Uses of Class
ubic.gemma.model.association.phenotype.PhenotypeAssociation

Packages that use PhenotypeAssociation

Package	Description
ubic.gemma.core.association.phenotype
ubic.gemma.model.association.phenotype
ubic.gemma.model.genome
ubic.gemma.model.genome.gene.phenotype.valueObject
ubic.gemma.persistence.service.association.phenotype
ubic.gemma.persistence.service.association.phenotype.service
ubic.gemma.rest
ubic.gemma.web.controller
ubic.gemma.web.controller.genome.gene

Uses of PhenotypeAssociation in ubic.gemma.core.association.phenotype

Methods in ubic.gemma.core.association.phenotype that return PhenotypeAssociation

Modifier and Type	Method	Description
PhenotypeAssociation	PhenotypeAssoManagerServiceHelper.valueObject2Entity(EvidenceValueObject<? extends PhenotypeAssociation> evidence)	Deprecated. Changes all type of evidenceValueObject to their corresponding entities
PhenotypeAssociation	PhenotypeAssoManagerServiceHelperImpl.valueObject2Entity(EvidenceValueObject<? extends PhenotypeAssociation> evidence)	Deprecated.

Methods in ubic.gemma.core.association.phenotype that return types with arguments of type PhenotypeAssociation

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 id
Collection<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 information
Collection<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 NCBI
Collection<EvidenceValueObject<? extends PhenotypeAssociation>>	PhenotypeAssociationManagerServiceImpl.findEvidenceByGeneNCBI(Integer geneNCBI)	Deprecated.
EvidenceValueObject<? extends PhenotypeAssociation>	PhenotypeAssociationManagerService.load(Long id)	Deprecated. Load an evidence
EvidenceValueObject<? extends PhenotypeAssociation>	PhenotypeAssociationManagerServiceImpl.load(Long id)	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 Database
Set<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 PhenotypeAssociation

Modifier and Type	Method	Description
void	PhenotypeAssoManagerServiceHelper.populateModifiedValues(EvidenceValueObject<? extends PhenotypeAssociation> evidenceValueObject, PhenotypeAssociation phenotypeAssociation)	Deprecated. load evidence from the database and populate it with the updated information
void	PhenotypeAssoManagerServiceHelperImpl.populateModifiedValues(EvidenceValueObject<? extends PhenotypeAssociation> evidenceValueObject, PhenotypeAssociation phenotypeAssociation)	Deprecated.

Method parameters in ubic.gemma.core.association.phenotype with type arguments of type PhenotypeAssociation

Modifier and Type	Method	Description
ValidateEvidenceValueObject	PhenotypeAssociationManagerService.makeEvidence(EvidenceValueObject<? extends PhenotypeAssociation> evidence)	Deprecated. Links an Evidence to a Gene
ValidateEvidenceValueObject	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 information
void	PhenotypeAssoManagerServiceHelperImpl.populateModifiedValues(EvidenceValueObject<? extends PhenotypeAssociation> evidenceValueObject, PhenotypeAssociation phenotypeAssociation)	Deprecated.
ValidateEvidenceValueObject	PhenotypeAssociationManagerService.update(EvidenceValueObject<? extends PhenotypeAssociation> evidenceValueObject)	Deprecated. Modify an existing evidence
ValidateEvidenceValueObject	PhenotypeAssociationManagerServiceImpl.update(EvidenceValueObject<? extends PhenotypeAssociation> modifiedEvidenceValueObject)	Deprecated.
ValidateEvidenceValueObject	PhenotypeAssociationManagerService.validateEvidence(EvidenceValueObject<PhenotypeAssociation> evidence)	Deprecated. Validate an Evidence before we create it
ValidateEvidenceValueObject	PhenotypeAssociationManagerServiceImpl.validateEvidence(EvidenceValueObject<PhenotypeAssociation> evidence)	Deprecated.
PhenotypeAssociation	PhenotypeAssoManagerServiceHelper.valueObject2Entity(EvidenceValueObject<? extends PhenotypeAssociation> evidence)	Deprecated. Changes all type of evidenceValueObject to their corresponding entities
PhenotypeAssociation	PhenotypeAssoManagerServiceHelperImpl.valueObject2Entity(EvidenceValueObject<? extends PhenotypeAssociation> evidence)	Deprecated.

Uses of PhenotypeAssociation in ubic.gemma.model.association.phenotype

Subclasses of PhenotypeAssociation in ubic.gemma.model.association.phenotype

Modifier and Type	Class	Description
class	DataAnalysisEvidence	Deprecated.
class	DifferentialExpressionEvidence	Deprecated.
class	ExperimentalEvidence	Deprecated.
class	GenericEvidence	Deprecated.
class	LiteratureEvidence	Deprecated.

Uses of PhenotypeAssociation in ubic.gemma.model.genome

Methods in ubic.gemma.model.genome that return types with arguments of type PhenotypeAssociation

Modifier and Type	Method	Description
Set<PhenotypeAssociation>	Gene.getPhenotypeAssociations()	Deprecated.

