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## Uses of Package
de.jstacs.scoringFunctions

Packages that use de.jstacs.scoringFunctions
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.models | Provides the interface `Model` and its abstract implementation `AbstractModel`, which is the super class of all other models.
de.jstacs.models.hmm.models | The package provides different implementations of hidden Markov models based on `AbstractHMM`
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer
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.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.scoringFunctions used by de.jstacs.classifier.scoringFunctionBased
ScoringFunction This interface is the main part of any `ScoreClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.classifier.scoringFunctionBased.gendismix
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.
ScoringFunction This interface is the main part of any `ScoreClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.classifier.scoringFunctionBased.logPrior
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.
ScoringFunction This interface is the main part of any `ScoreClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.classifier.scoringFunctionBased.msp
ScoringFunction This interface is the main part of any `ScoreClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.classifier.scoringFunctionBased.sampling
SamplingScoringFunction Interface for `NormalizableScoringFunction`s that can be used for Metropolis-Hastings sampling in a `SamplingScoreBasedClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.models
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.

Classes in de.jstacs.scoringFunctions used by de.jstacs.models.hmm.models
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.
SamplingScoringFunction Interface for `NormalizableScoringFunction`s that can be used for Metropolis-Hastings sampling in a `SamplingScoreBasedClassifier`.
ScoringFunction This interface is the main part of any `ScoreClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.motifDiscovery
ScoringFunction This interface is the main part of any `ScoreClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.scoringFunctions
AbstractNormalizableScoringFunction This class is the main part of any `ScoreClassifier`.
AbstractVariableLengthScoringFunction This abstract class implements some methods declared in `NormalizableScoringFunction` based on the declaration of methods in `VariableLengthScoringFunction`.
CMMScoringFunction This scoring function implements a cyclic Markov model of arbitrary order and periodicity for any sequence length.
IndependentProductScoringFunction This class enables the user to model parts of a sequence independent of each other.
MappingScoringFunction This class implements a `NormalizableScoringFunction` that works on mapped `Sequence`s.
MRFScoringFunction This class implements the scoring function for any MRF (Markov Random Field).
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.
NormalizedScoringFunction This class makes an unnormalized `NormalizableScoringFunction` to a normalized `NormalizableScoringFunction`.
ScoringFunction This interface is the main part of any `ScoreClassifier`.
VariableLengthScoringFunction This is an interface for all `NormalizableScoringFunction`s that allow to score subsequences of arbitrary length.

Classes in de.jstacs.scoringFunctions used by de.jstacs.scoringFunctions.directedGraphicalModels
AbstractNormalizableScoringFunction This class is the main part of any `ScoreClassifier`.
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.
SamplingScoringFunction Interface for `NormalizableScoringFunction`s that can be used for Metropolis-Hastings sampling in a `SamplingScoreBasedClassifier`.
ScoringFunction This interface is the main part of any `ScoreClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.scoringFunctions.homogeneous
AbstractNormalizableScoringFunction This class is the main part of any `ScoreClassifier`.
AbstractVariableLengthScoringFunction This abstract class implements some methods declared in `NormalizableScoringFunction` based on the declaration of methods in `VariableLengthScoringFunction`.
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.
ScoringFunction This interface is the main part of any `ScoreClassifier`.
VariableLengthScoringFunction This is an interface for all `NormalizableScoringFunction`s that allow to score subsequences of arbitrary length.

Classes in de.jstacs.scoringFunctions used by de.jstacs.scoringFunctions.mix
AbstractNormalizableScoringFunction This class is the main part of any `ScoreClassifier`.
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.
ScoringFunction This interface is the main part of any `ScoreClassifier`.
VariableLengthScoringFunction This is an interface for all `NormalizableScoringFunction`s that allow to score subsequences of arbitrary length.

Classes in de.jstacs.scoringFunctions used by de.jstacs.scoringFunctions.mix.motifSearch
AbstractNormalizableScoringFunction This class is the main part of any `ScoreClassifier`.
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.
ScoringFunction This interface is the main part of any `ScoreClassifier`.

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