Uses of Class
ubic.gemma.model.genome.gene.GeneSet
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Uses of GeneSet in ubic.gemma.core.genome.gene
Methods in ubic.gemma.core.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 entityGOGroupValueObject
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)
Method parameters in ubic.gemma.core.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 sizeList<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)
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Uses of GeneSet in ubic.gemma.core.genome.gene.service
Methods in ubic.gemma.core.genome.gene.service that return GeneSet Modifier and Type Method Description GeneSet
GeneSetService. create(GeneSet geneset)
GeneSet
GeneSetService. load(Long id)
GeneSet
GeneSetService. loadOrFail(Long id)
GeneSet
GeneSetService. save(GeneSet entity)
Methods in ubic.gemma.core.genome.gene.service that return types with arguments of type GeneSet Modifier and Type Method Description Collection<GeneSet>
GeneSetService. create(Collection<GeneSet> sets)
Collection<GeneSet>
GeneSetService. findByGene(Gene gene)
Return all sets that contain the given gene.Collection<GeneSet>
GeneSetServiceImpl. findByGene(Gene gene)
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>
GeneSetService. loadAll()
Collection<GeneSet>
GeneSetService. loadAll(Taxon tax)
Collection<GeneSet>
GeneSetServiceImpl. loadAll(Taxon tax)
Collection<GeneSet>
GeneSetService. loadMyGeneSets()
Returns theGeneSet
s for the currently logged inUser
- 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. save(Collection<GeneSet> entities)
Methods in ubic.gemma.core.genome.gene.service with parameters of type GeneSet Modifier and Type Method Description GeneSet
GeneSetService. create(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
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 genesTaxon
GeneSetServiceImpl. getTaxon(GeneSet geneSet)
DatabaseBackedGeneSetValueObject
GeneSetService. loadValueObject(GeneSet geneSet)
DatabaseBackedGeneSetValueObject
GeneSetServiceImpl. loadValueObject(GeneSet geneSet)
void
GeneSetService. remove(GeneSet entity)
GeneSet
GeneSetService. save(GeneSet entity)
void
GeneSetService. update(GeneSet entity)
Method parameters in ubic.gemma.core.genome.gene.service with type arguments of type GeneSet Modifier and Type Method Description Collection<GeneSet>
GeneSetService. create(Collection<GeneSet> sets)
List<DatabaseBackedGeneSetValueObject>
GeneSetService. loadValueObjects(Collection<GeneSet> entities)
void
GeneSetService. remove(Collection<GeneSet> entities)
Collection<GeneSet>
GeneSetService. save(Collection<GeneSet> entities)
void
GeneSetService. update(Collection<GeneSet> entities)
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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 persistentCollection<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 persistentCollection<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 GeneSetValueObjectsCollection<GeneSet>
GeneSetSearchImpl. findGeneSetsByName(String query, Long taxonId)
default Collection<SearchResult<GeneSet>>
SearchSource. searchGeneSet(SearchSettings settings)
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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)
Collection<SearchResult<GeneSet>>
DatabaseSearchSource. searchGeneSet(SearchSettings settings)
Collection<SearchResult<GeneSet>>
HibernateSearchSource. searchGeneSet(SearchSettings settings)
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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 Constructor Description DatabaseBackedGeneSetValueObject(GeneSet geneSet, Taxon taxon, Long size)
default constructor to satisfy java bean contractGeneSetValueObject(GeneSet geneSet, Taxon taxon, Long size)
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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
GeneSetDaoImpl. find(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>
GeneSetDao. findByGene(Gene gene)
Collection<GeneSet>
GeneSetDaoImpl. 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>
GeneSetDao. loadAll(Taxon tax)
Collection<GeneSet>
GeneSetDaoImpl. loadAll(Taxon tax)
Methods in ubic.gemma.persistence.service.genome.gene with parameters of type GeneSet Modifier and Type Method Description 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)
Taxon
GeneSetDao. getTaxon(GeneSet geneSet)
Returns the taxon of an arbitrary member of the set.Taxon
GeneSetDaoImpl. getTaxon(GeneSet geneSet)
DatabaseBackedGeneSetValueObject
GeneSetDaoImpl. loadValueObject(GeneSet geneSet)
void
GeneSetDaoImpl. remove(GeneSet entity)
void
GeneSetDao. thaw(GeneSet geneSet)
void
GeneSetDaoImpl. thaw(GeneSet geneSet)
void
GeneSetDaoImpl. 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>
GeneSetDaoImpl. loadValueObjects(Collection<GeneSet> entities)
void
GeneSetDaoImpl. remove(Collection<GeneSet> entities)
void
GeneSetDaoImpl. update(Collection<GeneSet> entities)
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