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

Packages that use FiniteAlphabet
org.biojava.bio.alignment: Classes to generate and describe sequence alignments.
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.search: Interfaces and classes for representing sequence similarity search results.
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.structure.io: Input and Output of Structures
org.biojava.bio.symbol: Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.utils.automata
org.biojava.utils.regex: This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets.
org.biojavax.bio.seq: Rich implementations of Sequences, Locations and Features.
org.biojavax.ga.util: Utility functions and helper classes

Uses of FiniteAlphabet in org.biojava.bio.alignment

Fields in org.biojava.bio.alignment declared as FiniteAlphabet
`protected FiniteAlphabet` `SubstitutionMatrix.alphabet`

Methods in org.biojava.bio.alignment that return FiniteAlphabet
`FiniteAlphabet` `SubstitutionMatrix.getAlphabet()` Gives the alphabet used by this matrix.

Constructors in org.biojava.bio.alignment with parameters of type FiniteAlphabet
`SubstitutionMatrix(FiniteAlphabet alpha, File matrixFile)` This constructs a `SubstitutionMatrix` object that contains two `Map` data structures having BioJava symbols as keys and the value being the index of the matrix containing the substitution score.
`SubstitutionMatrix(FiniteAlphabet alpha, short match, short replace)` Constructs a SubstitutionMatrix with every Match and every Replace having the same expenses given by the parameters.
`SubstitutionMatrix(FiniteAlphabet alpha, String matrixString, String name)` With this constructor it is possible to construct a SubstitutionMatrix object from a substitution matrix file.

Uses of FiniteAlphabet in org.biojava.bio.dist

Constructors in org.biojava.bio.dist with parameters of type FiniteAlphabet
`IndexedCount(FiniteAlphabet fa)` Get a new IdexedCount for an alphabet using the default indexer.
`SimpleDistribution(FiniteAlphabet alphabet)` make an instance of SimpleDistribution for the specified Alphabet.
`UniformDistribution(FiniteAlphabet alphabet)` Create a new UniformDistribution.
`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` `WMAsMM.stateAlphabet()`
`FiniteAlphabet` `SimpleMarkovModel.stateAlphabet()`
`FiniteAlphabet` `MarkovModel.stateAlphabet()` FiniteAlphabet of the states.
`FiniteAlphabet` `WMAsMM.transitionsFrom(State from)`
`FiniteAlphabet` `SimpleMarkovModel.transitionsFrom(State from)`
`FiniteAlphabet` `MarkovModel.transitionsFrom(State source)` Returns the FiniteAlphabet of all states that have a transition from 'source'.
`FiniteAlphabet` `WMAsMM.transitionsTo(State to)`
`FiniteAlphabet` `SimpleMarkovModel.transitionsTo(State to)`
`FiniteAlphabet` `MarkovModel.transitionsTo(State dest)` Returns the FiniteAlphabet of all states that have a transition to 'dest'.

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` `DataStore.getAlphabet()` The alphabet of symbol lists that can be searched against this DataStore.
`FiniteAlphabet` `CompactedDataStore.getAlphabet()`

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

Methods in org.biojava.bio.program.ssbind that return FiniteAlphabet
`static FiniteAlphabet` `AlphabetResolver.resolveAlphabet(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(File xffFile, 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.search

Constructors in org.biojava.bio.search with parameters of type FiniteAlphabet
`SeqContentPattern(FiniteAlphabet alpha)` Create a new SeqContentPattern over an alphabet.

Uses of FiniteAlphabet in org.biojava.bio.seq

Methods in org.biojava.bio.seq that return FiniteAlphabet
`static FiniteAlphabet` `ProteinTools.getAlphabet()` Gets the protein alphabet
`static FiniteAlphabet` `RNATools.getCodonAlphabet()` Gets the (RNA x RNA x RNA) Alphabet
`static FiniteAlphabet` `DNATools.getCodonAlphabet()` Gets the (DNA x DNA x DNA) Alphabet
`static FiniteAlphabet` `DNATools.getDNA()` Return the DNA alphabet.
`static FiniteAlphabet` `DNATools.getDNAxDNA()` Gets the (DNA x DNA) Alphabet
`static FiniteAlphabet` `NucleotideTools.getNucleotide()` Return the Nucleotide alphabet.
`static FiniteAlphabet` `RNATools.getRNA()` Return the RNA 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)` Deprecated. `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)` Construct a new NameTokenization, defaulting to case-insensitive.
`NameTokenization(FiniteAlphabet fab, boolean caseSensitive)`

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

Methods in org.biojava.bio.structure.io with parameters of type FiniteAlphabet
`static SubstitutionMatrix` `SeqRes2AtomAligner.getSubstitutionMatrix(FiniteAlphabet alphabet)`

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.
`class` `SoftMaskedAlphabet` Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.

Fields in org.biojava.bio.symbol declared as FiniteAlphabet
`static FiniteAlphabet` `Alphabet.EMPTY_ALPHABET` A really useful static alphabet that is always empty.

