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.

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