package jalview.gui;

import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GStructureChooser;
import jalview.util.MessageManager;
import jalview.ws.dbsources.PDBRestClient;
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import jalview.ws.uimodel.PDBSearchRequest;
import jalview.ws.uimodel.PDBSearchResponse;
import jalview.ws.uimodel.PDBSearchResponse.PDBResponseSummary;

import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;

import javax.swing.JOptionPane;

@SuppressWarnings("serial")
public class StructureChooser extends GStructureChooser
{

  private boolean structuresWereFound = false;

  private SequenceI selectedSequence;

  private SequenceI[] selectedSequences;

  public StructureChooser(AlignmentPanel ap, final SequenceI sequence)
  {
    this.ap = ap;
    this.selectedSequence = sequence;
    selectedSequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
    { sequence } : ap.av.getSequenceSelection());
    fetchStructures();
    populateFilterOptions();
    updateCurrentView();
  }

  @Override
  public void ok_ActionPerformed()
  {
    // TODO code to load selected structures to jmol or chimera
  }

  protected void populateFilterOptions()
  {
    if (structuresWereFound)
    {
      filterOptionsComboBox.addItem(new FilterOptions(
              "- Filter Criteria -", "",
              VIEWS_FILTER));
      filterOptionsComboBox.addItem(new FilterOptions("All", "all",
              VIEWS_FILTER));
      filterOptionsComboBox.addItem(new FilterOptions("Best Coverage",
              "coverage",
              VIEWS_FILTER));
      filterOptionsComboBox.addItem(new FilterOptions("Best Resolution",
              PDBDocField.RESOLUTION.getCode(),
              VIEWS_FILTER));
      filterOptionsComboBox.addItem(new FilterOptions("Best Quality",
              PDBDocField.OVERALL_QUALITY.getCode(),
              VIEWS_FILTER));

      // "number_of_polymers"), PROTEIN_CHAIN_COUNT(
      // "Protein Chain Count", "number_of_protein_chains"),
      // BOUND_MOLECULE_COUNT(
      // "Bound Molecule Count", "number_of_bound_molecules"),
      // POLYMER_RESIDUE_COUNT(
      // "Polymer Residue Count", "number_of_polymer_residues"),
      // UNIPROT_COVERAGE(
    }
    filterOptionsComboBox.addItem(new FilterOptions("Enter PDB Id", "-",
            VIEWS_ENTER_ID));
    filterOptionsComboBox.addItem(new FilterOptions("From File", "-",
            VIEWS_FROM_FILE));
  }

  private void fetchStructures()
  {
    long startTime = System.currentTimeMillis();
    // final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new
    // SequenceI[]
    // { sequence }
    // : ap.av.getSequenceSelection());

    int foundStructures = 0;
    List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
    wantedFields.add(PDBDocField.MOLECULE_TYPE);
    wantedFields.add(PDBDocField.PDB_ID);
    wantedFields.add(PDBDocField.GENUS);
    wantedFields.add(PDBDocField.GENE_NAME);
    wantedFields.add(PDBDocField.TITLE);

    PDBSearchRequest request = new PDBSearchRequest();
    request.setAllowEmptySeq(false);
    request.setResponseSize(500);
    request.setSearchTarget("(text:");
    request.setWantedFields(wantedFields);
    
    Collection<PDBResponseSummary> searchSummaries = new HashSet<PDBResponseSummary>();
    for (SequenceI seq : selectedSequences)
    {
      request.setSearchTerm(buildQuery(seq) + ")");
      PDBRestClient pdbRestCleint = new PDBRestClient();
      PDBSearchResponse resultList = pdbRestCleint
              .executeRequest(request);
      if (resultList.getSearchSummary() != null
              && !resultList.getSearchSummary().isEmpty())
      {
        searchSummaries.addAll(resultList.getSearchSummary());
      }
    }

