/*

 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
 * Copyright (C) 2014 The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */

package jalview.gui;

import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GStructureChooser;
import jalview.jbgui.PDBDocFieldPreferences;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.ws.dbsources.PDBRestClient;
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import jalview.ws.uimodel.PDBRestRequest;
import jalview.ws.uimodel.PDBRestResponse;
import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;

import java.awt.event.ItemEvent;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.LinkedHashSet;
import java.util.List;

import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.table.DefaultTableModel;


/**
 * Provides the behaviors for the Structure chooser Panel
 * 
 * @author tcnofoegbu
 *
 */
@SuppressWarnings("serial")
public class StructureChooser extends GStructureChooser
{
  private boolean structuresDiscovered = false;

  private SequenceI selectedSequence;

  private SequenceI[] selectedSequences;

  private IProgressIndicator progressIndicator;

  private Collection<PDBResponseSummary> discoveredStructuresSet;

  private PDBRestRequest lastPdbRequest;

  private PDBRestClient pdbRestCleint;

  private String selectedPdbFileName;

  private boolean isValidPBDEntry;

  private static Hashtable<String, PDBEntry> cachedEntryMap;

  public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
          AlignmentPanel ap)
  {
    this.ap = ap;
    this.selectedSequence = selectedSeq;
    this.selectedSequences = selectedSeqs;
    this.progressIndicator = (ap == null) ? null : ap.alignFrame;
    init();
  }

  /**
   * Initializes parameters used by the Structure Chooser Panel
   */
  public void init()
  {
    Thread discoverPDBStructuresThread = new Thread(new Runnable()
    {
      @Override
      public void run()
      {
        long startTime = System.currentTimeMillis();
        updateProgressIndicator(MessageManager
                .getString("status.loading_cached_pdb_entries"), startTime);
        loadLocalCachedPDBEntries();
        updateProgressIndicator(null, startTime);
        updateProgressIndicator(MessageManager
                .getString("status.searching_for_pdb_structures"),
                startTime);
        fetchStructuresMetaData();
        populateFilterComboBox();
        updateProgressIndicator(null, startTime);
        mainFrame.setVisible(true);
        updateCurrentView();
      }
    });
    discoverPDBStructuresThread.start();
  }

  /**
   * Updates the progress indicator with the specified message
   * 
   * @param message
   *          displayed message for the operation
   * @param id
   *          unique handle for this indicator
   */
  public void updateProgressIndicator(String message, long id)
  {
    if (progressIndicator != null)
    {
      progressIndicator.setProgressBar(message, id);
    }
  }

  /**
   * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
   * selection group
   */
  public void fetchStructuresMetaData()
  {
    long startTime = System.currentTimeMillis();
    Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
            .getStructureSummaryFields();

    discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
    HashSet<String> errors = new HashSet<String>();
    for (SequenceI seq : selectedSequences)
    {
      PDBRestRequest pdbRequest = new PDBRestRequest();
      pdbRequest.setAllowEmptySeq(false);
      pdbRequest.setResponseSize(500);
      pdbRequest.setFieldToSearchBy("(text:");
      pdbRequest.setWantedFields(wantedFields);
      pdbRequest.setSearchTerm(buildQuery(seq) + ")");
      pdbRequest.setAssociatedSequence(seq);
      pdbRestCleint = new PDBRestClient();
      PDBRestResponse resultList;
      try
      {
        resultList = pdbRestCleint.executeRequest(pdbRequest);
      } catch (Exception e)
      {
        e.printStackTrace();
        errors.add(e.getMessage());
        continue;
      }
      lastPdbRequest = pdbRequest;
      if (resultList.getSearchSummary() != null
              && !resultList.getSearchSummary().isEmpty())
      {
        discoveredStructuresSet.addAll(resultList.getSearchSummary());
        updateSequencePDBEntries(seq, resultList.getSearchSummary());
      }
    }

