Package org.biojava.bio.seq.io

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.

Interface Summary

Interface	Description
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

Class	Description
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

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