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

C

canBeCastedFromTo(DataType, DataType) - Static method in enum de.jstacs.DataType
Checks if the DataType from can be casted to the DataType to without loosing information.
cast(T...) - Static method in class de.jstacs.io.ArrayHandler
This method creates a new array of the super class of all elements of the given array and copies the elements.
CategoricalResult - Class in de.jstacs.results
A class for categorical results (i.e. non-numerical results) for primitives and Strings
CategoricalResult(StringBuffer) - Constructor for class de.jstacs.results.CategoricalResult
Creates a new CategoricalResult from its XML-representation.
CategoricalResult(DataType, String, String, Comparable) - Constructor for class de.jstacs.results.CategoricalResult
Creates a result of a primitive categorical datatype or a String
CategoricalResult(String, String, String) - Constructor for class de.jstacs.results.CategoricalResult
Creates a result of a String.
CategoricalResult(String, String, boolean) - Constructor for class de.jstacs.results.CategoricalResult
Creates a result of a boolean.
check(Sample) - Method in class de.jstacs.classifier.AbstractScoreBasedClassifier
This method checks if the given sample can be used.
check(Sequence) - Method in class de.jstacs.classifier.AbstractScoreBasedClassifier
This method checks if the given sequence can be used.
check(Sequence, int, int) - Method in class de.jstacs.models.discrete.DiscreteGraphicalModel
Checks some conditions on a sequence.
check(Sequence, int, int) - Method in class de.jstacs.models.discrete.inhomogeneous.InhomogeneousDGM
 
check(Object) - Method in interface de.jstacs.parameters.validation.Constraint
Checks value for the constraint defined in the Constraint.
check(Object) - Method in class de.jstacs.parameters.validation.ReferenceConstraint
 
check(Object) - Method in class de.jstacs.parameters.validation.SimpleReferenceConstraint
 
check(Object) - Method in class de.jstacs.parameters.validation.SimpleStaticConstraint
 
checkAcyclic(int, int[][]) - Static method in class de.jstacs.models.discrete.inhomogeneous.DAGModel
This method checks whether a given graph is acyclic.
checkConsistency(Alphabet) - Method in class de.jstacs.data.Alphabet
Checks if two alphabets are consistent, i.e. both alphabets use the same symbols.
checkConsistency(AlphabetContainer) - Method in class de.jstacs.data.AlphabetContainer
Checks whether to alphabets are consistent.
checkDatatype(DataType, Object) - Static method in class de.jstacs.results.Result
This method provides the possibility to check the compliance of some result value with one of the pre-defined DataTypes before creating a new Result and possibly running into an Exception.
checkLength(int, int) - Method in class de.jstacs.models.mixture.AbstractMixtureModel
This method checks if the length l of the model with index index is capable for the current instance.
checkModelsForGibbsSampling() - Method in class de.jstacs.models.mixture.AbstractMixtureModel
This method can be used to check whether the necessary models have implemented the GibbsSamplingComponent.
checkValue(Object) - Method in class de.jstacs.parameters.CollectionParameter
Returns true if the key specified by value is in the set of keys of this CollectionParameter.
checkValue(Object) - Method in class de.jstacs.parameters.FileParameter
 
checkValue(Object) - Method in class de.jstacs.parameters.MultiSelectionCollectionParameter
 
checkValue(Object) - Method in class de.jstacs.parameters.Parameter
Checks the value for correctness, e.g. for numerical parameters this might be checking if the value is within specified bounds
checkValue(Object) - Method in class de.jstacs.parameters.ParameterSetContainer
 
checkValue(Object) - Method in class de.jstacs.parameters.RangeParameter
 
checkValue(Object) - Method in class de.jstacs.parameters.SimpleParameter
 
checkValue(Object) - Method in class de.jstacs.parameters.validation.ConstraintValidator
 
checkValue(Object) - Method in class de.jstacs.parameters.validation.NumberValidator
 
