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

Packages that use Identifiable

Package	Description
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.util.mapper	Utilities for mapping Identifiable entities to external identifiers.
ubic.gemma.core.search
ubic.gemma.core.search.source
ubic.gemma.core.tasks	This package contains task definitions.
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.blacklist
ubic.gemma.model.common
ubic.gemma.model.common.auditAndSecurity
ubic.gemma.model.common.auditAndSecurity.curation
ubic.gemma.model.common.auditAndSecurity.eventType
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.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
ubic.gemma.web.taglib

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.loader.util.mapper

Classes in ubic.gemma.core.loader.util.mapper with type parameters of type Identifiable

Modifier and Type	Class	Description
class	ChainedEntityMapper<T extends Identifiable>	Implementation of a chain of entity mappers.
interface	EntityMapper<T extends Identifiable>	Map external identifiers to Gemma entities.
static interface	EntityMapper.StatefulEntityMapper<T extends Identifiable>	A stateful entity mapper keeps an internal state for a set of candidates to optimize the mapping process.
interface	HintingEntityMapper<T extends Identifiable>	Interface for mappers that can provide hints of identifier candidates.
class	MapBasedEntityMapper<T extends Identifiable>	A simple implementation of EntityMapper that uses a Map to store association between identifiers and entities.

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.core.tasks

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

Modifier and Type	Class	Description
class	EntityTaskCommand<T extends Identifiable>	A simple task command that contains an entity ID and class.

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	CellTypeAssignmentValueObject
class	Investigation	An abstract concept of a scientific study
class	ProtocolValueObject
class	SingleExperimentAnalysis	An analysis of a single experiment or subset.

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.
class	SampleCoexpressionMatrix	Holds the data of the sample coexpression matrix

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.
class	GeneDifferentialExpressionMetaAnalysisResult
class	HitListSize	The number of probes meeting a given q-value threshold in the result set.
class	PvalueDistribution

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	Eigenvalue
class	Eigenvector	A right singular vector (a.k.a. eigengenes)
class	PrincipalComponentAnalysis
class	ProbeLoading	Only stored for some of the probes (e.g. the top ones)

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.blacklist

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

Modifier and Type	Class	Description
class	BlacklistedEntity	Represents a blacklisted entity that should not be loaded into Gemma.
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	AbstractIdentifiable	Base class for identifiable entities.
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	GroupAuthority	Authority for groups (kind of like a "user role", but for group-based authorization)
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.

