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.uimodel.PDBSearchRequest;
import jalview.ws.uimodel.PDBSearchResponse;
import jalview.ws.uimodel.PDBSummaryListModel;
import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField;

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

import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;

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


  private SequenceI sequence;


  public StructureChooser(AlignmentPanel ap, final SequenceI sequence)
  {
    this.ap = ap;
    this.sequence = sequence;
    fetchStructures();
  }

  @Override
  public void ok_ActionPerformed()
  {
    jListFoundStructures.setSelectedValue("op1x", true);
  }

  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[]
            { sequence.getDisplayId(false) }));
    chooser.setToolTipText(MessageManager.formatMessage(
            "label.load_pdb_file_associate_with_sequence", new String[]
            { sequence.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, sequence, true,
              Desktop.instance);
    }

  }

  public void discoverPDB_actionPerformed()
  {

    final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
    { sequence }
            : ap.av.getSequenceSelection());
    Thread discpdb = new Thread(new Runnable()
    {
      @Override
      public void run()
      {

        new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
                .fetchDBRefs(false);
      }

    });
    discpdb.start();
  }

  // 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());
      sequence.getDatasetSequence().addPDBId(entry);
    }
  }

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

  @SuppressWarnings("unchecked")
  protected void populateFilterOptions()
  {
    filterOptions.addItem(new FilterOptions("- Filter Criteria -", "",
            VIEWS_AUTO));
    filterOptions.addItem(new FilterOptions("All", "all", VIEWS_AUTO));
    filterOptions
            .addItem(new FilterOptions("Best Coverage", "", VIEWS_AUTO));
    filterOptions.addItem(new FilterOptions("Best Resolution", "",
            VIEWS_AUTO));
    filterOptions
            .addItem(new FilterOptions("Best Quality", "", VIEWS_AUTO));
    filterOptions.addItem(new FilterOptions("Enter PDB Id", "", VIEWS_ID));
    filterOptions.addItem(new FilterOptions("From File", "", VIEWS_FILE));
  }

  protected void updateCurrentView()
  {
    String currentView = ((FilterOptions) filterOptions.getSelectedItem())
            .getView();
    switchableViewsLayout.show(switchableViewsPanel, currentView);
  }

  private void fetchStructures()
  {
    long startTime = System.currentTimeMillis();
    final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
    { sequence }
            : ap.av.getSequenceSelection());
    int foundStructures = 0;
    PDBSearchRequest request = new PDBSearchRequest();
    request.setAllowEmptySeq(false);
    request.setResponseSize(500);
    request.setSearchTarget("(text:");
    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);
    request.setWantedFields(wantedFields);
    
    Collection<PDBSummaryListModel> searchSummaries = new HashSet<PDBSummaryListModel>();
    // searchSummaries.
    for (SequenceI seq : sequences)
    {
      // System.out.println("Selected : " + seq.getName());
      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));
    }

    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())
      {
        System.out.println("dbref : " + dbRef.getAccessionId());
        queryBuilder.append("text:").append(dbRef.getAccessionId())
                .append(" OR ");
        ++count;
        if (count > 10)
        {
          break;
        }
      }
      // int beginIndex = queryBuilder. firstIndexOf("text");
      int endIndex = queryBuilder.lastIndexOf(" OR ");
      query = queryBuilder.toString().substring(5, endIndex);
    }
    System.out.println("------------> " + query);
    return query;
  }

  public class FilterOptions
  {
    private String name;

    private String value;

    private String view;

    public FilterOptions(String name, String value, String view)
    {
      this.name = name;
      this.value = value;
      this.view = view;
    }

    public String getName()
    {
      return name;
    }

    public void setName(String name)
    {
      this.name = name;
    }

    public String getValue()
    {
      return value;
    }

    public void setValue(String value)
    {
      this.value = value;
    }

    public String getView()
    {
      return view;
    }

    public void setView(String view)
    {
      this.view = view;
    }

    public String toString()
    {
      return this.name;
    }
  }
}