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

Packages that use FactorValue

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.singleCell	This package contains classes for analysing single-cell expression data.
ubic.gemma.core.analysis.singleCell.aggregate	This package contains classes for subsetting and aggregating single-cell data.
ubic.gemma.core.loader.expression	This package contains interfaces and classes for loading expression data.
ubic.gemma.core.loader.expression.singleCell	This package contains classes for loading single-cell expression data.
ubic.gemma.core.ontology
ubic.gemma.core.visualization.cellbrowser	This package contains classes related to the Cell Browser visualization tool.
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.util.args

Uses of FactorValue in ubic.gemma.core.analysis.expression.diff

Methods in ubic.gemma.core.analysis.expression.diff that return FactorValue

Modifier and Type	Method	Description
FactorValue	DifferentialExpressionAnalysisConfig.getSubsetFactorValue()	If this is non-null, this is a subset analysis for this factor value.

Methods in ubic.gemma.core.analysis.expression.diff that return types with arguments of type FactorValue

Modifier and Type	Method	Description
static Map<ExperimentalFactor, FactorValue>	BaselineSelection.getBaselineConditions(Collection<BioMaterial> samplesUsed, Collection<ExperimentalFactor> factors)
static Map<ExperimentalFactor, FactorValue>	BaselineSelection.getBaselineLevels(Collection<ExperimentalFactor> factors)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
static Map<ExperimentalFactor, FactorValue>	BaselineSelection.getBaselineLevels(Collection<ExperimentalFactor> factors, Collection<BioMaterial> samplesUsed)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
static List<FactorValue>	BaselineSelection.getExplicitBaselines(ExperimentalFactor factor, Collection<BioMaterial> samplesUsed)	The factor values a curator has EXPLICITLY marked as baseline on this factor, restricted to those the given samples actually use.

Methods in ubic.gemma.core.analysis.expression.diff with parameters of type FactorValue

Modifier and Type	Method	Description
static boolean	BaselineSelection.isBaselineCondition(FactorValue factorValue)	Check if a given factor value indicates a baseline condition.
static boolean	BaselineSelection.isForcedBaseline(FactorValue fv)	Check if this factor value is the baseline, overriding other possible baselines.
static String	DiffExAnalyzerUtils.nameForR(FactorValue fv, boolean isBaseline)	Create a name for the factor value that is suitable for R.
void	DifferentialExpressionAnalysisConfig.setSubsetFactorValue(FactorValue subsetFactorValue)	If this is non-null, this is a subset analysis for this factor value.

Method parameters in ubic.gemma.core.analysis.expression.diff with type arguments of type FactorValue

Modifier and Type	Method	Description
static ObjectMatrix<String,String,Object>	DiffExAnalyzerUtils.buildRDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor, FactorValue> baselines, boolean allowMissingValues)	A variant of DiffExAnalyzerUtils.buildRDesignMatrix(List, List, boolean) that allows for reusing baselines for repeated calls.
static Protocol	DiffExAnalyzerUtils.createProtocolForConfig(DifferentialExpressionAnalysisConfig config, Map<ExperimentalFactor, FactorValue> baselineFactorValues)
static void	DiffExAnalyzerUtils.populateFactorValuesFromBASet(BioAssaySet ee, ExperimentalFactor f, Collection<FactorValue> fvs)
Collection<DifferentialExpressionAnalysis>	DiffExAnalyzer.run(ExpressionExperiment expressionExperiment, Map<FactorValue, ExpressionExperimentSubSet> subsets, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Analyze a dataset with a pre-existing subset structure.
Collection<DifferentialExpressionAnalysis>	LinearModelAnalyzer.run(ExpressionExperiment ee, Map<FactorValue, ExpressionExperimentSubSet> subsets, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)

Uses of FactorValue in ubic.gemma.core.analysis.singleCell

Methods in ubic.gemma.core.analysis.singleCell that return types with arguments of type FactorValue

