Uses of Interface
org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface

Packages that use SequenceHeaderParserInterface

Package	Description
org.biojava.nbio.core.sequence.io
org.biojava.nbio.structure.io	Input and Output of Structures

Uses of SequenceHeaderParserInterface in org.biojava.nbio.core.sequence.io

Classes in org.biojava.nbio.core.sequence.io that implement SequenceHeaderParserInterface

Modifier and Type	Class and 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
class	GenericGenbankHeaderParser<S extends AbstractSequence<C>,C extends Compound>
class	PlainFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> The plain fasta header takes everything in the header as a single entity.

Constructors in org.biojava.nbio.core.sequence.io with parameters of type SequenceHeaderParserInterface

Constructor and Description
FastaReader(File file, SequenceHeaderParserInterface<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, SequenceHeaderParserInterface<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.
GenbankReader(File file, SequenceHeaderParserInterface<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.
GenbankReader(InputStream is, SequenceHeaderParserInterface<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 SequenceHeaderParserInterface in org.biojava.nbio.structure.io

Constructors in org.biojava.nbio.structure.io with parameters of type SequenceHeaderParserInterface

Constructor and Description
FastaStructureParser(File file, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)
FastaStructureParser(InputStream is, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)