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.
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.