package uk.ac.ebi.intenz.mapper;

 import java.sql.Connection;

 import java.sql.PreparedStatement;

 import java.sql.ResultSet;

 import java.sql.SQLException;

 import java.util.ArrayList;

 import java.util.List;

 import uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant;

 import uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant;

 import uk.ac.ebi.intenz.domain.constants.Status;

 import uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant;

 import uk.ac.ebi.intenz.domain.enzyme.EnzymeLink;

 import uk.ac.ebi.intenz.domain.exceptions.DomainException;

 /**

  * Maps link information to the corresponding database tables.

  * <p/>

  *

  * @author Michael Darsow

  * @version $Revision: 1.3 $ $Date: 2009/05/26 14:23:11 $

  */

 public class EnzymeLinkMapper {

   private static final String COLUMNS =

     "enzyme_id, url, display_name, status, source, web_view, data_comment";

   private static final String TABLES = "links";

   private static final String XREF_COLUMNS =

     "enzyme_id, database_code, database_ac, name, status, source, web_view, data_comment";

   private static final String XREF_TABLES = "xrefs";

 //  private static final Logger LOGGER = Logger.getLogger(EnzymeLinkMapper.class);

   public EnzymeLinkMapper() {

   }

   private String findStatement() {

     return "SELECT " + COLUMNS +

            " FROM " + TABLES +

            " WHERE links.enzyme_id = ?" +

            " ORDER BY links.display_name";

   }

   private String exportSibLinksStatement() {

     return "SELECT " + COLUMNS +

            " FROM " + TABLES +

            " WHERE links.enzyme_id = ? AND (links.web_view = ? OR links.web_view = ? OR links.web_view = ? OR links.web_view = ?)" +

            " ORDER BY links.display_name";

   }

   private String findXrefsStatement() {

     return "SELECT " + XREF_COLUMNS +

            " FROM " + XREF_TABLES +

            " WHERE xrefs.enzyme_id = ?" +

            " ORDER BY xrefs.name";

   }

   private String findSibXrefsStatement() {

     return "SELECT " + XREF_COLUMNS +

            " FROM " + XREF_TABLES +

            " WHERE xrefs.enzyme_id = ? AND (xrefs.web_view = ? OR xrefs.web_view = ? OR xrefs.web_view = ? OR xrefs.web_view = ?)" +

            " ORDER BY name";

   }

   private String insertStatement() {

     return "INSERT INTO links (enzyme_id, url, display_name, status, source, web_view, data_comment) VALUES (?, ?, ?, ?, ?, ?, ?)";

   }

   private String insertXrefStatement() {

     return "INSERT INTO xrefs (enzyme_id, database_code, database_ac, name, status, source, web_view, data_comment) VALUES (?, ?, ?, ?, ?, ?, ?, ?)";

   }

   private String updateLinkUrlStatement() {

     return "UPDATE links SET url = ?, status = ? WHERE enzyme_id = ? AND display_name = ?";

   }

   private String deleteStatement() {

     return "DELETE links WHERE enzyme_id = ? AND display_name = ? AND url = ?";

   }

   private String deleteAllStatement() {

     return "DELETE links WHERE enzyme_id = ?";

   }

   private String deleteXrefStatement() {

     return "DELETE xrefs WHERE enzyme_id = ? AND database_code = ? AND database_ac = ? AND name = ?";

   }

   private String deleteAllXrefStatement() {

     return "DELETE xrefs WHERE enzyme_id = ?";

   }

    private String deleteByCodeXrefStatement() {

     return "DELETE xrefs WHERE enzyme_id = ? AND database_code = ?";

   }

   private String deleteByNameStatement() {

     return "DELETE links WHERE enzyme_id = ? AND display_name = ?";

   }

   /**

    * Tries to find link information about an enzyme in tables LINKS and XREFS.

    *

    * @param enzymeId Enzyme ID of entry.

    * @param con      The logical connection.

    * @return a <code>Vector</code> containing <code>EnzymeLink</code>instances or <code>null</code> if nothing has been found.

