Package org.biojava3.core.sequence.io

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

java.lang.Object

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

Constructors

Constructor	Description
GenericFastaHeaderParser()

Method Summary

Modifier and Type	Method	Description
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

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

GenericFastaHeaderParser

public GenericFastaHeaderParser()

Method Details

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 -