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.