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

Class DifferentialExpressionAnalysisServiceImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractService<DifferentialExpressionAnalysis>

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

All Implemented Interfaces:

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

@Service
public class DifferentialExpressionAnalysisServiceImpl
extends AbstractService<DifferentialExpressionAnalysis>
implements DifferentialExpressionAnalysisService

Author:

paul, keshav

See Also:

• DifferentialExpressionAnalysisService

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractService

log

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionAnalysisServiceImpl(DifferentialExpressionAnalysisDao mainDao)

Method Summary

Modifier and Type	Method	Description
boolean	canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
Collection<DifferentialExpressionAnalysis>	findByExperiment(ExpressionExperiment experiment, boolean includeSubSets)
DifferentialExpressionAnalysis	findByExperimentAnalyzedAndId(ExpressionExperiment expressionExperiment, Long analysisId, boolean includeSubSets)
Map<Long,Collection<DifferentialExpressionAnalysis>>	findByExperimentIds(Collection<Long> experimentIds)
Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>>	findByExperiments(Collection<ExpressionExperiment> experiments, 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> experimentAnalyzedIds, boolean includeSubSets)	Obtain IDs of experiments that have analyses.
Collection<Long>	getExperimentsWithAnalysis(Taxon taxon)
DifferentialExpressionAnalysis	loadWithExperimentAnalyzed(Long id)
void	remove(Long id)	Removes the entity with given ID from the persistent storage.
void	remove(Collection<DifferentialExpressionAnalysis> entities)	Removes all the given entities from persistent storage.
void	remove(DifferentialExpressionAnalysis toDelete)	Removes the given entity from the persistent storage.
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)

Methods inherited from class ubic.gemma.persistence.service.AbstractService

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, save, save, streamAll, streamAll, update, update

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

countAll, getElementClass

Methods inherited from interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService

create, update

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

create, findOrCreate

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

Constructor Details

DifferentialExpressionAnalysisServiceImpl

@Autowired
public DifferentialExpressionAnalysisServiceImpl(DifferentialExpressionAnalysisDao mainDao)

Method Details

loadWithExperimentAnalyzed

@Transactional(readOnly=true)
public DifferentialExpressionAnalysis loadWithExperimentAnalyzed(Long id)

Specified by:

loadWithExperimentAnalyzed in interface DifferentialExpressionAnalysisService

findByFactor

@Transactional(readOnly=true)
public Collection<DifferentialExpressionAnalysis> findByFactor(ExperimentalFactor ef)

Specified by:

findByFactor in interface DifferentialExpressionAnalysisService

findByExperimentIds

@Transactional(readOnly=true)
public Map<Long,Collection<DifferentialExpressionAnalysis>> findByExperimentIds(Collection<Long> experimentIds)

Specified by:

findByExperimentIds in interface DifferentialExpressionAnalysisService

findExperimentsWithAnalyses

@Transactional(readOnly=true)
public Collection<BioAssaySet> findExperimentsWithAnalyses(Gene gene)

Specified by:

findExperimentsWithAnalyses in interface DifferentialExpressionAnalysisService

findByExperimentAnalyzedAndId

@Transactional(readOnly=true)
public DifferentialExpressionAnalysis findByExperimentAnalyzedAndId(ExpressionExperiment expressionExperiment,
 Long analysisId,
 boolean includeSubSets)

Specified by:

findByExperimentAnalyzedAndId in interface DifferentialExpressionAnalysisService

thaw

@Transactional(readOnly=true)
public Collection<DifferentialExpressionAnalysis> thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)

Specified by:

thaw in interface DifferentialExpressionAnalysisService

thaw

@Transactional(readOnly=true)
public DifferentialExpressionAnalysis thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)

Specified by:

thaw in interface DifferentialExpressionAnalysisService

thawFully

@Transactional(readOnly=true)
public DifferentialExpressionAnalysis thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)

Specified by:

thawFully in interface DifferentialExpressionAnalysisService

canDelete

@Transactional(readOnly=true)
public boolean canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)

Specified by:

canDelete in interface DifferentialExpressionAnalysisService

Parameters:

differentialExpressionAnalysis - analysis

Returns:

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

getAnalysesByExperiment

@Transactional(readOnly=true)
public Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>> getAnalysesByExperiment(Collection<Long> ids)

Description copied from interface: DifferentialExpressionAnalysisService

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.

Specified by:

getAnalysesByExperiment in interface DifferentialExpressionAnalysisService

Parameters:

ids - of experiments or experimentsubsets.

