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.svd
ubic.gemma.core.datastructure.matrix
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.persistence.service.expression.biomaterial
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.web.controller.expression.biomaterial
ubic.gemma.web.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 List<BioMaterial>	DifferentialExpressionAnalysisUtil.getBioMaterialsForBioAssays(ExpressionDataMatrix<?> matrix)	Returns a List of all the different types of biomaterials across all bioassays in the experiment.

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

Modifier and Type	Method	Description
static BioAssayDimension	LinearModelAnalyzer.createBADMap(List<BioMaterial> columnsToUse)	This bioAssayDimension shouldn't get persisted; it is only for dealing with subset diff ex.
static DoubleMatrix<String,String>	LinearModelAnalyzer.makeDataMatrix(ObjectMatrix<String,String,Object> designMatrix, DoubleMatrix<CompositeSequence,BioMaterial> namedMatrix)	Convert the data into a string-keyed matrix.

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<LocalFile> 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)

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
DoubleMatrix<Integer,BioMaterial>	ExpressionDataSVD.getV()

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

Modifier and Type	Method	Description
static void	SVDServiceHelperImpl.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	SVDServiceHelperImpl.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	BaseExpressionDataMatrix.getBioMaterialForColumn(int index)
BioMaterial	ExpressionDataMatrix.getBioMaterialForColumn(int index)

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

Modifier and Type	Method	Description
DoubleMatrix<CompositeSequence,BioMaterial>	ExpressionDataDoubleMatrix.getMatrix()
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(List<BioMaterial> start, Collection<ExperimentalFactor> factors)
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(List<BioMaterial> start, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(ExpressionDataMatrix<?> mat)
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(ExpressionDataMatrix<?> mat, ExperimentalFactor primaryFactor)

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

Modifier and Type	Method	Description
static String	ExpressionDataWriterUtils.constructBioAssayName(BioMaterial bioMaterial, Collection<BioAssay> bioAssays)
Integer	ExpressionDataIntegerMatrix.get(CompositeSequence designElement, BioMaterial bioMaterial)
int	BaseExpressionDataMatrix.getColumnIndex(BioMaterial bioMaterial)
int	ExpressionDataMatrix.getColumnIndex(BioMaterial bioMaterial)
static String	ExpressionDataWriterUtils.getExternalId(BioMaterial bioMaterial, Collection<BioAssay> bioAssays)

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

Modifier and Type	Method	Description
static Map<ExperimentalFactor,FactorValue>	ExpressionDataMatrixColumnSort.getBaselineLevels(List<BioMaterial> samplesUsed, Collection<ExperimentalFactor> factors)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(List<BioMaterial> start, Collection<ExperimentalFactor> factors)
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(List<BioMaterial> start, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)

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

Constructor	Description
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, List<BioMaterial> columnsToUse, BioAssayDimension reorderedDim)	Create a matrix based on another one's selected columns.
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, DoubleMatrix<CompositeSequence,BioMaterial> dataMatrix, Collection<QuantitationType> quantitationTypes)	Create a data matrix like sourceMatrix but use the values and quantitations from dataMatrix.
ExpressionDataDoubleMatrix(ExpressionExperiment ee, QuantitationType qt, DoubleMatrix<CompositeSequence,BioMaterial> matrix)	Create a matrix given a 'raw' matrix that uses the same samples as the experiment.

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
void	BioAssay.setSampleUsed(BioMaterial sampleUsed)

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

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

Modifier and Type	Method	Description
static BioMaterial	BioMaterial.Factory.newInstance()
static BioMaterial	BioMaterial.Factory.newInstance(String name)

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

Constructor	Description
BioMaterialValueObject(BioMaterial bm)
BioMaterialValueObject(BioMaterial bm, boolean basic)
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 List<BioMaterial>	ExperimentalDesignUtils.getOrderedSamples(ExpressionDataDoubleMatrix dmatrix, List<ExperimentalFactor> factors)	This puts the control samples up front if possible.
static ObjectMatrix<BioMaterial,ExperimentalFactor,Object>	ExperimentalDesignUtils.sampleInfoMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)

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

Modifier and Type	Method	Description
static Map<ExperimentalFactor,FactorValue>	ExperimentalDesignUtils.getBaselineConditions(List<BioMaterial> samplesUsed, List<ExperimentalFactor> factors)
static boolean	ExperimentalDesignUtils.isComplete(ExperimentalFactor factor, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)	Check if a factor has missing values (samples that lack an assigned value)

