Package ubic.gemma.persistence.service.analysis

Interface AnalysisService<T extends Analysis>

All Superinterfaces:

BaseImmutableService<T>, BaseReadOnlyService<T>

All Known Subinterfaces:

CoexpressionAnalysisService, DifferentialExpressionAnalysisService, GeneDiffExMetaAnalysisService, SingleExperimentAnalysisService<T>

All Known Implementing Classes:

CoexpressionAnalysisServiceImpl, DifferentialExpressionAnalysisServiceImpl, GeneDiffExMetaAnalysisServiceImpl

public interface AnalysisService<T extends Analysis>
extends BaseImmutableService<T>

Provides basic services for dealing with analyses

Author:

Gemma

Method Summary

Modifier and Type	Method	Description
Collection<T>	findByName(String name)
Collection<T>	findByTaxon(Taxon taxon)
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> idsToFilter)	Not secured: for internal use only
Collection<Long>	getExperimentsWithAnalysis(Taxon taxon)	Not secured: for internal use only
T	load(Long id)	Loads object with given ID.
Collection<T>	loadAll()	Loads all the entities of specific type.
void	remove(T toDelete)	Removes the given entity from the persistent storage.

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

create, create, findOrCreate, remove, remove

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

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

Method Detail

remove

@Secured({"GROUP_USER","ACL_ANALYSIS_EDIT"})
void remove(T toDelete)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<T extends Analysis>

Parameters:

toDelete - deletes the given analysis from the system

findByName

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<T> findByName(String name)

findByTaxon

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<T> findByTaxon(Taxon taxon)

getExperimentsWithAnalysis

Collection<Long> getExperimentsWithAnalysis(Collection<Long> idsToFilter)

Not secured: for internal use only

Parameters:

idsToFilter - starting list of bioassayset ids.

Returns:

the ones which have a coexpression analysis.

getExperimentsWithAnalysis

Collection<Long> getExperimentsWithAnalysis(Taxon taxon)

Not secured: for internal use only

Parameters:

taxon - taxon

Returns:

ids of bioassaysets from the given taxon that have a coexpression analysis

load

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
T load(Long id)

Description copied from interface: BaseReadOnlyService

Loads object with given ID.

Specified by:

load in interface BaseReadOnlyService<T extends Analysis>

Parameters:

id - id

Returns:

the analysis with the specified ID

loadAll

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<T> loadAll()

Description copied from interface: BaseReadOnlyService

Loads all the entities of specific type.

Specified by:

loadAll in interface BaseReadOnlyService<T extends Analysis>

Returns:

all of the analysis objects