Class DifferentialExpressionAnalysisReadServiceImpl

java.lang.Object

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

All Implemented Interfaces:

DifferentialExpressionAnalysisReadService

@Service("differentialExpressionAnalysisReadService")
public class DifferentialExpressionAnalysisReadServiceImpl
extends Object
implements DifferentialExpressionAnalysisReadService

Implementation of DifferentialExpressionAnalysisReadService.

All public methods are @Transactional(readOnly = true). ACL enforcement is the responsibility of the facade DifferentialExpressionAnalysisService interface -- this class is unsecured at the AOP boundary on purpose, so intra-gemma-core callers can bypass duplicate ACL checks once authenticated.

See Also:

• DifferentialExpressionAnalysisService

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionAnalysisReadServiceImpl(DifferentialExpressionAnalysisDao differentialExpressionAnalysisDao)

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)
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)
DifferentialExpressionAnalysis	loadWithExperimentAnalyzed(Long id)	Load an analysis by ID and eagerly initialize its experimentAnalyzed.
Collection<DifferentialExpressionAnalysis>	thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)	Thaw a collection of DifferentialExpressionAnalysis for full traversal.
DifferentialExpressionAnalysis	thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)	Thaw a single DifferentialExpressionAnalysis for full traversal.
DifferentialExpressionAnalysis	thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)	Thaw a single DifferentialExpressionAnalysis including all its result sets, results and contrasts.

Methods inherited from class Object

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

Constructor Details

DifferentialExpressionAnalysisReadServiceImpl

@Autowired
public DifferentialExpressionAnalysisReadServiceImpl(DifferentialExpressionAnalysisDao differentialExpressionAnalysisDao)

Method Details

loadWithExperimentAnalyzed

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

Description copied from interface: DifferentialExpressionAnalysisReadService

Load an analysis by ID and eagerly initialize its experimentAnalyzed.

Specified by:

loadWithExperimentAnalyzed in interface DifferentialExpressionAnalysisReadService

findByName

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

Specified by:

findByName in interface DifferentialExpressionAnalysisReadService

See Also:

• DifferentialExpressionAnalysisDao.findByName(String)

findByFactor

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

Specified by:

findByFactor in interface DifferentialExpressionAnalysisReadService

See Also:

• DifferentialExpressionAnalysisDao.findByFactor(ExperimentalFactor)

findExperimentsWithAnalyses

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

Specified by:

findExperimentsWithAnalyses in interface DifferentialExpressionAnalysisReadService

See Also:

• DifferentialExpressionAnalysisDao.findExperimentsWithAnalyses(Gene)

findByExperimentAndAnalysisId

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

Specified by:

findByExperimentAndAnalysisId in interface DifferentialExpressionAnalysisReadService

See Also:

• DifferentialExpressionAnalysisDao.findByExperimentAndAnalysisId(ExpressionExperiment, boolean, Long)

thaw

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

Description copied from interface: DifferentialExpressionAnalysisReadService

Thaw a collection of DifferentialExpressionAnalysis for full traversal.

Specified by:

thaw in interface DifferentialExpressionAnalysisReadService

thaw

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

Description copied from interface: DifferentialExpressionAnalysisReadService

Thaw a single DifferentialExpressionAnalysis for full traversal.

Specified by:

thaw in interface DifferentialExpressionAnalysisReadService

thawFully

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

Description copied from interface: DifferentialExpressionAnalysisReadService

Thaw a single DifferentialExpressionAnalysis including all its result sets, results and contrasts.

Specified by:

thawFully in interface DifferentialExpressionAnalysisReadService

canDelete

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

Specified by:

canDelete in interface DifferentialExpressionAnalysisReadService

Returns:

true if the analysis can be deleted (no other entity is keeping it around).

findByExperimentIds

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

Specified by:

findByExperimentIds in interface DifferentialExpressionAnalysisReadService

See Also:

• DifferentialExpressionAnalysisService.findByExperimentIds(Collection, boolean, boolean)

findByExperiment

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

Specified by:

findByExperiment in interface DifferentialExpressionAnalysisReadService

See Also:

• DifferentialExpressionAnalysisDao.findByExperiment(ExpressionExperiment, boolean)

findByExperiments

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

Specified by:

findByExperiments in interface DifferentialExpressionAnalysisReadService

See Also:

• DifferentialExpressionAnalysisDao.findByExperiments(Collection, boolean)

getExperimentsWithAnalysis

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

Specified by:

getExperimentsWithAnalysis in interface DifferentialExpressionAnalysisReadService

See Also:

• DifferentialExpressionAnalysisDao.getExperimentsWithAnalysis(Collection, boolean)