Uses of Class
ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject

Packages that use DoubleVectorValueObject

Package	Description
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.visualization
ubic.gemma.model.expression.bioAssayData
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.visualization

Uses of DoubleVectorValueObject in ubic.gemma.core.analysis.preprocess.svd

Methods in ubic.gemma.core.analysis.preprocess.svd that return types with arguments of type DoubleVectorValueObject

Modifier and Type	Method	Description
Map<ProbeLoading,DoubleVectorValueObject>	SVDService.getTopLoadedVectors(Long eeId, int component, int count)
Map<ProbeLoading,DoubleVectorValueObject>	SVDServiceHelper.getTopLoadedVectors(ExpressionExperiment ee, int component, int count)
Map<ProbeLoading,DoubleVectorValueObject>	SVDServiceHelperImpl.getTopLoadedVectors(ExpressionExperiment ee, int component, int count)
Map<ProbeLoading,DoubleVectorValueObject>	SVDServiceImpl.getTopLoadedVectors(Long eeId, int component, int count)

Uses of DoubleVectorValueObject in ubic.gemma.core.visualization

Method parameters in ubic.gemma.core.visualization with type arguments of type DoubleVectorValueObject

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

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

Subclasses of DoubleVectorValueObject in ubic.gemma.model.expression.bioAssayData

Modifier and Type	Class	Description
class	SlicedDoubleVectorValueObject

Constructors in ubic.gemma.model.expression.bioAssayData with parameters of type DoubleVectorValueObject

Constructor	Description
DataVectorValueObject(DoubleVectorValueObject dvvo)	Copy constructor
DoubleVectorValueObject(DoubleVectorValueObject dvvo)	Copy constructor.
SlicedDoubleVectorValueObject(DoubleVectorValueObject vec, ExpressionExperimentSubSet bioassaySet, BioAssayDimensionValueObject slicedBad)	Constructor for creating a slice.
VectorElementValueObject(DoubleVectorValueObject vector)

Constructor parameters in ubic.gemma.model.expression.bioAssayData with type arguments of type DoubleVectorValueObject

Constructor	Description
ExperimentExpressionLevelsValueObject(long datasetId, Map<Gene,List<DoubleVectorValueObject>> vectorsPerGene, boolean keepGeneNonSpecific, String conslidationMode)
GeneElementExpressionsValueObject(String geneOfficialSymbol, Integer geneNcbiId, List<DoubleVectorValueObject> vectors, boolean keepGeneNonSpecific, String mode)

Uses of DoubleVectorValueObject in ubic.gemma.persistence.service.expression.bioAssayData

Methods in ubic.gemma.persistence.service.expression.bioAssayData that return types with arguments of type DoubleVectorValueObject

Modifier and Type	Method	Description
List<DoubleVectorValueObject>	ProcessedExpressionDataVectorService.getDiffExVectors(Long resultSetId, double threshold, int maxNumberOfResults)
List<DoubleVectorValueObject>	ProcessedExpressionDataVectorServiceImpl.getDiffExVectors(Long resultSetId, double threshold, int maxNumberOfResults)
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorService.getProcessedDataArrays(Collection<? extends BioAssaySet> expressionExperiments, Collection<Long> genes)	Retrieve processed vectors by genes and experiments.
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorService.getProcessedDataArrays(BioAssaySet expressionExperiment)	Retrieve processed vectors for a given experiment or subset.
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorService.getProcessedDataArrays(BioAssaySet expressionExperiment, Collection<Long> genes)	Retrieve processed vectors by genes for a given experiment or subset.
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorServiceImpl.getProcessedDataArrays(Collection<? extends BioAssaySet> expressionExperiments, Collection<Long> genes)
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorServiceImpl.getProcessedDataArrays(BioAssaySet expressionExperiment)
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorServiceImpl.getProcessedDataArrays(BioAssaySet expressionExperiment, Collection<Long> genes)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorService.getProcessedDataArrays(Collection<ExpressionExperiment> expressionExperiments, Collection<Long> genes)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorService.getProcessedDataArrays(BioAssaySet bioAssaySet, Collection<Long> genes)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorService.getProcessedDataArrays(ExpressionExperiment expressionExperiment)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataArrays(Collection<ExpressionExperiment> expressionExperiments, Collection<Long> genes)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataArrays(BioAssaySet bioAssaySet, Collection<Long> genes)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataArrays(ExpressionExperiment expressionExperiment)
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorService.getProcessedDataArraysByProbe(Collection<? extends BioAssaySet> expressionExperiments, Collection<CompositeSequence> probes)	Retrieves processed vectors by probes and experiments
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorServiceImpl.getProcessedDataArraysByProbe(Collection<? extends BioAssaySet> ees, Collection<CompositeSequence> probes)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorService.getProcessedDataArraysByProbe(Collection<ExpressionExperiment> expressionExperiments, Collection<CompositeSequence> compositeSequences)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataArraysByProbe(Collection<ExpressionExperiment> expressionExperiments, Collection<CompositeSequence> compositeSequences)
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorService.getProcessedDataArraysByProbeIds(BioAssaySet ee, Collection<Long> probes)
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorServiceImpl.getProcessedDataArraysByProbeIds(BioAssaySet ee, Collection<Long> probes)
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorService.getRandomProcessedDataArrays(BioAssaySet expressionExperiment, int limit)	Retrieve random processed vectors for a given experiment or subset.
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorServiceImpl.getRandomProcessedDataArrays(BioAssaySet ee, int limit)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorService.getRandomProcessedDataArrays(ExpressionExperiment ee, int limit)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorServiceImpl.getRandomProcessedDataArrays(ExpressionExperiment ee, int limit)

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

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

Modifier and Type	Method	Description
Map<ExpressionExperimentValueObject,Map<Long,Collection<DoubleVectorValueObject>>>	DEDVController.getDEDV(Collection<Long> eeIds, Collection<Long> geneIds)	Given a collection of expression experiment Ids and a geneId returns a map of DEDV value objects to a collection of genes.

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

Constructors in ubic.gemma.web.controller.visualization with parameters of type DoubleVectorValueObject

Constructor	Description
ExpressionProfileDataObject(DoubleVectorValueObject data)
GeneExpressionProfile(DoubleVectorValueObject vector)
GeneExpressionProfile(DoubleVectorValueObject vector, Collection<GeneValueObject> genes)
GeneExpressionProfile(DoubleVectorValueObject vector, Collection<GeneValueObject> genes, String color, Integer factor, Double pValue)
GeneExpressionProfile(DoubleVectorValueObject vector, Collection<GeneValueObject> genes, String color, Integer factor, Double pValue, boolean standardize)
VisualizationValueObject(DoubleVectorValueObject dvvo)

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

Constructor	Description
VisualizationValueObject(Collection<DoubleVectorValueObject> vectors, Collection<GeneValueObject> genes, Double minPvalue, Collection<DifferentialExpressionValueObject> validatedProbes)
VisualizationValueObject(Collection<DoubleVectorValueObject> vectors, List<GeneValueObject> genes, Collection<Long> validatedProbeList)
VisualizationValueObject(Collection<DoubleVectorValueObject> vectors, List<GeneValueObject> genes, Collection<Long> validatedProbeIdList, Double minPvalue)