Coverage Report

Coverage Report - uk.ac.ebi.intenz.mapper.EnzymeNameMapper

Classes in this File

Line Coverage

Branch Coverage

Complexity

EnzymeNameMapper

63%

108/170

30%

47/154

5.105

 package uk.ac.ebi.intenz.mapper;
 
 import java.sql.Connection;
 import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.sql.Types;
 import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.log4j.Logger;
 
 import uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant;
 import uk.ac.ebi.intenz.domain.constants.EnzymeNameTypeConstant;
 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.enzyme.EnzymeName;
 
 /**
  * Maps enzyme names information to the corresponding database tables.
  *
  * @author Michael Darsow
  * @version $Revision: 1.3 $ $Date: 2009/05/26 14:59:09 $
  */
 public class EnzymeNameMapper {
 
   private static final Logger LOGGER =
           Logger.getLogger(EnzymeNameMapper.class.getName());
 
   private static final String COLUMNS = "enzyme_id, name, name_class, warning, status, source, note, order_in, web_view";
 
   public EnzymeNameMapper() {
   }
 
   private String exportSibNamesStatement() {
     return "SELECT " + COLUMNS +
            " FROM names WHERE enzyme_id = ?" +
            " AND (web_view = ? OR web_view = ? OR web_view = ? OR web_view = ?)" +
            " FOR UPDATE ORDER BY UPPER(name)";
   }
 
   private String findStatement() {
     return "SELECT " + COLUMNS +
            " FROM names" +
            " WHERE enzyme_id = ?" +
            " ORDER BY order_in";
   }
 
   private String findByClassStatement() {
     return "SELECT " + COLUMNS +
            " FROM names" +
            " WHERE enzyme_id = ? AND name_class = ?" +
            " ORDER BY order_in";
   }
 
   private String insertStatement() {
     return "INSERT INTO names (enzyme_id, name, name_class, warning, status, source, note, order_in, web_view) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)";
   }
 
   private String updateNameStatement() {
     return "UPDATE names SET name = ?, warning = ?, status = ?, source = ?, web_view = ? " +
            "WHERE enzyme_id = ? AND name_class = ?";
   }
 
   private String deleteNamesStatement() {
     return "DELETE names WHERE enzyme_id = ? AND name_class = ?";
   }
 
   /**
    * Tries to find name information about an enzyme.
    *
    * @param enzymeId Enzyme ID of entry.
    * @param con      The logical connection.
    * @return a <code>Vector</code> containing <code>EnzymeName</code>instances or <code>null</code> if nothing has been found.
    * @throws SQLException
    */
   public List<EnzymeName> find(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 findStatement = null;
     ResultSet rs = null;
     List<EnzymeName> result = new ArrayList<EnzymeName>();
     boolean noResult = true;
 
     try {
       // Core information.
       findStatement = con.prepareStatement(findStatement());
       findStatement.setLong(1, enzymeId.longValue());
       rs = findStatement.executeQuery();
       while (rs.next()) {
         EnzymeName name = doLoad(rs);
         if (name != null) {
           noResult = false;
           result.add(name);
         }
       }
     } finally {
             if (rs != null) rs.close();
       if (findStatement != null) findStatement.close();
     }
 
     if (noResult) return null;
     return result;
   }
 
   /**
    * Exports all names which are displayed in the ENZYME view.
    *
    * Affected table rows will be locked.
    *
    * @param enzymeId The enzyme ID used to retreive the related names.
    * @param con The database connection.
    * @return an {@link java.util.ArrayList} of names or <code>null</code> if no name could be found.
    * @throws SQLException if a database error occured.
    * @throws NullPointerException if either of the parameters is <code>null</code>.
    */
   public List<EnzymeName> exportSibNames(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 findStatement = null;
     ResultSet rs = null;
     List<EnzymeName> result = new ArrayList<EnzymeName>();
     boolean noResult = true;
 
