Uses of Class
ubic.gemma.model.expression.biomaterial.BioMaterial

Packages that use BioMaterial

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.preprocess.filter	This package contains classes for filtering expression data.
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.datastructure.matrix	This package contains data structures for representing matrices of gene expression.
ubic.gemma.core.datastructure.matrix.io	This package contains I/O utilities for reading and writing expression data matrices.
ubic.gemma.core.loader.expression	This package contains interfaces and classes for loading expression data.
ubic.gemma.core.loader.expression.cellxgene	This package contains classes for loading expression data from CELLxGENE.
ubic.gemma.core.loader.expression.singleCell	This package contains classes for loading single-cell expression data.
ubic.gemma.core.visualization.cellbrowser	This package contains classes related to the Cell Browser visualization tool.
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.persistence.service.expression.biomaterial
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util

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

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

Modifier and Type	Method	Description
static ObjectMatrix<BioMaterial, ExperimentalFactor, Object>	DiffExAnalyzerUtils.buildDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, boolean allowMissingValues)	Build a design matrix for the given factors and samples.
Set<BioMaterial>	DifferentialExpressionAnalysisFilterResult.getFinalSamples()	Final set of samples.
Set<BioMaterial>	DifferentialExpressionAnalysisFilterResult.getSamplesAfterMinimumCells()	Number of samples left after filtering for minimum number of cells.
Set<BioMaterial>	DifferentialExpressionAnalysisFilterResult.getSamplesAfterOutliers()
Set<BioMaterial>	DifferentialExpressionAnalysisFilterResult.getStartingSamples()	Starting set of samples prior to filtering.

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

Modifier and Type	Method	Description
static boolean	DiffExAnalyzerUtils.isAnalyzed(BioMaterial sample)	Check whether a sample takes part in a differential expression analysis.
static String	DiffExAnalyzerUtils.nameForR(BioMaterial sample)	Create a name for a sample suitable for R.

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

Modifier and Type	Method	Description
static boolean	DifferentialExpressionAnalysisUtil.blockComplete(Collection<BioMaterial> samples, Collection<ExperimentalFactor> factors)	A variant that judges from a given set of samples rather than every sample in the experiment.
static boolean	DifferentialExpressionAnalysisUtil.checkValidForLm(Collection<BioMaterial> samples, ExperimentalFactor experimentalFactor)	A variant that judges from a given set of samples rather than every sample in the experiment.
static BioAssayDimension	DiffExAnalyzerUtils.createBADMap(List<BioMaterial> columnsToUse)
static AnalysisType	DiffExAnalyzerUtils.determineAnalysisType(BioAssaySet bioAssaySet, DifferentialExpressionAnalysisConfig config, Collection<BioMaterial> samplesToAnalyze)	A variant that decides from a given set of samples rather than every sample in the experiment.
static Map<ExperimentalFactor, FactorValue>	BaselineSelection.getBaselineConditions(Collection<BioMaterial> samplesUsed, Collection<ExperimentalFactor> 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.
static DoubleMatrix<String,String>	DiffExAnalyzerUtils.makeDataMatrix(ObjectMatrix<String,String,Object> designMatrix, DoubleMatrix<CompositeSequence, BioMaterial> namedMatrix)	Convert the data into a string-keyed matrix.
static void	DiffExAnalyzerUtils.populateFactorValues(Collection<BioMaterial> samples, ExperimentalFactor f, Collection<FactorValue> fvs)	As above, over a given set of samples rather than every sample of the experiment or subset.
void	DifferentialExpressionAnalysisFilterResult.setFinalSamples(Set<BioMaterial> finalSamples)	Final set of samples.
void	DifferentialExpressionAnalysisFilterResult.setSamplesAfterMinimumCells(Set<BioMaterial> samplesAfterMinimumCells)	Number of samples left after filtering for minimum number of cells.
void	DifferentialExpressionAnalysisFilterResult.setSamplesAfterOutliers(Set<BioMaterial> samplesAfterOutliers)
void	DifferentialExpressionAnalysisFilterResult.setStartingSamples(Set<BioMaterial> startingSamples)	Starting set of samples prior to filtering.

