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

F

FALSE - Static variable in class de.jstacs.results.StorableResult

The model/classifier has been trained

FASTA - Static variable in class de.jstacs.io.AbstractStringExtractor

The comment-character for FastA-formatted files is '>'.

FastDirichletMRGParams - Class in de.jstacs.utils.random

The container for parameters of a Dirichlet random generator that uses the same hyperparameter at all positions.

FastDirichletMRGParams(double) - Constructor for class de.jstacs.utils.random.FastDirichletMRGParams

Creates the hyperparameter for a Dirichlet random generator which is used at all positions for the hyperparameter vector of the underlying Dirichlet distribution.

file - Variable in class de.jstacs.models.mixture.AbstractMixtureModel

The file in which the component probabilities are stored.

FileManager - Class in de.jstacs.io

This class is for handling files.

FileParameter - Class in de.jstacs.parameters

Class for a parameter that represents a local file.

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

Restores a file parameter from an XML representation.

FileParameter(String, String, String, boolean) - Constructor for class de.jstacs.parameters.FileParameter

Creates a file parameter.

FileParameter(String, String, String, boolean, ParameterValidator) - Constructor for class de.jstacs.parameters.FileParameter

Constructs a file parameter.

FileParameter.FileRepresentation - Class in de.jstacs.parameters

Class that represents a file

FileParameter.FileRepresentation(String, String) - Constructor for class de.jstacs.parameters.FileParameter.FileRepresentation

Created a file representation out of the filename and the file's contents

FileParameter.FileRepresentation(StringBuffer) - Constructor for class de.jstacs.parameters.FileParameter.FileRepresentation

Restores the file representation from an XML representation

filereader - Variable in class de.jstacs.models.mixture.AbstractMixtureModel

Reading component probabilities from a file.

filewriter - Variable in class de.jstacs.models.mixture.AbstractMixtureModel

Saving component probabilities in a file.

fill(double[]) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree

Fills all parameters with the probabilities given in fillEmptyWith.

fillComponentScores(Sequence, int) - Method in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction

Fills the internal array componentScore with the log scores of the components.

fillComponentScores(Sequence, int) - Method in class de.jstacs.scoringFunctions.mix.MixtureScoringFunction

fillTensor(Tensor, double[][]) - Static method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.Measure

Fills a Tensor t with the weights defined in weight.

fillTensor(Tensor, double[][][]) - Static method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.Measure

Fills a Tensor t with the weights defined in weight.

fillWithStandardFieldForClone(ReferenceConstraint) - Method in class de.jstacs.parameters.validation.ReferenceConstraint

Sets the standard-fields of clone to the values (or clones of them) of this instance.

filter(String, char, AlphabetContainer, int, String) - Static method in class de.jstacs.io.SymbolExtractor

This method allows the user to filter a file using a given alphabet container and a minimal sequence length.

filterBySuperclass(Class<S>, LinkedList<Class<? extends T>>) - Static method in class de.jstacs.utils.SubclassFinder

Returns a LinkedList of the Class objects for all classes in listToFilter that are sub-classes of superClass.

finalize() - Method in class de.jstacs.io.SparseStringExtractor

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

finalize() - Method in class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSampling

finalize() - Method in class de.jstacs.utils.GUIProgressUpdater

finalize() - Method in class de.jstacs.utils.REnvironment

finalize() - Method in class de.jstacs.utils.SafeOutputStream

find(int) - Method in class de.jstacs.algorithms.graphs.UnionFind

Finds the root of tree with node n and does path contraction.

findBracket(OneDimensionalFunction, double, double, double) - Static method in class de.jstacs.algorithms.optimization.Optimizer

This method returns a bracket containing a minimum.

findBracket(OneDimensionalFunction, double, double) - Static method in class de.jstacs.algorithms.optimization.Optimizer

This method returns a bracket containing a minimum.

findColumn(String) - Method in class de.jstacs.results.ResultSet

This method enables you to search for a column.

findInstantiableSubclasses(Class<T>, String) - Static method in class de.jstacs.utils.SubclassFinder

Returns all sub-classes of T that can be instantiated, i.e. are neither an interface nor abstract, and that are located in a package below startPackage.

findMax() - Method in class de.jstacs.algorithms.optimization.QuadraticFunction

This method returns the maximum.

findMin(double, double, double, double) - Method in class de.jstacs.algorithms.optimization.OneDimensionalFunction

This method returns a minimum x and the value f(x), starting the search at lower.

findMin() - Method in class de.jstacs.algorithms.optimization.QuadraticFunction

This method returns the minimum.