checkValue(Object) - Method in interface de.jstacs.parameters.validation.ParameterValidator
Returns true if the value is valid and false otherwise
checkValue(Object) - Method in class de.jstacs.parameters.validation.StorableValidator
Checks the value of value.
Chu_Liu_Edmonds - Class in de.jstacs.algorithms.graphs
This class implements the algorithm of Chu_Liu_Edmonds to determine an optimal branching (optimal directed graph of order 1).
CisRegulatoryModuleAnnotation - Class in de.jstacs.data.sequences.annotation
Annotation for a cis-regulatory module as defined by a set of MotifAnnotations of the motifs in the module.
CisRegulatoryModuleAnnotation(String, MotifAnnotation[], Result...) - Constructor for class de.jstacs.data.sequences.annotation.CisRegulatoryModuleAnnotation
Creates a new CisRegulatoryModuleAnnotation from a set of motifs and possibly additional annotations.
CisRegulatoryModuleAnnotation(StringBuffer) - Constructor for class de.jstacs.data.sequences.annotation.CisRegulatoryModuleAnnotation
Re-creates a CisRegulatoryModuleAnnotation from its XML-representation as returned by SequenceAnnotation.toXML().
ClassDimensionException - Exception in de.jstacs.classifier
This class indicates that the classifier should be defined for less than 2 classes or is defined over a different number of classes than given (e.g. by an array of Samples).
ClassDimensionException() - Constructor for exception de.jstacs.classifier.ClassDimensionException
This constructor creates an instance with default message.
ClassDimensionException(String) - Constructor for exception de.jstacs.classifier.ClassDimensionException
This constructor creates a instance with given message.
Classification - Class in de.jstacs.classifier
This class contains a main-method that allows to compute some performance measures in a very simple way.
Classification() - Constructor for class de.jstacs.classifier.Classification
 
ClassificationVisualizer - Class in de.jstacs.classifier.utils
This class enables you to visualize some classifier results.
ClassifierAssessment - Class in de.jstacs.classifier.assessment
Class defining an assessment of classifiers.
ClassifierAssessment(AbstractClassifier[], Model[][], boolean, boolean) - Constructor for class de.jstacs.classifier.assessment.ClassifierAssessment
Creates a new ClassifierAssessment from an array of AbstractClassifiers and a two-dimensional array of Models, which are combined to additional classifiers.
ClassifierAssessment(AbstractClassifier...) - Constructor for class de.jstacs.classifier.assessment.ClassifierAssessment
Creates a new ClassifierAssessment from a set of AbstractClassifiers.
ClassifierAssessment(boolean, Model[]...) - Constructor for class de.jstacs.classifier.assessment.ClassifierAssessment
Creates a new ClassifierAssessment from a set of Models.
ClassifierAssessment(AbstractClassifier[], boolean, Model[]...) - Constructor for class de.jstacs.classifier.assessment.ClassifierAssessment
This constructor allows to assess a collection of given AbstractClassifiers and those constructed using the given AbstractModels.
ClassifierAssessmentAssessParameterSet - Class in de.jstacs.classifier.assessment
This class is the super-class used by all ClassifierAssessmentAssessParameterSets.
ClassifierAssessmentAssessParameterSet(Class) - Constructor for class de.jstacs.classifier.assessment.ClassifierAssessmentAssessParameterSet
inherited from ParameterSet
ClassifierAssessmentAssessParameterSet() - Constructor for class de.jstacs.classifier.assessment.ClassifierAssessmentAssessParameterSet
inherited from ParameterSet
ClassifierAssessmentAssessParameterSet(StringBuffer) - Constructor for class de.jstacs.classifier.assessment.ClassifierAssessmentAssessParameterSet
inherited from ParameterSet
ClassifierAssessmentAssessParameterSet(int, boolean) - Constructor for class de.jstacs.classifier.assessment.ClassifierAssessmentAssessParameterSet
 
