A B C D E F G H I K L M N O P R S T V W

A

alpha - Variable in class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator

alphaElement(int, int) - Method in class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator

Returns an element of the alpha array.

B

BaumWelchLearner - Class in be.ac.ulg.montefiore.run.jahmm.learn

An implementation of the Baum-Welch learning algorithm.

BaumWelchLearner() - Constructor for class be.ac.ulg.montefiore.run.jahmm.learn.BaumWelchLearner

Initializes a Baum-Welch instance.

BaumWelchScaledLearner - Class in be.ac.ulg.montefiore.run.jahmm.learn

An implementation of the Baum-Welch learning algorithm.

BaumWelchScaledLearner() - Constructor for class be.ac.ulg.montefiore.run.jahmm.learn.BaumWelchScaledLearner

Initializes a Baum-Welch algorithm implementation.

be.ac.ulg.montefiore.run.distributions - package be.ac.ulg.montefiore.run.distributions

This package implements various pseudo-random distributions.

be.ac.ulg.montefiore.run.jahmm - package be.ac.ulg.montefiore.run.jahmm

This package is an Hidden Markov Model implementation.

be.ac.ulg.montefiore.run.jahmm.draw - package be.ac.ulg.montefiore.run.jahmm.draw

This classes help drawing Hidden Markov Model-related objects.

be.ac.ulg.montefiore.run.jahmm.io - package be.ac.ulg.montefiore.run.jahmm.io

This package holds classes that read and write Hidden Markov Model-related objects.

be.ac.ulg.montefiore.run.jahmm.learn - package be.ac.ulg.montefiore.run.jahmm.learn

This package holds Hidden Markov Model-related learning algorithms.

be.ac.ulg.montefiore.run.jahmm.toolbox - package be.ac.ulg.montefiore.run.jahmm.toolbox

This package holds Hidden Markov Model-related tool algorithms.

beta - Variable in class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator

betaElement(int, int) - Method in class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator

Returns an element of the beta array.

C

Centroid<O> - Interface in be.ac.ulg.montefiore.run.jahmm

The centroid (basically, the mean) of a cluster.

CentroidFactory<O> - Interface in be.ac.ulg.montefiore.run.jahmm

Creates a centroid for type .

CentroidObservationInteger - Class in be.ac.ulg.montefiore.run.jahmm

This class represents the centroid of a set of ObservationInteger.

CentroidObservationInteger(ObservationInteger) - Constructor for class be.ac.ulg.montefiore.run.jahmm.CentroidObservationInteger

CentroidObservationReal - Class in be.ac.ulg.montefiore.run.jahmm

This class represents the centroid of a set of ObservationReal.

CentroidObservationReal(ObservationReal) - Constructor for class be.ac.ulg.montefiore.run.jahmm.CentroidObservationReal

CentroidObservationVector - Class in be.ac.ulg.montefiore.run.jahmm

This class represents the centroid of a set of ObservationVector.

CentroidObservationVector(ObservationVector) - Constructor for class be.ac.ulg.montefiore.run.jahmm.CentroidObservationVector

Creates a new centroid that represents the mean value of a set of ObservationVectors.

clone() - Method in class be.ac.ulg.montefiore.run.jahmm.Hmm

clone() - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationVector

clone() - Method in interface be.ac.ulg.montefiore.run.jahmm.Opdf

clone() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfDiscrete

clone() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussian

clone() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

clone() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfInteger

clone() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussian

cluster(int) - Method in class be.ac.ulg.montefiore.run.jahmm.KMeansCalculator

Returns the elements of one of the clusters.

computeAlpha(Hmm<? super O>, List<O>) - Method in class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator

computeAlpha(Hmm<? super O>, List<O>) - Method in class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardScaledCalculator

computeAlphaInit(Hmm<? super O>, O, int) - Method in class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator

computeAlphaStep(Hmm<? super O>, O, int, int) - Method in class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator

computeBeta(Hmm<? super O>, List<O>) - Method in class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator

computeBeta(Hmm<? super O>, List<O>) - Method in class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardScaledCalculator

computeBetaStep(Hmm<? super O>, O, int, int) - Method in class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator

covariance() - Method in class be.ac.ulg.montefiore.run.distributions.MultiGaussianDistribution

Returns (a copy of) this distribution's covariance matrix.

covariance() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussian

Returns (a copy of) this distribution's covariance matrix.

covarianceDet() - Method in class be.ac.ulg.montefiore.run.distributions.MultiGaussianDistribution

Returns the covariance matrix determinant.

D

dimension() - Method in class be.ac.ulg.montefiore.run.distributions.MultiGaussianDistribution

dimension() - Method in interface be.ac.ulg.montefiore.run.distributions.MultiRandomDistribution

Returns the dimension of the vectors handled by this random distribution.

dimension() - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationVector

Returns the dimension of this vector.

dimension() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussian

Returns the dimension of the vectors handled by this distribution.

DiscreteDistribution - Interface in be.ac.ulg.montefiore.run.distributions

This interface must be implemented by all the package's classes implementing a discrete random distribution.

distance(O) - Method in interface be.ac.ulg.montefiore.run.jahmm.Centroid

Returns the distance from this centroid to a given element.

distance(ObservationInteger) - Method in class be.ac.ulg.montefiore.run.jahmm.CentroidObservationInteger

Returns the distance from this centroid to a given element.

distance(ObservationReal) - Method in class be.ac.ulg.montefiore.run.jahmm.CentroidObservationReal

Returns the distance from this centroid to a given element.

distance(ObservationVector) - Method in class be.ac.ulg.montefiore.run.jahmm.CentroidObservationVector

Returns the distance between this centroid and an element.

distance(Hmm<O>, Hmm<? super O>) - Method in class be.ac.ulg.montefiore.run.jahmm.toolbox.KullbackLeiblerDistanceCalculator

Computes the Kullback-Leibler distance between two HMMs.

distribution - Variable in class be.ac.ulg.montefiore.run.jahmm.OpdfDiscrete

distributions() - Method in class be.ac.ulg.montefiore.run.distributions.GaussianMixtureDistribution

Returns the distributions composing this mixture.