    int noOfStructuresFound = 0;
    String totalTime = (System.currentTimeMillis() - startTime)
            + " milli secs";
    if (discoveredStructuresSet != null
            && !discoveredStructuresSet.isEmpty())
    {
      tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
              discoveredStructuresSet));
      structuresDiscovered = true;
      noOfStructuresFound = discoveredStructuresSet.size();
      mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
              + " Found (" + totalTime + ")");
    }
    else
    {
      mainFrame
.setTitle("Structure Chooser - Manual association");
      if (errors.size() > 0)
      {
        StringBuilder errorMsg = new StringBuilder();
        // "Operation was unsuccessful due to the following: \n");
        for (String error : errors)
        {
          errorMsg.append(error).append("\n");
        }
        JOptionPane.showMessageDialog(this, errorMsg.toString(),
                "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
      }
    }
  }

  public void loadLocalCachedPDBEntries()
  {
    DefaultTableModel tableModel = new DefaultTableModel()
    {
      @Override
      public boolean isCellEditable(int row, int column)
      {
        return false;
      }
    };
    tableModel.addColumn("Ref Sequence");
    tableModel.addColumn("PDB Id");
    tableModel.addColumn("Chain");
    tableModel.addColumn("Type");
    tableModel.addColumn("File");
    cachedEntryMap = new Hashtable<String, PDBEntry>();
    for (SequenceI seq : selectedSequences)
    {
      if (seq.getDatasetSequence() != null
              && seq.getDatasetSequence().getPDBId() != null)
      {
        for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId())
        {

          String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry
                  .getChainCode();
          Object[] pdbEntryRowData = new Object[]
          { seq, pdbEntry.getId(),
 chain,
              pdbEntry.getType(),
              pdbEntry.getFile() };
          if (pdbEntry.getFile() != null)
          {
            tableModel.addRow(pdbEntryRowData);
          }
          cachedEntryMap.put(pdbEntry.getId().toLowerCase(),
                  pdbEntry);
        }
      }
    }
    tbl_local_pdb.setModel(tableModel);
  }

  /**
   * Update the PDBEntry for a given sequence with values retrieved from
   * PDBResponseSummary
   * 
   * @param seq
   *          the Sequence to update its DBRef entry
   * @param responseSummaries
   *          a collection of PDBResponseSummary
   */
  public void updateSequencePDBEntries(SequenceI seq,
          Collection<PDBResponseSummary> responseSummaries)
  {
    for (PDBResponseSummary response : responseSummaries)
    {
      String pdbIdStr = response.getPdbId();
      PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
      if (pdbEntry == null)
      {
        pdbEntry = new PDBEntry();
        pdbEntry.setId(pdbIdStr);
        pdbEntry.setType(PDBEntry.Type.PDB);
      }
      seq.getDatasetSequence().addPDBId(pdbEntry);
    }
  }

  /**
   * Builds a query string for a given sequences using its DBRef entries
   * 
   * @param seq
   *          the sequences to build a query for
   * @return the built query string
   */

  public static String buildQuery(SequenceI seq)
  {
    HashSet<String> seqRefs = new LinkedHashSet<String>();
    String seqName = seq.getName();
    String[] names = seqName.toLowerCase().split("\\|");
    for (String name : names)
    {
      // System.out.println("Found name : " + name);
      name.trim();
      if (isValidSeqName(name))
      {
        seqRefs.add(name);
      }
    }

    if (seq.getPDBId() != null)
    {
      for (PDBEntry entry : seq.getPDBId())
      {
        if (isValidSeqName(entry.getId()))
        {
          seqRefs.add(entry.getId());
        }
      }
    }

    if (seq.getDBRef() != null && seq.getDBRef().length != 0)
    {
      int count = 0;
      for (DBRefEntry dbRef : seq.getDBRef())
      {
        if (isValidSeqName(getDBRefId(dbRef)))
        {
          seqRefs.add(getDBRefId(dbRef));
        }
        ++count;
        if (count > 10)
        {
          break;
        }
      }
    }

    StringBuilder queryBuilder = new StringBuilder();
    for (String seqRef : seqRefs)
    {
      queryBuilder.append("text:").append(seqRef).append(" OR ");
    }
    int endIndex = queryBuilder.lastIndexOf(" OR ");
    String query = queryBuilder.toString().substring(5, endIndex);
    return query;
  }

