Uses of Interface
ubic.gemma.model.common.Identifiable
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Uses of Identifiable in ubic.gemma.core.genome.gene
Classes in ubic.gemma.core.genome.gene that implement Identifiable Modifier and Type Class Description class
FreeTextGeneResultsValueObject
*class
GOGroupValueObject
class
PhenotypeGroupValueObject
class
SessionBoundGeneSetValueObject
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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>
class
SearchResultSet<T extends Identifiable>
This is a special kind of set designed for holdingSearchResult
.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, Object source)
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, Object source)
Shorthand for#from(Class, Identifiable, double, String, Object)
if you don't need to set the score and highlighted text.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 whose result class differ from the object.static <T extends Identifiable>
SearchResult<T>SearchResult. from(SearchResult<?> original, T newResultObject)
Create a search result from an existing one, replacing the result object with the target one.<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.<T extends Identifiable,U extends IdentifiableValueObject<T>>
SearchResult<U>SearchService. loadValueObject(SearchResult<T> searchResult)
Convert aSearchResult
to its VO flavour.<T extends Identifiable,U extends IdentifiableValueObject<T>>
SearchResult<U>SearchServiceImpl. loadValueObject(SearchResult<T> searchResult)
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, Object source)
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, Object source)
Shorthand for#from(Class, Identifiable, double, String, Object)
if you don't need to set the score and highlighted text.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 whose result class differ from the object.List<SearchResult<?>>
SearchService.SearchResultMap. getByResultType(Class<? extends Identifiable> searchResultType)
void
IndexerService. index(Set<Class<? extends Identifiable>> classesToIndex, int numThreads)
Index all the given classes.void
IndexerServiceImpl. index(Set<Class<? extends Identifiable>> classesToIndex, int numThreads)
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Uses of Identifiable in ubic.gemma.core.search.source
Classes in ubic.gemma.core.search.source with type parameters of type Identifiable Modifier and Type Interface Description static interface
CompositeSearchSource.SearchFunction<T extends Identifiable>
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Uses of Identifiable in ubic.gemma.model
Classes in ubic.gemma.model with type parameters of type Identifiable Modifier and Type Class Description class
IdentifiableValueObject<O extends Identifiable>
Base implementations for value objects representing persistent objectsClasses in ubic.gemma.model that implement Identifiable Modifier and Type Class Description class
IdentifiableValueObject<O extends Identifiable>
Base implementations for value objects representing persistent objects -
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 anAnalysis
and a typical part of anAnalysisResultSet
.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 anAnalysisResultSet
to the public API.class
AnalysisResultValueObject<A extends AnalysisResult>
Wraps anAnalysisResult
to expose it on the public API.class
AnalysisValueObject<T extends Analysis>
class
Investigation
An abstract concept of a scientific studyclass
SingleExperimentAnalysis
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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 ExpressionExperimentsclass
ExpressionExperimentSet
A grouping of expression studies.class
FactorAssociatedAnalysisResultSet<R extends AnalysisResult>
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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 conditionsclass
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 anExpressionAnalysisResultSet
and expose it to the public API.class
DifferentialExpressionAnalysisResultValueObject
UnlikeDiffExResultSetSummaryValueObject
, this value object is meant for the public API.class
DifferentialExpressionAnalysisValueObject
Summary of a differential expression analysisclass
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
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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
Gene2OntologyEntryAssociation
class
Gene2OntologyEntryAssociationImpl
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.common
Subinterfaces of Identifiable in ubic.gemma.model.common Modifier and Type Interface Description interface
Auditable
Created by tesarst on 07/03/17.interface
Describable
Classes in ubic.gemma.model.common that implement Identifiable Modifier and Type Class Description class
AbstractAuditable
An entity which can have an audit trail attached to it.class
AbstractDescribable
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Uses of Identifiable in ubic.gemma.model.common.auditAndSecurity
Classes in ubic.gemma.model.common.auditAndSecurity that implement Identifiable Modifier and Type Class Description 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 neededclass
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.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 webclass
Characteristic
Instances of this are used to describe other entities.class
CharacteristicValueObject
Value object representation of aCharacteristic
.class
DatabaseEntry
A reference to a record in a database.class
DatabaseEntryValueObject
ValueObject for database entryclass
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
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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
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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 theQuantitationType
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Uses of Identifiable in ubic.gemma.model.expression
Classes in ubic.gemma.model.expression that implement Identifiable Modifier and Type Class Description class
BlacklistedEntity
class
BlacklistedValueObject
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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.class
BlacklistedPlatform
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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
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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
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. -
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
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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
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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
BioAssaySet
Represents a set of BioAssays.class
BlacklistedExperiment
TODO Document Meclass
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 ExpressionExperimentclass
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 theFactorValueBasicValueObject
.class
FreeTextExpressionExperimentResultsValueObject
class
Geeq
Represents quality information about a data set.class
GeeqAdminValueObject
Represents administrative geeq information.class
GeeqValueObject
Represents publicly available geeq informationclass
SessionBoundExpressionExperimentSetValueObject
class
Statement
A special kind of characteristic that act as a statement.class
StatementValueObject
Represents a VO for aStatement
, typically part of aFactorValueBasicValueObject
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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 chromosomeclass
ChromosomeFeature
Some part of a chromosomeclass
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 locationclass
Taxon
class
TaxonValueObject
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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
GeneAlias
class
GeneProduct
class
GeneProductValueObject
class
GeneSet
A grouping of genes that share a common relationshipclass
GeneSetMember
class
GeneSetValueObject
Represents a Gene group gene setclass
GeneValueObject
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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 objectsclass
ExperimentalEvidenceValueObject
Deprecated.class
GeneEvidenceValueObject
Deprecated.class
GenericEvidenceValueObject
class
LiteratureEvidenceValueObject
class
TreeCharacteristicValueObject
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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
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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 ofFilteringVoEnabledDao
based on the HibernateCriteria
API.class
AbstractDao<T extends Identifiable>
AbstractDao can find the generic type at runtime and simplify the code implementation of the BaseDao interfaceclass
AbstractFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>
Base implementation forFilteringVoEnabledDao
.class
AbstractFilteringVoEnabledService<O extends Identifiable,VO extends IdentifiableValueObject<O>>
Base implementation forFilteringVoEnabledService
.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 ofFilteringVoEnabledDao
based on the HibernateQuery
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 toCharacteristicDao.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 aHashSet
which would otherwise cause their initialization by accessingObject.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)
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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)
Obtain all annotations, grouped by applicable level.Map<Class<? extends Identifiable>,List<Characteristic>>
ExpressionExperimentDaoImpl. getAllAnnotations(ExpressionExperiment expressionExperiment)
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 givenExpressionExperiment
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
GenericValueObjectConverter<O extends Identifiable,VO extends IdentifiableValueObject<?>>
Generic value object converter.class
ServiceBasedEntityConverter<O extends Identifiable>
Performs conversion by identifier and collection of identifier for aBaseReadOnlyService
.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>
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)
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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 theid
andobjectClass
are omitted.static class
DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject
static class
DatasetsWebService.ExpressionExperimentWithSearchResultValueObject
static class
DatasetsWebService.TaxonWithUsageStatisticsValueObject
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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>>
BridgesArg
operating on entities with their correspondingFilteringService
.class
FilterArg<O extends Identifiable>
Represent a filter argument designed to generate aFilters
from user input.class
SortArg<O extends Identifiable>
Class representing an API argument that should be an integer.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
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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.
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