Uses of Class
ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject
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Uses of EvidenceValueObject in ubic.gemma.core.association.phenotype
Methods in ubic.gemma.core.association.phenotype that return EvidenceValueObject Modifier and Type Method Description EvidenceValueObject<? extends PhenotypeAssociation>
PhenotypeAssociationManagerService. load(Long id)
Deprecated.Load an evidenceEvidenceValueObject<? extends PhenotypeAssociation>
PhenotypeAssociationManagerServiceImpl. load(Long id)
Deprecated.Methods in ubic.gemma.core.association.phenotype that return types with arguments of type EvidenceValueObject Modifier and Type Method Description Collection<EvidenceValueObject<? extends PhenotypeAssociation>>
PhenotypeAssociationManagerService. findEvidenceByFilters(Long taxonId, int limit, String userName)
Deprecated.Return evidence satisfying the specified filters.Collection<EvidenceValueObject<? extends PhenotypeAssociation>>
PhenotypeAssociationManagerServiceImpl. findEvidenceByFilters(Long taxonId, int limit, String userName)
Deprecated.Collection<EvidenceValueObject<? extends PhenotypeAssociation>>
PhenotypeAssociationManagerService. findEvidenceByGeneId(Long geneId)
Deprecated.Return all evidence for a specific gene idCollection<EvidenceValueObject<? extends PhenotypeAssociation>>
PhenotypeAssociationManagerService. findEvidenceByGeneId(Long geneId, Set<String> phenotypesValuesUri, EvidenceFilter evidenceFilter)
Deprecated.Return all evidence for a specific gene id with evidence flagged, indicating more informationCollection<EvidenceValueObject<? extends PhenotypeAssociation>>
PhenotypeAssociationManagerServiceImpl. findEvidenceByGeneId(Long geneId)
Deprecated.Collection<EvidenceValueObject<? extends PhenotypeAssociation>>
PhenotypeAssociationManagerServiceImpl. findEvidenceByGeneId(Long geneId, Set<String> phenotypesValuesUri, EvidenceFilter evidenceFilter)
Deprecated.Collection<EvidenceValueObject<? extends PhenotypeAssociation>>
PhenotypeAssociationManagerService. findEvidenceByGeneNCBI(Integer geneNCBI)
Deprecated.Return all evidence for a specific gene NCBICollection<EvidenceValueObject<? extends PhenotypeAssociation>>
PhenotypeAssociationManagerServiceImpl. findEvidenceByGeneNCBI(Integer geneNCBI)
Deprecated.Set<EvidenceValueObject<? extends PhenotypeAssociation>>
PhenotypeAssociationManagerService. loadEvidenceWithExternalDatabaseName(String externalDatabaseName, int limit, int start)
Deprecated.use if we want to reimport data from a specific external DatabaseSet<EvidenceValueObject<? extends PhenotypeAssociation>>
PhenotypeAssociationManagerServiceImpl. loadEvidenceWithExternalDatabaseName(String externalDatabaseName, int limit, int start)
Deprecated.Collection<EvidenceValueObject<? extends PhenotypeAssociation>>
PhenotypeAssociationManagerService. loadEvidenceWithoutExternalDatabaseName()
Deprecated.Collection<EvidenceValueObject<? extends PhenotypeAssociation>>
PhenotypeAssociationManagerServiceImpl. loadEvidenceWithoutExternalDatabaseName()
Deprecated.Methods in ubic.gemma.core.association.phenotype with parameters of type EvidenceValueObject Modifier and Type Method Description ValidateEvidenceValueObject
PhenotypeAssociationManagerService. makeEvidence(EvidenceValueObject<? extends PhenotypeAssociation> evidence)
Deprecated.Links an Evidence to a GeneValidateEvidenceValueObject
PhenotypeAssociationManagerServiceImpl. makeEvidence(EvidenceValueObject<? extends PhenotypeAssociation> evidence)
Deprecated.void
PhenotypeAssoManagerServiceHelper. populateModifiedValues(EvidenceValueObject<? extends PhenotypeAssociation> evidenceValueObject, PhenotypeAssociation phenotypeAssociation)
Deprecated.load evidence from the database and populate it with the updated informationvoid
PhenotypeAssoManagerServiceHelperImpl. populateModifiedValues(EvidenceValueObject<? extends PhenotypeAssociation> evidenceValueObject, PhenotypeAssociation phenotypeAssociation)
Deprecated.ValidateEvidenceValueObject
PhenotypeAssociationManagerService. update(EvidenceValueObject<? extends PhenotypeAssociation> evidenceValueObject)
