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 two alphabets are consistent, i.e. both alphabets use the same symbols.
static AlphabetContainer	AlphabetContainer.getSimplifiedAlphabetContainer(Alphabet[] abc, int[] assignment) This method creates a new AlphabetContainer that uses as less as possible alphabets 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 alphabets into an existing AlphabetContainer.

Constructors in de.jstacs.data with parameters of type Alphabet

AlphabetContainer(Alphabet abc)
This constructor creates a simple AlphabetContainer.

AlphabetContainer(Alphabet[] abc)
This constructor creates an AlphabetContainer with different alphabets for each position.

AlphabetContainer(Alphabet[] abc, int[] assignment)
This constructor creates an AlphabetContainer that uses different alphabets.

AlphabetContainerParameterSet.AlphabetArrayParameterSet(Alphabet[] alphabets, AlphabetContainer.AlphabetContainerType type)
Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet from an array of Alphabets and the information if all alphabets are discrete.

AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(Alphabet[] alphabets, int[] indexes)
Creates a new AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet from an array of Alphabets, an array of indexes that define the index of the Alphabet in alphabets belonging to that position in indexes and a parameter if the alphabets may be discrete only.

AlphabetContainerParameterSet(Alphabet alph)
Creates a new AlphabetContainerParameterSet from a single Alphabet.

AlphabetContainerParameterSet(Alphabet[] alphabets)
Creates a new AlphabetContainerParameterSet from an array of Alphabets.

AlphabetContainerParameterSet(Alphabet[] alphabets, int[] indexes)
Creates a new AlphabetContainerParameterSet from an array of Alphabets and an array of ints defining the number of the alphabet in alphabets that is used for that position in indexes.

Constructor parameters in de.jstacs.data with type arguments of type Alphabet

Alphabet.AlphabetParameterSet(Class<? extends Alphabet> instanceClass)
Creates a new 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 Strings.
class	DNAAlphabet This class implements the alphabet that is used for DNA.

Methods in de.jstacs.data.alphabets with parameters of type Alphabet

int	DiscreteAlphabet.compareTo(Alphabet b)
int	ContinuousAlphabet.compareTo(Alphabet a)