Uses of Package
ubic.gemma.model.common

Packages that use ubic.gemma.model.common

Package	Description
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.expression.singleCell	This package contains classes for loading single-cell expression data.
ubic.gemma.core.loader.util
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.core.tasks.visualization
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.common.search
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.persister
ubic.gemma.persistence.service
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.common.auditAndSecurity
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.analysis.expression.diff
ubic.gemma.web.controller.expression.arrayDesign
ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.persistence
ubic.gemma.web.controller.util
ubic.gemma.web.taglib	This package contains custom JSP tag libraries used in the Gemma Web application.

Classes in ubic.gemma.model.common used by ubic.gemma.core.loader.expression.arrayDesign

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.core.loader.expression.geo

Class	Description
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.core.loader.expression.singleCell

Class	Description
NonUniqueDescribableByNameException	An exception that can be raised when trying to create a describable entity or add one to a collection with a name that is already being used.

Classes in ubic.gemma.model.common used by ubic.gemma.core.loader.util

Class	Description
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.core.loader.util.mapper

Class	Description
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.core.search

Class	Description
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.core.search.source

Class	Description
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.core.tasks

Class	Description
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.core.tasks.visualization

Class	Description
ValueObject	Annotate class representing value objects.

Classes in ubic.gemma.model.common used by ubic.gemma.model.analysis

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.analysis.expression

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.model.analysis.expression.coexpression

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.model.analysis.expression.diff

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects
ValueObject	Annotate class representing value objects.

Classes in ubic.gemma.model.common used by ubic.gemma.model.analysis.expression.pca

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.model.association

Class	Description
AbstractIdentifiable	Base class for identifiable entities.
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.model.association.coexpression

Class	Description
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.model.blacklist

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.common

Class	Description
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects
ValueObject	Annotate class representing value objects.

Classes in ubic.gemma.model.common used by ubic.gemma.model.common.auditAndSecurity

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.common.auditAndSecurity.curation

Class	Description
AbstractIdentifiable	Base class for identifiable entities.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.common.auditAndSecurity.eventType

Class	Description
AbstractIdentifiable	Base class for identifiable entities.
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.model.common.description

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.common.measurement

Class	Description
AbstractIdentifiable	Base class for identifiable entities.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.common.protocol

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.model.common.quantitationtype

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.common.search

Class	Description
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects
ValueObject	Annotate class representing value objects.

Classes in ubic.gemma.model.common used by ubic.gemma.model.expression.arrayDesign

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.expression.bioAssay

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.expression.bioAssayData

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.expression.biomaterial

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.expression.designElement

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.expression.experiment

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
GemmaSessionBackedValueObject
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.genome

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.genome.biosequence

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.model.genome.gene

Class	Description
AbstractDescribable
AbstractIdentifiable	Base class for identifiable entities.
Describable	Interface for entities that have a name and description.
GemmaSessionBackedValueObject
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.model.genome.sequenceAnalysis

Class	Description
AbstractIdentifiable	Base class for identifiable entities.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.persistence.persister

Class	Description
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.persistence.service

Class	Description
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.persistence.service.analysis.expression.diff

Class	Description
BaseValueObject

Classes in ubic.gemma.model.common used by ubic.gemma.persistence.service.common.auditAndSecurity

Class	Description
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.persistence.service.common.description

Class	Description
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.persistence.service.expression.experiment

Class	Description
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.persistence.util

Class	Description
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.rest

Class	Description
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.rest.util.args

Class	Description
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.web.controller.analysis.expression.diff

Class	Description
BaseValueObject

Classes in ubic.gemma.model.common used by ubic.gemma.web.controller.expression.arrayDesign

Class	Description
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.web.controller.expression.experiment

Class	Description
Describable	Interface for entities that have a name and description.
Identifiable	Interface for objects that have a numerical id.
IdentifiableValueObject	Base implementations for value objects representing persistent objects

Classes in ubic.gemma.model.common used by ubic.gemma.web.controller.persistence

Class	Description
GemmaSessionBackedValueObject

Classes in ubic.gemma.model.common used by ubic.gemma.web.controller.util

Class	Description
Identifiable	Interface for objects that have a numerical id.

Classes in ubic.gemma.model.common used by ubic.gemma.web.taglib

Class	Description
Identifiable	Interface for objects that have a numerical id.