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## E

Edge - Class in de.jstacs.algorithms.graphs
  This class is a representation of a weighted edge.
Edge(int, int, double) - Constructor for class de.jstacs.algorithms.graphs.Edge
  Creates a new weighted edge.
emit(int, int...) - Method in class de.jstacs.scoringFunctions.homogeneous.HMMScoringFunction
  This method returns a `Sample` object containing artificial sequence(s).
emitSample(int, int...) - Method in class de.jstacs.models.AbstractModel
emitSample(int, int...) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousModel
  Creates a `Sample` of a given number of `Sequence`s from a trained homogeneous model.
emitSample(int, int...) - Method in class de.jstacs.models.discrete.inhomogeneous.DAGModel
emitSample(int, int...) - Method in class de.jstacs.models.mixture.AbstractMixtureModel
emitSample(int, int...) - Method in interface de.jstacs.models.Model
  This method returns a `Sample` object containing artificial sequence(s).
emitSample(int, int...) - Method in class de.jstacs.models.UniformModel
emitSample(Model, int) - Static method in class de.jstacs.models.utils.DiscreteInhomogenousSampleEmitter
  This method emits a sample with `n`sequences from the discrete inhomogeneous model `m` .``
emitSampleUsingCurrentParameterSet(int, int...) - Method in class de.jstacs.models.mixture.AbstractMixtureModel
  The method returns an array of sequences using the current parameter set.
emitSampleUsingCurrentParameterSet(int, int...) - Method in class de.jstacs.models.mixture.MixtureModel
emitSampleUsingCurrentParameterSet(int, int...) - Method in class de.jstacs.models.mixture.motif.HiddenMotifMixture
  Standard implementation throwing an `OperationNotSupportedException`.
emitSampleUsingCurrentParameterSet(int, int...) - Method in class de.jstacs.models.mixture.StrandModel
EmptySampleException - Exception in de.jstacs.data
  An `EmptySampleException` will be thrown if no `Sequence` is in a `Sample` (i.e. the `Sample` is empty).
EmptySampleException() - Constructor for exception de.jstacs.data.EmptySampleException
  This constructor creates an instance with default error message ("The created Sample is empty.
encode(int[][]) - Static method in class de.jstacs.models.discrete.inhomogeneous.parameters.FSDAGMParameterSet
  This method can be used to encode an adjacency list to a graph description `String` (e.g. for the different constructors which requires graph description `String`s).
enumerate(Sample[], ScoringFunction[], int, int, double, OptimizableFunction, OutputStream) - Static method in class de.jstacs.motifDiscovery.MutableMotifDiscovererToolbox
  This method allows to enumerate all possible seeds for a motif in the `HiddenMotifsMixture` of a specific class.
enumerateHP(Tensor) - Static method in class de.jstacs.algorithms.graphs.DAG
  The method computes the HP(k) (see `DAG`).
EnumParameter - Class in de.jstacs.parameters
  This class implements a `CollectionParameter` based on an `Enum`.
EnumParameter(Class<? extends Enum>, String, boolean) - Constructor for class de.jstacs.parameters.EnumParameter
  The main constructor.
EnumParameter(StringBuffer) - Constructor for class de.jstacs.parameters.EnumParameter
  The standard constructor for the interface `Storable`.
eps - Variable in class de.jstacs.algorithms.optimization.NumericalDifferentiableFunction
  The constant used in the computation of the gradient.
EqualParts - Class in de.jstacs.utils.random
  This class is no real random generator it just returns 1/n for all values.
EqualParts() - Constructor for class de.jstacs.utils.random.EqualParts
equals(Object) - Method in class de.jstacs.data.Sequence
equals(Object) - Method in class de.jstacs.parameters.CollectionParameter
equals(Object) - Method in class de.jstacs.parameters.SequenceScoringParameterSet
equals(Object) - Method in class de.jstacs.parameters.SimpleParameter
EQUALS - Static variable in interface de.jstacs.parameters.validation.Constraint
  The condition is equality
equals(Object) - Method in class de.jstacs.results.SimpleResult
ErlangMRG - Class in de.jstacs.utils.random
  This class is a multivariate random generator based on a Dirichlet distribution for `alpha_i \in N`.
ErlangMRG() - Constructor for class de.jstacs.utils.random.ErlangMRG
  Constructor that creates a new multivariate random generator with underlying Erlang distribution.
ErlangMRGParams - Class in de.jstacs.utils.random
  The container for parameters of an Erlang multivariate random generator.