    * @throws SQLException

    */

   public List<EnzymeLink> find(Long enzymeId, Connection con) throws SQLException, DomainException {

     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

     PreparedStatement findStatement = null;

     ResultSet rs = null;

     List<EnzymeLink> result = new ArrayList<EnzymeLink>();

     try {

       findStatement = con.prepareStatement(findStatement());

       findStatement.setLong(1, enzymeId.longValue());

       rs = findStatement.executeQuery();

       while (rs.next()) {

         EnzymeLink link = doLoad(rs);

         if (link == null) continue;

         result.add(link);

       }

       List<EnzymeLink> xrefs = findXrefs(enzymeId, con);

       if (xrefs != null) result.addAll(xrefs);

     } finally {

             if (rs != null) rs.close();

       if (findStatement != null) findStatement.close();

     }

     if (result.size() == 0) return null;

     return result;

   }

   /**

    * Exports all links which are displayed in the ENZYME view.

    *

    * Affected table rows will be locked.

    *

    * @param enzymeId The enzyme ID used to retreive the related links.

    * @param con The database connection.

    * @return an {@link java.util.ArrayList} of links or <code>null</code> if no link could be found.

    * @throws SQLException if a database error occured.

    * @throws NullPointerException if either of the parameters is <code>null</code>.

    */

   public List<EnzymeLink> exportSibLinks(Long enzymeId, Connection con) throws SQLException, DomainException {

     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

     PreparedStatement findStatement = null;

     ResultSet rs = null;

     List<EnzymeLink> result = new ArrayList<EnzymeLink>();

     try {

       findStatement = con.prepareStatement(exportSibLinksStatement());

       findStatement.setLong(1, enzymeId.longValue());

       findStatement.setString(2, EnzymeViewConstant.INTENZ.toString());

       findStatement.setString(3, EnzymeViewConstant.IUBMB_SIB.toString());

       findStatement.setString(4, EnzymeViewConstant.SIB.toString());

       findStatement.setString(5, EnzymeViewConstant.SIB_INTENZ.toString());

       rs = findStatement.executeQuery();

       while (rs.next()) {

         EnzymeLink link = doLoad(rs);

         if (link == null) continue;

         result.add(link);

       }

       List<EnzymeLink> xrefs = findSibXrefs(enzymeId, con);

       if (xrefs != null) result.addAll(xrefs);

     } finally {

             if (rs != null) rs.close();

       if (findStatement != null) findStatement.close();

     }

     if (result.size() == 0) return null;

     return result;

   }

   /**

    * Tries to find SwissProt xref information about an enzyme.

    *

    * @param enzymeId Enzyme ID of entry.

    * @param con      The logical connection.

    * @return a <code>Vector</code> containing <code>EnzymeLink</code>instances or <code>null</code> if nothing has been found.

    * @throws SQLException

    */

   public List<EnzymeLink> findXrefs(Long enzymeId, Connection con) throws SQLException, DomainException {

     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

     PreparedStatement findStatement = null;

     ResultSet rs = null;

     List<EnzymeLink> result = new ArrayList<EnzymeLink>();

     boolean noResult = true;

     try {

       // Core information.

       findStatement = con.prepareStatement(findXrefsStatement());

       findStatement.setLong(1, enzymeId.longValue());

       rs = findStatement.executeQuery();

       while (rs.next()) {

         noResult = false;

         EnzymeLink link = doLoadXref(rs);

         if (link == null) continue;

         result.add(link);

       }

     } finally {

             if (rs != null) rs.close();

         if (findStatement != null) findStatement.close();

     }

     if (noResult) return null;

     return result;

   }

   /**

    * Finds all xrefs which are displayed in the ENZYME view.

    *

    * @param enzymeId The enzyme ID used to retreive the related xrefs.

    * @param con The database connection.

    * @return an {@link java.util.ArrayList} of xrefs or <code>null</code> if no xref could be found.

    * @throws SQLException if a database error occured.

    * @throws NullPointerException if either of the parameters is <code>null</code>.