Uses of BioMaterial in ubic.gemma.core.analysis.preprocess.batcheffects

Methods in ubic.gemma.core.analysis.preprocess.batcheffects that return types with arguments of type BioMaterial

Modifier and Type	Method	Description
Map<BioMaterial, Date>	BatchInfoParser.getBatchInfo(ExpressionExperiment ee, Collection<File> files)

Method parameters in ubic.gemma.core.analysis.preprocess.batcheffects with type arguments of type BioMaterial

Modifier and Type	Method	Description
ExperimentalFactor	BatchInfoPopulationHelperService.createBatchFactor(ExpressionExperiment ee, Map<BioMaterial, Date> dates)
ExperimentalFactor	BatchInfoPopulationHelperServiceImpl.createBatchFactor(ExpressionExperiment ee, Map<BioMaterial, Date> dates)
ExperimentalFactor	BatchInfoPopulationHelperService.createRnaSeqBatchFactor(ExpressionExperiment ee, Map<BioMaterial, String> headers)	For RNA-seq, we based the batching on the available device/run/flowcell/lane information
ExperimentalFactor	BatchInfoPopulationHelperServiceImpl.createRnaSeqBatchFactor(ExpressionExperiment ee, Map<BioMaterial, String> headers)	For RNA-seq, we based the batching on the available device/run/flowcell/lane information

Uses of BioMaterial in ubic.gemma.core.analysis.preprocess.filter

Methods in ubic.gemma.core.analysis.preprocess.filter that return types with arguments of type BioMaterial

Modifier and Type	Method	Description
static Set<BioMaterial>	ExpressionDataFilterUtils.getSamplesWithData(ExpressionDataDoubleMatrix dataMatrix)	Obtain the set of samples (columns) with data.

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

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

Modifier and Type	Method	Description
List<BioMaterial>	SVDResult.getBioMaterials()	Biomaterials used in the SVD analysis.
DoubleMatrix<Integer, BioMaterial>	ExpressionDataSVD.getV()
DoubleMatrix<BioMaterial, Integer>	SVDResult.getVMatrix()	Row names: biomaterials; column names: eigengene number (from 0)

Methods in ubic.gemma.core.analysis.preprocess.svd with parameters of type BioMaterial

Modifier and Type	Method	Description
static void	SVDServiceImpl.populateBMFMap(Map<ExperimentalFactor, Map<BioMaterial, Number>> bioMaterialFactorMap, BioMaterial bm)	Retrieve relationships between factors, biomaterials and factor values.

Method parameters in ubic.gemma.core.analysis.preprocess.svd with type arguments of type BioMaterial

Modifier and Type	Method	Description
static void	SVDServiceImpl.populateBMFMap(Map<ExperimentalFactor, Map<BioMaterial, Number>> bioMaterialFactorMap, BioMaterial bm)	Retrieve relationships between factors, biomaterials and factor values.

Uses of BioMaterial in ubic.gemma.core.datastructure.matrix

Methods in ubic.gemma.core.datastructure.matrix that return BioMaterial

Modifier and Type	Method	Description
BioMaterial	AbstractBulkExpressionDataMatrix.getBioMaterialForColumn(int index)
BioMaterial	AbstractMultiAssayExpressionDataMatrix.getBioMaterialForColumn(int index)
BioMaterial	BulkExpressionDataMatrix.getBioMaterialForColumn(int index)	Obtain a biomaterial corresponding to a column.
BioMaterial	EmptySingleCellExpressionDataMatrix.getBioMaterialForColumn(int j)
BioMaterial	MultiAssayBulkExpressionDataMatrix.getBioMaterialForColumn(int index)
BioMaterial	SingleCellExpressionDataDoubleMatrix.getBioMaterialForColumn(int j)
BioMaterial	SingleCellExpressionDataIntMatrix.getBioMaterialForColumn(int j)
BioMaterial	SingleCellExpressionDataMatrix.getBioMaterialForColumn(int j)

Methods in ubic.gemma.core.datastructure.matrix that return types with arguments of type BioMaterial

Modifier and Type	Method	Description
List<BioMaterial>	AbstractBulkExpressionDataMatrix.getBioMaterials()
List<BioMaterial>	AbstractMultiAssayExpressionDataMatrix.getBioMaterials()
List<BioMaterial>	BulkExpressionDataMatrix.getBioMaterials()
DoubleMatrix<CompositeSequence, BioMaterial>	ExpressionDataDoubleMatrix.getMatrix()
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(List<BioMaterial> start, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(BulkExpressionDataMatrix<?> dmatrix, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)

Methods in ubic.gemma.core.datastructure.matrix with parameters of type BioMaterial

