Package org.biojava.nbio.core.sequence.io

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

java.lang.Object

org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser<S,C>

All Implemented Interfaces:

SequenceHeaderParserInterface<S,C>

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

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor	Description
GenericFastaHeaderParser()

Method Summary

Modifier and Type	Method	Description
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 SequenceHeaderParserInterface<S extends AbstractSequence<C>,C extends Compound>

Parameters:

header -

sequence -