSearchSummary());
 174       }
 175     }
 176
 177     int noOfStructuresFound = 0;
 178     String totalTime = (System.currentTimeMillis() - startTime)
 179             + " milli secs";
 180     if (discoveredStructuresSet != null
 181             && !discoveredStructuresSet.isEmpty())
 182     {
 183       tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
 184               discoveredStructuresSet));
 185       structuresDiscovered = true;
 186       noOfStructuresFound = discoveredStructuresSet.size();
 187       mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
 188               + " Found (" + totalTime + ")");
 189     }
 190     else
 191     {
 192       mainFrame
 193 .setTitle("Structure Chooser - Manual association");
 194       if (errors.size() > 0)
 195       {
 196         StringBuilder errorMsg = new StringBuilder();
 197         // "Operation was unsuccessful due to the following: \n");
 198         for (String error : errors)
 199         {
 200           errorMsg.append(error).append("\n");
 201         }
 202         JOptionPane.showMessageDialog(this, errorMsg.toString(),
 203                 "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
 204       }
 205     }
 206   }
 207
 208   public void loadLocalCachedPDBEntries()
 209   {
 210     DefaultTableModel tableModel = new DefaultTableModel()
 211     {
 212       @Override
 213       public boolean isCellEditable(int row, int column)
 214       {
 215         return false;
 216       }
 217     };
 218     tableModel.addColumn("Ref Sequence");
 219     tableModel.addColumn("PDB Id");
 220     tableModel.addColumn("Chain");
 221     tableModel.addColumn("Type");
 222     tableModel.addColumn("File");
 223     cachedEntryMap = new Hashtable<String, PDBEntry>();
 224     for (SequenceI seq : selectedSequences)
 225     {
 226       if (seq.getDatasetSequence() != null
 227               && seq.getDatasetSequence().getPDBId() != null)
 228       {
 229         for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId())
 230         {
 231
 232           String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry
 233                   .getChainCode();
 234           Object[] pdbEntryRowData = new Object[]
 235           { seq, pdbEntry.getId(),
 236  chain,
 237               pdbEntry.getType(),
 238               pdbEntry.getFile() };
 239           if (pdbEntry.getFile() != null)
 240           {
 241             tableModel.addRow(pdbEntryRowData);
 242           }
 243           cachedEntryMap.put(pdbEntry.getId().toLowerCase(),
 244                   pdbEntry);
 245         }
 246       }
 247     }
 248     tbl_local_pdb.setModel(tableModel);
 249   }
 250
 251   /**
 252    * Update the PDBEntry for a given sequence with values retrieved from
 253    * PDBResponseSummary
 254    *
 255    * @param seq
 256    *          the Sequence to update its DBRef entry
 257    * @param responseSummaries
 258    *          a collection of PDBResponseSummary
 259    */
 260   public void updateSequencePDBEntries(SequenceI seq,
 261           Collection<PDBResponseSummary> responseSummaries)
 262   {
 263     for (PDBResponseSummary response : responseSummaries)
 264     {
 265       String pdbIdStr = response.getPdbId();
 266       PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
 267       if (pdbEntry == null)
 268       {
 269         pdbEntry = new PDBEntry();
 270         pdbEntry.setId(pdbIdStr);
 271         pdbEntry.setType(PDBEntry.Type.PDB);
 272       }
 273       seq.getDatasetSequence().addPDBId(pdbEntry);
 274     }
 275   }
 276
 277   /**
 278    * Builds a query string for a given sequences using its DBRef entries
 279    *
 280    * @param seq
 281    *          the sequences to build a query for
 282    * @return the built query string
 283    */
 284
 285   public static String buildQuery(SequenceI seq)
 286   {
 287     HashSet<String> seqRefs = new LinkedHashSet<String>();
 288     String seqName = seq.getName();
 289     String[] names = seqName.toLowerCase().split("\\|");
 290     for (String name : names)
 291     {
 292       // System.out.println("Found name : " + name);
 293       name.trim();
 294       if (isValidSeqName(name))
 295       {
 296         seqRefs.add(name);
 297       }
 298     }
 299
 300     if (seq.getPDBId() != null)
 301     {
 302       for (PDBEntry entry : seq.getPDBId())
 303       {
 304         if (isValidSeqName(entry.getId()))
 305         {
 306           seqRefs.add(entry.getId());
 307         }
 308       }
 309     }
 310
 311     if (seq.getDBRef() != null && seq.getDBRef().length != 0)
 312     {
 313       int count = 0;
