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

Interface DesignElementDataVectorDao<T extends DesignElementDataVector>

All Superinterfaces:

BaseDao<T>

All Known Subinterfaces:

ProcessedExpressionDataVectorDao, RawExpressionDataVectorDao

All Known Implementing Classes:

DesignElementDataVectorDaoImpl, ProcessedExpressionDataVectorDaoImpl, RawExpressionDataVectorDaoImpl

@Repository
public interface DesignElementDataVectorDao<T extends DesignElementDataVector>
extends BaseDao<T>

See Also:

DesignElementDataVector

Method Summary

Modifier and Type	Method	Description
Collection<T>	create(Collection<T> entities)	Creates a new instance of ubic.gemma.model.expression.bioAssayData.DesignElementDataVector and adds from the passed in entities collection
T	create(T designElementDataVector)	Create an object.
Collection<T>	find(Collection<QuantitationType> quantitationTypes)
Collection<T>	find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)
Collection<T>	find(QuantitationType quantitationType)
Collection<T>	find(ArrayDesign arrayDesign, QuantitationType quantitationType)
Collection<T>	find(BioAssayDimension bioAssayDimension)
Collection<T>	findByExpressionExperiment(ExpressionExperiment ee, QuantitationType quantitationType)	Find expression vectors by ExpressionExperiment.
Collection<DesignElementDataVector>	findRawAndProcessed(QuantitationType qt)
Collection<DesignElementDataVector>	findRawAndProcessed(BioAssayDimension dim)
T	load(Long id)	Loads the entity with given id from the persistent storage.
Collection<T>	loadAll()	Loads all entities of type DesignElementDataVector.
void	removeDataForCompositeSequence(CompositeSequence compositeSequence)
void	removeDataForQuantitationType(QuantitationType quantitationType)
void	removeRawAndProcessed(Collection<DesignElementDataVector> vectors)
void	thaw(Collection<T> designElementDataVectors)
void	thaw(T designElementDataVector)
void	thawRawAndProcessed(Collection<DesignElementDataVector> designElementDataVectors)

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

countAll, find, findOrCreate, load, remove, remove, remove, removeAll, save, save, update, update

Method Detail

removeRawAndProcessed

void removeRawAndProcessed(Collection<DesignElementDataVector> vectors)

findRawAndProcessed

Collection<DesignElementDataVector> findRawAndProcessed(BioAssayDimension dim)

findRawAndProcessed

Collection<DesignElementDataVector> findRawAndProcessed(QuantitationType qt)

thawRawAndProcessed

void thawRawAndProcessed(Collection<DesignElementDataVector> designElementDataVectors)

create

Collection<T> create(Collection<T> entities)

Creates a new instance of ubic.gemma.model.expression.bioAssayData.DesignElementDataVector and adds from the passed in entities collection

Specified by:

create in interface BaseDao<T extends DesignElementDataVector>

Parameters:

entities - the collection of ubic.gemma.model.expression.bioAssayData.DesignElementDataVector instances to create.

Returns:

the created instances.

create

T create(T designElementDataVector)

Description copied from interface: BaseDao

Create an object. If the entity type is immutable, this may also remove any existing entities identified by an appropriate 'find' method.

Specified by:

create in interface BaseDao<T extends DesignElementDataVector>

Parameters:

designElementDataVector - DE data vector

Returns:

Creates an instance of ubic.gemma.model.expression.bioAssayData.DesignElementDataVector and adds it to the persistent store.

load

T load(Long id)

Description copied from interface: BaseDao

Loads the entity with given id from the persistent storage.

Specified by:

load in interface BaseDao<T extends DesignElementDataVector>

Parameters:

id - id

Returns:

Loads an instance of ubic.gemma.model.expression.bioAssayData.DesignElementDataVector from the persistent store.

loadAll

Collection<T> loadAll()

Loads all entities of type DesignElementDataVector.

Specified by:

loadAll in interface BaseDao<T extends DesignElementDataVector>

Returns:

the loaded entities.

thaw

void thaw(Collection<T> designElementDataVectors)

thaw

void thaw(T designElementDataVector)

Parameters:

designElementDataVector - Thaws associations of the given DesignElementDataVector

find

Collection<T> find(BioAssayDimension bioAssayDimension)

find

Collection<T> find(Collection<QuantitationType> quantitationTypes)

find

Collection<T> find(QuantitationType quantitationType)

find

Collection<T> find(ArrayDesign arrayDesign,
                   QuantitationType quantitationType)

find

Collection<T> find(Collection<CompositeSequence> designElements,
                   QuantitationType quantitationType)

findByExpressionExperiment

Collection<T> findByExpressionExperiment(ExpressionExperiment ee,
                                         QuantitationType quantitationType)

Find expression vectors by ExpressionExperiment.

removeDataForCompositeSequence

void removeDataForCompositeSequence(CompositeSequence compositeSequence)

removeDataForQuantitationType

void removeDataForQuantitationType(QuantitationType quantitationType)