Uses of Class
ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
Packages that use AnnotationRelationDao.RelationQuery
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Uses of AnnotationRelationDao.RelationQuery in ubic.gemma.persistence.service.common.description
Methods in ubic.gemma.persistence.service.common.description that return AnnotationRelationDao.RelationQueryModifier and TypeMethodDescriptionAnnotationRelationDao.RelationQuery.bases(Set<AnnotationRelationBasis> v) AnnotationRelationDao.RelationQuery.excludedExperimentIds(Collection<Long> v) Hold experiments out of the evidence.AnnotationRelationDao.RelationQuery.excludedSubjectCategoryUris(Collection<String> v) Subject categories to leave out, for a caller that wants everything except one kind of implying term.AnnotationRelationDao.RelationQuery.includeRefuted(boolean v) Also return relations a source states do NOT hold.AnnotationRelationDao.RelationQuery.maximumObjectBreadth(int v) Drop relations whose object relates to more than this many distinct subjects.AnnotationRelationDao.RelationQuery.maximumSubjectBreadth(int v) Drop relations whose subject relates to more than this many distinct objects under the same predicate.AnnotationRelationDao.RelationQuery.maxResults(int v) AnnotationRelationDao.RelationQuery.minimumSpecificity(double v) Off by default, deliberately: no threshold has been tuned against curator judgement, and the shape of the distribution is worth seeing before one is fixed in the API.AnnotationRelationDao.RelationQuery.minimumSupport(int v) AnnotationRelationDao.RelationQuery.objectCategoryUris(Collection<String> v) AnnotationRelationDao.RelationQuery.objectValues(Collection<String> v) AnnotationRelationDao.RelationQuery.objectValueUris(Collection<String> v) AnnotationRelationDao.RelationQuery.predicateUris(Collection<String> v) AnnotationRelationDao.RelationQuery.seedDirection(AnnotationRelationDao.Direction v) Which side of the relation an experiment seed is matched against.AnnotationRelationDao.RelationQuery.seedFromExperimentId(Long v) Seed from every annotation an experiment carries, instead of from a list of terms.AnnotationRelationDao.RelationQuery.subjectCategoryUris(Collection<String> v) AnnotationRelationDao.RelationQuery.subjectValues(Collection<String> v) AnnotationRelationDao.RelationQuery.subjectValueUris(Collection<String> v) AnnotationRelationDao.RelationQuery.termLevelOnly(boolean v) Keep only relations that say something about the subject term, dropping per-experiment parameters.Methods in ubic.gemma.persistence.service.common.description with parameters of type AnnotationRelationDao.RelationQueryModifier and TypeMethodDescriptionAnnotationRelationDao.findRelations(AnnotationRelationDao.RelationQuery query) The ranked, evidenced read.AnnotationRelationDaoImpl.findRelations(AnnotationRelationDao.RelationQuery q) AnnotationRelationService.findRelations(AnnotationRelationDao.RelationQuery query) The ranked, evidenced read.AnnotationRelationServiceImpl.findRelations(AnnotationRelationDao.RelationQuery query)