org.biojava3.core.sequence.io
Class GenericFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound>

java.lang.Object
  extended by org.biojava3.core.sequence.io.GenericFastaHeaderParser<S,C>
All Implemented Interfaces:
FastaHeaderParserInterface<S,C>

public class GenericFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound>
extends Object
implements FastaHeaderParserInterface<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

Author:
Scooter Willis

Constructor Summary
GenericFastaHeaderParser()
           
 
Method Summary
static void main(String[] args)
           
 void parseHeader(String header, S sequence)
          Parse the header and set the values in the sequence
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

GenericFastaHeaderParser

public GenericFastaHeaderParser()
Method Detail

parseHeader

public void parseHeader(String header,
                        S sequence)
Parse the header and set the values in the sequence

Specified by:
parseHeader in interface FastaHeaderParserInterface<S extends AbstractSequence<C>,C extends Compound>
Parameters:
header -
sequence -

main

public static void main(String[] args)
Parameters:
args -