/*

 * 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.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.LinkedHashSet;
import java.util.List;
import java.util.Vector;

import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JLabel;

/**
 * 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;

  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();
        String msg = MessageManager.getString("status.fetching_db_refs");
        updateProgressIndicator(msg, 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>();
    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.getName());
      pdbRestCleint = new PDBRestClient();
      PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
      lastPdbRequest = pdbRequest;
      if (resultList.getSearchSummary() != null
              && !resultList.getSearchSummary().isEmpty())
      {
        discoveredStructuresSet.addAll(resultList.getSearchSummary());
        updateSequenceDbRef(seq, resultList.getSearchSummary());
      }
    }

    int noOfStructuresFound = 0;
    if (discoveredStructuresSet != null
            && !discoveredStructuresSet.isEmpty())
    {
      tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
              discoveredStructuresSet));
      structuresDiscovered = true;
      noOfStructuresFound = discoveredStructuresSet.size();
    }
    String totalTime = (System.currentTimeMillis() - startTime)
            + " milli secs";
    mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
            + " Found (" + totalTime + ")");
  }

  /**
   * Update the DBRef entry 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 updateSequenceDbRef(SequenceI seq,
          Collection<PDBResponseSummary> responseSummaries)
  {
    for (PDBResponseSummary response : responseSummaries)
    {
      PDBEntry newEntry = new PDBEntry();
      newEntry.setId(response.getPdbId());
      newEntry.setType("PDB");
      seq.getDatasetSequence().addPDBId(newEntry);
    }
  }

  /**
   * 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
   */
  @SuppressWarnings("unchecked")
  public static String buildQuery(SequenceI seq)
  {
    String query = seq.getName();
    StringBuilder queryBuilder = new StringBuilder();
    int count = 0;

    if (seq.getPDBId() != null)
    {
      for (PDBEntry entry : (Vector<PDBEntry>) seq.getPDBId())
      {
        queryBuilder.append("text:").append(entry.getId()).append(" OR ");
      }
    }

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

  /**
   * Filters a given list of discovered structures based on supplied argument
   * 
   * @param fieldToFilterBy
   *          the field to filter by
   */
  public void filterResultSet(final String fieldToFilterBy)
  {

    // SwingWorker aWorker = new SwingWorker()
    // {
    // long startTime = System.currentTimeMillis();
    //
    // @Override
    // protected Object doInBackground() throws Exception
    // {
    // lbl_loading.setVisible(true);
    //
    // Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
    // .getStructureSummaryFields();
    // Collection<PDBResponseSummary> filteredResponse = new
    // HashSet<PDBResponseSummary>();
    // 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.getName());
    // pdbRestCleint = new PDBRestClient();
    // PDBRestResponse resultList = pdbRestCleint
    // .executeRequest(pdbRequest);
    // lastPdbRequest = pdbRequest;
    // if (resultList.getSearchSummary() != null
    // && !resultList.getSearchSummary().isEmpty())
    // {
    // filteredResponse.addAll(resultList.getSearchSummary());
    // }
    // }
    //
    // 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 the model here
    // // ListSelectionModel model = tbl_summary.getSelectionModel();
    // // model.clearSelection();
    // // model.addSelectionInterval(0, filterResponseCount - 1);
    // // EventQueue.invokeLater(new Runnable()
    // // {
    // // public void run()
    // // {
    // // tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
    //
    // // }
    // // });
    // // Discard unwanted objects to make them eligible for garbage
    // // collection
    // reorderedStructuresSet = null;
    // }
    // return null;
    // }
    //
    // public void done()
    // {
    // lbl_loading.setVisible(false);
    // tbl_summary.addRowSelectionInterval(0, 2);
    // String totalTime = (System.currentTimeMillis() - startTime)
    // + " milli secs";
    // mainFrame.setTitle("Structure Chooser - Filter time (" + totalTime
    // + ")");
    // validateSelections();
    // }
    // };
    // aWorker.execute();

    Thread filterThread = new Thread(new Runnable()
    {
      @Override
      public void run()
      {
        long startTime = System.currentTimeMillis();
        try
        {
          lbl_loading.setVisible(true);

          Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
                  .getStructureSummaryFields();
          Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
          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.getName());
            pdbRestCleint = new PDBRestClient();
            PDBRestResponse resultList = pdbRestCleint
                    .executeRequest(pdbRequest);
            lastPdbRequest = pdbRequest;
            if (resultList.getSearchSummary() != null
                    && !resultList.getSearchSummary().isEmpty())
            {
              filteredResponse.addAll(resultList.getSearchSummary());
            }
          }

          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 the model here
            // ListSelectionModel model = tbl_summary.getSelectionModel();
            // model.clearSelection();
            // model.addSelectionInterval(0, filterResponseCount - 1);
            // EventQueue.invokeLater(new Runnable()
            // {
            // public void run()
            // {
            tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);

            // }
            // });
            // Discard unwanted objects to make them eligible for garbage
            // collection
            reorderedStructuresSet = null;
          }

          lbl_loading.setVisible(false);
          String totalTime = (System.currentTimeMillis() - startTime)
                  + " milli secs";
          mainFrame.setTitle("Structure Chooser - Filter time ("
                  + totalTime + ")");

          validateSelections();
        } catch (Exception e)
        {
          e.printStackTrace();
        }
      }
    });
    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));
  }

  /**
   * 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
    {
      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_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);
    if (selectedSequences.length == 1
            || !assSeqOpt.getName().equalsIgnoreCase(
                    "-Select Associated Seq-"))
    {
      txt_search.setEnabled(true);
      if (isValidPBDEntry)
      {
        btn_view.setEnabled(true);
        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 pdbIdCol = PDBRestClient.getPDBIdColumIndex(
              lastPdbRequest.getWantedFields(), true);
      int[] selectedRows = tbl_summary.getSelectedRows();
      PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
      int count = 0;
      for (int summaryRow : selectedRows)
      {
        String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
                .toString();
        PDBEntry pdbEntry = new PDBEntry();
        pdbEntry.setId(pdbIdStr);
        pdbEntry.setType("PDB");
        pdbEntriesToView[count++] = pdbEntry;
      }
      new StructureViewer(ap.getStructureSelectionManager())
              .viewStructures(ap, pdbEntriesToView,
                      ap.av.collateForPDB(pdbEntriesToView));
    }
    else if (currentView == VIEWS_ENTER_ID)
    {
      selectedSequence = ((AssociateSeqOptions) idInputAssSeqPanel
              .getCmb_assSeq().getSelectedItem()).getSequence();
      PDBEntry pdbEntry = new PDBEntry();
      pdbEntry.setId(txt_search.getText());
      pdbEntry.setType("PDB");
      selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
      PDBEntry[] pdbEntriesToView = new PDBEntry[]
      { pdbEntry };
      new StructureViewer(ap.getStructureSelectionManager())
              .viewStructures(ap, pdbEntriesToView,
                      ap.av.collateForPDB(pdbEntriesToView));
    }
    else if (currentView == VIEWS_FROM_FILE)
    {
      selectedSequence = ((AssociateSeqOptions) fileChooserAssSeqPanel
              .getCmb_assSeq().getSelectedItem()).getSequence();
      new AssociatePdbFileWithSeq().associatePdbWithSeq(
              selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
              selectedSequence, true, Desktop.instance);
    }
    mainFrame.dispose();
  }

  /**
   * 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()
  {
    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.getName());
      pdbRestCleint = new PDBRestClient();
      PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
      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();
    }
  }

}