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

Field Summary

protected uk.ac.ebi.rhea.mapper.db.RheaCompoundDbReader

rheaCompoundReader

Constructor Summary

EnzymeCofactorMapper()

Method Summary

void	close() Closes the underlying RheaCompoundDbReader.
void	deleteAll(Long enzymeId, Connection con) Deletes all cofactors related to one enzyme instance.
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.
void	insert(Collection<Object> cofactors, Long enzymeId, Status status, Connection con) Stores the given list of cofactors into the database.
void	reload(Collection<Object> cofactors, Long enzymeId, 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

Field Detail

rheaCompoundReader

protected uk.ac.ebi.rhea.mapper.db.RheaCompoundDbReader rheaCompoundReader

Constructor Detail

EnzymeCofactorMapper

public EnzymeCofactorMapper()

Method Detail

close

public void close()

Closes the underlying RheaCompoundDbReader.

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.

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,
                   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

reload

public void reload(Collection<Object> cofactors,
                   Long enzymeId,
                   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