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

Class NcbiGeneDomainObjectGenerator

java.lang.Object
ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator
public class NcbiGeneDomainObjectGenerator extends Object
Combines information from the gene2accession and gene_info files from NCBI Gene.
Author:
pavlidis

  • Constructor Details

    • NcbiGeneDomainObjectGenerator

      public NcbiGeneDomainObjectGenerator(Collection<Taxon> taxa)

  • Method Details

    • isDoDownload

      public boolean isDoDownload()

    • setDoDownload

      public void setDoDownload(boolean doDownload)

    • generate

      public void generate(BlockingQueue<NcbiGeneData> queue)

    • generateLocal

      public void generateLocal(String geneInfoFilePath, String gene2AccesionFilePath, String geneHistoryFilePath, String geneEnsemblFilePath, BlockingQueue<NcbiGeneData> queue)

    • isProducerDone

      public boolean isProducerDone()

    • setProducerDoneFlag

      public void setProducerDoneFlag(AtomicBoolean flag)

    • getSupportedTaxaWithNCBIGenes

      public Collection<Taxon> getSupportedTaxaWithNCBIGenes()
      Those taxa that are supported by GEMMA and have genes in NCBI.
      Returns:
      Collection of taxa that are supported by the GEMMA and have genes held by NCBI.

    • setStartingNcbiId

      public void setStartingNcbiId(Integer startingNcbiId)