Uses of Class
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

Packages that use BasicHigherOrderTransition.AbstractTransitionElement

Package	Description
de.jstacs.sequenceScores.statisticalModels.trainable.hmm	The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models	The package provides different implementations of hidden Markov models based on AbstractHMM.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions	The package provides all interfaces and classes for transitions used in hidden Markov models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements

Uses of BasicHigherOrderTransition.AbstractTransitionElement in de.jstacs.sequenceScores.statisticalModels.trainable.hmm

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm with parameters of type BasicHigherOrderTransition.AbstractTransitionElement

Modifier and Type	Method and Description
protected void	AbstractHMM.initTransition(BasicHigherOrderTransition.AbstractTransitionElement... te) This method creates the internal transition.

Uses of BasicHigherOrderTransition.AbstractTransitionElement in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models with parameters of type BasicHigherOrderTransition.AbstractTransitionElement

Constructor and Description
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 BasicHigherOrderTransition.AbstractTransitionElement in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions

Fields in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions declared as BasicHigherOrderTransition.AbstractTransitionElement

Modifier and Type	Field and Description
protected BasicHigherOrderTransition.AbstractTransitionElement[]	BasicHigherOrderTransition.transitions The internally used BasicHigherOrderTransition.AbstractTransitionElements.

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions that return BasicHigherOrderTransition.AbstractTransitionElement

Modifier and Type	Method and Description
BasicHigherOrderTransition.AbstractTransitionElement	BasicHigherOrderTransition.AbstractTransitionElement.clone()

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions with parameters of type BasicHigherOrderTransition.AbstractTransitionElement

Modifier and Type	Method and Description
void	BasicHigherOrderTransition.AbstractTransitionElement.joinStatistics(BasicHigherOrderTransition.AbstractTransitionElement... te) This method joins the statistics of different instances and sets this joined statistic as statistic of each instance.
void	BasicHigherOrderTransition.AbstractTransitionElement.setParameters(BasicHigherOrderTransition.AbstractTransitionElement t) Set values of parameters of the instance to the value of the parameters of the given instance.

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions with parameters of type BasicHigherOrderTransition.AbstractTransitionElement

Constructor and Description
BasicHigherOrderTransition(boolean[] isSilent, BasicHigherOrderTransition.AbstractTransitionElement... transitions) The main constructor.

Uses of BasicHigherOrderTransition.AbstractTransitionElement in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements

Subclasses of BasicHigherOrderTransition.AbstractTransitionElement in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements

Modifier and Type	Class and Description
class	BasicPluginTransitionElement Basic transition element without random initialization of parameters.
class	BasicTransitionElement This class implements the probability distribution for a given context, i.e.
class	DistanceBasedScaledTransitionElement Distance-based scaled transition element for an HMM with distance-scaled transition matrices (DSHMM).
class	ReferenceBasedTransitionElement This class implements transition elements that utilize a reference sequence to determine the transition probability.
class	ScaledTransitionElement Scaled transition element for an HMM with scaled transition matrices (SHMM).
class	TransitionElement This class implements an transition element implements method used for training via sampling or gradient based optimization approach.