     try {
       // Core information.
       findStatement = con.prepareStatement(exportSibNamesStatement());
       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()) {
         EnzymeName name = doLoad(rs);
         if (name != null) {
           noResult = false;
           result.add(name);
         }
       }
     } finally {
             if (rs != null) rs.close();
       if (findStatement != null) findStatement.close();
     }
 
     if (noResult) return null;
     return result;
   }
 
   /**
    * Finds only the common name of an entry.
    * <p/>
    * This method will be used to load a list of ghost entries.
    *
    * @param enzymeId Enzyme ID of entry.
    * @param con      The logical connection.
    * @return the name or <code>null</code> if nothing has been found.
    * @throws SQLException
    */
   public List<EnzymeName> findCommonNames(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 findStatement = null;
     ResultSet rs = null;
     boolean noResult = true;
     List<EnzymeName> commonNames = new ArrayList<EnzymeName>();
     EnzymeName result = null;
 
     try {
       // Core information.
       findStatement = con.prepareStatement(findByClassStatement());
       findStatement.setLong(1, enzymeId.longValue());
       findStatement.setString(2, EnzymeNameTypeConstant.COMMON_NAME.toString());
       rs = findStatement.executeQuery();
       while (rs.next()) {
         result = doLoad(rs);
         if (result != null) {
           noResult = false;
           commonNames.add(result);
         }
       }
     } finally {
             if (rs != null) rs.close();
       if (findStatement != null) findStatement.close();
     }
 
     if (noResult) return null;
     return commonNames;
   }
 
   /**
    * Finds only the systematic name of an entry.
    *
    * @param enzymeId Enzyme ID of entry.
    * @param con      The logical connection.
    * @return the name or <code>null</code> if nothing has been found.
    * @throws SQLException
    */
   public EnzymeName findSystematicName(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 findStatement = null;
     ResultSet rs = null;
     EnzymeName result = null;
     try {
       // Core information.
       findStatement = con.prepareStatement(findByClassStatement());
       findStatement.setLong(1, enzymeId.longValue());
       findStatement.setString(2, EnzymeNameTypeConstant.SYSTEMATIC_NAME.toString());
       rs = findStatement.executeQuery();
       if (rs.next()) {
         result = doLoad(rs);
       }
     } finally {
             if (rs != null) rs.close();
       if (findStatement != null) findStatement.close();
     }
 
     return result;
   }
 
   public void update(EnzymeName name, Long enzymeId, Status status, int orderIn, Connection con)
           throws SQLException {
     if (name == null) throw new NullPointerException("Parameter 'name' 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 (orderIn < 1) throw new IllegalArgumentException("Parameter 'orderIn' must not be < 1.");
     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
 
     PreparedStatement updateNameStatement = null;
     try {
       updateNameStatement = con.prepareStatement(updateNameStatement());
       doUpdate(name, enzymeId, status, orderIn, updateNameStatement);
       updateNameStatement.execute();
 //      con.commit();
 //    } catch (SQLException e) {
 //      con.rollback();
 //      throw e;
     } finally {
       if (updateNameStatement != null) updateNameStatement.close();
     }
   }
 
   public void insertNames(List<EnzymeName> names, Long enzymeId, Status status, Connection con)
           throws SQLException {
     if (names == null) throw new NullPointerException("Parameter 'names' 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.");
     for (int iii = 0; iii < names.size(); iii++) {
       insert(names.get(iii), enzymeId, status, (iii+1), con);
     }
   }
 
   public void insert(EnzymeName enzymeName, Long enzymeId, Status status, int orderIn, Connection con)
           throws SQLException {
     if (enzymeName == null) throw new NullPointerException("Parameter 'enzymeName' 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(enzymeName, enzymeId, status, orderIn, insertStatement);
       insertStatement.execute();
 //      con.commit();
 //    } catch (SQLException e) {
 //      con.rollback();
 //      throw e;
     } finally {
       if (insertStatement != null) insertStatement.close();
     }
   }
 
