Uses of Interface
ubic.gemma.model.common.Identifiable

Packages that use Identifiable

Package	Description
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.search
ubic.gemma.core.search.source
ubic.gemma.model.analysis
ubic.gemma.model.analysis.expression
ubic.gemma.model.analysis.expression.coexpression
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.analysis.expression.pca
ubic.gemma.model.association
ubic.gemma.model.association.coexpression
ubic.gemma.model.association.phenotype
ubic.gemma.model.blacklist
ubic.gemma.model.common
ubic.gemma.model.common.auditAndSecurity
ubic.gemma.model.common.auditAndSecurity.curation
ubic.gemma.model.common.description
ubic.gemma.model.common.measurement
ubic.gemma.model.common.protocol
ubic.gemma.model.common.quantitationtype
ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.designElement
ubic.gemma.model.expression.experiment
ubic.gemma.model.genome
ubic.gemma.model.genome.biosequence
ubic.gemma.model.genome.gene
ubic.gemma.model.genome.gene.phenotype.valueObject
ubic.gemma.model.genome.sequenceAnalysis
ubic.gemma.persistence.service
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.util.args
ubic.gemma.web.controller.expression.arrayDesign
ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.remote

Uses of Identifiable in ubic.gemma.core.loader.expression.arrayDesign

Classes in ubic.gemma.core.loader.expression.arrayDesign that implement Identifiable

Modifier and Type	Class	Description
class	Reporter	A "probe" (Affymetrix); for other types of arrays, there is no practical distinction between compositesequences and reporters, and all analysis would take place at the level of CompositeSequences.

Uses of Identifiable in ubic.gemma.core.search

Classes in ubic.gemma.core.search with type parameters of type Identifiable

Modifier and Type	Class	Description
class	SearchResult<T extends Identifiable>	Represents an individual search result.
class	SearchResultSet<T extends Identifiable>	This is a special kind of set designed for holding SearchResult.

Methods in ubic.gemma.core.search with type parameters of type Identifiable

Modifier and Type	Method	Description
static <T extends Identifiable> List<SearchResultDisplayObject>	SearchResultDisplayObject.convertSearchResults2SearchResultDisplayObjects(List<SearchResult<T>> results)	Creates a collection of SearchResultDisplayObjects from a collection of objects.
static <T extends Identifiable> SearchResult<T>	SearchResult.from(Class<? extends Identifiable> resultType, long entityId, double score, Map<String,String> highlights, Object source)	Create a new provisional search result with a result type and ID.
static <T extends Identifiable> SearchResult<T>	SearchResult.from(Class<? extends Identifiable> resultType, T entity, double score, Map<String,String> highlights, Object source)	Create a search result from a given identifiable entity.
<T extends Identifiable> List<SearchResult<T>>	SearchService.SearchResultMap.getByResultObjectType(Class<T> clazz)	Obtain results where the result object is of a given type, regardless of the result type.
static <T extends Identifiable> boolean	SearchSettingsUtils.isFilled(Collection<SearchResult<T>> results, SearchSettings settings)	Check if a collection of search results is already filled.
<T extends Identifiable,U extends IdentifiableValueObject<T>> SearchResult<U>	SearchService.loadValueObject(SearchResult<T> searchResult)	Convert a SearchResult to its VO flavour.
<T extends Identifiable,U extends IdentifiableValueObject<T>> SearchResult<U>	SearchServiceImpl.loadValueObject(SearchResult<T> searchResult)
<S extends Identifiable> SearchResult<S>	SearchResult.withResultObject(S resultObject)	Create a search result from an existing one, replacing the result object with the target one.

Methods in ubic.gemma.core.search that return types with arguments of type Identifiable

Modifier and Type	Method	Description
Set<Class<? extends Identifiable>>	SearchService.SearchResultMap.getResultTypes()
Set<Class<? extends Identifiable>>	SearchService.getSupportedResultTypes()	Returns a set of supported result types.
Set<Class<? extends Identifiable>>	SearchServiceImpl.getSupportedResultTypes()

Method parameters in ubic.gemma.core.search with type arguments of type Identifiable

