Uses of Class
de.jstacs.data.alphabets.DiscreteAlphabet

Packages that use DiscreteAlphabet

Package	Description
de.jstacs.clustering.distances
de.jstacs.data	Provides classes for the representation of data. The base classes to represent data are Alphabet and AlphabetContainer for representing alphabets, Sequence and its sub-classes to represent continuous and discrete sequences, and DataSet to represent data sets comprising a set of sequences.
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 DiscreteAlphabet in de.jstacs.clustering.distances

Methods in de.jstacs.clustering.distances with parameters of type DiscreteAlphabet

Modifier and Type	Method and Description
static CyclicSequenceAdaptor[]	RandomSequenceScoreDistance.createSequences(DiscreteAlphabet alphabet, int n) Creates a new random sequence of the given length and alphabet.

Constructors in de.jstacs.clustering.distances with parameters of type DiscreteAlphabet

Constructor and Description
RandomSequenceScoreDistance(DiscreteAlphabet alphabet, int n, boolean exp) Creates a distance using a random sequence of length .
SequenceScoreDistance(DiscreteAlphabet alphabet, int n, boolean exp) Creates a new distance.

Uses of DiscreteAlphabet in de.jstacs.data

Methods in de.jstacs.data with parameters of type DiscreteAlphabet

Modifier and Type	Method and Description
static CyclicSequenceAdaptor[]	DeBruijnSequenceGenerator.generate(DiscreteAlphabet alphabet, int n) Generates a De Bruijn sequence of length , where A denotes the alphabet.
static CyclicSequenceAdaptor[]	DeBruijnGraphSequenceGenerator.generate(DiscreteAlphabet alphabet, int n) Generates a De Bruijn sequence of length , where A denotes the alphabet.
static CyclicSequenceAdaptor	DeBruijnSequenceGenerator.generate(DiscreteAlphabet alphabet, int n, int alphabetShift) Generates a De Bruijn sequence using the supplied alphabet and the given alphabet shift, i.e., for a cyclic shift of the symbols of the alphabet.
static CyclicSequenceAdaptor	DeBruijnGraphSequenceGenerator.generate(DiscreteAlphabet alphabet, int n, int alphabetShift) Generates a De Bruijn sequence using the supplied alphabet and the given alphabet shift, i.e., for a cyclic shift of the symbols of the alphabet.

Uses of DiscreteAlphabet in de.jstacs.data.alphabets

Subclasses of DiscreteAlphabet in de.jstacs.data.alphabets

Modifier and Type	Class and Description
class	ComplementableDiscreteAlphabet This abstract class indicates that an alphabet can be used to compute the complement.
class	DNAAlphabet This class implements the discrete alphabet that is used for DNA.
class	GenericComplementableDiscreteAlphabet This class implements an generic complementable discrete alphabet.
class	IUPACDNAAlphabet This class implements a discrete alphabet for the IUPAC DNA code.
class	ProteinAlphabet This class implements the discrete alphabet that is used for proteins (one letter code).

Methods in de.jstacs.data.alphabets that return DiscreteAlphabet

Modifier and Type	Method and Description
DiscreteAlphabet	DiscreteAlphabetMapping.getNewAlphabet() Returns the new Alphabet that is used for mapping.

Constructors in de.jstacs.data.alphabets with parameters of type DiscreteAlphabet

Constructor and Description
DiscreteAlphabetMapping(int[] newValues, DiscreteAlphabet newAlphabet) The main constructor creating a DiscreteAlphabetMapping.

Constructor parameters in de.jstacs.data.alphabets with type arguments of type DiscreteAlphabet

Constructor and Description
DiscreteAlphabetParameterSet(Class<? extends DiscreteAlphabet> clazz) This constructor should only be used for parameter sets that are intended to created subclasses of DiscreteAlphabet.