Uses of Interface
org.biojava.bio.symbol.FiniteAlphabet

Packages that use FiniteAlphabet
org.biojava.bio.dist Probability distributions over Alphabets. 
org.biojava.bio.dp HMM and Dynamic Programming Algorithms. 
org.biojava.bio.gui Graphical interfaces for biojava objects. 
org.biojava.bio.program.abi ABI Trace Handling. 
org.biojava.bio.program.phred Parser for Phred output 
org.biojava.bio.program.ssaha SSAHA sequence searching API. 
org.biojava.bio.program.ssbind Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD. 
org.biojava.bio.program.xff Event-driven parsing system for the Extensible Feature Format (XFF). 
org.biojava.bio.proteomics Utilities to aid in performing various physical analysis of proteins. 
org.biojava.bio.seq Classes and interfaces for defining biological sequences and informatics objects. 
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 FiniteAlphabet in org.biojava.bio.dist
 

Constructors in org.biojava.bio.dist with parameters of type FiniteAlphabet
UniformDistribution(FiniteAlphabet alphabet)
           
SimpleDistribution(FiniteAlphabet alphabet)
           
IndexedCount(FiniteAlphabet fa)
           
UntrainableDistribution(FiniteAlphabet alpha)
          Construct a new untrainable distribution over the specified alphabet
 

Uses of FiniteAlphabet in org.biojava.bio.dp
 

Methods in org.biojava.bio.dp that return FiniteAlphabet
 FiniteAlphabet MarkovModel.stateAlphabet()
          FiniteAlphabet of the states.
 FiniteAlphabet MarkovModel.transitionsFrom(State source)
          Returns the FiniteAlphabet of all states that have a transition from 'source'.
 FiniteAlphabet MarkovModel.transitionsTo(State dest)
          Returns the FiniteAlphabet of all states that have a transition to 'dest'.
 FiniteAlphabet SimpleMarkovModel.stateAlphabet()
           
 FiniteAlphabet SimpleMarkovModel.transitionsFrom(State from)
           
 FiniteAlphabet SimpleMarkovModel.transitionsTo(State to)
           
 FiniteAlphabet WMAsMM.stateAlphabet()
           
 FiniteAlphabet WMAsMM.transitionsFrom(State from)
           
 FiniteAlphabet WMAsMM.transitionsTo(State to)
           
 

Uses of FiniteAlphabet in org.biojava.bio.gui
 

Constructors in org.biojava.bio.gui with parameters of type FiniteAlphabet
SimpleSymbolStyle(FiniteAlphabet alphabet)
           
 

Uses of FiniteAlphabet in org.biojava.bio.program.abi
 

Fields in org.biojava.bio.program.abi declared as FiniteAlphabet
static FiniteAlphabet ABITools.QUALITY
          The quality alphabet.
 

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

Methods in org.biojava.bio.program.phred that return FiniteAlphabet
static FiniteAlphabet PhredTools.getPhredAlphabet()
          Retrieves the PHRED alphabet from the AlphabetManager.
 

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

Methods in org.biojava.bio.program.ssaha that return FiniteAlphabet
 FiniteAlphabet CompactedDataStore.getAlphabet()
           
 FiniteAlphabet DataStore.getAlphabet()
          The alphabet of symbol lists that can be searched against this DataStore.
 

Uses of FiniteAlphabet in org.biojava.bio.program.ssbind
 

Methods in org.biojava.bio.program.ssbind that return FiniteAlphabet
static FiniteAlphabet AlphabetResolver.resolveAlphabet(java.lang.String identifier)
          resolveAlphabet returns an appropriate Alphabet for an arbitrary identifier.
 

