Uses of Package
de.jstacs.data.alphabets

Packages that use de.jstacs.data.alphabets

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.
de.jstacs.data.sequences	Provides classes for representing sequences. The implementations of sequences currently include DiscreteSequences prepared for alphabets of different sizes, and ArbitrarySequences that may contain continuous values as well. As sub-package provides the facilities to annotate Sequences.
de.jstacs.sequenceScores.statisticalModels.differentiable	Provides all DifferentiableStatisticalModels, which can compute the gradient with respect to their parameters for a given input Sequence.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture	Provides DifferentiableSequenceScores that are mixtures of other DifferentiableSequenceScores.
de.jstacs.utils	This package contains a bundle of useful classes and interfaces like ...

Classes in de.jstacs.data.alphabets used by de.jstacs.data

Alphabet
Class for a set of symbols, i.e.

DoubleSymbolException
A DoubleSymbolException is thrown if a symbol occurred more than once in an alphabet.

Classes in de.jstacs.data.alphabets used by de.jstacs.data.alphabets

Alphabet
Class for a set of symbols, i.e.

Alphabet.AlphabetParameterSet
The super class for the InstanceParameterSet of any Alphabet.

ComplementableDiscreteAlphabet
This abstract class indicates that an alphabet can be used to compute the complement.

ContinuousAlphabet.ContinuousAlphabetParameterSet
Class for the ParameterSet of a ContinuousAlphabet.

DiscreteAlphabet
Class for an alphabet that consists of arbitrary Strings.

DiscreteAlphabet.DiscreteAlphabetParameterSet
Class for the ParameterSet of a DiscreteAlphabet.

DNAAlphabet
This class implements the discrete alphabet that is used for DNA.

DNAAlphabet.DNAAlphabetParameterSet
The parameter set for a DNAAlphabet.

DNAAlphabetContainer
This class implements a singleton for an AlphabetContainer that can be used for DNA.

DNAAlphabetContainer.DNAAlphabetContainerParameterSet
This class implements a singleton for the ParameterSet of a DNAAlphabetContainer.

DoubleSymbolException
A DoubleSymbolException is thrown if a symbol occurred more than once in an alphabet.

GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet
This class is used as container for the parameters of a GenericComplementableDiscreteAlphabet.

ProteinAlphabet
This class implements the discrete alphabet that is used for proteins (one letter code).

ProteinAlphabet.ProteinAlphabetParameterSet
The parameter set for a ProteinAlphabet.

Classes in de.jstacs.data.alphabets used by de.jstacs.data.sequences

DiscreteAlphabetMapping
This class implements the transformation of discrete values to other discrete values which define a DiscreteAlphabet.

Classes in de.jstacs.data.alphabets used by de.jstacs.sequenceScores.statisticalModels.differentiable

DiscreteAlphabetMapping
This class implements the transformation of discrete values to other discrete values which define a DiscreteAlphabet.

Classes in de.jstacs.data.alphabets used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture

ComplementableDiscreteAlphabet
This abstract class indicates that an alphabet can be used to compute the complement.

Classes in de.jstacs.data.alphabets used by de.jstacs.utils

ComplementableDiscreteAlphabet
This abstract class indicates that an alphabet can be used to compute the complement.