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.gendismix	Provides an implementation of a classifier that allows to train the parameters of a set of NormalizableScoringFunctions 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 AbstractScoreBasedClassifiers that are based on SamplingScoringFunctions 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 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.gendismix

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.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.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 NormalizableScoringFunctions 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 ScoringFunctions.

Classes in de.jstacs.scoringFunctions used by de.jstacs.models.hmm.models

NormalizableScoringFunction
The interface for normalizable ScoringFunctions.

SamplingScoringFunction
Interface for NormalizableScoringFunctions 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 Sequences.

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 NormalizableScoringFunction to a normalized NormalizableScoringFunction.

ScoringFunction
This interface is the main part of any ScoreClassifier.

VariableLengthScoringFunction
This is an interface for all NormalizableScoringFunctions 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 ScoringFunctions.

SamplingScoringFunction
Interface for NormalizableScoringFunctions 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 ScoringFunctions.

ScoringFunction
This interface is the main part of any ScoreClassifier.

VariableLengthScoringFunction
This is an interface for all NormalizableScoringFunctions 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.

VariableLengthScoringFunction
This is an interface for all NormalizableScoringFunctions 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 ScoringFunctions.

ScoringFunction
This interface is the main part of any ScoreClassifier.