Package ubic.gemma.persistence.service.genome.gene

Interface GeneSetValueObjectHelper

All Known Implementing Classes:
GeneSetValueObjectHelperImpl
public interface GeneSetValueObjectHelper
* @author tvrossum

  • Method Details

    • convertToGOValueObject

      GOGroupValueObject convertToGOValueObject(GeneSet gs, String goId, String searchTerm)
      Method to create a GO group object from an ad hoc entity
      Parameters:
      gs - gene set
      goId - gene ontology id
      searchTerm - search term
      Returns:
      Go group VO

    • convertToLightValueObject

      DatabaseBackedGeneSetValueObject convertToLightValueObject(GeneSet gs)
      Constructor to build value object from GeneSet. This is a light version and *does not include member ids*! (But the size is set.) No security filtering is done here, assuming that if the user could load the experimentSet entity, they have access to it.
      Parameters:
      gs - the expressionExperimentSet entity to create a value object for
      Returns:
      a gene set value object with all fields filled except for gene members

    • convertToLightValueObjects

      List<DatabaseBackedGeneSetValueObject> convertToLightValueObjects(Collection<GeneSet> genesets, boolean includeOnesWithoutGenes)
      results will be sorted by size
      Parameters:
      genesets - gene sets
      includeOnesWithoutGenes - if true, even gene sets that lack genes will be returned.
      Returns:
      list of gene set value objects

    • convertToValueObject

      DatabaseBackedGeneSetValueObject convertToValueObject(GeneSet gs)
      Constructor to build value object from GeneSet. No security filtering is done here, assuming that if the user could load the experimentSet entity, they have access to it.
      Parameters:
      gs - an expressionExperimentSet entity to create a value object for
      Returns:
      a new DatabaseBackedGeneSetValueObject

    • convertToValueObjects

      List<DatabaseBackedGeneSetValueObject> convertToValueObjects(Collection<GeneSet> sets)
      Parameters:
      sets - gene sets
      Returns:
      results will be sorted by size gene sets that lack genes will be excluded

    • convertToValueObjects

      List<DatabaseBackedGeneSetValueObject> convertToValueObjects(Collection<GeneSet> geneSets, boolean includeOnesWithoutGenes)
      Parameters:
      geneSets - gene sets
      includeOnesWithoutGenes - if true, even gene sets that lack genes will be returned.
      Returns:
      results will be sorted by size