Returns:

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

getAnalysesByExperiment

@Transactional(readOnly=true)
public Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>> getAnalysesByExperiment(Collection<Long> ids,
 int offset,
 int limit)

Specified by:

getAnalysesByExperiment in interface DifferentialExpressionAnalysisService

remove

@Transactional
public void remove(DifferentialExpressionAnalysis toDelete)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<DifferentialExpressionAnalysis>

Specified by:

remove in interface SecurableBaseImmutableService<DifferentialExpressionAnalysis>

Overrides:

remove in class AbstractService<DifferentialExpressionAnalysis>

Parameters:

toDelete - the entity to be removed.

remove

public void remove(Collection<DifferentialExpressionAnalysis> entities)

Description copied from interface: BaseImmutableService

Removes all the given entities from persistent storage.

Specified by:

remove in interface BaseImmutableService<DifferentialExpressionAnalysis>

Specified by:

remove in interface SecurableBaseImmutableService<DifferentialExpressionAnalysis>

Overrides:

remove in class AbstractService<DifferentialExpressionAnalysis>

Parameters:

entities - the entities to be removed.

remove

public void remove(Long id)

Description copied from interface: BaseImmutableService

Removes the entity with given ID from the persistent storage.

Specified by:

remove in interface BaseImmutableService<DifferentialExpressionAnalysis>

Specified by:

remove in interface SecurableBaseImmutableService<DifferentialExpressionAnalysis>

Overrides:

remove in class AbstractService<DifferentialExpressionAnalysis>

Parameters:

id - the ID of entity to be removed.

removeForExperiment

@Transactional
public void removeForExperiment(ExpressionExperiment ee,
 boolean includeSubSets)

Description copied from interface: DifferentialExpressionAnalysisService

Removes all analyses for the given experiment

Specified by:

removeForExperiment in interface DifferentialExpressionAnalysisService

Parameters:

ee - the expriment to remove all analyses for

includeSubSets - also delete analyses of its ExpressionExperimentSubSet.

removeForExperimentAnalyzed

@Transactional
public void removeForExperimentAnalyzed(BioAssaySet experimentAnalyzed)

Specified by:

removeForExperimentAnalyzed in interface DifferentialExpressionAnalysisService

removeForExperimentalFactor

@Transactional
public int removeForExperimentalFactor(ExperimentalFactor experimentalFactor)

Description copied from interface: DifferentialExpressionAnalysisService

Remove analyses using the given factor.

Specified by:

removeForExperimentalFactor in interface DifferentialExpressionAnalysisService

Returns:

the number of analysis removed

removeForExperimentalFactors

@Transactional
public int removeForExperimentalFactors(Collection<ExperimentalFactor> experimentalFactors)

Specified by:

removeForExperimentalFactors in interface DifferentialExpressionAnalysisService

findByExperiment

@Transactional(readOnly=true)
public Collection<DifferentialExpressionAnalysis> findByExperiment(ExpressionExperiment experiment,
 boolean includeSubSets)

Specified by:

findByExperiment in interface DifferentialExpressionAnalysisService

Parameters:

experiment - experiment analyzed

includeSubSets - include analyses for its ExpressionExperimentSubSet

Returns:

find all the analyses that involved the given investigation

findByExperiments

@Transactional(readOnly=true)
public Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>> findByExperiments(Collection<ExpressionExperiment> experiments,
 boolean includeSubSets)

Specified by:

findByExperiments in interface DifferentialExpressionAnalysisService

Parameters:

experiments - 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

findByName

@Transactional(readOnly=true)
public Collection<DifferentialExpressionAnalysis> findByName(String name)

Specified by:

findByName in interface DifferentialExpressionAnalysisService

getExperimentsWithAnalysis

@Transactional(readOnly=true)
public Collection<Long> getExperimentsWithAnalysis(Collection<Long> experimentAnalyzedIds,
 boolean includeSubSets)

Description copied from interface: DifferentialExpressionAnalysisService

Obtain IDs of experiments that have analyses.

Not secured: for internal use only

Specified by:

getExperimentsWithAnalysis in interface DifferentialExpressionAnalysisService

Parameters:

experimentAnalyzedIds - starting list of experiment IDs

includeSubSets - include IDs of their subsets that have analyses

Returns:

the ones which have an analysis

getExperimentsWithAnalysis

@Transactional(readOnly=true)
public Collection<Long> getExperimentsWithAnalysis(Taxon taxon)

Specified by:

getExperimentsWithAnalysis in interface DifferentialExpressionAnalysisService