Uses of Class
ubic.gemma.model.common.description.CharacteristicValueObject

Packages that use CharacteristicValueObject

Package	Description
ubic.gemma.core.association.phenotype
ubic.gemma.core.ontology
ubic.gemma.model.common.description
ubic.gemma.model.genome.gene.phenotype.valueObject
ubic.gemma.persistence.service.association.phenotype
ubic.gemma.persistence.service.association.phenotype.service
ubic.gemma.persistence.service.common.description
ubic.gemma.web.controller
ubic.gemma.web.controller.expression.experiment

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

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

Modifier and Type	Method	Description
Collection<CharacteristicValueObject>	PhenotypeAssociationManagerService.findExperimentCategory()	Deprecated. Find category term that were used in the database, used to annotated Experiments
Collection<CharacteristicValueObject>	PhenotypeAssociationManagerServiceImpl.findExperimentCategory()	Deprecated.
Collection<CharacteristicValueObject>	PhenotypeAssociationManagerService.findExperimentOntologyValue(String givenQueryString, long timeout, TimeUnit timeUnit)	Deprecated. for a given search string look in the database and Ontology for matches
Collection<CharacteristicValueObject>	PhenotypeAssociationManagerServiceImpl.findExperimentOntologyValue(String givenQueryString, long timeout, TimeUnit timeUnit)	Deprecated.
Set<CharacteristicValueObject>	PhenotypeAssoOntologyHelper.findPhenotypesInOntology(String searchQuery)	Deprecated. search the disease,hp and mp ontology for a searchQuery and return an ordered set of CharacteristicVO
Set<CharacteristicValueObject>	PhenotypeAssoOntologyHelperImpl.findPhenotypesInOntology(String searchQuery)	Deprecated.
Collection<CharacteristicValueObject>	PhenotypeAssociationManagerService.searchInDatabaseForPhenotype(String searchQuery, int maxResults, long timeout, TimeUnit timeUnit)	Deprecated. For a given search string find all Ontology terms related, and then count their gene occurrence by taxon, including ontology children terms
Collection<CharacteristicValueObject>	PhenotypeAssociationManagerServiceImpl.searchInDatabaseForPhenotype(String searchQuery, int maxResults, long timeout, TimeUnit timeUnit)	Deprecated.
Collection<CharacteristicValueObject>	PhenotypeAssociationManagerService.searchOntologyForPhenotypes(String searchQuery, Long geneId)	Deprecated. Giving a phenotype searchQuery, returns a selection choice to the user
Collection<CharacteristicValueObject>	PhenotypeAssociationManagerServiceImpl.searchOntologyForPhenotypes(String searchQuery, Long geneId)	Deprecated.

Methods in ubic.gemma.core.association.phenotype with parameters of type CharacteristicValueObject

Modifier and Type	Method	Description
Characteristic	PhenotypeAssoOntologyHelper.characteristicValueObject2Characteristic(CharacteristicValueObject characteristicValueObject)	Deprecated. CharacteristicValueObject to Characteristic with no valueUri given
Characteristic	PhenotypeAssoOntologyHelperImpl.characteristicValueObject2Characteristic(CharacteristicValueObject characteristicValueObject)	Deprecated.

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

Modifier and Type	Method	Description
ValidateEvidenceValueObject	PhenotypeAssociationManagerService.makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId, SortedSet<CharacteristicValueObject> phenotypes, Double thresholdChosen)	Deprecated. creates the DifferentialExpressionEvidences using an DiffExpressionMetaAnalysis
ValidateEvidenceValueObject	PhenotypeAssociationManagerServiceImpl.makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId, SortedSet<CharacteristicValueObject> phenotypes, Double selectionThreshold)	Deprecated.

Uses of CharacteristicValueObject in ubic.gemma.core.ontology

Methods in ubic.gemma.core.ontology that return types with arguments of type CharacteristicValueObject

Modifier and Type	Method	Description
Collection<CharacteristicValueObject>	OntologyService.findExperimentsCharacteristicTags(String searchQuery, int maxResults, boolean useNeuroCartaOntology, long timeout, TimeUnit timeUnit)	Deprecated.
Collection<CharacteristicValueObject>	OntologyServiceImpl.findExperimentsCharacteristicTags(String searchQuery, int maxResults, boolean useNeuroCartaOntology, long timeout, TimeUnit timeUnit)	Using the ontology and values in the database, for a search searchQuery given by the client give an ordered list of possible choices
Collection<CharacteristicValueObject>	OntologyService.findTermsInexact(String givenQueryString, int maxResults, Taxon taxon, long timeout, TimeUnit timeUnit)	Given a search string will first look through the characteristic database for any entries that have a match.
Collection<CharacteristicValueObject>	OntologyServiceImpl.findTermsInexact(String queryString, int maxResults, Taxon taxon, long timeout, TimeUnit timeUnit)

