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## Uses of Package
de.jstacs.data

Packages that use de.jstacs.data
de.jstacs.algorithms | Provides classes for algorithms on graphs.
de.jstacs.classifier | This package provides the framework for any classifier.
de.jstacs.classifier.assessment | This package allows to assess classifiers.
de.jstacs.classifier.modelBased | Provides the classes for `Classifier`s that are based on `Model`s
de.jstacs.classifier.scoringFunctionBased | Provides the classes for `Classifier`s that are based on `ScoringFunction`s.
de.jstacs.classifier.scoringFunctionBased.cll | Provides the implementation of the log conditional likelihood as an `OptimizableFunction` and a classifier that uses log conditional likelihood or supervised posterior to learn the parameters of a set of `ScoringFunctions`
de.jstacs.classifier.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.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.models | Provides the interface `Model` and its abstract implementation `AbstractModel`, which is the super class of all other models.
de.jstacs.models.discrete |
de.jstacs.models.discrete.inhomogeneous | This package contains various inhomogeneous models.
de.jstacs.models.discrete.inhomogeneous.parameters |
de.jstacs.models.discrete.inhomogeneous.shared |
de.jstacs.models.mixture | This package is the super package for any mixture model.
de.jstacs.models.mixture.gibbssampling | This package contains many classes that can be used while a Gibbs sampling.
de.jstacs.models.utils |
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.scoringFunctions | Provides `ScoringFunction`s that can be used in a `ScoreClassifier`.
de.jstacs.scoringFunctions.directedGraphicalModels | Provides `ScoringFunction`s that are equivalent to directed graphical models.
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures | Provides the facilities to learn the structure of a `BayesianNetworkScoringFunction`.
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures | Provides the facilities to learn the structure of a `BayesianNetworkScoringFunction` as a Bayesian tree using a number of measures to define a rating of structures
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures | Provides the facilities to learn the structure of a `BayesianNetworkScoringFunction` as a permuted Markov model using a number of measures to define a rating of structures
de.jstacs.scoringFunctions.homogeneous | Provides `ScoringFunction`s that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.scoringFunctions.mix | Provides `ScoringFunction`s that are mixtures of other `ScoringFunction`s.

Classes in de.jstacs.data used by de.jstacs.algorithms
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.classifier
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .
Sample This is the class for any sample of sequences.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.classifier.assessment
Sample This is the class for any sample of sequences.
Sample.PartitionMethod This enum defines different partition method for a sample.

Classes in de.jstacs.data used by de.jstacs.classifier.modelBased
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .
Sample This is the class for any sample of sequences.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.classifier.scoringFunctionBased
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .
Sample This is the class for any sample of sequences.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.classifier.scoringFunctionBased.cll
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .
Sample This is the class for any sample of sequences.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.classifier.utils
Sample This is the class for any sample of sequences.

Classes in de.jstacs.data used by de.jstacs.data
Alphabet Class for an Alphabet.
Alphabet.AlphabetParameterSet The super class for the `ParameterSet` of any `Alphabet`.
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .
AlphabetContainerParameterSet Class for the `ParameterSet` of an `AlphabetContainer`.
AlphabetContainerParameterSet.AlphabetArrayParameterSet Class for the parameters of an array of `Alphabet`s of defined length.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet Class for the parameters of an array of `Alphabet`s where each alphabet may be used for one or more sections of positions.
EmptySampleException An EmptySampleException will be thrown if no sequence is in a Sample (i.e. the Sample is empty).
Sample This is the class for any sample of sequences.
Sample.PartitionMethod This enum defines different partition method for a sample.
Sample.WeightedSampleFactory.SortOperation This enum defines the different types of sort operation that can be performed while creating a `Sample.WeightedSampleFactory`.
Sequence This is the main class for all sequences.
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
Alphabet Class for an Alphabet.
Alphabet.AlphabetParameterSet The super class for the `ParameterSet` of any `Alphabet`.

Classes in de.jstacs.data used by de.jstacs.data.bioJava
Sample This is the class for any sample of sequences.

Classes in de.jstacs.data used by de.jstacs.data.sequences
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.io
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .

Classes in de.jstacs.data used by de.jstacs.models
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .
Sample This is the class for any sample of sequences.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.discrete
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .
Sample This is the class for any sample of sequences.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.discrete.inhomogeneous
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .
Sample This is the class for any sample of sequences.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.discrete.inhomogeneous.parameters
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .

Classes in de.jstacs.data used by de.jstacs.models.discrete.inhomogeneous.shared
Sample This is the class for any sample of sequences.

Classes in de.jstacs.data used by de.jstacs.models.mixture
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .
Sample This is the class for any sample of sequences.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.mixture.gibbssampling
Sample This is the class for any sample of sequences.

Classes in de.jstacs.data used by de.jstacs.models.utils
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .
Sample This is the class for any sample of sequences.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.parameters
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .

Classes in de.jstacs.data used by de.jstacs.results
Sample This is the class for any sample of sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .
Sample This is the class for any sample of sequences.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.directedGraphicalModels
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .
Sample This is the class for any sample of sequences.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures
Sample This is the class for any sample of sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures
Sample This is the class for any sample of sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures
Sample This is the class for any sample of sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.homogeneous
AlphabetContainer The container for some alphabets used in a sequence, sample, model or ... .
Sample This is the class for any sample of sequences.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.mix
Sample This is the class for any sample of sequences.
Sequence This is the main class for all sequences.

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