Uses of Package
org.biojava.bio.seq.io

Packages that use org.biojava.bio.seq.io

org.biojava.bio.program	Java wrappers for interacting with external bioinformatics tools.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.program.ssaha	SSAHA sequence searching API.
org.biojava.bio.program.xff	Event-driven parsing system for the Extensible Feature Format (XFF).
org.biojava.bio.seq.db	Collections of biological sequence data.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.io.game	Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.seq.io.game12	Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.seq.ragbag	The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.

Classes in org.biojava.bio.seq.io used by org.biojava.bio.program

SymbolTokenization
Encapsulate a mapping between BioJava Symbol objects and some string representation.

Classes in org.biojava.bio.seq.io used by org.biojava.bio.program.phred

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

SeqIOListener
Notification interface for objects which listen to a sequence stream parser.

SequenceFormat
Defines what a sequence format does.

StreamReader
Parses a stream into sequences.

SymbolTokenization
Encapsulate a mapping between BioJava Symbol objects and some string representation.

Classes in org.biojava.bio.seq.io used by org.biojava.bio.program.ssaha

SeqIOListener
Notification interface for objects which listen to a sequence stream parser.

SequenceFormat
Defines what a sequence format does.

SymbolTokenization
Encapsulate a mapping between BioJava Symbol objects and some string representation.

Classes in org.biojava.bio.seq.io used by org.biojava.bio.program.xff

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

SeqIOListener
Notification interface for objects which listen to a sequence stream parser.

Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.db

SequenceBuilderFactory
Simple factory for constructing new SequenceBuilder objects.

SequenceFormat
Defines what a sequence format does.

SymbolTokenization
Encapsulate a mapping between BioJava Symbol objects and some string representation.

Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.io

AlignmentFormat

FeatureTableParser
Simple parser for feature tables.

GenbankFileFormer
GenbankFileFormer performs the detailed formatting of Genbank entries for writing to a PrintStream.

GenbankProcessor
Simple filter which handles attribute lines from a Genbank file

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

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.

SequenceBuilderBase
Basic SequenceBuilder implementation which accumulates all notified information.

SequenceBuilderFactory
Simple factory for constructing new SequenceBuilder objects.

SequenceBuilderFilter
Base-class for builders that pass filtered events onto another builder.

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.

SymbolTokenization.TokenType

WordTokenization
Base class for tokenizations which accept whitespace-separated `words'.

Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.io.game

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

SeqIOListener
Notification interface for objects which listen to a sequence stream parser.

StreamParser
Parse a stream of characters into BioJava symbols.

Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.io.game12

SeqIOListener
Notification interface for objects which listen to a sequence stream parser.

Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.ragbag

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

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.

Classes in org.biojava.bio.seq.io used by org.biojava.bio.symbol

SymbolTokenization
Encapsulate a mapping between BioJava Symbol objects and some string representation.