Interface GeneSetSearch

All Known Implementing Classes:
GeneSetSearchImpl
public interface GeneSetSearch
Author:
paul

  • Method Details

    • findByGene

      Collection<GeneSet> findByGene(Gene gene)
      Parameters:
      gene - gene
      Returns:
      gene sets
      See Also:

    • findGeneSetValueObjectByGoId

      @Nullable GOGroupValueObject findGeneSetValueObjectByGoId(String goId, @Nullable Long taxonId)
      Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.
      Parameters:
      goId - go id
      taxonId - taxon id
      Returns:
      a GeneSet or null if nothing is found

    • findByGoId

      @Nullable GeneSet findByGoId(String goId, @Nullable Taxon taxon)
      Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.
      Parameters:
      goId - go id
      taxon - taxon
      Returns:
      a GeneSet or null if nothing is found

    • findByGoTermName

      Collection<GeneSet> findByGoTermName(String goTermName, Taxon taxon) throws SearchException
      finds gene sets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent
      Parameters:
      goTermName - go term name
      taxon - taxon
      Returns:
      a collection with the hits
      Throws:
      SearchException

    • findByGoTermName

      Collection<GeneSet> findByGoTermName(String goTermName, @Nullable Taxon taxon, @Nullable Integer maxGoTermsProcessed, @Nullable Integer maxGeneSetSize) throws SearchException
      finds genesets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent
      Parameters:
      goTermName - go term name
      taxon - taxon
      maxGoTermsProcessed - max go terms
      maxGeneSetSize - max gene set size
      Returns:
      a collection with the hits
      Throws:
      SearchException

    • findByName

      Collection<GeneSet> findByName(String name)
      Parameters:
      name - name
      Returns:
      gene sets
      See Also:

    • findByName

      Collection<GeneSet> findByName(String name, Taxon taxon)
      Parameters:
      name - name
      taxon - taxon
      Returns:
      gene sets

    • findGeneSetsByName

      Collection<GeneSet> findGeneSetsByName(String query, Long taxonId) throws SearchException
      Similar to method of same name in GeneSetController.java but here: - no taxon needed - GO groups always searched - GeneSet objects returned instead of GeneSetValueObjects
      Parameters:
      query - string to match to a gene set.
      taxonId - taxon id
      Returns:
      collection of GeneSet
      Throws:
      SearchException