Modifier and Type	Method	Description
static Map<Characteristic, Set<FactorValue>>	CellLevelCharacteristicsMappingUtils.createFullMappingByFactorValueCharacteristics(CellLevelCharacteristics clc, ExperimentalFactor factor)	Create a full mapping of cell types from a cell type assignment to factor values in a cell type factor.
static Map<Characteristic, FactorValue>	CellLevelCharacteristicsMappingUtils.createMappingByFactorValueCharacteristics(CellLevelCharacteristics cta, ExperimentalFactor factor)	Map the cell types from a cell type assignment to factor values in a cell type factor.
static Map<Characteristic, FactorValue>	CellLevelCharacteristicsMappingUtils.createMappingBySubSetCharacteristics(CellLevelCharacteristics clc, ExperimentalFactor factor, Map<FactorValue, ExpressionExperimentSubSet> subsets)	Infer the mapping of cell type assignments to factor values using a subset structure.
static Map<Characteristic, FactorValue>	CellLevelCharacteristicsMappingUtils.readMappingFromFile(CellLevelCharacteristics clc, ExperimentalFactor factor, Path cellTypeMappingFile)	Create a mapping of cell type assignments to factor values from a file.

Method parameters in ubic.gemma.core.analysis.singleCell with type arguments of type FactorValue

Modifier and Type	Method	Description
static Map<Characteristic, FactorValue>	CellLevelCharacteristicsMappingUtils.createMappingBySubSetCharacteristics(CellLevelCharacteristics clc, ExperimentalFactor factor, Map<FactorValue, ExpressionExperimentSubSet> subsets)	Infer the mapping of cell type assignments to factor values using a subset structure.
static String	CellLevelCharacteristicsMappingUtils.printMapping(Map<Characteristic, FactorValue> mappedCellTypeFactors)
static void	CellLevelCharacteristicsMappingUtils.printMapping(Map<Characteristic, FactorValue> mappedCellTypeFactors, Appendable details)
static void	CellLevelCharacteristicsMappingUtils.writeMapping(CellLevelCharacteristics cta, ExperimentalFactor factor, Map<Characteristic, FactorValue> cta2f, Writer dest)	Create a mapping of cell type assignments to factor values from a file.

Uses of FactorValue in ubic.gemma.core.analysis.singleCell.aggregate

Method parameters in ubic.gemma.core.analysis.singleCell.aggregate with type arguments of type FactorValue

Modifier and Type	Method	Description
QuantitationType	SingleCellExpressionExperimentAggregateService.aggregateVectors(ExpressionExperiment ee, QuantitationType qt, List<BioAssay> cellBAs, CellLevelCharacteristics cellLevelCharacteristics, ExperimentalFactor factor, Map<Characteristic, FactorValue> cellTypeMapping, SingleCellAggregationConfig config)	Aggregate preferred single-cell data vectors by the given cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentAggregateServiceImpl.aggregateVectors(ExpressionExperiment ee, QuantitationType qt, List<BioAssay> cellBAs, CellLevelCharacteristics cellLevelCharacteristics, ExperimentalFactor factor, Map<Characteristic, FactorValue> cellType2Factor, SingleCellAggregationConfig config)
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSubSetService.createSubSets(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic, FactorValue> cellTypeMapping, SingleCellExperimentSubSetsCreationConfig config)	Subset biomaterials and bioassays by the given CellLevelCharacteristics.
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSubSetServiceImpl.createSubSets(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic, FactorValue> mappedCellTypeFactors, SingleCellExperimentSubSetsCreationConfig config)
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateService.createSubSetsAndAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics cta, ExperimentalFactor cellTypeFactor, Map<Characteristic, FactorValue> c2f, SingleCellExperimentSubSetsCreationConfig singleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig config)	Create subsets and aggregate by any cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.createSubSetsAndAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor cellTypeFactor, Map<Characteristic, FactorValue> c2f, SingleCellExperimentSubSetsCreationConfig singleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig config)	See SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.createSubSetsAndAggregateByCellType(ExpressionExperiment, SingleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig) for why this is Propagation.NEVER.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateService.redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic, FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)	Re-aggregate a dataset by any cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic, FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)

Uses of FactorValue in ubic.gemma.core.loader.expression

Method parameters in ubic.gemma.core.loader.expression with type arguments of type FactorValue

Modifier and Type	Method	Description
Set<ExperimentalFactor>	AbstractDelegatingDataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial, Set<FactorValue>> factorValueAssignments)
Set<ExperimentalFactor>	DataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial, Set<FactorValue>> factorValueAssignments)	Load experimental factors present in the data.