  /**
   * Ensures sequence ref names are not less than 3 characters and does not
   * contain a database name
   * 
   * @param seqName
   * @return
   */
  public static boolean isValidSeqName(String seqName)
  {
    // System.out.println("seqName : " + seqName);
    String ignoreList = "pdb,uniprot,swiss-prot";
    if (seqName.length() < 3)
    {
      return false;
    }
    if (seqName.contains(":"))
    {
      return false;
    }
    seqName = seqName.toLowerCase();
    for (String ignoredEntry : ignoreList.split(","))
    {
      if (seqName.contains(ignoredEntry))
      {
        return false;
      }
    }
    return true;
  }

  public static String getDBRefId(DBRefEntry dbRef)
  {
    String ref = dbRef.getAccessionId().replaceAll("GO:", "");
    return ref;
  }

  /**
   * Filters a given list of discovered structures based on supplied argument
   * 
   * @param fieldToFilterBy
   *          the field to filter by
   */
  public void filterResultSet(final String fieldToFilterBy)
  {
    Thread filterThread = new Thread(new Runnable()
    {
      @Override
      public void run()
      {
        long startTime = System.currentTimeMillis();
        lbl_loading.setVisible(true);
        Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
                .getStructureSummaryFields();
        Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
        HashSet<String> errors = new HashSet<String>();
        for (SequenceI seq : selectedSequences)
        {
          PDBRestRequest pdbRequest = new PDBRestRequest();
          pdbRequest.setAllowEmptySeq(false);
          pdbRequest.setResponseSize(1);
          pdbRequest.setFieldToSearchBy("(text:");
          pdbRequest.setFieldToSortBy(fieldToFilterBy,
                  !chk_invertFilter.isSelected());
          pdbRequest.setSearchTerm(buildQuery(seq) + ")");
          pdbRequest.setWantedFields(wantedFields);
          pdbRequest.setAssociatedSequence(seq);
          pdbRestCleint = new PDBRestClient();
          PDBRestResponse resultList;
          try
          {
            resultList = pdbRestCleint.executeRequest(pdbRequest);
          } catch (Exception e)
          {
            e.printStackTrace();
            errors.add(e.getMessage());
            continue;
          }
          lastPdbRequest = pdbRequest;
          if (resultList.getSearchSummary() != null
                  && !resultList.getSearchSummary().isEmpty())
          {
            filteredResponse.addAll(resultList.getSearchSummary());
          }
        }

        String totalTime = (System.currentTimeMillis() - startTime)
                + " milli secs";
        if (!filteredResponse.isEmpty())
        {
          final int filterResponseCount = filteredResponse.size();
          Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
          reorderedStructuresSet.addAll(filteredResponse);
          reorderedStructuresSet.addAll(discoveredStructuresSet);
          tbl_summary.setModel(PDBRestResponse.getTableModel(
                  lastPdbRequest, reorderedStructuresSet));

          // Update table selection model here
          tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);

          mainFrame.setTitle("Structure Chooser - Filter time ("
                  + totalTime + ")");
        }
        else
        {
          mainFrame.setTitle("Structure Chooser - Filter time ("
                  + totalTime + ")");
          if (errors.size() > 0)
          {
            StringBuilder errorMsg = new StringBuilder();
            for (String error : errors)
            {
              errorMsg.append(error).append("\n");
            }
            JOptionPane.showMessageDialog(null, errorMsg.toString(),
                    "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
          }
        }

        lbl_loading.setVisible(false);

        validateSelections();
      }
    });
    filterThread.start();
  }


  /**
   * Handles action event for btn_pdbFromFile
   */
  public void pdbFromFile_actionPerformed()
  {
    jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
    chooser.setFileView(new jalview.io.JalviewFileView());
    chooser.setDialogTitle(MessageManager.formatMessage(
            "label.select_pdb_file_for", new String[]
            { selectedSequence.getDisplayId(false) }));
    chooser.setToolTipText(MessageManager.formatMessage(
            "label.load_pdb_file_associate_with_sequence", new String[]
            { selectedSequence.getDisplayId(false) }));

    int value = chooser.showOpenDialog(null);
    if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
    {
      selectedPdbFileName = chooser.getSelectedFile().getPath();
      jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
      validateSelections();
    }
  }