Deprecated.Modify an existing evidenceValidateEvidenceValueObject
PhenotypeAssociationManagerServiceImpl. update(EvidenceValueObject<? extends PhenotypeAssociation> modifiedEvidenceValueObject)
Deprecated.ValidateEvidenceValueObject
PhenotypeAssociationManagerService. validateEvidence(EvidenceValueObject<PhenotypeAssociation> evidence)
Deprecated.Validate an Evidence before we create itValidateEvidenceValueObject
PhenotypeAssociationManagerServiceImpl. validateEvidence(EvidenceValueObject<PhenotypeAssociation> evidence)
Deprecated.PhenotypeAssociation
PhenotypeAssoManagerServiceHelper. valueObject2Entity(EvidenceValueObject<? extends PhenotypeAssociation> evidence)
Deprecated.Changes all type of evidenceValueObject to their corresponding entitiesPhenotypeAssociation
PhenotypeAssoManagerServiceHelperImpl. valueObject2Entity(EvidenceValueObject<? extends PhenotypeAssociation> evidence)
Deprecated. -
Uses of EvidenceValueObject in ubic.gemma.model.genome.gene.phenotype.valueObject
Subclasses of EvidenceValueObject in ubic.gemma.model.genome.gene.phenotype.valueObject Modifier and Type Class Description class
DiffExpressionEvidenceValueObject
class
ExperimentalEvidenceValueObject
Deprecated.class
GenericEvidenceValueObject
class
LiteratureEvidenceValueObject
Methods in ubic.gemma.model.genome.gene.phenotype.valueObject that return types with arguments of type EvidenceValueObject Modifier and Type Method Description Collection<EvidenceValueObject<? extends PhenotypeAssociation>>
GeneEvidenceValueObject. getEvidence()
Deprecated.Methods in ubic.gemma.model.genome.gene.phenotype.valueObject with parameters of type EvidenceValueObject Modifier and Type Method Description int
EvidenceValueObject. compareTo(EvidenceValueObject<E> evidenceValueObject)
Method parameters in ubic.gemma.model.genome.gene.phenotype.valueObject with type arguments of type EvidenceValueObject Modifier and Type Method Description void
GeneEvidenceValueObject. setEvidence(Collection<EvidenceValueObject<? extends PhenotypeAssociation>> evidence)
Deprecated.Constructor parameters in ubic.gemma.model.genome.gene.phenotype.valueObject with type arguments of type EvidenceValueObject Constructor Description GeneEvidenceValueObject(Gene gene, Collection<EvidenceValueObject<? extends PhenotypeAssociation>> evidence)
Deprecated. -
Uses of EvidenceValueObject in ubic.gemma.rest
Methods in ubic.gemma.rest that return types with arguments of type EvidenceValueObject Modifier and Type Method Description ResponseDataObject<Set<EvidenceValueObject<? extends PhenotypeAssociation>>>
PhenotypeWebService. getPhenotypeEvidence(String database, OffsetArg offset, LimitArg limit)
Deprecated.Finds all evidence with the given external database name. -
Uses of EvidenceValueObject in ubic.gemma.web.controller
Methods in ubic.gemma.web.controller that return types with arguments of type EvidenceValueObject Modifier and Type Method Description Collection<EvidenceValueObject<? extends PhenotypeAssociation>>
PhenotypeController. findEvidenceByFilters(Long taxonId, Integer limit, String userName)
Methods in ubic.gemma.web.controller with parameters of type EvidenceValueObject Modifier and Type Method Description ValidateEvidenceValueObject
PhenotypeController. processPhenotypeAssociationForm(EvidenceValueObject<?> evidenceValueObject)
ValidateEvidenceValueObject
PhenotypeController. validatePhenotypeAssociationForm(EvidenceValueObject<PhenotypeAssociation> evidenceValueObject)
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Uses of EvidenceValueObject in ubic.gemma.web.controller.genome.gene
Methods in ubic.gemma.web.controller.genome.gene that return types with arguments of type EvidenceValueObject Modifier and Type Method Description Collection<EvidenceValueObject<? extends PhenotypeAssociation>>
GeneController. loadGeneEvidence(Long taxonId, boolean showOnlyEditable, Collection<Long> databaseIds, Long geneId, String[] phenotypeValueUris)
AJAX used to show gene info in the phenotype tab FIXME Why is the taxonId a parameter, since we have the gene ID?
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