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## Uses of Class
de.jstacs.data.Alphabet

Packages that use Alphabet
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

Uses of Alphabet in de.jstacs.data

Methods in de.jstacs.data that return Alphabet
`Alphabet` | `AlphabetContainer.getAlphabetAt(int pos)` Returns the underlying `Alphabet` of position `pos`.

Methods in de.jstacs.data with parameters of type Alphabet
`boolean` | `Alphabet.checkConsistency(Alphabet a)` Checks if this `Alphabet` is consistent consistent with another `Alphabet`, i.e. both `Alphabet`s use the same symbols.
`static AlphabetContainer` | `AlphabetContainer.getSimplifiedAlphabetContainer(Alphabet[] abc, int[] assignment)` This method creates a new `AlphabetContainer` that uses as less as possible `Alphabet`s to describe the container.
`static AlphabetContainer` | `AlphabetContainer.insertAlphabet(AlphabetContainer aC, Alphabet a, boolean[] useNewAlphabet)` This method may be used to construct a new `AlphabetContainer` by incorporating additional `Alphabet`s into an existing `AlphabetContainer`.

Constructors in de.jstacs.data with parameters of type Alphabet
`AlphabetContainer(Alphabet abc)` Creates a new simple `AlphabetContainer`.
`AlphabetContainer(Alphabet[] abc)` Creates a new `AlphabetContainer` with different `Alphabet`s for each position.
`AlphabetContainer(Alphabet[] abc, int[] assignment)` Creates a new `AlphabetContainer` that uses different `Alphabet`s.
`AlphabetContainerParameterSet.AlphabetArrayParameterSet(Alphabet[] alphabets, AlphabetContainer.AlphabetContainerType type)` Creates a new `AlphabetContainerParameterSet.AlphabetArrayParameterSet` from an array of `Alphabet`s and the information about the `type` of the `Alphabet`s.
`AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(Alphabet[] alphabets, int[] indexes)` Creates a new `AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet` from an array of `Alphabet`s and an array of indexes that define the index of the `Alphabet` in `alphabets` belonging to that position in `indexes`.
`AlphabetContainerParameterSet(Alphabet alph)` Creates a new `AlphabetContainerParameterSet` of a simple `AlphabetContainer` from a single `Alphabet`.
`AlphabetContainerParameterSet(Alphabet[] alphabets)` Creates a new `AlphabetContainerParameterSet` from an array of `Alphabet`s.
`AlphabetContainerParameterSet(Alphabet[] alphabets, int[] indexes)` Creates a new `AlphabetContainerParameterSet` from an array of `Alphabet`s and an array of `int`s defining the `Alphabet` index `i` in `alphabets` that is used for position `i`.

Constructor parameters in de.jstacs.data with type arguments of type Alphabet
`Alphabet.AlphabetParameterSet(Class<? extends Alphabet> instanceClass)` Creates a new `Alphabet.AlphabetParameterSet` from the class that can be instantiated using this `Alphabet.AlphabetParameterSet`.

Uses of Alphabet in de.jstacs.data.alphabets

Subclasses of Alphabet in de.jstacs.data.alphabets
`class` | `ComplementableDiscreteAlphabet` This abstract class indicates that an alphabet can be used to compute the complement.
`class` | `ContinuousAlphabet` Class for a continuous alphabet.
`class` | `DiscreteAlphabet` Class for an alphabet that consists of arbitrary `String`s.
`class` | `DNAAlphabet` This class implements the discrete alphabet that is used for DNA.
`class` | `GenericComplementableDiscreteAlphabet` This class implements an generic complementable discrete alphabet.

Methods in de.jstacs.data.alphabets with parameters of type Alphabet
`int` | `DiscreteAlphabet.compareTo(Alphabet b)`
`int` | `ContinuousAlphabet.compareTo(Alphabet a)`

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