Uses of FactorValue in ubic.gemma.core.loader.expression.singleCell

Method parameters in ubic.gemma.core.loader.expression.singleCell with type arguments of type FactorValue

Modifier and Type	Method	Description
Set<ExperimentalFactor>	AnnDataSingleCellDataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial, Set<FactorValue>> factorValueAssignments)
Set<ExperimentalFactor>	MexSingleCellDataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial, Set<FactorValue>> factorValueAssignments)	MEX does not provide experimental factors.
Set<ExperimentalFactor>	NullSingleCellDataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial, Set<FactorValue>> factorValueAssignments)

Uses of FactorValue in ubic.gemma.core.ontology

Methods in ubic.gemma.core.ontology with parameters of type FactorValue

Modifier and Type	Method	Description
static Map<String, FactorValueOntologyUtils.Annotation>	FactorValueOntologyUtils.getAnnotationsById(FactorValue fv)	Create a mapping of annotation IDs to annotations for a FactorValue.
static String	FactorValueOntologyUtils.getUri(FactorValue factorValue)	Obtain a suitable ontology ID for a given factor value.

Uses of FactorValue in ubic.gemma.core.visualization.cellbrowser

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

Modifier and Type	Method	Description
void	CellBrowserMetadataWriter.writeCell(BioAssay bioAssay, String cellId, int cellIndex, List<ExperimentalFactor> factors, Map<ExperimentalFactor, Map<BioMaterial, FactorValue>> factorValueMap, SortedMap<Category, Map<BioAssay, Characteristic>> bioAssayCharacteristics, SortedMap<Category, Map<BioMaterial, Characteristic>> sampleCharacteristics, List<CellLevelCharacteristics> clcs, Writer writer)

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

Methods in ubic.gemma.model.analysis.expression.diff that return FactorValue

Modifier and Type	Method	Description
FactorValue	DiffExResultSetSummaryValueObject.Prefetch.getBaselineGroup()
FactorValue	ExpressionAnalysisResultSet.getBaselineGroup()
FactorValue	Baseline.getFactorValue()
FactorValue	Contrast.getFactorValue()
FactorValue	ContrastResult.getFactorValue()
FactorValue	Baseline.getSecondFactorValue()
FactorValue	Contrast.getSecondFactorValue()
FactorValue	ContrastResult.getSecondFactorValue()
FactorValue	DifferentialExpressionAnalysis.getSubsetFactorValue()	If non-null, a factor value applicable to the ExpressionExperimentSubSet being analyzed.

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

Modifier and Type	Method	Description
List<FactorValue>	Contrast.getFactorValues()

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

Modifier and Type	Method	Description
static Baseline	Baseline.categorical(FactorValue fv)	Create a baseline for a single categorical factor.
static Contrast	Contrast.categorical(FactorValue fv)	Create a contrast for a categorical factor.
static Baseline	Baseline.interaction(FactorValue fv1, FactorValue fv2)	Create a baseline for an interaction of factors.
static Contrast	Contrast.interaction(FactorValue fv1, FactorValue fv2)	Create an interaction of two categorical factors.
static ContrastResult	ContrastResult.Factory.newInstance(Double pvalue, Double tstat, Double coefficient, Double logFoldChange, FactorValue factorValue, FactorValue secondFactorValue)
static ExpressionAnalysisResultSet	ExpressionAnalysisResultSet.Factory.newInstance(Set<ExperimentalFactor> experimentalFactors, Integer numberOfProbesTested, Integer numberOfGenesTested, FactorValue baselineGroup, Set<DifferentialExpressionAnalysisResult> results, DifferentialExpressionAnalysis analysis, PvalueDistribution pvalueDistribution, Set<HitListSize> hitListSizes)
void	ExpressionAnalysisResultSet.setBaselineGroup(FactorValue baselineGroup)
void	ContrastResult.setFactorValue(FactorValue factorValue)
void	ContrastResult.setSecondFactorValue(FactorValue secondFactorValue)
void	DifferentialExpressionAnalysis.setSubsetFactorValue(FactorValue subsetFactorValue)

