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## Uses of Package
de.jstacs.data.alphabets

Packages that use de.jstacs.data.alphabets
de.jstacs.data | Provides classes for the representation of data.
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
de.jstacs.data.sequences | Provides classes for representing sequences.
de.jstacs.sequenceScores.statisticalModels.differentiable | Provides all `DifferentiableStatisticalModel`s, which can compute the gradient with respect to their parameters for a given input `Sequence`.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture | Provides `DifferentiableSequenceScore`s that are mixtures of other `DifferentiableSequenceScore`s.

Classes in de.jstacs.data.alphabets used by de.jstacs.data
Alphabet Class for a set of symbols, i.e. an `Alphabet`.
DoubleSymbolException A `DoubleSymbolException` is thrown if a symbol occurred more than once in an alphabet.

Classes in de.jstacs.data.alphabets used by de.jstacs.data.alphabets
Alphabet Class for a set of symbols, i.e. an `Alphabet`.
Alphabet.AlphabetParameterSet 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.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`.
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`.
DoubleSymbolException A `DoubleSymbolException` is thrown if a symbol occurred more than once in an 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`.

Classes in de.jstacs.data.alphabets used by de.jstacs.data.sequences
DiscreteAlphabetMapping This class implements the transformation of discrete values to other discrete values which define a `DiscreteAlphabet`.

Classes in de.jstacs.data.alphabets used by de.jstacs.sequenceScores.statisticalModels.differentiable
DiscreteAlphabetMapping This class implements the transformation of discrete values to other discrete values which define a `DiscreteAlphabet`.

Classes in de.jstacs.data.alphabets used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture
ComplementableDiscreteAlphabet This abstract class indicates that an alphabet can be used to compute the complement.

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