Uses of Class
ubic.gemma.model.expression.experiment.ExperimentalDesign

Packages that use ExperimentalDesign

Package	Description
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util

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

Methods in ubic.gemma.model.analysis.expression.diff with parameters of type ExperimentalDesign

Modifier and Type	Method	Description
static DifferentialExpressionAnalysis	RandomDifferentialExpressionAnalysisUtils.randomAnalysis(BioAssaySet experimentAnalyzed, ExperimentalDesign design, ArrayDesign platform)

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

Subclasses with type arguments of type ExperimentalDesign in ubic.gemma.model.expression.experiment

Modifier and Type	Class	Description
class	ExperimentalDesignValueObject	Full structural representation of an ExperimentalDesign: factors, their factor values (with statements carrying stable database IDs), and the assignment of biomaterials to factor values.

Methods in ubic.gemma.model.expression.experiment that return ExperimentalDesign

Modifier and Type	Method	Description
ExperimentalDesign	ExperimentalFactor.getExperimentalDesign()
ExperimentalDesign	ExpressionExperiment.getExperimentalDesign()
static ExperimentalDesign	ExperimentalDesign.Factory.newInstance()

Methods in ubic.gemma.model.expression.experiment with parameters of type ExperimentalDesign

Modifier and Type	Method	Description
static Map<ExperimentalFactor, Map<BioMaterial, FactorValue>>	ExperimentalDesignUtils.getFactorValueMap(ExperimentalDesign experimentalDesign, Collection<BioMaterial> samples)	Create a mapping of samples to factor values for all factors in the experimental design.
static ExperimentalFactor	ExperimentalFactor.Factory.newInstance(ExperimentalDesign ed, String name, FactorType factorType)
void	ExperimentalFactor.setExperimentalDesign(ExperimentalDesign experimentalDesign)
void	ExpressionExperiment.setExperimentalDesign(ExperimentalDesign experimentalDesign)

Constructors in ubic.gemma.model.expression.experiment with parameters of type ExperimentalDesign

Modifier	Constructor	Description
	ExperimentalDesignValueObject(ExperimentalDesign ed, Collection<BioAssay> bioAssays)	Build the design VO from an ExperimentalDesign and the BioAssays of the owning experiment.

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

Subclasses with type arguments of type ExperimentalDesign in ubic.gemma.persistence.service.expression.experiment

Modifier and Type	Class	Description
class	ExperimentalDesignDaoImpl
class	ExperimentalDesignServiceImpl	Spring Service base class for ubic.gemma.model.expression.experiment.ExperimentalDesignService, provides access to all services and entities referenced by this service.

Subinterfaces with type arguments of type ExperimentalDesign in ubic.gemma.persistence.service.expression.experiment

Modifier and Type	Interface	Description
interface	ExperimentalDesignDao
interface	ExperimentalDesignService

Methods in ubic.gemma.persistence.service.expression.experiment that return ExperimentalDesign

Modifier and Type	Method	Description
ExperimentalDesign	ExperimentalDesignDaoImpl.find(ExperimentalDesign experimentalDesign)
ExperimentalDesign	ExperimentalDesignDao.getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign excludedDesign)	Pick a random experimental design that needs attention.
ExperimentalDesign	ExperimentalDesignDaoImpl.getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign excludedDesign)
ExperimentalDesign	ExperimentalDesignReadService.getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign excludeDesign)
ExperimentalDesign	ExperimentalDesignReadServiceImpl.getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign excludedDesign)
ExperimentalDesign	ExperimentalDesignService.getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign excludeDesign)	Obtain a random experimental design that needs attention.
ExperimentalDesign	ExperimentalDesignServiceImpl.getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign excludedDesign)
ExperimentalDesign	ExperimentalDesignReadService.loadWithExperimentalFactors(Long id)
ExperimentalDesign	ExperimentalDesignReadServiceImpl.loadWithExperimentalFactors(Long id)
ExperimentalDesign	ExperimentalDesignService.loadWithExperimentalFactors(Long id)
ExperimentalDesign	ExperimentalDesignServiceImpl.loadWithExperimentalFactors(Long id)

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type ExperimentalDesign

Modifier and Type	Method	Description
ExperimentalDesign	ExperimentalDesignDaoImpl.find(ExperimentalDesign experimentalDesign)
ExpressionExperiment	ExpressionExperimentDao.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentReadService.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentService.findByDesign(ExperimentalDesign ed)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByDesign(ExperimentalDesign ed)
Long	ExpressionExperimentDao.findIdByDesign(ExperimentalDesign design)
Long	ExpressionExperimentDaoImpl.findIdByDesign(ExperimentalDesign ed)
Long	ExpressionExperimentReadService.findIdByDesign(ExperimentalDesign design)
Long	ExpressionExperimentReadServiceImpl.findIdByDesign(ExperimentalDesign design)
Long	ExpressionExperimentService.findIdByDesign(ExperimentalDesign design)
Long	ExpressionExperimentServiceImpl.findIdByDesign(ExperimentalDesign design)
ExperimentalDesign	ExperimentalDesignDao.getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign excludedDesign)	Pick a random experimental design that needs attention.
ExperimentalDesign	ExperimentalDesignDaoImpl.getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign excludedDesign)
ExperimentalDesign	ExperimentalDesignReadService.getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign excludeDesign)
ExperimentalDesign	ExperimentalDesignReadServiceImpl.getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign excludedDesign)
ExperimentalDesign	ExperimentalDesignService.getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign excludeDesign)	Obtain a random experimental design that needs attention.
ExperimentalDesign	ExperimentalDesignServiceImpl.getRandomExperimentalDesignThatNeedsAttention(ExperimentalDesign excludedDesign)
Collection<FactorValue>	FactorValueDao.loadByExperimentalDesignWithCharacteristics(ExperimentalDesign ed)	Load all FactorValues belonging to the given ExperimentalDesign with their characteristics (and measurement, which is mapped fetch="join" so it is loaded with the FV itself) fetched in a single round-trip.
Collection<FactorValue>	FactorValueDaoImpl.loadByExperimentalDesignWithCharacteristics(ExperimentalDesign ed)

Uses of ExperimentalDesign in ubic.gemma.persistence.util

Subclasses with type arguments of type ExperimentalDesign in ubic.gemma.persistence.util

Modifier and Type	Class	Description
class	EntityUrlBuilder.ExperimentalDesignWebUrl