   public void reload(List<EnzymeName> names, Long enzymeId, EnzymeNameTypeConstant type, Status status,
                      Connection con)
           throws SQLException {
     deleteNames(enzymeId, type, con);
     insertNames(names, enzymeId, status, con);
   }
 
   public void deleteNames(Long enzymeId, EnzymeNameTypeConstant nameType, 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 deleteNamesStatement = null;
     try {
       deleteNamesStatement = con.prepareStatement(deleteNamesStatement());
       deleteNamesStatement.setLong(1, enzymeId.longValue());
       deleteNamesStatement.setString(2, nameType.toString());
       deleteNamesStatement.execute();
 //      con.commit();
 //    } catch (SQLException e) {
 //      con.rollback();
 //      throw e;
     } finally {
       if (deleteNamesStatement != null) deleteNamesStatement.close();
     }
   }
 
   // ------------------- PRIVATE METHODS ------------------------
 
   /**
    * Creates the <code>EnzymeName</code> object from the given result set.
    * <p/>
    * This method calls all related mappers for names, references, etc.
    *
    * @param rs The result set object.
    * @return an <code>EnzymeName</code> instance.
    * @throws SQLException
    */
   private EnzymeName doLoad(ResultSet rs) throws SQLException {
     assert rs != null : "Parameter 'rs' must not be null.";
 
     String name = "";
     String nameClass = "";
     String warning = "";
     String source = "";
     String webView = "";
 
     if (rs.getString("name") != null) name = rs.getString("name");
     if (rs.getString("name_class") != null) nameClass = rs.getString("name_class");
     if (rs.getString("warning") != null) warning = rs.getString("warning");
     if (rs.getString("source") != null) source = rs.getString("source");
     if (rs.getString("web_view") != null) webView = rs.getString("web_view");
 
     return EnzymeName.valueOf(name, EnzymeNameTypeConstant.valueOf(nameClass.toUpperCase()),
                               EnzymeNameQualifierConstant.valueOf(warning.toUpperCase()),
                               EnzymeSourceConstant.valueOf(source), EnzymeViewConstant.valueOf(webView));
   }
 
   /**
    * Sets the parameters of the insert statement
    *
    * @param name            ...
    * @param enzymeId        ...
    * @param status          ...
    * @param insertStatement ...
    * @throws SQLException
    */
   private void doInsert(EnzymeName name, Long enzymeId, Status status, int orderIn,
                         PreparedStatement insertStatement) throws SQLException {
     assert name != null : "Parameter 'name' must not be null.";
     assert enzymeId != null : "Parameter 'enzymeId' must not be null.";
     assert status != null : "Parameter 'status' must not be null.";
     assert orderIn > 0 : "Parameter 'orderIn' must not be < 1.";
     assert insertStatement != null : "Parameter 'insertStatement' must not be null.";
 
     insertStatement.setLong(1, enzymeId.longValue());
     insertStatement.setString(2, name.getName());
     insertStatement.setString(3, name.getType().toString());
     if (name.getQualifier() == EnzymeNameQualifierConstant.UNDEF)
       insertStatement.setNull(4, Types.VARCHAR);
     else
       insertStatement.setString(4, name.getQualifier().toString());
     insertStatement.setString(5, status.getCode());
     insertStatement.setString(6, name.getSource().toString());
     insertStatement.setNull(7, Types.VARCHAR);
     insertStatement.setInt(8, orderIn);
     insertStatement.setString(9, name.getView().toString());
   }
 
   private void doUpdate(EnzymeName name, Long enzymeId, Status status, int orderIn,
                         PreparedStatement updateStatement) throws SQLException {
     assert name != null : "Parameter 'name' must not be null.";
     assert enzymeId != null : "Parameter 'enzymeId' must not be null.";
     assert status != null : "Parameter 'status' must not be null.";
     assert orderIn > 0 : "Parameter 'orderIn' must not be < 1.";
     assert updateStatement != null : "Parameter 'updateStatement' must not be null.";
 
     updateStatement.setString(1, name.getName());
     if (name.getQualifier() == EnzymeNameQualifierConstant.UNDEF)
       updateStatement.setNull(2, Types.VARCHAR);
     else
       updateStatement.setString(2, name.getQualifier().toString());
     updateStatement.setString(3, status.getCode());
     updateStatement.setString(4, name.getSource().toString());
     updateStatement.setString(5, name.getView().toString());
     updateStatement.setLong(6, enzymeId.longValue());
     updateStatement.setString(7, name.getType().toString());
   }
 }

