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

Packages that use GeneSet

Package	Description
ubic.gemma.core.search
ubic.gemma.core.search.source
ubic.gemma.model.genome.gene
ubic.gemma.persistence.service.genome.gene

Uses of GeneSet in ubic.gemma.core.search

Methods in ubic.gemma.core.search that return GeneSet

Modifier and Type	Method	Description
GeneSet	GeneSetSearch.findByGoId(String goId, Taxon taxon)	Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.
GeneSet	GeneSetSearchImpl.findByGoId(String goId, Taxon taxon)

Methods in ubic.gemma.core.search that return types with arguments of type GeneSet

Modifier and Type	Method	Description
Collection<GeneSet>	GeneSetSearch.findByGene(Gene gene)
Collection<GeneSet>	GeneSetSearchImpl.findByGene(Gene gene)
Collection<GeneSet>	GeneSetSearch.findByGoTermName(String goTermName, Taxon taxon)	finds gene sets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent
Collection<GeneSet>	GeneSetSearch.findByGoTermName(String goTermName, Taxon taxon, Integer maxGoTermsProcessed, Integer maxGeneSetSize)	finds genesets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent
Collection<GeneSet>	GeneSetSearchImpl.findByGoTermName(String goTermName, Taxon taxon)
Collection<GeneSet>	GeneSetSearchImpl.findByGoTermName(String goTermName, Taxon taxon, Integer maxGoTermsProcessed, Integer maxGeneSetSize)
Collection<GeneSet>	GeneSetSearch.findByName(String name)
Collection<GeneSet>	GeneSetSearch.findByName(String name, Taxon taxon)
Collection<GeneSet>	GeneSetSearchImpl.findByName(String name)
Collection<GeneSet>	GeneSetSearchImpl.findByName(String name, Taxon taxon)
Collection<GeneSet>	GeneSetSearch.findGeneSetsByName(String query, Long taxonId)	Similar to method of same name in GeneSetController.java but here: - no taxon needed - GO groups always searched - GeneSet objects returned instead of GeneSetValueObjects
Collection<GeneSet>	GeneSetSearchImpl.findGeneSetsByName(String query, Long taxonId)
default Collection<SearchResult<GeneSet>>	SearchSource.searchGeneSet(SearchSettings settings, SearchContext context)

Uses of GeneSet in ubic.gemma.core.search.source

Methods in ubic.gemma.core.search.source that return types with arguments of type GeneSet

Modifier and Type	Method	Description
Collection<SearchResult<GeneSet>>	CompositeSearchSource.searchGeneSet(SearchSettings settings, SearchContext context)
Collection<SearchResult<GeneSet>>	DatabaseSearchSource.searchGeneSet(SearchSettings settings, SearchContext context)
Collection<SearchResult<GeneSet>>	HibernateSearchSource.searchGeneSet(SearchSettings settings, SearchContext context)

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

Methods in ubic.gemma.model.genome.gene that return GeneSet

Modifier and Type	Method	Description
static GeneSet	GeneSet.Factory.newInstance()

Methods in ubic.gemma.model.genome.gene with parameters of type GeneSet

Modifier and Type	Method	Description
static GeneSetMember	GeneSet.containsGene(Gene g, GeneSet gs)

Constructors in ubic.gemma.model.genome.gene with parameters of type GeneSet

Modifier	Constructor	Description
	DatabaseBackedGeneSetValueObject(GeneSet geneSet, Taxon taxon, Long size)	default constructor to satisfy java bean contract
	GeneSetValueObject(GeneSet geneSet, Taxon taxon, Long size)

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

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

Modifier and Type	Method	Description
GeneSet	GeneSetService.create(GeneSet geneset)
GeneSet	GeneSetDaoImpl.find(GeneSet entity)
GeneSet	GeneSetService.load(Long id)
GeneSet	GeneSetService.loadOrFail(Long id)
GeneSet	GeneSetService.save(GeneSet entity)