    */

   public List<EnzymeLink> findSibXrefs(Long enzymeId, Connection con) throws SQLException, DomainException {

     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

     PreparedStatement findStatement = null;

     ResultSet rs = null;

     List<EnzymeLink> result = new ArrayList<EnzymeLink>();

     boolean noResult = true;

     try {

       // Core information.

       findStatement = con.prepareStatement(findSibXrefsStatement());

       findStatement.setLong(1, enzymeId.longValue());

       findStatement.setString(2, EnzymeViewConstant.INTENZ.toString());

       findStatement.setString(3, EnzymeViewConstant.IUBMB_SIB.toString());

       findStatement.setString(4, EnzymeViewConstant.SIB.toString());

       findStatement.setString(5, EnzymeViewConstant.SIB_INTENZ.toString());

       rs = findStatement.executeQuery();

       while (rs.next()) {

         noResult = false;

         EnzymeLink link = doLoadXref(rs);

         if (link == null) continue;

         result.add(link);

       }

     } finally {

             if (rs != null) rs.close();

         if (findStatement != null) findStatement.close();

     }

     if (noResult) return null;

     return result;

   }

   /**

    * Stores the given list of links into the database.

    *

    * @param links    The vector of links.

    * @param enzymeId The enzyme ID.

    * @param status   ...

    * @param con      ...

    * @throws SQLException

    */

   public void insert(List<EnzymeLink> links, Long enzymeId, Status status, Connection con)

   throws SQLException {

     if (links == null) throw new NullPointerException("Parameter 'links' must not be null.");

     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

     if (status == null) throw new NullPointerException("Parameter 'status' must not be null.");

     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

     PreparedStatement insertStatement = null, insertXrefStatement = null;

     try {

       insertStatement = con.prepareStatement(insertStatement());

       insertXrefStatement = con.prepareStatement(insertXrefStatement());

       for (int iii = 0; iii < links.size(); iii++) {

         EnzymeLink link = links.get(iii);

         if (link.getXrefDatabaseConstant().isXref()) {

           doInsertXref(link, enzymeId, status, insertXrefStatement);

           insertXrefStatement.execute();

         } else {

           doInsert(link, enzymeId, status, insertStatement);

           insertStatement.execute();

         }

       }

     } finally {

       if (insertStatement != null) insertStatement.close();

       if (insertXrefStatement != null) insertXrefStatement.close();

     }

   }

   public void insertLink(EnzymeLink link, Long enzymeId, Status status, Connection con) throws SQLException {

     if (link == null) throw new NullPointerException("Parameter 'link' must not be null.");

     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

     if (status == null) throw new NullPointerException("Parameter 'status' must not be null.");

     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

     PreparedStatement insertStatement = null;

     try {

       insertStatement = con.prepareStatement(insertStatement());

       doInsert(link, enzymeId, status, insertStatement);

       insertStatement.execute();

     } finally {

       if (insertStatement != null) insertStatement.close();

     }

   }

   public void updateLinkUrl(EnzymeLink link, Long enzymeId, Status status, Connection con) throws SQLException {

     if (link == null) throw new NullPointerException("Parameter 'link' must not be null.");

     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

     if (status == null) throw new NullPointerException("Parameter 'status' must not be null.");

     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

     PreparedStatement updateStatement = null;

     try {

       updateStatement = con.prepareStatement(updateLinkUrlStatement());

       updateStatement.setString(1, link.getSpecificUrl());

       updateStatement.setString(2, status.getCode());

       updateStatement.setLong(3, enzymeId.longValue());

       if (link.getXrefDatabaseConstant().equals("NIST74"))

         updateStatement.setString(4, "GTD"); // TODO: Change to NIST 74 completely.

       else

         updateStatement.setString(4, link.getXrefDatabaseConstant().toString());

       updateStatement.execute();

     } finally {

       if (updateStatement != null) updateStatement.close();

     }

   }

   public void reloadLinks(List<EnzymeLink> links, Long enzymeId, Status status, Connection con) throws SQLException {

     if (links == null) throw new NullPointerException("Parameter 'links' must not be null.");

     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

     if (status == null) throw new NullPointerException("Parameter 'status' must not be null.");

     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

     deleteOtherLinks(links, enzymeId, con);

     insert(links, enzymeId, status, con);

   }

   public void delete(Long enzymeId, EnzymeLink link, Connection con) throws SQLException {

     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

     if (link == null) throw new NullPointerException("Parameter 'link' must not be null.");