 314       for (DBRefEntry dbRef : seq.getDBRef())
 315       {
 316         if (isValidSeqName(getDBRefId(dbRef)))
 317         {
 318           seqRefs.add(getDBRefId(dbRef));
 319         }
 320         ++count;
 321         if (count > 10)
 322         {
 323           break;
 324         }
 325       }
 326     }
 327
 328     StringBuilder queryBuilder = new StringBuilder();
 329     for (String seqRef : seqRefs)
 330     {
 331       queryBuilder.append("text:").append(seqRef).append(" OR ");
 332     }
 333     int endIndex = queryBuilder.lastIndexOf(" OR ");
 334     String query = queryBuilder.toString().substring(5, endIndex);
 335     return query;
 336   }
 337
 338   /**
 339    * Ensures sequence ref names are not less than 3 characters and does not
 340    * contain a database name
 341    *
 342    * @param seqName
 343    * @return
 344    */
 345   public static boolean isValidSeqName(String seqName)
 346   {
 347     // System.out.println("seqName : " + seqName);
 348     String ignoreList = "pdb,uniprot,swiss-prot";
 349     if (seqName.length() < 3)
 350     {
 351       return false;
 352     }
 353     if (seqName.contains(":"))
 354     {
 355       return false;
 356     }
 357     seqName = seqName.toLowerCase();
 358     for (String ignoredEntry : ignoreList.split(","))
 359     {
 360       if (seqName.contains(ignoredEntry))
 361       {
 362         return false;
 363       }
 364     }
 365     return true;
 366   }
 367
 368   public static String getDBRefId(DBRefEntry dbRef)
 369   {
 370     String ref = dbRef.getAccessionId().replaceAll("GO:", "");
 371     return ref;
 372   }
 373
 374   /**
 375    * Filters a given list of discovered structures based on supplied argument
 376    *
 377    * @param fieldToFilterBy
 378    *          the field to filter by
 379    */
 380   public void filterResultSet(final String fieldToFilterBy)
 381   {
 382     Thread filterThread = new Thread(new Runnable()
 383     {
 384       @Override
 385       public void run()
 386       {
 387         long startTime = System.currentTimeMillis();
 388         lbl_loading.setVisible(true);
 389         Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
 390                 .getStructureSummaryFields();
 391         Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
 392         HashSet<String> errors = new HashSet<String>();
 393         for (SequenceI seq : selectedSequences)
 394         {
 395           PDBRestRequest pdbRequest = new PDBRestRequest();
 396           pdbRequest.setAllowEmptySeq(false);
 397           pdbRequest.setResponseSize(1);
 398           pdbRequest.setFieldToSearchBy("(text:");
 399           pdbRequest.setFieldToSortBy(fieldToFilterBy,
 400                   !chk_invertFilter.isSelected());
 401           pdbRequest.setSearchTerm(buildQuery(seq) + ")");
 402           pdbRequest.setWantedFields(wantedFields);
 403           pdbRequest.setAssociatedSequence(seq);
 404           pdbRestCleint = new PDBRestClient();
 405           PDBRestResponse resultList;
 406           try
 407           {
 408             resultList = pdbRestCleint.executeRequest(pdbRequest);
 409           } catch (Exception e)
 410           {
 411             e.printStackTrace();
 412             errors.add(e.getMessage());
 413             continue;
 414           }
 415           lastPdbRequest = pdbRequest;
 416           if (resultList.getSearchSummary() != null
 417                   && !resultList.getSearchSummary().isEmpty())
 418           {
 419             filteredResponse.addAll(resultList.getSearchSummary());
 420           }
 421         }
 422
 423         String totalTime = (System.currentTimeMillis() - startTime)
 424                 + " milli secs";
 425         if (!filteredResponse.isEmpty())
 426         {
 427           final int filterResponseCount = filteredResponse.size();
 428           Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
 429           reorderedStructuresSet.addAll(filteredResponse);
 430           reorderedStructuresSet.addAll(discoveredStructuresSet);
 431           tbl_summary.setModel(PDBRestResponse.getTableModel(
 432                   lastPdbRequest, reorderedStructuresSet));
 433
 434           // Update table selection model here
 435           tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
 436
 437           mainFrame.setTitle("Structure Chooser - Filter time ("
 438                   + totalTime + ")");
 439         }
 440         else
 441         {
 442           mainFrame.setTitle("Structure Chooser - Filter time ("
 443                   + totalTime + ")");
