SigPath

Package org.sigpath.database

Core Database Managers.

See:
          Description

Interface Summary
DataSource  
JdoExtension  
SigPathManager Defines some basic operations for "mananger" classes in SigPath
SPIDManager  
SpidManagerDelegate Use Class.forName and the SpidManagerDelegate interface to avoid creating static references to thsi class.
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  
SpidManagerDelegateWebService This delegate requires the SpidGenerator web service stubs to compile.
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.


SigPath

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