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.