Uses of FiniteAlphabet in org.biojava.bio.program.xff
 

Methods in org.biojava.bio.program.xff with parameters of type FiniteAlphabet
static Sequence XFFTools.readXFF(java.io.File xffFile, java.lang.String seqID, FiniteAlphabet alpha)
           
 

Uses of FiniteAlphabet in org.biojava.bio.proteomics
 

Methods in org.biojava.bio.proteomics that return FiniteAlphabet
 FiniteAlphabet StructureTools.getStructure()
           
 

Uses of FiniteAlphabet in org.biojava.bio.seq
 

Methods in org.biojava.bio.seq that return FiniteAlphabet
static FiniteAlphabet NucleotideTools.getNucleotide()
          Return the Nucleotide alphabet.
static FiniteAlphabet RNATools.getRNA()
          Return the RNA alphabet.
static FiniteAlphabet RNATools.getCodonAlphabet()
          Gets the (RNA x RNA x RNA) Alphabet
static FiniteAlphabet DNATools.getDNA()
          Return the DNA alphabet.
static FiniteAlphabet DNATools.getCodonAlphabet()
          Gets the (DNA x DNA x DNA) Alphabet
static FiniteAlphabet ProteinTools.getAlphabet()
          Gets the protein alphabet
static FiniteAlphabet ProteinTools.getTAlphabet()
          Gets the protein alphabet including the translation termination symbols
 

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

Methods in org.biojava.bio.seq.io that return FiniteAlphabet
static FiniteAlphabet SeqIOTools.getAlphabet(int identifier)
          getAlphabet accepts a value which represents a sequence format and returns the relevant FiniteAlphabet object.
 

Constructors in org.biojava.bio.seq.io with parameters of type FiniteAlphabet
NameTokenization(FiniteAlphabet fab, boolean caseSensitive)
           
NameTokenization(FiniteAlphabet fab)
          Construct a new NameTokenization, defaulting to case-insensitive.
 

Uses of FiniteAlphabet in org.biojava.bio.symbol
 

Classes in org.biojava.bio.symbol that implement FiniteAlphabet
 class AbstractAlphabet
           An abstract implementation of Alphabet.
static class IntegerAlphabet.SubIntegerAlphabet
          A class to represent a finite contiguous subset of the infinite IntegerAlphabet
 class SimpleAlphabet
          A simple no-frills implementation of the FiniteAlphabet interface.
 class SingletonAlphabet
          An alphabet that contains a single atomic symbol.
 

Methods in org.biojava.bio.symbol that return FiniteAlphabet
 FiniteAlphabet Packing.getAlphabet()
          The FiniteAlphabet this packing is for.
 FiniteAlphabet AlphabetIndex.getAlphabet()
          Retrieve the alphabet that this indexes.
 FiniteAlphabet DNANoAmbPack.getAlphabet()
           
 FiniteAlphabet DNAAmbPack.getAlphabet()
           
 FiniteAlphabet SuffixTree.getAlphabet()
          Return the Alphabet containing all Symbols which might be found in this SuffixTree.
 

Methods in org.biojava.bio.symbol with parameters of type FiniteAlphabet
static Packing PackingFactory.getPacking(FiniteAlphabet alpha, boolean ambiguity)
          Get the default packing for an alphabet.
static Symbol AlphabetManager.getAllAmbiguitySymbol(FiniteAlphabet alpha)
          Return the ambiguity symbol which matches all symbols in a given alphabet.
static java.util.Set AlphabetManager.getAllSymbols(FiniteAlphabet alpha)
          Return a set containing all possible symbols which can be considered members of a given alphabet, including ambiguous symbols.
static AlphabetIndex AlphabetManager.getAlphabetIndex(FiniteAlphabet alpha)
          Get an indexer for a specified alphabet.
 

Constructors in org.biojava.bio.symbol with parameters of type FiniteAlphabet
SimpleReversibleTranslationTable(FiniteAlphabet source, FiniteAlphabet target)
          Construct a new translation table.
UkkonenSuffixTree(FiniteAlphabet alpha)
           
SimpleTranslationTable(FiniteAlphabet source, Alphabet target)
          Create a new translation table that will translate symbols from source to target.
SimpleTranslationTable(FiniteAlphabet source, Alphabet target, java.util.Map transMap)
          Create a new translation table that will translate symbols from source to target.
SuffixTree(FiniteAlphabet alphabet)
          Construct a new SuffixTree to contain motifs over the specified alphabet.
DummySymbolList(FiniteAlphabet alpha, int length)