  /**
   * Populates the filter combo-box options dynamically depending on discovered
   * structures
   */
  protected void populateFilterComboBox()
  {
    if (isStructuresDiscovered())
    {
      cmb_filterOption.addItem(new FilterOption("Best Quality",
              PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
      cmb_filterOption.addItem(new FilterOption("Best UniProt Coverage",
              PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER));
      cmb_filterOption.addItem(new FilterOption("Highest Resolution",
              PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
      cmb_filterOption.addItem(new FilterOption("Highest Protein Chain",
              PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER));
      cmb_filterOption.addItem(new FilterOption("Highest Bound Molecules",
              PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER));
      cmb_filterOption.addItem(new FilterOption("Highest Polymer Residues",
              PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER));
    }
    cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
            VIEWS_ENTER_ID));
    cmb_filterOption.addItem(new FilterOption("From File", "-",
            VIEWS_FROM_FILE));
    cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
            VIEWS_LOCAL_PDB));
  }

  /**
   * Updates the displayed view based on the selected filter option
   */
  protected void updateCurrentView()
  {
    FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
            .getSelectedItem());
    layout_switchableViews.show(pnl_switchableViews,
            selectedFilterOpt.getView());
    String filterTitle = mainFrame.getTitle();
    mainFrame.setTitle(frameTitle);
    chk_invertFilter.setVisible(false);
    if (selectedFilterOpt.getView() == VIEWS_FILTER)
    {
      mainFrame.setTitle(filterTitle);
      chk_invertFilter.setVisible(true);
      filterResultSet(selectedFilterOpt.getValue());
    }
    else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
            || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
    {
      mainFrame.setTitle(filterTitle);
      idInputAssSeqPanel.loadCmbAssSeq();
      fileChooserAssSeqPanel.loadCmbAssSeq();
    }
    validateSelections();
  }

  /**
   * Validates user selection and activates the view button if all parameters
   * are correct
   */
  public void validateSelections()
  {
    FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
            .getSelectedItem());
    btn_view.setEnabled(false);
    String currentView = selectedFilterOpt.getView();
    if (currentView == VIEWS_FILTER)
    {
      if (tbl_summary.getSelectedRows().length > 0)
      {
        btn_view.setEnabled(true);
      }
    }
    else if (currentView == VIEWS_LOCAL_PDB)
    {
      if (tbl_local_pdb.getSelectedRows().length > 0)
      {
        btn_view.setEnabled(true);
      }
    }
    else if (currentView == VIEWS_ENTER_ID)
    {
      validateAssociationEnterPdb();
    }
    else if (currentView == VIEWS_FROM_FILE)
    {
      validateAssociationFromFile();
    }
  }

  /**
   * Validates inputs from the Manual PDB entry panel
   */
  public void validateAssociationEnterPdb()
  {
    AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
            .getCmb_assSeq().getSelectedItem();
    lbl_pdbManualFetchStatus.setIcon(errorImage);
    lbl_pdbManualFetchStatus.setToolTipText("");
    if (txt_search.getText().length() > 0)
    {
      lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
              true, "No PDB entry found for \'" + txt_search.getText()
                      + "\'"));
    }

    if (errorWarning.length() > 0)
    {
      lbl_pdbManualFetchStatus.setIcon(warningImage);
      lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
              true, errorWarning.toString()));
    }

    if (selectedSequences.length == 1
            || !assSeqOpt.getName().equalsIgnoreCase(
                    "-Select Associated Seq-"))
    {
      txt_search.setEnabled(true);
      if (isValidPBDEntry)
      {
        btn_view.setEnabled(true);
        lbl_pdbManualFetchStatus.setToolTipText("");
        lbl_pdbManualFetchStatus.setIcon(goodImage);
      }
    }
    else
    {
      txt_search.setEnabled(false);
      lbl_pdbManualFetchStatus.setIcon(errorImage);
    }
  }

