Uses of Interface
ubic.gemma.persistence.service.BaseDao

Packages that use BaseDao

Package	Description
ubic.gemma.persistence.service
ubic.gemma.persistence.service.analysis
ubic.gemma.persistence.service.analysis.expression
ubic.gemma.persistence.service.analysis.expression.coexpression
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.analysis.expression.pca
ubic.gemma.persistence.service.association
ubic.gemma.persistence.service.association.coexpression
ubic.gemma.persistence.service.association.phenotype
ubic.gemma.persistence.service.blacklist	Service for managing blacklisted entities.
ubic.gemma.persistence.service.common.auditAndSecurity
ubic.gemma.persistence.service.common.auditAndSecurity.curation
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.common.measurement
ubic.gemma.persistence.service.common.protocol
ubic.gemma.persistence.service.common.quantitationtype
ubic.gemma.persistence.service.expression.arrayDesign
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.biomaterial
ubic.gemma.persistence.service.expression.designElement
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.service.genome
ubic.gemma.persistence.service.genome.biosequence
ubic.gemma.persistence.service.genome.gene
ubic.gemma.persistence.service.genome.sequenceAnalysis
ubic.gemma.persistence.service.genome.taxon

Uses of BaseDao in ubic.gemma.persistence.service

Subinterfaces of BaseDao in ubic.gemma.persistence.service

Modifier and Type	Interface	Description
interface	BaseVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Created by tesarst on 01/06/17.
interface	BrowsingDao<T>	Support for paging through the data.
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	FilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Interface for VO-enabled DAO with filtering capabilities.

Classes in ubic.gemma.persistence.service that implement BaseDao

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	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	AbstractVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>	Created by tesarst on 01/06/17.

Constructors in ubic.gemma.persistence.service with parameters of type BaseDao

Constructor	Description
AbstractService(BaseDao<O> mainDao)

Uses of BaseDao in ubic.gemma.persistence.service.analysis

Subinterfaces of BaseDao in ubic.gemma.persistence.service.analysis

Modifier and Type	Interface	Description
interface	AnalysisDao<T extends SingleExperimentAnalysis>
interface	AnalysisResultSetDao<K extends AnalysisResult,O extends AnalysisResultSet<K>>	Generic DAO for manipulating AnalysisResultSet.
interface	SingleExperimentAnalysisDao<T extends SingleExperimentAnalysis>

Classes in ubic.gemma.persistence.service.analysis that implement BaseDao

Modifier and Type	Class	Description
class	SingleExperimentAnalysisDaoBase<T extends SingleExperimentAnalysis>	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type SingleExperimentAnalysis.

Uses of BaseDao in ubic.gemma.persistence.service.analysis.expression

Subinterfaces of BaseDao in ubic.gemma.persistence.service.analysis.expression

Modifier and Type	Interface	Description
interface	ExpressionExperimentSetDao

Classes in ubic.gemma.persistence.service.analysis.expression that implement BaseDao

Modifier and Type	Class	Description
class	ExpressionExperimentSetDaoImpl

Uses of BaseDao in ubic.gemma.persistence.service.analysis.expression.coexpression

Subinterfaces of BaseDao in ubic.gemma.persistence.service.analysis.expression.coexpression

Modifier and Type	Interface	Description
interface	CoexpressionAnalysisDao

Classes in ubic.gemma.persistence.service.analysis.expression.coexpression that implement BaseDao

Modifier and Type	Class	Description
class	CoexpressionAnalysisDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis.