Modifier and Type	Method	Description
static <T extends Identifiable> SearchResult<T>	SearchResult.from(Class<? extends Identifiable> resultType, long entityId, double score, Map<String,String> highlights, Object source)	Create a new provisional search result with a result type and ID.
static <T extends Identifiable> SearchResult<T>	SearchResult.from(Class<? extends Identifiable> resultType, T entity, double score, Map<String,String> highlights, Object source)	Create a search result from a given identifiable entity.
List<SearchResult<?>>	SearchService.SearchResultMap.getByResultType(Class<? extends Identifiable> searchResultType)
Set<String>	FieldAwareSearchSource.getFields(Class<? extends Identifiable> entityClass)	Obtain a list of fields that can be searched on.
Set<String>	SearchService.getFields(Class<? extends Identifiable> resultType)	Obtain a list of fields that can be searched on for the given result type.
Set<String>	SearchServiceImpl.getFields(Class<? extends Identifiable> resultType)
void	IndexerService.index(Class<? extends Identifiable> classToIndex)	Index the given class.
void	IndexerServiceImpl.index(Class<? extends Identifiable> classToIndex)

Uses of Identifiable in ubic.gemma.core.search.source

Method parameters in ubic.gemma.core.search.source with type arguments of type Identifiable

Modifier and Type	Method	Description
Set<String>	HibernateSearchSource.getFields(Class<? extends Identifiable> entityClass)

Uses of Identifiable in ubic.gemma.model.analysis

Classes in ubic.gemma.model.analysis that implement Identifiable

Modifier and Type	Class	Description
class	Analysis	An analysis of one or more Investigations.
class	AnalysisResult	Abstract class representing a single result from an Analysis and a typical part of an AnalysisResultSet.
class	AnalysisResultSet<R extends AnalysisResult>	An abstract class representing a related set of generic analysis results, part of an analysis.
class	AnalysisResultSetValueObject<K extends AnalysisResult,R extends AnalysisResultSet<K>>	Exposes an AnalysisResultSet to the public API.
class	AnalysisResultValueObject<A extends AnalysisResult>	Wraps an AnalysisResult to expose it on the public API.
class	AnalysisValueObject<T extends Analysis>
class	Investigation	An abstract concept of a scientific study
class	SingleExperimentAnalysis

Uses of Identifiable in ubic.gemma.model.analysis.expression

Classes in ubic.gemma.model.analysis.expression that implement Identifiable

Modifier and Type	Class	Description
class	ExpressionAnalysis	An analysis of one or more ExpressionExperiments
class	ExpressionExperimentSet	A grouping of expression studies.
class	FactorAssociatedAnalysisResultSet<R extends AnalysisResult>

Uses of Identifiable in ubic.gemma.model.analysis.expression.coexpression

Classes in ubic.gemma.model.analysis.expression.coexpression that implement Identifiable

Modifier and Type	Class	Description
class	CoexpressionAnalysis	A coexpression analysis of one experiment.
class	SampleCoexpressionAnalysis	The 'analysis' in the name is a bit of a stretch here, as this object servers purely as an aggregator of all the sample coexpression matrices.

Uses of Identifiable in ubic.gemma.model.analysis.expression.diff

Classes in ubic.gemma.model.analysis.expression.diff that implement Identifiable

Modifier and Type	Class	Description
class	ContrastResult	Represents a contrast between "conditions".
class	ContrastResultValueObject	Represents a contrast result.
class	DifferentialExpressionAnalysis	An analysis of changes in expression levels across experimental conditions
class	DifferentialExpressionAnalysisResult	Result of an analysis of differences in expression levels -- a single test (e.g., for one gene or one probe), for one factor.
class	DifferentialExpressionAnalysisResultSetValueObject	Wraps an ExpressionAnalysisResultSet and expose it to the public API.
class	DifferentialExpressionAnalysisResultValueObject	Unlike DiffExResultSetSummaryValueObject, this value object is meant for the public API.
class	DifferentialExpressionAnalysisValueObject	Summary of a differential expression analysis
class	ExpressionAnalysisResultSet	A group of results for an ExpressionExperiment.
class	GeneDifferentialExpressionMetaAnalysis	Represents an analysis that combines the results of other analyses of differential expression.

Uses of Identifiable in ubic.gemma.model.analysis.expression.pca

Classes in ubic.gemma.model.analysis.expression.pca that implement Identifiable

Modifier and Type	Class	Description
class	PrincipalComponentAnalysis

Uses of Identifiable in ubic.gemma.model.association

Classes in ubic.gemma.model.association that implement Identifiable

Modifier and Type	Class	Description
class	BioSequence2GeneProduct	An association between a BioSequence and a Gene Product.
class	Gene2GeneAssociation	Entity representing a relationship between two genes.
class	Gene2GOAssociation
class	ReferenceAssociation	An association between a BioSequence and a GeneProduct based on external database identifiers.

