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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.homogeneous |
de.jstacs.models.discrete.homogeneous.parameters |
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.mixture.motif |
de.jstacs.models.utils |
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.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.
de.jstacs.scoringFunctions.mix.motifSearch |

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 `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
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 `Sequence`s.
Sample.PartitionMethod This `enum` defines different partition methods for a `Sample`.

Classes in de.jstacs.data used by de.jstacs.classifier.modelBased
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.classifier.scoringFunctionBased
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
AlphabetContainer.AlphabetContainerType This `enum` defines types of `AlphabetContainer`s.
Sample This is the class for any sample of `Sequence`s.
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 `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.

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

Classes in de.jstacs.data used by de.jstacs.data
Alphabet Class for a set of symbols, i.e. an `Alphabet`.
Alphabet.AlphabetParameterSet The super class for the `InstanceParameterSet` of any `Alphabet`.
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
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.
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 `Sequence`s.
Sample.PartitionMethod This `enum` defines different partition methods for a `Sample`.
Sample.WeightedSampleFactory.SortOperation This `enum` defines the different types of sort operations 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 a set of symbols, i.e. an `Alphabet`.
Alphabet.AlphabetParameterSet The super class for the `InstanceParameterSet` of any `Alphabet`.

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

Classes in de.jstacs.data used by de.jstacs.data.sequences
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sequence This is the main class for all sequences.

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

Classes in de.jstacs.data used by de.jstacs.models
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.discrete
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.discrete.homogeneous
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 `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.discrete.homogeneous.parameters
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .

Classes in de.jstacs.data used by de.jstacs.models.discrete.inhomogeneous
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
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 `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .

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

Classes in de.jstacs.data used by de.jstacs.models.mixture
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.mixture.gibbssampling
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.models.mixture.motif
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.utils
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

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

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

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

Classes in de.jstacs.data used by de.jstacs.scoringFunctions
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.directedGraphicalModels
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
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 `Sequence`s.

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

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

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.homogeneous
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
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 `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.mix.motifSearch
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.
WrongLengthException A `WrongLengthException` is thrown if a given (sub)sequence length is not correct.

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