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

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>	ExpressionExperimentReadService.getAnnotations(ExpressionExperiment expressionExperiment)
Set<AnnotationValueObject>	ExpressionExperimentReadService.getAnnotations(ExpressionExperiment expressionExperiment, boolean includeFreeText)
Set<AnnotationValueObject>	ExpressionExperimentReadService.getAnnotations(ExpressionExperimentSubSet ee)
Set<AnnotationValueObject>	ExpressionExperimentReadService.getAnnotations(ExpressionExperimentSubSet ee, boolean includeFreeText)
Set<AnnotationValueObject>	ExpressionExperimentReadServiceImpl.getAnnotations(ExpressionExperiment expressionExperiment)
Set<AnnotationValueObject>	ExpressionExperimentReadServiceImpl.getAnnotations(ExpressionExperiment expressionExperiment, boolean includeFreeText)
Set<AnnotationValueObject>	ExpressionExperimentReadServiceImpl.getAnnotations(ExpressionExperimentSubSet ee)
Set<AnnotationValueObject>	ExpressionExperimentReadServiceImpl.getAnnotations(ExpressionExperimentSubSet ee, boolean includeFreeText)
Set<AnnotationValueObject>	ExpressionExperimentService.getAnnotations(ExpressionExperiment ee)	Retrieve annotations for a given experiment.
Set<AnnotationValueObject>	ExpressionExperimentService.getAnnotations(ExpressionExperiment ee, boolean includeFreeText)	Retrieve annotations for a given experiment, optionally including unmapped ones.
Set<AnnotationValueObject>	ExpressionExperimentService.getAnnotations(ExpressionExperimentSubSet ee)	Retrieve annotations for a given experiment subset.
Set<AnnotationValueObject>	ExpressionExperimentService.getAnnotations(ExpressionExperimentSubSet ee, boolean includeFreeText)	Retrieve annotations for a given experiment subset, optionally including unmapped ones.
Set<AnnotationValueObject>	ExpressionExperimentServiceImpl.getAnnotations(ExpressionExperiment expressionExperiment)
Set<AnnotationValueObject>	ExpressionExperimentServiceImpl.getAnnotations(ExpressionExperiment expressionExperiment, boolean includeFreeText)
Set<AnnotationValueObject>	ExpressionExperimentServiceImpl.getAnnotations(ExpressionExperimentSubSet ee)
Set<AnnotationValueObject>	ExpressionExperimentServiceImpl.getAnnotations(ExpressionExperimentSubSet ee, boolean includeFreeText)

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 final 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<AnnotationValueObject>	DatasetsWebService.addSampleCharacteristic(DatasetArg<?> datasetArg, Long bioAssayId, DatasetsWebService.AnnotationTagInput body)
List<AnnotationValueObject>	AnnotationsWebService.AnnotationReplaceReport.getAdded()
ResponseDataObject<Set<AnnotationValueObject>>	DatasetsWebService.getDatasetAnnotations(DatasetArg<?> datasetArg, Boolean includeFreeText)	Retrieves the annotations for the given dataset.
List<AnnotationValueObject>	AnnotationsWebService.AnnotationReplaceReport.getRemoved()
ResponseDataObject<Set<AnnotationValueObject>>	DatasetsWebService.getSampleCharacteristics(DatasetArg<?> datasetArg, Long bioAssayId)
ResponseDataObject<AnnotationValueObject>	DatasetsWebService.removeSampleCharacteristic(DatasetArg<?> datasetArg, Long bioAssayId, Long characteristicId)
ResponseDataObject<Set<AnnotationValueObject>>	DatasetsWebService.updateDatasetAnnotations(DatasetArg<?> datasetArg, DatasetsWebService.AnnotationsUpdateRequest body)
ResponseDataObject<Set<AnnotationValueObject>>	DatasetsWebService.updateSampleCharacteristics(DatasetArg<?> datasetArg, Long bioAssayId, DatasetsWebService.AnnotationsUpdateRequest body)

Constructor parameters in ubic.gemma.rest with type arguments of type AnnotationValueObject

Modifier	Constructor	Description
	AnnotationReplaceReport(Long eeId, int before, int after, List<AnnotationValueObject> added, List<AnnotationValueObject> removed, int unchanged, List<Long> auditEventIds, List<String> unresolvedUris)	Creates a new AnnotationReplaceReport instance.

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)
Set<AnnotationValueObject>	DatasetArgService.getAnnotations(DatasetArg<?> arg, boolean includeFreeText)