Uses of Identifiable in ubic.gemma.model.association.coexpression

Classes in ubic.gemma.model.association.coexpression that implement Identifiable

Modifier and Type	Class	Description
class	GeneCoexpressionNodeDegree	Represents the coexpression node degree for a gene summarized across experiments, at each level of support.

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

Classes in ubic.gemma.model.association.phenotype that implement Identifiable

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

Uses of Identifiable in ubic.gemma.model.blacklist

Classes in ubic.gemma.model.blacklist that implement Identifiable

Modifier and Type	Class	Description
class	BlacklistedEntity
class	BlacklistedExperiment	TODO Document Me
class	BlacklistedPlatform
class	BlacklistedValueObject

Uses of Identifiable in ubic.gemma.model.common

Classes in ubic.gemma.model.common with type parameters of type Identifiable

Modifier and Type	Class	Description
class	IdentifiableValueObject<O extends Identifiable>	Base implementations for value objects representing persistent objects

Subinterfaces of Identifiable in ubic.gemma.model.common

Modifier and Type	Interface	Description
interface	Describable

Classes in ubic.gemma.model.common that implement Identifiable

Modifier and Type	Class	Description
class	AbstractDescribable
class	IdentifiableValueObject<O extends Identifiable>	Base implementations for value objects representing persistent objects

Uses of Identifiable in ubic.gemma.model.common.auditAndSecurity

Subinterfaces of Identifiable in ubic.gemma.model.common.auditAndSecurity

Modifier and Type	Interface	Description
interface	Auditable	Created by tesarst on 07/03/17.
interface	Securable
interface	SecuredChild
interface	SecuredNotChild

Classes in ubic.gemma.model.common.auditAndSecurity that implement Identifiable

Modifier and Type	Class	Description
class	AbstractAuditable	An entity which can have an audit trail attached to it.
class	AuditEvent	An event in the life of an object.
class	AuditEventValueObject
class	AuditTrail	The trail of events (create or update) that occurred in an objects lifetime.
class	Contact	Representing a person or organization that can be contacted about, or is the source of, data in the system.
class	JobInfo
class	Person	Deprecated. not needed
class	User	A user of the software system, who is authenticated.
class	UserGroup	An organized group of researchers with an identifiable leader and group members.
class	UserQuery

Uses of Identifiable in ubic.gemma.model.common.auditAndSecurity.curation

Subinterfaces of Identifiable in ubic.gemma.model.common.auditAndSecurity.curation

Modifier and Type	Interface	Description
interface	Curatable	Created by tesarst on 06/03/17.

Classes in ubic.gemma.model.common.auditAndSecurity.curation that implement Identifiable

Modifier and Type	Class	Description
class	AbstractCuratableValueObject<C extends Curatable>	Created by tesarst on 07/03/17.
class	CurationDetails	Class encapsulating all the curation information for Curatable objects.

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

Classes in ubic.gemma.model.common.description that implement Identifiable

Modifier and Type	Class	Description
class	AnnotationValueObject
class	BibliographicReference
class	BibliographicReferenceValueObject	represents a BibliographicReferenceValueObject when this value object is needed in core, the same value object exists in web
class	Characteristic	Instances of this are used to describe other entities.
class	CharacteristicValueObject	Value object representation of a Characteristic.
class	DatabaseEntry	A reference to a record in a database.
class	DatabaseEntryValueObject	ValueObject for database entry
class	ExternalDatabase
class	ExternalDatabaseValueObject
class	LocalFile	Not a persistent entity

Uses of Identifiable in ubic.gemma.model.common.measurement

Classes in ubic.gemma.model.common.measurement that implement Identifiable

Modifier and Type	Class	Description
class	Measurement
class	MeasurementValueObject
class	Unit

Uses of Identifiable in ubic.gemma.model.common.protocol

Classes in ubic.gemma.model.common.protocol that implement Identifiable

Modifier and Type	Class	Description
class	Protocol

Uses of Identifiable in ubic.gemma.model.common.quantitationtype

Classes in ubic.gemma.model.common.quantitationtype that implement Identifiable

Modifier and Type	Class	Description
class	QuantitationType
class	QuantitationTypeValueObject	Value object for the QuantitationType.

