Uses of Interface
org.biojava.bio.symbol.FiniteAlphabet
Packages that use FiniteAlphabet
Package
Description
Classes to generate and describe sequence alignments.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical interfaces for biojava objects.
ABI Trace Handling.
Parser for Phred output
SSAHA sequence searching API.
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
Event-driven parsing system for the Extensible Feature Format (XFF).
Utilities to aid in performing various physical analysis of proteins.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
Classes and interfaces for processing and producing flat-file representations
of sequences.
Representation of the Symbols that make up a sequence, and locations within
them.
This package is used to perform regular expression searches of
SymbolLists defined in arbitrary Alphabets.
Rich implementations of Sequences, Locations and Features.
Utility functions and helper classes
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Uses of FiniteAlphabet in org.biojava.bio.alignment
Methods in org.biojava.bio.alignment that return FiniteAlphabetModifier and TypeMethodDescriptionSubstitutionMatrix.getAlphabet()
Gives the alphabet used by this matrix.Methods in org.biojava.bio.alignment with parameters of type FiniteAlphabetModifier and TypeMethodDescriptionstatic SubstitutionMatrix
SubstitutionMatrix.getSubstitutionMatrix
(FiniteAlphabet alphabet, BufferedReader reader) Return a new substitution matrix with the specified alphabet.static SubstitutionMatrix
SubstitutionMatrix.getSubstitutionMatrix
(FiniteAlphabet alphabet, BufferedReader reader, String name) Return a new substitution matrix with the specified alphabet and name.Constructors in org.biojava.bio.alignment with parameters of type FiniteAlphabetModifierConstructorDescriptionSubstitutionMatrix
(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, File matrixFile) This constructs aSubstitutionMatrix
object that contains twoMap
data structures having BioJava symbols as keys and the value being the index of the matrix containing the substitution score.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 FiniteAlphabetModifierConstructorDescriptionGet 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.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 FiniteAlphabetModifier and TypeMethodDescriptionMarkovModel.stateAlphabet()
FiniteAlphabet of the states.SimpleMarkovModel.stateAlphabet()
WMAsMM.stateAlphabet()
MarkovModel.transitionsFrom
(State source) Returns the FiniteAlphabet of all states that have a transition from 'source'.SimpleMarkovModel.transitionsFrom
(State from) WMAsMM.transitionsFrom
(State from) MarkovModel.transitionsTo
(State dest) Returns the FiniteAlphabet of all states that have a transition to 'dest'.SimpleMarkovModel.transitionsTo
(State to) WMAsMM.transitionsTo
(State to) -
Uses of FiniteAlphabet in org.biojava.bio.gui
Constructors in org.biojava.bio.gui with parameters of type FiniteAlphabet -
Uses of FiniteAlphabet in org.biojava.bio.program.abi
Fields in org.biojava.bio.program.abi declared as FiniteAlphabetModifier and TypeFieldDescriptionstatic final FiniteAlphabet
ABITools.QUALITY
The quality alphabet. -
Uses of FiniteAlphabet in org.biojava.bio.program.phred
Methods in org.biojava.bio.program.phred that return FiniteAlphabetModifier and TypeMethodDescriptionstatic final 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 FiniteAlphabetModifier and TypeMethodDescriptionCompactedDataStore.getAlphabet()
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 FiniteAlphabetModifier and TypeMethodDescriptionstatic FiniteAlphabet
AlphabetResolver.resolveAlphabet
(String identifier) resolveAlphabet
returns an appropriateAlphabet
for an arbitrary identifier. -
Uses of FiniteAlphabet in org.biojava.bio.program.xff
Methods in org.biojava.bio.program.xff with parameters of type FiniteAlphabetModifier and TypeMethodDescriptionstatic 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 -
Uses of FiniteAlphabet in org.biojava.bio.search
Constructors in org.biojava.bio.search with parameters of type FiniteAlphabetModifierConstructorDescriptionSeqContentPattern