E

estimateGamma(double[][][], ForwardBackwardCalculator) - Method in class be.ac.ulg.montefiore.run.jahmm.learn.BaumWelchLearner

estimateXi(List<? extends O>, ForwardBackwardCalculator, Hmm<O>) - Method in class be.ac.ulg.montefiore.run.jahmm.learn.BaumWelchLearner

estimateXi(List<? extends O>, ForwardBackwardCalculator, Hmm<O>) - Method in class be.ac.ulg.montefiore.run.jahmm.learn.BaumWelchScaledLearner

ExponentialDistribution - Class in be.ac.ulg.montefiore.run.distributions

This class implements an generator of exponentially distributed reals.

ExponentialDistribution(double) - Constructor for class be.ac.ulg.montefiore.run.distributions.ExponentialDistribution

Creates a new pseudo-random, exponential distribution which is the distribution of waiting times between two events of a Poisson distribution with rate rate.

F

factor() - Method in interface be.ac.ulg.montefiore.run.jahmm.CentroidFactory

factor() - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationInteger

Returns the centroid matching this observation.

factor() - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationReal

Returns the centroid matching this observation.

factor() - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationVector

Returns the centroid matching this observation.

factor() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfDiscreteFactory

factor() - Method in interface be.ac.ulg.montefiore.run.jahmm.OpdfFactory

Generates a new observation probability distribution function.

factor() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianFactory

factor() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixtureFactory

factor() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfIntegerFactory

factor() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussianFactory

FileFormatException - Exception in be.ac.ulg.montefiore.run.jahmm.io

This exception reports the reading of an invalid (syntatically or lexically incorrect) file.

FileFormatException() - Constructor for exception be.ac.ulg.montefiore.run.jahmm.io.FileFormatException

Creates a new object reporting the reading of an invalid file.

FileFormatException(String) - Constructor for exception be.ac.ulg.montefiore.run.jahmm.io.FileFormatException

Creates a new object reporting the reading of an invalid file.

FileFormatException(int, String) - Constructor for exception be.ac.ulg.montefiore.run.jahmm.io.FileFormatException

Creates a new object reporting the reading of an invalid file.

fit(O...) - Method in interface be.ac.ulg.montefiore.run.jahmm.Opdf

Fits this observation probability (distribution) function to a (non empty) set of observations.

fit(Collection<? extends O>) - Method in interface be.ac.ulg.montefiore.run.jahmm.Opdf

Fits this observation probability (distribution) function to a (non empty) set of observations.

fit(O[], double[]) - Method in interface be.ac.ulg.montefiore.run.jahmm.Opdf

Fits this observation probability (distribution) function to a weighted (non empty) set of observations.

fit(Collection<? extends O>, double[]) - Method in interface be.ac.ulg.montefiore.run.jahmm.Opdf

Fits this observation probability (distribution) function to a weighted (non empty) set of observations.

fit(ObservationDiscrete<E>...) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfDiscrete

fit(Collection<? extends ObservationDiscrete<E>>) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfDiscrete

fit(ObservationDiscrete<E>[], double[]) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfDiscrete

fit(Collection<? extends ObservationDiscrete<E>>, double[]) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfDiscrete

fit(ObservationReal...) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussian

fit(Collection<? extends ObservationReal>) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussian

fit(ObservationReal[], double[]) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussian

fit(Collection<? extends ObservationReal>, double[]) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussian

fit(ObservationReal...) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

Fits this observation distribution function to a (non empty) set of observations.

fit(Collection<? extends ObservationReal>) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

Fits this observation distribution function to a (non empty) set of observations.

fit(ObservationReal[], double[]) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

Fits this observation distribution function to a (non empty) weighted set of observations.

fit(Collection<? extends ObservationReal>, double[]) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

Fits this observation distribution function to a (non empty) weighted set of observations.

fit(ObservationInteger...) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfInteger

fit(Collection<? extends ObservationInteger>) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfInteger

fit(ObservationInteger[], double[]) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfInteger

fit(Collection<? extends ObservationInteger>, double[]) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfInteger

fit(ObservationVector...) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussian

fit(Collection<? extends ObservationVector>) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussian

fit(ObservationVector[], double[]) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussian

fit(Collection<? extends ObservationVector>, double[]) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussian

ForwardBackwardCalculator - Class in be.ac.ulg.montefiore.run.jahmm

This class can be used to compute the probability of a given observations sequence for a given HMM.

ForwardBackwardCalculator() - Constructor for class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator

ForwardBackwardCalculator(List<? extends O>, Hmm<O>, EnumSet<ForwardBackwardCalculator.Computation>) - Constructor for class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator

Computes the probability of occurence of an observation sequence given a Hidden Markov Model.

ForwardBackwardCalculator(List<? extends O>, Hmm<O>) - Constructor for class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator

Computes the probability of occurence of an observation sequence given a Hidden Markov Model.

ForwardBackwardCalculator.Computation - Enum in be.ac.ulg.montefiore.run.jahmm

Flags used to explain how the observation sequence probability should be computed (either forward, using the alpha array, or backward, using the beta array).

ForwardBackwardScaledCalculator - Class in be.ac.ulg.montefiore.run.jahmm

This class can be used to compute the probability of a given observations sequence for a given HMM.

