uk.ac.roslin.ensembl.dao.database.factory

Class DBDAOCollectionCoreFactory

java.lang.Object

uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory

uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFactory

uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

All Implemented Interfaces:

DAOCollectionCoreFactory, DAOCollectionFactory, DAOCoreFactory, DAOFactory, DAOFactoryWithAnalyses, DAOSpeciesFactory

public class DBDAOCollectionCoreFactory
extends DBDAOCollectionFactory
implements DAOCollectionCoreFactory

Field Summary

Fields inherited from class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory

species

Fields inherited from class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

configuration, database, databaseName, databaseType, dBType, dbVersion, ensemblSchema, ibatisSchemaFilePath, mybatisSchemaFilePath, registry, schemaVersion, sqlSessionFactory, thisDBUrl

Constructor Summary

Constructors

Constructor and Description
DBDAOCollectionCoreFactory()
DBDAOCollectionCoreFactory(CollectionDatabase database, CollectionSpecies species)

Method Summary

Methods

Modifier and Type	Method and Description
DAAnalysis	getAnalysis(Integer id)
DBAnalysisDAO	getAnalysisDAO()
DBAssemblyDAO	getAssemblyDAO()
DBChromosomeDAO	getChromosomeDAO()
DBDAOComparaFactory	getComparaFactory(EnsemblComparaDivision comparaDivision)
DBCoordinateSystemDAO	getCoordinateSystemDAO()
CollectionCoreDatabase	getDatabase()
DBExonDAO	getExonDAO()
DBGeneDAO	getGeneDAO()
org.apache.ibatis.session.SqlSession	getNewSqlSession()
DBProteinFeatureDAO	getProteinFeatureDAO()
DBDNASequenceDAO	getSequenceDAO()
DBTranscriptDAO	getTranscriptDAO()
DBTranslationDAO	getTranslationDAO()
DAOVariationFactory	getVariationFactory()
DBXRefDAO	getXRefDAO()
boolean	hasVariationFactory()

Methods inherited from class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFactory

getSpecies, makeFactory

Methods inherited from class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory

setSpecies

Methods inherited from class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

getConfiguration, getDatabaseName, getDBType, getDBVersion, getEnsemblSchemaVersion, getMybatisSchemaFilePath, getRegistry, setDatabase, setDatabaseName, setDBType, setDBVersion, setEnsemblSchemaVersion, setMybatisSchemaFilePath

Methods inherited from class java.lang.Object

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

Methods inherited from interface uk.ac.roslin.ensembl.dao.factory.DAOCollectionFactory

getSpecies

Methods inherited from interface uk.ac.roslin.ensembl.dao.factory.DAOSpeciesFactory

setSpecies

Methods inherited from interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

getConfiguration, getDatabaseName, getDBType, getDBVersion, getEnsemblSchemaVersion, getMybatisSchemaFilePath, getRegistry, setDatabaseName, setDBType, setDBVersion, setEnsemblSchemaVersion, setMybatisSchemaFilePath

Constructor Detail

DBDAOCollectionCoreFactory

public DBDAOCollectionCoreFactory()

DBDAOCollectionCoreFactory

public DBDAOCollectionCoreFactory(CollectionDatabase database,
                          CollectionSpecies species)
                           throws DAOException

Throws:

DAOException

Method Detail

getDatabase

public CollectionCoreDatabase getDatabase()

Specified by:

getDatabase in interface DAOCollectionCoreFactory

Specified by:

getDatabase in interface DAOCoreFactory

Specified by:

getDatabase in interface DAOFactory

Overrides:

getDatabase in class DBDAOCollectionFactory

getCoordinateSystemDAO

public DBCoordinateSystemDAO getCoordinateSystemDAO()
                                             throws DAOException

Specified by:

getCoordinateSystemDAO in interface DAOCoreFactory

Throws:

DAOException

getChromosomeDAO

public DBChromosomeDAO getChromosomeDAO()
                                 throws DAOException

Specified by:

getChromosomeDAO in interface DAOCoreFactory

Throws:

DAOException

getGeneDAO

public DBGeneDAO getGeneDAO()
                     throws DAOException

Specified by:

getGeneDAO in interface DAOCoreFactory

Throws:

DAOException

getProteinFeatureDAO

public DBProteinFeatureDAO getProteinFeatureDAO()
                                         throws DAOException

Specified by:

getProteinFeatureDAO in interface DAOCoreFactory

Throws:

DAOException

getAssemblyDAO

public DBAssemblyDAO getAssemblyDAO()
                             throws DAOException

Specified by:

getAssemblyDAO in interface DAOCoreFactory

Throws:

DAOException

getSequenceDAO

public DBDNASequenceDAO getSequenceDAO()
                                throws DAOException

Specified by:

getSequenceDAO in interface DAOCoreFactory

Throws:

DAOException

getTranslationDAO

public DBTranslationDAO getTranslationDAO()
                                   throws DAOException

Specified by:

getTranslationDAO in interface DAOCoreFactory

Throws:

DAOException

getTranscriptDAO

public DBTranscriptDAO getTranscriptDAO()
                                 throws DAOException

Specified by:

getTranscriptDAO in interface DAOCoreFactory

Throws:

DAOException

getExonDAO

public DBExonDAO getExonDAO()
                     throws DAOException

Specified by:

getExonDAO in interface DAOCoreFactory

Throws:

DAOException

getComparaFactory

public DBDAOComparaFactory getComparaFactory(EnsemblComparaDivision comparaDivision)

Specified by:

getComparaFactory in interface DAOCoreFactory

getVariationFactory

public DAOVariationFactory getVariationFactory()

Specified by:

getVariationFactory in interface DAOCoreFactory

hasVariationFactory

public boolean hasVariationFactory()

Specified by:

hasVariationFactory in interface DAOCoreFactory

getAnalysisDAO

public DBAnalysisDAO getAnalysisDAO()
                             throws DAOException

Specified by:

getAnalysisDAO in interface DAOFactoryWithAnalyses

Throws:

DAOException

getAnalysis

public DAAnalysis getAnalysis(Integer id)

Specified by:

getAnalysis in interface DAOFactoryWithAnalyses

getXRefDAO

public DBXRefDAO getXRefDAO()
                     throws DAOException

Specified by:

getXRefDAO in interface DAOCoreFactory

Throws:

DAOException

getNewSqlSession

public org.apache.ibatis.session.SqlSession getNewSqlSession()
                                                      throws DAOException

Specified by:

getNewSqlSession in interface DAOFactory

Overrides:

getNewSqlSession in class DBDAOFactory

Throws:

DAOException