Uses of Interface
org.biojava.bio.symbol.FiniteAlphabet
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Packages that use FiniteAlphabet Package Description 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 outputorg.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.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 -
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Uses of FiniteAlphabet in org.biojava.bio.alignment
Methods in org.biojava.bio.alignment that return FiniteAlphabet Modifier and Type Method Description FiniteAlphabet
SubstitutionMatrix. getAlphabet()
Gives the alphabet used by this matrix.Methods in org.biojava.bio.alignment with parameters of type FiniteAlphabet Modifier and Type Method Description static 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 FiniteAlphabet Constructor Description 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, 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 FiniteAlphabet Constructor Description 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 Modifier and Type Method Description FiniteAlphabet
MarkovModel. stateAlphabet()
FiniteAlphabet of the states.FiniteAlphabet
SimpleMarkovModel. stateAlphabet()
FiniteAlphabet
WMAsMM. stateAlphabet()
FiniteAlphabet
MarkovModel. transitionsFrom(State source)
Returns the FiniteAlphabet of all states that have a transition from 'source'.FiniteAlphabet
SimpleMarkovModel. transitionsFrom(State from)
FiniteAlphabet
WMAsMM. transitionsFrom(State from)
FiniteAlphabet
MarkovModel. transitionsTo(State dest)
Returns the FiniteAlphabet of all states that have a transition to 'dest'.FiniteAlphabet
SimpleMarkovModel. transitionsTo(State to)
FiniteAlphabet
WMAsMM. transitionsTo(State to)
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Uses of FiniteAlphabet in org.biojava.bio.gui
Constructors in org.biojava.bio.gui with parameters of type FiniteAlphabet Constructor Description SimpleSymbolStyle(FiniteAlphabet alphabet)
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Uses of FiniteAlphabet in org.biojava.bio.program.abi
Fields in org.biojava.bio.program.abi declared as FiniteAlphabet Modifier and Type Field Description 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 Modifier and Type Method Description 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 Modifier and Type Method Description 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 Modifier and Type Method Description static 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 FiniteAlphabet Modifier and Type Method Description static Sequence
XFFTools. readXFF(File xffFile, String seqID, FiniteAlphabet alpha)
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Uses of FiniteAlphabet in org.biojava.bio.proteomics
Methods in org.biojava.bio.proteomics that return FiniteAlphabet Modifier and Type Method Description FiniteAlphabet
StructureTools. getStructure()
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Uses of FiniteAlphabet in org.biojava.bio.search
Constructors in org.biojava.bio.search with parameters of type FiniteAlphabet Constructor Description 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 Modifier and Type Method Description static 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 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 Modifier and Type Method Description static 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 FiniteAlphabet Constructor Description NameTokenization(FiniteAlphabet fab)
Construct a new NameTokenization, defaulting to case-insensitive.NameTokenization(FiniteAlphabet fab, boolean caseSensitive)
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Uses of FiniteAlphabet in org.biojava.bio.symbol
Classes in org.biojava.bio.symbol that implement FiniteAlphabet Modifier and Type Class Description class
AbstractAlphabet
An abstract implementation ofAlphabet
.static class
IntegerAlphabet.SubIntegerAlphabet
A class to represent a finite contiguous subset of the infinite IntegerAlphabetclass
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 Modifier and Type Field Description static FiniteAlphabet
Alphabet. EMPTY_ALPHABET
A really useful static alphabet that is always empty.Methods in org.biojava.bio.symbol that return FiniteAlphabet Modifier and Type Method Description FiniteAlphabet
AlphabetIndex. getAlphabet()
Retrieve the alphabet that this indexes.FiniteAlphabet
DNAAmbPack. getAlphabet()
FiniteAlphabet
DNANoAmbPack. getAlphabet()
FiniteAlphabet
Packing. getAlphabet()
The FiniteAlphabet this packing is for.FiniteAlphabet
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.FiniteAlphabet
SoftMaskedAlphabet. getMaskedAlphabet()
Gets theAlphabet
upon which masking is being appliedMethods in org.biojava.bio.symbol with parameters of type FiniteAlphabet Modifier and Type Method Description 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 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 FiniteAlphabet Constructor Description DummySymbolList(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)
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Uses of FiniteAlphabet in org.biojava.utils.automata
Constructors in org.biojava.utils.automata with parameters of type FiniteAlphabet Constructor Description Nfa(String name, FiniteAlphabet alfa)
PatternBlitz(FiniteAlphabet alfa, org.biojava.utils.automata.StateMachineToolkit factory)
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Uses of FiniteAlphabet in org.biojava.utils.regex
Methods in org.biojava.utils.regex that return FiniteAlphabet Modifier and Type Method Description FiniteAlphabet
Pattern. getAlphabet()
Methods in org.biojava.utils.regex with parameters of type FiniteAlphabet Modifier and Type Method Description 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 Constructor Description Search(FiniteAlphabet alfa)
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Uses of FiniteAlphabet in org.biojavax.bio.seq
Constructors in org.biojavax.bio.seq with parameters of type FiniteAlphabet Constructor Description 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 Modifier and Type Method Description static FiniteAlphabet
GATools. getBinaryAlphabet()
Gets a Reference to the FlyWeight GA_BinaryAlphabet
.Methods in org.biojavax.ga.util with parameters of type FiniteAlphabet Modifier and Type Method Description static 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).
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