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