ubic.gemma.persistence.service.expression.bioAssayData

Class AbstractDesignElementDataVectorService<T extends DesignElementDataVector>

java.lang.Object

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

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

All Implemented Interfaces:

BaseService<T>

Direct Known Subclasses:

ProcessedExpressionDataVectorServiceImpl, RawExpressionDataVectorServiceImpl

public abstract class AbstractDesignElementDataVectorService<T extends DesignElementDataVector>
extends AbstractService<T>

Field Summary

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

log

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractDesignElementDataVectorService(DesignElementDataVectorDao<T> mainDao)

Method Summary

Modifier and Type	Method and Description
Collection<T>	find(ArrayDesign arrayDesign, QuantitationType quantitationType) Find specific type (T) 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>	find(Collection<CompositeSequence> designElements, QuantitationType quantitationType) Find specific type (T) of vectors that meet the given criteria.
Collection<T>	find(Collection<QuantitationType> quantitationTypes) Find specific type (T) of vectors that meet the given criteria.
Collection<T>	find(QuantitationType quantitationType) Find specific type (T) of vectors that meet the given criteria.
Collection<T>	findByExpressionExperiment(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)
Collection<DesignElementDataVector>	findRawAndProcessed(BioAssayDimension dim) Finds all vectors for the given BA Dimension
Collection<DesignElementDataVector>	findRawAndProcessed(QuantitationType qt) Finds all vectors for the given quantitation type
void	removeDataForCompositeSequence(CompositeSequence compositeSequence) Removes specific type (T) of vectors for the given CS.
void	removeDataForQuantitationType(QuantitationType quantitationType) Removes specific type (T) of vectors for the given QT.
void	thaw(Collection<T> designElementDataVectors) Thaws the given vectors.
void	thawRawAndProcessed(Collection<DesignElementDataVector> vectors) Thaws all data vectors in the given collection
void	update(T dedv) Updates the given entity in the persistent storage.

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

countAll, create, create, find, findOrCreate, findOrFail, load, load, loadAll, loadOrFail, remove, remove, remove, removeAll, 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.BaseService

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

Constructor Detail

AbstractDesignElementDataVectorService

protected AbstractDesignElementDataVectorService(DesignElementDataVectorDao<T> mainDao)

Method Detail

thawRawAndProcessed

@Transactional(readOnly=true)
public void thawRawAndProcessed(Collection<DesignElementDataVector> vectors)

Thaws all data vectors in the given collection

Parameters:

vectors - the vectors to be thawed

findRawAndProcessed

@Transactional(readOnly=true)
public Collection<DesignElementDataVector> findRawAndProcessed(BioAssayDimension dim)

Finds all vectors for the given BA Dimension

Parameters:

dim - the BA dimension to limit the vector search to

Returns:

the found data vectors

findRawAndProcessed

@Transactional(readOnly=true)
public Collection<DesignElementDataVector> findRawAndProcessed(QuantitationType qt)

Finds all vectors for the given quantitation type

Parameters:

qt - the quantitation type to limit the vector search to

Returns:

the found data vectors

removeDataForCompositeSequence

@Transactional
public void removeDataForCompositeSequence(CompositeSequence compositeSequence)

Removes specific type (T) of vectors for the given CS.

Parameters:

compositeSequence - the sequence to remove the data for.

removeDataForQuantitationType

@Transactional
public void removeDataForQuantitationType(QuantitationType quantitationType)

Removes specific type (T) of vectors for the given QT.

Parameters:

quantitationType - the QT to remove the data for.

thaw

@Transactional(readOnly=true)
public void thaw(Collection<T> designElementDataVectors)

Thaws the given vectors.

Parameters:

designElementDataVectors - the vectors to thaw.

find

@Transactional(readOnly=true)
public Collection<T> find(ArrayDesign arrayDesign,
                                                        QuantitationType quantitationType)

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

Parameters:

arrayDesign - the AD

quantitationType - the QT

Returns:

the found vectors of type T.

find

@Transactional(readOnly=true)
public 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 T

find

@Transactional(readOnly=true)
public Collection<T> find(Collection<QuantitationType> quantitationTypes)

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

Parameters:

quantitationTypes - the QTs

Returns:

the found vectors of type T

find

@Transactional(readOnly=true)
public Collection<T> find(QuantitationType quantitationType)

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

Parameters:

quantitationType - the QT

Returns:

the found vectors of type T

find

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

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

Parameters:

designElements - design elements

quantitationType - the QT

Returns:

the found vectors of type T

findByExpressionExperiment

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

See Also:

DesignElementDataVectorDao.findByExpressionExperiment(ExpressionExperiment, QuantitationType)

update

@Secured(value="GROUP_USER")
public void update(T dedv)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<T extends DesignElementDataVector>

Parameters:

dedv - the entity to be updated.