Constructors in ubic.gemma.model.analysis.expression.diff with parameters of type FactorValue

Modifier	Constructor	Description
	Prefetch(Set<ExperimentalFactor> experimentalFactors, FactorValue baselineGroup)

Uses of FactorValue in ubic.gemma.model.expression.biomaterial

Methods in ubic.gemma.model.expression.biomaterial that return types with arguments of type FactorValue

Modifier and Type	Method	Description
Set<FactorValue>	BioMaterial.getAllFactorValues()	Obtain all the FactorValue associated to this biomaterial, including those inherited from its ancestors via BioMaterial.getSourceBioMaterial().
Set<FactorValue>	BioMaterial.getFactorValues()	Obtain the values that this BioAssay is associated with for the experiment.

Method parameters in ubic.gemma.model.expression.biomaterial with type arguments of type FactorValue

Modifier and Type	Method	Description
void	BioMaterial.setFactorValues(Set<FactorValue> factorValues)

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

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

Modifier and Type	Class	Description
class	AbstractFactorValueValueObject	The bare minimum to represent a factor value.

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

Modifier and Type	Method	Description
static FactorValue	FactorValue.Factory.newInstance()
static FactorValue	FactorValue.Factory.newInstance(ExperimentalFactor experimentalFactor)
static FactorValue	FactorValue.Factory.newInstance(ExperimentalFactor factor, Characteristic c)	Create a FactorValue with a single characteristic.
static FactorValue	FactorValue.Factory.newInstance(ExperimentalFactor factor, Measurement measurement)	Create a FactorValue with a measurement.
static FactorValue	FactorValue.Factory.newInstance(ExperimentalFactor factor, Statement c)	Create a FactorValue with a single statement.

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

Modifier and Type	Method	Description
static Map<ExperimentalFactor, Map<BioMaterial, FactorValue>>	ExperimentalDesignUtils.getFactorValueMap(Collection<ExperimentalFactor> factors, Collection<BioMaterial> samples)
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.
Set<FactorValue>	ExperimentalFactor.getFactorValues()

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

Modifier and Type	Method	Description
static String	FactorValueUtils.getSummaryString(FactorValue fv)	Produce a summary string for this factor value.
static String	FactorValueUtils.getSummaryString(FactorValue fv, String statementDelimiter)
static String	FactorValueUtils.getSummaryString(FactorValue fv, Characteristic category, String statementDelimiter)
static String	FactorValueUtils.getValue(FactorValue fv, String delimiter)	Produce a value for representing a factor value.
static String[]	FactorValueUtils.getValues(FactorValue fv)
static boolean	FactorValueUtils.isDeExcluded(FactorValue fv)	Check if a factor value marks its samples for exclusion from differential expression analysis.
static boolean	FactorValueUtils.isDeIncludeExcludeMarker(FactorValue fv)	Check if a factor value is one of the two DE_Include/DE_Exclude markers.

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

Modifier and Type	Method	Description
void	ExperimentalFactor.setFactorValues(Set<FactorValue> factorValues)

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

Modifier	Constructor	Description
protected	AbstractFactorValueValueObject(FactorValue fv, boolean includeExperimentalFactor)
	FactorValueBasicValueObject(FactorValue fv)
	FactorValueValueObject(FactorValue value)	Deprecated.
	FactorValueValueObject(FactorValue value, boolean includeExperimentalFactor)	Deprecated. Create a FactorValue VO.
	FactorValueValueObject(FactorValue fv, Statement c)	Deprecated. Create a FactorValue VO focusing on a specific statement.

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

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

Modifier and Type	Class	Description
class	FactorValueDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.experiment.FactorValue.
class	FactorValueServiceImpl	Spring Service base class for FactorValueService, provides access to all services and entities referenced by this service.

