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

Packages that use Alphabet

Package	Description
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 Alphabet in de.jstacs.data

Methods in de.jstacs.data that return Alphabet

Modifier and Type	Method and Description
Alphabet	AlphabetContainer.getAlphabetAt(int pos) Returns the underlying Alphabet of position pos.

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

Modifier and Type	Method and Description
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

Constructor and Description
AlphabetArrayParameterSet(Alphabet[] alphabets, AlphabetContainer.AlphabetContainerType type) Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet from an array of Alphabets and the information about the type of the Alphabets.
AlphabetContainer(Alphabet... abc) Creates a new AlphabetContainer with different Alphabets for each position.
AlphabetContainer(Alphabet abc) Creates a new simple AlphabetContainer.
AlphabetContainer(Alphabet[] abc, int[] assignment) Creates a new AlphabetContainer that uses different Alphabets.
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 Alphabets.
AlphabetContainerParameterSet(Alphabet[] alphabets, int[] indexes) Creates a new AlphabetContainerParameterSet from an array of Alphabets and an array of ints defining the Alphabet index i in alphabets that is used for position i.
AlphabetContainerParameterSet(Class<? extends AlphabetContainer> instanceClass, Alphabet... alphabets) /** Creates a new AlphabetContainerParameterSet from an array of Alphabets for a given sub-class of AlphabetContainer.
SectionDefinedAlphabetParameterSet(Alphabet[] alphabets, int[] indexes) Creates a new AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet from an array of Alphabets and an array of indexes that define the index of the Alphabet in alphabets belonging to that position in indexes.

Uses of Alphabet in de.jstacs.data.alphabets

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

Modifier and Type	Class and Description
static class	Alphabet.AlphabetParameterSet<T extends Alphabet> The super class for the InstanceParameterSet of any Alphabet.

Subclasses of Alphabet 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	ContinuousAlphabet Class for a continuous alphabet.
class	DiscreteAlphabet Class for an alphabet that consists of arbitrary Strings.
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 types with arguments of type Alphabet

Modifier and Type	Method and Description
abstract InstanceParameterSet<? extends Alphabet>	Alphabet.getCurrentParameterSet()

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

Modifier and Type	Method and Description
boolean	Alphabet.checkConsistency(Alphabet a) Checks if this Alphabet is consistent consistent with another Alphabet, i.e.
int	DiscreteAlphabet.compareTo(Alphabet b)
int	ContinuousAlphabet.compareTo(Alphabet a)