Modifier and Type	Method	Description
Integer	ExpressionDataIntegerMatrix.get(CompositeSequence designElement, BioMaterial bioMaterial)
int	AbstractBulkExpressionDataMatrix.getColumnIndex(BioMaterial bioMaterial)
int	AbstractMultiAssayExpressionDataMatrix.getColumnIndex(BioMaterial bioMaterial)
int	BulkExpressionDataMatrix.getColumnIndex(BioMaterial bioMaterial)
int	MultiAssayBulkExpressionDataMatrix.getColumnIndex(BioMaterial bioMaterial)
int[]	ExpressionDataDoubleMatrix.getNumberOfCellsForColumn(BioMaterial bioMaterial)
int[]	SingleCellDerivedBulkExpressionDataMatrix.getNumberOfCellsForColumn(BioMaterial bioMaterial)

Method parameters in ubic.gemma.core.datastructure.matrix with type arguments of type BioMaterial

Modifier and Type	Method	Description
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(List<BioMaterial> start, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)
protected void	AbstractMultiAssayExpressionDataMatrix.setUpColumnElements(LinkedHashMap<BioMaterial, Set<BioAssay>> bioMaterialMap)
BulkExpressionDataMatrix<Double>	BulkExpressionDataDoubleMatrix.sliceColumns(List<BioMaterial> bioMaterials)
BulkExpressionDataDoubleMatrix	BulkExpressionDataDoubleMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)
BulkExpressionDataMatrix<Integer>	BulkExpressionDataIntMatrix.sliceColumns(List<BioMaterial> bioMaterials)
BulkExpressionDataIntMatrix	BulkExpressionDataIntMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)
BulkExpressionDataMatrix<T>	BulkExpressionDataMatrix.sliceColumns(List<BioMaterial> bioMaterials)	Slice the requested samples (columns) from this matrix.
BulkExpressionDataMatrix<T>	BulkExpressionDataMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)	Slice the requested samples (columns) from this matrix.
BulkExpressionDataMatrix<Object>	EmptyBulkExpressionDataMatrix.sliceColumns(List<BioMaterial> bioMaterials)
EmptyBulkExpressionDataMatrix	EmptyBulkExpressionDataMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)
BulkExpressionDataMatrix<Object>	EmptyExpressionMatrix.sliceColumns(List<BioMaterial> bioMaterials)
EmptyExpressionMatrix	EmptyExpressionMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)
BulkExpressionDataMatrix<Boolean>	ExpressionDataBooleanMatrix.sliceColumns(List<BioMaterial> bioMaterials)
ExpressionDataBooleanMatrix	ExpressionDataBooleanMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)
ExpressionDataDoubleMatrix	ExpressionDataDoubleMatrix.sliceColumns(List<BioMaterial> bioMaterials)
ExpressionDataDoubleMatrix	ExpressionDataDoubleMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension reorderedDim)
BulkExpressionDataMatrix<Integer>	ExpressionDataIntegerMatrix.sliceColumns(List<BioMaterial> bioMaterials)
ExpressionDataIntegerMatrix	ExpressionDataIntegerMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)
BulkExpressionDataMatrix<String>	ExpressionDataStringMatrix.sliceColumns(List<BioMaterial> bioMaterials)
ExpressionDataStringMatrix	ExpressionDataStringMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)
ExpressionDataDoubleMatrix	ExpressionDataDoubleMatrix.withMatrix(DoubleMatrix<CompositeSequence, BioMaterial> matrix)	Create a copy of this matrix with the given data matrix.
ExpressionDataDoubleMatrix	ExpressionDataDoubleMatrix.withMatrix(DoubleMatrix<CompositeSequence, BioMaterial> matrix, Map<QuantitationType, QuantitationType> quantitationTypes)	Create a copy of this matrix with the given data matrix and quantitation types.

Constructor parameters in ubic.gemma.core.datastructure.matrix with type arguments of type BioMaterial

Modifier	Constructor	Description
	ExpressionDataDoubleMatrix(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, BioMaterial> dataMatrix, QuantitationType qt)	Create a matrix given a 'raw' matrix that uses the same samples as the experiment.

Uses of BioMaterial in ubic.gemma.core.datastructure.matrix.io

Methods in ubic.gemma.core.datastructure.matrix.io with parameters of type BioMaterial

Modifier and Type	Method	Description
static String	ExpressionDataWriterUtils.constructSampleName(BioMaterial bioMaterial, boolean useIds, boolean useRawColumnNames)
static String	ExpressionDataWriterUtils.constructSampleName(BioMaterial bioMaterial, Collection<BioAssay> bioAssays, boolean useIds, boolean useRawColumnNames, char assayDelimiter)	Construct a BioAssay column name prefixed by the BioMaterial from which it originates.
static String	ExpressionDataWriterUtils.constructSampleName(BioMaterial bm, BioAssay ba, boolean useIds, boolean useRawColumnNames)	Construct a sample name in case there is only one BioAssay attached to the corresponding BioMaterial.

