Interface DifferentialExpressionAnalysisService

All Superinterfaces:
AnalysisService<DifferentialExpressionAnalysis>, BaseImmutableService<DifferentialExpressionAnalysis>, BaseReadOnlyService<DifferentialExpressionAnalysis>, BaseService<DifferentialExpressionAnalysis>, SecurableBaseImmutableService<DifferentialExpressionAnalysis>, SecurableBaseReadOnlyService<DifferentialExpressionAnalysis>, SecurableBaseService<DifferentialExpressionAnalysis>
All Known Implementing Classes:
DifferentialExpressionAnalysisServiceImpl
public interface DifferentialExpressionAnalysisService extends AnalysisService<DifferentialExpressionAnalysis>, SecurableBaseService<DifferentialExpressionAnalysis>
Service interface for DifferentialExpressionAnalysis.

The methods here have two flavours: by experiments, which is always an ExpressionExperiment and by experiment analyzed which is either a ExpressionExperiment or ExpressionExperimentSubSet.

Author:
kelsey
See Also:

  • Method Details

    • loadWithExperimentAnalyzed

      @Nullable DifferentialExpressionAnalysis loadWithExperimentAnalyzed(Long id)

    • findByName

      @Secured("IS_AUTHENTICATED_ANONYMOUSLY") @PostFilter("hasPermission(filterObject, 'READ') or hasPermission(filterObject, 'ADMINISTRATION')") Collection<DifferentialExpressionAnalysis> findByName(String name)

    • findByFactor

      @Secured("IS_AUTHENTICATED_ANONYMOUSLY") Collection<DifferentialExpressionAnalysis> findByFactor(ExperimentalFactor ef)

    • findExperimentsWithAnalyses

      @Secured("IS_AUTHENTICATED_ANONYMOUSLY") @PostFilter("hasPermission(filterObject, 'READ') or hasPermission(filterObject, 'ADMINISTRATION')") Collection<BioAssaySet> findExperimentsWithAnalyses(Gene gene)

    • findByExperimentAndAnalysisId

      @Nullable @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) @PostAuthorize("returnObject == null or hasPermission(returnObject, 'READ') or hasPermission(returnObject, 'ADMINISTRATION')") DifferentialExpressionAnalysis findByExperimentAndAnalysisId(ExpressionExperiment expressionExperiment, boolean includeSubSets, Long analysisId)

    • thaw

      @CheckReturnValue @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"}) Collection<DifferentialExpressionAnalysis> thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)

    • thaw

      @CheckReturnValue @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) DifferentialExpressionAnalysis thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)

    • thawFully

      @CheckReturnValue @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) DifferentialExpressionAnalysis thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)

    • canDelete

      @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) boolean canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
      Parameters:
      differentialExpressionAnalysis - analysis
      Returns:
      Is the analysis deleteable, or is it tied up with another entity that keeps it from being removed.

    • findByExperimentIds

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"}) Map<ExpressionExperimentDetailsValueObject, Collection<DifferentialExpressionAnalysisValueObject>> findByExperimentIds(Collection<Long> experimentIds, boolean includeSubSets, boolean includeAssays)
      Given a set of ids, find experiments or subsets that have differential expression analyses.

      Subsets are handled two ways: if the ID given is of a subset, or if the ID is of an experiment that has subsets. In the latter case, the return value will contain experiments that were not explicitly queried for.

      Parameters:
      experimentIds - of ExpressionExperiment
      includeSubSets - include analysis of subsets of the requested experiments
      includeAssays - include assay information in the value objects
      Returns:
      map of detailed EE VOs to analyses VOs for each, subset analyses are mapped to their source experiment

    • removeForExperimentalFactor

      int removeForExperimentalFactor(ExperimentalFactor experimentalFactor)
      Remove analyses using the given factor.
      Returns:
      the number of analysis removed

    • removeForExperimentalFactors

      int removeForExperimentalFactors(Collection<ExperimentalFactor> experimentalFactors)

    • findByExperiment

      @Secured("IS_AUTHENTICATED_ANONYMOUSLY") @PostFilter("hasPermission(filterObject, 'READ') or hasPermission(filterObject, 'ADMINISTRATION')") Collection<DifferentialExpressionAnalysis> findByExperiment(ExpressionExperiment experimentAnalyzed, boolean includeSubSets)
      Parameters:
      experimentAnalyzed - experiment analyzed
      includeSubSets - include analyses for its ExpressionExperimentSubSet
      Returns:
      find all the analyses that involved the given investigation

    • findByExperiments

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"}) @PostFilter("hasPermission(filterObject.key, 'READ') or hasPermission(filterObject.key, 'ADMINISTRATION')") Map<ExpressionExperiment, Collection<DifferentialExpressionAnalysis>> findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)
      Parameters:
      experiments - investigations
      includeSubSets - include analyses for their ExpressionExperimentSubSet
      Returns:
      analyses grouped by experiment, subset analyses are mapped to their source experiment

    • getExperimentsWithAnalysis

      Collection<Long> getExperimentsWithAnalysis(Collection<Long> experimentIds, boolean includeSubSets)
      Obtain IDs of experiments that have analyses.

      Not secured: for internal use only

      Parameters:
      experimentIds - starting list of ExpressionExperiment IDs
      includeSubSets - include IDs of their subsets that have analyses
      Returns:
      the ones which have an analysis

    • removeForExperiment

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

    • removeForExperimentAnalyzed

      @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) void removeForExperimentAnalyzed(BioAssaySet experimentAnalyzed)
      Remove all analysis for the given experiment or subset.