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

Packages that use CharacteristicValueObject

Package	Description
ubic.gemma.core.ontology
ubic.gemma.model.analysis
ubic.gemma.model.common.description
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.common.description
ubic.gemma.rest
ubic.gemma.rest.ranking

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, boolean forceGeneOntology, long timeout, TimeUnit timeUnit)	Deprecated.
Collection<CharacteristicValueObject>	OntologyServiceImpl.findExperimentsCharacteristicTags(String searchQuery, int maxResults, boolean useNeuroCartaOntology, boolean forceGeneOntology, 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.analysis

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

Modifier and Type	Method	Description
Set<CharacteristicValueObject>	CellTypeAssignmentValueObject.getCellTypes()	A set of cell types that are assigned to individual cells.

Method parameters in ubic.gemma.model.analysis with type arguments of type CharacteristicValueObject

Modifier and Type	Method	Description
void	CellTypeAssignmentValueObject.setCellTypes(Set<CharacteristicValueObject> cellTypes)	A set of cell types that are assigned to individual cells.

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

Classes in ubic.gemma.model.common.description that implement interfaces with type arguments of type CharacteristicValueObject

Modifier and Type	Class	Description
class	CharacteristicValueObject	Value object representation of a Characteristic.

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.expression.bioAssayData

Methods in ubic.gemma.model.expression.bioAssayData that return types with arguments of type CharacteristicValueObject

Modifier and Type	Method	Description
Set<CharacteristicValueObject>	CellLevelCharacteristicsValueObject.getCharacteristics()	The distinct labels cells are grouped under; see CellLevelCharacteristics.

Method parameters in ubic.gemma.model.expression.bioAssayData with type arguments of type CharacteristicValueObject

Modifier and Type	Method	Description
void	CellLevelCharacteristicsValueObject.setCharacteristics(Set<CharacteristicValueObject> characteristics)	The distinct labels cells are grouped under; see CellLevelCharacteristics.

Uses of CharacteristicValueObject in ubic.gemma.model.expression.biomaterial

Methods in ubic.gemma.model.expression.biomaterial that return types with arguments of type CharacteristicValueObject

Modifier and Type	Method	Description
Collection<CharacteristicValueObject>	BioMaterialValueObject.getCharacteristics()

Method parameters in ubic.gemma.model.expression.biomaterial with type arguments of type CharacteristicValueObject

Modifier and Type	Method	Description
void	BioMaterialValueObject.setCharacteristics(Collection<CharacteristicValueObject> characteristics)

Uses of CharacteristicValueObject in ubic.gemma.model.expression.experiment

Methods in ubic.gemma.model.expression.experiment that return CharacteristicValueObject

Modifier and Type	Method	Description
CharacteristicValueObject	ExperimentalDesignValueObject.ExperimentalFactorEntry.getCategory()
CharacteristicValueObject	AbstractFactorValueValueObject.getExperimentalFactorCategory()	The experiment factor category.

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

Modifier and Type	Method	Description
List<CharacteristicValueObject>	AbstractFactorValueValueObject.getCharacteristics()	The characteristics associated with this factor value.
Collection<CharacteristicValueObject>	BioAssaySetValueObject.getCharacteristics()
Collection<CharacteristicValueObject>	ExpressionExperimentSubsetValueObject.getCharacteristics()
Set<CharacteristicValueObject>	ExpressionExperimentValueObject.getCharacteristics()

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

Modifier and Type	Method	Description
void	ExperimentalDesignValueObject.ExperimentalFactorEntry.setCategory(CharacteristicValueObject category)
void	AbstractFactorValueValueObject.setExperimentalFactorCategory(CharacteristicValueObject experimentalFactorCategory)	The experiment factor category.