     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

     PreparedStatement deleteStatement = null;

     try {

       deleteStatement = con.prepareStatement(deleteStatement());

       deleteStatement.setLong(1, enzymeId.longValue());

       if (link.getXrefDatabaseConstant().equals("NIST74"))

         deleteStatement.setString(2, "GTD");

       else

         deleteStatement.setString(2, link.getXrefDatabaseConstant().toString());

       deleteStatement.setString(3, link.getSpecificUrl());

       deleteStatement.execute();

 //      con.commit();

 //    } catch (SQLException e) {

 //      con.rollback();

 //      throw e;

     } finally {

       if (deleteStatement != null) deleteStatement.close();

     }

   }

   public void deleteAll(Long enzymeId, Connection con) throws SQLException {

     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

     PreparedStatement deleteStatement = null;

     try {

       deleteStatement = con.prepareStatement(deleteAllStatement());

       deleteStatement.setLong(1, enzymeId.longValue());

       deleteStatement.execute();

 //      con.commit();

 //    } catch (SQLException e) {

 //      con.rollback();

 //      throw e;

     } finally {

       if (deleteStatement != null) deleteStatement.close();

     }

   }

   public void deleteXref(Long enzymeId, EnzymeLink xref, Connection con) throws SQLException {

     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

     if (xref == null) throw new NullPointerException("Parameter 'xref' must not be null.");

     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

     PreparedStatement deleteXrefStatement = null;

     String dbCode = xref.getXrefDatabaseConstant().toString();

     if (dbCode.equals("Swiss-Prot")) dbCode = "S";

     if (dbCode.equals("PROSITE")) dbCode = "P";

     try {

       deleteXrefStatement = con.prepareStatement(deleteXrefStatement());

       deleteXrefStatement.setLong(1, enzymeId.longValue());

       deleteXrefStatement.setString(2, dbCode);

       deleteXrefStatement.setString(3, xref.getAccession());

       deleteXrefStatement.setString(4, xref.getName());

       deleteXrefStatement.execute();

 //      con.commit();

 //    } catch (SQLException e) {

 //      con.rollback();

 //      throw e;

     } finally {

       if (deleteXrefStatement != null) deleteXrefStatement.close();

     }

   }

   public void deleteAllXref(Long enzymeId, Connection con) throws SQLException {

     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

     PreparedStatement deleteXrefStatement = null;

     try {

       deleteXrefStatement = con.prepareStatement(deleteAllXrefStatement());

       deleteXrefStatement.setLong(1, enzymeId.longValue());

       deleteXrefStatement.execute();

 //      con.commit();

 //    } catch (SQLException e) {

 //      con.rollback();

 //      throw e;

     } finally {

       if (deleteXrefStatement != null) deleteXrefStatement.close();

     }

   }

   public void deleteByName(Long enzymeId, String displayName, Connection con) throws SQLException {

     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

     if (displayName == null) throw new NullPointerException("Parameter 'displayName' must not be null.");

     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

     PreparedStatement deleteByNameStatement = null;

     try {

       deleteByNameStatement = con.prepareStatement(deleteByNameStatement());

       deleteByNameStatement.setLong(1, enzymeId.longValue());

       deleteByNameStatement.setString(2, displayName);

       deleteByNameStatement.execute();

 //      con.commit();

 //    } catch (SQLException e) {

 //      con.rollback();

 //      throw e;

     } finally {

       if (deleteByNameStatement != null) deleteByNameStatement.close();

     }

   }

    public void deleteByCodeXref(Long enzymeId, String xrefCode, Connection con) throws SQLException {

        if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

        if (xrefCode == null) throw new NullPointerException("Parameter 'xrefCode' must not be null.");

        if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

        PreparedStatement deleteByNameStatement = null;

        if (xrefCode.equals(XrefDatabaseConstant.SWISSPROT.getDatabaseCode())) xrefCode = "S";

        if (xrefCode.equals(XrefDatabaseConstant.PROSITE.getDatabaseCode())) xrefCode = "P";

        try {

          deleteByNameStatement = con.prepareStatement(deleteByCodeXrefStatement());

          deleteByNameStatement.setLong(1, enzymeId.longValue());

          deleteByNameStatement.setString(2, xrefCode);

          deleteByNameStatement.execute();

 //         con.commit();

 //       } catch (SQLException e) {

 //         con.rollback();

 //         throw e;

        } finally {

          if (deleteByNameStatement != null) deleteByNameStatement.close();

        }

      }

   public void deleteOtherLinks(List<EnzymeLink> links, Long enzymeId, Connection con) throws SQLException {

     if (links == null) throw new NullPointerException("Parameter 'links' must not be null.");

     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");

     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");

     deleteAll(enzymeId, con);

     deleteAllXref(enzymeId, con);

   }

   // ------------------- PRIVATE METHODS ------------------------

   /**

    * Creates the <code>EnzymeLink</code> object from the given result set.