ForwardBackwardScaledCalculator(List<? extends O>, Hmm<O>, EnumSet<ForwardBackwardCalculator.Computation>) - Constructor for class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardScaledCalculator

Computes the probability of occurence of an observation sequence given a Hidden Markov Model.

ForwardBackwardScaledCalculator(List<? extends O>, Hmm<O>) - Constructor for class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardScaledCalculator

Computes the probability of occurence of an observation sequence given a Hidden Markov Model.

G

GaussianDistribution - Class in be.ac.ulg.montefiore.run.distributions

This class implements a Gaussian distribution.

GaussianDistribution() - Constructor for class be.ac.ulg.montefiore.run.distributions.GaussianDistribution

Creates a new pseudo-random, Gaussian distribution with zero mean and unitary variance.

GaussianDistribution(double, double) - Constructor for class be.ac.ulg.montefiore.run.distributions.GaussianDistribution

Creates a new pseudo-random, Gaussian distribution.

GaussianMixtureDistribution - Class in be.ac.ulg.montefiore.run.distributions

This class implements a Gaussian mixture distribution.

GaussianMixtureDistribution(int) - Constructor for class be.ac.ulg.montefiore.run.distributions.GaussianMixtureDistribution

Creates a new pseudo-random, Gaussian mixture distribution.

GaussianMixtureDistribution(double[], double[], double[]) - Constructor for class be.ac.ulg.montefiore.run.distributions.GaussianMixtureDistribution

Creates a new pseudo-random, Gaussian mixture distribution.

generate() - Method in interface be.ac.ulg.montefiore.run.distributions.DiscreteDistribution

Generates a pseudo-random number.

generate() - Method in class be.ac.ulg.montefiore.run.distributions.ExponentialDistribution

generate() - Method in class be.ac.ulg.montefiore.run.distributions.GaussianDistribution

generate() - Method in class be.ac.ulg.montefiore.run.distributions.GaussianMixtureDistribution

generate() - Method in class be.ac.ulg.montefiore.run.distributions.MultiGaussianDistribution

Generates a pseudo-random vector according to this distribution.

generate() - Method in interface be.ac.ulg.montefiore.run.distributions.MultiRandomDistribution

Generates a pseudo-random vector.

generate() - Method in class be.ac.ulg.montefiore.run.distributions.PoissonDistribution

generate() - Method in interface be.ac.ulg.montefiore.run.distributions.RandomDistribution

Generates a pseudo-random number.

generate() - Method in interface be.ac.ulg.montefiore.run.jahmm.Opdf

Generates a (pseudo) random observation according to this distribution.

generate() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfDiscrete

generate() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussian

generate() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

generate() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfInteger

generate() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussian

generateForwardBackwardCalculator(List<? extends O>, Hmm<O>) - Method in class be.ac.ulg.montefiore.run.jahmm.learn.BaumWelchLearner

generateForwardBackwardCalculator(List<? extends O>, Hmm<O>) - Method in class be.ac.ulg.montefiore.run.jahmm.learn.BaumWelchScaledLearner

GenericHmmDrawerDot - Class in be.ac.ulg.montefiore.run.jahmm.draw

An HMM to dot file converter.

GenericHmmDrawerDot() - Constructor for class be.ac.ulg.montefiore.run.jahmm.draw.GenericHmmDrawerDot

getAij(int, int) - Method in class be.ac.ulg.montefiore.run.jahmm.Hmm

Returns the probability associated with the transition going from state i to state j (a_i,j).

getNbIterations() - Method in class be.ac.ulg.montefiore.run.jahmm.learn.BaumWelchLearner

Returns the number of iterations performed by the BaumWelchLearner.learn(be.ac.ulg.montefiore.run.jahmm.Hmm, java.util.List>) method.

getNbSequences() - Method in class be.ac.ulg.montefiore.run.jahmm.toolbox.KullbackLeiblerDistanceCalculator

Returns the number of sequences generated to estimate a distance.

getOpdf(int) - Method in class be.ac.ulg.montefiore.run.jahmm.Hmm

Returns the opdf associated with a given state.

getPi(int) - Method in class be.ac.ulg.montefiore.run.jahmm.Hmm

Returns the pi value associated with a given state.

getSequencesLength() - Method in class be.ac.ulg.montefiore.run.jahmm.toolbox.KullbackLeiblerDistanceCalculator

Returns the length of sequences generated to estimate a distance.

H

Hmm<O extends Observation> - Class in be.ac.ulg.montefiore.run.jahmm

Main Hmm class; it implements an Hidden Markov Model.

Hmm(int, OpdfFactory<? extends Opdf<O>>) - Constructor for class be.ac.ulg.montefiore.run.jahmm.Hmm

Creates a new HMM.

Hmm(double[], double[][], List<? extends Opdf<O>>) - Constructor for class be.ac.ulg.montefiore.run.jahmm.Hmm

Creates a new HMM.

Hmm(int) - Constructor for class be.ac.ulg.montefiore.run.jahmm.Hmm

Creates a new HMM.

HmmBinaryReader - Class in be.ac.ulg.montefiore.run.jahmm.io

This class can read Hidden Markov Models from a byte stream.

HmmBinaryReader() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.HmmBinaryReader

HmmBinaryWriter - Class in be.ac.ulg.montefiore.run.jahmm.io

This class can write a Hidden Markov Models to a byte stream.

HmmBinaryWriter() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.HmmBinaryWriter

HmmReader - Class in be.ac.ulg.montefiore.run.jahmm.io

This class can read Hidden Markov Models represented as text files.

HmmReader() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.HmmReader

HmmWriter - Class in be.ac.ulg.montefiore.run.jahmm.io

Writes a HMM to a text file compatible with HmmReader.

