Package ubic.gemma.persistence.service.analysis

Interface SingleExperimentAnalysisService<T extends SingleExperimentAnalysis>

All Superinterfaces:

AnalysisService<T>, BaseImmutableService<T>, BaseReadOnlyService<T>

All Known Subinterfaces:

CoexpressionAnalysisService, DifferentialExpressionAnalysisService

All Known Implementing Classes:

CoexpressionAnalysisServiceImpl, DifferentialExpressionAnalysisServiceImpl

public interface SingleExperimentAnalysisService<T extends SingleExperimentAnalysis>
extends AnalysisService<T>

Interface for analysis service manipulating single experiments.

Author:

poirigiu

Method Summary

Modifier and Type	Method	Description
Collection<T>	findByExperiment(BioAssaySet investigation)
Map<BioAssaySet,Collection<T>>	findByExperiments(Collection<BioAssaySet> investigations)
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> idsToFilter)	Not secured: for internal use only
Collection<Long>	getExperimentsWithAnalysis(Taxon taxon)	Not secured: for internal use only
void	removeForExperiment(BioAssaySet ee)	Removes all analyses for the given experiment

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

findByName, findByTaxon, load, loadAll, remove

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

removeForExperiment

@Secured({"GROUP_USER","ACL_ANALYSIS_EDIT"})
void removeForExperiment(BioAssaySet ee)

Removes all analyses for the given experiment

Parameters:

ee - the expriment to remove all analyses for

findByExperiment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<T> findByExperiment(BioAssaySet investigation)

Parameters:

investigation - investigation

Returns:

find all the analyses that involved the given investigation

findByExperiments

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ","AFTER_ACL_MAP_READ"})
Map<BioAssaySet,Collection<T>> findByExperiments(Collection<BioAssaySet> investigations)

Parameters:

investigations - investigations

Returns:

Given a collection of investigations returns a Map of Analysis --> collection of Investigations The collection of investigations returned by the map will include all the investigations for the analysis key iff one of the investigations for that analysis was in the given collection started with

getExperimentsWithAnalysis

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

Not secured: for internal use only

Specified by:

getExperimentsWithAnalysis in interface AnalysisService<T extends SingleExperimentAnalysis>

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<T extends SingleExperimentAnalysis>

Parameters:

taxon - taxon

Returns:

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