  /**
   * Validates inputs for the manual PDB file selection options
   */
  public void validateAssociationFromFile()
  {
    AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
            .getCmb_assSeq().getSelectedItem();
    lbl_fromFileStatus.setIcon(errorImage);
    if (selectedSequences.length == 1
            || (assSeqOpt != null
            && !assSeqOpt.getName().equalsIgnoreCase(
                    "-Select Associated Seq-")))
    {
      btn_pdbFromFile.setEnabled(true);
      if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
      {
        btn_view.setEnabled(true);
        lbl_fromFileStatus.setIcon(goodImage);
      }
    }
    else
    {
      btn_pdbFromFile.setEnabled(false);
      lbl_fromFileStatus.setIcon(errorImage);
    }
  }

  @Override
  public void cmbAssSeqStateChanged()
  {
    validateSelections();
  }

  /**
   * Handles the state change event for the 'filter' combo-box and 'invert'
   * check-box
   */
  @Override
  protected void stateChanged(ItemEvent e)
  {
    if (e.getSource() instanceof JCheckBox)
    {
      updateCurrentView();
    }
    else
    {
      if (e.getStateChange() == ItemEvent.SELECTED)
      {
        updateCurrentView();
      }
    }

  }

  /**
   * Handles action event for btn_ok
   */
  @Override
  public void ok_ActionPerformed()
  {
    FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
            .getSelectedItem());
    String currentView = selectedFilterOpt.getView();
    if (currentView == VIEWS_FILTER)
    {
      int pdbIdColIndex = tbl_summary.getColumn(
              PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
      int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
              .getModelIndex();
      int[] selectedRows = tbl_summary.getSelectedRows();
      PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
      int count = 0;
      ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
      for (int summaryRow : selectedRows)
      {
        String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdColIndex)
                .toString();
        SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(
                summaryRow, refSeqColIndex);
        selectedSeqsToView.add(selectedSeq);
        PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
        if (pdbEntry == null)
        {
          pdbEntry = new PDBEntry();
          pdbEntry.setId(pdbIdStr);
          pdbEntry.setType(PDBEntry.Type.PDB);
        }
        pdbEntriesToView[count++] = pdbEntry;
      }
      SequenceI[] selectedSeqs = selectedSeqsToView
              .toArray(new SequenceI[selectedSeqsToView.size()]);
      launchStructureViewer(ap.getStructureSelectionManager(),
              pdbEntriesToView, ap, selectedSeqs);
    }
    else if(currentView == VIEWS_LOCAL_PDB){
      int[] selectedRows = tbl_local_pdb.getSelectedRows();
      PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
      int count = 0;
      int pdbIdColIndex = tbl_local_pdb.getColumn(
              PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
      int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
              .getModelIndex();
      ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
      for (int row : selectedRows)
      {
        String entryKey = tbl_local_pdb.getValueAt(row, pdbIdColIndex)
                .toString()
                .toLowerCase();
        pdbEntriesToView[count++] = cachedEntryMap.get(entryKey);
        SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
                refSeqColIndex);
        selectedSeqsToView.add(selectedSeq);

      }
      SequenceI[] selectedSeqs = selectedSeqsToView
              .toArray(new SequenceI[selectedSeqsToView.size()]);
      launchStructureViewer(ap.getStructureSelectionManager(),
              pdbEntriesToView, ap, selectedSeqs);
    }
    else if (currentView == VIEWS_ENTER_ID)
    {
      SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
              .getCmb_assSeq().getSelectedItem()).getSequence();
      if (userSelectedSeq != null)
      {
        selectedSequence = userSelectedSeq;
      }