Uses of Identifiable in ubic.gemma.model.expression.arrayDesign

Classes in ubic.gemma.model.expression.arrayDesign that implement Identifiable

Modifier and Type	Class	Description
class	ArrayDesign	Represents an assembly of design elements that are assayed all at once.
class	ArrayDesignValueObject	Value object for quickly displaying varied information about Array Designs.

Uses of Identifiable in ubic.gemma.model.expression.bioAssay

Classes in ubic.gemma.model.expression.bioAssay that implement Identifiable

Modifier and Type	Class	Description
class	BioAssay	Represents the bringing together of a biomaterial with an assay of some sort (typically an expression assay).
class	BioAssayValueObject

Uses of Identifiable in ubic.gemma.model.expression.bioAssayData

Classes in ubic.gemma.model.expression.bioAssayData that implement Identifiable

Modifier and Type	Class	Description
class	BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.
class	BioAssayDimensionValueObject
class	BooleanVectorValueObject	This is used to represent missing value data.
class	DataVector	An abstract class representing a one-dimensional vector of data about some aspect of an experiment.
class	DataVectorValueObject
class	DesignElementDataVector
class	DoubleVectorValueObject	Simple wrapper for a double[] that is derived from a DesignElementDataVector.
class	MeanVarianceRelation
class	ProcessedExpressionDataVector	Represents the processed data that is used for actual analyses.
class	RawExpressionDataVector	Data for one design element, across one or more bioassays, for a single quantitation type.
class	SlicedDoubleVectorValueObject

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

Classes in ubic.gemma.model.expression.biomaterial that implement Identifiable

Modifier and Type	Class	Description
class	BioMaterial	In MAGE, BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc...
class	BioMaterialValueObject
class	Compound
class	Treatment

Uses of Identifiable in ubic.gemma.model.expression.designElement

Classes in ubic.gemma.model.expression.designElement that implement Identifiable

Modifier and Type	Class	Description
class	CompositeSequence	A "Probe set" (Affymetrix) or a "Probe" (other types of arrays).
class	CompositeSequenceValueObject

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

Classes in ubic.gemma.model.expression.experiment that implement Identifiable

Modifier and Type	Class	Description
class	AbstractFactorValueValueObject	The bare minimum to represent a factor value.
class	BioAssaySet	Represents a set of BioAssays.
class	ExperimentalDesign
class	ExperimentalFactor	ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
class	ExperimentalFactorValueObject
class	ExpressionExperiment
class	ExpressionExperimentDetailsValueObject
class	ExpressionExperimentSetValueObject
class	ExpressionExperimentSubSet	A subset of samples from an ExpressionExperiment
class	ExpressionExperimentSubsetValueObject
class	ExpressionExperimentValueObject
class	FactorValue	The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"
class	FactorValueBasicValueObject	Each factorvalue can be associated with multiple characteristics (or with a measurement).
class	FactorValueValueObject	Deprecated. aim towards using the FactorValueBasicValueObject.
class	FreeTextExpressionExperimentResultsValueObject
class	Geeq	Represents quality information about a data set.
class	GeeqAdminValueObject	Represents administrative geeq information.
class	GeeqValueObject	Represents publicly available geeq information
class	SessionBoundExpressionExperimentSetValueObject
class	Statement	A special kind of characteristic that act as a statement.
class	StatementValueObject	Represents a VO for a Statement, typically part of a FactorValueBasicValueObject.

Uses of Identifiable in ubic.gemma.model.genome

Classes in ubic.gemma.model.genome that implement Identifiable

Modifier and Type	Class	Description
class	Chromosome	Immutable representation of a chromosome
class	ChromosomeFeature	Some part of a chromosome
class	ChromosomeLocation
class	Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
class	PhysicalLocation
class	PhysicalLocationValueObject	A very simple value object to represent a physical location
class	Taxon
class	TaxonValueObject

Uses of Identifiable in ubic.gemma.model.genome.biosequence

Classes in ubic.gemma.model.genome.biosequence that implement Identifiable

Modifier and Type	Class	Description
class	BioSequence	The sequence of a biological polymer such as a protein or DNA.

