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## Uses of Package
de.jstacs.data

Packages that use de.jstacs.data
de.jstacs.classifiers | This package provides the framework for any classifier.
de.jstacs.classifiers.assessment | This package allows to assess classifiers.
de.jstacs.classifiers.differentiableSequenceScoreBased | Provides the classes for `Classifier`s that are based on `SequenceScore`s.
de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix | Provides an implementation of a classifier that allows to train the parameters of a set of `DifferentiableStatisticalModel`s by a unified generative-discriminative learning principle
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling | Provides the classes for `AbstractScoreBasedClassifier`s that are based on `SamplingDifferentiableStatisticalModel`s and that sample parameters using the Metropolis-Hastings algorithm.
de.jstacs.classifiers.trainSMBased | Provides the classes for `Classifier`s that are based on `TrainableStatisticalModel`s
de.jstacs.classifiers.utils | Provides some useful classes for working with classifiers
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
de.jstacs.data.bioJava | Provides an adapter between the representation of data in BioJava and the representation used in Jstacs.
de.jstacs.data.sequences | Provides classes for representing sequences.
de.jstacs.data.sequences.annotation | Provides the facilities to annotate `Sequence`s using a number of pre-defined annotation types, or additional implementations of the `SequenceAnnotation` class
de.jstacs.io | Provides classes for reading data from and writing to a file and storing a number of datatypes, including all primitives, arrays of primitives, and `Storable`s to an XML-representation
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer
de.jstacs.parameters | This package provides classes for parameters that establish a general convention for the description of parameters as defined in the `Parameter`-interface.
de.jstacs.results | This package provides classes for results and sets of results.
de.jstacs.sampling | This package contains many classes that can be used while a sampling.
de.jstacs.sequenceScores | Provides all `SequenceScore`s, which can be used to score a `Sequence`, typically using some model assumptions.
de.jstacs.sequenceScores.differentiable |
de.jstacs.sequenceScores.differentiable.logistic |
de.jstacs.sequenceScores.statisticalModels | Provides all `StatisticalModel`s, which can compute a proper (i.e., normalized) likelihood over the input space of sequences.
de.jstacs.sequenceScores.statisticalModels.differentiable | Provides all `DifferentiableStatisticalModel`s, which can compute the gradient with respect to their parameters for a given input `Sequence`.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels | Provides `DifferentiableStatisticalModel`s that are directed graphical models.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures | Provides the facilities to learn the structure of a `BayesianNetworkDiffSM`.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures | Provides the facilities to learn the structure of a `BayesianNetworkDiffSM` as a Bayesian tree using a number of measures to define a rating of structures
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures | Provides the facilities to learn the structure of a `BayesianNetworkDiffSM` as a permuted Markov model using a number of measures to define a rating of structures
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous | Provides `DifferentiableStatisticalModel`s that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture | Provides `DifferentiableSequenceScore`s that are mixtures of other `DifferentiableSequenceScore`s.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif |
de.jstacs.sequenceScores.statisticalModels.trainable | Provides all `TrainableStatisticalModel`s, which can be learned from a single `DataSet`.
de.jstacs.sequenceScores.statisticalModels.trainable.discrete |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous | This package contains various inhomogeneous models.
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm | The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models | The package provides different implementations of hidden Markov models based on `AbstractHMM`
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states | The package provides all interfaces and classes for states used in hidden Markov models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete |
de.jstacs.sequenceScores.statisticalModels.trainable.mixture | This package is the super package for any mixture model.
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif |
de.jstacs.utils | This package contains a bundle of useful classes and interfaces like ...

