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

Class Summary

Class	Description
BufferedReaderBytesRead	Need to keep track of actual bytes read and take advantage of buffered reader performance.
CasePreservingProteinSequenceCreator	A sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence.
DNASequenceCreator	A helper class that allows different ways to read a string and create a DNA sequence.
FastaGeneWriter	A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.
FastaReader<S extends Sequence<?>,C extends Compound>	Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta files
FastaReaderHelper
FastaSequenceParser	Used to parse a stream of a fasta file to get the sequence
FastaWriter<S extends Sequence<?>,C extends Compound>	The FastaWriter writes a collection of sequences to an outputStream.
FastaWriterHelper	The class that should be used to write out fasta file of a sequence collection
FileProxyDNASequenceCreator	This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
FileProxyProteinSequenceCreator	This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
FileProxyRNASequenceCreator	This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
GenbankReader<S extends AbstractSequence<C>,C extends Compound>	Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the primary class used to read Genbank files
GenbankReaderHelper
GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound>
GenbankWriter<S extends Sequence<?>,C extends Compound>
GenbankWriterHelper	The class that should be used to write out genbank file of a sequence collection
GenericFastaHeaderFormat<S extends AbstractSequence<?>,C extends Compound>	We store the original header if the sequence is parsed from a fasta file and will use that exact sequence if we write out the sequences to a fasta file.
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
GenericGenbankHeaderFormat<S extends AbstractSequence<C>,C extends Compound>
GenericGenbankHeaderParser<S extends AbstractSequence<C>,C extends Compound>
GenericInsdcHeaderFormat<S extends AbstractSequence<C>,C extends Compound>
IUPACParser	Available translations 1 - UNIVERSAL 2 - VERTEBRATE_MITOCHONDRIAL 3 - YEAST_MITOCHONDRIAL 4 - MOLD_MITOCHONDRIAL 5 - INVERTEBRATE_MITOCHONDRIAL 6 - CILIATE_NUCLEAR 9 - ECHINODERM_MITOCHONDRIAL 10 - EUPLOTID_NUCLEAR 11 - BACTERIAL 12 - ALTERNATIVE_YEAST_NUCLEAR 13 - ASCIDIAN_MITOCHONDRIAL 14 - FLATWORM_MITOCHONDRIAL 15 - BLEPHARISMA_MACRONUCLEAR 16 - 2CHLOROPHYCEAN_MITOCHONDRIAL 21 - TREMATODE_MITOCHONDRIAL 23 - SCENEDESMUS_MITOCHONDRIAL Taken from	IUPACParser.IUPACTable	Holds the concept of a codon table from the IUPAC format
PlainFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound>	The plain fasta header takes everything in the header as a single entity.
ProteinSequenceCreator	Used to create a ProteinSequence from a String to allow for details about the location of the sequence etc.
RNASequenceCreator	Used to create a RNA sequence