Uses of Class
ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject
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Uses of GeneEvidenceValueObject in ubic.gemma.core.association.phenotype
Methods in ubic.gemma.core.association.phenotype that return types with arguments of type GeneEvidenceValueObject Modifier and Type Method Description Collection<GeneEvidenceValueObject>
PhenotypeAssociationManagerService. findCandidateGenes(Collection<String> phenotypesValuesUris, Taxon taxon)
Deprecated.Given an set of phenotypes returns the genes that have all those phenotypes or children phenotypesSet<GeneEvidenceValueObject>
PhenotypeAssociationManagerService. findCandidateGenes(EvidenceFilter evidenceFilter, Set<String> phenotypesValuesUri)
Deprecated.Given set of phenotypes returns the genes that have all those phenotypes or children phenotypesCollection<GeneEvidenceValueObject>
PhenotypeAssociationManagerServiceImpl. findCandidateGenes(Collection<String> phenotypeValueUris, Taxon taxon)
Deprecated.Set<GeneEvidenceValueObject>
PhenotypeAssociationManagerServiceImpl. findCandidateGenes(EvidenceFilter evidenceFilter, Set<String> phenotypesValuesUri)
Deprecated.List<GeneEvidenceValueObject>
PhenotypeAssociationManagerService. findGenesWithEvidence(String query, Long taxonId)
Deprecated.Does a Gene search (by name or symbol) for a query and return only Genes with evidenceList<GeneEvidenceValueObject>
PhenotypeAssociationManagerServiceImpl. findGenesWithEvidence(String query, Long taxonId)
Deprecated. -
Uses of GeneEvidenceValueObject in ubic.gemma.persistence.service.association.phenotype
Methods in ubic.gemma.persistence.service.association.phenotype that return types with arguments of type GeneEvidenceValueObject Modifier and Type Method Description Collection<GeneEvidenceValueObject>
PhenotypeAssociationDao. findGenesWithPhenotypes(Set<String> phenotypesValueUri, Taxon taxon, boolean showOnlyEditable, Collection<Long> externalDatabaseIds)
Collection<GeneEvidenceValueObject>
PhenotypeAssociationDaoImpl. findGenesWithPhenotypes(Set<String> phenotypeUris, Taxon taxon, boolean showOnlyEditable, Collection<Long> externalDatabaseIds)
Key method: find Genes link to a phenotype taking into account private and public evidence Here on the cases : 1- Admin - can see anything 2- user not logged in - only public data 3- user logged in only showing what he has read access - public, shared + owned 4- user logged in only showing what he has write access - owned. -
Uses of GeneEvidenceValueObject in ubic.gemma.persistence.service.association.phenotype.service
Methods in ubic.gemma.persistence.service.association.phenotype.service that return types with arguments of type GeneEvidenceValueObject Modifier and Type Method Description Collection<GeneEvidenceValueObject>
PhenotypeAssociationService. findGenesWithPhenotypes(Set<String> phenotypesValueUri, Taxon taxon, boolean showOnlyEditable, Collection<Long> externalDatabaseIds)
Collection<GeneEvidenceValueObject>
PhenotypeAssociationServiceImpl. findGenesWithPhenotypes(Set<String> phenotypesValueUris, Taxon taxon, boolean showOnlyEditable, Collection<Long> externalDatabaseIds)
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Uses of GeneEvidenceValueObject in ubic.gemma.rest
Methods in ubic.gemma.rest that return types with arguments of type GeneEvidenceValueObject Modifier and Type Method Description ResponseDataObject<Set<GeneEvidenceValueObject>>
TaxaWebService. findCandidateGenesInTaxon(TaxonArg<?> taxonArg, StringArrayArg phenotypes, Boolean editableOnly)
Deprecated.ResponseDataObject<List<GeneEvidenceValueObject>>
GeneWebService. getGeneEvidence(GeneArg<?> geneArg)
Deprecated.ResponseDataObject<List<GeneEvidenceValueObject>>
TaxaWebService. getGenesEvidenceInTaxon(TaxonArg<?> taxonArg, GeneArg<?> geneArg)
Deprecated. -
Uses of GeneEvidenceValueObject in ubic.gemma.rest.util.args
Methods in ubic.gemma.rest.util.args that return types with arguments of type GeneEvidenceValueObject Modifier and Type Method Description List<GeneEvidenceValueObject>
GeneArgService. getGeneEvidence(GeneArg<?> arg, Taxon taxon)
Deprecated. -
Uses of GeneEvidenceValueObject in ubic.gemma.web.controller
Methods in ubic.gemma.web.controller that return types with arguments of type GeneEvidenceValueObject Modifier and Type Method Description Collection<GeneEvidenceValueObject>
PhenotypeController. findCandidateGenes(Long taxonId, boolean showOnlyEditable, Collection<Long> databaseIds, String[] phenotypes)
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