    foundStructures = searchSummaries.size();
    if (searchSummaries != null)
    {
      jListFoundStructures.setModel(PDBSearchResponse
              .getListModel(searchSummaries));
      structuresWereFound = true;
    }
    String totalTime = (System.currentTimeMillis() - startTime)
            + " milli secs";
    mainFrame.setTitle("Structure Chooser - " + foundStructures
            + " Found (" + totalTime + ")");
  }

  private String buildQuery(SequenceI seq)
  {
    String query = seq.getName();
    StringBuilder queryBuilder = new StringBuilder();
    int count = 0;
    if (seq.getDBRef() != null && seq.getDBRef().length != 0)
    {
      for (DBRefEntry dbRef : seq.getDBRef())
      {
        queryBuilder.append("text:").append(dbRef.getAccessionId())
                .append(" OR ");
        ++count;
        if (count > 10)
        {
          break;
        }
      }
      int endIndex = queryBuilder.lastIndexOf(" OR ");
      query = queryBuilder.toString().substring(5, endIndex);
    }
    return query;
  }

  @Override
  protected void stateChanged()
  {
    updateCurrentView();
  }

  int debounceCount = 0;
  protected void updateCurrentView()
  {
    FilterOptions currentOption = ((FilterOptions) filterOptionsComboBox
            .getSelectedItem());
    switchableViewsLayout.show(switchableViewsPanel,
            currentOption.getView());
    ++debounceCount;
    if (currentOption.getView() == VIEWS_FILTER && debounceCount % 2 == 0)
    {
      filterResultSet(currentOption.getValue());
    }
  }

  public void filterResultSet(String filterTarget)
  {
    System.out.println("-----------------> Filter by : " + filterTarget);

    List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
    wantedFields.add(PDBDocField.MOLECULE_TYPE);
    wantedFields.add(PDBDocField.PDB_ID);
    wantedFields.add(PDBDocField.GENUS);
    wantedFields.add(PDBDocField.GENE_NAME);
    wantedFields.add(PDBDocField.TITLE);

    PDBSearchRequest request = new PDBSearchRequest();
    request.setAllowEmptySeq(false);
    request.setResponseSize(1);
    request.setSearchTarget("(text:");
    request.setSortTarget(filterTarget, true);

    request.setWantedFields(wantedFields);

    Collection<PDBResponseSummary> searchSummaries = new HashSet<PDBResponseSummary>();
    for (SequenceI seq : selectedSequences)
    {
      request.setSearchTerm(buildQuery(seq) + ")");
      PDBRestClient pdbRestCleint = new PDBRestClient();
      PDBSearchResponse resultList = pdbRestCleint.executeRequest(request);
      if (resultList.getSearchSummary() != null
              && !resultList.getSearchSummary().isEmpty())
      {
        searchSummaries.addAll(resultList.getSearchSummary());

      }
    }

    for (PDBResponseSummary summary : searchSummaries)
    {
      jListFoundStructures.setSelectedValue(summary, true);
      // jListFoundStructures.
      break;
    }
    System.out.println("Found item count : " + searchSummaries.size());
  }

  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)
    {
      String choice = chooser.getSelectedFile().getPath();
      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
      new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
              jalview.io.AppletFormatAdapter.FILE, selectedSequence, true,
              Desktop.instance);
    }

  }


  // rpdbview.addActionListener(new ActionListener()
  // {
  //
  // @Override
  // public void actionPerformed(ActionEvent e)
  // {
  // new StructureViewer(ap.getStructureSelectionManager())
  // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
  // }
  // });

  public void enterPDB_actionPerformed()
  {
    String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
            MessageManager.getString("label.enter_pdb_id"),
            MessageManager.getString("label.enter_pdb_id"),
            JOptionPane.QUESTION_MESSAGE);
    if (id != null && id.length() > 0)
    {
      PDBEntry entry = new PDBEntry();
      entry.setId(id.toUpperCase());
      selectedSequence.getDatasetSequence().addPDBId(entry);
    }
  }

  // public static void main(String[] args)
  // {
  // SwingUtilities.invokeLater(new Runnable()
  // {
  // public void run()
  // {
  // new StructureChooser(null, null);
  // }
  // });
  // }


}