classify(Sequence) - Method in class de.jstacs.classifier.AbstractClassifier
This method classifies a sequence and returns the index i, with 0 < i < getNumberOfClasses(), of the class to which the sequence is assigned.
classify(Sample) - Method in class de.jstacs.classifier.AbstractClassifier
This method classifies all sequences of a sample and returns the index i, with 0 < i < getNumberOfClasses(), of the class to which the sequence is assigned.
classify(Sequence) - Method in class de.jstacs.classifier.AbstractScoreBasedClassifier
 
classify(Sequence, boolean) - Method in class de.jstacs.classifier.AbstractScoreBasedClassifier
This method classifies a sequence.
classify(Sample) - Method in class de.jstacs.classifier.modelBased.ModelBasedClassifier
 
classMus - Variable in class de.jstacs.classifier.scoringFunctionBased.logPrior.SeparateLogPrior
The means for the class parameters, as specified by the user
classVars - Variable in class de.jstacs.classifier.scoringFunctionBased.logPrior.SeparateLogPrior
The variances for the class parameters, as specified by the user
clear() - Method in class de.jstacs.utils.DoubleList
Removes all elements from the list.
clear() - Method in class de.jstacs.utils.IntList
Removes all elements from the list.
CLLClassifier - Class in de.jstacs.classifier.scoringFunctionBased.cll
This class implements the conditional log likelihood classifier.
CLLClassifier(CLLClassifierParameterSet, ScoringFunction...) - Constructor for class de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifier
The default constructor.
CLLClassifier(CLLClassifierParameterSet, LogPrior, ScoringFunction...) - Constructor for class de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifier
The default constructor.
CLLClassifier(StringBuffer) - Constructor for class de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifier
This is the constructor for Storable.
CLLClassifierParameterSet - Class in de.jstacs.classifier.scoringFunctionBased.cll
This class contains the parameters for the CLLClassifier.
CLLClassifierParameterSet(StringBuffer) - Constructor for class de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifierParameterSet
This is the constructor for Storable.
CLLClassifierParameterSet(AlphabetContainer, int, byte, double, double, double, boolean, boolean, boolean) - Constructor for class de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifierParameterSet
The default constructor.
clone() - Method in class de.jstacs.algorithms.graphs.Edge
 
clone() - Method in class de.jstacs.classifier.AbstractClassifier
 
clone() - Method in class de.jstacs.classifier.AbstractScoreBasedClassifier
 
clone() - Method in class de.jstacs.classifier.modelBased.ModelBasedClassifier
 
clone() - Method in class de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifier
 
clone() - Method in class de.jstacs.classifier.scoringFunctionBased.ScoreClassifier
 
clone() - Method in class de.jstacs.data.Alphabet.AlphabetParameterSet
 
clone() - Method in class de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet
 
clone() - Method in class de.jstacs.data.AlphabetContainerParameterSet
 
clone() - Method in class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
 
clone(T...) - Static method in class de.jstacs.io.ArrayHandler
This method returns a deep copy of an array, i.e. for each element of the array the clone method will be invoked.
clone() - Method in class de.jstacs.models.AbstractModel
Follows the conventions of Object's clone-method.
clone() - Method in class de.jstacs.models.CompositeModel
 
clone() - Method in class de.jstacs.models.discrete.Constraint
 
clone() - Method in class de.jstacs.models.discrete.DGMParameterSet
 
clone() - Method in class de.jstacs.models.discrete.DiscreteGraphicalModel
 
clone() - Method in class de.jstacs.models.discrete.inhomogeneous.BayesianNetworkModel
 
clone() - Method in class de.jstacs.models.discrete.inhomogeneous.DAGModel
 
clone() - Method in class de.jstacs.models.discrete.inhomogeneous.InhCondProb
 
clone() - Method in class de.jstacs.models.discrete.inhomogeneous.InhConstraint
 
clone() - Method in class de.jstacs.models.discrete.inhomogeneous.InhomogeneousDGM
 
clone() - Method in class de.jstacs.models.discrete.inhomogeneous.MEMConstraint
 
clone() - Method in class de.jstacs.models.discrete.inhomogeneous.shared.SharedStructureClassifier
 