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

Modifier and Type	Interface	Description
interface	FactorValueDao
interface	FactorValueService
interface	FactorValueService

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

Modifier and Type	Method	Description
FactorValue	ExpressionExperimentService.addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue	ExpressionExperimentServiceImpl.addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue	ExpressionExperimentWriteService.addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue	ExpressionExperimentWriteServiceImpl.addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue	FactorValueDaoImpl.create(FactorValue factorValue)
FactorValue	FactorValueDaoImpl.find(FactorValue factorValue)
FactorValue	FactorValueReadService.loadWithExperimentalFactor(Long id)	Load a FactorValue by id and eagerly initialize its experimental factor.
FactorValue	FactorValueReadServiceImpl.loadWithExperimentalFactor(Long id)
FactorValue	FactorValueService.loadWithExperimentalFactor(Long id)
FactorValue	FactorValueServiceImpl.loadWithExperimentalFactor(Long id)
<T extends Exception> FactorValue	FactorValueReadService.loadWithExperimentalFactorOrFail(Long id, Function<String,T> exceptionSupplier)	Load a FactorValue with an initialized experimental factor, or throw the supplied exception if no such factor value exists.
<T extends Exception> FactorValue	FactorValueReadServiceImpl.loadWithExperimentalFactorOrFail(Long id, Function<String,T> exceptionSupplier)
<T extends Exception> FactorValue	FactorValueService.loadWithExperimentalFactorOrFail(Long id, Function<String,T> exceptionSupplier)	Load a FactorValue with an initialized experimental factor or fail.
<T extends Exception> FactorValue	FactorValueServiceImpl.loadWithExperimentalFactorOrFail(Long id, Function<String,T> exceptionSupplier)
FactorValue	FactorValueDao.loadWithOldStyleCharacteristics(Long id, boolean readOnly)	Deprecated.
FactorValue	FactorValueDaoImpl.loadWithOldStyleCharacteristics(Long id, boolean readOnly)	Deprecated.
FactorValue	FactorValueReadService.loadWithOldStyleCharacteristics(Long id, boolean readOnly)	Deprecated. do not use, this is only for migrating old-style characteristics to statements and will be removed
FactorValue	FactorValueReadServiceImpl.loadWithOldStyleCharacteristics(Long id, boolean readOnly)
FactorValue	FactorValueService.loadWithOldStyleCharacteristics(Long id, boolean readOnly)	Deprecated. do not use this, it is only meant for the purpose of migrating old-style characteristics to statements
FactorValue	FactorValueServiceImpl.loadWithOldStyleCharacteristics(Long id, boolean readOnly)	Deprecated.
FactorValue	FactorValueDaoImpl.save(FactorValue entity)

Methods in ubic.gemma.persistence.service.expression.experiment that return types with arguments of type FactorValue

