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

Interface CoexpressionAnalysisService

All Superinterfaces:

AnalysisService<CoexpressionAnalysis>, BaseImmutableService<CoexpressionAnalysis>, BaseReadOnlyService<CoexpressionAnalysis>, BaseService<CoexpressionAnalysis>, SingleExperimentAnalysisService<CoexpressionAnalysis>

All Known Implementing Classes:

CoexpressionAnalysisServiceImpl

public interface CoexpressionAnalysisService
extends BaseService<CoexpressionAnalysis>, SingleExperimentAnalysisService<CoexpressionAnalysis>

Deals with the Analysis objects for Coexpression - not the coexpression results themselves.

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
void	addCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment, CoexpCorrelationDistribution coexpd)	For backfilling of the coexpression distributions from flat files - remove when no longer needed.
CoexpressionAnalysis	create(CoexpressionAnalysis coexpressionAnalysis)	Creates the given entity in the persistent storage.
Collection<CoexpressionAnalysis>	findByTaxon(Taxon taxon)
CoexpCorrelationDistribution	getCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment)
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> idsToFilter)	Not secured: for internal use only
Collection<Long>	getExperimentsWithAnalysis(Taxon taxon)	Not secured: for internal use only
boolean	hasCoexpCorrelationDistribution(ExpressionExperiment ee)
void	removeForExperiment(BioAssaySet ee)	Removes all analyses for the given experiment
void	update(Collection<CoexpressionAnalysis> o)	Updates all entities in the given collection in the persistent storage.
void	update(CoexpressionAnalysis o)	Updates the given entity in the persistent storage.

Methods inherited from interface ubic.gemma.persistence.service.analysis.AnalysisService

findByName, load, loadAll, remove

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

create, findOrCreate, remove, remove

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

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

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

save, save

Methods inherited from interface ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisService

findByExperiment, findByExperiments

Method Detail

create

@Secured("GROUP_USER")
CoexpressionAnalysis create(CoexpressionAnalysis coexpressionAnalysis)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<CoexpressionAnalysis>

Parameters:

coexpressionAnalysis - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

update

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void update(CoexpressionAnalysis o)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<CoexpressionAnalysis>

Parameters:

o - the entity to be updated.

update

@Secured({"GROUP_USER","ACL_SECURABLE_COLLECTION_EDIT"})
void update(Collection<CoexpressionAnalysis> o)

Description copied from interface: BaseService

Updates all entities in the given collection in the persistent storage.

Specified by:

update in interface BaseService<CoexpressionAnalysis>

Parameters:

o - the entities to be updated.

getCoexpCorrelationDistribution

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
CoexpCorrelationDistribution getCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment)

addCoexpCorrelationDistribution

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_EDIT"})
void addCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment,
                                     CoexpCorrelationDistribution coexpd)

For backfilling of the coexpression distributions from flat files - remove when no longer needed.

Parameters:

coexpd - coexpd

expressionExperiment - ee

hasCoexpCorrelationDistribution

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
boolean hasCoexpCorrelationDistribution(ExpressionExperiment ee)

removeForExperiment

void removeForExperiment(BioAssaySet ee)

Description copied from interface: SingleExperimentAnalysisService

Removes all analyses for the given experiment

Specified by:

removeForExperiment in interface SingleExperimentAnalysisService<CoexpressionAnalysis>

Parameters:

ee - the expriment to remove all analyses for

findByTaxon

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

Specified by:

findByTaxon in interface AnalysisService<CoexpressionAnalysis>

getExperimentsWithAnalysis

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

Not secured: for internal use only

Specified by:

getExperimentsWithAnalysis in interface AnalysisService<CoexpressionAnalysis>

Specified by:

getExperimentsWithAnalysis in interface SingleExperimentAnalysisService<CoexpressionAnalysis>

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

Specified by:

getExperimentsWithAnalysis in interface AnalysisService<CoexpressionAnalysis>

Specified by:

getExperimentsWithAnalysis in interface SingleExperimentAnalysisService<CoexpressionAnalysis>

Parameters:

taxon - taxon

Returns:

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