clone() - Method in class de.jstacs.models.discrete.inhomogeneous.shared.SharedStructureMixture
 
clone() - Method in class de.jstacs.models.mixture.AbstractMixtureModel
 
clone() - Method in class de.jstacs.models.mixture.gibbssampling.BurnInTest
 
clone() - Method in class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSampling
In this method the reader is set to null
clone() - Method in interface de.jstacs.models.Model
Creates a clone (deep copy) of the current Model instance.
clone() - Method in class de.jstacs.models.UniformModel
 
clone() - Method in class de.jstacs.parameters.CollectionParameter
 
clone() - Method in class de.jstacs.parameters.ExpandableParameterSet
 
clone() - Method in class de.jstacs.parameters.FileParameter
 
clone() - Method in class de.jstacs.parameters.FileParameter.FileRepresentation
 
clone() - Method in class de.jstacs.parameters.InstanceParameterSet
 
clone() - Method in class de.jstacs.parameters.MultiSelectionCollectionParameter
 
clone() - Method in class de.jstacs.parameters.Parameter
 
clone() - Method in class de.jstacs.parameters.ParameterSet
Creates a full clone (deep copy) of this ParameterSet.
clone() - Method in class de.jstacs.parameters.ParameterSetContainer
 
clone() - Method in class de.jstacs.parameters.RangeParameter
 
clone() - Method in class de.jstacs.parameters.SimpleParameter
 
clone() - Method in class de.jstacs.parameters.SimpleParameterSet
 
clone() - Method in interface de.jstacs.parameters.validation.Constraint
This method returns a deep copy of the current instance.
clone() - Method in class de.jstacs.parameters.validation.ConstraintValidator
 
clone() - Method in class de.jstacs.parameters.validation.NumberValidator
 
clone() - Method in interface de.jstacs.parameters.validation.ParameterValidator
This method returns a deep copy of the current instance.
clone() - Method in class de.jstacs.parameters.validation.ReferenceConstraint
 
clone() - Method in class de.jstacs.parameters.validation.SimpleReferenceConstraint
 
clone() - Method in class de.jstacs.parameters.validation.SimpleStaticConstraint
 
clone() - Method in class de.jstacs.parameters.validation.StorableValidator
 
clone() - Method in class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
 
clone() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
 
clone() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
 
clone() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree
 
clone() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual
 
clone() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation
 
clone() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.InhomogeneousMarkov
 
clone() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.Measure
 
clone() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMExplainingAwayResidual
 
clone() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation
 
clone() - Method in class de.jstacs.scoringFunctions.homogeneous.HMM0ScoringFunction
 
clone() - Method in class de.jstacs.scoringFunctions.homogeneous.HMMScoringFunction
 
clone() - Method in class de.jstacs.scoringFunctions.IndependentProductScoringFunction
 
