Package org.biojavax.bio.seq.io

Classes to support the I/O of RichSequence and Bioentry objects.

See:
Description

Interface Summary

RichSeqIOListener	An interface for classes that listen to BioEntry or RichSequence I/O streams.
RichSequenceBuilder	An interface for objects that can build RichSequences.
RichSequenceBuilderFactory	Simple factory for constructing new RichSequenceBuilder objects.
RichSequenceFormat	Allows a file format to be read/written as RichSequences.

Class Summary

DebuggingRichSeqIOListener	This is purely for debugging purposes.
EMBLFormat	Format reader for EMBL files.
EMBLFormat.Terms	Implements some EMBL-specific terms.
EMBLxmlFormat	Format reader for EMBLxml files.
EMBLxmlFormat.Terms	Implements some EMBLxml-specific terms.
FastaFormat	Format object representing FASTA files.
GenbankFormat	Format reader for GenBank files.
GenbankFormat.Terms	Implements some GenBank-specific terms.
GenbankLocationParser	Parses Genbank location strings into RichLocation objects.
INSDseqFormat	Format reader for INSDseq files.
INSDseqFormat.Terms	Implements some INSDseq-specific terms.
RichSeqIOAdapter	This class implements all methods of RichSeqIOListener and takes no action.
RichSequenceFormat.BasicFormat	Provides a basic format with simple things like line-widths precoded.
RichSequenceFormat.HeaderlessFormat	Provides the basic implementation required for simple header/footer-less files such as Genbank.
RichStreamReader	Parses a stream into sequences.
RichStreamWriter	Writes all of the sequences from a SequenceIterator to a stream with a particular format.
SimpleRichSequenceBuilder	Constructs BioEntry objects by listening to events.
SimpleRichSequenceBuilderFactory	Generates RichSequenceBuilder objects.
UniProtCommentParser
UniProtCommentParser.Event	A class to describe events for alternative product comments.
UniProtCommentParser.Interaction	A class to describe protein-protein interactions.
UniProtCommentParser.Isoform	A class to describe isoforms for alternative product comments.
UniProtFormat	Format reader for UniProt files.
UniProtFormat.Terms	Implements some UniProt-specific terms.
UniProtLocationParser	Parses UniProt location strings into RichLocation objects.
UniProtXMLFormat	Format reader for UniProtXML files.
UniProtXMLFormat.Terms	Implements some UniProtXML-specific terms.

Package org.biojavax.bio.seq.io Description

Classes to support the I/O of RichSequence and Bioentry objects.