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

Packages that use Characteristic

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.association.phenotype
ubic.gemma.core.loader.expression.geo.model
ubic.gemma.core.ontology.providers
ubic.gemma.model.analysis
ubic.gemma.model.association
ubic.gemma.model.association.phenotype
ubic.gemma.model.common.description
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment
ubic.gemma.model.genome.gene
ubic.gemma.persistence.service.association
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.expression.biomaterial
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.web.controller.expression.experiment

Uses of Characteristic in ubic.gemma.core.analysis.expression.diff

Methods in ubic.gemma.core.analysis.expression.diff with parameters of type Characteristic

Modifier and Type	Method	Description
static boolean	BaselineSelection.isBaselineCondition(Characteristic c)	Check if a given characteristic indicate a baseline condition.

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

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

Modifier and Type	Method	Description
Characteristic	PhenotypeAssoOntologyHelper.characteristicValueObject2Characteristic(CharacteristicValueObject characteristicValueObject)	Deprecated. CharacteristicValueObject to Characteristic with no valueUri given
Characteristic	PhenotypeAssoOntologyHelperImpl.characteristicValueObject2Characteristic(CharacteristicValueObject characteristicValueObject)	Deprecated.
Characteristic	PhenotypeAssoOntologyHelper.valueUri2Characteristic(String valueUri)	Deprecated. Helper method.
Characteristic	PhenotypeAssoOntologyHelperImpl.valueUri2Characteristic(String valueUri)	Deprecated.

Uses of Characteristic in ubic.gemma.core.loader.expression.geo.model

Methods in ubic.gemma.core.loader.expression.geo.model that return Characteristic

Modifier and Type	Method	Description
Characteristic	GeoChannel.getMoleculeAsCharacteristic()	Convert the molecule into a MGED Ontology-based MaterialType Characteristic.

Uses of Characteristic in ubic.gemma.core.ontology.providers

Methods in ubic.gemma.core.ontology.providers with parameters of type Characteristic

Modifier and Type	Method	Description
static String	GeneOntologyUtils.asRegularGoId(Characteristic c)	Convert a characteristic to a regular GO ID.
GeneOntologyServiceImpl.GOAspect	GeneOntologyService.getTermAspect(Characteristic goId)
GeneOntologyServiceImpl.GOAspect	GeneOntologyServiceImpl.getTermAspect(Characteristic goId)

Uses of Characteristic in ubic.gemma.model.analysis

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

Modifier and Type	Method	Description
Set<Characteristic>	Investigation.getCharacteristics()

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

Modifier and Type	Method	Description
void	Investigation.setCharacteristics(Set<Characteristic> characteristics)

Uses of Characteristic in ubic.gemma.model.association

Methods in ubic.gemma.model.association that return Characteristic

Modifier and Type	Method	Description
Characteristic	Gene2GOAssociation.getOntologyEntry()

Methods in ubic.gemma.model.association with parameters of type Characteristic

Modifier and Type	Method	Description
static Gene2GOAssociation	Gene2GOAssociation.Factory.newInstance(Gene gene, Characteristic ontologyEntry, GOEvidenceCode evidenceCode)

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

Methods in ubic.gemma.model.association.phenotype that return Characteristic

Modifier and Type	Method	Description
Characteristic	PhenotypeAssociation.getAssociationType()	Deprecated.

Methods in ubic.gemma.model.association.phenotype that return types with arguments of type Characteristic

Modifier and Type	Method	Description
Set<Characteristic>	PhenotypeAssociation.getPhenotypes()	Deprecated.

Methods in ubic.gemma.model.association.phenotype with parameters of type Characteristic

Modifier and Type	Method	Description
void	PhenotypeAssociation.setAssociationType(Characteristic associationType)	Deprecated.

Method parameters in ubic.gemma.model.association.phenotype with type arguments of type Characteristic

Modifier and Type	Method	Description
void	PhenotypeAssociation.setPhenotypes(Set<Characteristic> phenotypes)	Deprecated.

