uk.ac.ebi.intenz.mapper
Class EnzymeReactionMapper

java.lang.Object
  uk.ac.ebi.intenz.mapper.EnzymeReactionMapper

public class EnzymeReactionMapper
extends Object

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

Version:

$Revision: 1.6 $ $Date: 2009/05/26 14:59:09 $

Author:

Michael Darsow, Rafael AlcÔøΩntara

Field Summary

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

rheaReader

Constructor Summary

EnzymeReactionMapper()

Method Summary

void	close()
EnzymaticReactions	exportSibReactions(Long enzymeId, Connection con) Exports all reactions which are displayed in the ENZYME view.
protected void	finalize()
EnzymaticReactions	find(Long enzymeId, Connection con) Tries to find reaction information about an enzyme.
void	insert(EnzymaticReactions reactions, Long enzymeId, Connection con) Stores the given list of reactions into the database.
void	insertMapping(Long enzymeId, Long reactionId, EnzymeViewConstant view, boolean iubmb, int orderIn, Connection con) Inserts a mapping reaction-enzyme into the database.
void	update(Long enzymeId, EnzymaticReactions reactions, Connection con) Replace the reactions in the database related to one enzyme with those passed as parameter.

Methods inherited from class java.lang.Object

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

Field Detail

rheaReader

protected uk.ac.ebi.rhea.mapper.db.RheaDbReader rheaReader

Constructor Detail

EnzymeReactionMapper

public EnzymeReactionMapper()

Method Detail

find

public EnzymaticReactions find(Long enzymeId,
                               Connection con)
                        throws SQLException,
                               uk.ac.ebi.rhea.mapper.MapperException

Tries to find reaction information about an enzyme.

Parameters:

enzymeId - Enzyme ID of entry.

con - The logical connection.

Returns:

a EnzymaticReactions object containing Reactioninstances 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 Rhea reactions.

exportSibReactions

public EnzymaticReactions exportSibReactions(Long enzymeId,
                                             Connection con)
                                      throws SQLException,
                                             uk.ac.ebi.rhea.mapper.MapperException

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

Parameters:

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

con - The database connection.

Returns:

an EnzymaticReactions containing reactions or null if no reaction could be found.

Throws:

SQLException - if a generic database error occured.

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

NullPointerException - if either of the parameters is null.

insert

public void insert(EnzymaticReactions reactions,
                   Long enzymeId,
                   Connection con)
            throws SQLException

Stores the given list of reactions into the database.

Parameters:

reactions - The vector of reactions.

enzymeId - The enzyme ID.

con - ...

Throws:

SQLException

insertMapping

public void insertMapping(Long enzymeId,
                          Long reactionId,
                          EnzymeViewConstant view,
                          boolean iubmb,
                          int orderIn,
                          Connection con)
                   throws SQLException

Inserts a mapping reaction-enzyme into the database.

Parameters:

enzymeId -

reactionId -

view -

iubmb -

orderIn -

con -

Throws:

SQLException

update

public void update(Long enzymeId,
                   EnzymaticReactions reactions,
                   Connection con)
            throws SQLException

Replace the reactions in the database related to one enzyme with those passed as parameter.

Parameters:

enzymeId - The enzyme ID.

reactions - The vector of reactions.

con -

Throws:

SQLException

close

public void close()
           throws uk.ac.ebi.rhea.mapper.MapperException

Throws:

uk.ac.ebi.rhea.mapper.MapperException

finalize

protected void finalize()
                 throws Throwable

Overrides:

finalize in class Object

Throws:

Throwable