 444           if (errors.size() > 0)
 445           {
 446             StringBuilder errorMsg = new StringBuilder();
 447             for (String error : errors)
 448             {
 449               errorMsg.append(error).append("\n");
 450             }
 451             JOptionPane.showMessageDialog(null, errorMsg.toString(),
 452                     "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
 453           }
 454         }
 455
 456         lbl_loading.setVisible(false);
 457
 458         validateSelections();
 459       }
 460     });
 461     filterThread.start();
 462   }
 463
 464
 465   /**
 466    * Handles action event for btn_pdbFromFile
 467    */
 468   public void pdbFromFile_actionPerformed()
 469   {
 470     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 471             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 472     chooser.setFileView(new jalview.io.JalviewFileView());
 473     chooser.setDialogTitle(MessageManager.formatMessage(
 474             "label.select_pdb_file_for", new String[]
 475             { selectedSequence.getDisplayId(false) }));
 476     chooser.setToolTipText(MessageManager.formatMessage(
 477             "label.load_pdb_file_associate_with_sequence", new String[]
 478             { selectedSequence.getDisplayId(false) }));
 479
 480     int value = chooser.showOpenDialog(null);
 481     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
 482     {
 483       selectedPdbFileName = chooser.getSelectedFile().getPath();
 484       jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
 485       validateSelections();
 486     }
 487   }
 488
 489   /**
 490    * Populates the filter combo-box options dynamically depending on discovered
 491    * structures
 492    */
 493   protected void populateFilterComboBox()
 494   {
 495     if (isStructuresDiscovered())
 496     {
 497       cmb_filterOption.addItem(new FilterOption("Best Quality",
 498               PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
 499       cmb_filterOption.addItem(new FilterOption("Best UniProt Coverage",
 500               PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER));
 501       cmb_filterOption.addItem(new FilterOption("Highest Resolution",
 502               PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
 503       cmb_filterOption.addItem(new FilterOption("Highest Protein Chain",
 504               PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER));
 505       cmb_filterOption.addItem(new FilterOption("Highest Bound Molecules",
 506               PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER));
 507       cmb_filterOption.addItem(new FilterOption("Highest Polymer Residues",
 508               PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER));
 509     }
 510     cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
 511             VIEWS_ENTER_ID));
 512     cmb_filterOption.addItem(new FilterOption("From File", "-",
 513             VIEWS_FROM_FILE));
 514     cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
 515             VIEWS_LOCAL_PDB));
 516   }
 517
 518   /**
 519    * Updates the displayed view based on the selected filter option
 520    */
 521   protected void updateCurrentView()
 522   {
 523     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 524             .getSelectedItem());
 525     layout_switchableViews.show(pnl_switchableViews,
 526             selectedFilterOpt.getView());
 527     String filterTitle = mainFrame.getTitle();
 528     mainFrame.setTitle(frameTitle);
 529     chk_invertFilter.setVisible(false);
 530     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 531     {
 532       mainFrame.setTitle(filterTitle);
 533       chk_invertFilter.setVisible(true);
 534       filterResultSet(selectedFilterOpt.getValue());
 535     }
 536     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 537             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 538     {
 539       mainFrame.setTitle(filterTitle);
 540       idInputAssSeqPanel.loadCmbAssSeq();
 541       fileChooserAssSeqPanel.loadCmbAssSeq();
 542     }
 543     validateSelections();
 544   }
 545
 546   /**
 547    * Validates user selection and activates the view button if all parameters
 548    * are correct
 549    */
 550   public void validateSelections()
 551   {
 552     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 553             .getSelectedItem());
 554     btn_view.setEnabled(false);
 555     String currentView = selectedFilterOpt.getView();
 556     if (currentView == VIEWS_FILTER)
 557     {
 558       if (tbl_summary.getSelectedRows().length > 0)