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

Classes in ubic.gemma.model.genome.gene that implement Identifiable

Modifier and Type	Class	Description
class	DatabaseBackedGeneSetValueObject
class	FreeTextGeneResultsValueObject	*
class	GeneAlias
class	GeneProduct
class	GeneProductValueObject
class	GeneSet	A grouping of genes that share a common relationship
class	GeneSetMember
class	GeneSetValueObject	Represents a Gene group gene set
class	GeneValueObject
class	GOGroupValueObject
class	PhenotypeGroupValueObject
class	SessionBoundGeneSetValueObject

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

Classes in ubic.gemma.model.genome.gene.phenotype.valueObject that implement Identifiable

Modifier and Type	Class	Description
class	DiffExpressionEvidenceValueObject
class	EvidenceSourceValueObject
class	EvidenceValueObject<E extends PhenotypeAssociation>	Parent class of all evidence value objects
class	ExperimentalEvidenceValueObject	Deprecated.
class	GeneEvidenceValueObject	Deprecated.
class	GenericEvidenceValueObject
class	LiteratureEvidenceValueObject
class	TreeCharacteristicValueObject

Uses of Identifiable in ubic.gemma.model.genome.sequenceAnalysis

Classes in ubic.gemma.model.genome.sequenceAnalysis that implement Identifiable

Modifier and Type	Class	Description
class	AnnotationAssociation	An association between BioSequence and GeneProduct that is provided through an external annotation source, rather than our own sequence analysis.
class	BioSequenceValueObject
class	BlatAssociation
class	BlatResult	Represents the result of a BLAT search.
class	BlatResultValueObject
class	SequenceSimilaritySearchResult

Uses of Identifiable in ubic.gemma.persistence.service

Classes in ubic.gemma.persistence.service with type parameters of type Identifiable

Modifier and Type	Class	Description
class	AbstractCriteriaFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Partial implementation of FilteringVoEnabledDao based on the Hibernate Criteria API.
class	AbstractDao<T extends Identifiable>	AbstractDao can find the generic type at runtime and simplify the code implementation of the BaseDao interface
class	AbstractFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Base implementation for FilteringVoEnabledDao.
class	AbstractFilteringVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Base implementation for FilteringVoEnabledService.
class	AbstractNoopFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Base class to use to pretend to offer filtering, but actually supporting no filterable properties.
class	AbstractQueryFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Partial implementation of FilteringVoEnabledDao based on the Hibernate Query API.
class	AbstractService<O extends Identifiable>	Base for all services handling DAO access.
class	AbstractVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Created by tesarst on 01/06/17.
class	AbstractVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Created by tesarst on 01/06/17.
interface	BaseImmutableService<O extends Identifiable>	Base service class for an immutable entity.
interface	BaseReadOnlyService<O extends Identifiable>	Interface for read-only services.
interface	BaseService<O extends Identifiable>	Interface that supports basic CRUD operations.
interface	BaseVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Created by tesarst on 01/06/17.
interface	BaseVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Created by tesarst on 01/06/17.
interface	CachedFilteringDao<O extends Identifiable>
interface	CachedFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>
interface	FilteringDao<O extends Identifiable>	Interface for filtering-capable DAO.
interface	FilteringService<O extends Identifiable>	Interface for filtering-capable services.
interface	FilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Interface for VO-enabled DAO with filtering capabilities.
interface	FilteringVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Interface VO-enabled service with filtering capabilities.

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

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

Modifier and Type	Method	Description
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicDao.findExperimentReferencesByUris(Collection<String> uris, Taxon taxon, int limit, boolean rankByLevel)	Similar to CharacteristicDao.findExperimentsByUris(Collection, Taxon, int, boolean), but returns proxies with instead of initializing all the EEs in bulk.
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicDaoImpl.findExperimentReferencesByUris(Collection<String> uris, Taxon taxon, int limit, boolean rankByLevel)	Since proxies are returned, they cannot be collected in a HashSet which would otherwise cause their initialization by accessing Object.hashCode().
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicDao.findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean rankByLevel)	This search looks at direct annotations, factor values and biomaterials in that order.
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicDaoImpl.findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean rankByLevel)
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicService.findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicServiceImpl.findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
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 Identifiable in ubic.gemma.persistence.service.expression.experiment

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

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)

Method parameters in ubic.gemma.persistence.service.expression.experiment with type arguments of type Identifiable

Modifier and Type	Method	Description
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.

