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

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

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.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, inhomogenous 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.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 message.

encode(int[][]) - Static method in class de.jstacs.models.discrete.inhomogeneous.parameters.FSDAGMParameterSet

This method can be used to encode adjacency list to a graph description string.

enumerateHP(Tensor) - Static method in class de.jstacs.algorithms.graphs.DAG

The method computes the HP(k).

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

Restores an instance of EnumParameter from a string representation

eps - Variable in class de.jstacs.algorithms.optimization.NumericalDifferentiableFunction

The constant used in the computation of the gradient.

equalDistributed() - Static method in class de.jstacs.utils.random.UnivariateRandomGenerator

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.InstanceParameterSet

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

erlangDistributed(int) - Static method in class de.jstacs.utils.random.UnivariateRandomGenerator

gamma distributed for alpha \in N.

erlangDistributed(int, Random) - Static method in class de.jstacs.utils.random.UnivariateRandomGenerator

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

ErlangMRGParams - Class in de.jstacs.utils.random

The container for paramater of a Erlang random generator.

ErlangMRGParams(int, int) - Constructor for class de.jstacs.utils.random.ErlangMRGParams

ErlangMRGParams(int[]) - Constructor for class de.jstacs.utils.random.ErlangMRGParams

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

estimate(double) - Method in class de.jstacs.models.discrete.Constraint

Estimates the (smoothed) relative frequencies using the ess.

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 respectively posterior.

estimateUnConditional(int, int, double, boolean) - Method in class de.jstacs.models.discrete.Constraint

Estimates unconditionally.

estimateUnConditional(double, double) - Method in class de.jstacs.models.discrete.inhomogeneous.InhCondProb

Estimates the unconditional frequencies using the ess.

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 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

evaluateClassifier(MeasureParameters, ClassifierAssessmentAssessParameterSet, Sample[], ProgressUpdater) - Method in class de.jstacs.classifier.assessment.RepeatedHoldOutExperiment

evaluateClassifier(MeasureParameters, ClassifierAssessmentAssessParameterSet, Sample[], ProgressUpdater) - Method in class de.jstacs.classifier.assessment.RepeatedSubSamplingExperiment

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.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 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 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 message

ExpandableParameterSet - Class in de.jstacs.parameters

A class for a ParameterSet that can be expanded by additional Parameters at runtime.

ExpandableParameterSet(Class, 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 ParameterSetContainers enclosing the ParameterSets.

ExpandableParameterSet(Class, 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 ParameterSetContainers enclosing the ParameterSets.

ExpandableParameterSet(StringBuffer) - Constructor for class de.jstacs.parameters.ExpandableParameterSet

Creates a new ExpandableParameterSet from its XML-representation.

ExpandableParameterSet(Class, ParameterSet[], String, String) - Constructor for class de.jstacs.parameters.ExpandableParameterSet

Creates a new ExpandableParameterSet from a ParameterSet-array.

exponentialDistributed() - Static method in class de.jstacs.utils.random.UnivariateRandomGenerator

extendSampling(int) - Method in class de.jstacs.models.mixture.AbstractMixtureModel

This method prepares the model to extend a 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 constraint of a String and returns an ArrayList of byte[].

extractAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.Constraint

This method parses additional information from the StringBuffer that are not parsed in the base class.

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

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

Returns the substring between start and end tag as 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.scoringFunctions.mix.AbstractMixtureScoringFunction

This method is the opposite of AbstractMixtureScoringFunction.getFurtherInformation().

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 fromXML-method to extract the main information (name, comment, datatype).

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.