Coverage Report

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

Classes in this File

Line Coverage

Branch Coverage

Complexity

EnzymeSubclassMapper

0/70

0/44

3.889

 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.Statement;
 import java.util.ArrayList;
 import java.util.List;
 
 import uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber;
 import uk.ac.ebi.intenz.domain.enzyme.EnzymeSubSubclass;
 import uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass;
 import uk.ac.ebi.intenz.domain.exceptions.DomainException;
 
 /**
  * Maps enzyme subclass information to the corresponding database tables.
  *
  * @author Michael Darsow
  * @version $Revision: 1.3 $ $Date: 2009/05/26 14:59:09 $
  */
 public class EnzymeSubclassMapper {
 
   private static final String COLUMNS = "s.ec1, s.ec2, s.name, c.name, s.description";
 
   private static final String SELECT_ALL = "SELECT " + COLUMNS + " FROM subclasses s, classes c";
   
   public EnzymeSubclassMapper() {
   }
 
   private String findStatement() {
     return "SELECT " + COLUMNS + " FROM subclasses s, classes c WHERE c.ec1 = ? AND s.ec1 = ? AND s.ec2 = ? ORDER BY s.ec1, s.ec2";
   }
 
   private String findListStatement() {
     return "SELECT " + COLUMNS + " FROM subclasses s, classes c WHERE c.ec1 = ? AND s.ec1 = ? ORDER BY s.ec1, s.ec2";
   }
 
   private String findSubclassOnlyStatement() {
     return "SELECT ec1 FROM subclasses WHERE ec1 = ? AND ec2 = ?";
   }
 
   /**
    * Tries to find Subclass information about an enzyme.
    *
    * @param ec1 Number of class to search for.
    * @param ec2 Number of subclass to search for.
    * @param con The logical connection.
    * @return an <code>EnzymeClass</code> instance or <code>null</code> if nothing has been found.
    * @throws NullPointerException if any of the parameters is <code>null</code>.
    * @throws SQLException         if a database error occurs.
    * @throws DomainException      if any error related to domain information occurs.
    */
   public EnzymeSubclass find(String ec1, String ec2, Connection con) throws SQLException, DomainException {
     if (ec1 == null) throw new NullPointerException("Parameter 'ec1' must not be null.");
     if (ec2 == null) throw new NullPointerException("Parameter 'ec2' must not be null.");
     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
 
     PreparedStatement findStatement = null;
     ResultSet rs = null;
     EnzymeSubclass result = null;
     List<EnzymeSubSubclass> subSubclasses;
 
     // Get sub-subclasses.
     EnzymeSubSubclassMapper subSubclassMapper = new EnzymeSubSubclassMapper();
     subSubclasses = subSubclassMapper.findList(ec1, ec2, con);
 
     try {
       findStatement = con.prepareStatement(findStatement());
       findStatement.setString(1, ec1);
       findStatement.setString(2, ec1);
       findStatement.setString(3, ec2);
       rs = findStatement.executeQuery();
       if (rs.next()) {
         result = doLoad(rs, subSubclasses);
       }
     } finally {
             if (rs != null) rs.close();
       if (findStatement != null) findStatement.close();
     }
 
     return result;
   }
 
   /**
    * Tries to find all Subclasses requested.
    *
    * @param ec1 Number/Wildcard of class to search for.
    * @param con The logical connection.
    * @return a <code>Vector</code> of <code>EnzymeClass</code> instances or <code>null</code> if nothing has been found.
    * @throws SQLException
    */
   public List<EnzymeSubclass> findList(String ec1, Connection con) throws SQLException, DomainException {
     PreparedStatement findListStatement = null;
     ResultSet rs = null;
     List<EnzymeSubclass> result = new ArrayList<EnzymeSubclass>();
     boolean noResult = true;
 
     try {
       findListStatement = con.prepareStatement(findListStatement());
       findListStatement.setString(1, ec1);
       findListStatement.setString(2, ec1);
       rs = findListStatement.executeQuery();
       while (rs.next()) {
         noResult = false;
         result.add(doLoad(rs, null));
       }
     } finally {
             if (rs != null) rs.close();
       if (findListStatement != null) findListStatement.close();
     }
 
     if (noResult) return null;
     return result;
   }
   
   /**
    * 
    * @param con
    * @return A <code>List</code> of <code>EnzymeSubclass</code>es (without
    *    subsubclass information).
  * @throws SQLException 
  * @throws DomainException 
    */
   public List<EnzymeSubclass> findAll(Connection con) throws SQLException, DomainException{
       List<EnzymeSubclass> result = new ArrayList<EnzymeSubclass>();
       Statement stm = null;
       ResultSet rs = null;
       try {
           stm = con.createStatement();
           rs = stm.executeQuery(SELECT_ALL);
           while (rs.next()){
               result.add(doLoad(rs, null));
           }
       } finally {
               if (rs != null) rs.close();
           if (stm != null) stm.close();
       }
       return result;
   }
 
