Interface ExpressionExperimentSetDao

All Superinterfaces:
BaseDao<ExpressionExperimentSet>, BaseVoEnabledDao<ExpressionExperimentSet, ExpressionExperimentSetValueObject>
All Known Implementing Classes:
ExpressionExperimentSetDaoImpl
public interface ExpressionExperimentSetDao extends BaseVoEnabledDao<ExpressionExperimentSet, ExpressionExperimentSetValueObject>
See Also:

  • Method Details

    • find

      Collection<ExpressionExperimentSet> find(ExpressionExperiment ee)
      Parameters:
      ee - bio assay set
      Returns:
      expressionExperimentSets that contain the given ee.

    • findByName

      Collection<ExpressionExperimentSet> findByName(String name)

    • findByAccession

      Collection<ExpressionExperimentSet> findByAccession(String accession)

    • findByAccession

      Collection<ExpressionExperimentSet> findByAccession(String accession, ExternalDatabase externalDatabase)

    • getExperimentsInSet

      Collection<ExpressionExperiment> getExperimentsInSet(Long id)
      Parameters:
      id - id
      Returns:
      the security-filtered list of experiments in a set. It is possible for the return to be empty even if the set is not (due to security filters). Use this instead of expressionExperimentSet.getExperiments.

    • loadAllExperimentSetsWithTaxon

      Collection<ExpressionExperimentSet> loadAllExperimentSetsWithTaxon()
      Returns:
      ExpressionExperimentSets that have more than 1 experiment in them & have a taxon value.

    • thaw

      void thaw(ExpressionExperimentSet expressionExperimentSet)

    • loadAllValueObjects

      Collection<ExpressionExperimentSetValueObject> loadAllValueObjects(boolean loadEEIds)
      Parameters:
      loadEEIds - whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.
      Returns:
      ee vos

    • loadValueObjects

      List<ExpressionExperimentSetValueObject> loadValueObjects(Collection<Long> eeSetIds, boolean loadEEIds)
      Parameters:
      eeSetIds - ids
      loadEEIds - whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.
      Returns:
      ee vos

    • getExperimentValueObjectsInSet

      Collection<ExpressionExperimentDetailsValueObject> getExperimentValueObjectsInSet(Long id)

    • loadValueObject

      @Nullable ExpressionExperimentSetValueObject loadValueObject(Long id, boolean loadEEIds)
      Parameters:
      id - id
      loadEEIds - whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.
      Returns:
      ee vos