Uses of Class
ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject

Packages that use DatabaseBackedGeneSetValueObject

Package	Description
ubic.gemma.persistence.service.genome.gene

Uses of DatabaseBackedGeneSetValueObject in ubic.gemma.persistence.service.genome.gene

Methods in ubic.gemma.persistence.service.genome.gene that return DatabaseBackedGeneSetValueObject

Modifier and Type	Method	Description
DatabaseBackedGeneSetValueObject	GeneSetValueObjectHelper.convertToLightValueObject(GeneSet gs)	Constructor to build value object from GeneSet.
DatabaseBackedGeneSetValueObject	GeneSetValueObjectHelperImpl.convertToLightValueObject(GeneSet gs)
DatabaseBackedGeneSetValueObject	GeneSetValueObjectHelper.convertToValueObject(GeneSet gs)	Constructor to build value object from GeneSet.
DatabaseBackedGeneSetValueObject	GeneSetValueObjectHelperImpl.convertToValueObject(GeneSet gs)
DatabaseBackedGeneSetValueObject	GeneSetDaoImpl.loadValueObject(GeneSet geneSet)
DatabaseBackedGeneSetValueObject	GeneSetServiceImpl.loadValueObject(GeneSet geneSet)
DatabaseBackedGeneSetValueObject	GeneSetDaoImpl.loadValueObjectById(Long id)
DatabaseBackedGeneSetValueObject	GeneSetDao.loadValueObjectByIdLite(Long id)
DatabaseBackedGeneSetValueObject	GeneSetDaoImpl.loadValueObjectByIdLite(Long id)
DatabaseBackedGeneSetValueObject	GeneSetService.loadValueObjectByIdLite(Long id)
DatabaseBackedGeneSetValueObject	GeneSetServiceImpl.loadValueObjectByIdLite(Long id)
DatabaseBackedGeneSetValueObject	GeneSetService.updateDatabaseEntityNameDesc(DatabaseBackedGeneSetValueObject geneSetVO)	AJAX Updates the database entity (permission permitting) with the name and description fields of the param value object
DatabaseBackedGeneSetValueObject	GeneSetServiceImpl.updateDatabaseEntityNameDesc(DatabaseBackedGeneSetValueObject geneSetVO)

Methods in ubic.gemma.persistence.service.genome.gene that return types with arguments of type DatabaseBackedGeneSetValueObject

Modifier and Type	Method	Description
List<DatabaseBackedGeneSetValueObject>	GeneSetValueObjectHelper.convertToLightValueObjects(Collection<GeneSet> genesets, boolean includeOnesWithoutGenes)	results will be sorted by size
List<DatabaseBackedGeneSetValueObject>	GeneSetValueObjectHelperImpl.convertToLightValueObjects(Collection<GeneSet> geneSets, boolean includeOnesWithoutGenes)
List<DatabaseBackedGeneSetValueObject>	GeneSetValueObjectHelper.convertToValueObjects(Collection<GeneSet> sets)
List<DatabaseBackedGeneSetValueObject>	GeneSetValueObjectHelper.convertToValueObjects(Collection<GeneSet> geneSets, boolean includeOnesWithoutGenes)
List<DatabaseBackedGeneSetValueObject>	GeneSetValueObjectHelperImpl.convertToValueObjects(Collection<GeneSet> sets)
List<DatabaseBackedGeneSetValueObject>	GeneSetValueObjectHelperImpl.convertToValueObjects(Collection<GeneSet> genesets, boolean includeOnesWithoutGenes)
Collection<DatabaseBackedGeneSetValueObject>	GeneSetService.getUsersGeneGroupsValueObjects(boolean privateOnly, Long taxonId)	Returns just the current users gene sets
Collection<DatabaseBackedGeneSetValueObject>	GeneSetServiceImpl.getUsersGeneGroupsValueObjects(boolean privateOnly, Long taxonId)
List<DatabaseBackedGeneSetValueObject>	GeneSetDaoImpl.loadAllValueObjects()
List<DatabaseBackedGeneSetValueObject>	GeneSetDaoImpl.loadValueObjects(Collection<GeneSet> entities)
List<DatabaseBackedGeneSetValueObject>	GeneSetDaoImpl.loadValueObjectsByIds(Collection<Long> ids)
List<DatabaseBackedGeneSetValueObject>	GeneSetServiceImpl.loadValueObjectsByIds(Collection<Long> ids)
List<DatabaseBackedGeneSetValueObject>	GeneSetDao.loadValueObjectsByIdsLite(Collection<Long> geneSetIds)
List<DatabaseBackedGeneSetValueObject>	GeneSetDaoImpl.loadValueObjectsByIdsLite(Collection<Long> ids)
List<DatabaseBackedGeneSetValueObject>	GeneSetService.loadValueObjectsByIdsLite(Collection<Long> geneSetIds)
List<DatabaseBackedGeneSetValueObject>	GeneSetServiceImpl.loadValueObjectsByIdsLite(Collection<Long> genesetIds)
Collection<DatabaseBackedGeneSetValueObject>	GeneSetService.updateDatabaseEntity(Collection<DatabaseBackedGeneSetValueObject> geneSetVos)	AJAX Updates the database entity (permission permitting) with the fields of the param value object
Collection<DatabaseBackedGeneSetValueObject>	GeneSetServiceImpl.updateDatabaseEntity(Collection<DatabaseBackedGeneSetValueObject> geneSetVos)

Methods in ubic.gemma.persistence.service.genome.gene with parameters of type DatabaseBackedGeneSetValueObject

Modifier and Type	Method	Description
void	GeneSetService.deleteDatabaseEntity(DatabaseBackedGeneSetValueObject geneSetVO)	Security is handled within method, when the set is loaded
void	GeneSetServiceImpl.deleteDatabaseEntity(DatabaseBackedGeneSetValueObject geneSetVO)
DatabaseBackedGeneSetValueObject	GeneSetService.updateDatabaseEntityNameDesc(DatabaseBackedGeneSetValueObject geneSetVO)	AJAX Updates the database entity (permission permitting) with the name and description fields of the param value object
DatabaseBackedGeneSetValueObject	GeneSetServiceImpl.updateDatabaseEntityNameDesc(DatabaseBackedGeneSetValueObject geneSetVO)

Method parameters in ubic.gemma.persistence.service.genome.gene with type arguments of type DatabaseBackedGeneSetValueObject

Modifier and Type	Method	Description
void	GeneSetService.deleteDatabaseEntities(Collection<DatabaseBackedGeneSetValueObject> vos)	Security is handled within method
void	GeneSetServiceImpl.deleteDatabaseEntities(Collection<DatabaseBackedGeneSetValueObject> vos)
Collection<DatabaseBackedGeneSetValueObject>	GeneSetService.updateDatabaseEntity(Collection<DatabaseBackedGeneSetValueObject> geneSetVos)	AJAX Updates the database entity (permission permitting) with the fields of the param value object
Collection<DatabaseBackedGeneSetValueObject>	GeneSetServiceImpl.updateDatabaseEntity(Collection<DatabaseBackedGeneSetValueObject> geneSetVos)