   /**
    * Checks if the given subclass numbers are valid.
    *
    * @param ec1 The class number.
    * @param ec2 The subclass number.
    * @param con The connection.
    * @return <code>true</code> if the class exists.
    * @throws SQLException
    */
   public boolean subclassExists(String ec1, String ec2, Connection con) throws SQLException {
     PreparedStatement findStatement = null;
     ResultSet rs = null;
     try {
       findStatement = con.prepareStatement(findSubclassOnlyStatement());
       findStatement.setString(1, ec1);
       findStatement.setString(2, ec2);
       rs = findStatement.executeQuery();
       if (rs.next()) {
         return true;
       }
     } finally {
             if (rs != null) rs.close();
       if (findStatement != null) findStatement.close();
     }
 
     return false;
   }
 
 
   // ------------------- PRIVATE METHODS ------------------------
 
   /**
    * Creates the <code>EnzymeSubclass</code> object.
    *
    * @param rs The result set object.
    * @return an <code>EnzymeSubclass</code> instance.
    * @throws SQLException
    */
   private EnzymeSubclass doLoad(ResultSet rs, List<EnzymeSubSubclass> subSubclasses)
   throws SQLException, DomainException {
     int ec1 = 0;
     int ec2 = 0;
     String className = "";
     String name = "";
     String description = "";
 
     if (rs.getInt(1) > 0) ec1 = rs.getInt(1);
     if (rs.getInt(2) > 0) ec2 = rs.getInt(2);
     if (rs.getString(3) != null) name = rs.getString(3);
     if (rs.getString(4) != null) className = rs.getString(4);
     if (rs.getString(5) != null) description = rs.getString(5);
 
     return new EnzymeSubclass(EnzymeCommissionNumber.valueOf(ec1, ec2), className, name, description, subSubclasses);
   }
 }