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

Methods in ubic.gemma.model.common.description that return Characteristic

Modifier and Type	Method	Description
static Characteristic	CharacteristicUtils.getCategory(Characteristic t)	Create a new characteristic that represents the category of a given characteristic.
static Characteristic	Characteristic.Factory.newInstance()
static Characteristic	Characteristic.Factory.newInstance(String name, String description, String value, String valueUri, String category, String categoryUri, GOEvidenceCode evidenceCode)

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

Modifier and Type	Method	Description
Set<Characteristic>	BibliographicReference.getAnnotations()	Deprecated.
static Comparator<Characteristic>	Characteristic.getByCategoryAndValueComparator()	Obtain a comparator to order terms by value URI (or value if null) in a case-insensitive manner.
static Comparator<Characteristic>	Characteristic.getByCategoryComparator()	Obtain a comparator to compare terms by category URI (or category if null) in a case-insensitive manner.
static Comparator<Characteristic>	Characteristic.getComparator()	Obtain a full comparator for characteristics that fallbacks on the ID if everything else is equal.

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

Modifier and Type	Method	Description
int	Characteristic.compareTo(Characteristic characteristic)
static Characteristic	CharacteristicUtils.getCategory(Characteristic t)	Create a new characteristic that represents the category of a given characteristic.
static boolean	CharacteristicUtils.isFreeText(Characteristic c)	Check if the given characteristic is a free-text value.
static boolean	CharacteristicUtils.isFreeTextCategory(Characteristic c)	Check if the given characteristic has or is a free-text category.
static boolean	CharacteristicUtils.isUncategorized(Characteristic c)	Check if the given characteristic is uncategorized.

Method parameters in ubic.gemma.model.common.description with type arguments of type Characteristic

Modifier and Type	Method	Description
static Collection<CharacteristicValueObject>	CharacteristicValueObject.characteristic2CharacteristicVO(Collection<? extends Characteristic> characteristics)
void	BibliographicReference.setAnnotations(Set<Characteristic> annotations)	Deprecated.

Constructors in ubic.gemma.model.common.description with parameters of type Characteristic

Constructor	Description
AnnotationValueObject(Characteristic c)
AnnotationValueObject(Characteristic c, Class<?> objectClass)
CharacteristicValueObject(Characteristic characteristic)

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

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

Modifier and Type	Method	Description
Set<Characteristic>	BioMaterial.getCharacteristics()

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

Modifier and Type	Method	Description
void	BioMaterial.setCharacteristics(Set<Characteristic> characteristics)

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

Subclasses of Characteristic in ubic.gemma.model.expression.experiment

Modifier and Type	Class	Description
class	Statement	A special kind of characteristic that act as a statement.

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

Modifier and Type	Method	Description
Characteristic	ExperimentalFactor.getCategory()	Obtain the category of this experimental factor.

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

Modifier and Type	Method	Description
Set<Characteristic>	ExpressionExperiment.getAllCharacteristics()	Obtain all characteristics associated to this EE.
Set<Characteristic>	ExperimentalFactor.getAnnotations()	Deprecated.
Set<Characteristic>	ExpressionExperiment.getCharacteristics()
Set<Characteristic>	FactorValue.getOldStyleCharacteristics()	Deprecated.
Set<Characteristic>	ExperimentalDesign.getTypes()

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

Modifier and Type	Method	Description
int	Statement.compareTo(Characteristic characteristic)
static boolean	ExperimentalDesignUtils.isBatch(Characteristic category)
void	ExperimentalFactor.setCategory(Characteristic category)

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

Modifier and Type	Method	Description
void	ExpressionExperiment.setAllCharacteristics(Set<Characteristic> allCharacteristics)
void	ExperimentalFactor.setAnnotations(Set<Characteristic> annotations)	Deprecated.
void	FactorValue.setOldStyleCharacteristics(Set<Characteristic> oldCharacteristics)	Deprecated.
void	ExperimentalDesign.setTypes(Set<Characteristic> types)

Uses of Characteristic in ubic.gemma.model.genome.gene

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

Modifier and Type	Method	Description
Set<Characteristic>	GeneSet.getCharacteristics()

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

Modifier and Type	Method	Description
void	GeneSet.setCharacteristics(Set<Characteristic> characteristics)

Uses of Characteristic in ubic.gemma.persistence.service.association

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

Modifier and Type	Method	Description
Collection<Characteristic>	Gene2GOAssociationDao.findByGene(Gene gene)
Collection<Characteristic>	Gene2GOAssociationDaoImpl.findByGene(Gene gene)
Collection<Characteristic>	Gene2GOAssociationService.findByGene(Gene gene)
Collection<Characteristic>	Gene2GOAssociationServiceImpl.findByGene(Gene gene)
Map<Gene,Collection<Characteristic>>	Gene2GOAssociationDao.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<Characteristic>>	Gene2GOAssociationDaoImpl.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<Characteristic>>	Gene2GOAssociationService.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<Characteristic>>	Gene2GOAssociationServiceImpl.findByGenes(Collection<Gene> genes)