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.auditAndSecurity.eventType

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

Modifier and Type	Class	Description
class	AlignmentBasedGeneMappingEvent	Signifies a mapping based on sequence alignment performed by the system.
class	AnalysisSuitabilityEvent	Used for indication of the suitability, or unsuitability, of an entity for a particular type of analysis.
class	AnnotationBasedGeneMappingEvent	To signify the array design was mapped from an external source, not by our own sequence analysis.
class	AnnotationEvent
class	ArrayDesignAnalysisEvent	An event involving the analysis of an ArrayDesign
class	ArrayDesignGeneMappingEvent	The mapping of probes to genes for an ArrayDesign
class	ArrayDesignMergeEvent
class	ArrayDesignProbeRenamingEvent	Signifies that the probes were renamed from their original values.
class	ArrayDesignRepeatAnalysisEvent
class	ArrayDesignSequenceAnalysisEvent	The sequence alignment analysis of an ArrayDesign
class	ArrayDesignSequenceRemoveEvent	Used to indicate that all associations that this array design has with BioSequences have been removed.
class	ArrayDesignSequenceUpdateEvent	The updating of the sequences associated with an ArrayDesign
class	ArrayDesignSubsumeCheckEvent
class	AuditEventType
class	AutomatedAnnotationEvent	Deprecated. this event type was used by the auto-tagger, which has been removed.
class	BatchCorrectionEvent
class	BatchInformationEvent	Abstract class for events related to batch information.
class	BatchInformationFetchingEvent	Indicates that batch information was successfully obtained.
class	BatchInformationMissingEvent	Indicate that batch information has been looked for and was missing.
class	BatchProblemsUpdateEvent	Event that tracks when batch effects or problems are detected.
class	BioMaterialMappingUpdate	Indicates that the biomaterial to bioassay mapping of the expression experiment was modified.
class	CellLevelCharacteristicsAddedEvent	Event emitted when a cell-level characteristics is removed.
class	CellLevelCharacteristicsEvent	Event emitted when a cell-level characteristics is modified (either added or removed).
class	CellLevelCharacteristicsRemovedEvent	Event emitted when a cell-level characteristics is removed.
class	CellTypeAssignmentAddedEvent	Event emitted when a CellTypeAssignmentEvent is added.
class	CellTypeAssignmentEvent	Event emitted when a cell type assignment is modified (either added or removed).
class	CellTypeAssignmentRemovedEvent	Event emitted when a CellTypeAssignmentEvent is removed.
class	CommentedEvent	An event indicating a comment was added to the auditable.
class	CurationDetailsEvent	Event types that can change CurationDetails of Curatable objects.
class	CurationNoteUpdateEvent	Indicates that previous validation is being invalidated
class	DataAddedEvent	Indicates that a data type (for a specific QuantitationType, possibly new) was added.
class	DataRemovedEvent	Indicates that a data type (for a specific QuantitationType, possibly new) was removed.
class	DataReplacedEvent	Signifies that the data for the experiment was replaced (or filled in) after the experiment was loaded into the system.
class	DifferentialExpressionAnalysisEvent	Indicates the experiment was the subject of a differential expression analysis.
class	DifferentialExpressionSuitabilityEvent	Used to indicate the suitability status of an ExpressionExperiment for differential expression analysis.
class	DoesNotNeedAttentionEvent	An event that occurs when a curator has validated the entity and indicated that it is "approved".
class	ExperimentalDesignUpdatedEvent	Describes an event that involved a change of assignment of factor value to bio material, or other changes in the experimental design.
class	ExpressionExperimentAnalysisEvent	An event involving an ExpressionExperiment
class	ExpressionExperimentPlatformSwitchEvent	The event that this experiment has had its array design switched (typically to a 'merged' one.
class	ExpressionExperimentUpdateFromGEOEvent	Indicates that we have updated an expression experiment's information from GEO, after it was already loaded in Gemma.
class	ExpressionExperimentVectorMergeEvent	Indicates that the "Vector merging" has been done on the associated experiment.
class	FactorValueNeedsAttentionEvent	Indicates that a factor value needs attention.
class	FailedBatchInformationFetchingEvent	Indicates that the attempt to get batch information failed due to an error.
class	FailedBatchInformationMissingEvent	Deprecated. use BatchInformationMissingEvent
class	FailedDataReplacedEvent	Represents a failed data replace.
class	FailedDifferentialExpressionAnalysisEvent
class	FailedLinkAnalysisEvent
class	FailedMeanVarianceUpdateEvent
class	FailedMissingValueAnalysisEvent
class	FailedPCAAnalysisEvent
class	FailedProcessedVectorComputationEvent
class	FailedSampleCorrelationAnalysisEvent
class	GeeqEvent
class	LinkAnalysisEvent	Computing coexpression links for an expression experiment
class	MakePrivateEvent	Indicate that an entity has been made private.
class	MakePublicEvent	Indicate that an entity has been made public.
class	ManualAnnotationEvent
class	MeanVarianceUpdateEvent
class	MissingValueAnalysisEvent	Computing missing values for an expression experiment
class	NeedsAttentionAlteringEvent	Base class for events altering CurationDetails.getNeedsAttention().
class	NeedsAttentionEvent	Indicates that previous validation is being invalidated
class	NotTroubledStatusFlagEvent	This event type resets the trouble flag of curation details of a curatable object.
class	OutlierAnalysisEvent
class	OutlierFoundAnalysisEvent
class	OutliersNotFoundAnalysisEvent
class	PCAAnalysisEvent
class	PermissionChangeEvent	Represents a change in permissions of an Auditable entity.
class	ProcessedVectorComputationEvent	Computation of the "processed" expression data with the ranking (by 'expression level') information filled in, for an Expression Experiment
class	RankComputationEvent	Deprecated.
class	ReleaseDetailsUpdateEvent	Event triggered when the release details of a Versioned entity are updated.
class	ResetSuitabilityForDifferentialExpressionAnalysisEvent	Used to indicate that the suitability status of an experiment is the default.
class	SampleCorrelationAnalysisEvent
class	SampleRemovalEvent	Event used when a sample is removed from an experiment (typically due to QC concerns or when marked as an outlier).
class	SampleRemovalReversionEvent	Indicates that samples that were previously removed have been "put back", e.g. un-marked as an outlier.
class	SingleBatchDeterminationEvent	Indicates that we got batch information, but there was (as far as we can tell) just one batch.
class	SingleCellSubSetsCreatedEvent	Emitted when a collection of ExpressionExperimentSubSet for holding aggregated single-cell data is created.
class	SingletonBatchInvalidEvent	Indiates that there was at least one batch with only one sample.
class	TooSmallDatasetLinkAnalysisEvent	Indicates that the data set had too few samples or probes to be analyzed (after filtering), and was skipped
class	TroubledStatusFlagAlteringEvent	Base class for events that alter the CurationDetails.getTroubled() flag.
class	TroubledStatusFlagEvent	Sets the trouble flag of curation details of any Curatable object.
class	UninformativeFASTQHeadersForBatchingEvent	Indicates that FASTQ headers were present, but they were not usable for determining batches, typically because of invalid formatting or lack of information.
class	UnsuitableForDifferentialExpressionAnalysisEvent	Indicates that the associated Experiment is NOT suitable for differential expression analysis.
class	VersionedEvent	Base class for events relating to a Versioned entity.