1		package uk.ac.ebi.intenz.mapper;
2
3		import java.sql.Connection;
4		import java.sql.PreparedStatement;
5		import java.sql.ResultSet;
6		import java.sql.SQLException;
7		import java.sql.Types;
8		import java.util.ArrayList;
9		import java.util.List;
10
11		import org.apache.log4j.Logger;
12
13		import uk.ac.ebi.intenz.domain.constants.EnzymeNameQualifierConstant;
14		import uk.ac.ebi.intenz.domain.constants.EnzymeNameTypeConstant;
15		import uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant;
16		import uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant;
17		import uk.ac.ebi.intenz.domain.constants.Status;
18		import uk.ac.ebi.intenz.domain.enzyme.EnzymeName;
19
20		/**
21		* Maps enzyme names information to the corresponding database tables.
22		*
23		* @author Michael Darsow
24		* @version $Revision: 1.3 $ $Date: 2009/05/26 14:59:09 $
25		*/
26	1	public class EnzymeNameMapper {
27
28	1	private static final Logger LOGGER =
29		Logger.getLogger(EnzymeNameMapper.class.getName());
30
31		private static final String COLUMNS = "enzyme_id, name, name_class, warning, status, source, note, order_in, web_view";
32
33	2	public EnzymeNameMapper() {
34	2	}
35
36		private String exportSibNamesStatement() {
37	0	return "SELECT " + COLUMNS +
38		" FROM names WHERE enzyme_id = ?" +
39		" AND (web_view = ? OR web_view = ? OR web_view = ? OR web_view = ?)" +
40		" FOR UPDATE ORDER BY UPPER(name)";
41		}
42
43		private String findStatement() {
44	2	return "SELECT " + COLUMNS +
45		" FROM names" +
46		" WHERE enzyme_id = ?" +
47		" ORDER BY order_in";
48		}
49
50		private String findByClassStatement() {
51	2	return "SELECT " + COLUMNS +
52		" FROM names" +
53		" WHERE enzyme_id = ? AND name_class = ?" +
54		" ORDER BY order_in";
55		}
56
57		private String insertStatement() {
58	2	return "INSERT INTO names (enzyme_id, name, name_class, warning, status, source, note, order_in, web_view) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)";
59		}
60
61		private String updateNameStatement() {
62	0	return "UPDATE names SET name = ?, warning = ?, status = ?, source = ?, web_view = ? " +
63		"WHERE enzyme_id = ? AND name_class = ?";
64		}
65
66		private String deleteNamesStatement() {
67	4	return "DELETE names WHERE enzyme_id = ? AND name_class = ?";
68		}
69
70		/**
71		* Tries to find name information about an enzyme.
72		*
73		* @param enzymeId Enzyme ID of entry.
74		* @param con The logical connection.
75		* @return a <code>Vector</code> containing <code>EnzymeName</code>instances or <code>null</code> if nothing has been found.
76		* @throws SQLException
77		*/
78		public List<EnzymeName> find(Long enzymeId, Connection con) throws SQLException {
79	2	if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
80	2	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
81
82	2	PreparedStatement findStatement = null;
83	2	ResultSet rs = null;
84	2	List<EnzymeName> result = new ArrayList<EnzymeName>();
85	2	boolean noResult = true;
86
87		try {
88		// Core information.
89	2	findStatement = con.prepareStatement(findStatement());
90	2	findStatement.setLong(1, enzymeId.longValue());
91	2	rs = findStatement.executeQuery();
92	17	while (rs.next()) {
93	15	EnzymeName name = doLoad(rs);
94	15	if (name != null) {
95	15	noResult = false;
96	15	result.add(name);
97		}
98	15	}
99		} finally {
100	2	if (rs != null) rs.close();
101	2	if (findStatement != null) findStatement.close();
102		}
103
104	2	if (noResult) return null;
105	2	return result;
106		}
107
108		/**
109		* Exports all names which are displayed in the ENZYME view.
110		*
111		* Affected table rows will be locked.
112		*
113		* @param enzymeId The enzyme ID used to retreive the related names.
