Package org.sigpath.database

Core Database Managers.

See:
Description

Interface Summary

DataSource
JdoExtension
SigPathManager	Defines some basic operations for "mananger" classes in SigPath
SPIDManager
TransactionManager	TransactionManager Interface that defines base database transaction processes.

Class Summary

AllExportableInstanceSource
DBInformation	The DBInformation class returns information about the current FastObjects Database.
EntityCollectionDataSource	Data source backed by a collection of entities.
EntityManager	EntityManager Provides database functionality regarding SigPathEntity objects.
FOJdoExtension
JDOResultCollection	JDOResultCollection is a collection that is being retrieved by JDO Queries.
JDOResultIterator	JDOResultIterator is and iterator over a collection that is being retrieved by JDO Queries.
JDORICreateDataStore	Creates a datastore that can be used with the JDO Reference implementation (jdori).
KODOJdoExtension
NamingManager
PureJdoExtension
QueryManager	QueryManager Provides JDO query convenience utilities.
ReactionTyper	User: Fabien Campagne Date: May 2, 2004 Time: 11:40:32 AM
SimpleSPIDManager	SPIDManager provides methods to work with a SPID (SigPath Id) or a BID (Background Data Identifier) in an object oriented database.
SPDBManager	SPDBManager Central point for database access in the SigPath system.
SpidCollectionDataSource
SPIDManagerImpl	SPIDManagerImpl handles init, allocation, and update of current and marked spid range values.
SpidManagerWithSpidRanges	This is the old SPIDManager.
StandaloneDataSource	A data source that computes the set instances that compose a standalone XML submission.
UnitManager	Manages all SigPath Units.
Units	Represents units known to SigPath.
UserManager	UserManager Contains all business logic relating to Users.

Exception Summary

SigPathDatabaseException

SigPathDatabaseException contains an Exception.

Package org.sigpath.database Description

Core Database Managers.

All access to the database goes through this package. The SPDBManager is responsible for hiding database specific issues from the client code. This makes client code easier to read, and much more maintainable.

The other managers, including ProteinManager and SmallMoleculeManager provide public methods for adding / querying molecules.