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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 indicates 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
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, `false` otherwise.
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.ParameterSetTagger
  This method allows to check whether all tagged parameters that require a value also have some value.
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
hashCodeForPos(int) - Method in class de.jstacs.data.Sequence
  This method is used in `Sequence.hashCode()` and the hash code for one specific position.
hashCodeForPos(int) - Method in class de.jstacs.data.Sequence.RecursiveSequence
hashCodeForPos(int) - Method in class de.jstacs.data.sequences.ArbitrarySequence
hashCodeForPos(int) - Method in class de.jstacs.data.sequences.MultiDimensionalDiscreteSequence
hashCodeForPos(int) - Method in class de.jstacs.data.sequences.SimpleDiscreteSequence
hasMoreElements() - Method in class de.jstacs.data.DiscreteSequenceEnumerator
hasMoreElements() - Method in class de.jstacs.data.Sample.ElementEnumerator
hasMoreElements() - Method in class de.jstacs.data.SampleKMerEnumerator
hasMoreElements() - Method in class de.jstacs.data.SequenceEnumeration
hasMoreElements() - Method in class de.jstacs.io.InfixStringExtractor
hasMoreElements() - Method in class de.jstacs.io.LimitedStringExtractor
hasMoreElements() - Method in class de.jstacs.io.SimpleStringExtractor
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
hasNext() - Method in class de.jstacs.data.Sample.ElementEnumerator
hasTag(StringBuffer, String, Map<String, String>, Map<String, String>) - Static method in class de.jstacs.io.XMLParser
  This method allows to check whether an XML contains a tagged entry.
helpArray - Variable in class de.jstacs.classifier.scoringFunctionBased.gendismix.LogGenDisMixFunction
HiddenMotifMixture - Class in de.jstacs.models.mixture.motif
  This is the main class that every generative motif discoverer should implement.
HiddenMotifMixture(Model[], boolean[], int, int, boolean, double[], double[], PositionPrior, AbstractMixtureModel.Algorithm, double, TerminationCondition, AbstractMixtureModel.Parameterization, int, int, BurnInTest) - Constructor for class de.jstacs.models.mixture.motif.HiddenMotifMixture
  Creates a new `HiddenMotifMixture`.
HiddenMotifMixture(StringBuffer) - Constructor for class de.jstacs.models.mixture.motif.HiddenMotifMixture
  The standard constructor for the interface `Storable`.
HiddenMotifsMixture - Class in de.jstacs.scoringFunctions.mix.motifSearch
  This class handles mixtures with at least one hidden motif.
HiddenMotifsMixture(boolean, int, int, boolean, HomogeneousScoringFunction, NormalizableScoringFunction, DurationScoringFunction, boolean) - Constructor for class de.jstacs.scoringFunctions.mix.motifSearch.HiddenMotifsMixture
  This constructor creates an instance of `HiddenMotifsMixture` that is either an OOPS or a ZOOPS model depending on the chosen `type`.
HiddenMotifsMixture(boolean, int, int, boolean, HomogeneousScoringFunction, NormalizableScoringFunction[], DurationScoringFunction[], boolean) - Constructor for class de.jstacs.scoringFunctions.mix.motifSearch.HiddenMotifsMixture
  This constructor creates an instance of `HiddenMotifsMixture` that allows to have one site of the specified motifs in a `Sequence`.
HiddenMotifsMixture(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.mix.motifSearch.HiddenMotifsMixture
  This is the 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.
History - Interface in de.jstacs.motifDiscovery.history
  This interface is used to manage the history of some process.
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, int) - Constructor for class de.jstacs.scoringFunctions.homogeneous.HMMScoringFunction
  This is a convenience constructor for creating an instance of a homogeneous Markov model of arbitrary order.
HMMScoringFunction(AlphabetContainer, int, double, double[], boolean, boolean, int) - Constructor for class de.jstacs.scoringFunctions.homogeneous.HMMScoringFunction
  This is the main constructor that creates an instance of a homogeneous Markov model of arbitrary order.
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 standard constructor for the interface `Storable`.
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
  Creates a new `HomMMParameterSet` with `AlphabetContainer`, ess (equivalent sample size), description and order of the homogeneous Markov model.
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 new homogeneous Markov model from a parameter set.
HomogeneousMM(StringBuffer) - Constructor for class de.jstacs.models.discrete.homogeneous.HomogeneousMM
  The standard constructor for the interface `Storable`.
HomogeneousModel - Class in de.jstacs.models.discrete.homogeneous
  This class implements homogeneous models of arbitrary order.
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
  The standard constructor for the interface `Storable`.
HomogeneousModel.HomCondProb - Class in de.jstacs.models.discrete.homogeneous
  This class handles the (conditional) probabilities of a homogeneous model 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
  The standard constructor for the interface `Storable` .
HomogeneousModel.HomCondProb(HomogeneousModel.HomCondProb) - Constructor for class de.jstacs.models.discrete.homogeneous.HomogeneousModel.HomCondProb
  Creates a new `HomogeneousModel.HomCondProb` instance from a given one.
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 standard constructor for the interface `Storable`.
HomogeneousModelParameterSet(Class<? extends HomogeneousModel>) - Constructor for class de.jstacs.models.discrete.homogeneous.parameters.HomogeneousModelParameterSet
  This is the constructor that creates an empty `HomogeneousModelParameterSet` from the class that can be instantiated using this `HomogeneousModelParameterSet`.
HomogeneousModelParameterSet(Class<? extends HomogeneousModel>, AlphabetContainer, double, String, byte) - Constructor for class de.jstacs.models.discrete.homogeneous.parameters.HomogeneousModelParameterSet
  Creates a new `HomogeneousModelParameterSet` with `AlphabetContainer`, ess (equivalent sample size), description and order of the homogeneous Markov model.
HomogeneousScoringFunction - Class in de.jstacs.scoringFunctions.homogeneous
  This is the main class for all homogeneous `ScoringFunction`s.
HomogeneousScoringFunction(AlphabetContainer) - Constructor for class de.jstacs.scoringFunctions.homogeneous.HomogeneousScoringFunction
  This is the main constructor that creates an instance of a `HomogeneousScoringFunction` that models sequences of arbitrary length.
HomogeneousScoringFunction(AlphabetContainer, int) - Constructor for class de.jstacs.scoringFunctions.homogeneous.HomogeneousScoringFunction
  This is the main constructor that creates an instance of a `HomogeneousScoringFunction` that models sequences of a given length.
HomogeneousScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.homogeneous.HomogeneousScoringFunction
  This is the constructor for `Storable`.

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