HmmWriter() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.HmmWriter

I

isTerminated() - Method in class be.ac.ulg.montefiore.run.jahmm.learn.KMeansLearner

Returns true if the algorithm has reached a fix point, else returns false.

iterate(Hmm<O>, List<? extends List<? extends O>>) - Method in class be.ac.ulg.montefiore.run.jahmm.learn.BaumWelchLearner

Performs one iteration of the Baum-Welch algorithm.

iterate() - Method in class be.ac.ulg.montefiore.run.jahmm.learn.KMeansLearner

Performs one iteration of the K-Means algorithm.

K

KMeansCalculator<K extends CentroidFactory<? super K>> - Class in be.ac.ulg.montefiore.run.jahmm

This class can be used to divide a set of elements in clusters using the k-means algorithm.

KMeansCalculator(int, List<? extends K>) - Constructor for class be.ac.ulg.montefiore.run.jahmm.KMeansCalculator

This class divides a set of elements in a given number of clusters.

KMeansLearner<O extends Observation & CentroidFactory<? super O>> - Class in be.ac.ulg.montefiore.run.jahmm.learn

An implementation of the K-Means learning algorithm.

KMeansLearner(int, OpdfFactory<? extends Opdf<O>>, List<? extends List<? extends O>>) - Constructor for class be.ac.ulg.montefiore.run.jahmm.learn.KMeansLearner

Initializes a K-Means algorithm implementation.

KullbackLeiblerDistanceCalculator - Class in be.ac.ulg.montefiore.run.jahmm.toolbox

Computes the distance between HMMs.

KullbackLeiblerDistanceCalculator() - Constructor for class be.ac.ulg.montefiore.run.jahmm.toolbox.KullbackLeiblerDistanceCalculator

L

learn(Hmm<O>, List<? extends List<? extends O>>) - Method in class be.ac.ulg.montefiore.run.jahmm.learn.BaumWelchLearner

Does a fixed number of iterations (see BaumWelchLearner.getNbIterations()) of the Baum-Welch algorithm.

learn() - Method in class be.ac.ulg.montefiore.run.jahmm.learn.KMeansLearner

Does iterations of the K-Means algorithm until a fix point is reached.

lnProbability() - Method in class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardScaledCalculator

Return the neperian logarithm of the probability of the sequence that generated this object.

lnProbability(List<? extends O>) - Method in class be.ac.ulg.montefiore.run.jahmm.Hmm

Returns the neperian logarithm of observation sequence's probability given this HMM.

lnProbability() - Method in class be.ac.ulg.montefiore.run.jahmm.ViterbiCalculator

Returns the neperian logarithm of the probability of the given observation sequence on the most likely state sequence of the given HMM.

M

MarkovGenerator<O extends Observation> - Class in be.ac.ulg.montefiore.run.jahmm.toolbox

Generates sequences of markovian observations given a HMM.

MarkovGenerator(Hmm<O>) - Constructor for class be.ac.ulg.montefiore.run.jahmm.toolbox.MarkovGenerator

Initializes a Markovian generator.

mean() - Method in class be.ac.ulg.montefiore.run.distributions.GaussianDistribution

Returns this distribution's mean value.

mean() - Method in class be.ac.ulg.montefiore.run.distributions.MultiGaussianDistribution

Returns (a copy of) this distribution's mean vector.

mean() - Method in class be.ac.ulg.montefiore.run.distributions.PoissonDistribution

Returns this distribution's mean.

mean() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussian

Returns this distribution's mean value.

mean() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussian

Returns (a copy of) this distribution's mean vector.

means() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

Returns the mean value of each distribution composing this mixture.

minus(ObservationVector) - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationVector

Returns a new observation that is the difference between this observation and another one.

mostLikelyStateSequence(List<? extends O>) - Method in class be.ac.ulg.montefiore.run.jahmm.Hmm

Returns an array containing the most likely state sequence matching an observation sequence given this HMM.

MultiGaussianDistribution - Class in be.ac.ulg.montefiore.run.distributions

This class implements a multi-variate Gaussian distribution.

MultiGaussianDistribution(double[], double[][]) - Constructor for class be.ac.ulg.montefiore.run.distributions.MultiGaussianDistribution

Creates a new pseudo-random, multivariate gaussian distribution.

MultiGaussianDistribution(int) - Constructor for class be.ac.ulg.montefiore.run.distributions.MultiGaussianDistribution

Creates a new pseudo-random, multivariate gaussian distribution with zero mean and identity covariance.

MultiRandomDistribution - Interface in be.ac.ulg.montefiore.run.distributions

This interface must be implemented by all the package's classes implementing a multi-variate random distribution.

N

nbClusters() - Method in class be.ac.ulg.montefiore.run.jahmm.KMeansCalculator

Returns the number of clusters.

nbEntries() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfInteger

Returns how many integers are associated to probabilities by this distribution.

nbGaussians() - Method in class be.ac.ulg.montefiore.run.distributions.GaussianMixtureDistribution

Returns the number of Gaussians composing this mixture.

nbGaussians() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

Returns the number of distributions composing this mixture.

nbStates() - Method in class be.ac.ulg.montefiore.run.jahmm.Hmm

Returns the number of states of this HMM.

newSequence() - Method in class be.ac.ulg.montefiore.run.jahmm.toolbox.MarkovGenerator

Finds a new state according to the initial (pi) probabilities of each state.

O

Observation - Class in be.ac.ulg.montefiore.run.jahmm

Observations generated by a Markovian process.

Observation() - Constructor for class be.ac.ulg.montefiore.run.jahmm.Observation

observation() - Method in class be.ac.ulg.montefiore.run.jahmm.toolbox.MarkovGenerator

Generates a new (pseudo) random observation.

