Package ubic.gemma.core.loader.genome.gene.ncbi.homology

Interface HomologeneService

All Known Implementing Classes:
HomologeneServiceImpl
public interface HomologeneService
Author:
paul

  • Method Details

    • getHomologue

      Gene getHomologue(Gene gene, Taxon taxon)
      Parameters:
      gene - gene
      taxon - desired taxon to find homologue in
      Returns:
      Finds the homologue of the given gene for the taxon specified, or null if there is no homologue

    • getHomologues

      Collection<Gene> getHomologues(Gene gene)
      Parameters:
      gene - gene
      Returns:
      Collection of genes found in Gemma that are homologous with the given gene. Empty if no homologues or gene lacks homologue information, or null if not ready.

    • getHomologues

      Collection<Long> getHomologues(Long ncbiId)
      Parameters:
      ncbiId - gene ncbi id
      Returns:
      A collection of NCBI gene ids that are homologous with the given NCBI Gene Id

    • getHomologueValueObject

      GeneValueObject getHomologueValueObject(Long geneId, String taxonCommonName)
      Parameters:
      geneId - gene id
      taxonCommonName - desired taxon to find homologue in
      Returns:
      Finds the homologue of the given gene for the taxon specified, or null if there is no homologue

    • getNCBIGeneIdsInGroup

      Collection<Long> getNCBIGeneIdsInGroup(long homologeneGroupId)

    • refresh

      void refresh() throws IOException
      Refresh homologene data.
      Throws:
      IOException