Uses of Class
ubic.gemma.model.expression.bioAssay.BioAssayValueObject

Packages that use BioAssayValueObject

Package	Description
ubic.gemma.core.visualization
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.rest
ubic.gemma.rest.util.args

Uses of BioAssayValueObject in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization that return types with arguments of type BioAssayValueObject

Modifier and Type	Method	Description
Map<Long, LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>>>	ExperimentalDesignVisualizationService.sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs, ExperimentalFactor primaryFactor)	Put data vectors in the order you'd want to display the experimental design.
Map<Long, LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>>>	ExperimentalDesignVisualizationServiceImpl.sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs, ExperimentalFactor primaryFactor)

Uses of BioAssayValueObject in ubic.gemma.model.analysis.expression.diff

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

Modifier and Type	Method	Description
Collection<BioAssayValueObject>	DifferentialExpressionAnalysisValueObject.getBioAssaysAnalyzed()	The BioAssays analyzed in this differential expression analysis.
Collection<BioAssayValueObject>	DiffExResultSetSummaryValueObject.getBioAssaysAnalyzed()	List of BioAssays analyzed

Method parameters in ubic.gemma.model.analysis.expression.diff with type arguments of type BioAssayValueObject

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisValueObject.setBioAssaysAnalyzed(Collection<BioAssayValueObject> bioAssaysAnalyzed)	The BioAssays analyzed in this differential expression analysis.
void	DiffExResultSetSummaryValueObject.setBioAssaysAnalyzed(Collection<BioAssayValueObject> bioAssaysAnalyzed)	List of BioAssays analyzed

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

Methods in ubic.gemma.model.expression.bioAssayData that return types with arguments of type BioAssayValueObject

Modifier and Type	Method	Description
List<BioAssayValueObject>	BioAssayDimensionValueObject.getBioAssays()
List<BioAssayValueObject>	DataVectorValueObject.getBioAssays()

Method parameters in ubic.gemma.model.expression.bioAssayData with type arguments of type BioAssayValueObject

Modifier and Type	Method	Description
void	BioAssayDimensionValueObject.addBioAssays(List<BioAssayValueObject> bvos)
void	BioAssayDimensionValueObject.reorder(List<BioAssayValueObject> newOrdering)

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

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

Modifier and Type	Method	Description
Collection<BioAssayValueObject>	ExpressionExperimentSubsetValueObject.getBioAssays()

Method parameters in ubic.gemma.model.expression.experiment with type arguments of type BioAssayValueObject

Modifier and Type	Method	Description
void	ExpressionExperimentSubsetValueObject.setBioAssays(Collection<BioAssayValueObject> bioAssays)

Uses of BioAssayValueObject in ubic.gemma.persistence.service.expression.bioAssay

Subclasses with type arguments of type BioAssayValueObject in ubic.gemma.persistence.service.expression.bioAssay

Modifier and Type	Class	Description
class	BioAssayDaoImpl
class	BioAssayServiceImpl

Subinterfaces with type arguments of type BioAssayValueObject in ubic.gemma.persistence.service.expression.bioAssay

Modifier and Type	Interface	Description
interface	BioAssayDao
interface	BioAssayService

Methods in ubic.gemma.persistence.service.expression.bioAssay that return BioAssayValueObject

Modifier and Type	Method	Description
protected BioAssayValueObject	BioAssayDaoImpl.doLoadValueObject(BioAssay entity)

Methods in ubic.gemma.persistence.service.expression.bioAssay that return types with arguments of type BioAssayValueObject

Modifier and Type	Method	Description
List<BioAssayValueObject>	BioAssayDao.loadValueObjects(Collection<BioAssay> entities, Map<ArrayDesign, ArrayDesignValueObject> ad2vo, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
List<BioAssayValueObject>	BioAssayDaoImpl.loadValueObjects(Collection<BioAssay> entities, Map<ArrayDesign, ArrayDesignValueObject> ad2vo, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
List<BioAssayValueObject>	BioAssayReadService.loadValueObjects(Collection<BioAssay> entities, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
List<BioAssayValueObject>	BioAssayReadServiceImpl.loadValueObjects(Collection<BioAssay> entities, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
List<BioAssayValueObject>	BioAssayService.loadValueObjects(Collection<BioAssay> entities, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
List<BioAssayValueObject>	BioAssayServiceImpl.loadValueObjects(Collection<BioAssay> entities, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
CursorPage<BioAssayValueObject>	BioAssayDao.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee, Cursor cursor, int limit)	Cursor-paged listing of BioAssayValueObjects for a single ExpressionExperiment, sorted by ascending id — see CURSOR_PAGINATION_STEP1_PLAN.md step 1k.
CursorPage<BioAssayValueObject>	BioAssayDaoImpl.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	BioAssayReadService.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	BioAssayReadServiceImpl.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	BioAssayService.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee, Cursor cursor, int limit)	Cursor-mode counterpart to the legacy unpaginated BioAssayDao EE-scoped sample listing — see CURSOR_PAGINATION_STEP1_PLAN.md step 1k.
CursorPage<BioAssayValueObject>	BioAssayServiceImpl.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	BioAssayDao.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)	Cursor-paged listing of BioAssayValueObjects for a single ExpressionExperimentSubSet, sorted by ascending id — see CURSOR_PAGINATION_STEP1_PLAN.md step 1u (the subset-scoped twin of step 1k).
CursorPage<BioAssayValueObject>	BioAssayDaoImpl.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	BioAssayReadService.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	BioAssayReadServiceImpl.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	BioAssayService.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)	Cursor-mode counterpart to the legacy unpaginated subset-scoped sample listing — see CURSOR_PAGINATION_STEP1_PLAN.md step 1u.
CursorPage<BioAssayValueObject>	BioAssayServiceImpl.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)