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

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

Modifier and Type	Method	Description
Characteristic	CharacteristicService.create(Characteristic c)
Characteristic	CharacteristicDao.findBestByUri(String uri)	Return the characteristic with the most frequently used non-null value by URI.
Characteristic	CharacteristicDaoImpl.findBestByUri(String uri)
Characteristic	CharacteristicService.findBestByUri(String uri)	Find the best possible characteristic for a given URI.
Characteristic	CharacteristicServiceImpl.findBestByUri(String uri)

Methods in ubic.gemma.persistence.service.common.description that return types with arguments of type Characteristic

Modifier and Type	Method	Description
List<Characteristic>	CharacteristicDao.browse(int start, int limit)	Browse through the characteristics, excluding GO annotations.
List<Characteristic>	CharacteristicDao.browse(int start, int limit, String sortField, boolean descending)	Browse through the characteristics, excluding GO annotations, with sorting.
List<Characteristic>	CharacteristicDaoImpl.browse(int start, int limit)
List<Characteristic>	CharacteristicDaoImpl.browse(int start, int limit, String orderField, boolean descending)
List<Characteristic>	CharacteristicService.browse(int start, int limit)	Browse through the characteristics, excluding GO annotations.
List<Characteristic>	CharacteristicService.browse(int start, int limit, String sortField, boolean descending)	Browse through the characteristics, excluding GO annotations.
List<Characteristic>	CharacteristicServiceImpl.browse(int start, int limit)
List<Characteristic>	CharacteristicServiceImpl.browse(int start, int limit, String sortField, boolean descending)
Collection<? extends Characteristic>	CharacteristicService.findByAnyUri(String uri)	Find a characteristic or statement by any URI it contains including its category, value, predicates and objects.
Collection<? extends Characteristic>	CharacteristicServiceImpl.findByAnyUri(String uri)
Collection<? extends Characteristic>	CharacteristicService.findByAnyValue(String value)	Find a characteristic by any value it contains including its category, value, predicates and objects.
Collection<? extends Characteristic>	CharacteristicServiceImpl.findByAnyValue(String value)
Collection<? extends Characteristic>	CharacteristicService.findByAnyValueStartingWith(String value)	Find a characteristic by any value it contains including its category, value, predicates and objects that starts with the given query.
Collection<? extends Characteristic>	CharacteristicServiceImpl.findByAnyValueStartingWith(String value)
Collection<Characteristic>	CharacteristicDao.findByCategory(String value)
Collection<Characteristic>	CharacteristicDaoImpl.findByCategory(String value)
Collection<Characteristic>	CharacteristicDao.findByCategoryLike(String query)
Collection<Characteristic>	CharacteristicDaoImpl.findByCategoryLike(String query)
Collection<Characteristic>	CharacteristicService.findByCategoryStartingWith(String queryPrefix)
Collection<Characteristic>	CharacteristicServiceImpl.findByCategoryStartingWith(String query)
Collection<Characteristic>	CharacteristicDao.findByCategoryUri(String uri)
Collection<Characteristic>	CharacteristicDaoImpl.findByCategoryUri(String uri)
Collection<Characteristic>	CharacteristicService.findByCategoryUri(String query)
Collection<Characteristic>	CharacteristicServiceImpl.findByCategoryUri(String query)
Collection<Characteristic>	CharacteristicDao.findByUri(String searchString)
Collection<Characteristic>	CharacteristicDao.findByUri(Collection<String> uris)
Collection<Characteristic>	CharacteristicDaoImpl.findByUri(String uri)
Collection<Characteristic>	CharacteristicDaoImpl.findByUri(Collection<String> uris)
Collection<Characteristic>	CharacteristicService.findByUri(String searchString)	Looks for an exact match of the give string to a valueUri in the characteristic database
Collection<Characteristic>	CharacteristicService.findByUri(Collection<String> uris)	given a collection of strings that represent URI's will find all the characteristics that are used in the system with URI's matching anyone in the given collection
Collection<Characteristic>	CharacteristicServiceImpl.findByUri(String searchString)
Collection<Characteristic>	CharacteristicServiceImpl.findByUri(Collection<String> uris)
Collection<Characteristic>	CharacteristicDao.findByValue(String search)
Collection<Characteristic>	CharacteristicDaoImpl.findByValue(String value)
Collection<Characteristic>	CharacteristicDao.findByValueLike(String search)	Finds all Characteristics whose value match the given search term
Collection<Characteristic>	CharacteristicDaoImpl.findByValueLike(String search)
Collection<Characteristic>	CharacteristicService.findByValueLike(String search)	Returns a collection of characteristics that have a value matching the given SQL LIKE pattern.
Collection<Characteristic>	CharacteristicServiceImpl.findByValueLike(String search)
Map<String,Characteristic>	CharacteristicDao.findByValueLikeGroupedByNormalizedValue(String valueLike, Collection<Class<?>> parentClasses)	Find characteristics by value matching the provided LIKE pattern.
Map<String,Characteristic>	CharacteristicDaoImpl.findByValueLikeGroupedByNormalizedValue(String valueLike, Collection<Class<?>> parentClasses)
Collection<Characteristic>	CharacteristicService.findByValueStartingWith(String search)	Returns a collection of characteristics that have a value starting with the given string.
Collection<Characteristic>	CharacteristicServiceImpl.findByValueStartingWith(String search)
Map<String,Characteristic>	CharacteristicDao.findByValueUriGroupedByNormalizedValue(String valueUri, Collection<Class<?>> parentClasses)	Find characteristics by URI.
Map<String,Characteristic>	CharacteristicDaoImpl.findByValueUriGroupedByNormalizedValue(String valueUri, Collection<Class<?>> parentClasses)
Map<String,Characteristic>	CharacteristicService.findByValueUriOrValueLike(String search, Collection<Class<?>> parentClasses)
Map<String,Characteristic>	CharacteristicServiceImpl.findByValueUriOrValueLike(String search, Collection<Class<?>> parentClasses)
Map<Characteristic,Identifiable>	CharacteristicDao.getParents(Collection<Characteristic> characteristics, Collection<Class<?>> parentClasses, int maxResults)	Obtain the parents (i.e.
Map<Characteristic,Identifiable>	CharacteristicDaoImpl.getParents(Collection<Characteristic> characteristics, Collection<Class<?>> parentClasses, int maxResults)
Map<Characteristic,Identifiable>	CharacteristicService.getParents(Collection<Characteristic> characteristics, Collection<Class<?>> parentClasses, int maxResults)
Map<Characteristic,Identifiable>	CharacteristicServiceImpl.getParents(Collection<Characteristic> characteristics, Collection<Class<?>> parentClasses, int maxResults)