Modifier and Type	Method	Description
Collection<FactorValue>	FactorValueDao.findByValueStartingWith(String valuePrefix, int maxResults)	Deprecated.
Collection<FactorValue>	FactorValueDaoImpl.findByValueStartingWith(String valuePrefix, int maxResults)
Collection<FactorValue>	FactorValueReadService.findByValueStartingWith(String valuePrefix, int maxResults)	Deprecated. because FactorValue.getValue() is deprecated
Collection<FactorValue>	FactorValueReadServiceImpl.findByValueStartingWith(String valuePrefix, int maxResults)
Collection<FactorValue>	FactorValueService.findByValueStartingWith(String valuePrefix, int maxResults)	Deprecated. because FactorValue.getValue() is deprecated
Collection<FactorValue>	FactorValueServiceImpl.findByValueStartingWith(String valuePrefix, int maxResults)	Deprecated.
Map<FactorValue, Characteristic>	FactorValueDao.getExperimentalFactorCategories(Collection<FactorValue> factorValues)
Map<FactorValue, Characteristic>	FactorValueDaoImpl.getExperimentalFactorCategories(Collection<FactorValue> factorValues)
Map<FactorValue, Characteristic>	FactorValueReadService.getExperimentalFactorCategoriesIgnoreAcls(Collection<FactorValue> factorValues)	Return the experimental factor categories of the given factor values.
Map<FactorValue, Characteristic>	FactorValueReadServiceImpl.getExperimentalFactorCategoriesIgnoreAcls(Collection<FactorValue> factorValues)
Map<FactorValue, Characteristic>	FactorValueService.getExperimentalFactorCategoriesIgnoreAcls(Collection<FactorValue> factorValues)	Obtain the categories of the given factor values.
Map<FactorValue, Characteristic>	FactorValueServiceImpl.getExperimentalFactorCategoriesIgnoreAcls(Collection<FactorValue> factorValues)
Map<FactorValue, ExpressionExperiment>	FactorValueDao.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)
Map<FactorValue, ExpressionExperiment>	FactorValueDaoImpl.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)
Map<FactorValue, ExpressionExperiment>	FactorValueReadService.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)	Return the ExpressionExperiment that owns each of the given factor values.
Map<FactorValue, ExpressionExperiment>	FactorValueReadServiceImpl.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)
Map<FactorValue, ExpressionExperiment>	FactorValueService.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)	For efficiency, only the ID, short name and name of the EEs are populated.
Map<FactorValue, ExpressionExperiment>	FactorValueServiceImpl.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)
Collection<FactorValue>	ExpressionExperimentSubSetDao.getFactorValuesUsed(Long subSetId, Long experimentalFactor)
Collection<FactorValue>	ExpressionExperimentSubSetDao.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)	Obtain the FactorValue used by the samples from this subset in the given factor.
Collection<FactorValue>	ExpressionExperimentSubSetDaoImpl.getFactorValuesUsed(Long subSetId, Long experimentalFactor)
Collection<FactorValue>	ExpressionExperimentSubSetDaoImpl.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Collection<FactorValue>	ExpressionExperimentSubSetReadService.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)	Obtain the FactorValues used by samples in the given subset for the given factor.
Collection<FactorValue>	ExpressionExperimentSubSetReadServiceImpl.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Collection<FactorValue>	ExpressionExperimentSubSetService.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Collection<FactorValue>	ExpressionExperimentSubSetServiceImpl.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Map<ExperimentalFactor, Map<FactorValue, ExpressionExperimentSubSet>>	ExpressionExperimentService.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment.
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment and factor.
Map<ExperimentalFactor, Map<FactorValue, ExpressionExperimentSubSet>>	ExpressionExperimentServiceImpl.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)
Map<ExperimentalFactor, Map<FactorValue, ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadService.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Reconstitute the FV-to-subset mapping for a given experiment along all separating factors.
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadService.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV-to-subset mapping for a given experiment and factor.
Map<ExperimentalFactor, Map<FactorValue, ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment and factor.
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadService.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV-to-subset mapping for a given experiment and factor, with subset characteristics initialized and assays thawed.
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)
Slice<FactorValue>	FactorValueDao.loadAll(int offset, int limit)	Load a slice of FactorValues.
Slice<FactorValue>	FactorValueDaoImpl.loadAll(int offset, int limit)
Slice<FactorValue>	FactorValueReadService.loadAll(int offset, int limit)
Slice<FactorValue>	FactorValueReadServiceImpl.loadAll(int offset, int limit)
Slice<FactorValue>	FactorValueService.loadAll(int offset, int limit)	Load a slice of FactorValues.
Slice<FactorValue>	FactorValueServiceImpl.loadAll(int offset, int limit)
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)
Collection<FactorValue>	FactorValueReadService.loadIgnoreAcls(Set<Long> ids)	Load FactorValues by IDs, ignoring ACLs.
Collection<FactorValue>	FactorValueReadServiceImpl.loadIgnoreAcls(Set<Long> ids)
Collection<FactorValue>	FactorValueService.loadIgnoreAcls(Set<Long> ids)	Load FactorValues by IDs, ignoring ACLs.
Collection<FactorValue>	FactorValueServiceImpl.loadIgnoreAcls(Set<Long> ids)

