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

Class NCBIGeneInfo

  • public class NCBIGeneInfo
extends Object

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

       ===========================================================================
   gene_info
   ---------------------------------------------------------------------------
   This file can be considered as the logical equivalent of
   ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL.out
   tab-delimited
   one line per GeneID
   ---------------------------------------------------------------------------
   tax_id:
   the unique identifier provided by NCBI Taxonomy
   for the species or strain/isolate
   GeneID:
   the unique identifier for a gene
   ASN1:  geneid
   --note:  for genomes previously available from LocusLink,
   the identifiers are equivalent
   Symbol:
   the default symbol for the gene
   ASN1:  gene->locus
   LocusTag:
   the LocusTag value
   ASN1:  gene->locus-tag
   Synonyms:
   bar-delimited set of unoffical symbols for the gene
   dbXrefs:
   bar-delimited set of identifiers in other databases
   for this gene.  The unit of the set is database:value.
   chromosome:
   the chromosome on which this gene is placed
   map location:
   the map location for this gene
   description
   a descriptive name for this gene
   type of gene:
   the type assigned to the gene according to the list of options
   provided in http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
   Symbol from nomenclature authority:
   when not '-', indicates that this symbol is from a
   a nomenclature authority
   Full name from nomenclature authority:
   when not '-', indicates that this full name is from a
   a nomenclature authority
   Nomenclature status
   when not '-', indicates the status of the name from the
   nomenclature authority (O for official, I for interim)
    Author:
    pavlidis

    • Constructor Detail

      • NCBIGeneInfo

        public NCBIGeneInfo()

    • Method Detail

      • typeStringToGeneType

        public static NCBIGeneInfo.GeneType typeStringToGeneType​(String typeString)
        Convert string to GeneType. See http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
        Parameters:
        typeString - type string
        Returns:
        gene type

      • addToDbXRefs

        public void addToDbXRefs​(String dbName,
                         String identifier)

      • addToSynonyms

        public void addToSynonyms​(String synonym)

      • getChromosome

        public String getChromosome()
        Returns:
        Returns the chromosome.

      • setChromosome

        public void setChromosome​(String chromosome)
        Parameters:
        chromosome - The chromosome to set.

      • getDbXrefs

        public Map<String,​String> getDbXrefs()
        Returns:
        Returns the dbXrefs.

      • getDefaultSymbol

        public String getDefaultSymbol()
        Returns:
        Returns the defaultSymbol.

      • setDefaultSymbol

        public void setDefaultSymbol​(String defaultSymbol)
        Parameters:
        defaultSymbol - The defaultSymbol to set.

      • getDescription

        public String getDescription()
        Returns:
        Returns the description.

      • setDescription

        public void setDescription​(String description)
        Parameters:
        description - The description to set.

      • getDiscontinuedId

        public String getDiscontinuedId()
        Returns:
        The NCBI gene ID that was 'discontinued' for the gene that matches this symbol and taxon. These correspond to the lines in gene_history that have a '-' in the second column. But because we are matching only on the symbol+taxon, we have to be a bit careful using it.

      • setDiscontinuedId

        public void setDiscontinuedId​(String discontinuedIdForGene)

      • getEnsemblId

        public String getEnsemblId()

      • setEnsemblId

        public void setEnsemblId​(String ensemblId)

      • getGeneId

        public String getGeneId()
        Returns:
        Returns the geneId.

      • setGeneId

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

      • setGeneType

        public void setGeneType​(NCBIGeneInfo.GeneType geneType)
        Parameters:
        geneType - The geneType to set.

      • setHistory

        public void setHistory​(NcbiGeneHistory history)
        Parameters:
        history - the history to set

      • getLocusTag

        public String getLocusTag()
        Returns:
        Returns the locusTag.

      • setLocusTag

        public void setLocusTag​(String locusTag)
        Parameters:
        locusTag - The locusTag to set.

      • getMapLocation

        public String getMapLocation()
        Returns:
        Returns the mapLocation.

      • setMapLocation

        public void setMapLocation​(String mapLocation)
        Parameters:
        mapLocation - The mapLocation to set.

      • setNomenclatureStatus

        public void setNomenclatureStatus​(NCBIGeneInfo.NomenclatureStatus nomenclatureStatus)
        Parameters:
        nomenclatureStatus - The nomenclatureStatus to set.

      • getSynonyms

        public Collection<String> getSynonyms()
        Returns:
        Returns the synonyms.

      • getTaxId

        public int getTaxId()
        Returns:
        Returns the taxId.

      • setTaxId

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

      • isNameIsFromAuthority

        public boolean isNameIsFromAuthority()
        Returns:
        Returns the nameIsFromAuthority.

      • setNameIsFromAuthority

        public void setNameIsFromAuthority​(boolean nameIsFromAuthority)
        Parameters:
        nameIsFromAuthority - The nameIsFromAuthority to set.

      • isSymbolIsFromAuthority

        public boolean isSymbolIsFromAuthority()
        Returns:
        Returns the symbolIsFromAuthority.

      • setSymbolIsFromAuthority

        public void setSymbolIsFromAuthority​(boolean symbolIsFromAuthority)
        Parameters:
        symbolIsFromAuthority - The symbolIsFromAuthority to set.