Uses of Interface
org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface
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Packages that use SequenceHeaderParserInterface Package Description org.biojava.nbio.core.sequence.io org.biojava.nbio.structure.io Input and Output of Structures -
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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 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 FastaHeaderParserInterfaceclass
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 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 useFileProxyProteinSequenceCreator
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 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)
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