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 BioIndex.getSymbolParser()
           
 SymbolTokenization IndexStore.getSymbolParser()
          Retrieve the symbol parser used to turn the sequence characters into Symobl objects.
 SymbolTokenization EmblCDROMIndexStore.getSymbolParser()
           
 SymbolTokenization TabIndexStore.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 SequenceFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          Read a sequence and pass data on to a SeqIOListener.
 boolean FastaFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol)
           
 boolean GAMEFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          this version only reads annotations (no symbols)
 boolean EmblLikeFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
           
 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.
 

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 IntegerAlphabet.getTokenization(java.lang.String name)
          Creates a new parser (Mark Schreiber 3 May 2001).
 SymbolTokenization IntegerAlphabet.SubIntegerAlphabet.getTokenization(java.lang.String name)
           
 SymbolTokenization AbstractAlphabet.getTokenization(java.lang.String name)
           
 SymbolTokenization DoubleAlphabet.getTokenization(java.lang.String name)
           
 SymbolTokenization DoubleAlphabet.SubDoubleAlphabet.getTokenization(java.lang.String name)
           
 SymbolTokenization SingletonAlphabet.getTokenization(java.lang.String name)
           
 SymbolTokenization Alphabet.getTokenization(java.lang.String name)
           Get a SymbolTokenization by 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.