Uses of Class
ubic.gemma.model.common.description.AnnotationValueObject

Packages that use AnnotationValueObject

Package	Description
ubic.gemma.core.tasks.maintenance
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.service.genome.gene
ubic.gemma.persistence.service.genome.sequenceAnalysis
ubic.gemma.rest
ubic.gemma.rest.util.args
ubic.gemma.web.controller.common
ubic.gemma.web.controller.expression.biomaterial
ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.genome.gene

Uses of AnnotationValueObject in ubic.gemma.core.tasks.maintenance

Methods in ubic.gemma.core.tasks.maintenance that return types with arguments of type AnnotationValueObject

Modifier and Type	Method	Description
Collection<AnnotationValueObject>	CharacteristicUpdateCommand.getAnnotationValueObjects()

Method parameters in ubic.gemma.core.tasks.maintenance with type arguments of type AnnotationValueObject

Modifier and Type	Method	Description
void	CharacteristicUpdateCommand.setAnnotationValueObjects(Collection<AnnotationValueObject> annotationValueObjects)

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

Methods in ubic.gemma.persistence.service.expression.experiment that return types with arguments of type AnnotationValueObject

Modifier and Type	Method	Description
Set<AnnotationValueObject>	ExpressionExperimentService.getAnnotationsById(Long eeId)	Obtain experiment annotations.
Set<AnnotationValueObject>	ExpressionExperimentServiceImpl.getAnnotationsById(Long eeId)

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

Methods in ubic.gemma.persistence.service.genome.gene that return types with arguments of type AnnotationValueObject

Modifier and Type	Method	Description
Collection<AnnotationValueObject>	GeneService.findGOTerms(Long geneId)
Collection<AnnotationValueObject>	GeneServiceImpl.findGOTerms(Long geneId)

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

Methods in ubic.gemma.persistence.service.genome.sequenceAnalysis that return types with arguments of type AnnotationValueObject

Modifier and Type	Method	Description
Collection<AnnotationValueObject>	AnnotationAssociationService.removeRootTerms(Collection<AnnotationValueObject> associations)
Collection<AnnotationValueObject>	AnnotationAssociationServiceImpl.removeRootTerms(Collection<AnnotationValueObject> associations)	Remove root terms, like "molecular_function", "biological_process" and "cellular_component" Also removes any null objects.

Method parameters in ubic.gemma.persistence.service.genome.sequenceAnalysis with type arguments of type AnnotationValueObject

Modifier and Type	Method	Description
Collection<AnnotationValueObject>	AnnotationAssociationService.removeRootTerms(Collection<AnnotationValueObject> associations)
Collection<AnnotationValueObject>	AnnotationAssociationServiceImpl.removeRootTerms(Collection<AnnotationValueObject> associations)	Remove root terms, like "molecular_function", "biological_process" and "cellular_component" Also removes any null objects.

Uses of AnnotationValueObject in ubic.gemma.rest

Subclasses of AnnotationValueObject in ubic.gemma.rest

Modifier and Type	Class	Description
static class	DatasetsWebService.AnnotationWithUsageStatisticsValueObject	This is an aggregated entity across value URI and value, thus the id and objectClass are omitted.

Methods in ubic.gemma.rest that return types with arguments of type AnnotationValueObject

Modifier and Type	Method	Description
ResponseDataObject<Set<AnnotationValueObject>>	DatasetsWebService.getDatasetAnnotations(DatasetArg<?> datasetArg)	Retrieves the annotations for the given dataset.

Uses of AnnotationValueObject in ubic.gemma.rest.util.args

Methods in ubic.gemma.rest.util.args that return types with arguments of type AnnotationValueObject

Modifier and Type	Method	Description
Set<AnnotationValueObject>	DatasetArgService.getAnnotations(DatasetArg<?> arg)

Uses of AnnotationValueObject in ubic.gemma.web.controller.common

Methods in ubic.gemma.web.controller.common that return types with arguments of type AnnotationValueObject

Modifier and Type	Method	Description
JsonReaderResponse<AnnotationValueObject>	CharacteristicBrowserController.browse(ListBatchCommand batch)
Collection<AnnotationValueObject>	CharacteristicBrowserController.findCharacteristics(String valuePrefix)
Collection<AnnotationValueObject>	CharacteristicBrowserController.findCharacteristicsCustom(String queryString, boolean searchNos, boolean searchEEs, boolean searchBMs, boolean searchFVs, boolean searchFVVs, boolean searchCategories, String categoryConstraint)

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

Modifier and Type	Method	Description
void	CharacteristicBrowserController.removeCharacteristics(Collection<AnnotationValueObject> chars)
void	CharacteristicBrowserController.updateCharacteristics(Collection<AnnotationValueObject> avos)	Update characteristics associated with entities.

Uses of AnnotationValueObject in ubic.gemma.web.controller.expression.biomaterial

Methods in ubic.gemma.web.controller.expression.biomaterial that return types with arguments of type AnnotationValueObject

Modifier and Type	Method	Description
Collection<AnnotationValueObject>	BioMaterialController.getAnnotation(EntityDelegator<BioMaterial> bm)

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

Methods in ubic.gemma.web.controller.expression.experiment that return types with arguments of type AnnotationValueObject

Modifier and Type	Method	Description
Collection<AnnotationValueObject>	ExpressionExperimentController.getAnnotation(EntityDelegator<ExpressionExperiment> e)	AJAX

Uses of AnnotationValueObject in ubic.gemma.web.controller.genome.gene

Methods in ubic.gemma.web.controller.genome.gene that return types with arguments of type AnnotationValueObject

Modifier and Type	Method	Description
Collection<AnnotationValueObject>	GeneController.findGOTerms(Long geneId)