114		* @param con The database connection.
115		* @return an {@link java.util.ArrayList} of names or <code>null</code> if no name could be found.
116		* @throws SQLException if a database error occured.
117		* @throws NullPointerException if either of the parameters is <code>null</code>.
118		*/
119		public List<EnzymeName> exportSibNames(Long enzymeId, Connection con) throws SQLException {
120	0	if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
121	0	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
122
123	0	PreparedStatement findStatement = null;
124	0	ResultSet rs = null;
125	0	List<EnzymeName> result = new ArrayList<EnzymeName>();
126	0	boolean noResult = true;
127
128		try {
129		// Core information.
130	0	findStatement = con.prepareStatement(exportSibNamesStatement());
131	0	findStatement.setLong(1, enzymeId.longValue());
132	0	findStatement.setString(2, EnzymeViewConstant.INTENZ.toString());
133	0	findStatement.setString(3, EnzymeViewConstant.IUBMB_SIB.toString());
134	0	findStatement.setString(4, EnzymeViewConstant.SIB.toString());
135	0	findStatement.setString(5, EnzymeViewConstant.SIB_INTENZ.toString());
136	0	rs = findStatement.executeQuery();
137	0	while (rs.next()) {
138	0	EnzymeName name = doLoad(rs);
139	0	if (name != null) {
140	0	noResult = false;
141	0	result.add(name);
142		}
143	0	}
144		} finally {
145	0	if (rs != null) rs.close();
146	0	if (findStatement != null) findStatement.close();
147		}
148
149	0	if (noResult) return null;
150	0	return result;
151		}
152
153		/**
154		* Finds only the common name of an entry.
155		* <p/>
156		* This method will be used to load a list of ghost entries.
157		*
158		* @param enzymeId Enzyme ID of entry.
159		* @param con The logical connection.
160		* @return the name or <code>null</code> if nothing has been found.
161		* @throws SQLException
162		*/
163		public List<EnzymeName> findCommonNames(Long enzymeId, Connection con) throws SQLException {
164	1	if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
165	1	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
166
167	1	PreparedStatement findStatement = null;
168	1	ResultSet rs = null;
169	1	boolean noResult = true;
170	1	List<EnzymeName> commonNames = new ArrayList<EnzymeName>();
171	1	EnzymeName result = null;
172
173		try {
174		// Core information.
175	1	findStatement = con.prepareStatement(findByClassStatement());
176	1	findStatement.setLong(1, enzymeId.longValue());
177	1	findStatement.setString(2, EnzymeNameTypeConstant.COMMON_NAME.toString());
178	1	rs = findStatement.executeQuery();
179	2	while (rs.next()) {
180	1	result = doLoad(rs);
181	1	if (result != null) {
182	1	noResult = false;
183	1	commonNames.add(result);
184		}
185		}
186		} finally {
187	1	if (rs != null) rs.close();
188	1	if (findStatement != null) findStatement.close();
189		}
190
191	1	if (noResult) return null;
192	1	return commonNames;
193		}
194
195		/**
196		* Finds only the systematic name of an entry.
197		*
198		* @param enzymeId Enzyme ID of entry.
199		* @param con The logical connection.
200		* @return the name or <code>null</code> if nothing has been found.
201		* @throws SQLException
202		*/
203		public EnzymeName findSystematicName(Long enzymeId, Connection con) throws SQLException {
204	1	if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
205	1	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
206
207	1	PreparedStatement findStatement = null;
208	1	ResultSet rs = null;
209	1	EnzymeName result = null;
210		try {
211		// Core information.
212	1	findStatement = con.prepareStatement(findByClassStatement());
213	1	findStatement.setLong(1, enzymeId.longValue());
214	1	findStatement.setString(2, EnzymeNameTypeConstant.SYSTEMATIC_NAME.toString());