Uses of BaseDao in ubic.gemma.persistence.service.analysis.expression.diff

Subinterfaces of BaseDao in ubic.gemma.persistence.service.analysis.expression.diff

Modifier and Type	Interface	Description
interface	DifferentialExpressionAnalysisDao
interface	DifferentialExpressionResultDao
interface	ExpressionAnalysisResultSetDao
interface	GeneDiffExMetaAnalysisDao

Classes in ubic.gemma.persistence.service.analysis.expression.diff that implement BaseDao

Modifier and Type	Class	Description
class	DifferentialExpressionResultDaoImpl	This is a key class for queries to retrieve differential expression results (as well as standard CRUD aspects of working with DifferentialExpressionResults).
class	ExpressionAnalysisResultSetDaoImpl
class	GeneDiffExMetaAnalysisDaoImpl

Uses of BaseDao in ubic.gemma.persistence.service.analysis.expression.pca

Subinterfaces of BaseDao in ubic.gemma.persistence.service.analysis.expression.pca

Modifier and Type	Interface	Description
interface	PrincipalComponentAnalysisDao

Classes in ubic.gemma.persistence.service.analysis.expression.pca that implement BaseDao

Modifier and Type	Class	Description
class	PrincipalComponentAnalysisDaoImpl

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

Subinterfaces of BaseDao in ubic.gemma.persistence.service.association

Modifier and Type	Interface	Description
interface	Gene2GOAssociationDao
interface	ReferenceAssociationDao

Classes in ubic.gemma.persistence.service.association that implement BaseDao

Modifier and Type	Class	Description
class	Gene2GOAssociationDaoImpl
class	ReferenceAssociationDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ReferenceAssociation.

Uses of BaseDao in ubic.gemma.persistence.service.association.coexpression

Subinterfaces of BaseDao in ubic.gemma.persistence.service.association.coexpression

Modifier and Type	Interface	Description
interface	CoexpressionNodeDegreeDao

Classes in ubic.gemma.persistence.service.association.coexpression that implement BaseDao

Modifier and Type	Class	Description
class	CoexpressionNodeDegreeDaoImpl

Uses of BaseDao in ubic.gemma.persistence.service.association.phenotype

Subinterfaces of BaseDao in ubic.gemma.persistence.service.association.phenotype

Modifier and Type	Interface	Description
interface	DifferentialExpressionEvidenceDao
interface	ExperimentalEvidenceDao
interface	GenericEvidenceDao
interface	GenericExperimentDao
interface	LiteratureEvidenceDao
interface	PhenotypeAssociationDao

Classes in ubic.gemma.persistence.service.association.phenotype that implement BaseDao

Modifier and Type	Class	Description
class	DifferentialExpressionEvidenceDaoImpl
class	ExperimentalEvidenceDaoImpl
class	GenericEvidenceDaoImpl
class	GenericExperimentDaoImpl
class	LiteratureEvidenceDaoImpl
class	PhenotypeAssociationDaoImpl	deals with all basic queries used by Neurocarta

Uses of BaseDao in ubic.gemma.persistence.service.blacklist

Subinterfaces of BaseDao in ubic.gemma.persistence.service.blacklist

Modifier and Type	Interface	Description
interface	BlacklistedEntityDao

Classes in ubic.gemma.persistence.service.blacklist that implement BaseDao

Modifier and Type	Class	Description
class	BlacklistedEntityDaoImpl

Uses of BaseDao in ubic.gemma.persistence.service.common.auditAndSecurity

Subinterfaces of BaseDao in ubic.gemma.persistence.service.common.auditAndSecurity

Modifier and Type	Interface	Description
interface	AuditEventDao
interface	AuditTrailDao
interface	ContactDao
interface	PersonDao	Deprecated. as Person is deprecated
interface	UserDao
interface	UserGroupDao

Classes in ubic.gemma.persistence.service.common.auditAndSecurity that implement BaseDao

Modifier and Type	Class	Description
class	AuditEventDaoImpl
class	AuditTrailDaoImpl
class	ContactDaoImpl
class	PersonDaoImpl	Deprecated. as Person is deprecated
class	UserDaoImpl	DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.common.auditAndSecurity.User.
class	UserGroupDaoImpl

Uses of BaseDao in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Classes in ubic.gemma.persistence.service.common.auditAndSecurity.curation that implement BaseDao

Modifier and Type	Class	Description
class	AbstractCuratableDao<C extends Curatable,VO extends AbstractCuratableValueObject<C>>	Created by tesarst on 07/03/17.

