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

Class GeneDiffExMetaAnalysisServiceImpl

java.lang.Object

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

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

All Implemented Interfaces:

AnalysisService<GeneDifferentialExpressionMetaAnalysis>, GeneDiffExMetaAnalysisService, BaseImmutableService<GeneDifferentialExpressionMetaAnalysis>, BaseReadOnlyService<GeneDifferentialExpressionMetaAnalysis>, BaseService<GeneDifferentialExpressionMetaAnalysis>

@Service
public class GeneDiffExMetaAnalysisServiceImpl
extends AbstractService<GeneDifferentialExpressionMetaAnalysis>
implements GeneDiffExMetaAnalysisService

Author:

Paul

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
GeneDiffExMetaAnalysisServiceImpl(GeneDiffExMetaAnalysisDao mainDao)

Method Summary

Modifier and Type	Method	Description
BaseValueObject	delete(Long id)
Collection<GeneDifferentialExpressionMetaAnalysis>	findByName(String name)
Collection<GeneDifferentialExpressionMetaAnalysis>	findByTaxon(Taxon taxon)
Collection<IncludedResultSetInfoValueObject>	findIncludedResultSetsInfoById(long analysisId)
Collection<GeneDifferentialExpressionMetaAnalysisSummaryValueObject>	findMetaAnalyses(Collection<Long> metaAnalysisIds)
Collection<GeneDifferentialExpressionMetaAnalysisResultValueObject>	findResultsById(long analysisId)
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> idsToFilter)	Not secured: for internal use only
Collection<Long>	getExperimentsWithAnalysis(Taxon taxon)	Not secured: for internal use only
GeneDifferentialExpressionMetaAnalysisResult	loadResult(Long idResult)
GeneDifferentialExpressionMetaAnalysis	loadWithResultId(Long idResult)

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

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, remove, remove, remove, 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, remove

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

create, findOrCreate, remove, remove

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

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

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

create

Constructor Detail

GeneDiffExMetaAnalysisServiceImpl

@Autowired
public GeneDiffExMetaAnalysisServiceImpl(GeneDiffExMetaAnalysisDao mainDao)

Method Detail

delete

@Transactional
public BaseValueObject delete(Long id)

Specified by:

delete in interface GeneDiffExMetaAnalysisService

findByTaxon

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

Specified by:

findByTaxon in interface AnalysisService<GeneDifferentialExpressionMetaAnalysis>

Specified by:

findByTaxon in interface GeneDiffExMetaAnalysisService

findIncludedResultSetsInfoById

@Transactional(readOnly=true)
public Collection<IncludedResultSetInfoValueObject> findIncludedResultSetsInfoById(long analysisId)

Specified by:

findIncludedResultSetsInfoById in interface GeneDiffExMetaAnalysisService

findMetaAnalyses

@Transactional(readOnly=true)
public Collection<GeneDifferentialExpressionMetaAnalysisSummaryValueObject> findMetaAnalyses(Collection<Long> metaAnalysisIds)

Specified by:

findMetaAnalyses in interface GeneDiffExMetaAnalysisService

findResultsById

@Transactional(readOnly=true)
public Collection<GeneDifferentialExpressionMetaAnalysisResultValueObject> findResultsById(long analysisId)

Specified by:

findResultsById in interface GeneDiffExMetaAnalysisService

loadResult

@Transactional(readOnly=true)
public GeneDifferentialExpressionMetaAnalysisResult loadResult(Long idResult)

Specified by:

loadResult in interface GeneDiffExMetaAnalysisService

loadWithResultId

@Transactional(readOnly=true)
public GeneDifferentialExpressionMetaAnalysis loadWithResultId(Long idResult)

Specified by:

loadWithResultId in interface GeneDiffExMetaAnalysisService

findByName

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

Specified by:

findByName in interface AnalysisService<GeneDifferentialExpressionMetaAnalysis>

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<GeneDifferentialExpressionMetaAnalysis>

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<GeneDifferentialExpressionMetaAnalysis>

Parameters:

taxon - taxon

Returns:

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