Package org.biojavax.bio.seq.io

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

Interface Summary

Interface	Description
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

Class	Description
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.