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

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

See:
Description

Interface Summary
AlignmentFormat
SeqFileFormer: Objects implementing the `SeqFileFormer` interface are responsible for the detailed formatting of sequence data prior to writing to a `PrintStream`.
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.
CharacterTokenization: Implementation of SymbolTokenization which binds symbols to single unicode characters.
ChunkedSymbolListBuilder
ChunkedSymbolListFactory: class that makes ChunkedSymbolLists with the chunks implemented as SymbolLists themselves.
CrossProductTokenization: Tokenization for cross-product alphabets.
DoubleTokenization
EmblFileFormer: `EmblFileFormer` performs the detailed formatting of EMBL entries for writing to a `PrintStream`.
EmblLikeFormat: Format processor for handling EMBL records and similar files.
EmblLikeLocationParser: `EmblLikeLocationParser` parses EMBL/Genbank style locations.
EmblProcessor: Simple filter which handles attribute lines from an EMBL file.
EmblProcessor.Factory: Factory which wraps SequenceBuilders in an EmblProcessor
FastaAlignmentFormat: This class implements the AlignmentFormat interface to read FASTA alignments.
FastaDescriptionLineParser: Simple filter which performs a default extraction of data from the description lines of FASTA files.
FastaDescriptionLineParser.Factory: Factory which wraps SequenceBuilders in a FastaDescriptionLineParser
FastaFormat: Format object representing FASTA files.
FeatureTableParser: Simple parser for feature tables.
GAMEFormat: A rudimentary read-only GAME 1.2 Format object.
GenbankFileFormer: `GenbankFileFormer` performs the detailed formatting of Genbank entries for writing to a `PrintStream`.
GenbankFormat: Format reader for GenBank files.
GenbankProcessor: Simple filter which handles attribute lines from a Genbank file
GenbankProcessor.Factory: Factory which wraps sequence builders in a GenbankProcessor
IntegerTokenization
MSFAlignmentFormat
NameTokenization: Simple implementation of SymbolTokenization which uses the `name' field of the symbols.
OrganismParser: A parser that is able to generate Taxon entries for sequence builder event streams.
OrganismParser.Factory: Factory which wraps SequenceBuilders in an OrganismParser.
ProteinRefSeqFileFormer: This class performs the detailed formatting of refseq protein entries.
ProteinRefSeqProcessor: Class description
ProteinRefSeqProcessor.Factory: Factory which wraps sequence builders in a ProteinRefSeqProcessor
SeqAlignReadWrite: Title: File2Biojava Description: This project will take in a file of any common bioinformatics file formats and convert it to the appropriate Biojava object.
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.
SeqIOFilter: Base-class for listeners that pass filtered events onto another listener.
SeqIOTools: A set of convenience methods for handling common file formats.
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.
SwissprotFileFormer: Formats a sequence into Swissprot/TrEMBL format.
SwissprotProcessor: Simple filter which handles attribute lines from an Swissprot entry.
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.