Methods in org.biojava.bio.symbol that return FiniteAlphabet
`FiniteAlphabet` `SuffixTree.getAlphabet()` Return the Alphabet containing all Symbols which might be found in this SuffixTree.
`FiniteAlphabet` `Packing.getAlphabet()` The FiniteAlphabet this packing is for.
`FiniteAlphabet` `DNANoAmbPack.getAlphabet()`
`FiniteAlphabet` `DNAAmbPack.getAlphabet()`
`FiniteAlphabet` `AlphabetIndex.getAlphabet()` Retrieve the alphabet that this indexes.
`protected FiniteAlphabet` `SoftMaskedAlphabet.getDelegate()` The compound alpha that holds the symbols used by this wrapper
`static FiniteAlphabet` `CodonPrefTools.getDinucleotideAlphabet()` returns an RNA dinucleotide alphabet.
`FiniteAlphabet` `SoftMaskedAlphabet.getMaskedAlphabet()` Gets the `Alphabet` upon which masking is being applied

Methods in org.biojava.bio.symbol with parameters of type FiniteAlphabet
`static Symbol` `AlphabetManager.getAllAmbiguitySymbol(FiniteAlphabet alpha)` Return the ambiguity symbol which matches all symbols in a given alphabet.
`static 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.
`static SoftMaskedAlphabet` `SoftMaskedAlphabet.getInstance(FiniteAlphabet alphaToMask)` Generates a soft masked Alphabet where lowercase tokens are assumed to be soft masked.
`static SoftMaskedAlphabet` `SoftMaskedAlphabet.getInstance(FiniteAlphabet alphaToMask, SoftMaskedAlphabet.MaskingDetector maskingDetector)` Creates a compound alphabet that is a hybrid of the alphabet that is to be soft masked and a binary alphabet that indicates if any `Symbol` is soft masked or not.
`static Packing` `PackingFactory.getPacking(FiniteAlphabet alpha, boolean ambiguity)` Get the default packing for an alphabet.

Constructors in org.biojava.bio.symbol with parameters of type FiniteAlphabet
`DummySymbolList(FiniteAlphabet alpha, int length)`
`SimpleGeneticCodeTable(FiniteAlphabet source, FiniteAlphabet target)` Creates a new instance of SimpleGeneticCodeTable
`SimpleManyToOneTranslationTable(FiniteAlphabet source, FiniteAlphabet target)` Construct a new translation table.
`SimpleReversibleTranslationTable(FiniteAlphabet source, FiniteAlphabet target)` Construct a new translation table.
`SimpleTranslationTable(FiniteAlphabet source, Alphabet target)` Create a new translation table that will translate symbols from source to target.
`SimpleTranslationTable(FiniteAlphabet source, Alphabet target, 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.
`UkkonenSuffixTree(FiniteAlphabet alpha)`

Uses of FiniteAlphabet in org.biojava.utils.automata

Constructors in org.biojava.utils.automata with parameters of type FiniteAlphabet
`Nfa(String name, FiniteAlphabet alfa)`
`PatternBlitz(FiniteAlphabet alfa, org.biojava.utils.automata.StateMachineToolkit factory)`

Uses of FiniteAlphabet in org.biojava.utils.regex

Methods in org.biojava.utils.regex that return FiniteAlphabet
`FiniteAlphabet` `Pattern.getAlphabet()`

Methods in org.biojava.utils.regex with parameters of type FiniteAlphabet
`static PatternFactory` `PatternFactory.makeFactory(FiniteAlphabet alfa)` Returns a factory for Patterns in the specified Alphabet.

Constructors in org.biojava.utils.regex with parameters of type FiniteAlphabet
`Search(FiniteAlphabet alfa)`

Uses of FiniteAlphabet in org.biojavax.bio.seq

Constructors in org.biojavax.bio.seq with parameters of type FiniteAlphabet
`InfinitelyAmbiguousSymbolList(FiniteAlphabet fa)` Creates a new instance of InfinitelyAmbiguousSymbolList

Uses of FiniteAlphabet in org.biojavax.ga.util

Methods in org.biojavax.ga.util that return FiniteAlphabet
`static FiniteAlphabet` `GATools.getBinaryAlphabet()` Gets a Reference to the FlyWeight GA_Binary `Alphabet`.

Methods in org.biojavax.ga.util with parameters of type FiniteAlphabet
`static OrderNDistribution` `GATools.standardMutationDistribution(FiniteAlphabet a)` Makes a mutation `Distribution` where the probability of a `Symbol` being mutated to itself is zero and the probability of it being changed to any other `Symbol` in the `Alphabet a` is `1.0 / (a.size() - 1.0)`
`static OrderNDistribution` `GATools.uniformMutationDistribution(FiniteAlphabet a)` Makes a 1st order distribution which is infact uniform (equivalent to a uniform zero order distribution).