ObservationDiscrete<E extends java.lang.Enum<E>> - Class in be.ac.ulg.montefiore.run.jahmm

This class implements observations whose values are taken out of a finite set implemented as an enumeration.

ObservationDiscrete(E) - Constructor for class be.ac.ulg.montefiore.run.jahmm.ObservationDiscrete

ObservationInteger - Class in be.ac.ulg.montefiore.run.jahmm

This class holds an integer observation.

ObservationInteger(int) - Constructor for class be.ac.ulg.montefiore.run.jahmm.ObservationInteger

An observation that can be described by an integer.

ObservationIntegerReader - Class in be.ac.ulg.montefiore.run.jahmm.io

Reads an ObservationInteger up to (and including) a semi-colon.

ObservationIntegerReader() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.ObservationIntegerReader

Constructs a reader of ObservationInteger.

ObservationIntegerReader(int) - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.ObservationIntegerReader

Constructs a reader of ObservationInteger.

ObservationIntegerWriter - Class in be.ac.ulg.montefiore.run.jahmm.io

Writes an ObservationInteger up to (and including) the semi-colon.

ObservationIntegerWriter() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.ObservationIntegerWriter

ObservationReader<O extends Observation> - Class in be.ac.ulg.montefiore.run.jahmm.io

Reads an observation up to (and including) the semi-colon.

ObservationReader() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.ObservationReader

ObservationReal - Class in be.ac.ulg.montefiore.run.jahmm

This class implements observations made of a real value.

ObservationReal(double) - Constructor for class be.ac.ulg.montefiore.run.jahmm.ObservationReal

An observation that can be described by a real.

ObservationRealReader - Class in be.ac.ulg.montefiore.run.jahmm.io

Reads an ObservationReal up to (and including) a semi-colon.

ObservationRealReader() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.ObservationRealReader

ObservationRealWriter - Class in be.ac.ulg.montefiore.run.jahmm.io

Writes an ObservationReal up to (and including) the semi-colon.

ObservationRealWriter() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.ObservationRealWriter

observationSequence(int) - Method in class be.ac.ulg.montefiore.run.jahmm.toolbox.MarkovGenerator

Generates a new (pseudo) random observation sequence and start a new one.

ObservationSequencesReader - Class in be.ac.ulg.montefiore.run.jahmm.io

This class can read observations sequences from file.

ObservationSequencesReader() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.ObservationSequencesReader

ObservationSequencesWriter - Class in be.ac.ulg.montefiore.run.jahmm.io

This class can write a set of observation sequences to a Writer.

ObservationSequencesWriter() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.ObservationSequencesWriter

ObservationVector - Class in be.ac.ulg.montefiore.run.jahmm

This class holds an Observation described by a vector of reals.

ObservationVector(int) - Constructor for class be.ac.ulg.montefiore.run.jahmm.ObservationVector

An observation whose components are 0.

ObservationVector(double[]) - Constructor for class be.ac.ulg.montefiore.run.jahmm.ObservationVector

An observation that can be described by a vector of reals.

ObservationVectorReader - Class in be.ac.ulg.montefiore.run.jahmm.io

Reads an ObservationVector up to (and including) a semi-colon.

ObservationVectorReader() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.ObservationVectorReader

Constructs a reader of ObservationVector.

ObservationVectorReader(int) - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.ObservationVectorReader

Constructs a reader of ObservationVector.

ObservationVectorWriter - Class in be.ac.ulg.montefiore.run.jahmm.io

Writes an ObservationReal up to (and including) the semi-colon.

ObservationVectorWriter() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.ObservationVectorWriter

ObservationWriter<O extends Observation> - Class in be.ac.ulg.montefiore.run.jahmm.io

Writes an observation up to (and including) the semi-colon.

ObservationWriter() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.ObservationWriter

Opdf<O extends Observation> - Interface in be.ac.ulg.montefiore.run.jahmm

Objects implementing this interface represent an observation probability (distribution) function.

OpdfDiscrete<E extends java.lang.Enum<E>> - Class in be.ac.ulg.montefiore.run.jahmm

This class implements a distribution over a finite set of elements.

OpdfDiscrete(Class<E>) - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfDiscrete

Builds a new probability distribution which operates on a finite set of values.

OpdfDiscrete(Class<E>, double[]) - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfDiscrete

Builds a new probability distribution which operates on integer values.

OpdfDiscreteFactory<E extends java.lang.Enum<E>> - Class in be.ac.ulg.montefiore.run.jahmm

This class can build OpdfInteger observation probability distribution functions.

OpdfDiscreteFactory(Class<E>) - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfDiscreteFactory

Creates a factory for OpdfDiscrete objects.

OpdfFactory<D extends Opdf<?>> - Interface in be.ac.ulg.montefiore.run.jahmm

Classes implementing this interface are able to generate observation probability distribution functions.

OpdfGaussian - Class in be.ac.ulg.montefiore.run.jahmm

This class represents a (monovariate) gaussian distribution function.

OpdfGaussian() - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfGaussian

Builds a new gaussian probability distribution with zero mean and unit variance.

OpdfGaussian(double, double) - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfGaussian

Builds a new gaussian probability distribution with a given mean and covariance matrix.

OpdfGaussianFactory - Class in be.ac.ulg.montefiore.run.jahmm

This class can build OpdfMultiGaussian observation probability functions.

OpdfGaussianFactory() - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianFactory

OpdfGaussianMixture - Class in be.ac.ulg.montefiore.run.jahmm

This class implements a mixture of monovariate gaussian distributions.

OpdfGaussianMixture(int) - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

Creates a Gaussian mixture distribution.

OpdfGaussianMixture(double[], double[], double[]) - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

Creates a Gaussian mixture distribution.

