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

Class 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 Detail

      • NCBIGene2Accession

        public NCBIGene2Accession()

    • Method Detail

      • 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.