Package ubic.gemma.persistence.service.analysis.expression

Interface ExpressionExperimentSetDao

All Superinterfaces:

BaseDao<ExpressionExperimentSet>, BaseVoEnabledDao<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

All Known Implementing Classes:

ExpressionExperimentSetDaoImpl

public interface ExpressionExperimentSetDao
extends BaseVoEnabledDao<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

See Also:

• ExpressionExperimentSet

Method Summary

Modifier and Type	Method	Description
Collection<ExpressionExperimentSet>	find(ExpressionExperiment ee)
Collection<ExpressionExperimentSet>	findByAccession(String accession)
Collection<ExpressionExperimentSet>	findByAccession(String accession, ExternalDatabase externalDatabase)
Collection<ExpressionExperimentSet>	findByName(String name)
Collection<ExpressionExperiment>	getExperimentsInSet(Long id)
Collection<ExpressionExperimentDetailsValueObject>	getExperimentValueObjectsInSet(Long id)
Collection<ExpressionExperimentSet>	loadAllExperimentSetsWithTaxon()
Collection<ExpressionExperimentSetValueObject>	loadAllValueObjects(boolean loadEEIds)
ExpressionExperimentSetValueObject	loadValueObject(Long id, boolean loadEEIds)
List<ExpressionExperimentSetValueObject>	loadValueObjects(Collection<Long> eeSetIds, boolean loadEEIds)
void	thaw(ExpressionExperimentSet expressionExperimentSet)

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

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

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Method Details

find

Collection<ExpressionExperimentSet> find(ExpressionExperiment ee)

Parameters:

ee - bio assay set

Returns:

expressionExperimentSets that contain the given ee.

findByName

Collection<ExpressionExperimentSet> findByName(String name)

findByAccession

Collection<ExpressionExperimentSet> findByAccession(String accession)

findByAccession

Collection<ExpressionExperimentSet> findByAccession(String accession,
 ExternalDatabase externalDatabase)

getExperimentsInSet

Collection<ExpressionExperiment> getExperimentsInSet(Long id)

Parameters:

id - id

Returns:

the security-filtered list of experiments in a set. It is possible for the return to be empty even if the set is not (due to security filters). Use this instead of expressionExperimentSet.getExperiments.

loadAllExperimentSetsWithTaxon

Collection<ExpressionExperimentSet> loadAllExperimentSetsWithTaxon()

Returns:

ExpressionExperimentSets that have more than 1 experiment in them & have a taxon value.

thaw

void thaw(ExpressionExperimentSet expressionExperimentSet)

loadAllValueObjects

Collection<ExpressionExperimentSetValueObject> loadAllValueObjects(boolean loadEEIds)

Parameters:

loadEEIds - whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.

Returns:

ee vos

loadValueObjects

List<ExpressionExperimentSetValueObject> loadValueObjects(Collection<Long> eeSetIds,
 boolean loadEEIds)

Parameters:

eeSetIds - ids

loadEEIds - whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.

Returns:

ee vos

getExperimentValueObjectsInSet

Collection<ExpressionExperimentDetailsValueObject> getExperimentValueObjectsInSet(Long id)

loadValueObject

@Nullable
ExpressionExperimentSetValueObject loadValueObject(Long id,
 boolean loadEEIds)

Parameters:

id - id

loadEEIds - whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.

Returns:

ee vos