## 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
`SimpleDistribution(FiniteAlphabet alphabet)`
`UniformDistribution(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` `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)`
`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'.

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(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` `RNATools.getRNA()` Return the RNA alphabet.
`static FiniteAlphabet` `RNATools.getCodonAlphabet()` Gets the (RNA x RNA x RNA) Alphabet
`static FiniteAlphabet` `NucleotideTools.getNucleotide()` Return the Nucleotide 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` `DNANoAmbPack.getAlphabet()`
`FiniteAlphabet` `AlphabetIndex.getAlphabet()` Retrieve the alphabet that this indexes.
`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.
`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.
`DummySymbolList(FiniteAlphabet alpha, int length)`
`UkkonenSuffixTree(FiniteAlphabet alpha)`
`SuffixTree(FiniteAlphabet alphabet)` Construct a new SuffixTree to contain motifs over the specified alphabet.