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

Class NCBIGene2Accession

java.lang.Object
ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
public class NCBIGene2Accession extends Object

See ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/README 

 gene2accession
 ---------------------------------------------------------------------------
 This file is a comprehensive report of the accessions that are
 related to a GeneID.  It includes sequences from the international
 sequence collaboration, Swiss-Prot, and RefSeq.
 This file can be considered as the logical equivalent of
 ftp://ftp.ncbi.nih.gov/refseq/LocusLink/loc2ref
 AND
 ftp://ftp.ncbi.nih.gov/refseq/LocusLink/loc2acc
 tab-delimited
 one line per genomic/RNA/protein set of sequence accessions
 ---------------------------------------------------------------------------
 tax_id:
 the unique identifier provided by NCBI Taxonomy
 for the species or strain/isolate
 GeneID:
 the unique identifier for a gene
 --note:  for genomes previously available from LocusLink,
 the identifiers are equivalent
 status:
 status of the RefSeq if a refseq, else '-'
 RNA nucleotide accession.version
 may be null (-) for some genomes
 RNA nucleotide gi
 the gi for an RNA nucleotide accession, '-' if not applicable
 protein accession.version
 will be null (-) for RNA-coding genes
 protein gi:
 the gi for a protein accession, '-' if not applicable
 genomic nucleotide accession.version
 may be null (-)
 genomic nucleotide gi
 the gi for a genomic nucleotide accession, '-' if not applicable
 start position on the genomic accession
 position of the gene feature on the genomic accession,
 '-' if not applicable
 position 0-based
 end position on the genomic accession
 position of the gene feature on the genomic accession,
 '-' if not applicable
 position 0-based
 orientation
 orientation of the gene feature on the genomic accession,
 '?' if not applicable
Author:
pavlidis

  • Constructor Details

    • NCBIGene2Accession

      public NCBIGene2Accession()

  • Method Details

    • getGenomicNucleotideAccession

      public String getGenomicNucleotideAccession()
      Returns:
      the genomicNucleotideAccession

    • setGenomicNucleotideAccession

      public void setGenomicNucleotideAccession(String genomicNucleotideAccession)
      Parameters:
      genomicNucleotideAccession - the genomicNucleotideAccession to set

    • getGenomicNucleotideAccessionVersion

      public String getGenomicNucleotideAccessionVersion()
      Returns:
      the genomicNucleotideAccessionVersion

    • setGenomicNucleotideAccessionVersion

      public void setGenomicNucleotideAccessionVersion(String genomicNucleotideAccessionVersion)
      Parameters:
      genomicNucleotideAccessionVersion - the genomicNucleotideAccessionVersion to set

    • getProteinAccessionVersion

      public String getProteinAccessionVersion()
      Returns:
      the proteinAccessionVersion

    • setProteinAccessionVersion

      public void setProteinAccessionVersion(String proteinAccessionVersion)
      Parameters:
      proteinAccessionVersion - the proteinAccessionVersion to set

    • getRnaNucleotideAccession

      public String getRnaNucleotideAccession()
      Returns:
      the rnaNucleotideAccession

    • setRnaNucleotideAccession

      public void setRnaNucleotideAccession(String rnaNucleotideAccession)
      Parameters:
      rnaNucleotideAccession - the rnaNucleotideAccession to set

    • getRnaNucleotideAccessionVersion

      public String getRnaNucleotideAccessionVersion()
      Returns:
      the rnaNucleotideAccessionVersion

    • setRnaNucleotideAccessionVersion

      public void setRnaNucleotideAccessionVersion(String rnaNucleotideAccessionVersion)
      Parameters:
      rnaNucleotideAccessionVersion - the rnaNucleotideAccessionVersion to set

    • getRnaNucleotideGI

      public String getRnaNucleotideGI()
      Returns:
      the rnaNucleotideGI

    • setRnaNucleotideGI

      public void setRnaNucleotideGI(String rnaNucleotideGI)
      Parameters:
      rnaNucleotideGI - the rnaNucleotideGI to set

    • getInfo

      public NCBIGeneInfo getInfo()
      Returns:
      Returns the info.

    • setInfo

      public void setInfo(NCBIGeneInfo info)
      Parameters:
      info - The info to set.

    • getEndPosition

      public Long getEndPosition()
      Returns:
      Returns the endPosition.

    • setEndPosition

      public void setEndPosition(Long endPosition)
      Parameters:
      endPosition - The endPosition to set.

    • getGeneId

      public String getGeneId()
      Returns:
      Returns the geneId.

    • setGeneId

      public void setGeneId(String geneId)
      Parameters:
      geneId - The geneId to set.

    • getGenomicNucleotideGI

      public String getGenomicNucleotideGI()
      Returns:
      Returns the genomicNucleotideGI.

    • setGenomicNucleotideGI

      public void setGenomicNucleotideGI(String genomicNucleotideGI)
      Parameters:
      genomicNucleotideGI - The genomicNucleotideGI to set.

    • getOrientation

      public String getOrientation()
      Returns:
      Returns the orientation.

    • setOrientation

      public void setOrientation(String orientation)
      Parameters:
      orientation - The orientation to set.

    • getProteinAccession

      public String getProteinAccession()
      Returns:
      Returns the proteinAccessionVersion.

    • setProteinAccession

      public void setProteinAccession(String proteinAccession)
      Parameters:
      proteinAccession - The proteinAccessionVersion to set.

    • getProteinGI

      public String getProteinGI()
      Returns:
      Returns the proteinGI.

    • setProteinGI

      public void setProteinGI(String proteinGI)
      Parameters:
      proteinGI - The proteinGI to set.

    • getStartPosition

      public Long getStartPosition()
      Returns:
      Returns the startPosition.

    • setStartPosition

      public void setStartPosition(Long startPosition)
      Parameters:
      startPosition - The startPosition to set.

    • getStatus

      public String getStatus()
      Returns:
      Returns the status.

    • setStatus

      public void setStatus(String status)
      Parameters:
      status - The status to set.

    • getTaxId

      public int getTaxId()
      Returns:
      Returns the taxId.

    • setTaxId

      public void setTaxId(int taxId)
      Parameters:
      taxId - The taxId to set.