OpdfGaussianMixtureFactory - Class in be.ac.ulg.montefiore.run.jahmm

Implements a factory of Gaussian mixtures distributions.

OpdfGaussianMixtureFactory(int) - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixtureFactory

Creates a new factory of Gaussian mixtures.

OpdfGaussianMixtureReader - Class in be.ac.ulg.montefiore.run.jahmm.io

This class implements a OpdfGaussian reader.

OpdfGaussianMixtureReader() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.OpdfGaussianMixtureReader

OpdfGaussianMixtureWriter - Class in be.ac.ulg.montefiore.run.jahmm.io

This class implements a OpdfGaussianMixture writer.

OpdfGaussianMixtureWriter() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.OpdfGaussianMixtureWriter

OpdfGaussianReader - Class in be.ac.ulg.montefiore.run.jahmm.io

This class implements a OpdfGaussian reader.

OpdfGaussianReader() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.OpdfGaussianReader

OpdfGaussianWriter - Class in be.ac.ulg.montefiore.run.jahmm.io

This class implements a OpdfGaussian writer.

OpdfGaussianWriter() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.OpdfGaussianWriter

OpdfGenericReader - Class in be.ac.ulg.montefiore.run.jahmm.io

OpdfGenericReader() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.OpdfGenericReader

OpdfInteger - Class in be.ac.ulg.montefiore.run.jahmm

This class represents a distribution of a finite number of positive integer observations.

OpdfInteger(int) - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfInteger

Builds a new probability distribution which operates on integer values.

OpdfInteger(double[]) - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfInteger

Builds a new probability distribution which operates on integer values.

OpdfIntegerFactory - Class in be.ac.ulg.montefiore.run.jahmm

This class can build OpdfInteger observation probability functions.

OpdfIntegerFactory(int) - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfIntegerFactory

Creates a factory for OpdfInteger objects.

OpdfIntegerReader - Class in be.ac.ulg.montefiore.run.jahmm.io

This class implements a OpdfInteger reader.

OpdfIntegerReader() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.OpdfIntegerReader

Implements a reader of distributions over integer observations.

OpdfIntegerReader(int) - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.OpdfIntegerReader

Implements a reader of distributions over integer observations.

OpdfIntegerWriter - Class in be.ac.ulg.montefiore.run.jahmm.io

This class can write a textual description of an OpdfInteger.

OpdfIntegerWriter() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.OpdfIntegerWriter

OpdfMultiGaussian - Class in be.ac.ulg.montefiore.run.jahmm

This class represents a multivariate gaussian distribution function.

OpdfMultiGaussian(int) - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussian

Builds a new gaussian probability distribution with zero mean and identity covariance matrix.

OpdfMultiGaussian(double[], double[][]) - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussian

Builds a new gaussian probability distribution with a given mean and covariance matrix.

OpdfMultiGaussianFactory - Class in be.ac.ulg.montefiore.run.jahmm

This class can build OpdfMultiGaussian observation probability functions.

OpdfMultiGaussianFactory(int) - Constructor for class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussianFactory

Generates a new multivariate gaussian observation probability distribution function.

OpdfMultiGaussianReader - Class in be.ac.ulg.montefiore.run.jahmm.io

This class implements a OpdfMultiGaussian reader.

OpdfMultiGaussianReader() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.OpdfMultiGaussianReader

OpdfMultiGaussianWriter - Class in be.ac.ulg.montefiore.run.jahmm.io

This class implements a OpdfMultiGaussian writer.

OpdfMultiGaussianWriter() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.OpdfMultiGaussianWriter

OpdfReader<O extends Opdf<?>> - Class in be.ac.ulg.montefiore.run.jahmm.io

Reads an observation distribution textual description.

OpdfReader() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.OpdfReader

OpdfWriter<O extends Opdf<?>> - Class in be.ac.ulg.montefiore.run.jahmm.io

Writes an observation distribution textual description.

OpdfWriter() - Constructor for class be.ac.ulg.montefiore.run.jahmm.io.OpdfWriter

P

plus(ObservationVector) - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationVector

Returns a new observation that is the sum of this observation and another one.

PoissonDistribution - Class in be.ac.ulg.montefiore.run.distributions

This class implements a generator of Poisson distributed numbers.

PoissonDistribution(double) - Constructor for class be.ac.ulg.montefiore.run.distributions.PoissonDistribution

Creates a new pseudo-random Poisson distribution.

probability(int) - Method in interface be.ac.ulg.montefiore.run.distributions.DiscreteDistribution

Returns the probability of a given number.

probability(double) - Method in class be.ac.ulg.montefiore.run.distributions.ExponentialDistribution

probability(double) - Method in class be.ac.ulg.montefiore.run.distributions.GaussianDistribution

probability(double) - Method in class be.ac.ulg.montefiore.run.distributions.GaussianMixtureDistribution

probability(double[]) - Method in class be.ac.ulg.montefiore.run.distributions.MultiGaussianDistribution

probability(double[]) - Method in interface be.ac.ulg.montefiore.run.distributions.MultiRandomDistribution

Returns the probability (density) of a given vector.

probability(int) - Method in class be.ac.ulg.montefiore.run.distributions.PoissonDistribution

probability(double) - Method in interface be.ac.ulg.montefiore.run.distributions.RandomDistribution

Returns the probability (density) of a given number.

probability - Variable in class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator

probability() - Method in class be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator

Return the probability of the sequence that generated this object.

probability(List<? extends O>) - Method in class be.ac.ulg.montefiore.run.jahmm.Hmm

Returns the probability of an observation sequence given this HMM.

probability(List<? extends O>, int[]) - Method in class be.ac.ulg.montefiore.run.jahmm.Hmm

Returns the probability of an observation sequence along a state sequence given this HMM.

probability(O) - Method in interface be.ac.ulg.montefiore.run.jahmm.Opdf

Returns the probability (density) of an observation given a distribution.

probability(ObservationDiscrete) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfDiscrete

probability(ObservationReal) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussian

probability(ObservationReal) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

probability(ObservationInteger) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfInteger

probability(ObservationVector) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussian

proportions() - Method in class be.ac.ulg.montefiore.run.distributions.GaussianMixtureDistribution

Returns the proportions of the distributions in this mixture.

proportions() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

Returns the mixing proportions of each gaussian distribution.

