de.jstacs.data.alphabets

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Package de.jstacs.data.alphabets

Provides classes for the representation of discrete and continuous alphabets, including a DNAAlphabet for the most common case of DNA-sequences

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Description

Class Summary
Alphabet	Class for a set of symbols, i.e. an `Alphabet`.
Alphabet.AlphabetParameterSet<T extends Alphabet>	The super class for the `InstanceParameterSet` of any `Alphabet`.
ComplementableDiscreteAlphabet	This abstract class indicates that an alphabet can be used to compute the complement.
ContinuousAlphabet	Class for a continuous alphabet.
ContinuousAlphabet.ContinuousAlphabetParameterSet	Class for the `ParameterSet` of a `ContinuousAlphabet`.
DiscreteAlphabet	Class for an alphabet that consists of arbitrary `String`s.
DiscreteAlphabet.DiscreteAlphabetParameterSet	Class for the `ParameterSet` of a `DiscreteAlphabet`.
DiscreteAlphabetMapping	This class implements the transformation of discrete values to other discrete values which define a `DiscreteAlphabet`.
DNAAlphabet	This class implements the discrete alphabet that is used for DNA.
DNAAlphabet.DNAAlphabetParameterSet	The parameter set for a `DNAAlphabet`.
DNAAlphabetContainer	This class implements a singleton for an `AlphabetContainer` that can be used for DNA.
DNAAlphabetContainer.DNAAlphabetContainerParameterSet	This class implements a singleton for the `ParameterSet` of a `DNAAlphabetContainer`.
GenericComplementableDiscreteAlphabet	This class implements an generic complementable discrete alphabet.
GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet	This class is used as container for the parameters of a `GenericComplementableDiscreteAlphabet`.
ProteinAlphabet	This class implements the discrete alphabet that is used for proteins (one letter code).
ProteinAlphabet.ProteinAlphabetParameterSet	The parameter set for a `ProteinAlphabet`.

Exception Summary
DoubleSymbolException	A `DoubleSymbolException` is thrown if a symbol occurred more than once in an alphabet.

Package de.jstacs.data.alphabets Description

Provides classes for the representation of discrete and continuous alphabets, including a DNAAlphabet for the most common case of DNA-sequences.