Uses of Class
de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction

Packages that use AbstractNormalizableScoringFunction

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

Uses of AbstractNormalizableScoringFunction in de.jstacs.scoringFunctions

Subclasses of AbstractNormalizableScoringFunction in de.jstacs.scoringFunctions

class	AbstractVariableLengthScoringFunction This abstract class implements some methods declared in NormalizableScoringFunction based on the declaration of methods in VariableLengthScoringFunction.
class	CMMScoringFunction This scoring function implements a cyclic Markov model of arbitrary order and periodicity for any sequence length.
class	IndependentProductScoringFunction This class enables the user to model parts of a sequence independent of each other.
class	MappingScoringFunction This class implements a NormalizableScoringFunction that works on mapped Sequences.
class	MRFScoringFunction This class implements the scoring function for any MRF (Markov Random Field).
class	NormalizedScoringFunction This class makes an unnormalized NormalizableScoringFunction to a normalized NormalizableScoringFunction.
class	UniformScoringFunction This ScoringFunction does nothing.

Methods in de.jstacs.scoringFunctions that return AbstractNormalizableScoringFunction

AbstractNormalizableScoringFunction

AbstractNormalizableScoringFunction.clone()

Uses of AbstractNormalizableScoringFunction in de.jstacs.scoringFunctions.directedGraphicalModels

Subclasses of AbstractNormalizableScoringFunction in de.jstacs.scoringFunctions.directedGraphicalModels

class	BayesianNetworkScoringFunction This class implements a scoring function that is a moral directed graphical model, i.e. a moral Bayesian network.
class	MutableMarkovModelScoringFunction This class implements a AbstractNormalizableScoringFunction for an inhomogeneous Markov model.

Uses of AbstractNormalizableScoringFunction in de.jstacs.scoringFunctions.homogeneous

Subclasses of AbstractNormalizableScoringFunction in de.jstacs.scoringFunctions.homogeneous

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 AbstractNormalizableScoringFunction in de.jstacs.scoringFunctions.mix

Subclasses of AbstractNormalizableScoringFunction in de.jstacs.scoringFunctions.mix

class	AbstractMixtureScoringFunction This main abstract class for any mixture scoring function (e.g.
class	MixtureScoringFunction This class implements a real mixture model.
class	StrandScoringFunction This class enables the user to search on both strand.
class	VariableLengthMixtureScoringFunction This class implements a mixture of VariableLengthScoringFunction by extending MixtureScoringFunction and implementing the methods of VariableLengthScoringFunction.

Uses of AbstractNormalizableScoringFunction in de.jstacs.scoringFunctions.mix.motifSearch

Subclasses of AbstractNormalizableScoringFunction in de.jstacs.scoringFunctions.mix.motifSearch

class	DurationScoringFunction This class is the super class for all one dimensional position scoring functions that can be used as durations for semi Markov models.
class	HiddenMotifsMixture This class handles mixtures with at least one hidden motif.
class	MixtureDuration This class implements a mixture of DurationScoringFunctions.
class	PositionScoringFunction This class implements a position scoring function that enables the user to get a score without using a Sequence object.
class	SkewNormalLikeScoringFunction This class implements a skew normal like discrete truncated distribution.
class	UniformDurationScoringFunction This scoring function implements a uniform distribution for positions.