Interface SingleExperimentAnalysisService<T extends SingleExperimentAnalysis>

All Superinterfaces:
AnalysisService<T>, BaseImmutableService<T>, BaseReadOnlyService<T>, SecurableBaseImmutableService<T>, SecurableBaseReadOnlyService<T>
All Known Subinterfaces:
CoexpressionAnalysisService, DifferentialExpressionAnalysisService
All Known Implementing Classes:
CoexpressionAnalysisServiceImpl, DifferentialExpressionAnalysisServiceImpl
public interface SingleExperimentAnalysisService<T extends SingleExperimentAnalysis> extends AnalysisService<T>, SecurableBaseImmutableService<T>
Interface for analysis service manipulating single experiments.
Author:
poirigui

  • Method Details

    • findByExperiment

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<T> findByExperiment(BioAssaySet experimentAnalyzed, boolean includeSubSets)
      Parameters:
      experimentAnalyzed - experiment analyzed
      includeSubSets - if the experiment is a ExpressionExperiment, include analyses for its ExpressionExperimentSubSet
      Returns:
      find all the analyses that involved the given investigation

    • findByExperiments

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ","AFTER_ACL_MAP_READ"}) Map<BioAssaySet, Collection<T>> findByExperiments(Collection<BioAssaySet> investigations, boolean includeSubSets)
      Parameters:
      investigations - investigations
      includeSubSets - if the experiment is a ExpressionExperiment, include analyses for its ExpressionExperimentSubSet
      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

    • getExperimentsWithAnalysis

      Collection<Long> getExperimentsWithAnalysis(Collection<Long> experimentAnalyzedIds, boolean includeSubSets)
      Not secured: for internal use only
      Parameters:
      experimentAnalyzedIds - starting list of experiment or subset IDs
      includeSubSets - retain IDs of experiments that have subset analyses
      Returns:
      the ones which have an 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

    • removeForExperiment

      @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) void removeForExperiment(BioAssaySet ee, boolean includeSubSets)
      Removes all analyses for the given experiment
      Parameters:
      ee - the expriment to remove all analyses for
      includeSubSets - if the experiment is a ExpressionExperiment, also delete analyses of its ExpressionExperimentSubSet.