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

Methods in ubic.gemma.core.loader.expression that return types with arguments of type BioMaterial

Modifier and Type	Method	Description
Map<BioMaterial, Set<Characteristic>>	AbstractDelegatingDataLoader.getSamplesCharacteristics(Collection<BioAssay> samples)
Map<BioMaterial, Set<Characteristic>>	DataLoader.getSamplesCharacteristics(Collection<BioAssay> samples)	Load samples characteristics present in the data.

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

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 BioMaterial in ubic.gemma.core.loader.expression.cellxgene

Methods in ubic.gemma.core.loader.expression.cellxgene that return types with arguments of type BioMaterial

Modifier and Type	Method	Description
Map<BioMaterial, Set<Characteristic>>	CellXGeneAnnDataSingleCellDataLoader.getSamplesCharacteristics(Collection<BioAssay> samples)

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

Methods in ubic.gemma.core.loader.expression.singleCell that return types with arguments of type BioMaterial

Modifier and Type	Method	Description
Map<BioMaterial, Set<Characteristic>>	AnnDataSingleCellDataLoader.getSamplesCharacteristics(Collection<BioAssay> samples)
Map<BioMaterial, Set<Characteristic>>	MexSingleCellDataLoader.getSamplesCharacteristics(Collection<BioAssay> samples)	MEX does not provide sample characteristics.
Map<BioMaterial, Set<Characteristic>>	NullSingleCellDataLoader.getSamplesCharacteristics(Collection<BioAssay> samples)

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

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 BioMaterial in ubic.gemma.core.visualization.cellbrowser

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

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 BioMaterial in ubic.gemma.model.expression.bioAssay

Methods in ubic.gemma.model.expression.bioAssay that return BioMaterial

Modifier and Type	Method	Description
BioMaterial	BioAssay.getSampleUsed()

Methods in ubic.gemma.model.expression.bioAssay with parameters of type BioMaterial

Modifier and Type	Method	Description
static BioAssay	BioAssay.Factory.newInstance(String name, ArrayDesign arrayDesignUsed, BioMaterial sampleUsed)
void	BioAssay.setSampleUsed(BioMaterial sampleUsed)

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

Subclasses with type arguments of type BioMaterial in ubic.gemma.model.expression.biomaterial

Modifier and Type	Class	Description
class	BioMaterialValueObject

Fields in ubic.gemma.model.expression.biomaterial with type parameters of type BioMaterial

Modifier and Type	Field	Description
static final Comparator<BioMaterial>	BioMaterial.COMPARATOR

Methods in ubic.gemma.model.expression.biomaterial that return BioMaterial

Modifier and Type	Method	Description
BioMaterial	BioMaterial.getSourceBioMaterial()	Parent biomaterial or null if this is a top-level biomaterial.
static BioMaterial	BioMaterial.Factory.newInstance()
static BioMaterial	BioMaterial.Factory.newInstance(String name)
static BioMaterial	BioMaterial.Factory.newInstance(String name, Taxon taxon)

Methods in ubic.gemma.model.expression.biomaterial with parameters of type BioMaterial

Modifier and Type	Method	Description
void	BioMaterial.setSourceBioMaterial(BioMaterial sourceBioMaterial)

Constructors in ubic.gemma.model.expression.biomaterial with parameters of type BioMaterial

Modifier	Constructor	Description
	BioMaterialValueObject(BioMaterial bm)
	BioMaterialValueObject(BioMaterial bm, boolean basic, boolean allFactorValuesAndCharacteristics)
	BioMaterialValueObject(BioMaterial bm, BioAssay ba)

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

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

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.

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

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.

Uses of BioMaterial in ubic.gemma.persistence.persister

Methods in ubic.gemma.persistence.persister that return BioMaterial

Modifier and Type	Method	Description
BioMaterial	EeWriteServiceImpl.persistBioMaterial(BioMaterial bioMaterial)	Persister-shrink S4c: public typed entry point for standalone BioMaterial persistence.

Methods in ubic.gemma.persistence.persister with parameters of type BioMaterial

Modifier and Type	Method	Description
BioMaterial	EeWriteServiceImpl.persistBioMaterial(BioMaterial bioMaterial)	Persister-shrink S4c: public typed entry point for standalone BioMaterial persistence.