clone() - Method in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
 
clone() - Method in class de.jstacs.scoringFunctions.MRFScoringFunction
 
clone() - Method in interface de.jstacs.scoringFunctions.ScoringFunction
Creates a clone (deep copy) of the current ScoringFunction instance.
cloneFunctions(NormalizableScoringFunction[]) - Method in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
This method clones the given array of function and enables the user to do some postprocessing.
close() - Method in class de.jstacs.utils.NullProgressUpdater
closes the supervision
close() - Method in class de.jstacs.utils.REnvironment
Close the Renviroment and removes all files from the server.
close() - Method in class de.jstacs.utils.SafeOutputStream
Closes this SafeOutputStream by closing the OutputStream this stream was constructed of.
CollectionParameter - Class in de.jstacs.parameters
Class for a collection parameter, i.e. a parameter that provides some collection of possible values the user can choose from.
CollectionParameter(ParameterSet, int, int, boolean, String, String, boolean, DataType, String, boolean) - Constructor for class de.jstacs.parameters.CollectionParameter
Creates a new CollectionParameter from the necessary field.
CollectionParameter(DataType, String[], Object[], String, String, boolean) - Constructor for class de.jstacs.parameters.CollectionParameter
Constructor for a CollectionParameter.
CollectionParameter(DataType, String[], Object[], String[], String, String, boolean) - Constructor for class de.jstacs.parameters.CollectionParameter
Constructor for a CollectionParameter.
CollectionParameter(ParameterSet[], String, String, boolean) - Constructor for class de.jstacs.parameters.CollectionParameter
Constructor for a CollectionParameter from an array of ParameterSets.
CollectionParameter(StringBuffer) - Constructor for class de.jstacs.parameters.CollectionParameter
Restores an instance of CollectionParameter from a string representation
CollectionParameter.InconsistentCollectionException - Exception in de.jstacs.parameters
This exception is thrown if the CollectionParameter is inconsistent for some reason
CollectionParameter.InconsistentCollectionException(String) - Constructor for exception de.jstacs.parameters.CollectionParameter.InconsistentCollectionException
Constructs a new InconsistentCollectionExceptionmessage
CombinationIterator - Class in de.jstacs.models.discrete.inhomogeneous
This class can be used for iterating of all possible combinations
CombinationIterator(int, int) - Constructor for class de.jstacs.models.discrete.inhomogeneous.CombinationIterator
Creates a new CombinationIterator with n elements and at most max selected elements.
comment - Variable in class de.jstacs.parameters.SimpleParameter
A comment on the parameter
comment - Variable in class de.jstacs.results.Result
The comment for the result.
commentTemplate - Variable in class de.jstacs.parameters.ExpandableParameterSet
A template for the comment of the enclosing ParameterSetContainer
ComparableElement<E,C extends Comparable> - Class in de.jstacs.utils
This class is a container for any objects that have to be compared.
ComparableElement(E, C) - Constructor for class de.jstacs.utils.ComparableElement
Creates a new ComparableElement.
compareTo(Edge) - Method in class de.jstacs.algorithms.graphs.Edge
 
compareTo(AlphabetContainer) - Method in class de.jstacs.data.AlphabetContainer
 
compareTo(Alphabet) - Method in class de.jstacs.data.alphabets.ContinuousAlphabet
 
compareTo(Alphabet) - Method in class de.jstacs.data.alphabets.DiscreteAlphabet
 
compareTo(Sequence) - Method in class de.jstacs.data.Sequence
 
compareTo(SimpleResult) - Method in class de.jstacs.results.SimpleResult
 
compareTo(ComparableElement<E, C>) - Method in class de.jstacs.utils.ComparableElement
 
complement() - Method in class de.jstacs.data.Sequence
This method returns a new instance of sequence containing the complementary current sequence.
complement(int, int) - Method in class de.jstacs.data.Sequence
This method returns a new instance of sequence containing a part of the complementary current sequence.
complement(int, int) - Method in class de.jstacs.data.sequences.SparseSequence
 
ComplementableDiscreteAlphabet - Class in de.jstacs.data.alphabets
This abstract class indicates that an alphabet can be used for to compute the complement.
ComplementableDiscreteAlphabet(StringBuffer) - Constructor for class de.jstacs.data.alphabets.ComplementableDiscreteAlphabet
The constructor for the Storable interface.
ComplementableDiscreteAlphabet(String[], boolean) - Constructor for class de.jstacs.data.alphabets.ComplementableDiscreteAlphabet
The main constructor.
componentHyperParams - Variable in class de.jstacs.models.mixture.AbstractMixtureModel
The hyperparameters for estimating the probabilities of the components
componentScore - Variable in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
This array is used while computing the score.
CompositeModel - Class in de.jstacs.models
This class is for modelling sequences by modelling the different positions of the each sequence by different models.
CompositeModel(AlphabetContainer, int[], Model...) - Constructor for class de.jstacs.models.CompositeModel
 
