## Package org.biojava.bio.seq.io

Classes and interfaces for processing and producing flat-file representations of sequences.

See:
Description

Interface Summary
AlignmentFormat
SeqFileFormer: Deprecated. Use org.biojavax.bio.seq.io framework instead
SeqIOListener: Notification interface for objects which listen to a sequence stream parser.
SequenceBuilder: Interface for objects which accumulate state via SeqIOListener, then construct a Sequence object.
SequenceBuilderFactory: Simple factory for constructing new SequenceBuilder objects.
SequenceFormat: Defines what a sequence format does.
StreamParser: Parse a stream of characters into BioJava symbols.
SymbolReader: Encapsulate a stream of Symbols being parsed from some input stream.
SymbolTokenization: Encapsulate a mapping between BioJava Symbol objects and some string representation.

Class Summary
AlignIOConstants: `AlignIOConstants` contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing alignments.
AlternateTokenization: Implementation of SymbolTokenization which binds symbols to strings of characters.
CharacterTokenization: Implementation of SymbolTokenization which binds symbols to single unicode characters.
ChunkedSymbolListFactory: class that makes ChunkedSymbolLists with the chunks implemented as SymbolLists themselves.
CrossProductTokenization: Tokenization for cross-product alphabets.
DoubleTokenization
EmblFileFormer: Deprecated. Use org.biojavax.bio.seq.io framework instead
EmblLikeFormat: Deprecated. Use org.biojavax.bio.seq.io.EMBLFormat instead
EmblLikeLocationParser: Deprecated. Use org.biojavax.bio.seq.io framework instead
EmblProcessor: Deprecated. Use org.biojavax.bio.seq.io framework instead
EmblProcessor.Factory: Factory which wraps SequenceBuilders in an EmblProcessor
EmblReferenceComparator
FastaAlignmentFormat: This class implements the AlignmentFormat interface to read FASTA alignments.
FastaDescriptionLineParser: Deprecated. Use org.biojavax.bio.seq.io.FastaFormat
FastaDescriptionLineParser.Factory: Factory which wraps SequenceBuilders in a FastaDescriptionLineParser
FastaFormat: Deprecated. Use org.biojavax.bio.seq.io.FastaFormat
FeatureTableParser: Deprecated. Use org.biojavax.bio.seq.io framework instead
GAMEFormat: A rudimentary read-only GAME 1.2 Format object.
GenbankFileFormer: Deprecated. Use org.biojavax.bio.seq.io framework instead
GenbankFormat: Deprecated. Use org.biojavax.bio.seq.io.GenbankFormat
GenbankProcessor: Deprecated. Use org.biojavax.bio.seq.io framework instead
GenbankProcessor.Factory: Factory which wraps sequence builders in a GenbankProcessor
GenbankXmlFormat: Deprecated. Use org.biojavax.bio.seq.io.INSDseqFormat
GenEmblFeatureComparator: Deprecated. Use org.biojavax.bio.seq.io framework instead
GenEmblPropertyComparator: Deprecated. Use org.biojavax.bio.seq.io framework instead
GenpeptFormat: Deprecated. Use org.biojavax.bio.seq.io framework instead
IntegerTokenization
MSFAlignmentFormat
NameTokenization: Simple implementation of SymbolTokenization which uses the `name' field of the symbols.
OrganismParser: Deprecated. Use org.biojavax.bio.taxa framework instead
OrganismParser.Factory: Factory which wraps SequenceBuilders in an OrganismParser.
ProteinRefSeqFileFormer: Deprecated. Use org.biojavax.bio.seq.io framework instead
ProteinRefSeqProcessor: Deprecated. Use org.biojavax.bio.seq.io framework instead
ProteinRefSeqProcessor.Factory: Factory which wraps sequence builders in a ProteinRefSeqProcessor
ReferenceAnnotation: Deprecated. Use org.biojavax.bio.seq.io framework instead
SeqIOAdapter: Adapter class for SeqIOListener that has empty methods.
SeqIOConstants: `SeqIOConstants` contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing sequences.
SeqIOEventEmitter: Deprecated. Use org.biojavax.bio.seq.io framework instead
SeqIOFilter: Base-class for listeners that pass filtered events onto another listener.
SeqIOTools: Deprecated. use org.biojavax.bio.seq.RichSequence.IOTools
SequenceBuilderBase: Basic SequenceBuilder implementation which accumulates all notified information.
SequenceBuilderFilter: Base-class for builders that pass filtered events onto another builder.
SequenceDBSequenceBuilder: This SequenceBuilder has a variety of modes of operation.
SimpleAssemblyBuilder: Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly.
SimpleSequenceBuilder: Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleSequence.
SmartSequenceBuilder: Basic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence.
StreamReader: Parses a stream into sequences.
StreamWriter: Writes all of the sequences from a SequenceIterator to a stream with a particular format.
SubIntegerTokenization
SwissprotFileFormer: Deprecated. Use org.biojavax.bio.seq.io framework instead
SwissprotProcessor: Deprecated. Use org.biojavax.bio.seq.io framework instead
SwissprotProcessor.Factory: Factory which wraps SequenceBuilders in a SwissprotProcessor
SymbolListCharSequence: `SymbolListCharSequence` is a `CharSequence` implementation which wraps a `SymbolList`.
SymbolTokenization.TokenType
WordTokenization: Base class for tokenizations which accept whitespace-separated `words'.

Exception Summary
ParseException: ParseException should be thrown to indicate that there was a problem with parsing sequence information.

## Package org.biojava.bio.seq.io Description

Classes and interfaces for processing and producing flat-file representations of sequences.

These interfaces define how to read and write arbitrary file formats. The file format is decoupled from the type of sequence that will be produced or written. For example, you could read in entries from a Fasta database and generate ACeDB sequences within an ACeDB database for each entry just by configuring a StreamReader with a FastaFormat and an AceSequenceFactory.