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

Methods in ubic.gemma.persistence.service.expression.bioAssay with parameters of type BioMaterial

Modifier and Type	Method	Description
void	BioAssayService.addBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)	Associates a bioMaterial with a specified bioAssay.
void	BioAssayServiceImpl.addBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)
void	BioAssayService.removeBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)	Removes the association between a specific bioMaterial and a bioAssay.
void	BioAssayServiceImpl.removeBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)

Uses of BioMaterial in ubic.gemma.persistence.service.expression.biomaterial

Subclasses with type arguments of type BioMaterial in ubic.gemma.persistence.service.expression.biomaterial

Modifier and Type	Class	Description
class	BioMaterialDaoImpl
class	BioMaterialServiceImpl

Subinterfaces with type arguments of type BioMaterial in ubic.gemma.persistence.service.expression.biomaterial

Modifier and Type	Interface	Description
interface	BioMaterialDao
interface	BioMaterialService
interface	BioMaterialService

Methods in ubic.gemma.persistence.service.expression.biomaterial that return BioMaterial

Modifier and Type	Method	Description
BioMaterial	BioMaterialDao.copy(BioMaterial bioMaterial)
BioMaterial	BioMaterialDaoImpl.copy(BioMaterial bioMaterial)
BioMaterial	BioMaterialReadService.copy(BioMaterial bioMaterial)	Copy a BioMaterial.
BioMaterial	BioMaterialReadServiceImpl.copy(BioMaterial bioMaterial)
BioMaterial	BioMaterialService.copy(BioMaterial bioMaterial)	Copies a bioMaterial.
BioMaterial	BioMaterialServiceImpl.copy(BioMaterial bioMaterial)
BioMaterial	BioMaterialDaoImpl.create(BioMaterial entity)
BioMaterial	BioMaterialDaoImpl.find(BioMaterial bioMaterial)
<T extends Exception> BioMaterial	BioMaterialReadService.loadAndThawOrFail(Long bmId, Function<String,T> exceptionSupplier, String message)	Load a BioMaterial by ID and thaw it eagerly, or throw the supplied exception if no such biomaterial exists.
<T extends Exception> BioMaterial	BioMaterialReadServiceImpl.loadAndThawOrFail(Long bmId, Function<String,T> exceptionSupplier, String message)
<T extends Exception> BioMaterial	BioMaterialService.loadAndThawOrFail(Long bmId, Function<String,T> exceptionSupplier, String message)
<T extends Exception> BioMaterial	BioMaterialServiceImpl.loadAndThawOrFail(Long bmId, Function<String,T> exceptionSupplier, String message)
BioMaterial	BioMaterialDaoImpl.save(BioMaterial entity)
BioMaterial	BioMaterialReadService.thaw(BioMaterial bioMaterial)	Thaw a single BioMaterial for full traversal.
BioMaterial	BioMaterialReadServiceImpl.thaw(BioMaterial bioMaterial)
BioMaterial	BioMaterialService.thaw(BioMaterial bioMaterial)
BioMaterial	BioMaterialServiceImpl.thaw(BioMaterial bioMaterial)

Methods in ubic.gemma.persistence.service.expression.biomaterial that return types with arguments of type BioMaterial

