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

Class CoexpressionAnalysisDaoImpl

java.lang.Object

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

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

All Implemented Interfaces:

AnalysisDao<CoexpressionAnalysis>, CoexpressionAnalysisDao, SingleExperimentAnalysisDao<CoexpressionAnalysis>, BaseDao<CoexpressionAnalysis>

@Repository
public class CoexpressionAnalysisDaoImpl
extends AbstractDao<CoexpressionAnalysis>
implements CoexpressionAnalysisDao, SingleExperimentAnalysisDao<CoexpressionAnalysis>

Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis.

See Also:

CoexpressionAnalysis

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
CoexpressionAnalysisDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
boolean	existsByExperiment(BioAssaySet ee, boolean includeSubSets)	Indicate if there is an analysis (or at least one) for the given experiment.
Collection<CoexpressionAnalysis>	findByExperiment(BioAssaySet experiment, boolean includeSubSets)	Find by associated experiment via SingleExperimentAnalysis.getExperimentAnalyzed().
Map<BioAssaySet,Collection<CoexpressionAnalysis>>	findByExperiments(Collection<? extends BioAssaySet> experiments, boolean includeSubSets)	Given a collection of experiments returns a Map of Analysis --> collection of Experiments 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
Collection<CoexpressionAnalysis>	findByTaxon(Taxon taxon)
CoexpCorrelationDistribution	getCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment)
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> idsToFilter)
boolean	hasCoexpCorrelationDistribution(ExpressionExperiment ee)

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

countAll, create, create, find, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, streamQuery, 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.BaseDao

countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, update, update

Constructor Detail

CoexpressionAnalysisDaoImpl

@Autowired
public CoexpressionAnalysisDaoImpl(SessionFactory sessionFactory)

Method Detail

findByExperiment

public Collection<CoexpressionAnalysis> findByExperiment(BioAssaySet experiment,
                                                         boolean includeSubSets)

Description copied from interface: SingleExperimentAnalysisDao

Find by associated experiment via SingleExperimentAnalysis.getExperimentAnalyzed().

Specified by:

findByExperiment in interface SingleExperimentAnalysisDao<CoexpressionAnalysis>

includeSubSets - include subsets of the specified experiments

findByExperiments

public Map<BioAssaySet,Collection<CoexpressionAnalysis>> findByExperiments(Collection<? extends BioAssaySet> experiments,
                                                                                 boolean includeSubSets)

Description copied from interface: SingleExperimentAnalysisDao

Given a collection of experiments returns a Map of Analysis --> collection of Experiments 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

Specified by:

findByExperiments in interface SingleExperimentAnalysisDao<CoexpressionAnalysis>

Parameters:

experiments - experiments

includeSubSets - include subsets of the specified experiments

Returns:

map to analyses

findByTaxon

public Collection<CoexpressionAnalysis> findByTaxon(Taxon taxon)

Specified by:

findByTaxon in interface CoexpressionAnalysisDao

existsByExperiment

public boolean existsByExperiment(BioAssaySet ee,
                                  boolean includeSubSets)

Description copied from interface: SingleExperimentAnalysisDao

Indicate if there is an analysis (or at least one) for the given experiment.

Specified by:

existsByExperiment in interface SingleExperimentAnalysisDao<CoexpressionAnalysis>

includeSubSets - include subsets of the specified experiments

getCoexpCorrelationDistribution

public CoexpCorrelationDistribution getCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment)

Specified by:

getCoexpCorrelationDistribution in interface CoexpressionAnalysisDao

getExperimentsWithAnalysis

public Collection<Long> getExperimentsWithAnalysis(Collection<Long> idsToFilter)

Specified by:

getExperimentsWithAnalysis in interface CoexpressionAnalysisDao

hasCoexpCorrelationDistribution

public boolean hasCoexpCorrelationDistribution(ExpressionExperiment ee)

Specified by:

hasCoexpCorrelationDistribution in interface CoexpressionAnalysisDao