Package ubic.gemma.persistence.service.genome

Interface GeneDao

All Superinterfaces:
BaseDao<Gene>, BaseVoEnabledDao<Gene,GeneValueObject>, FilteringDao<Gene>, FilteringVoEnabledDao<Gene,GeneValueObject>
All Known Implementing Classes:
GeneDaoImpl
public interface GeneDao extends FilteringVoEnabledDao<Gene,GeneValueObject>
See Also:

  • Field Details

  • Method Details

    • find

      Collection<Gene> find(PhysicalLocation physicalLocation)
      Find all genes at a physical location. All overlapping genes are returned. The location can be a point or a region. If strand is non-null, only genes on the same strand are returned.
      Parameters:
      physicalLocation - physical location
      Returns:
      found genes

    • findByAccession

      @Nullable Gene findByAccession(String accession, @Nullable ExternalDatabase source)

    • findByAlias

      Collection<Gene> findByAlias(String search)
      Locate genes that match the given alias string
      Parameters:
      search - search string
      Returns:
      found genes

    • findByEnsemblId

      @Nullable Gene findByEnsemblId(String exactString)

    • findByNcbiId

      @Nullable Gene findByNcbiId(Integer accession)

    • findByOfficialSymbol

      Collection<Gene> findByOfficialSymbol(String officialSymbol)

    • findByOfficialName

      Collection<Gene> findByOfficialName(String officialName)

    • findByOfficialNameInexact

      Collection<Gene> findByOfficialNameInexact(String officialName)

    • findByOfficialSymbol

      @Nullable Gene findByOfficialSymbol(String symbol, Taxon taxon)

    • findByOfficialSymbolInexact

      Collection<Gene> findByOfficialSymbolInexact(String officialSymbol)

    • findByOfficialSymbols

      Map<String,Gene> findByOfficialSymbols(Collection<String> query, Long taxonId)
      Quickly load exact matches.
      Parameters:
      query - query
      taxonId - taxon id
      Returns:
      map of gene symbol (toLowerCase()) to the gene. The actual query that led to the gene is not retained.

    • findByNcbiIds

      Map<Integer,Gene> findByNcbiIds(Collection<Integer> ncbiIds)
      Quickly load exact matches.
      Parameters:
      ncbiIds - ncbi ids
      Returns:
      map of NCBI Id to the gene.

    • findByPhysicalLocation

      @Deprecated Collection<Gene> findByPhysicalLocation(PhysicalLocation location)
      Deprecated.

    • getCompositeSequenceCount

      long getCompositeSequenceCount(Gene gene, boolean includeDummyProducts)
      Obtain the number of platform elements (e.g. probes) associated to this gene, totalled up over all platforms.

      Note that ACLs are applied to the platforms.

      Parameters:
      includeDummyProducts - if true, include platform elements related via dummy GeneProducts

    • getCompositeSequenceCountById

      long getCompositeSequenceCountById(long id, boolean includeDummyProducts)
      See Also:

    • getCompositeSequences

      Collection<CompositeSequence> getCompositeSequences(Gene gene, ArrayDesign arrayDesign, boolean includeDummyProducts)
      Get the composite sequences (e.g. probes) associated with this gene via a particular platform.
      Parameters:
      arrayDesign - platform to restrict composite sequences to
      includeDummyProducts - if true, include platform elements related via dummy GeneProducts

    • getCompositeSequences

      Collection<CompositeSequence> getCompositeSequences(Gene gene, boolean includeDummyProducts)
      Get the composite sequences (e.g. probes) associated with this gene, for any platform.
      Parameters:
      includeDummyProducts - if true, include platform elements related via dummy GeneProducts

    • getCompositeSequencesById

      Collection<CompositeSequence> getCompositeSequencesById(long id, boolean includeDummyProducts)
      See Also:

    • getMicroRnaByTaxon

      Collection<Gene> getMicroRnaByTaxon(Taxon taxon)
      Parameters:
      taxon - taxon
      Returns:
      a collection of genes that are actually MicroRNA for a given taxon

    • getPlatformCountById

      long getPlatformCountById(Long id, boolean includeDummyProducts)
      Parameters:
      id - id
      includeDummyProducts - include platforms related via dummy GeneProducts in the count
      Returns:
      how many platforms have a representation of this gene

    • loadKnownGenes

      Collection<Gene> loadKnownGenes(Taxon taxon)
      Parameters:
      taxon - taxon
      Returns:
      a collection of genes for the specified taxon (not all genes, ie not probe aligned regions and predicted genes)

    • loadThawed

      List<Gene> loadThawed(Collection<Long> ids)

    • loadThawedLiter

      Collection<Gene> loadThawedLiter(Collection<Long> ids)

    • thaw

      Gene thaw(Gene gene)

    • thawAliases

      Gene thawAliases(Gene gene)

    • thawLite

      Collection<Gene> thawLite(Collection<Gene> genes)

    • thawLite

      Gene thawLite(Gene gene)

    • thawLiter

      Gene thawLiter(Gene gene)

    • removeAll

      int removeAll()