(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 FiniteAlphabetModifier and TypeMethodDescriptionstatic final FiniteAlphabet
ProteinTools.getAlphabet()
Gets the protein alphabetstatic FiniteAlphabet
DNATools.getCodonAlphabet()
Gets the (DNA x DNA x DNA) Alphabetstatic FiniteAlphabet
RNATools.getCodonAlphabet()
Gets the (RNA x RNA x RNA) Alphabetstatic FiniteAlphabet
DNATools.getDNA()
Return the DNA alphabet.static FiniteAlphabet
DNATools.getDNAxDNA()
Gets the (DNA x DNA) Alphabetstatic FiniteAlphabet
NucleotideTools.getNucleotide()
Return the Nucleotide alphabet.static FiniteAlphabet
RNATools.getRNA()
Return the RNA alphabet.static final 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 FiniteAlphabetModifier and TypeMethodDescriptionstatic FiniteAlphabet
SeqIOTools.getAlphabet
(int identifier) Deprecated.getAlphabet
accepts a value which represents a sequence format and returns the relevantFiniteAlphabet
object.Constructors in org.biojava.bio.seq.io with parameters of type FiniteAlphabetModifierConstructorDescriptionConstruct a new NameTokenization, defaulting to case-insensitive.NameTokenization
(FiniteAlphabet fab, boolean caseSensitive) -
Uses of FiniteAlphabet in org.biojava.bio.symbol
Classes in org.biojava.bio.symbol that implement FiniteAlphabetModifier and TypeClassDescriptionclass
An abstract implementation ofAlphabet
.static class
A class to represent a finite contiguous subset of the infinite IntegerAlphabetclass
A simple no-frills implementation of the FiniteAlphabet interface.class
An alphabet that contains a single atomic symbol.final class
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 FiniteAlphabetModifier and TypeFieldDescriptionstatic final FiniteAlphabet
Alphabet.EMPTY_ALPHABET
A really useful static alphabet that is always empty.Methods in org.biojava.bio.symbol that return FiniteAlphabetModifier and TypeMethodDescriptionAlphabetIndex.getAlphabet()
Retrieve the alphabet that this indexes.DNAAmbPack.getAlphabet()
DNANoAmbPack.getAlphabet()
Packing.getAlphabet()
The FiniteAlphabet this packing is for.SuffixTree.getAlphabet()
Return the Alphabet containing all Symbols which might be found in this SuffixTree.protected FiniteAlphabet
SoftMaskedAlphabet.getDelegate()
The compound alpha that holds the symbols used by this wrapperstatic FiniteAlphabet
CodonPrefTools.getDinucleotideAlphabet()
returns an RNA dinucleotide alphabet.SoftMaskedAlphabet.getMaskedAlphabet()
Gets theAlphabet
upon which masking is being appliedMethods in org.biojava.bio.symbol with parameters of type FiniteAlphabetModifier and TypeMethodDescriptionstatic 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 anySymbol
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 FiniteAlphabetModifierConstructorDescriptionDummySymbolList
(FiniteAlphabet alpha, int length) SimpleGeneticCodeTable
(FiniteAlphabet source, FiniteAlphabet target) Creates a new instance of SimpleGeneticCodeTableSimpleManyToOneTranslationTable
(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 FiniteAlphabetModifierConstructorDescriptionNfa
(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 FiniteAlphabetMethods in org.biojava.utils.regex with parameters of type FiniteAlphabetModifier and TypeMethodDescriptionstatic 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 -
Uses of FiniteAlphabet in org.biojavax.bio.seq
Constructors in org.biojavax.bio.seq with parameters of type FiniteAlphabetModifierConstructorDescriptionCreates a new instance of InfinitelyAmbiguousSymbolList -
Uses of FiniteAlphabet in org.biojavax.ga.util
Methods in org.biojavax.ga.util that return FiniteAlphabetModifier and TypeMethodDescriptionstatic FiniteAlphabet
GATools.getBinaryAlphabet()
Gets a Reference to the FlyWeight GA_BinaryAlphabet
.Methods in org.biojavax.ga.util with parameters of type FiniteAlphabetModifier and TypeMethodDescriptionstatic OrderNDistribution
GATools.standardMutationDistribution
(FiniteAlphabet a) Makes a mutationDistribution
where the probability of aSymbol
being mutated to itself is zero and the probability of it being changed to any otherSymbol
in theAlphabet a
is1.0 / (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).