Modifier and Type	Method	Description
static Map<Category, Map<BioMaterial, Collection<Characteristic>>>	BioMaterialUtils.createCharacteristicMap(Collection<BioMaterial> samples)	Create a mapping of biomaterial to characteristics for each category.
Collection<BioMaterial>	BioMaterialDao.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialDaoImpl.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialReadService.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialReadServiceImpl.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialService.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialServiceImpl.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialDao.findByFactor(ExperimentalFactor experimentalFactor)
Collection<BioMaterial>	BioMaterialDaoImpl.findByFactor(ExperimentalFactor experimentalFactor)
Collection<BioMaterial>	BioMaterialReadService.findByFactor(ExperimentalFactor experimentalFactor)
Collection<BioMaterial>	BioMaterialReadServiceImpl.findByFactor(ExperimentalFactor experimentalFactor)
Collection<BioMaterial>	BioMaterialService.findByFactor(ExperimentalFactor experimentalFactor)
Collection<BioMaterial>	BioMaterialServiceImpl.findByFactor(ExperimentalFactor experimentalFactor)
Collection<BioMaterial>	BioMaterialReadService.findSiblings(BioMaterial bioMaterial)	Find the siblings of a given biomaterial (other direct sub-materials of the same source).
Collection<BioMaterial>	BioMaterialReadServiceImpl.findSiblings(BioMaterial bioMaterial)
Collection<BioMaterial>	BioMaterialService.findSiblings(BioMaterial bioMaterial)	Find the siblings of a given biomaterial.
Collection<BioMaterial>	BioMaterialServiceImpl.findSiblings(BioMaterial bioMaterial)
List<BioMaterial>	BioMaterialDao.findSubBioMaterials(Collection<BioMaterial> bioMaterials, boolean direct)	Find all the sub-biomaterials for a given biomaterial related by BioMaterial.getSourceBioMaterial().
List<BioMaterial>	BioMaterialDao.findSubBioMaterials(BioMaterial bioMaterial, boolean direct)	Find all the sub-biomaterials for a given biomaterial related by BioMaterial.getSourceBioMaterial().
List<BioMaterial>	BioMaterialDaoImpl.findSubBioMaterials(Collection<BioMaterial> bioMaterials, boolean direct)
List<BioMaterial>	BioMaterialDaoImpl.findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
Collection<BioMaterial>	BioMaterialReadService.findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
Collection<BioMaterial>	BioMaterialReadServiceImpl.findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
Collection<BioMaterial>	BioMaterialService.findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
Collection<BioMaterial>	BioMaterialServiceImpl.findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialDao.getExpressionExperiments(BioMaterial bm)	Obtain all the experiments a biomaterial is used in from its hierarchy.
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialDaoImpl.getExpressionExperiments(BioMaterial bm)
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialReadService.getExpressionExperiments(BioMaterial bm)	Return the ExpressionExperiment occurrences of a given biomaterial, organized by BioAssay.
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialReadServiceImpl.getExpressionExperiments(BioMaterial bm)
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialService.getExpressionExperiments(BioMaterial bm)
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialServiceImpl.getExpressionExperiments(BioMaterial bm)
Collection<BioMaterial>	BioMaterialReadService.thaw(Collection<BioMaterial> bioMaterials)	Thaw a collection of BioMaterial for full traversal.
Collection<BioMaterial>	BioMaterialReadServiceImpl.thaw(Collection<BioMaterial> bioMaterials)
Collection<BioMaterial>	BioMaterialService.thaw(Collection<BioMaterial> bioMaterials)
Collection<BioMaterial>	BioMaterialServiceImpl.thaw(Collection<BioMaterial> bioMaterials)
Collection<BioMaterial>	BioMaterialService.updateBioMaterials(Collection<BioMaterialValueObject> valueObjects)	Update the biomaterials that are described by the given valueObjects.
Collection<BioMaterial>	BioMaterialServiceImpl.updateBioMaterials(Collection<BioMaterialValueObject> valueObjects)

Methods in ubic.gemma.persistence.service.expression.biomaterial with parameters of type BioMaterial

