Uses of Package
de.jstacs.scoringFunctions

Packages that use de.jstacs.scoringFunctions

de.jstacs.classifier.scoringFunctionBased	Provides the classes for Classifiers that are based on ScoringFunctions.
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.scoringFunctionBased.logPrior	Provides a general definition of a parameter log-prior and a number of implementations of Laplace and Gaussian priors
de.jstacs.motifDiscovery	This package provides the framework including the interface for any de novo motif discoverer
de.jstacs.scoringFunctions	Provides ScoringFunctions that can be used in a ScoreClassifier.
de.jstacs.scoringFunctions.directedGraphicalModels	Provides ScoringFunctions that are equivalent to directed graphical models.
de.jstacs.scoringFunctions.homogeneous	Provides ScoringFunctions that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.scoringFunctions.mix	Provides ScoringFunctions that are mixtures of other ScoringFunctions.
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.cll

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 ScoringFunctions.

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.

IndependentProductScoringFunction
This class enables the user to model parts of a sequence independent of each other.

MRFScoringFunction
This class implements the scoring function for any MRF (Markov Random Field).

NormalizableScoringFunction
The interface for normalizable ScoringFunctions.

NormalizedScoringFunction
This class makes an unnormalized ScoringFunction to a normalized ScoringFunction.

ScoringFunction
This interface is the main part of any ScoreClassifier.

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 ScoringFunctions.

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.

NormalizableScoringFunction
The interface for normalizable ScoringFunctions.

ScoringFunction
This interface is the main part of any ScoreClassifier.

VariableLengthScoringFunction
This is the main class for all ScoringFunctions 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 ScoringFunctions.

ScoringFunction
This interface is the main part of any ScoreClassifier.

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 ScoringFunctions.

ScoringFunction
This interface is the main part of any ScoreClassifier.