      String pdbIdStr = txt_search.getText();
      PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
      if (pdbEntry == null)
      {
        pdbEntry = new PDBEntry();
        pdbEntry.setId(txt_search.getText());
        pdbEntry.setType(PDBEntry.Type.PDB);
      }

      selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
      PDBEntry[] pdbEntriesToView = new PDBEntry[]
      { pdbEntry };
      launchStructureViewer(ap.getStructureSelectionManager(),
              pdbEntriesToView, ap, new SequenceI[]
              { selectedSequence });
    }
    else if (currentView == VIEWS_FROM_FILE)
    {
      SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
              .getCmb_assSeq().getSelectedItem()).getSequence();
      if (userSelectedSeq != null)
      {
        selectedSequence = userSelectedSeq;
      }
      PDBEntry fileEntry = new AssociatePdbFileWithSeq()
              .associatePdbWithSeq(
              selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
              selectedSequence, true, Desktop.instance);

      launchStructureViewer(ap.getStructureSelectionManager(),
              new PDBEntry[]
              { fileEntry }, ap, new SequenceI[]
              { selectedSequence });
    }
    mainFrame.dispose();
  }

  private void launchStructureViewer(StructureSelectionManager ssm,
          PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
          SequenceI[] sequences)
  {
    StructureViewer sViewer = new StructureViewer(ssm);
    if (pdbEntriesToView.length > 1)
    {
      ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
      for (SequenceI seq : sequences)
      {
        seqsMap.add(new SequenceI[]
        { seq });
      }
      SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
      sViewer.viewStructures(pdbEntriesToView, collatedSeqs,
              alignPanel);
      // sViewer.viewStructures(pdbEntriesToView,
      // alignPanel.av.collateForPDB(pdbEntriesToView),
      // alignPanel);
    }
    else
    {
      sViewer.viewStructures(pdbEntriesToView[0], sequences,
              alignPanel);
    }
  }

  /**
   * Populates the combo-box used in associating manually fetched structures to
   * a unique sequence when more than one sequence selection is made.
   */
  public void populateCmbAssociateSeqOptions(
          JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
  {
    cmb_assSeq.removeAllItems();
    cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
            null));
    // cmb_assSeq.addItem(new AssociateSeqOptions("Auto Detect", null));
    lbl_associateSeq.setVisible(false);
    if (selectedSequences.length > 1)
    {
      for (SequenceI seq : selectedSequences)
      {
        cmb_assSeq.addItem(new AssociateSeqOptions(seq));
      }
    }
    else
    {
      String seqName = selectedSequence.getDisplayId(false);
      seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
      lbl_associateSeq.setText(seqName);
      lbl_associateSeq.setVisible(true);
      cmb_assSeq.setVisible(false);
    }
  }

  public boolean isStructuresDiscovered()
  {
    return structuresDiscovered;
  }

  public void setStructuresDiscovered(boolean structuresDiscovered)
  {
    this.structuresDiscovered = structuresDiscovered;
  }

  public Collection<PDBResponseSummary> getDiscoveredStructuresSet()
  {
    return discoveredStructuresSet;
  }

  @Override
  protected void txt_search_ActionPerformed()
  {
    errorWarning.setLength(0);
    isValidPBDEntry = false;
    if (txt_search.getText().length() > 0)
    {
      List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
      wantedFields.add(PDBDocField.PDB_ID);
      PDBRestRequest pdbRequest = new PDBRestRequest();
      pdbRequest.setAllowEmptySeq(false);
      pdbRequest.setResponseSize(1);
      pdbRequest.setFieldToSearchBy("(pdb_id:");
      pdbRequest.setWantedFields(wantedFields);
      pdbRequest.setSearchTerm(txt_search.getText() + ")");
      pdbRequest.setAssociatedSequence(selectedSequence);
      pdbRestCleint = new PDBRestClient();
      PDBRestResponse resultList;
      try
      {
        resultList = pdbRestCleint.executeRequest(pdbRequest);
      } catch (Exception e)
      {
        errorWarning.append(e.getMessage());
        return;
      } finally
      {
        validateSelections();
      }
      if (resultList.getSearchSummary() != null
              && resultList.getSearchSummary().size() > 0)
      {
        isValidPBDEntry = true;
      }
    }
    validateSelections();
  }

  @Override
  public void tabRefresh()
  {
    if (selectedSequences != null)
    {
      Thread refreshThread = new Thread(new Runnable()
      {
        @Override
        public void run()
        {
          fetchStructuresMetaData();
          filterResultSet(((FilterOption) cmb_filterOption
                  .getSelectedItem()).getValue());
        }
      });
      refreshThread.start();
    }
  }

}