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

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	BioMaterialService.copy(BioMaterial bioMaterial)	Copies a bioMaterial.
BioMaterial	BioMaterialServiceImpl.copy(BioMaterial bioMaterial)
BioMaterial	BioMaterialDaoImpl.create(BioMaterial entity)
BioMaterial	BioMaterialService.create(BioMaterial bioMaterial)
BioMaterial	BioMaterialDaoImpl.find(BioMaterial bioMaterial)
BioMaterial	BioMaterialService.findOrCreate(BioMaterial bioMaterial)
BioMaterial	BioMaterialService.load(Long id)
BioMaterial	BioMaterialDaoImpl.save(BioMaterial entity)
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
Collection<BioMaterial>	BioMaterialDao.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialDaoImpl.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialService.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialServiceImpl.findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	BioMaterialService.load(Collection<Long> ids)
Collection<BioMaterial>	BioMaterialService.loadAll()
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
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	BioMaterialService.copy(BioMaterial bioMaterial)	Copies a bioMaterial.
BioMaterial	BioMaterialServiceImpl.copy(BioMaterial bioMaterial)
BioMaterial	BioMaterialDaoImpl.create(BioMaterial entity)
BioMaterial	BioMaterialService.create(BioMaterial bioMaterial)
protected BioMaterialValueObject	BioMaterialDaoImpl.doLoadValueObject(BioMaterial entity)
BioMaterial	BioMaterialDaoImpl.find(BioMaterial bioMaterial)
BioMaterial	BioMaterialService.findOrCreate(BioMaterial bioMaterial)
void	BioMaterialService.remove(BioMaterial bioMaterial)
void	BioMaterialService.removeCharacteristic(BioMaterial bm, Characteristic vc)	Remove the given characteristic from the given biomaterial
void	BioMaterialServiceImpl.removeCharacteristic(BioMaterial bm, Characteristic characterId)
BioMaterial	BioMaterialDaoImpl.save(BioMaterial entity)
void	BioMaterialDao.thaw(BioMaterial bioMaterial)	Thaw the given BioMaterial.
void	BioMaterialDaoImpl.thaw(BioMaterial bioMaterial)
BioMaterial	BioMaterialService.thaw(BioMaterial bioMaterial)
BioMaterial	BioMaterialServiceImpl.thaw(BioMaterial bioMaterial)
void	BioMaterialDaoImpl.update(BioMaterial entity)
void	BioMaterialService.update(BioMaterial bioMaterial)

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)
String	BioMaterialService.getBioMaterialIdList(Collection<BioMaterial> bioMaterials)
String	BioMaterialServiceImpl.getBioMaterialIdList(Collection<BioMaterial> bioMaterials)
Collection<BioMaterial>	BioMaterialService.thaw(Collection<BioMaterial> bioMaterials)
Collection<BioMaterial>	BioMaterialServiceImpl.thaw(Collection<BioMaterial> bioMaterials)

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

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

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

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

Modifier and Type	Method	Description
ExpressionExperiment	ExpressionExperimentDao.findByBioMaterial(BioMaterial bm)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByBioMaterial(BioMaterial bm)
ExpressionExperiment	ExpressionExperimentService.findByBioMaterial(BioMaterial bm)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByBioMaterial(BioMaterial bm)

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

Uses of BioMaterial in ubic.gemma.persistence.util

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

Modifier and Type	Method	Description
static void	BusinessKey.addRestrictions(Criteria queryObject, BioMaterial bioMaterial)

Uses of BioMaterial in ubic.gemma.web.controller.expression.biomaterial

Methods in ubic.gemma.web.controller.expression.biomaterial that return types with arguments of type BioMaterial

Modifier and Type	Method	Description
Collection<BioMaterial>	BioMaterialController.getBioMaterials(Collection<Long> ids)
Collection<BioMaterial>	BioMaterialController.getBioMaterialsForEE(Long id)

Method parameters in ubic.gemma.web.controller.expression.biomaterial with type arguments of type BioMaterial

Modifier and Type	Method	Description
Collection<AnnotationValueObject>	BioMaterialController.getAnnotation(EntityDelegator<BioMaterial> bm)
Collection<FactorValueValueObject>	BioMaterialController.getFactorValues(EntityDelegator<BioMaterial> bm)

Uses of BioMaterial in ubic.gemma.web.util

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

Modifier and Type	Method	Description
static String	AnchorTagUtil.getBioMaterialLink(BioMaterial bm, String link, javax.servlet.ServletContext servletContext)