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## 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`.

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