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

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	findByExperimentAndAnalysisId(ExpressionExperiment expressionExperiment, boolean includeSubSets, Long analysisId)
Map<ExpressionExperimentDetailsValueObject,Collection<DifferentialExpressionAnalysisValueObject>>	findByExperimentIds(Collection<Long> experimentIds, boolean includeSubSets, boolean includeAssays)	Given a set of ids, find experiments or subsets that have differential expression analyses.
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)
Collection<DifferentialExpressionAnalysis>	findByFactor(ExperimentalFactor ef)
Collection<DifferentialExpressionAnalysis>	findByName(String name)
Collection<BioAssaySet>	findExperimentsWithAnalyses(Gene gene)
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> experimentIds, boolean includeSubSets)	Obtain IDs of experiments that have analyses.
DifferentialExpressionAnalysis	loadWithExperimentAnalyzed(Long id)
void	remove(Collection<DifferentialExpressionAnalysis> entities)
void	remove(DifferentialExpressionAnalysis toDelete)
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)	Remove all analysis for the given experiment or subset.
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, 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, loadOrFail, loadOrFail

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

create, 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, 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

findExperimentsWithAnalyses

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

Specified by:

findExperimentsWithAnalyses in interface DifferentialExpressionAnalysisService

findByExperimentAndAnalysisId

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

Specified by:

findByExperimentAndAnalysisId 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.

findByExperimentIds

@Transactional(readOnly=true)
public Map<ExpressionExperimentDetailsValueObject,Collection<DifferentialExpressionAnalysisValueObject>> findByExperimentIds(Collection<Long> experimentIds,
 boolean includeSubSets,
 boolean includeAssays)

Description copied from interface: DifferentialExpressionAnalysisService

Given a set of ids, find experiments or subsets 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:

findByExperimentIds in interface DifferentialExpressionAnalysisService

Parameters:

experimentIds - of ExpressionExperiment

includeSubSets - include analysis of subsets of the requested experiments

includeAssays - include assay information in the value objects

Returns:

map of detailed EE VOs to analyses VOs for each, subset analyses are mapped to their source experiment

remove

@Transactional
public void remove(DifferentialExpressionAnalysis toDelete)

Specified by:

remove in interface BaseImmutableService<DifferentialExpressionAnalysis>

Specified by:

remove in interface SecurableBaseImmutableService<DifferentialExpressionAnalysis>

Overrides:

remove in class AbstractService<DifferentialExpressionAnalysis>

See Also:

• BaseDao.remove(Identifiable)

remove

public void remove(Collection<DifferentialExpressionAnalysis> entities)

Specified by:

remove in interface BaseImmutableService<DifferentialExpressionAnalysis>

Specified by:

remove in interface SecurableBaseImmutableService<DifferentialExpressionAnalysis>

Overrides:

remove in class AbstractService<DifferentialExpressionAnalysis>

See Also:

• BaseDao.remove(Collection)

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)

Description copied from interface: DifferentialExpressionAnalysisService

Remove all analysis for the given experiment or subset.

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

Specified by:

findByExperiments in interface DifferentialExpressionAnalysisService

Parameters:

experiments - investigations

includeSubSets - include analyses for their ExpressionExperimentSubSet

Returns:

analyses grouped by experiment, subset analyses are mapped to their source experiment

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> experimentIds,
 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:

experimentIds - starting list of ExpressionExperiment IDs

includeSubSets - include IDs of their subsets that have analyses

Returns:

the ones which have an analysis