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

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

Package	Description
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.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.ontology.io	Tools for loading and saving ontologies.
org.biojava.ontology.obo
org.biojavax.bio.phylo.io.nexus	Classes to support the I/O of Nexus files.
org.biojavax.bio.phylo.io.phylip	Classes to support the reading and writing of PHYLIP format.
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.
org.biojavax.bio.taxa.io

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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
AlignmentFormat
FeatureTableParser Deprecated. Use org.biojavax.bio.seq.io framework instead
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
ParseException ParseException should be thrown to indicate that there was a problem with parsing sequence information.
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.
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

Class and Description
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

Class and Description
StreamParser Parse a stream of characters into BioJava symbols.

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

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

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

Class and Description
SeqIOListener Notification interface for objects which listen to a sequence stream parser.
StreamParser Parse a stream of characters into BioJava symbols.
SymbolTokenization Encapsulate a mapping between BioJava Symbol objects and some string representation.
SymbolTokenization.TokenType

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

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

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

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

Classes in org.biojava.bio.seq.io used by org.biojavax.bio.phylo.io.nexus

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

Classes in org.biojava.bio.seq.io used by org.biojavax.bio.phylo.io.phylip

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

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

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

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

Class and Description
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.
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.biojavax.bio.taxa.io

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