 559       {
 560         btn_view.setEnabled(true);
 561       }
 562     }
 563     else if (currentView == VIEWS_LOCAL_PDB)
 564     {
 565       if (tbl_local_pdb.getSelectedRows().length > 0)
 566       {
 567         btn_view.setEnabled(true);
 568       }
 569     }
 570     else if (currentView == VIEWS_ENTER_ID)
 571     {
 572       validateAssociationEnterPdb();
 573     }
 574     else if (currentView == VIEWS_FROM_FILE)
 575     {
 576       validateAssociationFromFile();
 577     }
 578   }
 579
 580   /**
 581    * Validates inputs from the Manual PDB entry panel
 582    */
 583   public void validateAssociationEnterPdb()
 584   {
 585     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 586             .getCmb_assSeq().getSelectedItem();
 587     lbl_pdbManualFetchStatus.setIcon(errorImage);
 588     lbl_pdbManualFetchStatus.setToolTipText("");
 589     if (txt_search.getText().length() > 0)
 590     {
 591       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
 592               true, "No PDB entry found for \'" + txt_search.getText()
 593                       + "\'"));
 594     }
 595
 596     if (errorWarning.length() > 0)
 597     {
 598       lbl_pdbManualFetchStatus.setIcon(warningImage);
 599       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
 600               true, errorWarning.toString()));
 601     }
 602
 603     if (selectedSequences.length == 1
 604             || !assSeqOpt.getName().equalsIgnoreCase(
 605                     "-Select Associated Seq-"))
 606     {
 607       txt_search.setEnabled(true);
 608       if (isValidPBDEntry)
 609       {
 610         btn_view.setEnabled(true);
 611         lbl_pdbManualFetchStatus.setToolTipText("");
 612         lbl_pdbManualFetchStatus.setIcon(goodImage);
 613       }
 614     }
 615     else
 616     {
 617       txt_search.setEnabled(false);
 618       lbl_pdbManualFetchStatus.setIcon(errorImage);
 619     }
 620   }
 621
 622   /**
 623    * Validates inputs for the manual PDB file selection options
 624    */
 625   public void validateAssociationFromFile()
 626   {
 627     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
 628             .getCmb_assSeq().getSelectedItem();
 629     lbl_fromFileStatus.setIcon(errorImage);
 630     if (selectedSequences.length == 1
 631             || (assSeqOpt != null
 632             && !assSeqOpt.getName().equalsIgnoreCase(
 633                     "-Select Associated Seq-")))
 634     {
 635       btn_pdbFromFile.setEnabled(true);
 636       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
 637       {
 638         btn_view.setEnabled(true);
 639         lbl_fromFileStatus.setIcon(goodImage);
 640       }
 641     }
 642     else
 643     {
 644       btn_pdbFromFile.setEnabled(false);
 645       lbl_fromFileStatus.setIcon(errorImage);
 646     }
 647   }
 648
 649   @Override
 650   public void cmbAssSeqStateChanged()
 651   {
 652     validateSelections();
 653   }
 654
 655   /**
 656    * Handles the state change event for the 'filter' combo-box and 'invert'
 657    * check-box
 658    */
 659   @Override
 660   protected void stateChanged(ItemEvent e)
 661   {
 662     if (e.getSource() instanceof JCheckBox)
 663     {
 664       updateCurrentView();
 665     }
 666     else
 667     {
 668       if (e.getStateChange() == ItemEvent.SELECTED)
 669       {
 670         updateCurrentView();
 671       }
 672     }
 673
 674   }
 675
 676   /**
 677    * Handles action event for btn_ok
 678    */
 679   @Override
 680   public void ok_ActionPerformed()
 681   {
 682     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 683             .getSelectedItem());
 684     String currentView = selectedFilterOpt.getView();
 685     if (currentView == VIEWS_FILTER)
 686     {
 687       int pdbIdColIndex = tbl_summary.getColumn(
 688               PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
 689       int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
 690               .getModelIndex();
 691       int[] selectedRows = tbl_summary.getSelectedRows();
 692       PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 693       int count = 0;
 694       ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
 695       for (int summaryRow : selectedRows)
 696       {
 697         String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdColIndex)
 698                 .toString();
 699         SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(
 700                 summaryRow, refSeqColIndex);
 701         selectedSeqsToView.add(selectedSeq);
 702         PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