R

RandomDistribution - Interface in be.ac.ulg.montefiore.run.distributions

This interface must be implemented by all the package's classes implementing a mono-variate random distribution.

rate() - Method in class be.ac.ulg.montefiore.run.distributions.ExponentialDistribution

Returns this distribution's rate.

read(InputStream) - Static method in class be.ac.ulg.montefiore.run.jahmm.io.HmmBinaryReader

Reads a HMM from a byte stream.

read(Reader, OpdfReader<? extends Opdf<O>>) - Static method in class be.ac.ulg.montefiore.run.jahmm.io.HmmReader

Reads a HMM from a text file.

read(StreamTokenizer) - Method in class be.ac.ulg.montefiore.run.jahmm.io.ObservationIntegerReader

Reads an ObservationInteger reader, as explained in ObservationReader.

read(StreamTokenizer) - Method in class be.ac.ulg.montefiore.run.jahmm.io.ObservationReader

Reads an Observation (followed by a semi-colon) out of a StreamTokenizer.

read(StreamTokenizer) - Method in class be.ac.ulg.montefiore.run.jahmm.io.ObservationRealReader

Reads an ObservationReal reader, as explained in ObservationReader.

read(StreamTokenizer) - Method in class be.ac.ulg.montefiore.run.jahmm.io.ObservationVectorReader

An ObservationInteger reader, as explained in ObservationReader.

read(StreamTokenizer) - Method in class be.ac.ulg.montefiore.run.jahmm.io.OpdfGaussianMixtureReader

read(StreamTokenizer) - Method in class be.ac.ulg.montefiore.run.jahmm.io.OpdfGaussianReader

read(StreamTokenizer) - Method in class be.ac.ulg.montefiore.run.jahmm.io.OpdfGenericReader

read(StreamTokenizer) - Method in class be.ac.ulg.montefiore.run.jahmm.io.OpdfIntegerReader

read(StreamTokenizer) - Method in class be.ac.ulg.montefiore.run.jahmm.io.OpdfMultiGaussianReader

read(StreamTokenizer) - Method in class be.ac.ulg.montefiore.run.jahmm.io.OpdfReader

Reads an Opdf out of a StreamTokenizer.

read(StreamTokenizer, int) - Static method in class be.ac.ulg.montefiore.run.jahmm.io.OpdfReader

Reads a sequence of numbers.

readSequence(ObservationReader<O>, Reader) - Static method in class be.ac.ulg.montefiore.run.jahmm.io.ObservationSequencesReader

Reads an observation sequence out of a file Reader.

readSequences(ObservationReader<O>, Reader) - Static method in class be.ac.ulg.montefiore.run.jahmm.io.ObservationSequencesReader

Reads observation sequences file.

reevaluateAdd(O, List<? extends O>) - Method in interface be.ac.ulg.montefiore.run.jahmm.Centroid

Reevalue the value of this centroid, knowing that it currently is the centroid of the observations composing v and that we want it to be the centroid of v plus the value of the observation e.

reevaluateAdd(ObservationInteger, List<? extends ObservationInteger>) - Method in class be.ac.ulg.montefiore.run.jahmm.CentroidObservationInteger

reevaluateAdd(ObservationReal, List<? extends ObservationReal>) - Method in class be.ac.ulg.montefiore.run.jahmm.CentroidObservationReal

reevaluateAdd(ObservationVector, List<? extends ObservationVector>) - Method in class be.ac.ulg.montefiore.run.jahmm.CentroidObservationVector

reevaluateRemove(O, List<? extends O>) - Method in interface be.ac.ulg.montefiore.run.jahmm.Centroid

Reevalue the value of this centroid, knowing that it currently is the centroid of the observations composing v and that we want it to be the centroid of v minus the value of the observation e.

reevaluateRemove(ObservationInteger, List<? extends ObservationInteger>) - Method in class be.ac.ulg.montefiore.run.jahmm.CentroidObservationInteger

reevaluateRemove(ObservationReal, List<? extends ObservationReal>) - Method in class be.ac.ulg.montefiore.run.jahmm.CentroidObservationReal

reevaluateRemove(ObservationVector, List<? extends ObservationVector>) - Method in class be.ac.ulg.montefiore.run.jahmm.CentroidObservationVector

S

setAij(int, int, double) - Method in class be.ac.ulg.montefiore.run.jahmm.Hmm

Sets the probability associated to the transition going from state i to state j (A_i,j).

setNbIterations(int) - Method in class be.ac.ulg.montefiore.run.jahmm.learn.BaumWelchLearner

Sets the number of iterations performed by the BaumWelchLearner.learn(be.ac.ulg.montefiore.run.jahmm.Hmm, java.util.List>) method.

setNbSequences(int) - Method in class be.ac.ulg.montefiore.run.jahmm.toolbox.KullbackLeiblerDistanceCalculator

Sets the number of sequences generated to estimate a distance.

setOpdf(int, Opdf<O>) - Method in class be.ac.ulg.montefiore.run.jahmm.Hmm

Sets the opdf associated with a given state.

setPi(int, double) - Method in class be.ac.ulg.montefiore.run.jahmm.Hmm

Sets the pi value associated with a given state.

setSequencesLength(int) - Method in class be.ac.ulg.montefiore.run.jahmm.toolbox.KullbackLeiblerDistanceCalculator

Sets the length of sequences generated to estimate a distance.

stateNb() - Method in class be.ac.ulg.montefiore.run.jahmm.toolbox.MarkovGenerator

Returns the state number of the current state.

stateSequence() - Method in class be.ac.ulg.montefiore.run.jahmm.ViterbiCalculator

Returns a (clone of) the array containing the computed most likely state sequence.