Modifier and Type	Method	Description
Characteristic	BioMaterialService.addAnnotation(ExpressionExperiment owner, BioMaterial bm, Characteristic vc)	Per-tag add of a characteristic to a biomaterial, the sample-level counterpart of ExpressionExperimentService.addAnnotation(ExpressionExperiment, Characteristic).
Characteristic	BioMaterialService.addAnnotation(ExpressionExperiment owner, BioMaterial bm, Characteristic vc, String reason)	As BioMaterialService.addAnnotation(ExpressionExperiment, BioMaterial, Characteristic), with a caller-supplied reason appended to the audit note after the server's own description.
Characteristic	BioMaterialServiceImpl.addAnnotation(ExpressionExperiment owner, BioMaterial bm, Characteristic vc)
Characteristic	BioMaterialServiceImpl.addAnnotation(ExpressionExperiment owner, BioMaterial bm, Characteristic vc, String reason)	Reason-carrying overload.
void	BioMaterialService.addCharacteristic(BioMaterial bm, Characteristic vc)	Will persist the give vocab characteristic to the given biomaterial
void	BioMaterialServiceImpl.addCharacteristic(BioMaterial bm, Characteristic vc)
BioMaterial	BioMaterialDao.copy(BioMaterial bioMaterial)
BioMaterial	BioMaterialDaoImpl.copy(BioMaterial bioMaterial)
BioMaterial	BioMaterialReadService.copy(BioMaterial bioMaterial)	Copy a BioMaterial.
BioMaterial	BioMaterialReadServiceImpl.copy(BioMaterial bioMaterial)
BioMaterial	BioMaterialService.copy(BioMaterial bioMaterial)	Copies a bioMaterial.
BioMaterial	BioMaterialServiceImpl.copy(BioMaterial bioMaterial)
BioMaterial	BioMaterialDaoImpl.create(BioMaterial entity)
protected BioMaterialValueObject	BioMaterialDaoImpl.doLoadValueObject(BioMaterial entity)
BioMaterial	BioMaterialDaoImpl.find(BioMaterial bioMaterial)
Collection<BioMaterial>	BioMaterialReadService.findSiblings(BioMaterial bioMaterial)	Find the siblings of a given biomaterial (other direct sub-materials of the same source).
Collection<BioMaterial>	BioMaterialReadServiceImpl.findSiblings(BioMaterial bioMaterial)
Collection<BioMaterial>	BioMaterialService.findSiblings(BioMaterial bioMaterial)	Find the siblings of a given biomaterial.
Collection<BioMaterial>	BioMaterialServiceImpl.findSiblings(BioMaterial bioMaterial)
List<BioMaterial>	BioMaterialDao.findSubBioMaterials(BioMaterial bioMaterial, boolean direct)	Find all the sub-biomaterials for a given biomaterial related by BioMaterial.getSourceBioMaterial().
List<BioMaterial>	BioMaterialDaoImpl.findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
Collection<BioMaterial>	BioMaterialReadService.findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
Collection<BioMaterial>	BioMaterialReadServiceImpl.findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
Collection<BioMaterial>	BioMaterialService.findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
Collection<BioMaterial>	BioMaterialServiceImpl.findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialDao.getExpressionExperiments(BioMaterial bm)	Obtain all the experiments a biomaterial is used in from its hierarchy.
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialDaoImpl.getExpressionExperiments(BioMaterial bm)
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialReadService.getExpressionExperiments(BioMaterial bm)	Return the ExpressionExperiment occurrences of a given biomaterial, organized by BioAssay.
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialReadServiceImpl.getExpressionExperiments(BioMaterial bm)
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialService.getExpressionExperiments(BioMaterial bm)
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	BioMaterialServiceImpl.getExpressionExperiments(BioMaterial bm)
void	BioMaterialDaoImpl.remove(BioMaterial entity)
Characteristic	BioMaterialService.removeAnnotation(ExpressionExperiment owner, BioMaterial bm, Long annotationId)	Per-tag remove of a characteristic from a biomaterial by id, the sample-level counterpart of ExpressionExperimentService.removeAnnotation(ExpressionExperiment, Long).
Characteristic	BioMaterialService.removeAnnotation(ExpressionExperiment owner, BioMaterial bm, Long annotationId, String reason)	As BioMaterialService.removeAnnotation(ExpressionExperiment, BioMaterial, Long), with a caller-supplied reason appended to the audit note.
Characteristic	BioMaterialServiceImpl.removeAnnotation(ExpressionExperiment owner, BioMaterial bm, Long annotationId)
Characteristic	BioMaterialServiceImpl.removeAnnotation(ExpressionExperiment owner, BioMaterial bm, Long annotationId, String reason)	Reason-carrying overload; see BioMaterialServiceImpl.addAnnotation(ExpressionExperiment, BioMaterial, Characteristic, String).
void	BioMaterialService.removeCharacteristics(BioMaterial bm, Collection<Characteristic> vc)	Remove the given characteristic from the given biomaterial
void	BioMaterialServiceImpl.removeCharacteristics(BioMaterial bm, Collection<Characteristic> characteristicsToRemove)
BioMaterial	BioMaterialDaoImpl.save(BioMaterial entity)
BioMaterial	BioMaterialReadService.thaw(BioMaterial bioMaterial)	Thaw a single BioMaterial for full traversal.
BioMaterial	BioMaterialReadServiceImpl.thaw(BioMaterial bioMaterial)
BioMaterial	BioMaterialService.thaw(BioMaterial bioMaterial)
BioMaterial	BioMaterialServiceImpl.thaw(BioMaterial bioMaterial)
void	BioMaterialDaoImpl.update(BioMaterial entity)
int	BioMaterialService.updateAnnotations(ExpressionExperiment owner, BioMaterial bm, Collection<Characteristic> desired)	Idempotent set-replace for a biomaterial's direct characteristic set, the sample-level counterpart of ExpressionExperimentService.updateAnnotations(ExpressionExperiment, Collection).
int	BioMaterialServiceImpl.updateAnnotations(ExpressionExperiment owner, BioMaterial bm, Collection<Characteristic> desired)
static void	BioMaterialUtils.visitBioMaterials(BioMaterial bioMaterial, Consumer<BioMaterial> visitor)	Visit all the biomaterials in the hierarchy.