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

Modifier and Type	Method	Description
FactorValue	ExpressionExperimentService.addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue	ExpressionExperimentServiceImpl.addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue	ExpressionExperimentWriteService.addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue	ExpressionExperimentWriteServiceImpl.addFactorValue(ExpressionExperiment ee, FactorValue fv)
void	FactorValueNeedsAttentionService.clearNeedsAttentionFlag(FactorValue factorValue, String note)	Clear a needs attention flag on a given factor value.
void	FactorValueNeedsAttentionServiceImpl.clearNeedsAttentionFlag(FactorValue factorValue, String note)
FactorValue	FactorValueDaoImpl.create(FactorValue factorValue)
Statement	FactorValueService.createStatement(FactorValue factorValue, Statement statement)	Create a given statement and add it to the given factor value.
Statement	FactorValueServiceImpl.createStatement(FactorValue factorValue, Statement statement)
protected FactorValueValueObject	FactorValueDaoImpl.doLoadValueObject(FactorValue entity)
FactorValue	FactorValueDaoImpl.find(FactorValue factorValue)
ExpressionExperiment	ExpressionExperimentDao.findByFactorValue(FactorValue fv)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByFactorValue(FactorValue fv)
ExpressionExperiment	ExpressionExperimentReadService.findByFactorValue(FactorValue factorValue)
ExpressionExperiment	ExpressionExperimentReadServiceImpl.findByFactorValue(FactorValue factorValue)
ExpressionExperiment	ExpressionExperimentService.findByFactorValue(FactorValue factorValue)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByFactorValue(FactorValue factorValue)
Long	ExpressionExperimentDao.findIdByFactorValue(FactorValue factorValue)
Long	ExpressionExperimentDaoImpl.findIdByFactorValue(FactorValue fv)
Long	ExpressionExperimentReadService.findIdByFactorValue(FactorValue factorValue)
Long	ExpressionExperimentReadServiceImpl.findIdByFactorValue(FactorValue factorValue)
Long	ExpressionExperimentService.findIdByFactorValue(FactorValue factor)
Long	ExpressionExperimentServiceImpl.findIdByFactorValue(FactorValue factorValue)
void	FactorValueNeedsAttentionService.markAsNeedsAttention(FactorValue factorValue, String note)	Mark a given factor value as needs attention.
void	FactorValueNeedsAttentionServiceImpl.markAsNeedsAttention(FactorValue factorValue, String note)
void	FactorValueDaoImpl.remove(FactorValue factorValue)
void	FactorValueServiceImpl.remove(FactorValue entity)
void	FactorValueService.removeStatement(FactorValue fv, Statement c)	Remove a statement from a factor value.
void	FactorValueServiceImpl.removeStatement(FactorValue fv, Statement statement)
FactorValue	FactorValueDaoImpl.save(FactorValue entity)
Statement	FactorValueService.saveStatement(FactorValue fv, Statement statement)	Create a given statement as per FactorValueService.createStatement(FactorValue, Statement) if it is transient, otherwise update an existing statement.
Statement	FactorValueServiceImpl.saveStatement(FactorValue fv, Statement statement)
Statement	FactorValueService.saveStatementIgnoreAcl(FactorValue fv, Statement statement)	Deprecated. do not use this, it is meant for FactorValue migration only
Statement	FactorValueServiceImpl.saveStatementIgnoreAcl(FactorValue fv, Statement statement)
void	FactorValueDaoImpl.update(FactorValue entity)
void	FactorValueDao.updateIgnoreAcl(FactorValue fv)	Deprecated. do not use this, it is only a workaround to make FV migration faster
void	FactorValueDaoImpl.updateIgnoreAcl(FactorValue fv)

Method parameters in ubic.gemma.persistence.service.expression.experiment with type arguments of type FactorValue

