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 used 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 exsisting 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, boolean discrete)
          Creates a new AlphabetArrayParameterSet from an array of Alphabets and the information if all alphabets are discrete
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(Alphabet[] alphabets, int[] indexes, boolean discrete)
          Creates a new SectionDefinedAlphabetParameterSet from an array of Alphabets, an array of indexes that define the index of the Alphabet<>/code> in alphabets/code> 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 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 for 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)