215	1	rs = findStatement.executeQuery();
216	1	if (rs.next()) {
217	1	result = doLoad(rs);
218		}
219		} finally {
220	1	if (rs != null) rs.close();
221	1	if (findStatement != null) findStatement.close();
222		}
223
224	1	return result;
225		}
226
227		public void update(EnzymeName name, Long enzymeId, Status status, int orderIn, Connection con)
228		throws SQLException {
229	0	if (name == null) throw new NullPointerException("Parameter 'name' must not be null.");
230	0	if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
231	0	if (status == null) throw new NullPointerException("Parameter 'status' must not be null.");
232	0	if (orderIn < 1) throw new IllegalArgumentException("Parameter 'orderIn' must not be < 1.");
233	0	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
234
235	0	PreparedStatement updateNameStatement = null;
236		try {
237	0	updateNameStatement = con.prepareStatement(updateNameStatement());
238	0	doUpdate(name, enzymeId, status, orderIn, updateNameStatement);
239	0	updateNameStatement.execute();
240		// con.commit();
241		// } catch (SQLException e) {
242		// con.rollback();
243		// throw e;
244		} finally {
245	0	if (updateNameStatement != null) updateNameStatement.close();
246		}
247	0	}
248
249		public void insertNames(List<EnzymeName> names, Long enzymeId, Status status, Connection con)
250		throws SQLException {
251	0	if (names == null) throw new NullPointerException("Parameter 'names' must not be null.");
252	0	if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
253	0	if (status == null) throw new NullPointerException("Parameter 'status' must not be null.");
254	0	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
255	0	for (int iii = 0; iii < names.size(); iii++) {
256	0	insert(names.get(iii), enzymeId, status, (iii+1), con);
257		}
258	0	}
259
260		public void insert(EnzymeName enzymeName, Long enzymeId, Status status, int orderIn, Connection con)
261		throws SQLException {
262	2	if (enzymeName == null) throw new NullPointerException("Parameter 'enzymeName' must not be null.");
263	2	if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
264	2	if (status == null) throw new NullPointerException("Parameter 'status' must not be null.");
265	2	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
266
267	2	PreparedStatement insertStatement = null;
268		try {
269	2	insertStatement = con.prepareStatement(insertStatement());
270	2	doInsert(enzymeName, enzymeId, status, orderIn, insertStatement);
271	2	insertStatement.execute();
272		// con.commit();
273		// } catch (SQLException e) {
274		// con.rollback();
275		// throw e;
276		} finally {
277	2	if (insertStatement != null) insertStatement.close();
278		}
279	2	}
280
281		public void reload(List<EnzymeName> names, Long enzymeId, EnzymeNameTypeConstant type, Status status,
282		Connection con)
283		throws SQLException {
284	0	deleteNames(enzymeId, type, con);
285	0	insertNames(names, enzymeId, status, con);
286	0	}
287
288		public void deleteNames(Long enzymeId, EnzymeNameTypeConstant nameType, Connection con) throws SQLException {
289	4	if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
290	4	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
291
292	4	PreparedStatement deleteNamesStatement = null;
293		try {
294	4	deleteNamesStatement = con.prepareStatement(deleteNamesStatement());
295	4	deleteNamesStatement.setLong(1, enzymeId.longValue());
296	4	deleteNamesStatement.setString(2, nameType.toString());
297	4	deleteNamesStatement.execute();
298		// con.commit();
299		// } catch (SQLException e) {
300		// con.rollback();
301		// throw e;
302		} finally {
303	4	if (deleteNamesStatement != null) deleteNamesStatement.close();
304		}
305	4	}
306
307		// ------------------- PRIVATE METHODS ------------------------
