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

Class RawAndProcessedExpressionDataVectorServiceImpl

java.lang.Object

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

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

ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceImpl

All Implemented Interfaces:

BaseImmutableService<DesignElementDataVector>, BaseReadOnlyService<DesignElementDataVector>, BaseService<DesignElementDataVector>, RawAndProcessedExpressionDataVectorService

@Service
public class RawAndProcessedExpressionDataVectorServiceImpl
extends AbstractDesignElementDataVectorService<DesignElementDataVector>
implements RawAndProcessedExpressionDataVectorService

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
RawAndProcessedExpressionDataVectorServiceImpl(RawAndProcessedExpressionDataVectorDao 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<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<DesignElementDataVector>	findAndThaw(Collection<QuantitationType> quantitationTypes)
Collection<T>	findAndThaw(QuantitationType quantitationType)	Find and thaw specific type (DesignElementDataVectorService) of vectors that meet the given criteria.
Collection<DesignElementDataVector>	findAndThaw(BioAssayDimension bioAssayDimension)
int	removeByCompositeSequence(CompositeSequence cs)
Collection<DesignElementDataVector>	thaw(Collection<DesignElementDataVector> vectors)	Deprecated.

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

find, find, find, findAndThaw

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, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail

Constructor Detail

RawAndProcessedExpressionDataVectorServiceImpl

@Autowired
public RawAndProcessedExpressionDataVectorServiceImpl(RawAndProcessedExpressionDataVectorDao mainDao)

Method Detail

removeByCompositeSequence

@Transactional
public int removeByCompositeSequence(CompositeSequence cs)

Specified by:

removeByCompositeSequence in interface RawAndProcessedExpressionDataVectorService

See Also:

RawAndProcessedExpressionDataVectorDao.removeByCompositeSequence(CompositeSequence)

findAndThaw

public Collection<DesignElementDataVector> findAndThaw(BioAssayDimension bioAssayDimension)

Overrides:

findAndThaw in class AbstractDesignElementDataVectorService<DesignElementDataVector>

findAndThaw

public Collection<DesignElementDataVector> findAndThaw(Collection<QuantitationType> quantitationTypes)

Overrides:

findAndThaw in class AbstractDesignElementDataVectorService<DesignElementDataVector>

thaw

@Deprecated
@Transactional(readOnly=true)
public Collection<DesignElementDataVector> thaw(Collection<DesignElementDataVector> vectors)

Deprecated.

Description copied from interface: RawAndProcessedExpressionDataVectorService

Thaw both raw and processed vectors.

This method thaws by first splitting the vectors into raw and processed groups and then thawing each group with the corresponding vector service. If you know the type of vector a collection holds, favour using a specific service instead.

Specified by:

thaw in interface RawAndProcessedExpressionDataVectorService

Overrides:

thaw in class AbstractDesignElementDataVectorService<DesignElementDataVector>

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

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

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.