Interface CoexpressionAnalysisService

All Superinterfaces:

AnalysisService<CoexpressionAnalysis>, BaseImmutableService<CoexpressionAnalysis>, BaseReadOnlyService<CoexpressionAnalysis>, BaseService<CoexpressionAnalysis>, SecurableBaseImmutableService<CoexpressionAnalysis>, SecurableBaseReadOnlyService<CoexpressionAnalysis>, SecurableBaseService<CoexpressionAnalysis>, SingleExperimentAnalysisService<CoexpressionAnalysis>

All Known Implementing Classes:

CoexpressionAnalysisServiceImpl

public interface CoexpressionAnalysisService
extends SingleExperimentAnalysisService<CoexpressionAnalysis>, SecurableBaseService<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.
Collection<CoexpressionAnalysis>	findByTaxon(Taxon taxon)
CoexpCorrelationDistribution	getCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment)
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> experimentAnalyzedIds, boolean includeSubSets)	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, boolean includeSubSets)	Removes all analyses for the given experiment

Methods inherited from interface BaseReadOnlyService

countAll, getElementClass

Methods inherited from interface SecurableBaseImmutableService

create, create, findOrCreate, remove, remove, remove

Methods inherited from interface SecurableBaseReadOnlyService

find, findOrFail, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Methods inherited from interface SecurableBaseService

save, save, update, update

Methods inherited from interface SingleExperimentAnalysisService

findByExperiment, findByExperiments

Method Details

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:

expressionExperiment - ee

coexpd - coexpd

hasCoexpCorrelationDistribution

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

removeForExperiment

void removeForExperiment(BioAssaySet ee,
 boolean includeSubSets)

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

includeSubSets - if the experiment is a ExpressionExperiment, also delete analyses of its ExpressionExperimentSubSet.

findByTaxon

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

getExperimentsWithAnalysis

Collection<Long> getExperimentsWithAnalysis(Collection<Long> experimentAnalyzedIds,
 boolean includeSubSets)

Not secured: for internal use only

Specified by:

getExperimentsWithAnalysis in interface SingleExperimentAnalysisService<CoexpressionAnalysis>

Parameters:

experimentAnalyzedIds - starting list of bioassayset ids.

includeSubSets -

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 SingleExperimentAnalysisService<CoexpressionAnalysis>

Parameters:

taxon - taxon

Returns:

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