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

H

hasBeenOptimized - Variable in class de.jstacs.classifier.scoringFunctionBased.ScoreClassifier

This boolean indicates whether the classifier has been optimized with the method AbstractClassifier.train(Sample[]) or the weighted version.

hasBeenOptimized() - Method in class de.jstacs.classifier.scoringFunctionBased.ScoreClassifier

This method returns true if the classifier has been optimized by a train-method.

hasDefault() - Method in class de.jstacs.parameters.CollectionParameter

Returns true, if this CollectionParameter has a default value.

hasDefaultOrIsSet() - Method in class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet

hasDefaultOrIsSet() - Method in class de.jstacs.models.discrete.DGMParameterSet

hasDefaultOrIsSet() - Method in class de.jstacs.models.discrete.homogeneous.parameters.HomogeneousModelParameterSet

hasDefaultOrIsSet() - Method in class de.jstacs.parameters.ArrayParameterSet

hasDefaultOrIsSet() - Method in class de.jstacs.parameters.CollectionParameter

Returns true if all the parameters in this collection are either set by the user or have default values

hasDefaultOrIsSet() - Method in class de.jstacs.parameters.FileParameter

hasDefaultOrIsSet() - Method in class de.jstacs.parameters.MultiSelectionCollectionParameter

hasDefaultOrIsSet() - Method in class de.jstacs.parameters.Parameter

Returns true if the parameter either has a default value or the value was set by the user.

hasDefaultOrIsSet() - Method in class de.jstacs.parameters.ParameterSet

Returns true if all parameters in this ParameterSet are either set by the user or have default values.

hasDefaultOrIsSet() - Method in class de.jstacs.parameters.ParameterSetContainer

hasDefaultOrIsSet() - Method in class de.jstacs.parameters.RangeParameter

hasDefaultOrIsSet() - Method in class de.jstacs.parameters.SequenceScoringParameterSet

hasDefaultOrIsSet() - Method in class de.jstacs.parameters.SimpleParameter

hashCode() - Method in class de.jstacs.data.Sequence

hasMoreElements() - Method in class de.jstacs.data.DiscreteSequenceEnumerator

hasMoreElements() - Method in class de.jstacs.data.Sample.ElementEnumerator

hasMoreElements() - Method in class de.jstacs.io.SparseStringExtractor

hasMoreElements() - Method in class de.jstacs.io.StringExtractor

hasMoreElements() - Method in class de.jstacs.io.SymbolExtractor

hasNext() - Method in class de.jstacs.data.bioJava.SimpleSequenceIterator

HiddenMotifMixture - Class in de.jstacs.models.mixture.motif

This is the main class that every generative motif discoverer should implement.

HiddenMotifMixture(Model[], int, boolean, double[], double[], PositionPrior, boolean, AbstractMixtureModel.Algorithm, double, double, AbstractMixtureModel.Parameterization, int, int, BurnInTest) - Constructor for class de.jstacs.models.mixture.motif.HiddenMotifMixture

Creates a new AbstractMixtureModel.

HiddenMotifMixture(StringBuffer) - Constructor for class de.jstacs.models.mixture.motif.HiddenMotifMixture

The standard constructor for the interface Storable.

hiddenParameter - Variable in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction

This array contains the hidden parameters of the instance.

hiddenPotential - Variable in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction

This array contains the hidden potentials of the instance.

HMM0ScoringFunction - Class in de.jstacs.scoringFunctions.homogeneous

This scoring function implements a homogeneous Markov model of order zero (hMM(0)) for a fixed sequence length.

HMM0ScoringFunction(AlphabetContainer, int, double, boolean, boolean) - Constructor for class de.jstacs.scoringFunctions.homogeneous.HMM0ScoringFunction

The main constructor that creates an instance of a homogeneous Markov model of order 0.

HMM0ScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.homogeneous.HMM0ScoringFunction

This is the constructor for Storable.

HMMScoringFunction - Class in de.jstacs.scoringFunctions.homogeneous

This scoring function implements a homogeneous Markov model of arbitrary order for any sequence length.

HMMScoringFunction(AlphabetContainer, int, double, double[], boolean, boolean, int) - Constructor for class de.jstacs.scoringFunctions.homogeneous.HMMScoringFunction

This is the main constructor.

HMMScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.homogeneous.HMMScoringFunction

This is the constructor for Storable.

HomMMParameterSet - Class in de.jstacs.models.discrete.homogeneous.parameters

This class implements a container for all parameters of a homogeneous Markov model

HomMMParameterSet(StringBuffer) - Constructor for class de.jstacs.models.discrete.homogeneous.parameters.HomMMParameterSet

The constructor for the Storable interface.

HomMMParameterSet() - Constructor for class de.jstacs.models.discrete.homogeneous.parameters.HomMMParameterSet

An empty constructor.

HomMMParameterSet(AlphabetContainer, double, String, byte) - Constructor for class de.jstacs.models.discrete.homogeneous.parameters.HomMMParameterSet

The constructor that sets already the ALphabetContainer, ESS, description and order.

HomogeneousMM - Class in de.jstacs.models.discrete.homogeneous

This class implements homogeneous Markov models (hMM) of arbitrary order.

HomogeneousMM(HomMMParameterSet) - Constructor for class de.jstacs.models.discrete.homogeneous.HomogeneousMM

Creates a homogeneous Markov model from a parameter set.

HomogeneousMM(StringBuffer) - Constructor for class de.jstacs.models.discrete.homogeneous.HomogeneousMM

Creates a homogeneous Markov model from a StringBuffer.

HomogeneousModel - Class in de.jstacs.models.discrete.homogeneous

This class implements homogeneous models.

HomogeneousModel(HomogeneousModelParameterSet) - Constructor for class de.jstacs.models.discrete.homogeneous.HomogeneousModel

Creates a homogeneous model from a parameter set.

HomogeneousModel(StringBuffer) - Constructor for class de.jstacs.models.discrete.homogeneous.HomogeneousModel

Creates a homogeneous model from a StringBuffer.

HomogeneousModel.HomCondProb - Class in de.jstacs.models.discrete.homogeneous

This class handles the (conditional) homogeneous probabilities in a fast way.

HomogeneousModel.HomCondProb(int[], int) - Constructor for class de.jstacs.models.discrete.homogeneous.HomogeneousModel.HomCondProb

The main constructor.

HomogeneousModel.HomCondProb(StringBuffer) - Constructor for class de.jstacs.models.discrete.homogeneous.HomogeneousModel.HomCondProb

Creates an instance from a StringBuffer (see Storable).

HomogeneousModel.HomCondProb(HomogeneousModel.HomCondProb) - Constructor for class de.jstacs.models.discrete.homogeneous.HomogeneousModel.HomCondProb

This constructor is used for cloning instances, since any instance is an inner instance of a HomogeneousModel.

HomogeneousModelParameterSet - Class in de.jstacs.models.discrete.homogeneous.parameters

This class implements a container for all parameters of any homogeneous model.

HomogeneousModelParameterSet(StringBuffer) - Constructor for class de.jstacs.models.discrete.homogeneous.parameters.HomogeneousModelParameterSet

The constructor for the Storable interface.

HomogeneousModelParameterSet(Class<? extends HomogeneousModel>) - Constructor for class de.jstacs.models.discrete.homogeneous.parameters.HomogeneousModelParameterSet

An empty constructor.

HomogeneousModelParameterSet(Class<? extends HomogeneousModel>, AlphabetContainer, double, String, byte) - Constructor for class de.jstacs.models.discrete.homogeneous.parameters.HomogeneousModelParameterSet

The constructor for models, that can handle variable lengths.

HomogeneousScoringFunction - Class in de.jstacs.scoringFunctions.homogeneous

This is the main class for all homogeneous ScoringFunctions.

HomogeneousScoringFunction(AlphabetContainer) - Constructor for class de.jstacs.scoringFunctions.homogeneous.HomogeneousScoringFunction

This is the main constructor that creates an instance that models sequence s of arbitrary length.

HomogeneousScoringFunction(AlphabetContainer, int) - Constructor for class de.jstacs.scoringFunctions.homogeneous.HomogeneousScoringFunction

This is the main constructor that creates an instance that models sequence s of a given length.

HomogeneousScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.homogeneous.HomogeneousScoringFunction

This is the constructor for Storable.