Class CoexpressionAnalysisServiceImpl
- java.lang.Object
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- ubic.gemma.persistence.service.AbstractService<CoexpressionAnalysis>
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- ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl
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- 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
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Field Summary
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Fields inherited from class ubic.gemma.persistence.service.AbstractService
log
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Constructor Summary
Constructors Constructor Description CoexpressionAnalysisServiceImpl(CoexpressionAnalysisDao mainDao, CoexpressionService coexpressionService)
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Method Summary
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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
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface ubic.gemma.persistence.service.analysis.AnalysisService
load, loadAll
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Methods inherited from interface ubic.gemma.persistence.service.BaseImmutableService
create, findOrCreate
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Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService
countAll, find, findOrFail, getElementClass, load, loadOrFail, loadOrFail, loadOrFail, loadOrFail
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Methods inherited from interface ubic.gemma.persistence.service.BaseService
save, save
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Methods inherited from interface ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService
create, update, update
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Constructor Detail
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CoexpressionAnalysisServiceImpl
@Autowired public CoexpressionAnalysisServiceImpl(CoexpressionAnalysisDao mainDao, CoexpressionService coexpressionService)
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Method Detail
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findByTaxon
@Transactional(readOnly=true) public Collection<CoexpressionAnalysis> findByTaxon(Taxon taxon)
- Specified by:
findByTaxon
in interfaceAnalysisService<CoexpressionAnalysis>
- Specified by:
findByTaxon
in interfaceCoexpressionAnalysisService
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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 interfaceAnalysisService<CoexpressionAnalysis>
- Specified by:
getExperimentsWithAnalysis
in interfaceCoexpressionAnalysisService
- Specified by:
getExperimentsWithAnalysis
in interfaceSingleExperimentAnalysisService<CoexpressionAnalysis>
- Parameters:
idsToFilter
- starting list of bioassayset ids.- Returns:
- the ones which have a coexpression analysis.
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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 interfaceAnalysisService<CoexpressionAnalysis>
- Specified by:
getExperimentsWithAnalysis
in interfaceCoexpressionAnalysisService
- Specified by:
getExperimentsWithAnalysis
in interfaceSingleExperimentAnalysisService<CoexpressionAnalysis>
- Parameters:
taxon
- taxon- Returns:
- ids of bioassaysets from the given taxon that have a coexpression analysis
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getCoexpCorrelationDistribution
@Transactional(readOnly=true) public CoexpCorrelationDistribution getCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment)
- Specified by:
getCoexpCorrelationDistribution
in interfaceCoexpressionAnalysisService
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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 interfaceCoexpressionAnalysisService
- Parameters:
expressionExperiment
- eecoexpd
- coexpd
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hasCoexpCorrelationDistribution
@Transactional(readOnly=true) public Boolean hasCoexpCorrelationDistribution(ExpressionExperiment ee)
- Specified by:
hasCoexpCorrelationDistribution
in interfaceCoexpressionAnalysisService
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remove
@Transactional public void remove(CoexpressionAnalysis toDelete)
Description copied from interface:BaseImmutableService
Removes the given entity from the persistent storage.- Specified by:
remove
in interfaceAnalysisService<CoexpressionAnalysis>
- Specified by:
remove
in interfaceBaseImmutableService<CoexpressionAnalysis>
- Overrides:
remove
in classAbstractService<CoexpressionAnalysis>
- Parameters:
toDelete
- the entity to be removed.
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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 interfaceBaseImmutableService<CoexpressionAnalysis>
- Overrides:
remove
in classAbstractService<CoexpressionAnalysis>
- Parameters:
entities
- the entities to be removed.
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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 interfaceBaseImmutableService<CoexpressionAnalysis>
- Overrides:
remove
in classAbstractService<CoexpressionAnalysis>
- Parameters:
id
- the ID of entity to be removed.
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findByExperiment
@Transactional(readOnly=true) public Collection<CoexpressionAnalysis> findByExperiment(BioAssaySet investigation)
- Specified by:
findByExperiment
in interfaceSingleExperimentAnalysisService<CoexpressionAnalysis>
- Parameters:
investigation
- investigation- Returns:
- find all the analyses that involved the given investigation
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findByExperiments
@Transactional(readOnly=true) public Map<BioAssaySet,Collection<CoexpressionAnalysis>> findByExperiments(Collection<BioAssaySet> investigations)
- Specified by:
findByExperiments
in interfaceSingleExperimentAnalysisService<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
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findByName
@Transactional(readOnly=true) public Collection<CoexpressionAnalysis> findByName(String name)
- Specified by:
findByName
in interfaceAnalysisService<CoexpressionAnalysis>
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removeForExperiment
@Transactional public void removeForExperiment(BioAssaySet ee)
Description copied from interface:SingleExperimentAnalysisService
Removes all analyses for the given experiment- Specified by:
removeForExperiment
in interfaceCoexpressionAnalysisService
- Specified by:
removeForExperiment
in interfaceSingleExperimentAnalysisService<CoexpressionAnalysis>
- Parameters:
ee
- the expriment to remove all analyses for
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