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

Subinterfaces of BaseDao in ubic.gemma.persistence.service.common.description

Modifier and Type	Interface	Description
interface	BibliographicReferenceDao
interface	CharacteristicDao
interface	DatabaseEntryDao
interface	ExternalDatabaseDao

Classes in ubic.gemma.persistence.service.common.description that implement BaseDao

Modifier and Type	Class	Description
class	BibliographicReferenceDaoImpl
class	CharacteristicDaoImpl
class	DatabaseEntryDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type DatabaseEntry.
class	ExternalDatabaseDaoImpl

Uses of BaseDao in ubic.gemma.persistence.service.common.measurement

Subinterfaces of BaseDao in ubic.gemma.persistence.service.common.measurement

Modifier and Type	Interface	Description
interface	UnitDao

Classes in ubic.gemma.persistence.service.common.measurement that implement BaseDao

Modifier and Type	Class	Description
class	UnitDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.common.measurement.Unit.

Uses of BaseDao in ubic.gemma.persistence.service.common.protocol

Subinterfaces of BaseDao in ubic.gemma.persistence.service.common.protocol

Modifier and Type	Interface	Description
interface	ProtocolDao

Classes in ubic.gemma.persistence.service.common.protocol that implement BaseDao

Modifier and Type	Class	Description
class	ProtocolDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type Protocol.

Uses of BaseDao in ubic.gemma.persistence.service.common.quantitationtype

Subinterfaces of BaseDao in ubic.gemma.persistence.service.common.quantitationtype

Modifier and Type	Interface	Description
interface	QuantitationTypeDao

Classes in ubic.gemma.persistence.service.common.quantitationtype that implement BaseDao

Modifier and Type	Class	Description
class	QuantitationTypeDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type QuantitationType.

Uses of BaseDao in ubic.gemma.persistence.service.expression.arrayDesign

Subinterfaces of BaseDao in ubic.gemma.persistence.service.expression.arrayDesign

Modifier and Type	Interface	Description
interface	ArrayDesignDao	Created by tesarst on 13/03/17.

Classes in ubic.gemma.persistence.service.expression.arrayDesign that implement BaseDao

Modifier and Type	Class	Description
class	ArrayDesignDaoImpl

Uses of BaseDao in ubic.gemma.persistence.service.expression.bioAssay

Subinterfaces of BaseDao in ubic.gemma.persistence.service.expression.bioAssay

Modifier and Type	Interface	Description
interface	BioAssayDao

Classes in ubic.gemma.persistence.service.expression.bioAssay that implement BaseDao

Modifier and Type	Class	Description
class	BioAssayDaoImpl

Uses of BaseDao in ubic.gemma.persistence.service.expression.bioAssayData

Subinterfaces of BaseDao in ubic.gemma.persistence.service.expression.bioAssayData

Modifier and Type	Interface	Description
interface	BioAssayDimensionDao
interface	DesignElementDataVectorDao<T extends DesignElementDataVector>
interface	ProcessedExpressionDataVectorDao
interface	RawAndProcessedExpressionDataVectorDao
interface	RawExpressionDataVectorDao

Classes in ubic.gemma.persistence.service.expression.bioAssayData that implement BaseDao

Modifier and Type	Class	Description
class	AbstractDesignElementDataVectorDao<T extends DesignElementDataVector>
class	BioAssayDimensionDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.bioAssayData.BioAssayDimension.
class	ProcessedExpressionDataVectorDaoImpl
class	RawAndProcessedExpressionDataVectorDaoImpl
class	RawExpressionDataVectorDaoImpl

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

Subinterfaces of BaseDao in ubic.gemma.persistence.service.expression.biomaterial

Modifier and Type	Interface	Description
interface	BioMaterialDao
interface	CompoundDao

Classes in ubic.gemma.persistence.service.expression.biomaterial that implement BaseDao

Modifier and Type	Class	Description
class	BioMaterialDaoImpl
class	CompoundDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.biomaterial.Compound.