CompositeModel(StringBuffer) - Constructor for class de.jstacs.models.CompositeModel
The constructor for the Storable interface.
compProb - Variable in class de.jstacs.models.mixture.AbstractMixtureModel
This array is used while training to avoid creating many new objects.
computeFreqs(double, Constraint...) - Static method in class de.jstacs.models.discrete.ConstraintManager
This method computes the (smoothed) relative frequencies.
computeGammaNorm() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree
Computes the Gamma-normalization for the prior
computeHiddenParameter(double[]) - Method in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
This method has to be invoked during an initialization.
computeLogGammaSum() - Method in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
This method is used to precompute the sum of the logarithm of the gamma functions that is used in the prior.
computeMaximalHP(Tensor) - Static method in class de.jstacs.algorithms.graphs.DAG
The method computes the HP(k).
computeMaximalKDAG(Tensor) - Static method in class de.jstacs.algorithms.graphs.DAG
Computes the maximal k-DAG, i.e. the k-DAG that maximize the score given by the tensor.
computeMaxKDAG(SymmetricTensor) - Static method in class de.jstacs.algorithms.graphs.DAG
Computes the maximal k-DAG, i.e. the k-DAG that maximize the score given by the tensor.
ConfusionMatrix - Class in de.jstacs.classifier
This class holds the confusion matrix of a classifier.
ConfusionMatrix(int) - Constructor for class de.jstacs.classifier.ConfusionMatrix
This constructor creates an instance with a given number of classes.
ConfusionMatrix(StringBuffer) - Constructor for class de.jstacs.classifier.ConfusionMatrix
This is the constructor for Storable.
CONJUGATE_GRADIENTS_FR - Static variable in class de.jstacs.algorithms.optimization.Optimizer
This constant can be used to specify that conjugate gradients (by Fletcher and Reeves) should be used in the optimize-method.
CONJUGATE_GRADIENTS_PRP - Static variable in class de.jstacs.algorithms.optimization.Optimizer
This constant can be used to specify that conjugate gradients (by Polak and Ribiere should be used in the optimize-method.
conjugateGradientsFR(DifferentiableFunction, double[], Optimizer.TerminationCondition, double, double, StartDistanceForecaster, SafeOutputStream, Time) - Static method in class de.jstacs.algorithms.optimization.Optimizer
The conjugate gradient algorithm by Fletcher and Reeves.
conjugateGradientsPR(DifferentiableFunction, double[], Optimizer.TerminationCondition, double, double, StartDistanceForecaster, SafeOutputStream, Time) - Static method in class de.jstacs.algorithms.optimization.Optimizer
The conjugate gradient algorithm by Polak and Ribiere.
conjugateGradientsPRP(DifferentiableFunction, double[], Optimizer.TerminationCondition, double, double, StartDistanceForecaster, SafeOutputStream, Time) - Static method in class de.jstacs.algorithms.optimization.Optimizer
The conjugate gradient algorithm by Polak and Ribiere called Polak-Ribiere-Positive.
ConstantStartDistance - Class in de.jstacs.algorithms.optimization
The most simple StartDistanceForecaster that returns always the same value.
ConstantStartDistance(double) - Constructor for class de.jstacs.algorithms.optimization.ConstantStartDistance
This constructor creates an instance that returns always the given value
Constraint - Class in de.jstacs.models.discrete
The main class for all constraints on models.
Constraint(int[], int) - Constructor for class de.jstacs.models.discrete.Constraint