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

Modifier and Type	Method	Description
Collection<GeneSet>	GeneSetService.create(Collection<GeneSet> sets)
Collection<GeneSet>	GeneSetDao.findByGene(Gene gene)
Collection<GeneSet>	GeneSetDaoImpl.findByGene(Gene gene)
Collection<GeneSet>	GeneSetService.findByGene(Gene gene)	Return all sets that contain the given gene.
Collection<GeneSet>	GeneSetServiceImpl.findByGene(Gene gene)
Collection<GeneSet>	GeneSetDao.findByName(String name)
Collection<GeneSet>	GeneSetDao.findByName(String name, Taxon taxon)
Collection<GeneSet>	GeneSetDaoImpl.findByName(String name)
Collection<GeneSet>	GeneSetDaoImpl.findByName(String name, Taxon taxon)
Collection<GeneSet>	GeneSetService.findByName(String name)
Collection<GeneSet>	GeneSetService.findByName(String name, Taxon taxon)
Collection<GeneSet>	GeneSetServiceImpl.findByName(String name)
Collection<GeneSet>	GeneSetServiceImpl.findByName(String name, Taxon taxon)
Collection<GeneSet>	GeneSetService.getUsersGeneGroups(boolean privateOnly, Long taxonId, boolean sharedPublicOnly)
Collection<GeneSet>	GeneSetServiceImpl.getUsersGeneGroups(boolean privateOnly, Long taxonId, boolean sharedPublicOnly)
Collection<GeneSet>	GeneSetService.load(Collection<Long> ids)
Collection<GeneSet>	GeneSetDao.loadAll(Taxon tax)
Collection<GeneSet>	GeneSetDaoImpl.loadAll(Taxon tax)
Collection<GeneSet>	GeneSetService.loadAll()
Collection<GeneSet>	GeneSetService.loadAll(Taxon tax)
Collection<GeneSet>	GeneSetServiceImpl.loadAll(Taxon tax)
Collection<GeneSet>	GeneSetService.loadMyGeneSets()	Returns the GeneSets for the currently logged in User - i.e, ones for which the current user has specific read permissions on (as opposed to data sets which are public).
Collection<GeneSet>	GeneSetService.loadMyGeneSets(Taxon tax)
Collection<GeneSet>	GeneSetServiceImpl.loadMyGeneSets()
Collection<GeneSet>	GeneSetServiceImpl.loadMyGeneSets(Taxon tax)
Collection<GeneSet>	GeneSetService.loadMySharedGeneSets(Taxon tax)
Collection<GeneSet>	GeneSetServiceImpl.loadMySharedGeneSets(Taxon tax)
Collection<GeneSet>	GeneSetService.loadWithMembers(Collection<Long> ids)	Load the gene sets with their members initialized.
Collection<GeneSet>	GeneSetServiceImpl.loadWithMembers(Collection<Long> ids)
Collection<GeneSet>	GeneSetService.save(Collection<GeneSet> entities)

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

Modifier and Type	Method	Description
GOGroupValueObject	GeneSetValueObjectHelper.convertToGOValueObject(GeneSet gs, String goId, String searchTerm)	Method to create a GO group object from an ad hoc entity
GOGroupValueObject	GeneSetValueObjectHelperImpl.convertToGOValueObject(GeneSet gs, String goId, String searchTerm)
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)
GeneSet	GeneSetService.create(GeneSet geneset)
GeneSet	GeneSetDaoImpl.find(GeneSet entity)
List<Taxon>	GeneSetDao.getTaxa(GeneSet geneSet)	Return all the taxa of the gene set members.
List<Taxon>	GeneSetDaoImpl.getTaxa(GeneSet geneSet)
Set<Taxon>	GeneSetService.getTaxa(GeneSet geneSet)	Obtain all the taxa for the members of a given gene set.
Set<Taxon>	GeneSetServiceImpl.getTaxa(GeneSet geneSet)
Taxon	GeneSetDao.getTaxon(GeneSet geneSet)	Returns the taxon of an arbitrary member of the set.
Taxon	GeneSetDaoImpl.getTaxon(GeneSet geneSet)
Taxon	GeneSetService.getTaxon(GeneSet geneSet)	get the taxon for the gene set parameter, assumes that the taxon of the first gene will be representational of all the genes
Taxon	GeneSetServiceImpl.getTaxon(GeneSet geneSet)
DatabaseBackedGeneSetValueObject	GeneSetDaoImpl.loadValueObject(GeneSet geneSet)
DatabaseBackedGeneSetValueObject	GeneSetService.loadValueObject(GeneSet geneSet)
DatabaseBackedGeneSetValueObject	GeneSetServiceImpl.loadValueObject(GeneSet geneSet)
final void	GeneSetDaoImpl.remove(GeneSet entity)
void	GeneSetService.remove(GeneSet entity)
GeneSet	GeneSetService.save(GeneSet entity)
void	GeneSetDao.thaw(GeneSet geneSet)
void	GeneSetDaoImpl.thaw(GeneSet geneSet)
final void	GeneSetDaoImpl.update(GeneSet entity)
void	GeneSetService.update(GeneSet entity)

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

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<GeneSet>	GeneSetService.create(Collection<GeneSet> sets)
List<DatabaseBackedGeneSetValueObject>	GeneSetDaoImpl.loadValueObjects(Collection<GeneSet> entities)
List<DatabaseBackedGeneSetValueObject>	GeneSetService.loadValueObjects(Collection<GeneSet> entities)
final void	GeneSetDaoImpl.remove(Collection<GeneSet> entities)
void	GeneSetService.remove(Collection<GeneSet> entities)
Collection<GeneSet>	GeneSetService.save(Collection<GeneSet> entities)
final void	GeneSetDaoImpl.update(Collection<GeneSet> entities)
void	GeneSetService.update(Collection<GeneSet> entities)