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

Interface CoexpressionAnalysisService

All Superinterfaces:
AnalysisService<CoexpressionAnalysis>, BaseImmutableService<CoexpressionAnalysis>, BaseReadOnlyService<CoexpressionAnalysis>, BaseService<CoexpressionAnalysis>, SecurableBaseImmutableService<CoexpressionAnalysis>, SecurableBaseReadOnlyService<CoexpressionAnalysis>, SecurableBaseService<CoexpressionAnalysis>
All Known Implementing Classes:
CoexpressionAnalysisServiceImpl
public interface CoexpressionAnalysisService extends AnalysisService<CoexpressionAnalysis>, SecurableBaseService<CoexpressionAnalysis>
Deals with the Analysis objects for Coexpression - not the coexpression results themselves.
Author:
kelsey

  • Method Details

    • findByExperimentAnalyzed

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<CoexpressionAnalysis> findByExperimentAnalyzed(ExpressionExperiment experimentAnalyzed)
      Parameters:
      experimentAnalyzed - experiment analyzed
      Returns:
      find all the analyses that involved the given investigation

    • findByExperimentsAnalyzed

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ","AFTER_ACL_MAP_READ"}) Map<ExpressionExperiment,Collection<CoexpressionAnalysis>> findByExperimentsAnalyzed(Collection<ExpressionExperiment> experimentsAnalyzed)
      Parameters:
      experimentsAnalyzed - 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

    • removeForExperimentAnalyzed

      @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) void removeForExperimentAnalyzed(ExpressionExperiment ee)

    • getCoexpCorrelationDistribution

      @Nullable @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) CoexpCorrelationDistribution getCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment)

    • addCoexpCorrelationDistribution

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_EDIT"}) void addCoexpCorrelationDistribution(ExpressionExperiment expressionExperiment, CoexpCorrelationDistribution coexpd)
      For backfilling of the coexpression distributions from flat files - remove when no longer needed.
      Parameters:
      expressionExperiment - ee
      coexpd - coexpd

    • findByTaxon

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<CoexpressionAnalysis> findByTaxon(Taxon taxon)

    • getExperimentsWithAnalysis

      Collection<Long> getExperimentsWithAnalysis(Collection<Long> eeIds)
      Not secured: for internal use only
      Parameters:
      eeIds - expression experiment IDs
      Returns:
      the ones which have a coexpression analysis.

    • getExperimentsWithAnalysis

      Collection<Long> getExperimentsWithAnalysis(Taxon taxon)
      Not secured: for internal use only
      Parameters:
      taxon - taxon
      Returns:
      ids of bioassaysets from the given taxon that have a coexpression analysis