 703         if (pdbEntry == null)
 704         {
 705           pdbEntry = new PDBEntry();
 706           pdbEntry.setId(pdbIdStr);
 707           pdbEntry.setType(PDBEntry.Type.PDB);
 708         }
 709         pdbEntriesToView[count++] = pdbEntry;
 710       }
 711       SequenceI[] selectedSeqs = selectedSeqsToView
 712               .toArray(new SequenceI[selectedSeqsToView.size()]);
 713       launchStructureViewer(ap.getStructureSelectionManager(),
 714               pdbEntriesToView, ap, selectedSeqs);
 715     }
 716     else if(currentView == VIEWS_LOCAL_PDB){
 717       int[] selectedRows = tbl_local_pdb.getSelectedRows();
 718       PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 719       int count = 0;
 720       int pdbIdColIndex = tbl_local_pdb.getColumn(
 721               PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
 722       int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
 723               .getModelIndex();
 724       ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
 725       for (int row : selectedRows)
 726       {
 727         String entryKey = tbl_local_pdb.getValueAt(row, pdbIdColIndex)
 728                 .toString()
 729                 .toLowerCase();
 730         pdbEntriesToView[count++] = cachedEntryMap.get(entryKey);
 731         SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
 732                 refSeqColIndex);
 733         selectedSeqsToView.add(selectedSeq);
 734       }
 735       SequenceI[] selectedSeqs = selectedSeqsToView
 736               .toArray(new SequenceI[selectedSeqsToView.size()]);
 737       launchStructureViewer(ap.getStructureSelectionManager(),
 738               pdbEntriesToView, ap, selectedSeqs);
 739     }
 740     else if (currentView == VIEWS_ENTER_ID)
 741     {
 742       SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
 743               .getCmb_assSeq().getSelectedItem()).getSequence();
 744       if (userSelectedSeq != null)
 745       {
 746         selectedSequence = userSelectedSeq;
 747       }
 748
 749       String pdbIdStr = txt_search.getText();
 750       PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
 751       if (pdbEntry == null)
 752       {
 753         pdbEntry = new PDBEntry();
 754         pdbEntry.setId(txt_search.getText());
 755         pdbEntry.setType(PDBEntry.Type.PDB);
 756       }
 757
 758       selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
 759       PDBEntry[] pdbEntriesToView = new PDBEntry[]
 760       { pdbEntry };
 761       launchStructureViewer(ap.getStructureSelectionManager(),
 762               pdbEntriesToView, ap, new SequenceI[]
 763               { selectedSequence });
 764     }
 765     else if (currentView == VIEWS_FROM_FILE)
 766     {
 767       SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
 768               .getCmb_assSeq().getSelectedItem()).getSequence();
 769       if (userSelectedSeq != null)
 770       {
 771         selectedSequence = userSelectedSeq;
 772       }
 773       PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 774               .associatePdbWithSeq(
 775               selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
 776               selectedSequence, true, Desktop.instance);
 777
 778       launchStructureViewer(ap.getStructureSelectionManager(),
 779               new PDBEntry[]
 780               { fileEntry }, ap, new SequenceI[]
 781               { selectedSequence });
 782     }
 783     mainFrame.dispose();
 784   }
 785
 786   private void launchStructureViewer(StructureSelectionManager ssm,
 787           PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
 788           SequenceI[] sequences)
 789   {
 790     StructureViewer sViewer = new StructureViewer(ssm);
 791     if (pdbEntriesToView.length > 1)
 792     {
 793       ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
 794       for (SequenceI seq : sequences)
 795       {
 796         seqsMap.add(new SequenceI[]
 797         { seq });
 798       }
 799       SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
 800       sViewer.viewStructures(pdbEntriesToView, collatedSeqs,
 801               alignPanel);
 802       // sViewer.viewStructures(pdbEntriesToView,
 803       // alignPanel.av.collateForPDB(pdbEntriesToView),
 804       // alignPanel);
 805     }
 806     else
 807     {
 808       sViewer.viewStructures(pdbEntriesToView[0], sequences,
 809               alignPanel);
 810     }
 811   }
 812
 813   /**
 814    * Populates the combo-box used in associating manually fetched structures to
 815    * a unique sequence when more than one sequence selection is made.