Method parameters in ubic.gemma.persistence.service.expression.biomaterial with type arguments of type BioMaterial

Modifier and Type	Method	Description
<T> void	BioMaterialService.associateBatchFactor(Map<BioMaterial, T> descriptors, Map<T, FactorValue> d2fv)	Associate dates with bioassays and any new factors with the biomaterials.
<T> void	BioMaterialServiceImpl.associateBatchFactor(Map<BioMaterial, T> descriptors, Map<T, FactorValue> d2fv)
static Map<Category, Map<BioMaterial, Collection<Characteristic>>>	BioMaterialUtils.createCharacteristicMap(Collection<BioMaterial> samples)	Create a mapping of biomaterial to characteristics for each category.
List<BioMaterial>	BioMaterialDao.findSubBioMaterials(Collection<BioMaterial> bioMaterials, boolean direct)	Find all the sub-biomaterials for a given biomaterial related by BioMaterial.getSourceBioMaterial().
List<BioMaterial>	BioMaterialDaoImpl.findSubBioMaterials(Collection<BioMaterial> bioMaterials, boolean direct)
Collection<BioMaterial>	BioMaterialReadService.thaw(Collection<BioMaterial> bioMaterials)	Thaw a collection of BioMaterial for full traversal.
Collection<BioMaterial>	BioMaterialReadServiceImpl.thaw(Collection<BioMaterial> bioMaterials)
Collection<BioMaterial>	BioMaterialService.thaw(Collection<BioMaterial> bioMaterials)
Collection<BioMaterial>	BioMaterialServiceImpl.thaw(Collection<BioMaterial> bioMaterials)
static void	BioMaterialUtils.visitBioMaterials(BioMaterial bioMaterial, Consumer<BioMaterial> visitor)	Visit all the biomaterials in the hierarchy.

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

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

Modifier and Type	Method	Description
BioMaterial	EeWriteService.persistBioMaterial(BioMaterial bioMaterial)	Persist a standalone BioMaterial.

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

Modifier and Type	Method	Description
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentDao.findByBioMaterials(Collection<BioMaterial> bms)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentDaoImpl.findByBioMaterials(Collection<BioMaterial> bms)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentReadService.findByBioMaterials(Collection<BioMaterial> biomaterials)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentReadServiceImpl.findByBioMaterials(Collection<BioMaterial> biomaterials)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentService.findByBioMaterials(Collection<BioMaterial> biomaterials)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentServiceImpl.findByBioMaterials(Collection<BioMaterial> biomaterials)

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

Modifier and Type	Method	Description
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<Long>	ExpressionExperimentDao.findIdsByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<Long>	ExpressionExperimentDaoImpl.findIdsByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<Long>	ExpressionExperimentReadService.findIdsByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<Long>	ExpressionExperimentReadServiceImpl.findIdsByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<Long>	ExpressionExperimentService.findIdsByBioMaterial(BioMaterial bm, boolean includeSubSets)
Collection<Long>	ExpressionExperimentServiceImpl.findIdsByBioMaterial(BioMaterial bm, boolean includeSubSets)
BioMaterial	EeWriteService.persistBioMaterial(BioMaterial bioMaterial)	Persist a standalone BioMaterial.

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

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)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentDao.findByBioMaterials(Collection<BioMaterial> bms)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentDaoImpl.findByBioMaterials(Collection<BioMaterial> bms)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentReadService.findByBioMaterials(Collection<BioMaterial> biomaterials)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentReadServiceImpl.findByBioMaterials(Collection<BioMaterial> biomaterials)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentService.findByBioMaterials(Collection<BioMaterial> biomaterials)
Map<ExpressionExperiment, Collection<BioMaterial>>	ExpressionExperimentServiceImpl.findByBioMaterials(Collection<BioMaterial> biomaterials)

Uses of BioMaterial in ubic.gemma.persistence.util

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

Modifier and Type	Method	Description
static BioMaterial	BusinessKey.find(Session session, BioMaterial bioMaterial)

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

Modifier and Type	Method	Description
static BioMaterial	BusinessKey.find(Session session, BioMaterial bioMaterial)
static List<jakarta.persistence.criteria.Predicate>	BusinessKey.matches(jakarta.persistence.criteria.CriteriaBuilder cb, jakarta.persistence.criteria.From<?, BioMaterial> from, BioMaterial bioMaterial)
static void	Thaws.thawBioMaterial(BioMaterial bm2)	Thaw the given BioMaterial.

Method parameters in ubic.gemma.persistence.util with type arguments of type BioMaterial

Modifier and Type	Method	Description
static List<jakarta.persistence.criteria.Predicate>	BusinessKey.matches(jakarta.persistence.criteria.CriteriaBuilder cb, jakarta.persistence.criteria.From<?, BioMaterial> from, BioMaterial bioMaterial)