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## 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.

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