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.Statement;
8		import java.util.ArrayList;
9		import java.util.List;
10
11		import uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber;
12		import uk.ac.ebi.intenz.domain.enzyme.EnzymeSubSubclass;
13		import uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass;
14		import uk.ac.ebi.intenz.domain.exceptions.DomainException;
15
16		/**
17		* Maps enzyme subclass information to the corresponding database tables.
18		*
19		* @author Michael Darsow
20		* @version $Revision: 1.3 $ $Date: 2009/05/26 14:59:09 $
21		*/
22		public class EnzymeSubclassMapper {
23
24		private static final String COLUMNS = "s.ec1, s.ec2, s.name, c.name, s.description";
25
26		private static final String SELECT_ALL = "SELECT " + COLUMNS + " FROM subclasses s, classes c";
27
28	0	public EnzymeSubclassMapper() {
29	0	}
30
31		private String findStatement() {
32	0	return "SELECT " + COLUMNS + " FROM subclasses s, classes c WHERE c.ec1 = ? AND s.ec1 = ? AND s.ec2 = ? ORDER BY s.ec1, s.ec2";
33		}
34
35		private String findListStatement() {
36	0	return "SELECT " + COLUMNS + " FROM subclasses s, classes c WHERE c.ec1 = ? AND s.ec1 = ? ORDER BY s.ec1, s.ec2";
37		}
38
39		private String findSubclassOnlyStatement() {
40	0	return "SELECT ec1 FROM subclasses WHERE ec1 = ? AND ec2 = ?";
41		}
42
43		/**
44		* Tries to find Subclass information about an enzyme.
45		*
46		* @param ec1 Number of class to search for.
47		* @param ec2 Number of subclass to search for.
48		* @param con The logical connection.
49		* @return an <code>EnzymeClass</code> instance or <code>null</code> if nothing has been found.
50		* @throws NullPointerException if any of the parameters is <code>null</code>.
51		* @throws SQLException if a database error occurs.
52		* @throws DomainException if any error related to domain information occurs.
53		*/
54		public EnzymeSubclass find(String ec1, String ec2, Connection con) throws SQLException, DomainException {
55	0	if (ec1 == null) throw new NullPointerException("Parameter 'ec1' must not be null.");
56	0	if (ec2 == null) throw new NullPointerException("Parameter 'ec2' must not be null.");
57	0	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
58
59	0	PreparedStatement findStatement = null;
60	0	ResultSet rs = null;
61	0	EnzymeSubclass result = null;
62		List<EnzymeSubSubclass> subSubclasses;
63
64		// Get sub-subclasses.
65	0	EnzymeSubSubclassMapper subSubclassMapper = new EnzymeSubSubclassMapper();
66	0	subSubclasses = subSubclassMapper.findList(ec1, ec2, con);
67
68		try {
69	0	findStatement = con.prepareStatement(findStatement());
70	0	findStatement.setString(1, ec1);
71	0	findStatement.setString(2, ec1);
72	0	findStatement.setString(3, ec2);
73	0	rs = findStatement.executeQuery();
74	0	if (rs.next()) {
75	0	result = doLoad(rs, subSubclasses);
76		}
77		} finally {
78	0	if (rs != null) rs.close();
79	0	if (findStatement != null) findStatement.close();
80		}
81
82	0	return result;
83		}
84
85		/**
86		* Tries to find all Subclasses requested.
87		*
88		* @param ec1 Number/Wildcard of class to search for.
89		* @param con The logical connection.
90		* @return a <code>Vector</code> of <code>EnzymeClass</code> instances or <code>null</code> if nothing has been found.
91		* @throws SQLException
92		*/
93		public List<EnzymeSubclass> findList(String ec1, Connection con) throws SQLException, DomainException {
94	0	PreparedStatement findListStatement = null;
95	0	ResultSet rs = null;
96	0	List<EnzymeSubclass> result = new ArrayList<EnzymeSubclass>();
97	0	boolean noResult = true;
98
99		try {
100	0	findListStatement = con.prepareStatement(findListStatement());
101	0	findListStatement.setString(1, ec1);
102	0	findListStatement.setString(2, ec1);
103	0	rs = findListStatement.executeQuery();
104	0	while (rs.next()) {
105	0	noResult = false;
106	0	result.add(doLoad(rs, null));
107		}
108		} finally {
109	0	if (rs != null) rs.close();
110	0	if (findListStatement != null) findListStatement.close();
111		}
112
113	0	if (noResult) return null;
114	0	return result;
115		}
116
117		/**
118		*
119		* @param con
120		* @return A <code>List</code> of <code>EnzymeSubclass</code>es (without
121		* subsubclass information).
122		* @throws SQLException
123		* @throws DomainException
124		*/
125		public List<EnzymeSubclass> findAll(Connection con) throws SQLException, DomainException{
126	0	List<EnzymeSubclass> result = new ArrayList<EnzymeSubclass>();
127	0	Statement stm = null;
128	0	ResultSet rs = null;
129		try {
130	0	stm = con.createStatement();
131	0	rs = stm.executeQuery(SELECT_ALL);
132	0	while (rs.next()){
133	0	result.add(doLoad(rs, null));
134		}
135		} finally {
136	0	if (rs != null) rs.close();
137	0	if (stm != null) stm.close();
138		}
139	0	return result;
140		}
141
142		/**
143		* Checks if the given subclass numbers are valid.
144		*
145		* @param ec1 The class number.
146		* @param ec2 The subclass number.
147		* @param con The connection.
148		* @return <code>true</code> if the class exists.
149		* @throws SQLException
150		*/
151		public boolean subclassExists(String ec1, String ec2, Connection con) throws SQLException {
152	0	PreparedStatement findStatement = null;
153	0	ResultSet rs = null;
154		try {
155	0	findStatement = con.prepareStatement(findSubclassOnlyStatement());
156	0	findStatement.setString(1, ec1);
157	0	findStatement.setString(2, ec2);
158	0	rs = findStatement.executeQuery();
159	0	if (rs.next()) {
160	0	return true;
161		}
162		} finally {
163	0	if (rs != null) rs.close();
164	0	if (findStatement != null) findStatement.close();
165		}
166
167	0	return false;
168		}
169
170
171		// ------------------- PRIVATE METHODS ------------------------
172
173		/**
174		* Creates the <code>EnzymeSubclass</code> object.
175		*
176		* @param rs The result set object.
177		* @return an <code>EnzymeSubclass</code> instance.
178		* @throws SQLException
179		*/
180		private EnzymeSubclass doLoad(ResultSet rs, List<EnzymeSubSubclass> subSubclasses)
181		throws SQLException, DomainException {
182	0	int ec1 = 0;
183	0	int ec2 = 0;
184	0	String className = "";
185	0	String name = "";
186	0	String description = "";
187
188	0	if (rs.getInt(1) > 0) ec1 = rs.getInt(1);
189	0	if (rs.getInt(2) > 0) ec2 = rs.getInt(2);
190	0	if (rs.getString(3) != null) name = rs.getString(3);
191	0	if (rs.getString(4) != null) className = rs.getString(4);
192	0	if (rs.getString(5) != null) description = rs.getString(5);
193
194	0	return new EnzymeSubclass(EnzymeCommissionNumber.valueOf(ec1, ec2), className, name, description, subSubclasses);
195		}
196		}