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

Packages that use SequenceHeaderParserInterface

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

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
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.