ErlangMRGParams(int, int) - Constructor for class de.jstacs.utils.random.ErlangMRGParams
  Constructor which creates a new hyperparameter vector for an Erlang random generator.
ErlangMRGParams(int[]) - Constructor for class de.jstacs.utils.random.ErlangMRGParams
  Constructor which creates a new hyperparameter vector for an Erlang random generator.
errorMessage - Variable in class de.jstacs.parameters.CollectionParameter
  If a value was illegal for the collection parameter, this field holds the error message.
errorMessage - Variable in class de.jstacs.parameters.ParameterSet
  The error message of the last error or `null`
errorMessage - Variable in class de.jstacs.parameters.ParameterSetContainer
  The message of the last error or `null` if no error occurred.
errorMessage - Variable in class de.jstacs.parameters.validation.ReferenceConstraint
  The message of the last error or `null`.
ess - Variable in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
  The equivalent sample size.
ess - Variable in class de.jstacs.scoringFunctions.mix.motifSearch.DurationScoringFunction
  The equivalent sample size.
estimate(double) - Method in class de.jstacs.models.discrete.Constraint
  Estimates the (smoothed) relative frequencies using the ess (equivalent sample size).
estimate(double) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousModel.HomCondProb
estimate(double) - Method in class de.jstacs.models.discrete.inhomogeneous.InhCondProb
estimate(double) - Method in class de.jstacs.models.discrete.inhomogeneous.MEMConstraint
estimateComponentProbs - Variable in class de.jstacs.models.mixture.AbstractMixtureModel
  The switch for estimating the component probabilities or not.
estimateParameters(Sample, double[]) - Method in class de.jstacs.models.discrete.inhomogeneous.DAGModel
  This method estimates the parameter of the model from the likelihood or the posterior, respectively.
estimateUnConditional(int, int, double, boolean) - Method in class de.jstacs.models.discrete.Constraint
  Estimates unconditionally.
estimateUnConditional(int, int, double, boolean) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousModel.HomCondProb
estimateUnConditional(double, double) - Method in class de.jstacs.models.discrete.inhomogeneous.InhCondProb
  Estimates the unconditional frequencies using the ess (equivalent sample size).
estimateUnConditional(int, int, double, boolean) - Method in class de.jstacs.models.discrete.inhomogeneous.InhCondProb
eval(String) - Method in class de.jstacs.utils.REnvironment
  Evaluates the `String` as R commands.
evaluate(MeasureParameters, boolean, Sample...) - Method in class de.jstacs.classifier.AbstractClassifier
  This method evaluates the classifier and computes all numerical results as, for instance, the sensitivity for a given specificity, the area under the ROC curve and so on.
evaluateAll(MeasureParameters, boolean, Sample...) - Method in class de.jstacs.classifier.AbstractClassifier
  This method evaluates the classifier and computes all results.
evaluateClassifier(MeasureParameters, ClassifierAssessmentAssessParameterSet, Sample[], ProgressUpdater) - Method in class de.jstacs.classifier.assessment.ClassifierAssessment
  This method must be implemented in all subclasses.
evaluateClassifier(MeasureParameters, ClassifierAssessmentAssessParameterSet, Sample[], ProgressUpdater) - Method in class de.jstacs.classifier.assessment.KFoldCrossValidation
  Evaluates a classifier.
evaluateClassifier(MeasureParameters, ClassifierAssessmentAssessParameterSet, Sample[], ProgressUpdater) - Method in class de.jstacs.classifier.assessment.RepeatedHoldOutExperiment
  Evaluates the classifier.
evaluateClassifier(MeasureParameters, ClassifierAssessmentAssessParameterSet, Sample[], ProgressUpdater) - Method in class de.jstacs.classifier.assessment.RepeatedSubSamplingExperiment
  Evaluates the classifier.
evaluateClassifier(MeasureParameters, ClassifierAssessmentAssessParameterSet, Sample[], ProgressUpdater) - Method in class de.jstacs.classifier.assessment.Sampled_RepeatedHoldOutExperiment
evaluateFunction(double[]) - Method in interface de.jstacs.algorithms.optimization.Function
  Evaluates the function at a certain vector (in mathematical sense) `x`.
evaluateFunction(double[]) - Method in class de.jstacs.algorithms.optimization.NegativeDifferentiableFunction
evaluateFunction(double[]) - Method in class de.jstacs.algorithms.optimization.NegativeFunction
evaluateFunction(double[]) - Method in class de.jstacs.algorithms.optimization.NegativeOneDimensionalFunction
evaluateFunction(double) - Method in class de.jstacs.algorithms.optimization.NegativeOneDimensionalFunction
evaluateFunction(double[]) - Method in class de.jstacs.algorithms.optimization.OneDimensionalFunction
evaluateFunction(double) - Method in class de.jstacs.algorithms.optimization.OneDimensionalFunction
  Evaluates the function at position `x`.