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	BibRefAnnotation
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	Keyword
class	MedicalSubjectHeading

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	AlternateName
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

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

Modifier and Type	Interface	Description
interface	CellLevelCharacteristics	Characteristics applicable to individual cells in a SingleCellDimension.

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	Value object for a BulkExpressionDataVector containing booleans.
class	BulkExpressionDataVector	A data vector storing bulk expression data.
class	CellLevelCharacteristicsValueObject
class	CellTypeAssignment	Represents a cell type assignment where cells from a given dataset are assigned cell types.
class	DataVector	An abstract class representing a one-dimensional vector of data about some aspect of an ExpressionExperiment.
class	DataVectorValueObject	Base class for value objects of BulkExpressionDataVector.
class	DesignElementDataVector	Data vector associated to a CompositeSequence.
class	DoubleVectorValueObject	Value object for a BulkExpressionDataVector containing doubles.
class	GenericCellLevelCharacteristics	Generic cell-level characteristics.
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	SingleCellDimension	Represents a single-cell dimension, holding shared information for a set of SingleCellExpressionDataVector.
class	SingleCellDimensionValueObject	Value object for a single-cell dimension.
class	SingleCellExpressionDataVector	An expression data vector that contains data at the resolution of individual cells.
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

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

Modifier and Type	Interface	Description
interface	BioAssaySetValueObject	Interface for VOs deriving from BioAssaySet.

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	Multifunctionality
class	SessionBoundGeneSetValueObject

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. owners) of the given characteristics.
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	EntityUrlBuilder.AllEntitiesUrl<T extends Identifiable>
class	EntityUrlBuilder.AllRestEntitiesUrl<T extends Identifiable>
class	EntityUrlBuilder.AllWebEntitiesUrl<T extends Identifiable>
class	EntityUrlBuilder.EntityUrl<T extends Identifiable>	Represents a URL for an Identifiable entity.
class	EntityUrlBuilder.OntologyEntityUrl<T extends Identifiable>
class	EntityUrlBuilder.RestEntityUrl<T extends Identifiable>	Generate a URL for Gemma REST.
class	EntityUrlBuilder.SomeEntitiesUrl<T extends Identifiable>
class	EntityUrlBuilder.SomeRestEntitiesUrl<T extends Identifiable>
class	EntityUrlBuilder.SomeWebEntitiesUrl<T extends Identifiable>
class	EntityUrlBuilder.WebEntityUrl<U extends Identifiable>	Generate a URL for Gemma Web.
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.

Fields in ubic.gemma.persistence.util declared as Identifiable

Modifier and Type	Field	Description
protected T	EntityUrlBuilder.EntityUrl.entity

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

Modifier and Type	Method	Description
<T extends Identifiable> EntityUrlBuilder.AllEntitiesUrl<T>	EntityUrlBuilder.EntityUrlChooser.all(Class<T> entityType)
static <T extends Identifiable> List<List<T>>	QueryUtils.batchIdentifiableParameterList(Collection<T> list, int batchSize)
<T extends Identifiable> EntityUrlBuilder.EntityUrl<T>	EntityUrlBuilder.EntityUrlChooser.entity(Class<T> entityType, Long id)
<T extends Identifiable> EntityUrlBuilder.EntityUrl<T>	EntityUrlBuilder.EntityUrlChooser.entity(T entity)
static <T extends Identifiable> boolean	IdentifiableUtils.equals(T a, T b)	Compare two identifiables of the same type without risking initializing them.
static <T extends Identifiable> Map<Long,T>	IdentifiableUtils.getIdMap(Collection<T> entities)	Given a set of entities, create a map of their ids to the entities.
static <T extends Identifiable> List<Long>	IdentifiableUtils.getIds(Collection<T> entities)	Convert a collection of identifiable to their IDs.
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.
<T extends Identifiable> EntityUrlBuilder.SomeEntitiesUrl<T>	EntityUrlBuilder.EntityUrlChooser.some(Class<T> entityType, Collection<Long> ids)
<T extends Identifiable> EntityUrlBuilder.SomeEntitiesUrl<T>	EntityUrlBuilder.EntityUrlChooser.some(Collection<T> 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.

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

Modifier and Type	Method	Description
static int	IdentifiableUtils.hash(Identifiable... identifiables)	Hash identifiables in a proxy-safe way using their IDs.

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.ExpressionExperimentSubsetWithFactorValuesObject
static class	DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject
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.

Uses of Identifiable in ubic.gemma.web.taglib

Methods in ubic.gemma.web.taglib with parameters of type Identifiable

Modifier and Type	Method	Description
void	EntityLinkTag.setEntity(Identifiable entity)