Uses of Enum Class
ubic.gemma.model.common.description.AnnotationRelationBasis

Packages that use AnnotationRelationBasis

Package	Description
ubic.gemma.model.common.description
ubic.gemma.persistence.service.common.description

Uses of AnnotationRelationBasis in ubic.gemma.model.common.description

Subclasses with type arguments of type AnnotationRelationBasis in ubic.gemma.model.common.description

Modifier and Type	Class	Description
enum	AnnotationRelationBasis	How an AnnotationRelation came to be known, ranked best first.

Methods in ubic.gemma.model.common.description that return AnnotationRelationBasis

Modifier and Type	Method	Description
AnnotationRelationBasis	AnnotationRelation.getBasis()
static AnnotationRelationBasis	AnnotationRelationBasis.valueOf(String name)	Returns the enum constant of this class with the specified name.
static AnnotationRelationBasis[]	AnnotationRelationBasis.values()	Returns an array containing the constants of this enum class, in the order they are declared.

Methods in ubic.gemma.model.common.description with parameters of type AnnotationRelationBasis

Modifier and Type	Method	Description
void	AnnotationRelation.setBasis(AnnotationRelationBasis basis)

Uses of AnnotationRelationBasis in ubic.gemma.persistence.service.common.description

Methods in ubic.gemma.persistence.service.common.description that return AnnotationRelationBasis

Modifier and Type	Method	Description
AnnotationRelationBasis	AnnotationRelationDao.RelationSummary.getBasis()

Methods in ubic.gemma.persistence.service.common.description that return types with arguments of type AnnotationRelationBasis

Modifier and Type	Method	Description
Set<AnnotationRelationBasis>	AnnotationRelationDao.RelationQuery.getBases()

Methods in ubic.gemma.persistence.service.common.description with parameters of type AnnotationRelationBasis

Modifier and Type	Method	Description
AnnotationRelationDao.RelationSummary.RelationSummaryBuilder	AnnotationRelationDao.RelationSummary.RelationSummaryBuilder.basis(AnnotationRelationBasis basis)
int	AnnotationRelationDao.removeByBasis(AnnotationRelationBasis basis, Long experimentId)	Remove every derived row for a basis, optionally for one experiment.
int	AnnotationRelationDao.removeByBasis(AnnotationRelationBasis basis, Long experimentId, String source)	The same rebuild delete, narrowed to one source.
int	AnnotationRelationDaoImpl.removeByBasis(AnnotationRelationBasis basis, Long experimentId)
int	AnnotationRelationDaoImpl.removeByBasis(AnnotationRelationBasis basis, Long experimentId, String source)

Method parameters in ubic.gemma.persistence.service.common.description with type arguments of type AnnotationRelationBasis

Modifier and Type	Method	Description
AnnotationRelationDao.RelationQuery	AnnotationRelationDao.RelationQuery.bases(Set<AnnotationRelationBasis> v)
List<String[]>	AnnotationRelationDao.findRelatedTerms(Collection<String> seedValueUris, Collection<String> seedValues, AnnotationRelationDao.Direction direction, Set<AnnotationRelationBasis> bases, Collection<String> predicateUris, Long taxonId, Collection<Long> excludedExperimentIds, int maximumObjectBreadth, int maxResults)	Set membership: every term related to any of the seeds, with no counting, no ranking and no ambiguity to resolve.
List<String[]>	AnnotationRelationDaoImpl.findRelatedTerms(Collection<String> seedValueUris, Collection<String> seedValues, AnnotationRelationDao.Direction direction, Set<AnnotationRelationBasis> bases, Collection<String> predicateUris, Long taxonId, Collection<Long> excludedExperimentIds, int maximumObjectBreadth, int maxResults)
List<String[]>	AnnotationRelationService.findRelatedTermsForSearch(Collection<String> seedValueUris, Collection<String> seedValues, AnnotationRelationDao.Direction direction, Set<AnnotationRelationBasis> bases, Long taxonId, Collection<Long> excludedExperimentIds, int maximumObjectBreadth, int maxResults)	Terms related to the seeds, for widening a query or testing membership.
List<String[]>	AnnotationRelationServiceImpl.findRelatedTermsForSearch(Collection<String> seedValueUris, Collection<String> seedValues, AnnotationRelationDao.Direction direction, Set<AnnotationRelationBasis> bases, Long taxonId, Collection<Long> excludedExperimentIds, int maximumObjectBreadth, int maxResults)
List<AnnotationRelationDao.RelationSummary>	AnnotationRelationService.findRelationsForExperiment(ExpressionExperiment ee, AnnotationRelationDao.Direction direction, Set<AnnotationRelationBasis> bases, int maxResults)	What this experiment's own annotations imply, for display beside them.
List<AnnotationRelationDao.RelationSummary>	AnnotationRelationServiceImpl.findRelationsForExperiment(ExpressionExperiment ee, AnnotationRelationDao.Direction direction, Set<AnnotationRelationBasis> bases, int maxResults)

Constructors in ubic.gemma.persistence.service.common.description with parameters of type AnnotationRelationBasis

Modifier	Constructor	Description
	RelationSummary(String subjectValue, String subjectValueUri, String subjectCategory, String subjectCategoryUri, String predicate, String predicateUri, String objectValue, String objectValueUri, String objectCategory, String objectCategoryUri, Long taxonId, String taxonCommonName, Integer taxonNcbiId, AnnotationRelationBasis basis, AnnotationRelationStatus status, String source, String sourceVersion, long numberOfExperiments, long numberOfExperimentsAtFactorValue, long numberOfExperimentsAtTag, long numberOfExperimentsAtBioMaterial, Long exampleExperimentId, long numberOfExperimentsWithSubject, long objectBreadth, long subjectBreadth, String evidence)	🛑 Build one with AnnotationRelationDao.RelationSummary.builder(), not with this. Twenty-six positional arguments, a dozen of them long and most of the rest String, is a constructor where a transposition compiles and passes — and adding a field to it broke a stale test class three times in one day, because Maven does not recompile a test whose source has not changed and the mismatch therefore arrives at runtime as NoSuchMethodError rather than at compile time.