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

Class DifferentialExpressionAnalysisServiceImpl

java.lang.Object

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

All Implemented Interfaces:

AnalysisService<DifferentialExpressionAnalysis>, DifferentialExpressionAnalysisService

@Service
public class DifferentialExpressionAnalysisServiceImpl
extends Object
implements DifferentialExpressionAnalysisService

Author:

paul, keshav

See Also:

DifferentialExpressionAnalysisService

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionAnalysisServiceImpl()

Method Summary

Modifier and Type	Method	Description
boolean	canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
Integer	countDownregulated(ExpressionAnalysisResultSet par, double threshold)
Integer	countProbesMeetingThreshold(ExpressionAnalysisResultSet ears, double threshold)
Integer	countUpregulated(ExpressionAnalysisResultSet par, double threshold)
DifferentialExpressionAnalysis	create(DifferentialExpressionAnalysis analysis)
Collection<DifferentialExpressionAnalysis>	find(Gene gene, ExpressionAnalysisResultSet resultSet, double threshold)
Collection<DifferentialExpressionAnalysis>	findByFactor(ExperimentalFactor ef)
Collection<DifferentialExpressionAnalysis>	findByInvestigation(Investigation investigation)
Map<Long,Collection<DifferentialExpressionAnalysis>>	findByInvestigationIds(Collection<Long> investigationIds)
Map<Investigation,Collection<DifferentialExpressionAnalysis>>	findByInvestigations(Collection<? extends Investigation> investigations)
Collection<DifferentialExpressionAnalysis>	findByName(String name)
Collection<DifferentialExpressionAnalysis>	findByTaxon(Taxon taxon)
DifferentialExpressionAnalysis	findByUniqueInvestigations(Collection<? extends Investigation> investigations)
Collection<BioAssaySet>	findExperimentsWithAnalyses(Gene gene)
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)
Collection<DifferentialExpressionAnalysis>	getAnalyses(BioAssaySet expressionExperiment)
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> idsToFilter)	Not secured: for internal use only
Collection<Long>	getExperimentsWithAnalysis(Taxon taxon)	Not secured: for internal use only
DifferentialExpressionAnalysis	load(Long id)
Collection<DifferentialExpressionAnalysis>	loadAll()
void	remove(DifferentialExpressionAnalysis toDelete)
void	removeForExperiment(ExpressionExperiment ee)	Removes all analyses for the given experiment
void	thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)
void	thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)
DifferentialExpressionAnalysis	thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)
void	update(DifferentialExpressionAnalysis o)
void	update(ExpressionAnalysisResultSet a)

Methods inherited from class java.lang.Object

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

Constructor Detail

DifferentialExpressionAnalysisServiceImpl

public DifferentialExpressionAnalysisServiceImpl()

Method Detail

countDownregulated

@Transactional(readOnly=true)
public Integer countDownregulated(ExpressionAnalysisResultSet par,
                                  double threshold)

Specified by:

countDownregulated in interface DifferentialExpressionAnalysisService

Parameters:

par - result set

threshold - for corrected pvalue. Results may not be accurate for 'unreasonable' thresholds.

Returns:

number of downregulated elements

countProbesMeetingThreshold

@Transactional(readOnly=true)
public Integer countProbesMeetingThreshold(ExpressionAnalysisResultSet ears,
                                           double threshold)

Specified by:

countProbesMeetingThreshold in interface DifferentialExpressionAnalysisService

Parameters:

ears - result sets

threshold - (double) for corrected pvalue. Results may not be accurate for 'unreasonable' thresholds.

Returns:

an integer count of all the probes that met the given threshold in the given expressionAnalysisResultSet

countUpregulated

@Transactional(readOnly=true)
public Integer countUpregulated(ExpressionAnalysisResultSet par,
                                double threshold)

Specified by:

countUpregulated in interface DifferentialExpressionAnalysisService

Parameters:

par - result set

threshold - for corrected pvalue. Results may not be accurate for 'unreasonable' thresholds.

create

@Transactional
public DifferentialExpressionAnalysis create(DifferentialExpressionAnalysis analysis)

Specified by:

create in interface DifferentialExpressionAnalysisService

find

@Transactional(readOnly=true)
public Collection<DifferentialExpressionAnalysis> find(Gene gene,
                                                       ExpressionAnalysisResultSet resultSet,
                                                       double threshold)

