Class RawExpressionDataVectorDaoImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractDao<RawExpressionDataVector>

ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao<RawExpressionDataVector>

ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoImpl

All Implemented Interfaces:

BaseDao<RawExpressionDataVector>, DesignElementDataVectorDao<RawExpressionDataVector>, RawExpressionDataVectorDao

@Repository
public class RawExpressionDataVectorDaoImpl
extends AbstractDesignElementDataVectorDao<RawExpressionDataVector>
implements RawExpressionDataVectorDao

Author:

paul

Field Summary

Fields inherited from class AbstractDao

log

Constructor Summary

Constructors

Constructor	Description
RawExpressionDataVectorDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
Collection<RawExpressionDataVector>	find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)
Collection<RawExpressionDataVector>	find(ArrayDesign arrayDesign, QuantitationType quantitationType)
RawExpressionDataVector	find(RawExpressionDataVector designElementDataVector)	Does a look-up for the given entity in the persistent storage, usually looking for a specific identifier if Identifiable.getId() is set or a business key.
Collection<RawExpressionDataVector>	getRandomRawVectors(QuantitationType quantitationType, int limit)	Fetch up to limit raw vectors for the given quantitation type, chosen uniformly at random.

Methods inherited from class AbstractDesignElementDataVectorDao

find, find, find, findByExpressionExperiment, thaw, thaw

Methods inherited from class AbstractDao

countAll, create, create, findByProperty, findByPropertyIn, findIdByProperty, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getEntityName, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, streamQuery, update, update

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface BaseDao

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

Methods inherited from interface DesignElementDataVectorDao

find, find, find, findByExpressionExperiment, thaw, thaw

Constructor Details

RawExpressionDataVectorDaoImpl

@Autowired
public RawExpressionDataVectorDaoImpl(SessionFactory sessionFactory)

Method Details

find

public Collection<RawExpressionDataVector> find(ArrayDesign arrayDesign,
 QuantitationType quantitationType)

Specified by:

find in interface RawExpressionDataVectorDao

find

public Collection<RawExpressionDataVector> find(Collection<CompositeSequence> designElements,
 QuantitationType quantitationType)

Specified by:

find in interface RawExpressionDataVectorDao

getRandomRawVectors

public Collection<RawExpressionDataVector> getRandomRawVectors(QuantitationType quantitationType,
 int limit)

Description copied from interface: RawExpressionDataVectorDao

Fetch up to limit raw vectors for the given quantitation type, chosen uniformly at random.

Mirrors ProcessedExpressionDataVectorDao#getRandomProcessedVectors: a cheap id-only scan is shuffled in Java and only the picked vectors are fetched (with the design-element / array-design / bioAssayDimension / quantitationType join fetches), avoiding an ORDER BY RAND() sort and a whole-matrix load. Unlike the processed variant there is no rankByMean preference — raw vectors carry no rank, so the sample is uniform.

Specified by:

getRandomRawVectors in interface RawExpressionDataVectorDao

find

public RawExpressionDataVector find(RawExpressionDataVector designElementDataVector)

Description copied from interface: BaseDao

Does a look-up for the given entity in the persistent storage, usually looking for a specific identifier if Identifiable.getId() is set or a business key.

Specified by:

find in interface BaseDao<RawExpressionDataVector>

Overrides:

find in class AbstractDao<RawExpressionDataVector>

Parameters:

designElementDataVector - the entity to look for.

Returns:

an entity that was found in the persistent storage, or null if no such entity was found.