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

Interface CoexpressionAnalysisService

All Superinterfaces:

AnalysisService<CoexpressionAnalysis>, SingleExperimentAnalysisService<CoexpressionAnalysis>

All Known Implementing Classes:

CoexpressionAnalysisServiceImpl

public interface CoexpressionAnalysisService
extends SingleExperimentAnalysisService<CoexpressionAnalysis>

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

Author:

kelsey

Method Summary

Modifier and Type	Method and 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)
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(CoexpressionAnalysis o)

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

findByExperiment, findByExperiments

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

findByName, load, loadAll, remove

Method Detail

create

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

update

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

getCoexpCorrelationDistribution

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

addCoexpCorrelationDistribution

@Secured(value={"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(value={"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(value={"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