| 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. |
| 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 ...
|
| Class and Description |
|---|
| DiscreteAlphabet
Class for an alphabet that consists of arbitrary
Strings. |
| Class and Description |
|---|
| Alphabet
Class for a set of symbols, i.e.
|
| DiscreteAlphabet
Class for an alphabet that consists of arbitrary
Strings. |
| DoubleSymbolException
A
DoubleSymbolException is thrown if a symbol occurred more than once
in an alphabet. |
| Class and Description |
|---|
| 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. |
| 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. |
| Class and Description |
|---|
| DiscreteAlphabetMapping
This class implements the transformation of discrete values to other discrete values
which define a
DiscreteAlphabet. |
| Class and Description |
|---|
| DiscreteAlphabetMapping
This class implements the transformation of discrete values to other discrete values
which define a
DiscreteAlphabet. |
| Class and Description |
|---|
| ComplementableDiscreteAlphabet
This abstract class indicates that an alphabet can be used to compute the
complement.
|
| Class and Description |
|---|
| ComplementableDiscreteAlphabet
This abstract class indicates that an alphabet can be used to compute the
complement.
|