    * <p/>

    *

    * @param rs The result set object.

    * @return an <code>EnzymeLink</code> instance.

    * @throws SQLException

    */

   private EnzymeLink doLoad(ResultSet rs) throws SQLException, DomainException {

     assert rs != null : "Parameter 'rs' must not be null.";

     EnzymeLink result = null;

     String displayName = "";

     String url = "";

     String source = "";

     String webView = "";

     String dataComment = null;

     if (rs.getString("display_name") != null) displayName = rs.getString("display_name");

     if (rs.getString("url") != null) url = rs.getString("url");

     if (rs.getString("source") != null) source = rs.getString("source");

     if (rs.getString("web_view") != null) webView = rs.getString("web_view");

     if (rs.getString("data_comment") != null) dataComment = rs.getString("data_comment");

     if (displayName.equals("UM-BBD")) displayName = "UMBBD";

     if (displayName.equals("NIST 74")) displayName = "NIST74";

         // Check for static links.

     if (displayName.equals(EnzymeLink.BRENDA.getXrefDatabaseConstant().getDatabaseCode())){

         result = EnzymeLink.BRENDA;

     } else if (displayName.equals(EnzymeLink.KEGG.getXrefDatabaseConstant().getDatabaseCode())){

         result = EnzymeLink.KEGG;

     } else if (displayName.equals(EnzymeLink.EXPASY.getXrefDatabaseConstant().getDatabaseCode())){

         return null;//return EnzymeLink.EXPASY; // These links are not necessary anymore.

     } else if (displayName.equals(EnzymeLink.GO.getXrefDatabaseConstant().getDatabaseCode())){

         result = EnzymeLink.GO;

     } else if (displayName.equals(EnzymeLink.NIST74.getXrefDatabaseConstant().getDisplayName()) ||

             displayName.equals("GTD")){

         result = EnzymeLink.NIST74;

     } else if (displayName.equals(EnzymeLink.ERGO.getXrefDatabaseConstant().getDatabaseCode()) ||

             displayName.equals(EnzymeLink.WIT.getXrefDatabaseConstant().getDatabaseCode())) {

         result = EnzymeLink.ERGO;

     } else if (displayName.equals(XrefDatabaseConstant.CAS.getDatabaseCode())) {

         if(url.trim().equals("")) return null;

         result = EnzymeLink.valueOf(XrefDatabaseConstant.CAS, "", url, "",

                         EnzymeSourceConstant.valueOf(source), EnzymeViewConstant.valueOf(webView), dataComment);

     }

     if (result == null){ // not a static link

         result = EnzymeLink.valueOf(XrefDatabaseConstant.valueOf(displayName), url, "", "",

                 EnzymeSourceConstant.valueOf(source), EnzymeViewConstant.valueOf(webView), dataComment);    

     } else if (dataComment != null){ // static link with a comment!

         result = EnzymeLink.valueOf(XrefDatabaseConstant.valueOf(displayName), result.getSpecificUrl(),

                 result.getAccession(), result.getName(), result.getSource(), result.getView(), dataComment);

     }

     return result;

   }

   /**

    * Creates the <code>EnzymeLink</code> object from the given xref result set.

    * <p/>

    *

    * @param rs The result set object.

    * @return an <code>EnzymeLink</code> instance.

