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

Interface DifferentialExpressionAnalysisService

All Superinterfaces:

AnalysisService<DifferentialExpressionAnalysis>, BaseImmutableService<DifferentialExpressionAnalysis>, BaseReadOnlyService<DifferentialExpressionAnalysis>, BaseService<DifferentialExpressionAnalysis>, SecurableBaseImmutableService<DifferentialExpressionAnalysis>, SecurableBaseReadOnlyService<DifferentialExpressionAnalysis>, SecurableBaseService<DifferentialExpressionAnalysis>

All Known Implementing Classes:

DifferentialExpressionAnalysisServiceImpl

public interface DifferentialExpressionAnalysisService
extends AnalysisService<DifferentialExpressionAnalysis>, SecurableBaseService<DifferentialExpressionAnalysis>

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
boolean	canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
DifferentialExpressionAnalysis	create(DifferentialExpressionAnalysis analysis)	Creates the given entity in the persistent storage.
Collection<DifferentialExpressionAnalysis>	findByExperiment(ExpressionExperiment experimentAnalyzed, boolean includeSubSets)
DifferentialExpressionAnalysis	findByExperimentAnalyzedAndId(ExpressionExperiment expressionExperiment, Long analysisId, boolean includeSubSets)
Map<Long,Collection<DifferentialExpressionAnalysis>>	findByExperimentIds(Collection<Long> investigationIds)
Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>>	findByExperiments(Collection<ExpressionExperiment> investigations, boolean includeSubSets)
Collection<DifferentialExpressionAnalysis>	findByFactor(ExperimentalFactor ef)
Collection<DifferentialExpressionAnalysis>	findByName(String name)
Collection<BioAssaySet>	findExperimentsWithAnalyses(Gene gene)
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>>	getAnalysesByExperiment(Collection<Long> ids)	Given a set of ids, find experiments or experimentsubsets that have differential expression analyses.
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>>	getAnalysesByExperiment(Collection<Long> ids, int offset, int limit)
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> eeIds, boolean includeSubSets)	Obtain IDs of experiments that have analyses.
Collection<Long>	getExperimentsWithAnalysis(Taxon taxon)
DifferentialExpressionAnalysis	loadWithExperimentAnalyzed(Long id)
void	removeForExperiment(ExpressionExperiment ee, boolean includeSubSets)	Removes all analyses for the given experiment
int	removeForExperimentalFactor(ExperimentalFactor experimentalFactor)	Remove analyses using the given factor.
int	removeForExperimentalFactors(Collection<ExperimentalFactor> experimentalFactors)
void	removeForExperimentAnalyzed(BioAssaySet experimentAnalyzed)
Collection<DifferentialExpressionAnalysis>	thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)
DifferentialExpressionAnalysis	thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)
DifferentialExpressionAnalysis	thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)
void	update(DifferentialExpressionAnalysis o)	Updates the given entity in the persistent storage.

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

countAll, getElementClass, loadOrFail, loadOrFail

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService

create, findOrCreate, remove, remove, remove

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService

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

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService

save, save, update

Method Details

loadWithExperimentAnalyzed

@Nullable
DifferentialExpressionAnalysis loadWithExperimentAnalyzed(Long id)

create

@Secured("GROUP_USER")
DifferentialExpressionAnalysis create(DifferentialExpressionAnalysis analysis)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<DifferentialExpressionAnalysis>

Specified by:

create in interface SecurableBaseImmutableService<DifferentialExpressionAnalysis>

Parameters:

analysis - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

findByName

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

findByFactor

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Collection<DifferentialExpressionAnalysis> findByFactor(ExperimentalFactor ef)

findByExperimentIds

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Map<Long,Collection<DifferentialExpressionAnalysis>> findByExperimentIds(Collection<Long> investigationIds)

findExperimentsWithAnalyses

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioAssaySet> findExperimentsWithAnalyses(Gene gene)

findByExperimentAnalyzedAndId

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ","AFTER_ACL_READ"})
DifferentialExpressionAnalysis findByExperimentAnalyzedAndId(ExpressionExperiment expressionExperiment,
 Long analysisId,
 boolean includeSubSets)

thaw

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"})
Collection<DifferentialExpressionAnalysis> thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)

thaw

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
DifferentialExpressionAnalysis thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)

thawFully

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
DifferentialExpressionAnalysis thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)

update

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

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<DifferentialExpressionAnalysis>

Specified by:

update in interface SecurableBaseService<DifferentialExpressionAnalysis>

Parameters:

o - the entity to be updated.

canDelete

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
boolean canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)

Parameters:

differentialExpressionAnalysis - analysis

Returns:

Is the analysis deleteable, or is it tied up with another entity that keeps it from being removed.

getAnalysesByExperiment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>> getAnalysesByExperiment(Collection<Long> ids)

Given a set of ids, find experiments or experimentsubsets that have differential expression analyses. Subsets are handled two ways: if the ID given is of a subset, or if the ID is of an experiment that has subsets. In the latter case, the return value will contain experiments that were not explicitly queried for.

Parameters:

ids - of experiments or experimentsubsets.

Returns:

map of bioassayset (valueobjects) to analyses (valueobjects) for each.

getAnalysesByExperiment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>> getAnalysesByExperiment(Collection<Long> ids,
 int offset,
 int limit)

removeForExperimentalFactor

int removeForExperimentalFactor(ExperimentalFactor experimentalFactor)

Remove analyses using the given factor.

Returns:

the number of analysis removed

removeForExperimentalFactors

int removeForExperimentalFactors(Collection<ExperimentalFactor> experimentalFactors)

findByExperiment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<DifferentialExpressionAnalysis> findByExperiment(ExpressionExperiment experimentAnalyzed,
 boolean includeSubSets)

Parameters:

experimentAnalyzed - experiment analyzed

includeSubSets - include analyses for its ExpressionExperimentSubSet

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<DifferentialExpressionAnalysis>> findByExperiments(Collection<ExpressionExperiment> investigations,
 boolean includeSubSets)

Parameters:

investigations - investigations

includeSubSets - include analyses for their ExpressionExperimentSubSet

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> eeIds,
 boolean includeSubSets)

Obtain IDs of experiments that have analyses.

Not secured: for internal use only

Parameters:

eeIds - starting list of experiment IDs

includeSubSets - include IDs of their subsets that have analyses

Returns:

the ones which have an analysis

getExperimentsWithAnalysis

Collection<Long> getExperimentsWithAnalysis(Taxon taxon)

removeForExperiment

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeForExperiment(ExpressionExperiment ee,
 boolean includeSubSets)

Removes all analyses for the given experiment

Parameters:

ee - the expriment to remove all analyses for

includeSubSets - also delete analyses of its ExpressionExperimentSubSet.

removeForExperimentAnalyzed

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeForExperimentAnalyzed(BioAssaySet experimentAnalyzed)