Package ubic.gemma.persistence.service.expression.biomaterial

Interface BioMaterialDao

All Superinterfaces:

BaseDao<BioMaterial>, BaseVoEnabledDao<BioMaterial,BioMaterialValueObject>

All Known Implementing Classes:

BioMaterialDaoImpl

public interface BioMaterialDao
extends BaseVoEnabledDao<BioMaterial,BioMaterialValueObject>

See Also:

• BioMaterial

Method Summary

Modifier and Type	Method	Description
BioMaterial	copy(BioMaterial bioMaterial)
Collection<BioMaterial>	findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	findByFactor(ExperimentalFactor experimentalFactor)
List<BioMaterial>	findSubBioMaterials(Collection<BioMaterial> bioMaterials, boolean direct)	Find all the sub-biomaterials for a given biomaterial related by BioMaterial.getSourceBioMaterial().
List<BioMaterial>	findSubBioMaterials(BioMaterial bioMaterial, boolean direct)	Find all the sub-biomaterials for a given biomaterial related by BioMaterial.getSourceBioMaterial().
Map<BioMaterial,Map<BioAssay,ExpressionExperiment>>	getExpressionExperiments(BioMaterial bm)	Obtain all the experiments a biomaterial is used in from its hierarchy.

Methods inherited from interface ubic.gemma.persistence.service.BaseDao

countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, update, update

Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledDao

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Method Details

copy

BioMaterial copy(BioMaterial bioMaterial)

findSubBioMaterials

List<BioMaterial> findSubBioMaterials(BioMaterial bioMaterial,
 boolean direct)

Find all the sub-biomaterials for a given biomaterial related by BioMaterial.getSourceBioMaterial().

Parameters:

direct - if true, only direct sub-biomaterials are retained, otherwise the entire hierarchy is visited recursively.

findSubBioMaterials

List<BioMaterial> findSubBioMaterials(Collection<BioMaterial> bioMaterials,
 boolean direct)

Find all the sub-biomaterials for a given biomaterial related by BioMaterial.getSourceBioMaterial().

Parameters:

bioMaterials - a collection of biomaterials to visit

direct - if true, only direct sub-biomaterials are retained, otherwise the entire hierarchy is visited recursively.

findByExperiment

Collection<BioMaterial> findByExperiment(ExpressionExperiment experiment)

findByFactor

Collection<BioMaterial> findByFactor(ExperimentalFactor experimentalFactor)

getExpressionExperiments

Map<BioMaterial,Map<BioAssay,ExpressionExperiment>> getExpressionExperiments(BioMaterial bm)

Obtain all the experiments a biomaterial is used in from its hierarchy.

This also includes experiments that are using this via one of their parent?