Modifier and Type	Method	Description
void	ExpressionExperimentService.addFactorValues(ExpressionExperiment ee, Map<BioMaterial, FactorValue> fvs)	Intended with the case of a continuous factor being added.
void	ExpressionExperimentServiceImpl.addFactorValues(ExpressionExperiment ee, Map<BioMaterial, FactorValue> fvs)
void	ExpressionExperimentWriteService.addFactorValues(ExpressionExperiment ee, Map<BioMaterial, FactorValue> fvs)
void	ExpressionExperimentWriteServiceImpl.addFactorValues(ExpressionExperiment ee, Map<BioMaterial, FactorValue> fvs)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByFactorValues(Collection<FactorValue> fvs)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByFactorValues(Collection<FactorValue> fvs)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByFactorValues(Collection<FactorValue> factorValues)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByFactorValues(Collection<FactorValue> factorValues)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByFactorValues(Collection<FactorValue> factorValues)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByFactorValues(Collection<FactorValue> factorValues)
Map<FactorValue, Characteristic>	FactorValueDao.getExperimentalFactorCategories(Collection<FactorValue> factorValues)
Map<FactorValue, Characteristic>	FactorValueDaoImpl.getExperimentalFactorCategories(Collection<FactorValue> factorValues)
Map<FactorValue, Characteristic>	FactorValueReadService.getExperimentalFactorCategoriesIgnoreAcls(Collection<FactorValue> factorValues)	Return the experimental factor categories of the given factor values.
Map<FactorValue, Characteristic>	FactorValueReadServiceImpl.getExperimentalFactorCategoriesIgnoreAcls(Collection<FactorValue> factorValues)
Map<FactorValue, Characteristic>	FactorValueService.getExperimentalFactorCategoriesIgnoreAcls(Collection<FactorValue> factorValues)	Obtain the categories of the given factor values.
Map<FactorValue, Characteristic>	FactorValueServiceImpl.getExperimentalFactorCategoriesIgnoreAcls(Collection<FactorValue> factorValues)
Map<FactorValue, ExpressionExperiment>	FactorValueDao.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)
Map<FactorValue, ExpressionExperiment>	FactorValueDaoImpl.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)
Map<FactorValue, ExpressionExperiment>	FactorValueReadService.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)	Return the ExpressionExperiment that owns each of the given factor values.
Map<FactorValue, ExpressionExperiment>	FactorValueReadServiceImpl.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)
Map<FactorValue, ExpressionExperiment>	FactorValueService.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)	For efficiency, only the ID, short name and name of the EEs are populated.
Map<FactorValue, ExpressionExperiment>	FactorValueServiceImpl.getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)
void	FactorValueServiceImpl.remove(Collection<FactorValue> entities)

Uses of FactorValue in ubic.gemma.persistence.util

Classes in ubic.gemma.persistence.util that implement interfaces with type arguments of type FactorValue

Modifier and Type	Class	Description
class	FactorValueComparator

Methods in ubic.gemma.persistence.util that return FactorValue

Modifier and Type	Method	Description
static FactorValue	BusinessKey.find(Session session, FactorValue factorValue)

Methods in ubic.gemma.persistence.util that return types with arguments of type FactorValue

Modifier and Type	Method	Description
Collection<FactorValue>	FactorValueVector.getValuesForFactor(ExperimentalFactor factor)

Methods in ubic.gemma.persistence.util with parameters of type FactorValue

Modifier and Type	Method	Description
static void	BusinessKey.checkKey(FactorValue factorValue)
int	FactorValueComparator.compare(FactorValue v1, FactorValue v2)
static FactorValue	BusinessKey.find(Session session, FactorValue factorValue)

Uses of FactorValue in ubic.gemma.rest

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

Modifier	Constructor	Description
	ExpressionExperimentSubsetWithFactorValuesObject(ExpressionExperimentSubSet subset, Set<FactorValue> factorValues, Map<ArrayDesign, ArrayDesignValueObject> id2advo, boolean includeAssays, Map<BioAssay,BioAssay> assay2sourceAssayMap)

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

Subclasses with type arguments of type FactorValue in ubic.gemma.rest.util.args

Modifier and Type	Class	Description
class	FactorValueArg<A>	Represents an API arguments that maps to a FactorValue by its ID or name.