Uses of Class ubic.gemma.model.genome.gene.GeneSetValueObject (Gemma 1.31.12-SNAPSHOT API)

Packages that use GeneSetValueObject
Package	Description
ubic.gemma.core.search
ubic.gemma.model.genome.gene
ubic.gemma.persistence.service.genome.gene
ubic.gemma.web.controller.diff
ubic.gemma.web.controller.genome.gene

Uses of GeneSetValueObject in ubic.gemma.core.search

Methods in ubic.gemma.core.search that return types with arguments of type GeneSetValueObject
Modifier and Type	Method	Description
`Collection<GeneSetValueObject>`	GeneSetSearch.`findByPhenotypeName(String phenotypeQuery, Taxon taxon)`
`Collection<GeneSetValueObject>`	GeneSetSearchImpl.`findByPhenotypeName(String phenotypeQuery, Taxon taxon)`

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`	`PhenotypeGroupValueObject`
`class`	`SessionBoundGeneSetValueObject`

Methods in ubic.gemma.model.genome.gene with parameters of type GeneSetValueObject
Modifier and Type	Method	Description
`static PhenotypeGroupValueObject`	PhenotypeGroupValueObject.`convertFromGeneSetValueObject(GeneSetValueObject gsvo, String searchTerm)`

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.diff

Methods in ubic.gemma.web.controller.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.