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).