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

import javax.swing.JCheckBox;
import javax.swing.JOptionPane;
import javax.swing.JTable;
import javax.swing.ListSelectionModel;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumnModel;

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

  private boolean structuresWereFound = false;

  private SequenceI selectedSequence;

  private SequenceI[] selectedSequences;

  IProgressIndicator af;

  Collection<PDBResponseSummary> discoveredStructuresSet = new HashSet<PDBResponseSummary>();

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

  private void init()
  {
    Thread discPDBThread = new Thread(new Runnable()
    {
      @Override
      public void run()
      {
        long startTime = System.currentTimeMillis();
        af.setProgressBar(
                MessageManager.getString("status.fetching_db_refs"),
                startTime);

        fetchStructures();
        populateFilterOptions();
        af.setProgressBar(null, startTime);
        mainFrame.setVisible(true);
        updateCurrentView();
      }
    });
    discPDBThread.start();
  }

  private void fetchStructures()
  {
    long startTime = System.currentTimeMillis();
    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.setFieldToSearchBy("(text:");
    request.setWantedFields(wantedFields);

    for (SequenceI seq : selectedSequences)
    {
      request.setSearchTerm(buildQuery(seq) + ")");
      request.setAssociatedSequence(seq.getName());
      PDBRestClient pdbRestCleint = new PDBRestClient();
      PDBSearchResponse resultList = pdbRestCleint.executeRequest(request);
      if (resultList.getSearchSummary() != null
              && !resultList.getSearchSummary().isEmpty())
      {
        discoveredStructuresSet.addAll(resultList.getSearchSummary());
      }
    }

    int noOfStructuresFound = 0;
    if (discoveredStructuresSet != null)
    {
      jListFoundStructures.setModel(PDBSearchResponse
              .getListModel(discoveredStructuresSet));
      summaryTable.setModel(PDBSearchResponse.getTableModel(request,
              discoveredStructuresSet));
      // resizeColumnWidth(summaryTable);
      structuresWereFound = true;
      noOfStructuresFound = discoveredStructuresSet.size();
    }
    String totalTime = (System.currentTimeMillis() - startTime)
            + " milli secs";
    mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
            + " Found (" + totalTime + ")");
  }

  public void resizeColumnWidth(JTable table)
  {
    // table.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
    final TableColumnModel columnModel = table.getColumnModel();
    for (int column = 0; column < table.getColumnCount(); column++)
    {
      int width = 50; // Min width
      for (int row = 0; row < table.getRowCount(); row++)
      {
        TableCellRenderer renderer = table.getCellRenderer(row, column);
        Component comp = table.prepareRenderer(renderer, row, column);
        width = Math.max(comp.getPreferredSize().width, width);
      }
      columnModel.getColumn(column).setPreferredWidth(width);
    }
  }

  protected void populateFilterOptions()
  {
    if (structuresWereFound)
    {
      filterOptionsComboBox.addItem(new FilterOptions("Best Quality",
              PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
      filterOptionsComboBox.addItem(new FilterOptions(
              "Best UniProt Coverage", PDBDocField.UNIPROT_COVERAGE
                      .getCode(), VIEWS_FILTER));
      filterOptionsComboBox.addItem(new FilterOptions("Highest Resolution",
              PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
      filterOptionsComboBox.addItem(new FilterOptions(
              "Highest Protein Chain", PDBDocField.PROTEIN_CHAIN_COUNT
                      .getCode(), VIEWS_FILTER));
      filterOptionsComboBox.addItem(new FilterOptions(
              "Highest Bound Molecules", PDBDocField.BOUND_MOLECULE_COUNT
                      .getCode(), VIEWS_FILTER));
      filterOptionsComboBox.addItem(new FilterOptions(
              "Highest Polymer Residues", PDBDocField.POLYMER_RESIDUE_COUNT
                      .getCode(), VIEWS_FILTER));
    }
    filterOptionsComboBox.addItem(new FilterOptions("Enter PDB Id", "-",
            VIEWS_ENTER_ID));
    filterOptionsComboBox.addItem(new FilterOptions("From File", "-",
            VIEWS_FROM_FILE));
  }

  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;
  }

  protected void updateCurrentView()
  {
    FilterOptions currentOption = ((FilterOptions) filterOptionsComboBox
            .getSelectedItem());
    switchableViewsLayout.show(switchableViewsPanel,
            currentOption.getView());
    invertFilter.setEnabled(false);
    if (currentOption.getView() == VIEWS_FILTER)
    {
      invertFilter.setEnabled(true);
      filterResultSet(currentOption.getValue());
    }
  }

  public void filterResultSet(final String fieldToFilterBy)
  {
    Thread filterThread = new Thread(new Runnable()
    {
      @Override
      public void run()
      {
        try
        {
        loadingImageLabel.setVisible(true);
        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.setFieldToSearchBy("(text:");
        request.setFieldToSortBy(fieldToFilterBy,
                !invertFilter.isSelected());

        request.setWantedFields(wantedFields);

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


        if (filteredResponse != null)
        {
            //
            // for (PDBResponseSummary s : filteredResponse)
            // {
            // System.out.println("-----------> " + s.getPdbId());
            // }

          int filterResponseCount = filteredResponse.size();
          List<PDBResponseSummary> list = new ArrayList<PDBResponseSummary>(
                  discoveredStructuresSet);
          list.removeAll(filteredResponse);

          Collection<PDBResponseSummary> newSet = new ArrayList<PDBResponseSummary>();
          newSet.addAll(filteredResponse);
          newSet.addAll(list);

          jListFoundStructures.setModel(PDBSearchResponse
                  .getListModel(newSet));
          summaryTable.setModel(PDBSearchResponse.getTableModel(request,
                  newSet));
          // resizeColumnWidth(summaryTable);
          list = null;
          newSet = null;

          int[] filterIndice = new int[filterResponseCount];
          ListSelectionModel model = summaryTable.getSelectionModel();
          model.clearSelection();
          // int x = 0;
          for (int x = 0; x < filterResponseCount; x++)
          {
            filterIndice[x] = x;
            model.addSelectionInterval(x, x);
          }
          jListFoundStructures.setSelectedIndices(filterIndice);
        }

        loadingImageLabel.setVisible(false);
        } catch (Exception e)
        {
          e.printStackTrace();
        }
      }
    });
    filterThread.start();

  }

  @Override
  protected void stateChanged(ItemEvent e)
  {
    if (e.getSource() instanceof JCheckBox)
    {
      updateCurrentView();
    }
    else
    {
      if (e.getStateChange() == ItemEvent.SELECTED)
      {
        updateCurrentView();
      }
    }

  }

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

  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);
    }
  }

}