Uses of Interface
ubic.gemma.model.common.auditAndSecurity.Securable

Packages that use Securable

Package	Description
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.phenotype
ubic.gemma.model.common.auditAndSecurity
ubic.gemma.model.common.auditAndSecurity.curation
ubic.gemma.model.common.description
ubic.gemma.model.common.protocol
ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment
ubic.gemma.model.genome.gene
ubic.gemma.persistence.service.common.auditAndSecurity
ubic.gemma.persistence.util
ubic.gemma.web.controller.common.auditAndSecurity

Uses of Securable in ubic.gemma.model.analysis

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

Modifier and Type	Class	Description
class	Investigation	An abstract concept of a scientific study
class	SingleExperimentAnalysis

Methods in ubic.gemma.model.analysis that return Securable

Modifier and Type	Method	Description
Securable	SingleExperimentAnalysis.getSecurityOwner()

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

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

Modifier and Type	Class	Description
class	ExpressionExperimentSet	A grouping of expression studies.

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

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

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 Securable in ubic.gemma.model.analysis.expression.diff

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

Modifier and Type	Class	Description
class	DifferentialExpressionAnalysis	An analysis of changes in expression levels across experimental conditions
class	ExpressionAnalysisResultSet	A group of results for an ExpressionExperiment.
class	GeneDifferentialExpressionMetaAnalysis	Represents an analysis that combines the results of other analyses of differential expression.

Methods in ubic.gemma.model.analysis.expression.diff that return Securable

Modifier and Type	Method	Description
Securable	ExpressionAnalysisResultSet.getSecurityOwner()

Methods in ubic.gemma.model.analysis.expression.diff that return types with arguments of type Securable

Modifier and Type	Method	Description
Class<? extends Securable>	GeneDifferentialExpressionMetaAnalysisSummaryValueObject.getSecurableClass()

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

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

Modifier and Type	Class	Description
class	PrincipalComponentAnalysis

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

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

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 Securable in ubic.gemma.model.common.auditAndSecurity

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

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

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

Modifier and Type	Class	Description
class	AbstractAuditable	An entity which can have an audit trail attached to it.
class	JobInfo
class	UserGroup	An organized group of researchers with an identifiable leader and group members.
class	UserQuery

Methods in ubic.gemma.model.common.auditAndSecurity that return Securable

Modifier and Type	Method	Description
Securable	SecuredChild.getSecurityOwner()

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

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

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

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

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

Modifier and Type	Class	Description
class	ExternalDatabase

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

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

Modifier and Type	Class	Description
class	Protocol

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

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

Modifier and Type	Class	Description
class	ArrayDesign	Represents an assembly of design elements that are assayed all at once.

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

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

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

Methods in ubic.gemma.model.expression.bioAssay that return Securable

Modifier and Type	Method	Description
Securable	BioAssay.getSecurityOwner()

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

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

Modifier and Type	Class	Description
class	MeanVarianceRelation

Methods in ubic.gemma.model.expression.bioAssayData that return Securable

Modifier and Type	Method	Description
Securable	MeanVarianceRelation.getSecurityOwner()

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

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

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...

Methods in ubic.gemma.model.expression.biomaterial that return Securable

Modifier and Type	Method	Description
Securable	BioMaterial.getSecurityOwner()

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

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

Modifier and Type	Class	Description
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	ExpressionExperiment
class	ExpressionExperimentSubSet	A subset of samples from an ExpressionExperiment
class	FactorValue	The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"

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

Modifier and Type	Method	Description
Securable	ExperimentalDesign.getSecurityOwner()
Securable	ExperimentalFactor.getSecurityOwner()
Securable	ExpressionExperimentSubSet.getSecurityOwner()

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

Modifier and Type	Method	Description
Class<? extends Securable>	ExpressionExperimentSetValueObject.getSecurableClass()
Class<? extends Securable>	ExpressionExperimentSubsetValueObject.getSecurableClass()
Class<? extends Securable>	ExpressionExperimentValueObject.getSecurableClass()

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

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

Modifier and Type	Class	Description
class	GeneSet	A grouping of genes that share a common relationship

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

Modifier and Type	Method	Description
Class<? extends Securable>	GeneSetValueObject.getSecurableClass()

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

Classes in ubic.gemma.persistence.service.common.auditAndSecurity with type parameters of type Securable

Modifier and Type	Interface	Description
interface	SecurableBaseImmutableService<C extends Securable>
interface	SecurableBaseReadOnlyService<C extends Securable>
interface	SecurableBaseService<C extends Securable>	A base service for securable entities.
interface	SecurableBaseVoEnabledService<C extends Securable,VO extends IdentifiableValueObject<C>>
interface	SecurableFilteringVoEnabledService<C extends Securable,VO extends IdentifiableValueObject<C>>	A base service for securable entities with filtering and VO capabilities.

Uses of Securable in ubic.gemma.persistence.util

Method parameters in ubic.gemma.persistence.util with type arguments of type Securable

Modifier and Type	Method	Description
static void	AclQueryUtils.addAclParameters(Query query, Class<? extends Securable> aoiType)	Bind Query parameters to a join clause generated with AclQueryUtils.formAclRestrictionClause(String) and add ACL restriction parameters defined in AclQueryUtils.formAclRestrictionClause(String).
static void	EE2CAclQueryUtils.addAclParameters(Query query, Class<? extends Securable> aoiType)
static Criterion	AclCriteriaUtils.formAclRestrictionClause(String aoiIdColumn, Class<? extends Securable> aoiType)	Form a restriction clause for ACL using the read permission.
static Criterion	AclCriteriaUtils.formAclRestrictionClause(String aoiIdColumn, Class<? extends Securable> aoiType, int mask)	Form a restriction clause for ACL.

Uses of Securable in ubic.gemma.web.controller.common.auditAndSecurity

Method parameters in ubic.gemma.web.controller.common.auditAndSecurity with type arguments of type Securable

Modifier and Type	Method	Description
SecurityInfoValueObject	SecurityController.getSecurityInfo(EntityDelegator<? extends Securable> ed)
boolean	SecurityController.makeGroupReadable(EntityDelegator<? extends Securable> ed, String groupName)
boolean	SecurityController.makeGroupWriteable(EntityDelegator<? extends Securable> ed, String groupName)
boolean	SecurityController.makePrivate(EntityDelegator<? extends Securable> ed)
boolean	SecurityController.makePublic(EntityDelegator<? extends Securable> ed)
boolean	SecurityController.removeGroupReadable(EntityDelegator<? extends Securable> ed, String groupName)
boolean	SecurityController.removeGroupWriteable(EntityDelegator<? extends Securable> ed, String groupName)

Constructors in ubic.gemma.web.controller.common.auditAndSecurity with parameters of type Securable

Constructor	Description
SecurityInfoValueObject(Securable s)