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

Methods in ubic.gemma.model.common.description that return types with arguments of type CharacteristicValueObject

Modifier and Type	Method	Description
static Collection<CharacteristicValueObject>	CharacteristicValueObject.characteristic2CharacteristicVO(Collection<? extends Characteristic> characteristics)

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

Modifier and Type	Method	Description
int	CharacteristicValueObject.compareTo(CharacteristicValueObject that)

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

Subclasses of CharacteristicValueObject in ubic.gemma.model.genome.gene.phenotype.valueObject

Modifier and Type	Class	Description
class	TreeCharacteristicValueObject

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

Modifier and Type	Method	Description
Collection<CharacteristicValueObject>	ExperimentalEvidenceValueObject.getExperimentCharacteristics()	Deprecated.
Set<CharacteristicValueObject>	EvidenceValueObject.getPhenotypes()
Set<CharacteristicValueObject>	BibliographicPhenotypesValueObject.getPhenotypesValues()

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

Modifier and Type	Method	Description
void	ExperimentalEvidenceValueObject.setExperimentCharacteristics(Collection<CharacteristicValueObject> experimentCharacteristics)	Deprecated.
void	EvidenceValueObject.setPhenotypes(Set<CharacteristicValueObject> phenotypes)
void	BibliographicPhenotypesValueObject.setPhenotypesValues(Set<CharacteristicValueObject> phenotypesValues)

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

Constructor	Description
BibliographicPhenotypesValueObject(String geneName, Integer geneNCBI, Set<CharacteristicValueObject> phenotypesValues)
DiffExpressionEvidenceValueObject(Long id, GeneDifferentialExpressionMetaAnalysis geneDifferentialExpressionMetaAnalysis, GeneDifferentialExpressionMetaAnalysisResult geneDifferentialExpressionMetaAnalysisResult, SortedSet<CharacteristicValueObject> phenotypes, String evidenceCode, Double selectionThreshold)
EvidenceValueObject(Long id, Integer geneNCBI, Set<CharacteristicValueObject> phenotypes, String description, String evidenceCode, boolean isNegativeEvidence, EvidenceSourceValueObject evidenceSource)
GenericEvidenceValueObject(Long id, Integer geneNCBI, SortedSet<CharacteristicValueObject> phenotypes, String description, String evidenceCode, boolean isNegativeEvidence, EvidenceSourceValueObject evidenceSource)

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

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

Modifier and Type	Method	Description
Collection<CharacteristicValueObject>	PhenotypeAssociationDao.findEvidenceCategoryTerms()
Collection<CharacteristicValueObject>	PhenotypeAssociationDaoImpl.findEvidenceCategoryTerms()	find category terms currently used in the database by evidence

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

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

Modifier and Type	Method	Description
Collection<CharacteristicValueObject>	PhenotypeAssociationService.findEvidenceCategoryTerms()
Collection<CharacteristicValueObject>	PhenotypeAssociationServiceImpl.findEvidenceCategoryTerms()

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

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

Modifier and Type	Method	Description
protected CharacteristicValueObject	CharacteristicDaoImpl.doLoadValueObject(Characteristic entity)

Uses of CharacteristicValueObject in ubic.gemma.web.controller

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

Modifier and Type	Method	Description
Collection<CharacteristicValueObject>	PhenotypeController.findExperimentCategory()	Returns available efo category terms.
Collection<CharacteristicValueObject>	PhenotypeController.findExperimentOntologyValue(String givenQueryString, String categoryUri, Long taxonId)
Collection<CharacteristicValueObject>	PhenotypeController.searchOntologyForPhenotypes(String query, Long geneId)	Returns all phenotypes satisfied the given search criteria.

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

Modifier and Type	Method	Description
ValidateEvidenceValueObject	PhenotypeController.makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId, SortedSet<CharacteristicValueObject> phenotypes, Double selectionThreshold)

Uses of CharacteristicValueObject in ubic.gemma.web.controller.expression.experiment

Methods in ubic.gemma.web.controller.expression.experiment that return types with arguments of type CharacteristicValueObject

Modifier and Type	Method	Description
Collection<CharacteristicValueObject>	AnnotationController.findTerm(String givenQueryString, Long taxonId)	AJAX.
Collection<CharacteristicValueObject>	ExperimentalDesignController.getBioMaterialCharacteristicCategories(Long experimentalDesignID)	Extract just the categories from the biomaterial's characteristics.

Methods in ubic.gemma.web.controller.expression.experiment with parameters of type CharacteristicValueObject

Modifier and Type	Method	Description
void	ExperimentalDesignController.createFactorValueCharacteristic(EntityDelegator<FactorValue> e, CharacteristicValueObject cvo)