Uses of BaseDao in ubic.gemma.persistence.service.expression.designElement

Subinterfaces of BaseDao in ubic.gemma.persistence.service.expression.designElement

Modifier and Type	Interface	Description
interface	CompositeSequenceDao

Classes in ubic.gemma.persistence.service.expression.designElement that implement BaseDao

Modifier and Type	Class	Description
class	CompositeSequenceDaoImpl

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

Subinterfaces of BaseDao in ubic.gemma.persistence.service.expression.experiment

Modifier and Type	Interface	Description
interface	ExperimentalDesignDao
interface	ExperimentalFactorDao
interface	ExpressionExperimentDao	Created by tesarst on 13/03/17.
interface	ExpressionExperimentSubSetDao
interface	FactorValueDao
interface	GeeqDao
interface	StatementDao

Classes in ubic.gemma.persistence.service.expression.experiment that implement BaseDao

Modifier and Type	Class	Description
class	ExperimentalDesignDaoImpl
class	ExperimentalFactorDaoImpl
class	ExpressionExperimentDaoImpl
class	ExpressionExperimentSubSetDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet.
class	FactorValueDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.experiment.FactorValue.
class	GeeqDaoImpl
class	StatementDaoImpl

Uses of BaseDao in ubic.gemma.persistence.service.genome

Subinterfaces of BaseDao in ubic.gemma.persistence.service.genome

Modifier and Type	Interface	Description
interface	ChromosomeDao
interface	GeneDao

Classes in ubic.gemma.persistence.service.genome that implement BaseDao

Modifier and Type	Class	Description
class	ChromosomeDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.genome.Chromosome.
class	GeneDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type Gene.

Uses of BaseDao in ubic.gemma.persistence.service.genome.biosequence

Subinterfaces of BaseDao in ubic.gemma.persistence.service.genome.biosequence

Modifier and Type	Interface	Description
interface	BioSequenceDao

Classes in ubic.gemma.persistence.service.genome.biosequence that implement BaseDao

Modifier and Type	Class	Description
class	BioSequenceDaoImpl

Uses of BaseDao in ubic.gemma.persistence.service.genome.gene

Subinterfaces of BaseDao in ubic.gemma.persistence.service.genome.gene

Modifier and Type	Interface	Description
interface	GeneAliasDao
interface	GeneProductDao
interface	GeneSetDao	The interface for managing groupings of genes.

Classes in ubic.gemma.persistence.service.genome.gene that implement BaseDao

Modifier and Type	Class	Description
class	GeneAliasDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.genome.gene.GeneAlias.
class	GeneProductDaoImpl
class	GeneSetDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.genome.gene.GeneSet.
class	GeneSetMemberDaoImpl

Uses of BaseDao in ubic.gemma.persistence.service.genome.sequenceAnalysis

Subinterfaces of BaseDao in ubic.gemma.persistence.service.genome.sequenceAnalysis

Modifier and Type	Interface	Description
interface	AnnotationAssociationDao
interface	BlatAssociationDao
interface	BlatResultDao

Classes in ubic.gemma.persistence.service.genome.sequenceAnalysis that implement BaseDao

Modifier and Type	Class	Description
class	AnnotationAssociationDaoImpl
class	BlatAssociationDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type BlatAssociation.
class	BlatResultDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.genome.sequenceAnalysis.BlatResult.

Uses of BaseDao in ubic.gemma.persistence.service.genome.taxon

Subinterfaces of BaseDao in ubic.gemma.persistence.service.genome.taxon

Modifier and Type	Interface	Description
interface	TaxonDao

Classes in ubic.gemma.persistence.service.genome.taxon that implement BaseDao

Modifier and Type	Class	Description
class	TaxonDaoImpl