Uses of BioAssayValueObject in ubic.gemma.rest

Subclasses with type arguments of type BioAssayValueObject in ubic.gemma.rest

Modifier and Type	Class	Description
static class	DatasetsWebService.CursorPaginatedResponseDataObjectBioAssayValueObject	Cursor-mode response shape for DatasetsWebService.getDatasetSamples(DatasetArg, QuantitationTypeArg, boolean, CursorArg, LimitArg, ExcludeArg, boolean).
static class	DatasetsWebService.ResponseDataObjectListBioAssayValueObject	Legacy-mode response shape for DatasetsWebService.getDatasetSamples(DatasetArg, QuantitationTypeArg, boolean, CursorArg, LimitArg, ExcludeArg, boolean).

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

Modifier and Type	Method	Description
ResponseDataObject<BioAssayValueObject>	DatasetsWebService.markDatasetSampleOutlier(DatasetArg<?> datasetArg, Long bioAssayId, DatasetsWebService.SampleOutlierRequest body)	Mark (or unmark) a BioAssay as a sample outlier.

Method parameters in ubic.gemma.rest with type arguments of type BioAssayValueObject

Modifier and Type	Method	Description
Object	DatasetsWebService.getDatasetSamples(DatasetArg<?> datasetArg, QuantitationTypeArg<?> quantitationTypeArg, boolean useProcessedQuantitationType, CursorArg cursorArg, LimitArg limitArg, ExcludeArg<BioAssayValueObject> excludeArg, boolean includePredictedOutliers)	Retrieves the samples for the given dataset.

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

Modifier	Constructor	Description
	CursorPaginatedResponseDataObjectBioAssayValueObject(CursorPage<BioAssayValueObject> payload, String[] groupBy)
	ResponseDataObjectListBioAssayValueObject(List<BioAssayValueObject> payload)

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

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

Modifier and Type	Method	Description
List<BioAssayValueObject>	DatasetArgService.getSamples(DatasetArg<?> arg, boolean includePredictedOutliers)
List<BioAssayValueObject>	DatasetArgService.getSamples(DatasetArg<?> datasetArg, QuantitationType qt, boolean includePredictedOutliers)	Obtain a collection of BioAssays that represent the experiments samples for a particular quantitation type.
CursorPage<BioAssayValueObject>	DatasetArgService.getSamplesByCursor(DatasetArg<?> arg, Cursor cursor, int limit, boolean includePredictedOutliers)	Cursor-mode counterpart to DatasetArgService.getSamples(DatasetArg, boolean) for the GET /datasets/{dataset}/samples endpoint — see CURSOR_PAGINATION_STEP1_PLAN.md step 1k.
List<BioAssayValueObject>	DatasetArgService.getSubSetSamples(DatasetArg<?> datasetArg, Long subSetId, boolean includePredictedOutliers)
CursorPage<BioAssayValueObject>	DatasetArgService.getSubSetSamplesByCursor(DatasetArg<?> datasetArg, Long subSetId, Cursor cursor, int limit, boolean includePredictedOutliers)	Cursor-mode counterpart to DatasetArgService.getSubSetSamples(DatasetArg, Long, boolean) for the GET /datasets/{dataset}/subSets/{subSet}/samples endpoint — see CURSOR_PAGINATION_STEP1_PLAN.md step 1u (the subset-scoped twin of step 1k for GET /datasets/{dataset}/samples).

Method parameters in ubic.gemma.rest.util.args with type arguments of type BioAssayValueObject

Modifier and Type	Method	Description
void	DatasetArgService.populateOutliers(ExpressionExperiment ee, Collection<BioAssayValueObject> bioAssayValueObjects)	Set BioAssayValueObject.getPredictedOutlier() from the median-correlation algorithm.