 816    */
 817   public void populateCmbAssociateSeqOptions(
 818           JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
 819   {
 820     cmb_assSeq.removeAllItems();
 821     cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
 822             null));
 823     // cmb_assSeq.addItem(new AssociateSeqOptions("Auto Detect", null));
 824     lbl_associateSeq.setVisible(false);
 825     if (selectedSequences.length > 1)
 826     {
 827       for (SequenceI seq : selectedSequences)
 828       {
 829         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
 830       }
 831     }
 832     else
 833     {
 834       String seqName = selectedSequence.getDisplayId(false);
 835       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
 836       lbl_associateSeq.setText(seqName);
 837       lbl_associateSeq.setVisible(true);
 838       cmb_assSeq.setVisible(false);
 839     }
 840   }
 841
 842   public boolean isStructuresDiscovered()
 843   {
 844     return structuresDiscovered;
 845   }
 846
 847   public void setStructuresDiscovered(boolean structuresDiscovered)
 848   {
 849     this.structuresDiscovered = structuresDiscovered;
 850   }
 851
 852   public Collection<PDBResponseSummary> getDiscoveredStructuresSet()
 853   {
 854     return discoveredStructuresSet;
 855   }
 856
 857   @Override
 858   protected void txt_search_ActionPerformed()
 859   {
 860     errorWarning.setLength(0);
 861     isValidPBDEntry = false;
 862     if (txt_search.getText().length() > 0)
 863     {
 864       List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
 865       wantedFields.add(PDBDocField.PDB_ID);
 866       PDBRestRequest pdbRequest = new PDBRestRequest();
 867       pdbRequest.setAllowEmptySeq(false);
 868       pdbRequest.setResponseSize(1);
 869       pdbRequest.setFieldToSearchBy("(pdb_id:");
 870       pdbRequest.setWantedFields(wantedFields);
 871       pdbRequest.setSearchTerm(txt_search.getText() + ")");
 872       pdbRequest.setAssociatedSequence(selectedSequence);
 873       pdbRestCleint = new PDBRestClient();
 874       PDBRestResponse resultList;
 875       try
 876       {
 877         resultList = pdbRestCleint.executeRequest(pdbRequest);
 878       } catch (Exception e)
 879       {
 880         errorWarning.append(e.getMessage());
 881         return;
 882       } finally
 883       {
 884         validateSelections();
 885       }
 886       if (resultList.getSearchSummary() != null
 887               && resultList.getSearchSummary().size() > 0)
 888       {
 889         isValidPBDEntry = true;
 890       }
 891     }
 892     validateSelections();
 893   }
 894
 895   @Override
 896   public void tabRefresh()
 897   {
 898     if (selectedSequences != null)
 899     {
 900       Thread refreshThread = new Thread(new Runnable()
 901       {
 902         @Override
 903         public void run()
 904         {
 905           fetchStructuresMetaData();
 906           filterResultSet(((FilterOption) cmb_filterOption
 907                   .getSelectedItem()).getValue());
 908         }
 909       });
 910       refreshThread.start();
 911     }
 912   }
 913
 914 }