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

Packages that use GeneSetValueObject

Package	Description
ubic.gemma.model.genome.gene
ubic.gemma.persistence.service.genome.gene
ubic.gemma.web.controller.analysis.expression.diff
ubic.gemma.web.controller.genome.gene

Uses of GeneSetValueObject in ubic.gemma.model.genome.gene

Subclasses of GeneSetValueObject in ubic.gemma.model.genome.gene

Modifier and Type	Class	Description
class	DatabaseBackedGeneSetValueObject
class	FreeTextGeneResultsValueObject	*
class	GOGroupValueObject
class	SessionBoundGeneSetValueObject

Methods in ubic.gemma.model.genome.gene that return types with arguments of type GeneSetValueObject

Modifier and Type	Method	Description
Collection<GeneSetValueObject>	GeneValueObject.getGeneSets()

Method parameters in ubic.gemma.model.genome.gene with type arguments of type GeneSetValueObject

Modifier and Type	Method	Description
void	GeneValueObject.setGeneSets(Collection<GeneSetValueObject> geneSets)

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

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

Modifier and Type	Method	Description
GeneSetValueObject	GeneSetService.createDatabaseEntity(GeneSetValueObject gsvo)	create an entity in the database based on the value object parameter
GeneSetValueObject	GeneSetServiceImpl.createDatabaseEntity(GeneSetValueObject geneSetVo)

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

Modifier and Type	Method	Description
Collection<GeneSetValueObject>	GeneSetService.findGeneSetsByGene(Long geneId)	Given a Gemma Gene Id, find all the gene groups it is a member of (filtering is handled when gene sets are loaded)
Collection<GeneSetValueObject>	GeneSetServiceImpl.findGeneSetsByGene(Long geneId)
Collection<GeneSetValueObject>	GeneSetService.findGeneSetsByName(String query, Long taxonId)
Collection<GeneSetValueObject>	GeneSetServiceImpl.findGeneSetsByName(String query, Long taxonId)

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

Modifier and Type	Method	Description
GeneSetValueObject	GeneSetService.createDatabaseEntity(GeneSetValueObject gsvo)	create an entity in the database based on the value object parameter
GeneSetValueObject	GeneSetServiceImpl.createDatabaseEntity(GeneSetValueObject geneSetVo)
Collection<Long>	GeneSetService.getGeneIdsInGroup(GeneSetValueObject geneSetVO)
Collection<Long>	GeneSetServiceImpl.getGeneIdsInGroup(GeneSetValueObject object)
Collection<GeneValueObject>	GeneSetService.getGenesInGroup(GeneSetValueObject object)	Get the gene value objects for the members of the group param
Collection<GeneValueObject>	GeneSetServiceImpl.getGenesInGroup(GeneSetValueObject object)
int	GeneSetService.getSize(GeneSetValueObject geneSetVO)
int	GeneSetServiceImpl.getSize(GeneSetValueObject object)

Uses of GeneSetValueObject in ubic.gemma.web.controller.analysis.expression.diff

Methods in ubic.gemma.web.controller.analysis.expression.diff with parameters of type GeneSetValueObject

Modifier and Type	Method	Description
String	DifferentialExpressionSearchController.scheduleDiffExpSearchTask(Long taxonId, ExpressionExperimentSetValueObject eevo, GeneSetValueObject gsvo)	AJAX - method used for main display metaheatmap.

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

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

Modifier and Type	Method	Description
Collection<GeneSetValueObject>	GeneSetController.addUserAndSessionGroups(Collection<GeneSetValueObject> geneSetVos)	AJAX adds the gene group to the session
Collection<GeneSetValueObject>	GeneSetController.create(Collection<GeneSetValueObject> geneSetVos)	AJAX create an entities in the database based on the value objects passed in
Collection<GeneSetValueObject>	GeneSetController.findGeneSetsByGene(Long geneId)	Given a Gemma Gene Id will find all gene groups that the current user is allowed to use
Collection<GeneSetValueObject>	GeneSetController.findGeneSetsByName(String query, Long taxonId)
Collection<GeneSetValueObject>	GeneSetController.getUserAndSessionGeneGroups(boolean privateOnly, Long taxonId)	AJAX Returns the current users gene sets as well as their session gene sets
Collection<GeneSetValueObject>	GeneSetController.removeUserAndSessionGroups(Collection<GeneSetValueObject> vos)	AJAX Given valid gene groups will remove them from the session or the database appropriately.
Collection<GeneSetValueObject>	GeneSetController.updateUserAndSessionGroups(Collection<GeneSetValueObject> vos)	AJAX Updates the session group and user database groups.

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

Modifier and Type	Method	Description
String	GeneSetController.canCurrentUserEditGroup(GeneSetValueObject gsvo)	AJAX returns a JSON string encoding whether the current user owns the group and whether the group is db-backed

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

Modifier and Type	Method	Description
Collection<GeneSetValueObject>	GeneSetController.addUserAndSessionGroups(Collection<GeneSetValueObject> geneSetVos)	AJAX adds the gene group to the session
Collection<GeneSetValueObject>	GeneSetController.create(Collection<GeneSetValueObject> geneSetVos)	AJAX create an entities in the database based on the value objects passed in
Collection<GeneSetValueObject>	GeneSetController.removeUserAndSessionGroups(Collection<GeneSetValueObject> vos)	AJAX Given valid gene groups will remove them from the session or the database appropriately.
Collection<GeneSetValueObject>	GeneSetController.updateUserAndSessionGroups(Collection<GeneSetValueObject> vos)	AJAX Updates the session group and user database groups.