uk.ac.ebi.intenz.mapper

Class EnzymeCofactorMapper

java.lang.Object

uk.ac.ebi.intenz.mapper.EnzymeCofactorMapper

public class EnzymeCofactorMapper
extends Object

Maps reaction information to the corresponding database tables.
IMPORTANT: after using instances of this class, call the close() method, otherwise the underlying Rhea mapper objects will keep their statements open.

Version:

$Revision: 1.10 $ $Date: 2009/05/26 14:59:09 $

Author:

Michael Darsow

Constructor Summary

Constructors

Constructor and Description
EnzymeCofactorMapper()

Method Summary

Methods

Modifier and Type	Method and Description
void	close()
void	deleteAll(Long enzymeId, Connection con) Deletes all cofactors related to one enzyme instance.
void	deleteCompound(Long compoundId, Connection con) Deletes a cofactor from the COMPOUND_DATA table.
Set<Object>	exportSibCofactors(Long enzymeId, Connection con) Exports all cofactors which are displayed in the ENZYME view.
protected void	finalize()
Set<Object>	find(Long enzymeId, Connection con) Tries to find cofactor information about an enzyme.
Map<uk.ac.ebi.rhea.domain.Compound,Map<Long,String>>	findAll(Connection con) Retrieves a list of compounds acting as cofactors in the database, along with the identifiers for the enzymes they appear in.
uk.ac.ebi.rhea.domain.Compound	findByChebiId(String chebiId, Connection con) Retrieves one cofactor from the IntEnz database by its ChEBI ID.
uk.ac.ebi.rhea.domain.Compound	getCompound(Connection connection, Long compoundId) Retrieves a compound (cofactor) from the database.
void	insert(Collection<Object> cofactors, Long enzymeId, uk.ac.ebi.intenz.domain.constants.Status status, Connection con) Stores the given list of cofactors into the database.
Long	insertCompound(uk.ac.ebi.rhea.domain.Compound compound, Connection con) Inserts one compound (cofactor) into the COMPOUND_DATA table.
void	reload(Collection<Object> cofactors, Long enzymeId, uk.ac.ebi.intenz.domain.constants.Status status, Connection con) Reloads the given list of cofactors into the database.
void	update(uk.ac.ebi.rhea.domain.Compound oldCf, uk.ac.ebi.rhea.domain.Compound newCf, Connection con) Updates the ChEBI mapping of a cofactor, and the name if needed too.

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

EnzymeCofactorMapper

public EnzymeCofactorMapper()

Method Detail

close

public void close()

finalize

protected void finalize()
                 throws Throwable

Overrides:

finalize in class Object

Throws:

Throwable

find

public Set<Object> find(Long enzymeId,
               Connection con)
                 throws SQLException,
                        uk.ac.ebi.rhea.mapper.MapperException

Tries to find cofactor information about an enzyme.

Parameters:

enzymeId - Enzyme ID of entry.

con - The logical connection.

Returns:

a Set containing Cofactor instances, or OperatorSet instances filled with Cofactor objects, or null if nothing has been found.

Throws:

SQLException - in case of a generic database problem.

uk.ac.ebi.rhea.mapper.MapperException - in case of problem retrieving the cofactors.

findByChebiId

public uk.ac.ebi.rhea.domain.Compound findByChebiId(String chebiId,
                                           Connection con)
                                             throws SQLException

Retrieves one cofactor from the IntEnz database by its ChEBI ID.

Parameters:

chebiId - the ChEBI ID of the cofactor.

con - a connection to IntEnz database.

Returns:

a Compound, or null if it does not exist in IntEnz.

Throws:

SQLException - in case of problem retrieving the cofactor.

Since:

4.6.0

exportSibCofactors

public Set<Object> exportSibCofactors(Long enzymeId,
                             Connection con)
                               throws SQLException,
                                      uk.ac.ebi.rhea.mapper.MapperException

Exports all cofactors which are displayed in the ENZYME view. Affected table rows will be locked.

Parameters:

enzymeId - The enzyme ID used to retreive the related cofactors.

con - The database connection.

Returns:

an ArrayList of cofactors or null if no cofactor could be found.

Throws:

SQLException - in case of a generic database problem.

uk.ac.ebi.rhea.mapper.MapperException - in case of problem retrieving the cofactors.

NullPointerException - if either of the parameters is null.

findAll

public Map<uk.ac.ebi.rhea.domain.Compound,Map<Long,String>> findAll(Connection con)
                                                             throws SQLException,
                                                                    uk.ac.ebi.rhea.mapper.MapperException

Retrieves a list of compounds acting as cofactors in the database, along with the identifiers for the enzymes they appear in.

Parameters:

con - a database connection

Returns:

a map of compounds (cofactors) to pairs enzyme ID/EC number.

Throws:

SQLException - in case of a generic database problem.

uk.ac.ebi.rhea.mapper.MapperException - in case of problem retrieving compounds.

uk.ac.ebi.rhea.mapper.MapperException

insert

public void insert(Collection<Object> cofactors,
          Long enzymeId,
          uk.ac.ebi.intenz.domain.constants.Status status,
          Connection con)
            throws SQLException

Stores the given list of cofactors into the database.

Parameters:

cofactors - The vector of cofactors.

enzymeId - The enzyme ID.

status -

con - ...

Throws:

SQLException

insertCompound

public Long insertCompound(uk.ac.ebi.rhea.domain.Compound compound,
                  Connection con)
                    throws SQLException

Inserts one compound (cofactor) into the COMPOUND_DATA table.

Parameters:

compound - a compound.

con - a connection to the IntEnz database.

Returns:

the internal ID of the compound in the table.

Throws:

SQLException - in case of problem inserting the row.

Since:

4.6.0

deleteCompound

public void deleteCompound(Long compoundId,
                  Connection con)
                    throws SQLException

Deletes a cofactor from the COMPOUND_DATA table.

Parameters:

compoundId - the internal ID of the compound.

con - a connection to the IntEnz database.

Throws:

SQLException - in case of problem with the database.

Since:

4.6.0

reload

public void reload(Collection<Object> cofactors,
          Long enzymeId,
          uk.ac.ebi.intenz.domain.constants.Status status,
          Connection con)
            throws SQLException

Reloads the given list of cofactors into the database.

Parameters:

cofactors - The vector of cofactors.

enzymeId - The enzyme ID.

status -

con - ...

Throws:

SQLException

update

public void update(uk.ac.ebi.rhea.domain.Compound oldCf,
          uk.ac.ebi.rhea.domain.Compound newCf,
          Connection con)
            throws SQLException

Updates the ChEBI mapping of a cofactor, and the name if needed too.

Parameters:

oldCf - the old cofactor

newCf - the new cofactor

con -

Throws:

SQLException

deleteAll

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

Deletes all cofactors related to one enzyme instance.

Parameters:

enzymeId - Enzyme ID of the enzyme instance.

con - ...

Throws:

SQLException

getCompound

public uk.ac.ebi.rhea.domain.Compound getCompound(Connection connection,
                                         Long compoundId)
                                           throws SQLException

Retrieves a compound (cofactor) from the database.

Parameters:

connection -

compoundId - the internal compound ID.

Returns:

a cofactor.

Throws:

SQLException