Methods in ubic.gemma.persistence.service.common.description with parameters of type Characteristic

Modifier and Type	Method	Description
Characteristic	CharacteristicService.create(Characteristic c)
protected CharacteristicValueObject	CharacteristicDaoImpl.doLoadValueObject(Characteristic entity)
String	CharacteristicDao.normalizeByValue(Characteristic characteristic)	Normalize a characteristic by value.
String	CharacteristicDaoImpl.normalizeByValue(Characteristic characteristic)
void	CharacteristicService.remove(Characteristic c)

Method parameters in ubic.gemma.persistence.service.common.description with type arguments of type Characteristic

Modifier and Type	Method	Description
Map<Characteristic,Identifiable>	CharacteristicDao.getParents(Collection<Characteristic> characteristics, Collection<Class<?>> parentClasses, int maxResults)	Obtain the parents (i.e.
Map<Characteristic,Identifiable>	CharacteristicDaoImpl.getParents(Collection<Characteristic> characteristics, Collection<Class<?>> parentClasses, int maxResults)
Map<Characteristic,Identifiable>	CharacteristicService.getParents(Collection<Characteristic> characteristics, Collection<Class<?>> parentClasses, int maxResults)
Map<Characteristic,Identifiable>	CharacteristicServiceImpl.getParents(Collection<Characteristic> characteristics, Collection<Class<?>> parentClasses, int maxResults)

Uses of Characteristic in ubic.gemma.persistence.service.expression.biomaterial

Methods in ubic.gemma.persistence.service.expression.biomaterial with parameters of type Characteristic

