Uses of Interface
de.jstacs.scoringFunctions.NormalizableScoringFunction

Packages that use NormalizableScoringFunction
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.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. 
 

Uses of NormalizableScoringFunction in de.jstacs.classifier.scoringFunctionBased.logPrior
 

Fields in de.jstacs.classifier.scoringFunctionBased.logPrior declared as NormalizableScoringFunction
protected  NormalizableScoringFunction[] SeparateLogPrior.funs
          The ScoringFunctions using the parameters that shall be penalized
 

Uses of NormalizableScoringFunction in de.jstacs.scoringFunctions
 

Classes in de.jstacs.scoringFunctions that implement NormalizableScoringFunction
 class AbstractNormalizableScoringFunction
          This class is the main part of any ScoreClassifier.
 class IndependentProductScoringFunction
          This class enables the user to model parts of the sequence independent of each other.
 class MRFScoringFunction
          This class implements the scoring function for any MRF.
 class UniformScoringFunction
          This scoring function does nothing.
 class VariableLengthScoringFunction
          This is the main class for all ScoringFunctions that allow to score subsequences of arbitrary length.
 

Methods in de.jstacs.scoringFunctions with parameters of type NormalizableScoringFunction
static boolean AbstractNormalizableScoringFunction.isNormalized(NormalizableScoringFunction... function)
          This method checks whether all given NormalizableScoringFunctions are normalized.
 

Constructors in de.jstacs.scoringFunctions with parameters of type NormalizableScoringFunction
IndependentProductScoringFunction(NormalizableScoringFunction... functions)
          This constructor creates an instance of a given series of independent NormalizableScoringFunctions.
IndependentProductScoringFunction(NormalizableScoringFunction[] functions, int[] length)
          This constructor creates an instance of a given series of independent NormalizableScoringFunctions and lengths.
 

Uses of NormalizableScoringFunction in de.jstacs.scoringFunctions.directedGraphicalModels
 

Classes in de.jstacs.scoringFunctions.directedGraphicalModels that implement NormalizableScoringFunction
 class BayesianNetworkScoringFunction
          This class implements a scoring function that is a moral directed graphical model, i.e. a moral Bayesian network.
 

Uses of NormalizableScoringFunction in de.jstacs.scoringFunctions.homogeneous
 

Classes in de.jstacs.scoringFunctions.homogeneous that implement NormalizableScoringFunction
 class HMM0ScoringFunction
          This scoring function implements a homogeneous Markov model of order zero (hMM(0)) for a fixed sequence length.
 class HMMScoringFunction
          This scoring function implements a homogeneous Markov model of arbitrary order for any sequence length.
 class HomogeneousScoringFunction
          This is the main class for all homogeneous ScoringFunctions.
 class UniformHomogeneousScoringFunction
          This scoring function does nothing.
 

Uses of NormalizableScoringFunction in de.jstacs.scoringFunctions.mix
 

Classes in de.jstacs.scoringFunctions.mix that implement NormalizableScoringFunction
 class AbstractMixtureScoringFunction
          This main abstract class for any mixture (e.g.
 class MixtureScoringFunction
          This class implements a real mixture model.
 

Fields in de.jstacs.scoringFunctions.mix declared as NormalizableScoringFunction
protected  NormalizableScoringFunction[] AbstractMixtureScoringFunction.function
          This array contains the internal functions that are used to determine the score.
 

Methods in de.jstacs.scoringFunctions.mix that return NormalizableScoringFunction
 NormalizableScoringFunction AbstractMixtureScoringFunction.getFunction(int index)
          This method returns a specific internal function
 NormalizableScoringFunction[] AbstractMixtureScoringFunction.getFunctions()
          This method returns an array of clones of the internal used functions.
 NormalizableScoringFunction[] AbstractMixtureScoringFunction.getScoringFunctions()
          Returns a deep copy of all internal used ScoringFunctions
 

Methods in de.jstacs.scoringFunctions.mix with parameters of type NormalizableScoringFunction
protected  void AbstractMixtureScoringFunction.cloneFunctions(NormalizableScoringFunction[] originalFunctions)
          This method clones the given array of function and enables the user to do some postprocessing.
 

Constructors in de.jstacs.scoringFunctions.mix with parameters of type NormalizableScoringFunction
AbstractMixtureScoringFunction(int length, int starts, int dimension, boolean optimizeHidden, boolean plugIn, NormalizableScoringFunction... function)
          This constructor creates an AbstractMixtureScoringFunction.
MixtureScoringFunction(int starts, boolean plugIn, NormalizableScoringFunction... component)
          This constructor creates a mixture.