The main constructor.
Constraint(StringBuffer) - Constructor for class de.jstacs.models.discrete.Constraint
The constructor for creating an object from an StringBuffer.
Constraint - Interface in de.jstacs.parameters.validation
Interface for a constraint that must be fulfilled in a ConstraintValidator
ConstraintManager - Class in de.jstacs.models.discrete
The class manipulate some constraints.
constraintParameter - Variable in class de.jstacs.parameters.validation.ReferenceConstraint
The reference to the Parameter that is part of the condition
constraints - Variable in class de.jstacs.models.discrete.inhomogeneous.DAGModel
The constraints for the model.
ConstraintValidator - Class in de.jstacs.parameters.validation
Class for a ParameterValidator that is based on Constraints.
ConstraintValidator() - Constructor for class de.jstacs.parameters.validation.ConstraintValidator
Creates a new ConstraintValidator having an empty list of Constraints, i.e. the constraints of this ConstraintValidator are always fulfilled before additional Constraints are added using the addConstraint()-method.
ConstraintValidator(StringBuffer) - Constructor for class de.jstacs.parameters.validation.ConstraintValidator
Creates a new ConstraintValidator from its XML-representation.
content - Variable in class de.jstacs.data.sequences.RecursiveSequence
The internal sequence
context - Variable in class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
The context of this parameter.
continueIterations(double[], double[][]) - Method in class de.jstacs.models.mixture.AbstractMixtureModel
This method will run the train algorithm for the current model on the internal sample.
continueIterations(double[], double[][], int, int) - Method in class de.jstacs.models.mixture.AbstractMixtureModel
This method will run the train algorithm for the current model on the internal sample.
ContinuousAlphabet - Class in de.jstacs.data.alphabets
Class for a continuous alphabet.
ContinuousAlphabet(ContinuousAlphabet.ContinuousAlphabetParameterSet) - Constructor for class de.jstacs.data.alphabets.ContinuousAlphabet
The constructor for the InstantiableFromParameterSet interface.
ContinuousAlphabet(double, double) - Constructor for class de.jstacs.data.alphabets.ContinuousAlphabet
Creates a new ContinuousAlphabet from a minimum and a maximum value
ContinuousAlphabet(StringBuffer) - Constructor for class de.jstacs.data.alphabets.ContinuousAlphabet
Extracts the alphabet from the StringBuffer.
ContinuousAlphabet.ContinuousAlphabetParameterSet - Class in de.jstacs.data.alphabets
Class for the ParameterSet of a ContinuousAlphabet.
ContinuousAlphabet.ContinuousAlphabetParameterSet() - Constructor for class de.jstacs.data.alphabets.ContinuousAlphabet.ContinuousAlphabetParameterSet
Creates a new ContinuousAlphabetParameterSet with empty values.
ContinuousAlphabet.ContinuousAlphabetParameterSet(double, double) - Constructor for class de.jstacs.data.alphabets.ContinuousAlphabet.ContinuousAlphabetParameterSet
Creates a new ContinuousAlphabetParameterSet from a minimum and a maximum value
ContinuousAlphabet.ContinuousAlphabetParameterSet(StringBuffer) - Constructor for class de.jstacs.data.alphabets.ContinuousAlphabet.ContinuousAlphabetParameterSet
Creates a new ContinousParameterSet from its XML-representation.
continuousVal(int) - Method in class de.jstacs.data.Sequence
Returns the continuous value of position pos.
continuousVal(int) - Method in class de.jstacs.data.sequences.ArbitrarySequence
 
