Uses of Class
de.jstacs.models.hmm.HMMTrainingParameterSet

Packages that use HMMTrainingParameterSet

de.jstacs.models.hmm	The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.models.hmm.models	The package provides different implementations of hidden Markov models based on AbstractHMM
de.jstacs.models.hmm.training	The package provides all classes used to determine the training algorithm of a hidden Markov model

Uses of HMMTrainingParameterSet in de.jstacs.models.hmm

Fields in de.jstacs.models.hmm declared as HMMTrainingParameterSet

protected HMMTrainingParameterSet

AbstractHMM.trainingParameter The ParameterSet containing all Parameters for the training of the HMM.

Methods in de.jstacs.models.hmm with parameters of type HMMTrainingParameterSet

static AbstractHMM	HMMFactory.createErgodicHMM(HMMTrainingParameterSet pars, int order, double ess, double selfTranistionPart, double expectedSequenceLength, Emission... emission) This method creates an ergodic, i.e. a completely connected, HMM using the given emissions.
static AbstractHMM	HMMFactory.createSunflowerHMM(HMMTrainingParameterSet pars, AlphabetContainer con, double ess, int expectedSequenceLength, boolean startCentral, int... motifLength) This method creates a first order sunflower HMM.
static AbstractHMM	HMMFactory.createSunflowerHMM(HMMTrainingParameterSet pars, AlphabetContainer con, double ess, int expectedSequenceLength, boolean startCentral, PhyloTree[] t, double[] motifProb, int[] motifLength) This method creates a first order sunflower HMM allowing phylogenetic emissions.

Constructors in de.jstacs.models.hmm with parameters of type HMMTrainingParameterSet

AbstractHMM(HMMTrainingParameterSet trainingParameterSet, String[] name, int[] emissionIdx, boolean[] forward, Emission[] emission)
This is the main constructor for an HMM.

Uses of HMMTrainingParameterSet in de.jstacs.models.hmm.models

Constructors in de.jstacs.models.hmm.models with parameters of type HMMTrainingParameterSet

HigherOrderHMM(HMMTrainingParameterSet trainingParameterSet, String[] name, Emission[] emission, BasicHigherOrderTransition.AbstractTransitionElement... te)
This is a convenience constructor.

HigherOrderHMM(HMMTrainingParameterSet trainingParameterSet, String[] name, int[] emissionIdx, boolean[] forward, Emission[] emission, BasicHigherOrderTransition.AbstractTransitionElement... te)
This is the main constructor.

Uses of HMMTrainingParameterSet in de.jstacs.models.hmm.training

Subclasses of HMMTrainingParameterSet in de.jstacs.models.hmm.training

class	BaumWelchParameterSet This class implements an HMMTrainingParameterSet for the Baum-Welch training of an AbstractHMM.
class	MaxHMMTrainingParameterSet This class is the super class for any HMMTrainingParameterSet that is used for a maximizing training algorithm of a hidden Markov model.
class	NumericalHMMTrainingParameterSet This class implements an ParameterSet for numerical training of an AbstractHMM.
class	SamplingHMMTrainingParameterSet This class contains the parameters for training training an AbstractHMM using a sampling strategy.
class	ViterbiParameterSet This class implements an ParameterSet for the viterbi training of an AbstractHMM.