Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV LETTER NEXT LETTER | FRAMES NO FRAMES

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 `DataType`s 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 `MotifAnnotation`s 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 `AbstractClassifier`s and a two-dimensional array of `Model`s, which are combined to additional classifiers.
ClassifierAssessment(AbstractClassifier...) - Constructor for class de.jstacs.classifier.assessment.ClassifierAssessment
  Creates a new `ClassifierAssessment` from a set of `AbstractClassifier`s.
ClassifierAssessment(boolean, Model[]...) - Constructor for class de.jstacs.classifier.assessment.ClassifierAssessment
  Creates a new `ClassifierAssessment` from a set of `Model`s.
ClassifierAssessment(AbstractClassifier[], boolean, Model[]...) - Constructor for class de.jstacs.classifier.assessment.ClassifierAssessment
  This constructor allows to assess a collection of given `AbstractClassifier`s and those constructed using the given `AbstractModel`s.
ClassifierAssessmentAssessParameterSet - Class in de.jstacs.classifier.assessment
  This class is the super-class used by all `ClassifierAssessmentAssessParameterSet`s.
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 `InconsistentCollectionException`message
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 `Constraint`s.
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 `Constraint`s 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.

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV LETTER NEXT LETTER | FRAMES NO FRAMES

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