Method parameters in ubic.gemma.model.genome with type arguments of type PhenotypeAssociation

Modifier and Type	Method	Description
void	Gene.setPhenotypeAssociations(Set<PhenotypeAssociation> phenotypeAssociations)	Deprecated.

Uses of PhenotypeAssociation in ubic.gemma.model.genome.gene.phenotype.valueObject

Classes in ubic.gemma.model.genome.gene.phenotype.valueObject with type parameters of type PhenotypeAssociation

Modifier and Type	Class	Description
class	EvidenceValueObject<E extends PhenotypeAssociation>	Parent class of all evidence value objects

Methods in ubic.gemma.model.genome.gene.phenotype.valueObject that return types with arguments of type PhenotypeAssociation

Modifier and Type	Method	Description
Collection<EvidenceValueObject<? extends PhenotypeAssociation>>	GeneEvidenceValueObject.getEvidence()	Deprecated.

Method parameters in ubic.gemma.model.genome.gene.phenotype.valueObject with type arguments of type PhenotypeAssociation

Modifier and Type	Method	Description
static Collection<BibliographicPhenotypesValueObject>	BibliographicPhenotypesValueObject.phenotypeAssociations2BibliographicPhenotypesValueObjects(Collection<PhenotypeAssociation> phenotypeAssociations)
void	GeneEvidenceValueObject.setEvidence(Collection<EvidenceValueObject<? extends PhenotypeAssociation>> evidence)	Deprecated.

Constructors in ubic.gemma.model.genome.gene.phenotype.valueObject with parameters of type PhenotypeAssociation

Constructor	Description
BibliographicPhenotypesValueObject(PhenotypeAssociation phenotypeAssociation)

Constructor parameters in ubic.gemma.model.genome.gene.phenotype.valueObject with type arguments of type PhenotypeAssociation

Constructor	Description
GeneEvidenceValueObject(Gene gene, Collection<EvidenceValueObject<? extends PhenotypeAssociation>> evidence)	Deprecated.

Uses of PhenotypeAssociation in ubic.gemma.persistence.service.association.phenotype

Methods in ubic.gemma.persistence.service.association.phenotype that return PhenotypeAssociation

Modifier and Type	Method	Description
PhenotypeAssociation	PhenotypeAssociationDaoImpl.find(PhenotypeAssociation entity)
PhenotypeAssociation	PhenotypeAssociationDaoImpl.load(Long id)

Methods in ubic.gemma.persistence.service.association.phenotype that return types with arguments of type PhenotypeAssociation

Modifier and Type	Method	Description
Collection<PhenotypeAssociation>	PhenotypeAssociationDao.findEvidencesWithExternalDatabaseName(String externalDatabaseName, int limit, int start)
Collection<PhenotypeAssociation>	PhenotypeAssociationDaoImpl.findEvidencesWithExternalDatabaseName(String externalDatabaseName, int limit, int start)	loads all evidences from a specific external database
Collection<PhenotypeAssociation>	PhenotypeAssociationDao.findEvidencesWithoutExternalDatabaseName()
Collection<PhenotypeAssociation>	PhenotypeAssociationDaoImpl.findEvidencesWithoutExternalDatabaseName()	find all evidence that doesn't come from an external course
Collection<PhenotypeAssociation>	PhenotypeAssociationDao.findPhenotypeAssociationForGeneId(Long geneId)
Collection<PhenotypeAssociation>	PhenotypeAssociationDaoImpl.findPhenotypeAssociationForGeneId(Long geneId)	find all PhenotypeAssociation for a specific gene id
Collection<PhenotypeAssociation>	PhenotypeAssociationDao.findPhenotypeAssociationForGeneIdAndDatabases(Long geneId, Collection<Long> externalDatabaseIds)
Collection<PhenotypeAssociation>	PhenotypeAssociationDaoImpl.findPhenotypeAssociationForGeneIdAndDatabases(Long geneId, Collection<Long> externalDatabaseIds)	find all PhenotypeAssociation for a specific gene id and external Databases ids
Collection<PhenotypeAssociation>	PhenotypeAssociationDao.findPhenotypeAssociationForGeneNCBI(Integer geneNCBI)
Collection<PhenotypeAssociation>	PhenotypeAssociationDao.findPhenotypeAssociationForGeneNCBI(Integer geneNCBI, Set<String> phenotype)
Collection<PhenotypeAssociation>	PhenotypeAssociationDaoImpl.findPhenotypeAssociationForGeneNCBI(Integer geneNCBI)	find all PhenotypeAssociation for a specific NCBI id
Collection<PhenotypeAssociation>	PhenotypeAssociationDaoImpl.findPhenotypeAssociationForGeneNCBI(Integer geneNCBI, Set<String> phenotype)	find all PhenotypeAssociation for a specific NCBI id and phenotypes valueUri
Collection<PhenotypeAssociation>	PhenotypeAssociationDao.findPhenotypeAssociationWithIds(Collection<Long> ids)
Collection<PhenotypeAssociation>	PhenotypeAssociationDaoImpl.findPhenotypeAssociationWithIds(Collection<Long> paIds)	find PhenotypeAssociation satisfying the given filters: paIds, taxonId and limit
Collection<PhenotypeAssociation>	PhenotypeAssociationDao.findPhenotypesForBibliographicReference(String pubMedID)
Collection<PhenotypeAssociation>	PhenotypeAssociationDaoImpl.findPhenotypesForBibliographicReference(String pubMedID)	find PhenotypeAssociations associated with a BibliographicReference

