Package ubic.gemma.persistence.service.expression.bioAssayData

Class RawExpressionDataVectorServiceImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractService<T>

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

ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorServiceImpl

All Implemented Interfaces:

BaseImmutableService<RawExpressionDataVector>, BaseReadOnlyService<RawExpressionDataVector>, BaseService<RawExpressionDataVector>, RawExpressionDataVectorService

@Service
public class RawExpressionDataVectorServiceImpl
extends AbstractDesignElementDataVectorService<RawExpressionDataVector>
implements RawExpressionDataVectorService

Provides methods that can be applied to both RawExpressionDataVector and ProcessedExpressionDataVector

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractService

log

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	RawExpressionDataVectorServiceImpl(RawExpressionDataVectorDao mainDao)

Method Summary

Modifier and Type	Method	Description
Collection<T>	find(Collection<QuantitationType> quantitationTypes)	Find specific type (DesignElementDataVectorService) of vectors that meet the given criteria.
Collection<RawExpressionDataVector>	find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)
Collection<T>	find(QuantitationType quantitationType)	Find specific type (DesignElementDataVectorService) of vectors that meet the given criteria.
Collection<T>	find(BioAssayDimension bioAssayDimension)	Find specific type (raw or processed, depending on the service) of vectors that meet the given criteria.
Collection<T>	findAndThaw(Collection<QuantitationType> quantitationTypes)
Collection<T>	findAndThaw(QuantitationType quantitationType)	Find and thaw specific type (DesignElementDataVectorService) of vectors that meet the given criteria.
Collection<T>	findAndThaw(BioAssayDimension bioAssayDimension)
Collection<RawExpressionDataVector>	findByExpressionExperiment(ExpressionExperiment ee, QuantitationType quantitationType)
Collection<T>	thaw(Collection<T> vectors)	Deprecated. Use findAndThaw(QuantitationType), findAndThaw(Collection) or findAndThaw(BioAssayDimension) instead, it's much more efficient.

Methods inherited from class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorService

find, find, find, findAndThaw, findAndThaw, findAndThaw, thaw

Methods inherited from class ubic.gemma.persistence.service.AbstractService

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, remove, remove, remove, save, save, update, update

Methods inherited from class java.lang.Object

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

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

countAll, find, findOrFail, getElementClass, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail

Methods inherited from interface ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService

load

Constructor Detail

RawExpressionDataVectorServiceImpl

@Autowired
protected RawExpressionDataVectorServiceImpl(RawExpressionDataVectorDao mainDao)

Method Detail

findByExpressionExperiment

@Transactional(readOnly=true)
public Collection<RawExpressionDataVector> findByExpressionExperiment(ExpressionExperiment ee,
                                                                      QuantitationType quantitationType)

Specified by:

findByExpressionExperiment in interface RawExpressionDataVectorService

find

@Transactional(readOnly=true)
public Collection<RawExpressionDataVector> find(Collection<CompositeSequence> designElements,
                                                QuantitationType quantitationType)

Specified by:

find in interface RawExpressionDataVectorService

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DATAVECTOR_COLLECTION_READ"})
public abstract Collection<T> find(BioAssayDimension bioAssayDimension)

Find specific type (raw or processed, depending on the service) of vectors that meet the given criteria.

Parameters:

bioAssayDimension - the BA dimension

Returns:

the found vectors of type DesignElementDataVectorService

findAndThaw

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DATAVECTOR_COLLECTION_READ"})
public abstract Collection<T> findAndThaw(BioAssayDimension bioAssayDimension)

find

@Secured("GROUP_ADMIN")
public abstract Collection<T> find(Collection<QuantitationType> quantitationTypes)

Find specific type (DesignElementDataVectorService) of vectors that meet the given criteria.

Parameters:

quantitationTypes - the QTs

Returns:

the found vectors of type DesignElementDataVectorService

findAndThaw

@Secured("GROUP_ADMIN")
public abstract Collection<T> findAndThaw(Collection<QuantitationType> quantitationTypes)

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DATAVECTOR_COLLECTION_READ"})
public abstract Collection<T> find(QuantitationType quantitationType)

Find specific type (DesignElementDataVectorService) of vectors that meet the given criteria.

Parameters:

quantitationType - the QT

Returns:

the found vectors of type DesignElementDataVectorService

findAndThaw

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DATAVECTOR_COLLECTION_READ"})
public abstract Collection<T> findAndThaw(QuantitationType quantitationType)

Find and thaw specific type (DesignElementDataVectorService) of vectors that meet the given criteria.

thaw

@CheckReturnValue
@Deprecated
public abstract Collection<T> thaw(Collection<T> vectors)

Deprecated.

Use findAndThaw(QuantitationType), findAndThaw(Collection) or findAndThaw(BioAssayDimension) instead, it's much more efficient.

Thaw the given vectors.