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

Packages that use BioAssayValueObject

Package	Description
ubic.gemma.core.visualization
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.rest
ubic.gemma.rest.util.args
ubic.gemma.web.controller.expression.bioAssay
ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.visualization
ubic.gemma.web.taglib.expression.experiment

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.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

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>	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)

Uses of BioAssayValueObject in ubic.gemma.rest

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

Modifier and Type	Method	Description
ResponseDataObject<List<BioAssayValueObject>>	DatasetsWebService.getDatasetSamples(DatasetArg<?> datasetArg, QuantitationTypeArg<?> quantitationTypeArg, boolean useProcessedQuantitationType)	Retrieves the samples for the given dataset.
ResponseDataObject<List<BioAssayValueObject>>	DatasetsWebService.getDatasetSubSetSamples(DatasetArg<?> datasetArg, Long subSetId)

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)
List<BioAssayValueObject>	DatasetArgService.getSamples(DatasetArg<?> datasetArg, QuantitationType qt)	Obtain a collection of BioAssays that represent the experiments samples for a particular quantitation type.
List<BioAssayValueObject>	DatasetArgService.getSubSetSamples(DatasetArg<?> datasetArg, Long subSetId)

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)

Uses of BioAssayValueObject in ubic.gemma.web.controller.expression.bioAssay

Methods in ubic.gemma.web.controller.expression.bioAssay that return types with arguments of type BioAssayValueObject

Modifier and Type	Method	Description
Collection<BioAssayValueObject>	BioAssayController.getBioAssays(Long eeId)

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

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

Modifier and Type	Method	Description
Collection<BioAssayValueObject>	ExpressionExperimentEditController.ExpressionExperimentEditForm.getBioAssays()
Collection<BioAssayValueObject>	ExpressionExperimentEditValueObject.getBioAssays()

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

Modifier and Type	Method	Description
void	ExpressionExperimentEditController.ExpressionExperimentEditForm.setBioAssays(Collection<BioAssayValueObject> bioAssays)
void	ExpressionExperimentEditValueObject.setBioAssays(Collection<BioAssayValueObject> bioAssays)

Uses of BioAssayValueObject in ubic.gemma.web.controller.visualization

Method parameters in ubic.gemma.web.controller.visualization with type arguments of type BioAssayValueObject

Modifier and Type	Method	Description
void	VisualizationValueObject.setUpFactorProfiles(LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>> layout)	Initialize the factor profiles.

Constructor parameters in ubic.gemma.web.controller.visualization with type arguments of type BioAssayValueObject

Modifier	Constructor	Description
	FactorProfile(ExperimentalFactor ef, LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>> layouts)

Uses of BioAssayValueObject in ubic.gemma.web.taglib.expression.experiment

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

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