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.