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

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hasAnySelfTransitions() - Method in interface de.jstacs.models.hmm.Transition

This method answers the question whether the instance models any self transitions.

hasAnySelfTransitions() - Method in class de.jstacs.models.hmm.transitions.BasicHigherOrderTransition

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.models.hmm.training.BaumWelchParameterSet

hasDefaultOrIsSet() - Method in class de.jstacs.models.hmm.training.ViterbiParameterSet

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

hasSampled - Variable in class de.jstacs.models.hmm.models.SamplingHigherOrderHMM

This boolean indicates if the parameters for the model were sampled

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

General temporary array

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.

HigherOrderHMM - Class in de.jstacs.models.hmm.models

This class implements a higher order hidden Markov model.

HigherOrderHMM(HMMTrainingParameterSet, String[], Emission[], BasicHigherOrderTransition.AbstractTransitionElement...) - Constructor for class de.jstacs.models.hmm.models.HigherOrderHMM

This is a convenience constructor.

HigherOrderHMM(HMMTrainingParameterSet, String[], int[], boolean[], Emission[], BasicHigherOrderTransition.AbstractTransitionElement...) - Constructor for class de.jstacs.models.hmm.models.HigherOrderHMM

This is the main constructor.

HigherOrderHMM(StringBuffer) - Constructor for class de.jstacs.models.hmm.models.HigherOrderHMM

The standard constructor for the interface Storable.

HigherOrderHMM.Type - Enum in de.jstacs.models.hmm.models

This enum defined different types of computations that will be done using the backward algorithm.

HigherOrderTransition - Class in de.jstacs.models.hmm.transitions

This class can be used in any AbstractHMM allowing to use gradient based or sampling training algorithm.

HigherOrderTransition(boolean[], TransitionElement...) - Constructor for class de.jstacs.models.hmm.transitions.HigherOrderTransition

The main constructor.

HigherOrderTransition(StringBuffer) - Constructor for class de.jstacs.models.hmm.transitions.HigherOrderTransition

The standard constructor for the interface Storable.

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.

HMMFactory - Class in de.jstacs.models.hmm

This class allows to create some frequently used HMMs.

HMMFactory() - Constructor for class de.jstacs.models.hmm.HMMFactory

HMMFactory.HMMType - Enum in de.jstacs.models.hmm

This enum defines some standard architecture of profile HMMs.

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.

HMMTrainingParameterSet - Class in de.jstacs.models.hmm

This class implements an abstract ParameterSet that is used for the training of an AbstractHMM.

HMMTrainingParameterSet() - Constructor for class de.jstacs.models.hmm.HMMTrainingParameterSet

This is the empty constructor that can be used to fill the parameters after creation.

HMMTrainingParameterSet(int) - Constructor for class de.jstacs.models.hmm.HMMTrainingParameterSet

This constructor can be used to create an instance with a specified number of starts.

HMMTrainingParameterSet(StringBuffer) - Constructor for class de.jstacs.models.hmm.HMMTrainingParameterSet

The standard constructor for the interface 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 ScoringFunctions.

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.

hyperParameters - Variable in class de.jstacs.models.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

The hyperparameters of the prior over the parameters.

hyperParams - Variable in class de.jstacs.models.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission

The hyper-parameters for the prior on the parameters