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## Uses of Package
de.jstacs

Packages that use de.jstacs
de.jstacs | This package is the root package for the most and important packages.
de.jstacs.algorithms.optimization.termination |
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.gendismix | Provides an implementation of a classifier that allows to train the parameters of a set of `NormalizableScoringFunction`s by a unified generative-discriminative learning principle
de.jstacs.classifier.scoringFunctionBased.logPrior | Provides a general definition of a parameter log-prior and a number of implementations of Laplace and Gaussian priors
de.jstacs.classifier.scoringFunctionBased.msp | Provides an implementation of a classifier that allows to train the parameters of a set of `ScoringFunctions` either by maximum supervised posterior (MSP) or by maximum conditional likelihood (MCL)
de.jstacs.classifier.scoringFunctionBased.sampling | Provides the classes for `AbstractScoreBasedClassifier`s that are based on `SamplingScoringFunction`s and that sample parameters using the Metropolis-Hastings algorithm.
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.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.hmm | The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.models.hmm.models | The package provides different implementations of hidden Markov models based on `AbstractHMM`
de.jstacs.models.hmm.states.emissions |
de.jstacs.models.hmm.states.emissions.continuous |
de.jstacs.models.hmm.states.emissions.discrete |
de.jstacs.models.hmm.training | The package provides all classes used to determine the training algorithm of a hidden Markov model
de.jstacs.models.hmm.transitions | The package provides all interfaces and classes for transitions used in hidden Markov models.
de.jstacs.models.hmm.transitions.elements |
de.jstacs.models.mixture | This package is the super package for any mixture model.
de.jstacs.models.mixture.motif |
de.jstacs.models.mixture.motif.positionprior |
de.jstacs.models.phylo |
de.jstacs.models.phylo.parser |
de.jstacs.models.utils |
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer
de.jstacs.motifDiscovery.history |
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.parameters.validation | Provides classes for the validation of `Parameter` values
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.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 |
de.jstacs.utils | This package contains a bundle of useful classes and interfaces like ...
de.jstacs.utils.galaxy |

Classes in de.jstacs used by de.jstacs
DataType This `enum` defines a number of data types that can be used for `Parameter`s and `Result` s.

Classes in de.jstacs used by de.jstacs.algorithms.optimization.termination
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.classifier
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
NotTrainedException A `NotTrainedException` is thrown if the user tries to use an untrained model.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.classifier.assessment
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.classifier.modelBased
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
NotTrainedException A `NotTrainedException` is thrown if the user tries to use an untrained model.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased.gendismix
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased.logPrior
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased.msp
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased.sampling
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
NotTrainedException A `NotTrainedException` is thrown if the user tries to use an untrained model.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.data
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.data.alphabets
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.data.bioJava
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.data.sequences
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.data.sequences.annotation
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.io
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs used by de.jstacs.models
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
NotTrainedException A `NotTrainedException` is thrown if the user tries to use an untrained model.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.models.discrete
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
NotTrainedException A `NotTrainedException` is thrown if the user tries to use an untrained model.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.models.discrete.homogeneous
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
NotTrainedException A `NotTrainedException` is thrown if the user tries to use an untrained model.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.models.discrete.homogeneous.parameters
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.models.discrete.inhomogeneous
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
NotTrainedException A `NotTrainedException` is thrown if the user tries to use an untrained model.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.models.discrete.inhomogeneous.parameters
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.models.discrete.inhomogeneous.shared
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
NotTrainedException A `NotTrainedException` is thrown if the user tries to use an untrained model.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.models.hmm
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
NotTrainedException A `NotTrainedException` is thrown if the user tries to use an untrained model.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.models.hmm.models
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
NotTrainedException A `NotTrainedException` is thrown if the user tries to use an untrained model.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.models.hmm.states.emissions
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.models.hmm.states.emissions.continuous
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.models.hmm.states.emissions.discrete
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.models.hmm.training
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.models.hmm.transitions
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.models.hmm.transitions.elements
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.models.mixture
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
NotTrainedException A `NotTrainedException` is thrown if the user tries to use an untrained model.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.models.mixture.motif
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.models.mixture.motif.positionprior
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.models.phylo
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.models.phylo.parser
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs used by de.jstacs.models.utils
NotTrainedException A `NotTrainedException` is thrown if the user tries to use an untrained model.

Classes in de.jstacs used by de.jstacs.motifDiscovery
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.motifDiscovery.history
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.parameters
DataType This `enum` defines a number of data types that can be used for `Parameter`s and `Result` s.
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.parameters.validation
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.results
DataType This `enum` defines a number of data types that can be used for `Parameter`s and `Result` s.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.sampling
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.scoringFunctions
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.scoringFunctions.directedGraphicalModels
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.scoringFunctions.homogeneous
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.scoringFunctions.mix
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.scoringFunctions.mix.motifSearch
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.

Classes in de.jstacs used by de.jstacs.utils
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

Classes in de.jstacs used by de.jstacs.utils.galaxy
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
Storable This is the root interface for all immutable objects that must be stored in e.g. a file or a database.

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