    * @throws SQLException

    */

   private EnzymeLink doLoadXref(ResultSet rs) throws SQLException, DomainException {

     assert rs != null : "Parameter 'rs' must not be null.";

     String databaseCode = "";

     String accession = "";

     String name = "";

     String source = "";

     String webView = "";

     String dataComment = null;

     if (rs.getString("database_code") != null) databaseCode = rs.getString("database_code");

     if (rs.getString("database_ac") != null) accession = rs.getString("database_ac");

     if (rs.getString("name") != null) name = rs.getString("name");

     if (rs.getString("source") != null) source = rs.getString("source");

     if (rs.getString("web_view") != null) webView = rs.getString("web_view");

     if (rs.getString("data_comment") != null) dataComment = rs.getString("data_comment");

     if (databaseCode.equals("S")) databaseCode = "SWISSPROT";

     if (databaseCode.equals("P")) databaseCode = "PROSITE";

     if (databaseCode.equals("DIAGR")) {

       databaseCode = "DIAGRAM";

       return EnzymeLink.valueOf(XrefDatabaseConstant.DIAGRAM, accession, "", name,

                       EnzymeSourceConstant.valueOf(source), EnzymeViewConstant.valueOf(webView), dataComment); // Accession is the URL for DIAGRAMS.

     }

     return EnzymeLink.valueOf(XrefDatabaseConstant.valueOf(databaseCode), "", accession, name,

         EnzymeSourceConstant.valueOf(source), EnzymeViewConstant.valueOf(webView), dataComment);

   }

   /**

    * Sets the parameters of the prepared statement.

    *

    * @param link            ...

    * @param enzymeId        ...

    * @param status          ...

    * @param insertStatement ...

    * @throws SQLException

    */

   private void doInsert(EnzymeLink link, Long enzymeId, Status status,

                         PreparedStatement insertStatement) throws SQLException {

     assert link != null : "Parameter 'link' must not be null.";

     assert enzymeId != null : "Parameter 'enzymeId' must not be null.";

     assert status != null : "Parameter 'status' must not be null.";

     assert insertStatement != null : "Parameter 'insertStatement' must not be null.";

     insertStatement.setLong(1, enzymeId.longValue());

     if (link.getXrefDatabaseConstant() == XrefDatabaseConstant.CAS) {

       insertStatement.setString(2, link.getAccession());

     } else {

       insertStatement.setString(2, link.getSpecificUrl());

     }

     if (link.getXrefDatabaseConstant().equals("NIST74")) // TODO: Change to NIST 74 completely.

       insertStatement.setString(3, "GTD");

     else

       insertStatement.setString(3, link.getXrefDatabaseConstant().toString());

     insertStatement.setString(4, status.getCode());

     insertStatement.setString(5, link.getSource().toString());

     insertStatement.setString(6, link.getView().toString());

     if (link.getDataComment() == null || link.getDataComment().equals("")){

         insertStatement.setNull(7, java.sql.Types.VARCHAR);

     } else {

         insertStatement.setString(7, link.getDataComment());

     }

   }

   private void doInsertXref(EnzymeLink xref, Long enzymeId, Status status,

                             PreparedStatement insertXrefStatement) throws SQLException {

     assert xref != null : "Parameter 'xref' must not be null.";

     assert enzymeId != null : "Parameter 'enzymeId' must not be null.";

     assert status != null : "Parameter 'status' must not be null.";

     assert insertXrefStatement != null : "Parameter 'insertXrefStatement' must not be null.";

     String dbCode = xref.getXrefDatabaseConstant().getDatabaseCode();

     if (dbCode.equals("SWISSPROT")) dbCode = "S";

     if (dbCode.equals("PROSITE")) dbCode = "P";

 //    if (dbCode.equals("DIAGRAM")) dbCode = "DIAGR";

     insertXrefStatement.setLong(1, enzymeId.longValue());

     insertXrefStatement.setString(2, dbCode);

     if (dbCode.equals("DIAGR"))

       insertXrefStatement.setString(3, xref.getSpecificUrl());

     else

       insertXrefStatement.setString(3, xref.getAccession());

     insertXrefStatement.setString(4, xref.getName());

     insertXrefStatement.setString(5, status.getCode());

     insertXrefStatement.setString(6, xref.getSource().toString());

     insertXrefStatement.setString(7, xref.getView().toString());

     if (xref.getDataComment() == null || xref.getDataComment().equals("")){

         insertXrefStatement.setNull(8, java.sql.Types.VARCHAR);

     } else {

         insertXrefStatement.setString(8, xref.getDataComment());

     }

   }

 }