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
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionstatic void
void
parseHeader
(String header, S sequence) Parse the header and set the values in the sequence
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Constructor Details
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GenericFastaHeaderParser
public GenericFastaHeaderParser()
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Method Details
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parseHeader
Parse the header and set the values in the sequence- Specified by:
parseHeader
in interfaceSequenceHeaderParserInterface<S extends AbstractSequence<C>,
C extends Compound> - Parameters:
header
-sequence
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main
- Parameters:
args
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