## 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.
FastaHeader: This class is used by `FastaFormat` to determine which fields are in the fasta header.
GenbankFormat: Format reader for GenBank files.
GenbankFormat.Terms: Implements some GenBank-specific terms.
GenbankLocationParser: Parses Genbank location strings into RichLocation objects.
HashedFastaIterator: Iterates over a Fasta file that is kept in memory for optimized access.
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.
UniProtCommentParser.SeqCaution: A class to describe seq caution entries.
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.