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

Packages that use DatabaseBackedGeneSetValueObject

Package	Description
ubic.gemma.persistence.service.genome.gene
ubic.gemma.web.controller.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	GeneSetService.loadValueObject(GeneSet geneSet)
DatabaseBackedGeneSetValueObject	GeneSetServiceImpl.loadValueObject(GeneSet geneSet)
DatabaseBackedGeneSetValueObject	GeneSetDaoImpl.loadValueObjectById(Long id)
DatabaseBackedGeneSetValueObject	GeneSetService.loadValueObjectById(Long entityId)
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>	GeneSetService.loadAllValueObjects()
List<DatabaseBackedGeneSetValueObject>	GeneSetDaoImpl.loadValueObjects(Collection<GeneSet> entities)
List<DatabaseBackedGeneSetValueObject>	GeneSetService.loadValueObjects(Collection<GeneSet> entities)
List<DatabaseBackedGeneSetValueObject>	GeneSetDaoImpl.loadValueObjectsByIds(Collection<Long> ids)
List<DatabaseBackedGeneSetValueObject>	GeneSetService.loadValueObjectsByIds(Collection<Long> ids)	Ids of member genes will be filled in
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)

Uses of DatabaseBackedGeneSetValueObject in ubic.gemma.web.controller.genome.gene

Methods in ubic.gemma.web.controller.genome.gene that return DatabaseBackedGeneSetValueObject

Modifier and Type	Method	Description
DatabaseBackedGeneSetValueObject	GeneSetController.load(Long id)	AJAX - load with the IDs filled in
DatabaseBackedGeneSetValueObject	GeneSetController.updateNameDesc(DatabaseBackedGeneSetValueObject geneSetVO)	AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.

Methods in ubic.gemma.web.controller.genome.gene that return types with arguments of type DatabaseBackedGeneSetValueObject

Modifier and Type	Method	Description
Collection<DatabaseBackedGeneSetValueObject>	GeneSetController.getUsersGeneGroups(boolean privateOnly, Long taxonId)	AJAX Returns just the current users gene sets
Collection<DatabaseBackedGeneSetValueObject>	GeneSetController.remove(Collection<DatabaseBackedGeneSetValueObject> vos)	AJAX Given a valid gene group will remove it from db (if the user has permissons to do so).
Collection<DatabaseBackedGeneSetValueObject>	GeneSetController.update(Collection<DatabaseBackedGeneSetValueObject> geneSetVos)	AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.

Methods in ubic.gemma.web.controller.genome.gene with parameters of type DatabaseBackedGeneSetValueObject

Modifier and Type	Method	Description
DatabaseBackedGeneSetValueObject	GeneSetController.updateNameDesc(DatabaseBackedGeneSetValueObject geneSetVO)	AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.

Method parameters in ubic.gemma.web.controller.genome.gene with type arguments of type DatabaseBackedGeneSetValueObject

Modifier and Type	Method	Description
Collection<DatabaseBackedGeneSetValueObject>	GeneSetController.remove(Collection<DatabaseBackedGeneSetValueObject> vos)	AJAX Given a valid gene group will remove it from db (if the user has permissons to do so).
Collection<DatabaseBackedGeneSetValueObject>	GeneSetController.update(Collection<DatabaseBackedGeneSetValueObject> geneSetVos)	AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.