Method parameters in ubic.gemma.model.expression.experiment with type arguments of type CharacteristicValueObject

Modifier and Type	Method	Description
void	AbstractFactorValueValueObject.setCharacteristics(List<CharacteristicValueObject> characteristics)	The characteristics associated with this factor value.
void	ExpressionExperimentSubsetValueObject.setCharacteristics(Collection<CharacteristicValueObject> characteristics)
void	ExpressionExperimentValueObject.setCharacteristics(Set<CharacteristicValueObject> characteristics)

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

Subclasses with type arguments of type CharacteristicValueObject in ubic.gemma.persistence.service.common.description

Modifier and Type	Class	Description
class	CharacteristicDaoImpl
class	CharacteristicServiceImpl

Subinterfaces with type arguments of type CharacteristicValueObject in ubic.gemma.persistence.service.common.description

Modifier and Type	Interface	Description
interface	CharacteristicDao
interface	CharacteristicService

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.rest

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

Modifier and Type	Method	Description
List<CharacteristicValueObject>	DatasetsWebService.FilteredAndInferredAndCursorPaginatedResponseDataObject.getInferredTerms()
List<CharacteristicValueObject>	DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject.getInferredTerms()
List<CharacteristicValueObject>	DatasetsWebService.QueriedAndFilteredAndInferredAndCursorPaginatedResponseDataObject.getInferredTerms()
List<CharacteristicValueObject>	DatasetsWebService.QueriedAndFilteredAndInferredAndLimitedResponseDataObject.getInferredTerms()
List<CharacteristicValueObject>	DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObject.getInferredTerms()
List<CharacteristicValueObject>	DatasetsWebService.QueriedAndFilteredAndInferredResponseDataObject.getInferredTerms()

Uses of CharacteristicValueObject in ubic.gemma.rest.ranking

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

Modifier and Type	Method	Description
List<CharacteristicValueObject>	AnnotationSearchRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri)	Re-order rawHits according to this strategy.
default List<CharacteristicValueObject>	AnnotationSearchRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri, Map<String,Integer> stringPriorByUri)	Re-order rawHits with the per-string corpus prior available in addition to the usage counts.
default List<CharacteristicValueObject>	AnnotationSearchRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri, Map<String,Integer> stringPriorByUri, Map<String,String> matchedTextByUri)	Re-order rawHits with the per-URI matched text available in addition to the counts.
List<CharacteristicValueObject>	CommonalityRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri)
List<CharacteristicValueObject>	CommonalityRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri, Map<String,Integer> stringPriorByUri)
List<CharacteristicValueObject>	CompositeRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri)
List<CharacteristicValueObject>	CompositeRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri, Map<String,Integer> stringPriorByUri, Map<String,String> matchedTextByUri)
List<CharacteristicValueObject>	LuceneOrderRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri)
List<CharacteristicValueObject>	TokenCoverageRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri)
List<CharacteristicValueObject>	UsageWeightedRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri)

Method parameters in ubic.gemma.rest.ranking with type arguments of type CharacteristicValueObject

Modifier and Type	Method	Description
List<CharacteristicValueObject>	AnnotationSearchRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri)	Re-order rawHits according to this strategy.
default List<CharacteristicValueObject>	AnnotationSearchRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri, Map<String,Integer> stringPriorByUri)	Re-order rawHits with the per-string corpus prior available in addition to the usage counts.
default List<CharacteristicValueObject>	AnnotationSearchRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri, Map<String,Integer> stringPriorByUri, Map<String,String> matchedTextByUri)	Re-order rawHits with the per-URI matched text available in addition to the counts.
List<CharacteristicValueObject>	CommonalityRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri)
List<CharacteristicValueObject>	CommonalityRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri, Map<String,Integer> stringPriorByUri)
List<CharacteristicValueObject>	CompositeRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri)
List<CharacteristicValueObject>	CompositeRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri, Map<String,Integer> stringPriorByUri, Map<String,String> matchedTextByUri)
List<CharacteristicValueObject>	LuceneOrderRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri)
List<CharacteristicValueObject>	TokenCoverageRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri)
List<CharacteristicValueObject>	UsageWeightedRankingStrategy.rank(String originalQuery, List<CharacteristicValueObject> rawHits, Map<String,Integer> usageCountsByUri)