308
309		/**
310		* Creates the <code>EnzymeName</code> object from the given result set.
311		* <p/>
312		* This method calls all related mappers for names, references, etc.
313		*
314		* @param rs The result set object.
315		* @return an <code>EnzymeName</code> instance.
316		* @throws SQLException
317		*/
318		private EnzymeName doLoad(ResultSet rs) throws SQLException {
319	17	assert rs != null : "Parameter 'rs' must not be null.";
320
321	17	String name = "";
322	17	String nameClass = "";
323	17	String warning = "";
324	17	String source = "";
325	17	String webView = "";
326
327	17	if (rs.getString("name") != null) name = rs.getString("name");
328	17	if (rs.getString("name_class") != null) nameClass = rs.getString("name_class");
329	17	if (rs.getString("warning") != null) warning = rs.getString("warning");
330	17	if (rs.getString("source") != null) source = rs.getString("source");
331	17	if (rs.getString("web_view") != null) webView = rs.getString("web_view");
332
333	17	return EnzymeName.valueOf(name, EnzymeNameTypeConstant.valueOf(nameClass.toUpperCase()),
334		EnzymeNameQualifierConstant.valueOf(warning.toUpperCase()),
335		EnzymeSourceConstant.valueOf(source), EnzymeViewConstant.valueOf(webView));
336		}
337
338		/**
339		* Sets the parameters of the insert statement
340		*
341		* @param name ...
342		* @param enzymeId ...
343		* @param status ...
344		* @param insertStatement ...
345		* @throws SQLException
346		*/
347		private void doInsert(EnzymeName name, Long enzymeId, Status status, int orderIn,
348		PreparedStatement insertStatement) throws SQLException {
349	2	assert name != null : "Parameter 'name' must not be null.";
350	2	assert enzymeId != null : "Parameter 'enzymeId' must not be null.";
351	2	assert status != null : "Parameter 'status' must not be null.";
352	2	assert orderIn > 0 : "Parameter 'orderIn' must not be < 1.";
353	2	assert insertStatement != null : "Parameter 'insertStatement' must not be null.";
354
355	2	insertStatement.setLong(1, enzymeId.longValue());
356	2	insertStatement.setString(2, name.getName());
357	2	insertStatement.setString(3, name.getType().toString());
358	2	if (name.getQualifier() == EnzymeNameQualifierConstant.UNDEF)
359	2	insertStatement.setNull(4, Types.VARCHAR);
360		else
361	0	insertStatement.setString(4, name.getQualifier().toString());
362	2	insertStatement.setString(5, status.getCode());
363	2	insertStatement.setString(6, name.getSource().toString());
364	2	insertStatement.setNull(7, Types.VARCHAR);
365	2	insertStatement.setInt(8, orderIn);
366	2	insertStatement.setString(9, name.getView().toString());
367	2	}
368
369		private void doUpdate(EnzymeName name, Long enzymeId, Status status, int orderIn,
370		PreparedStatement updateStatement) throws SQLException {
371	0	assert name != null : "Parameter 'name' must not be null.";
372	0	assert enzymeId != null : "Parameter 'enzymeId' must not be null.";
373	0	assert status != null : "Parameter 'status' must not be null.";
374	0	assert orderIn > 0 : "Parameter 'orderIn' must not be < 1.";
375	0	assert updateStatement != null : "Parameter 'updateStatement' must not be null.";
376
377	0	updateStatement.setString(1, name.getName());
378	0	if (name.getQualifier() == EnzymeNameQualifierConstant.UNDEF)
379	0	updateStatement.setNull(2, Types.VARCHAR);
380		else
381	0	updateStatement.setString(2, name.getQualifier().toString());
382	0	updateStatement.setString(3, status.getCode());
383	0	updateStatement.setString(4, name.getSource().toString());
384	0	updateStatement.setString(5, name.getView().toString());
385	0	updateStatement.setLong(6, enzymeId.longValue());
386	0	updateStatement.setString(7, name.getType().toString());
387	0	}
388		}