Uses of Identifiable in ubic.gemma.persistence.util

Classes in ubic.gemma.persistence.util with type parameters of type Identifiable

Modifier and Type	Class	Description
class	ServiceBasedEntityConverter<O extends Identifiable>	Performs conversion by identifier and collection of identifier for a BaseReadOnlyService.
class	ServiceBasedValueObjectConverter<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Perform conversion to value object by entity, ID and collections of entities and IDs and also to entity by ID and collection of IDs.

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

Modifier and Type	Method	Description
static <T extends Identifiable> List<List<T>>	QueryUtils.batchIdentifiableParameterList(Collection<T> list, int batchSize)
static <T extends Identifiable> Map<Long,T>	EntityUtils.getIdMap(Collection<T> entities)	Given a set of entities, create a map of their ids to the entities.
static <T extends Identifiable> List<Long>	EntityUtils.getIds(Collection<T> entities)
static <S extends Identifiable,T> List<T>	QueryUtils.listByIdentifiableBatch(Query query, String batchParam, Collection<S> list, int batchSize)
static <S extends Identifiable,T> List<T>	QueryUtils.listByIdentifiableBatch(Query query, String batchParam, Collection<S> list, int batchSize, int maxResults)
static <T extends Identifiable> Collection<T>	QueryUtils.optimizeIdentifiableParameterList(Collection<T> list)	Optimize a collection of Identifiable entities.
static <T,K extends Identifiable,U> Collector<T,?,Map<K,U>>	IdentifiableUtils.toIdentifiableMap(Function<? super T,? extends K> keyMapper, Function<? super T,? extends U> valueMapper)	Collect results into an identifiable map.
static <T extends Identifiable> Collector<T,?,Set<T>>	IdentifiableUtils.toIdentifiableSet()	Collect results into an identifiable set.
static <T extends Identifiable> String	IdentifiableUtils.toString(T identifiable, Class<T> clazz)	Converts an identifiable to string, avoiding its initialization of it is a proxy.

Uses of Identifiable in ubic.gemma.rest

Classes in ubic.gemma.rest that implement Identifiable

Modifier and Type	Class	Description
static class	DatasetsWebService.AnnotationWithUsageStatisticsValueObject	This is an aggregated entity across value URI and value, thus the id and objectClass are omitted.
static class	DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject
static class	DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject
static class	DatasetsWebService.ExpressionExperimentWithSearchResultValueObject
static class	DatasetsWebService.TaxonWithUsageStatisticsValueObject

Uses of Identifiable in ubic.gemma.rest.util.args

Classes in ubic.gemma.rest.util.args with type parameters of type Identifiable

Modifier and Type	Class	Description
class	AbstractEntityArg<T,O extends Identifiable,S extends FilteringService<O>>	Interface representing and API call argument that can represent various identifiers of different types.
class	AbstractEntityArgService<T extends Identifiable,S extends FilteringService<T>>
class	AbstractEntityArrayArg<O extends Identifiable,S extends FilteringService<O>>
interface	EntityArgService<T extends Identifiable,S extends FilteringService<T>>	Bridges Arg operating on entities with their corresponding FilteringService.
class	FilterArg<O extends Identifiable>	Represent a filter argument designed to generate a Filters from user input.
class	SortArg<O extends Identifiable>	Represents an API argument for sorting.

Methods in ubic.gemma.rest.util.args with type parameters of type Identifiable

Modifier and Type	Method	Description
static <O extends Identifiable> FilterArg<O>	FilterArg.valueOf(String s)	Used by RS to parse value of request parameters.
static <T extends Identifiable> SortArg<T>	SortArg.valueOf(String s)	Used by RS to parse value of request parameters.

Uses of Identifiable in ubic.gemma.web.controller.expression.arrayDesign

Classes in ubic.gemma.web.controller.expression.arrayDesign that implement Identifiable

Modifier and Type	Class	Description
class	ArrayDesignValueObjectExt	Extended value object to carry more data to client.

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

Classes in ubic.gemma.web.controller.expression.experiment that implement Identifiable

Modifier and Type	Class	Description
class	ExperimentalFactorValueWebUIObject
class	ExpressionExperimentEditValueObject

Uses of Identifiable in ubic.gemma.web.remote

Classes in ubic.gemma.web.remote with type parameters of type Identifiable

Modifier and Type	Class	Description
class	EntityDelegator<T extends Identifiable>	Bean to expose for remote access via AJAX, when all that is needed is the ID and a way to know what the class is.