Class EbiFormat

  • All Implemented Interfaces:
    TaxonParser

    public class EbiFormat
    extends java.lang.Object
    implements TaxonParser
    Deprecated.
    replaced by classes in org.biojavax.bio.taxa
    Encapsulate the 'EBI' species format used in Embl, Genbank and Swissprot files. The Taxon objects created by this process have the following annotations:

     key=PROPERTY_NCBI_TAXON, value=String representation of the NCBI taxon id
     key=PROPERTY_TAXON_NAMES, value=Map from name-class to name (see ncbi names.dmp)
     
    Author:
    Matthew Pocock, Len Trigg
    • Field Detail

      • PROPERTY_NCBI_TAXON

        public static final java.lang.String PROPERTY_NCBI_TAXON
        Deprecated.
      • PROPERTY_TAXON_NAMES

        public static final java.lang.String PROPERTY_TAXON_NAMES
        Deprecated.
    • Constructor Detail

      • EbiFormat

        public EbiFormat()
        Deprecated.
    • Method Detail

      • getInstance

        public static final EbiFormat getInstance()
        Deprecated.
      • serialize

        public java.lang.String serialize​(Taxon taxon)
        Deprecated.
        Description copied from interface: TaxonParser
        Convert a Taxon into a stringified representation.
        Specified by:
        serialize in interface TaxonParser
        Parameters:
        taxon - the Taxon to serialize
        Returns:
        the stringified version of Taxon
      • serializeSource

        public java.lang.String serializeSource​(Taxon taxon)
        Deprecated.
      • serializeXRef

        public java.lang.String serializeXRef​(Taxon taxon)
        Deprecated.