Uses of Interface
org.biojava3.core.sequence.io.template.FastaHeaderParserInterface

Packages that use FastaHeaderParserInterface

Package	Description
bacnet.reader
org.biojava3.core.sequence.io

Uses of FastaHeaderParserInterface in bacnet.reader

Classes in bacnet.reader that implement FastaHeaderParserInterface

Modifier and Type	Class	Description
class	NCBIFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound>	My own implementation of a FastaHeaderParserInterface to parse Fasta files from NCBI ftp NCBI fna (genome and plasmids) gi|gi-number|ref|accession|name gi|16802048|ref|NC_003210.1| Listeria monocytogenes EGD-e, complete genome NCBI ffn (coding) ref|refGenome gi-number|:start-end name ref|NC_003210.1|:318-1673 chromosomal replication initiation protein [Listeria monocytogenes EGD-e] NCBI frn (non-coding) ref|refGenome gi-number|:start-end| name| [locus-tag] ref|NC_003210|:82705-82777|Lys tRNA| [locus_tag=lmot01] NCBI faa (proteins) gi|gi-number|ref|accession|name gi|16802049|ref|NP_463534.1| chromosomal replication initiation protein [Listeria monocytogenes EGD-e]

Constructors in bacnet.reader with parameters of type FastaHeaderParserInterface

Modifier	Constructor	Description
	FastaFileReader(File file, FastaHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)	If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.
	FastaFileReader(InputStream is, FastaHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)	If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.

Uses of FastaHeaderParserInterface in org.biojava3.core.sequence.io

Classes in org.biojava3.core.sequence.io that implement FastaHeaderParserInterface

Modifier and Type	Class	Description
class	GenericFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound>	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

Constructors in org.biojava3.core.sequence.io with parameters of type FastaHeaderParserInterface

Modifier	Constructor	Description
	FastaReader(File file, FastaHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)	If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.
	FastaReader(InputStream is, FastaHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)	If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.