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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 Parameter
s 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 ParameterSetContainer
s enclosing the ParameterSet
s.
- 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 ParameterSetContainer
s enclosing the ParameterSet
s.
- 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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