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

Class CoexpressionAnalysisServiceImpl

java.lang.Object

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

ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl

All Implemented Interfaces:

AnalysisService<CoexpressionAnalysis>, CoexpressionAnalysisService, SingleExperimentAnalysisService<CoexpressionAnalysis>, BaseImmutableService<CoexpressionAnalysis>, BaseReadOnlyService<CoexpressionAnalysis>, BaseService<CoexpressionAnalysis>

@Service
public class CoexpressionAnalysisServiceImpl
extends AbstractService<CoexpressionAnalysis>
implements CoexpressionAnalysisService

Author:

paul

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
CoexpressionAnalysisServiceImpl(CoexpressionAnalysisDao mainDao, CoexpressionService coexpressionService)

Method Summary

Modifier and Type	Method	Description
void	addCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment, CoexpCorrelationDistribution coexpd)	For backfilling of the coexpression distributions from flat files - remove when no longer needed.
Collection<CoexpressionAnalysis>	findByExperiment(BioAssaySet investigation)
Map<BioAssaySet,Collection<CoexpressionAnalysis>>	findByExperiments(Collection<BioAssaySet> investigations)
Collection<CoexpressionAnalysis>	findByName(String name)
Collection<CoexpressionAnalysis>	findByTaxon(Taxon taxon)
CoexpCorrelationDistribution	getCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment)
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> idsToFilter)	Not secured: for internal use only
Collection<Long>	getExperimentsWithAnalysis(Taxon taxon)	Not secured: for internal use only
Boolean	hasCoexpCorrelationDistribution(ExpressionExperiment ee)
void	remove(Long id)	Removes the entity with given ID from the persistent storage.
void	remove(Collection<CoexpressionAnalysis> entities)	Removes all the given entities from persistent storage.
void	remove(CoexpressionAnalysis toDelete)	Removes the given entity from the persistent storage.
void	removeForExperiment(BioAssaySet ee)	Removes all analyses for the given experiment

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, 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.analysis.AnalysisService

load, loadAll

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

create, findOrCreate

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

countAll, find, findOrFail, getElementClass, load, loadOrFail, loadOrFail, loadOrFail, loadOrFail

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

save, save

Methods inherited from interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService

create, update, update

Constructor Detail

CoexpressionAnalysisServiceImpl

@Autowired
public CoexpressionAnalysisServiceImpl(CoexpressionAnalysisDao mainDao,
                                       CoexpressionService coexpressionService)

Method Detail

findByTaxon

@Transactional(readOnly=true)
public Collection<CoexpressionAnalysis> findByTaxon(Taxon taxon)

Specified by:

findByTaxon in interface AnalysisService<CoexpressionAnalysis>

Specified by:

findByTaxon in interface CoexpressionAnalysisService

getExperimentsWithAnalysis

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

Description copied from interface: CoexpressionAnalysisService

Not secured: for internal use only

Specified by:

getExperimentsWithAnalysis in interface AnalysisService<CoexpressionAnalysis>

Specified by:

getExperimentsWithAnalysis in interface CoexpressionAnalysisService

Specified by:

getExperimentsWithAnalysis in interface SingleExperimentAnalysisService<CoexpressionAnalysis>

Parameters:

idsToFilter - starting list of bioassayset ids.

Returns:

the ones which have a coexpression analysis.

getExperimentsWithAnalysis

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

Description copied from interface: CoexpressionAnalysisService

Not secured: for internal use only

Specified by:

getExperimentsWithAnalysis in interface AnalysisService<CoexpressionAnalysis>

Specified by:

getExperimentsWithAnalysis in interface CoexpressionAnalysisService

Specified by:

getExperimentsWithAnalysis in interface SingleExperimentAnalysisService<CoexpressionAnalysis>

Parameters:

taxon - taxon

Returns:

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

getCoexpCorrelationDistribution

@Transactional(readOnly=true)
public CoexpCorrelationDistribution getCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment)

Specified by:

getCoexpCorrelationDistribution in interface CoexpressionAnalysisService

addCoexpCorrelationDistribution

@Transactional
public void addCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment,
                                            CoexpCorrelationDistribution coexpd)

Description copied from interface: CoexpressionAnalysisService

For backfilling of the coexpression distributions from flat files - remove when no longer needed.

Specified by:

addCoexpCorrelationDistribution in interface CoexpressionAnalysisService

Parameters:

expressionExperiment - ee

coexpd - coexpd

hasCoexpCorrelationDistribution

@Transactional(readOnly=true)
public Boolean hasCoexpCorrelationDistribution(ExpressionExperiment ee)

Specified by:

hasCoexpCorrelationDistribution in interface CoexpressionAnalysisService

remove

@Transactional
public void remove(CoexpressionAnalysis toDelete)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface AnalysisService<CoexpressionAnalysis>

Specified by:

remove in interface BaseImmutableService<CoexpressionAnalysis>

Overrides:

remove in class AbstractService<CoexpressionAnalysis>

Parameters:

toDelete - the entity to be removed.

remove

@Transactional
public void remove(Collection<CoexpressionAnalysis> entities)

Description copied from interface: BaseImmutableService

Removes all the given entities from persistent storage.

Specified by:

remove in interface BaseImmutableService<CoexpressionAnalysis>

Overrides:

remove in class AbstractService<CoexpressionAnalysis>

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<CoexpressionAnalysis>

Overrides:

remove in class AbstractService<CoexpressionAnalysis>

Parameters:

id - the ID of entity to be removed.

findByExperiment

@Transactional(readOnly=true)
public Collection<CoexpressionAnalysis> findByExperiment(BioAssaySet investigation)

Specified by:

findByExperiment in interface SingleExperimentAnalysisService<CoexpressionAnalysis>

Parameters:

investigation - investigation

Returns:

find all the analyses that involved the given investigation

findByExperiments

@Transactional(readOnly=true)
public Map<BioAssaySet,Collection<CoexpressionAnalysis>> findByExperiments(Collection<BioAssaySet> investigations)

Specified by:

findByExperiments in interface SingleExperimentAnalysisService<CoexpressionAnalysis>

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

findByName

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

Specified by:

findByName in interface AnalysisService<CoexpressionAnalysis>

removeForExperiment

@Transactional
public void removeForExperiment(BioAssaySet ee)

Description copied from interface: SingleExperimentAnalysisService

Removes all analyses for the given experiment

Specified by:

removeForExperiment in interface CoexpressionAnalysisService

Specified by:

removeForExperiment in interface SingleExperimentAnalysisService<CoexpressionAnalysis>

Parameters:

ee - the expriment to remove all analyses for