continuousVal(int) - Method in class de.jstacs.data.sequences.DiscreteSequence
 
continuousVal(int) - Method in class de.jstacs.data.sequences.RecursiveSequence
 
copy(String, String) - Static method in class de.jstacs.io.FileManager
This method copies a file in a faster manner.
copy(String, String, byte[]) - Static method in class de.jstacs.io.FileManager
This method copies a file in a faster manner using a specified buffer.
copy(ParameterTree) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree
Copies the values of the parameters from another ParameterTree
copyDiff(File, File, Date, boolean, FileFilter) - Static method in class de.jstacs.io.FileManager
This method copies all files and directories, if selected, from a source to a target that have been modified after a predefined date
copyFileFromServer(String, String, boolean) - Method in class de.jstacs.utils.REnvironment
Copies a file from the server to the local machine.
copyFileFromServer(String, String, RConnection) - Static method in class de.jstacs.utils.RUtils
This method copies a file from the server to the client.
copyFileToServer(String, String, boolean) - Method in class de.jstacs.utils.REnvironment
Copies a file from the local machine to the server.
copyFileToServer(File, String, RConnection) - Static method in class de.jstacs.utils.RUtils
Copies a file to the R side.
copyFileToServer(String, String, RConnection) - Static method in class de.jstacs.utils.RUtils
Copies a file to the R side.
count(int[][], byte) - Method in class de.jstacs.models.discrete.inhomogeneous.BayesianNetworkModel
Counts the occurrence of the different indegrees and check if the conventions are met.
count - Variable in class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
The counts for this parameter.
countElements() - Method in class de.jstacs.io.SymbolExtractor
Counts the number of elements that can initially be received.
counter - Variable in class de.jstacs.models.mixture.AbstractMixtureModel
The current index of the parameter set while adjustment (optimization).
counter - Variable in class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSampling
The counter for the sampling steps of each sampling
countInhomogeneous(AlphabetContainer, int, Sample, double[], boolean, Constraint...) - Static method in class de.jstacs.models.discrete.ConstraintManager
Fills the (inhomogeneous) constr with the weighted absolute frequency of the sample data and computes the frequencies will not be computed.
counts - Variable in class de.jstacs.models.discrete.Constraint
The counts for each specific constraint
create(CLLClassifierParameterSet, LogPrior, ScoringFunction[]...) - Static method in class de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifier
This method creates an array of CLLClassifier by using the cross-product of the given ScoringFunctions.
create(AlphabetContainer, String) - Static method in class de.jstacs.data.Sequence
Creates a sequence from a string based on the given AlphabetContainer using the standard delimiter for this AlphabetContainer.
create(AlphabetContainer, String, String) - Static method in class de.jstacs.data.Sequence
Creates a sequence from a string based on the given AlphabetContainer using the given delimiter.
create(AlphabetContainer, SequenceAnnotation[], String, String) - Static method in class de.jstacs.data.Sequence
Creates a sequence from a string based on the given AlphabetContainer using the given delimiter.
createConstraints(AbstractList<int[]>, int[], int[]) - Static method in class de.jstacs.models.discrete.ConstraintManager
Creates the constraints for a part of a model
createConstraints(AbstractList<int[]>, int[]) - Static method in class de.jstacs.models.discrete.ConstraintManager
Creates the constraints of a model
createConstraints(int[][]) - Method in class de.jstacs.models.discrete.inhomogeneous.DAGModel
This method creates the constraints for a given structure.
createDefaultClassWeights(int, double) - Method in class de.jstacs.classifier.AbstractScoreBasedClassifier
This method creates new class weights.
createMatrix(String, int[][]) - Method in class de.jstacs.utils.REnvironment
Creates a matrix of integers.
createMatrix(String, double[][]) - Method in class de.jstacs.utils.REnvironment
Creates a matrix of doubles.
createParameterSet(Object[], String[], String[]) - Method in class de.jstacs.parameters.CollectionParameter
Creates a new ParameterSet from an array of values, an array of names, and an array of comments.
createResult(String, String, DataType, Object) - Static method in class de.jstacs.results.Result
Factory method to create a new Result.
createSeqWeightsArray() - Method in class de.jstacs.models.mixture.AbstractMixtureModel
Creates an array that can be used for weighting sequences in the algorithm.
createStructure(Sample[], double[][]) - Method in class de.jstacs.classifier.scoringFunctionBased.ScoreClassifier
Creates the structure that will be used in the optimization.
createTrees(Sample[], double[][]) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
Creates the tree structures that represent the context (array BayesianNetworkScoringFunction.trees) and the parameter objects BayesianNetworkScoringFunction.parameters using the given Measure BayesianNetworkScoringFunction.structureMeasure.
createVector(String, String[]) - Method in class de.jstacs.utils.REnvironment
Creates a vector of Strings.
createVector(String, int[]) - Method in class de.jstacs.utils.REnvironment
Creates a vector of integers.
createVector(String, long[]) - Method in class de.jstacs.utils.REnvironment
Creates a vector of longs.
createVector(String, double[]) - Method in class de.jstacs.utils.REnvironment
Creates a vector of doubles.

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