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

Packages that use Describable

Package	Description
ubic.gemma.core.loader.expression.arrayDesign
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.blacklist
ubic.gemma.model.common
ubic.gemma.model.common.auditAndSecurity
ubic.gemma.model.common.description
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.persistence.util
ubic.gemma.rest
ubic.gemma.web.controller.expression.experiment

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

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

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 Describable in ubic.gemma.model.analysis

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

Modifier and Type	Class	Description
class	Analysis	An analysis of one or more Investigations.
class	Investigation	An abstract concept of a scientific study
class	SingleExperimentAnalysis<T extends BioAssaySet>	An analysis of a single experiment or subset.

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

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

Modifier and Type	Class	Description
class	ExpressionAnalysis	An analysis of one or more ExpressionExperiments
class	ExpressionExperimentSet	A grouping of expression studies.

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

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

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

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

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

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

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

Modifier and Type	Class	Description
class	PrincipalComponentAnalysis

Uses of Describable in ubic.gemma.model.blacklist

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

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

Uses of Describable in ubic.gemma.model.common

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

Modifier and Type	Class	Description
class	AbstractDescribable

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

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

Modifier and Type	Class	Description
class	AbstractAuditable	An entity which can have an audit trail attached to it.
class	Contact	Representing a person or organization that can be contacted about, or is the source of, data in the system.
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 Describable in ubic.gemma.model.common.description

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

Modifier and Type	Class	Description
class	BibliographicReference
class	Characteristic	Instances of this are used to describe other entities.
class	ExternalDatabase

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

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

Modifier and Type	Class	Description
class	Protocol

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

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

Modifier and Type	Class	Description
class	QuantitationType

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

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

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

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

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

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

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

Subinterfaces of Describable 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 Describable

Modifier and Type	Class	Description
class	CellTypeAssignment	Represents a cell type assignment where cells from a given dataset are assigned cell types.
class	GenericCellLevelCharacteristics	Generic cell-level characteristics.

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

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

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	Compound
class	Treatment

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

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

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

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

Subinterfaces of Describable 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 Describable

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	ExpressionExperimentDetailsValueObject
class	ExpressionExperimentSubSet	A subset of samples from an ExpressionExperiment
class	ExpressionExperimentSubsetValueObject
class	ExpressionExperimentValueObject
class	Statement	A special kind of characteristic that act as a statement.

Uses of Describable in ubic.gemma.model.genome

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

Modifier and Type	Class	Description
class	ChromosomeFeature	Some part of a chromosome
class	Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

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

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

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

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

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

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

Uses of Describable in ubic.gemma.persistence.util

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

Modifier and Type	Method	Description
int	DescribableComparator.compare(Describable d1, Describable d2)

Uses of Describable in ubic.gemma.rest

Classes in ubic.gemma.rest that implement Describable

Modifier and Type	Class	Description
static class	DatasetsWebService.ExpressionExperimentSubsetWithFactorValuesObject
static class	DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject
static final class	DatasetsWebService.ExpressionExperimentWithSearchResultValueObject

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

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

Modifier and Type	Class	Description
class	ExpressionExperimentEditValueObject