## Uses of Interface
org.biojava.bio.seq.io.SymbolTokenization

Packages that use SymbolTokenization
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.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.symbol: Representation of the Symbols that make up a sequence, and locations within them.

Uses of SymbolTokenization in org.biojava.bio.program

Constructors in org.biojava.bio.program with parameters of type SymbolTokenization
`Meme(java.io.InputStream is, SymbolTokenization symParser)`

Uses of SymbolTokenization in org.biojava.bio.program.phred

Methods in org.biojava.bio.program.phred with parameters of type SymbolTokenization
`boolean` `PhredFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol)`

Uses of SymbolTokenization in org.biojava.bio.program.ssaha

Constructors in org.biojava.bio.program.ssaha with parameters of type SymbolTokenization
`SequenceStreamer.FileStreamer(SequenceFormat format, SymbolTokenization toke, java.util.List files)`
`SequenceStreamer.FileStreamer(SequenceFormat format, SymbolTokenization toke, java.io.File f)`

Uses of SymbolTokenization in org.biojava.bio.seq.db

Methods in org.biojava.bio.seq.db that return SymbolTokenization
`SymbolTokenization` `EmblCDROMIndexStore.getSymbolParser()`
`SymbolTokenization` `TabIndexStore.getSymbolParser()`
`SymbolTokenization` `IndexStore.getSymbolParser()` Retrieve the symbol parser used to turn the sequence characters into Symobl objects.
`SymbolTokenization` `BioIndex.getSymbolParser()`

Constructors in org.biojava.bio.seq.db with parameters of type SymbolTokenization
`EmblCDROMIndexStore(java.io.File divisionLkp, java.io.File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser)` Creates a new `EmblCDROMIndexStore` backed by a random access binary index.
`EmblCDROMIndexStore(java.io.File pathPrefix, java.io.File divisionLkp, java.io.File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser)` Creates a new `EmblCDROMIndexStore` backed by a random access binary index.
`TabIndexStore(java.io.File storeFile, java.io.File indexFile, java.lang.String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser)`

Uses of SymbolTokenization in org.biojava.bio.seq.io

Classes in org.biojava.bio.seq.io that implement SymbolTokenization
`class` `CharacterTokenization` Implementation of SymbolTokenization which binds symbols to single unicode characters.
`class` `CrossProductTokenization` Tokenization for cross-product alphabets.
`class` `DoubleTokenization`
`class` `IntegerTokenization`
`class` `NameTokenization` Simple implementation of SymbolTokenization which uses the `name' field of the symbols.
`class` `WordTokenization` Base class for tokenizations which accept whitespace-separated `words'.

Methods in org.biojava.bio.seq.io with parameters of type SymbolTokenization
`boolean` `GenbankFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.
`boolean` `SequenceFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` Read a sequence and pass data on to a SeqIOListener.
`boolean` `GAMEFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` this version only reads annotations (no symbols)
`boolean` `FastaFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol)`
`boolean` `EmblLikeFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)`

Constructors in org.biojava.bio.seq.io with parameters of type SymbolTokenization
`StreamReader(java.io.InputStream is, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf)`
`StreamReader(java.io.BufferedReader reader, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf)`

Uses of SymbolTokenization in org.biojava.bio.symbol

Methods in org.biojava.bio.symbol that return SymbolTokenization
`SymbolTokenization` `SingletonAlphabet.getTokenization(java.lang.String name)`
`SymbolTokenization` `AbstractAlphabet.getTokenization(java.lang.String name)`
`SymbolTokenization` `Alphabet.getTokenization(java.lang.String name)` Get a SymbolTokenization by name.
`SymbolTokenization` `DoubleAlphabet.getTokenization(java.lang.String name)`
`SymbolTokenization` `DoubleAlphabet.SubDoubleAlphabet.getTokenization(java.lang.String name)`
`SymbolTokenization` `IntegerAlphabet.getTokenization(java.lang.String name)` Creates a new parser (Mark Schreiber 3 May 2001).
`SymbolTokenization` `IntegerAlphabet.SubIntegerAlphabet.getTokenization(java.lang.String name)`

Methods in org.biojava.bio.symbol with parameters of type SymbolTokenization
`void` `AbstractAlphabet.putTokenization(java.lang.String name, SymbolTokenization parser)` Assigns a symbol parser to a String object.

Constructors in org.biojava.bio.symbol with parameters of type SymbolTokenization
`SimpleSymbolList(SymbolTokenization parser, java.lang.String seqString)` Construct a SymbolList from a string.