Package 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.

See: Description

Class Summary

Class	Description
Alphabet	Class for a set of symbols, i.e.
Alphabet.AlphabetParameterSet<T extends Alphabet>	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	Class for a continuous alphabet.
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.
DiscreteAlphabetMapping	This class implements the transformation of discrete values to other discrete values which define 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.
GenericComplementableDiscreteAlphabet	This class implements an generic complementable discrete alphabet.
GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet	This class is used as container for the parameters of a GenericComplementableDiscreteAlphabet.
IUPACDNAAlphabet	This class implements a discrete alphabet for the IUPAC DNA code.
IUPACDNAAlphabet.IUPACDNAAlphabetParameterSet	The parameter set for a IUPACDNAAlphabet.
ProteinAlphabet	This class implements the discrete alphabet that is used for proteins (one letter code).
ProteinAlphabet.ProteinAlphabetParameterSet	The parameter set for a ProteinAlphabet.

Exception Summary

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

Package de.jstacs.data.alphabets Description

Provides classes for the representation of discrete and continuous alphabets, including a DNAAlphabet for the most common case of DNA-sequences.