evaluateFunction(double) - Method in class de.jstacs.algorithms.optimization.OneDimensionalSubFunction
evaluateFunction(double) - Method in class de.jstacs.algorithms.optimization.QuadraticFunction
evaluateFunction(double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.cll.NormConditionalLogLikelihood
evaluateFunction(double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.CompositeLogPrior
evaluateFunction(double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.DoesNothingLogPrior
evaluateFunction(double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.SeparateGaussianLogPrior
evaluateFunction(double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.SeparateLaplaceLogPrior
evaluateFunction(double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.SimpleGaussianSumLogPrior
evaluateGradientOfFunction(double[]) - Method in class de.jstacs.algorithms.optimization.DifferentiableFunction
  Evaluates the gradient of a function at a certain vector (in mathematical sense) `x`.
evaluateGradientOfFunction(double[]) - Method in class de.jstacs.algorithms.optimization.NegativeDifferentiableFunction
evaluateGradientOfFunction(double[]) - Method in class de.jstacs.algorithms.optimization.NumericalDifferentiableFunction
  Evaluates the gradient of a function at a certain vector (in mathematical sense) `x` numerically.
evaluateGradientOfFunction(double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.cll.NormConditionalLogLikelihood
evaluateGradientOfFunction(double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.LogPrior
EvaluationException - Exception in de.jstacs.algorithms.optimization
  This class indicates that there was a problem to evaluate a function or the gradient of the function.
EvaluationException(String) - Constructor for exception de.jstacs.algorithms.optimization.EvaluationException
  This constructor creates an `EvaluationException` with given error `message`.
ExpandableParameterSet - Class in de.jstacs.parameters
  A class for a `ParameterSet` that can be expanded by additional `Parameter`s at runtime.
ExpandableParameterSet(ParameterSet, String, String) - Constructor for class de.jstacs.parameters.ExpandableParameterSet
  Creates a new `ExpandableParameterSet` from a `Class` that can be instantiated using this `ExpandableParameterSet` and templates for the `ParameterSet` in each element of the array, the name and the comment that are displayed for the `ParameterSetContainer`s enclosing the `ParameterSet`s.
ExpandableParameterSet(ParameterSet, String, String, int) - Constructor for class de.jstacs.parameters.ExpandableParameterSet
  Creates a new `ExpandableParameterSet` from a `Class` that can be instantiated using this `ExpandableParameterSet` and templates for the `ParameterSet` in each element of the array, the name and the comment that are displayed for the `ParameterSetContainer`s enclosing the `ParameterSet`s.
ExpandableParameterSet(StringBuffer) - Constructor for class de.jstacs.parameters.ExpandableParameterSet
  The standard constructor for the interface `Storable`.
ExpandableParameterSet(ParameterSet[], String, String) - Constructor for class de.jstacs.parameters.ExpandableParameterSet
  Creates a new `ExpandableParameterSet` from a `ParameterSet` -array.
extendSampling(int) - Method in class de.jstacs.models.mixture.AbstractMixtureModel
  This method prepares the model to extend an existing sampling.
extendSampling(int, boolean) - Method in class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSampling
extendSampling(int, boolean) - Method in interface de.jstacs.models.mixture.gibbssampling.GibbsSamplingComponent
  This method allows to extend a sampling.
extract(int, String) - Static method in class de.jstacs.models.discrete.ConstraintManager
  Extracts the constraints of a `String` and returns an `ArrayList` of `int[]`.
extractAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.Constraint
  This method parses additional information from the `StringBuffer` that is not parsed in the base class.
extractAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousModel.HomCondProb
extractAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.inhomogeneous.InhCondProb
extractAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.inhomogeneous.InhConstraint
extractAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.inhomogeneous.MEMConstraint
extractAdditionalInformation(StringBuffer) - Method in class de.jstacs.models.mixture.motif.positionprior.GaussianLikePositionPrior
extractAdditionalInformation(StringBuffer) - Method in class de.jstacs.models.mixture.motif.positionprior.PositionPrior
  This method extracts additional information from a `StringBuffer`.
extractAdditionalInformation(StringBuffer) - Method in class de.jstacs.models.mixture.motif.positionprior.UniformPositionPrior
extractBoolean2ArrayForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as a two dimensional `boolean` array.
extractBoolean2ArrayForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as a two dimensional `boolean` array.
extractBooleanArrayForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as a `boolean` array.
extractBooleanArrayForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as a `boolean` array.
extractBooleanForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as `boolean`.
extractBooleanForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as `boolean`.
extractByte2ArrayForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as a two dimensional `byte` array.
extractByte2ArrayForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as a two dimensional `byte` array.
extractByteArrayForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as a `byte` array.
extractByteArrayForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as a `byte` array.
extractByteForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as `byte`.
extractByteForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as `byte`.
extractCollection(StringBuffer) - Method in class de.jstacs.parameters.CollectionParameter
  Extracts the internal `ParameterSet` from its XML representation ( `ParameterSet.toXML()`).
extractCollection(StringBuffer) - Method in class de.jstacs.parameters.EnumParameter
extractDouble2ArrayForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as a two dimensional `double` array.
extractDouble2ArrayForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as a two dimensional `double` array.
extractDoubleArrayForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as a `double` array.
extractDoubleArrayForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as a `double` array.
extractDoubleForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as `double` .
extractDoubleForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as `double`.
extractEnumForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the enumeration between equal start and end tags as `Enum`.
extractEnumForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the enumeration between start and end tag as `Enum`.
extractForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Extracts the code between equal start and end tags and returns the substring between the tags as new `StringBuffer`.
extractForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Extracts the code between start and end tag and returns the substring between the tags as new `StringBuffer`.
extractFurtherClassifierInfosFromXML(StringBuffer) - Method in class de.jstacs.classifier.AbstractClassifier
  Extracts further information of a classifier from an XML representation.
extractFurtherClassifierInfosFromXML(StringBuffer) - Method in class de.jstacs.classifier.AbstractScoreBasedClassifier
extractFurtherClassifierInfosFromXML(StringBuffer) - Method in class de.jstacs.classifier.MappingClassifier
extractFurtherClassifierInfosFromXML(StringBuffer) - Method in class de.jstacs.classifier.modelBased.ModelBasedClassifier
extractFurtherClassifierInfosFromXML(StringBuffer) - Method in class de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifier
extractFurtherClassifierInfosFromXML(StringBuffer) - Method in class de.jstacs.classifier.scoringFunctionBased.ScoreClassifier
extractFurtherClassifierInfosFromXML(StringBuffer) - Method in class de.jstacs.models.discrete.inhomogeneous.shared.SharedStructureClassifier
extractFurtherInformation(StringBuffer) - Method in class de.jstacs.models.mixture.AbstractMixtureModel
  This method is used in the subclasses to extract further information from the XML representation and to set these as values of the instance.
extractFurtherInformation(StringBuffer) - Method in class de.jstacs.models.mixture.motif.HiddenMotifMixture
extractFurtherInformation(StringBuffer) - Method in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
  This method is the opposite of `AbstractMixtureScoringFunction.getFurtherInformation()`.
extractFurtherInformation(StringBuffer) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.HiddenMotifsMixture
extractFurtherInformation(StringBuffer) - Method in class de.jstacs.scoringFunctions.mix.StrandScoringFunction
extractInt2ArrayForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as a two dimensional `int` array.
extractInt2ArrayForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as a two dimensional `int` array.
extractIntArrayForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as an `int` array.
extractIntArrayForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as an `int` array.
extractIntForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as `int`.
extractIntForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as `int`.
extractLongForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as `long`.
extractLongForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as `long`.
extractMainInfo(StringBuffer) - Method in class de.jstacs.results.Result
  This method can be used in the method `Result.fromXML(StringBuffer)` to extract the main information (name, comment, data type).
extractStorable2ArrayForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as a two dimensional `Storable` array.
extractStorable2ArrayForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as a two dimensional `Storable` array.
extractStorable3ArrayForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as a three dimensional `Storable` array.
extractStorable3ArrayForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as a three dimensional `Storable` array.
extractStorableArrayForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as a `Storable` array.
extractStorableArrayForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as a `Storable` array.
extractStorableForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as `Storable`.
extractStorableForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as `Storable`.
extractStorableOrNullForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as `Storable` or `null`.
extractStorableOrNullForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as `Storable` or `null`.
extractString2ArrayForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as a two dimensional `String` array.
extractString2ArrayForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as a two dimensional `String` array.
extractStringArrayForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as a `String` array.
extractStringArrayForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as a `String` array.
extractStringForTag(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between equal start and end tags as a `String`.
extractStringForTag(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Returns the value between start and end tag as a `String`.

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