Class GenericFastaHeaderParser<S extends AbstractSequence<C>,​C extends Compound>

  • All Implemented Interfaces:

    public class GenericFastaHeaderParser<S extends AbstractSequence<C>,​C extends Compound>
    extends Object
    implements SequenceHeaderParserInterface<S,​C>
    The default fasta header parser where some headers are well defined based on the source database which allows us to set the source of the protein sequence and the identifier that can be used in future implementations to load features from external sources If the user has a custom header with local data then they can create their own implementation of a FastaHeaderParserInterface
     GenBank                           gi|gi-number|gb|accession|locus
     ENA Data Library                  gi|gi-number|emb|accession|locus
     DDBJ, DNA Database of Japan       gi|gi-number|dbj|accession|locus
     NBRF PIR                          pir||entry
     Protein Research Foundation       prf||name
     SWISS-PROT                        sp|accession|name
     Brookhaven Protein Data Bank (1)  pdb|entry|chain
     Brookhaven Protein Data Bank (2)  entry:chain|PDBID|CHAIN|SEQUENCE
     PDB EBI                           PDB:1ECY_A mol:protein length:142  ECOTIN
     Patents                           pat|country|number
     GenInfo Backbone Id               bbs|number
     General database identifier       gnl|database|identifier
     NCBI Reference Sequence           ref|accession|locus
     Local Sequence identifier         lcl|identifier
    Scooter Willis