## 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.agave: Classes for converting between AGAVE XML and BioJava objects.
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.agave
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.io.game
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.