Classes in de.jstacs.data used by de.jstacs.classifiers
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.classifiers.assessment
DataSet This is the class for any data set of `Sequence`s.
DataSet.PartitionMethod This `enum` defines different partition methods for a `DataSet`.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs.data used by de.jstacs.classifiers.differentiableSequenceScoreBased
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
AlphabetContainer.AlphabetContainerType This `enum` defines types of `AlphabetContainer`s.
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.classifiers.differentiableSequenceScoreBased.sampling
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.classifiers.trainSMBased
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.classifiers.utils
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.data
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
AlphabetContainer.AbstractAlphabetContainerParameterSet This class is the super class of any `InstanceParameterSet` for `AlphabetContainer`.
AlphabetContainer.AlphabetContainerType This `enum` defines types of `AlphabetContainer`s.
AlphabetContainerParameterSet Class for the `AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet` of an `AlphabetContainer`.
AlphabetContainerParameterSet.AlphabetArrayParameterSet Class for the parameters of an array of `Alphabet`s of defined length.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet Class for the parameter set of an array of `Alphabet`s where each `Alphabet` may be used for one or more sections of positions.
DataSet This is the class for any data set of `Sequence`s.
DataSet.PartitionMethod This `enum` defines different partition methods for a `DataSet`.
DataSet.WeightedDataSetFactory.SortOperation This `enum` defines the different types of sort operations that can be performed while creating a `DataSet.WeightedDataSetFactory`.
DinucleotideProperty This `enum` defines physicochemical, conformational, and letter-based dinucleotide properties of nucleotide sequences.
DinucleotideProperty.HowCreated This enum defines the origins of nucleotide properties
DinucleotideProperty.Smoothing Abstract class for methods that smooth a series of real values.
DinucleotideProperty.Type This enum defines the types of dinucleotide properties.
EmptyDataSetException An `EmptyDataSetException` will be thrown if no `Sequence` is in a `DataSet` (i.e. the `DataSet` is empty).
RecyclableSequenceEnumerator This interface extends `Enumeration` of `Sequence`s by declaring an additional method that allows to reuse the Enumeration.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.
WrongLengthException A `WrongLengthException` is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.data.alphabets
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
AlphabetContainer.AbstractAlphabetContainerParameterSet This class is the super class of any `InstanceParameterSet` for `AlphabetContainer`.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs.data used by de.jstacs.data.bioJava
DataSet This is the class for any data set of `Sequence`s.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs.data used by de.jstacs.data.sequences
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.
EmptyDataSetException An `EmptyDataSetException` will be thrown if no `Sequence` is in a `DataSet` (i.e. the `DataSet` is empty).
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.
WrongLengthException A `WrongLengthException` is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.data.sequences.annotation
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .

Classes in de.jstacs.data used by de.jstacs.io
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .

Classes in de.jstacs.data used by de.jstacs.motifDiscovery
DataSet This is the class for any data set of `Sequence`s.
DataSet.WeightedDataSetFactory This class enables you to eliminate `Sequence`s that occur more than once in one or more `DataSet`s.
DataSet.WeightedDataSetFactory.SortOperation This `enum` defines the different types of sort operations that can be performed while creating a `DataSet.WeightedDataSetFactory`.
RecyclableSequenceEnumerator This interface extends `Enumeration` of `Sequence`s by declaring an additional method that allows to reuse the Enumeration.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.
WrongLengthException A `WrongLengthException` is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.parameters
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
AlphabetContainer.AlphabetContainerType This `enum` defines types of `AlphabetContainer`s.

Classes in de.jstacs.data used by de.jstacs.results
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.sampling
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.sequenceScores
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.differentiable
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.
WrongLengthException A `WrongLengthException` is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.differentiable.logistic
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture
DataSet This is the class for any data set of `Sequence`s.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.
WrongLengthException A `WrongLengthException` is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.
EmptyDataSetException An `EmptyDataSetException` will be thrown if no `Sequence` is in a `DataSet` (i.e. the `DataSet` is empty).
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared
DataSet This is the class for any data set of `Sequence`s.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .
DataSet This is the class for any data set of `Sequence`s.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models
DataSet This is the class for any data set of `Sequence`s.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.
WrongLengthException A `WrongLengthException` is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states
WrongLengthException A `WrongLengthException` is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ... .

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture
DataSet This is the class for any data set of `Sequence`s.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif
DataSet This is the class for any data set of `Sequence`s.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs.data used by de.jstacs.utils
DataSet This is the class for any data set of `Sequence`s.

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