Specified by:

find in interface DifferentialExpressionAnalysisService

findByFactor

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

Specified by:

findByFactor in interface DifferentialExpressionAnalysisService

findByInvestigationIds

@Transactional(readOnly=true)
public Map<Long,Collection<DifferentialExpressionAnalysis>> findByInvestigationIds(Collection<Long> investigationIds)

Specified by:

findByInvestigationIds in interface DifferentialExpressionAnalysisService

findByTaxon

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

Specified by:

findByTaxon in interface AnalysisService<DifferentialExpressionAnalysis>

Specified by:

findByTaxon in interface DifferentialExpressionAnalysisService

findExperimentsWithAnalyses

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

Specified by:

findExperimentsWithAnalyses in interface DifferentialExpressionAnalysisService

getAnalyses

@Transactional(readOnly=true)
public Collection<DifferentialExpressionAnalysis> getAnalyses(BioAssaySet expressionExperiment)

Specified by:

getAnalyses in interface DifferentialExpressionAnalysisService

getAnalyses

@Transactional(readOnly=true)
public Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>> getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)

Specified by:

getAnalyses in interface DifferentialExpressionAnalysisService

Parameters:

expressionExperiments - ees

Returns:

quite deeply thawed analyses (not the results themselves, but metadata)

thaw

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

Specified by:

thaw in interface DifferentialExpressionAnalysisService

thaw

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

Specified by:

thaw in interface DifferentialExpressionAnalysisService

thawFully

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

Specified by:

thawFully in interface DifferentialExpressionAnalysisService

update

@Transactional
public void update(DifferentialExpressionAnalysis o)

Specified by:

update in interface DifferentialExpressionAnalysisService

update

@Transactional
public void update(ExpressionAnalysisResultSet a)

Specified by:

update 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)

Specified by:

remove in interface AnalysisService<DifferentialExpressionAnalysis>

Parameters:

toDelete - deletes the given analysis from the system

removeForExperiment

public void removeForExperiment(ExpressionExperiment ee)

Description copied from interface: AnalysisService

Removes all analyses for the given experiment

Specified by:

removeForExperiment in interface AnalysisService<DifferentialExpressionAnalysis>

Parameters:

ee - the expriment to remove all analyses for

findByInvestigation

@Transactional(readOnly=true)
public Collection<DifferentialExpressionAnalysis> findByInvestigation(Investigation investigation)

Specified by:

findByInvestigation in interface AnalysisService<DifferentialExpressionAnalysis>

Parameters:

investigation - investigation

Returns:

find all the analyses that involved the given investigation

findByInvestigations

@Transactional(readOnly=true)
public Map<Investigation,Collection<DifferentialExpressionAnalysis>> findByInvestigations(Collection<? extends Investigation> investigations)

Specified by:

findByInvestigations in interface AnalysisService<DifferentialExpressionAnalysis>

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<DifferentialExpressionAnalysis> findByName(String name)

Specified by:

findByName in interface AnalysisService<DifferentialExpressionAnalysis>

findByUniqueInvestigations

@Transactional(readOnly=true)
public DifferentialExpressionAnalysis findByUniqueInvestigations(Collection<? extends Investigation> investigations)

Specified by:

findByUniqueInvestigations in interface AnalysisService<DifferentialExpressionAnalysis>

Parameters:

investigations - investigations

Returns:

An analysis is uniquely determined by its set of investigations. Only returns an analysis if the collection of investigations given exactly matches other wise returns null

getExperimentsWithAnalysis

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

Description copied from interface: AnalysisService

Not secured: for internal use only

Specified by:

getExperimentsWithAnalysis in interface AnalysisService<DifferentialExpressionAnalysis>

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: AnalysisService

Not secured: for internal use only

Specified by:

getExperimentsWithAnalysis in interface AnalysisService<DifferentialExpressionAnalysis>

Parameters:

taxon - taxon

Returns:

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

load

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

Specified by:

load in interface AnalysisService<DifferentialExpressionAnalysis>

Parameters:

id - id

Returns:

the analysis with the specified ID

loadAll

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

Specified by:

loadAll in interface AnalysisService<DifferentialExpressionAnalysis>

Returns:

all of the analysis objects