Methods in ubic.gemma.persistence.service.association.phenotype with parameters of type PhenotypeAssociation

Modifier and Type	Method	Description
PhenotypeAssociation	PhenotypeAssociationDaoImpl.find(PhenotypeAssociation entity)
void	PhenotypeAssociationDaoImpl.remove(PhenotypeAssociation entity)

Uses of PhenotypeAssociation in ubic.gemma.persistence.service.association.phenotype.service

Methods in ubic.gemma.persistence.service.association.phenotype.service that return PhenotypeAssociation

Modifier and Type	Method	Description
PhenotypeAssociation	PhenotypeAssociationService.create(PhenotypeAssociation p)
PhenotypeAssociation	PhenotypeAssociationService.load(Long id)

Methods in ubic.gemma.persistence.service.association.phenotype.service that return types with arguments of type PhenotypeAssociation

Modifier and Type	Method	Description
Collection<PhenotypeAssociation>	PhenotypeAssociationService.findEvidencesWithExternalDatabaseName(String externalDatabaseName, int limit, int start)
Collection<PhenotypeAssociation>	PhenotypeAssociationServiceImpl.findEvidencesWithExternalDatabaseName(String externalDatabaseName, int limit, int start)
Collection<PhenotypeAssociation>	PhenotypeAssociationService.findEvidencesWithoutExternalDatabaseName()
Collection<PhenotypeAssociation>	PhenotypeAssociationServiceImpl.findEvidencesWithoutExternalDatabaseName()
Collection<PhenotypeAssociation>	PhenotypeAssociationService.findPhenotypeAssociationForGeneId(Long geneId)
Collection<PhenotypeAssociation>	PhenotypeAssociationServiceImpl.findPhenotypeAssociationForGeneId(Long geneId)
Collection<PhenotypeAssociation>	PhenotypeAssociationService.findPhenotypeAssociationForGeneIdAndDatabases(Long geneId, Collection<Long> externalDatabaseIds)
Collection<PhenotypeAssociation>	PhenotypeAssociationServiceImpl.findPhenotypeAssociationForGeneIdAndDatabases(Long geneId, Collection<Long> externalDatabaseIds)
Collection<PhenotypeAssociation>	PhenotypeAssociationService.findPhenotypeAssociationForGeneNCBI(Integer geneNCBI)
Collection<PhenotypeAssociation>	PhenotypeAssociationService.findPhenotypeAssociationForGeneNCBI(Integer geneNCBI, Set<String> phenotype)
Collection<PhenotypeAssociation>	PhenotypeAssociationServiceImpl.findPhenotypeAssociationForGeneNCBI(Integer geneNCBI)
Collection<PhenotypeAssociation>	PhenotypeAssociationServiceImpl.findPhenotypeAssociationForGeneNCBI(Integer geneNCBI, Set<String> phenotype)
Collection<PhenotypeAssociation>	PhenotypeAssociationService.findPhenotypeAssociationWithIds(Collection<Long> paIds)
Collection<PhenotypeAssociation>	PhenotypeAssociationServiceImpl.findPhenotypeAssociationWithIds(Collection<Long> ids)
Collection<PhenotypeAssociation>	PhenotypeAssociationService.findPhenotypesForBibliographicReference(String pubMedId)
Collection<PhenotypeAssociation>	PhenotypeAssociationServiceImpl.findPhenotypesForBibliographicReference(String pubMedId)
Collection<PhenotypeAssociation>	PhenotypeAssociationService.loadAll()

Methods in ubic.gemma.persistence.service.association.phenotype.service with parameters of type PhenotypeAssociation

Modifier and Type	Method	Description
PhenotypeAssociation	PhenotypeAssociationService.create(PhenotypeAssociation p)
void	PhenotypeAssociationService.remove(PhenotypeAssociation p)
void	PhenotypeAssociationService.update(PhenotypeAssociation evidence)

Uses of PhenotypeAssociation in ubic.gemma.rest

Methods in ubic.gemma.rest that return types with arguments of type PhenotypeAssociation

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 PhenotypeAssociation in ubic.gemma.web.controller

Methods in ubic.gemma.web.controller that return types with arguments of type PhenotypeAssociation

Modifier and Type	Method	Description
Collection<EvidenceValueObject<? extends PhenotypeAssociation>>	PhenotypeController.findEvidenceByFilters(Long taxonId, Integer limit, String userName)

Method parameters in ubic.gemma.web.controller with type arguments of type PhenotypeAssociation

Modifier and Type	Method	Description
ValidateEvidenceValueObject	PhenotypeController.validatePhenotypeAssociationForm(EvidenceValueObject<PhenotypeAssociation> evidenceValueObject)

Uses of PhenotypeAssociation in ubic.gemma.web.controller.genome.gene

Methods in ubic.gemma.web.controller.genome.gene that return types with arguments of type PhenotypeAssociation

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?