Modifier and Type	Method	Description
void	BioMaterialService.addCharacteristic(BioMaterial bm, Characteristic vc)	Will persist the give vocab characteristic to the given biomaterial
void	BioMaterialServiceImpl.addCharacteristic(BioMaterial bm, Characteristic vc)
void	BioMaterialService.removeCharacteristic(BioMaterial bm, Characteristic vc)	Remove the given characteristic from the given biomaterial
void	BioMaterialServiceImpl.removeCharacteristic(BioMaterial bm, Characteristic characterId)

Uses of Characteristic in ubic.gemma.persistence.service.expression.experiment

Methods in ubic.gemma.persistence.service.expression.experiment that return types with arguments of type Characteristic

Modifier and Type	Method	Description
Map<Class<? extends Identifiable>,List<Characteristic>>	ExpressionExperimentDao.getAllAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)	Obtain all annotations, grouped by applicable level.
Map<Class<? extends Identifiable>,List<Characteristic>>	ExpressionExperimentDaoImpl.getAllAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)
Map<Characteristic,Long>	ExpressionExperimentDao.getAnnotationsUsageFrequency(Collection<Long> expressionExperimentIds, Class<? extends Identifiable> level, int maxResults, int minFrequency, String category, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris)	Obtain annotations usage frequency for a set of given ExpressionExperiment IDs.
Map<Characteristic,Long>	ExpressionExperimentDaoImpl.getAnnotationsUsageFrequency(Collection<Long> eeIds, Class<? extends Identifiable> level, int maxResults, int minFrequency, String category, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris)	We're making two assumptions: a dataset cannot have a characteristic more than once and a dataset cannot have the same characteristic at multiple levels to make counting more efficient.
List<Characteristic>	ExpressionExperimentDao.getBioMaterialAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)	Obtain sample-level annotations.
List<Characteristic>	ExpressionExperimentDaoImpl.getBioMaterialAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)
Map<Characteristic,Long>	ExpressionExperimentDao.getCategoriesUsageFrequency(Collection<Long> eeIds, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, int maxResults)
Map<Characteristic,Long>	ExpressionExperimentDaoImpl.getCategoriesUsageFrequency(Collection<Long> eeIds, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, int maxResults)
Map<Characteristic,Long>	ExpressionExperimentService.getCategoriesUsageFrequency(Filters filters, Set<Long> extraIds, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, int maxResults)	Obtain category usage frequency for datasets matching the given filter.
Map<Characteristic,Long>	ExpressionExperimentServiceImpl.getCategoriesUsageFrequency(Filters filters, Set<Long> extraIds, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, int maxResults)
List<Characteristic>	ExpressionExperimentDao.getExperimentalDesignAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)	Obtain experimental design-level annotations.
List<Characteristic>	ExpressionExperimentDaoImpl.getExperimentalDesignAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)
Collection<Characteristic>	ExpressionExperimentDao.getExperimentAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)	Obtain experiment-level annotations.
List<Characteristic>	ExpressionExperimentDaoImpl.getExperimentAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type Characteristic

Modifier and Type	Method	Description
void	ExpressionExperimentService.addCharacteristic(ExpressionExperiment ee, Characteristic vc)	Will add the vocab characteristic to the expression experiment and persist the changes.
void	ExpressionExperimentServiceImpl.addCharacteristic(ExpressionExperiment ee, Characteristic vc)	Will add the characteristic to the expression experiment and persist the changes.

Uses of Characteristic in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util with parameters of type Characteristic

Modifier and Type	Method	Description
static void	BusinessKey.attachCriteria(Criteria queryObject, Characteristic ontologyEntry, String propertyName)	Restricts the query to the provided OntologyEntry.
static void	BusinessKey.checkKey(Characteristic ontologyEntry)
static Conjunction	BusinessKey.createCharacteristicRestriction(Characteristic characteristic)
static Criteria	BusinessKey.createQueryObject(Session session, Characteristic ontologyEntry)

Uses of Characteristic in ubic.gemma.rest

Constructors in ubic.gemma.rest with parameters of type Characteristic

Constructor	Description
AnnotationWithUsageStatisticsValueObject(Characteristic c, Long numberOfExpressionExperiments, Set<DatasetsWebService.OntologyTermValueObject> parentTerms)

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

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

Modifier and Type	Method	Description
void	AnnotationController.createBiomaterialTag(Characteristic vc, Long id)
void	AnnotationController.createExperimentTag(Characteristic vc, Long id)	Ajax
void	AnnotationController.removeBiomaterialTag(Characteristic vc, Long id)