T

times(double) - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationVector

Returns a new observation that is the product of this observation by a scalar.

toIntegerMap - Variable in class be.ac.ulg.montefiore.run.jahmm.OpdfDiscrete

toString(NumberFormat) - Method in class be.ac.ulg.montefiore.run.jahmm.Hmm

Gives a description of this HMM.

toString() - Method in class be.ac.ulg.montefiore.run.jahmm.Hmm

Gives a description of this HMM.

toString(NumberFormat) - Method in class be.ac.ulg.montefiore.run.jahmm.Observation

Formats this observation using a number formatter.

toString() - Method in class be.ac.ulg.montefiore.run.jahmm.Observation

Converts this Observation to a String.

toString() - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationDiscrete

toString(NumberFormat) - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationDiscrete

toString(NumberFormat) - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationInteger

toString(NumberFormat) - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationReal

toString(NumberFormat) - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationVector

toString(NumberFormat) - Method in interface be.ac.ulg.montefiore.run.jahmm.Opdf

Returns a String describing this distribution.

toString() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfDiscrete

toString(NumberFormat) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfDiscrete

toString() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussian

toString(NumberFormat) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussian

toString() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

toString(NumberFormat) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

toString() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfInteger

toString(NumberFormat) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfInteger

toString() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussian

toString(NumberFormat) - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfMultiGaussian

V

value - Variable in class be.ac.ulg.montefiore.run.jahmm.ObservationDiscrete

This observation value.

value - Variable in class be.ac.ulg.montefiore.run.jahmm.ObservationInteger

The observation's value.

value - Variable in class be.ac.ulg.montefiore.run.jahmm.ObservationReal

The observation's value.

value(int) - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationVector

Returns one of the values composing the observation.

valueOf(String) - Static method in enum be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator.Computation

Returns the enum constant of this type with the specified name.

values() - Static method in enum be.ac.ulg.montefiore.run.jahmm.ForwardBackwardCalculator.Computation

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Method in class be.ac.ulg.montefiore.run.jahmm.ObservationVector

Returns the values composing this observation.

values - Variable in class be.ac.ulg.montefiore.run.jahmm.OpdfDiscrete

valuesClass - Variable in class be.ac.ulg.montefiore.run.jahmm.OpdfDiscreteFactory

variance() - Method in class be.ac.ulg.montefiore.run.distributions.GaussianDistribution

Returns this distribution's variance.

variance() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussian

Returns this distribution's variance.

variances() - Method in class be.ac.ulg.montefiore.run.jahmm.OpdfGaussianMixture

Returns the mean value of each distribution composing this mixture.

ViterbiCalculator - Class in be.ac.ulg.montefiore.run.jahmm

This class can be used to compute the most probable state sequence matching a given observation sequence (given an HMM).

ViterbiCalculator(List<? extends O>, Hmm<O>) - Constructor for class be.ac.ulg.montefiore.run.jahmm.ViterbiCalculator

Computes the most likely state sequence matching an observation sequence given an HMM.

W

write(OutputStream, Hmm<?>) - Static method in class be.ac.ulg.montefiore.run.jahmm.io.HmmBinaryWriter

Writes a HMM to byte stream.

write(Writer, OpdfWriter<? extends Opdf<O>>, Hmm<O>) - Static method in class be.ac.ulg.montefiore.run.jahmm.io.HmmWriter

Writes a HMM description.

write(ObservationInteger, Writer) - Method in class be.ac.ulg.montefiore.run.jahmm.io.ObservationIntegerWriter

write(ObservationReal, Writer) - Method in class be.ac.ulg.montefiore.run.jahmm.io.ObservationRealWriter

write(Writer, ObservationWriter<? super O>, List<? extends List<O>>) - Static method in class be.ac.ulg.montefiore.run.jahmm.io.ObservationSequencesWriter

Writes a set of sequences to file.

write(ObservationVector, Writer) - Method in class be.ac.ulg.montefiore.run.jahmm.io.ObservationVectorWriter

write(O, Writer) - Method in class be.ac.ulg.montefiore.run.jahmm.io.ObservationWriter

Writes an Observation (followed by a semi-colon) using a Writer.

write(Writer, OpdfGaussianMixture) - Method in class be.ac.ulg.montefiore.run.jahmm.io.OpdfGaussianMixtureWriter

write(Writer, OpdfGaussian) - Method in class be.ac.ulg.montefiore.run.jahmm.io.OpdfGaussianWriter

write(Writer, OpdfInteger) - Method in class be.ac.ulg.montefiore.run.jahmm.io.OpdfIntegerWriter

write(Writer, OpdfMultiGaussian) - Method in class be.ac.ulg.montefiore.run.jahmm.io.OpdfMultiGaussianWriter

write(Writer, O) - Method in class be.ac.ulg.montefiore.run.jahmm.io.OpdfWriter

Writes a textual description of a given Opdf compatible with the corresponding OpdfReader.

write(Writer, double[]) - Method in class be.ac.ulg.montefiore.run.jahmm.io.OpdfWriter

Writes a sequence of numbers.

A B C D E F G H I K L M N O P R S T V W