findOneDimensionalMin(double[], double[], double, double, double, double) - Method in class de.jstacs.algorithms.optimization.DifferentiableFunction

This method is used to find an approximation of an one-dimensional subfunction.

findSubclasses(Class<T>, String) - Static method in class de.jstacs.utils.SubclassFinder

Returns all sub-classes of T including interfaces and abstract classes that are located in a package below startPackage.

flatCloneWithoutAnnotation() - Method in class de.jstacs.data.Sequence.CompositeSequence

flatCloneWithoutAnnotation() - Method in class de.jstacs.data.Sequence

Works in analogy to Object.clone(), but does not clone the annotation.

flatCloneWithoutAnnotation() - Method in class de.jstacs.data.Sequence.SubSequence

flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.ArbitrarySequence

flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.ByteSequence

flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.IntSequence

flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.PermutedSequence

flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.ShortSequence

flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.SparseSequence

flush() - Method in class de.jstacs.utils.SafeOutputStream

forward(ParameterTree[]) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree

Computes the forward-part of the normalization constant starting from this ParameterTree.

freeParameters - Variable in class de.jstacs.classifier.scoringFunctionBased.logPrior.SeparateLogPrior

Indicates, if only free parameters shall be used and hence penalized

freeParams - Variable in class de.jstacs.classifier.scoringFunctionBased.AbstractOptimizableFunction

Whether only the free parameters or all should be used.

freq - Variable in class de.jstacs.models.discrete.Constraint

The frequencies estimated from the counts

fromStringArray(String[], AlphabetContainer) - Static method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree

Re-creates an array of ParameterTrees from their XML-representation as given in strs.

fromXML(StringBuffer) - Method in class de.jstacs.classifier.AbstractScoreBasedClassifier.DoubleTableResult

fromXML(StringBuffer) - Method in class de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet

fromXML(StringBuffer) - Method in class de.jstacs.data.AlphabetContainerParameterSet

fromXML(StringBuffer) - Method in class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet

fromXML(StringBuffer) - Method in class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation

fromXML(StringBuffer) - Method in class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength

fromXML(StringBuffer) - Method in class de.jstacs.data.sequences.annotation.SequenceAnnotation

fromXML(StringBuffer) - Method in class de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength

fromXML(StringBuffer) - Method in class de.jstacs.models.AbstractModel

This method should only be used by the constructor that works on StringBuffer.

fromXML(StringBuffer) - Method in class de.jstacs.models.CompositeModel

fromXML(StringBuffer) - Method in class de.jstacs.models.discrete.DiscreteGraphicalModel

fromXML(StringBuffer) - Method in class de.jstacs.models.discrete.inhomogeneous.shared.SharedStructureMixture

fromXML(StringBuffer) - Method in class de.jstacs.models.mixture.AbstractMixtureModel

fromXML(StringBuffer) - Method in class de.jstacs.models.UniformModel

fromXML(StringBuffer) - Method in class de.jstacs.parameters.ArrayParameterSet

fromXML(StringBuffer) - Method in class de.jstacs.parameters.CollectionParameter

fromXML(StringBuffer) - Method in class de.jstacs.parameters.ExpandableParameterSet

fromXML(StringBuffer) - Method in class de.jstacs.parameters.FileParameter

fromXML(StringBuffer) - Method in class de.jstacs.parameters.InstanceParameterSet

fromXML(StringBuffer) - Method in class de.jstacs.parameters.MultiSelectionCollectionParameter

fromXML(StringBuffer) - Method in class de.jstacs.parameters.Parameter

Parses a Parameter from an XML-representation as returned by Parameter.toXML().

fromXML(StringBuffer) - Method in class de.jstacs.parameters.ParameterSet

Parses the instance fields of a ParameterSet from the XML-representation as returned by ParameterSet.toXML().

fromXML(StringBuffer) - Method in class de.jstacs.parameters.ParameterSetContainer

fromXML(StringBuffer) - Method in class de.jstacs.parameters.RangeParameter

fromXML(StringBuffer) - Method in class de.jstacs.parameters.SequenceScoringParameterSet

fromXML(StringBuffer) - Method in class de.jstacs.parameters.SimpleParameter

fromXML(StringBuffer) - Method in class de.jstacs.parameters.validation.ConstraintValidator

Parses a ConstraintValidator from the XML-representation as returned by ConstraintValidator.toXML().

fromXML(StringBuffer) - Method in class de.jstacs.parameters.validation.NumberValidator

Parses a NumberValidator from the XML-representation as returned by NumberValidator.toXML().

fromXML(StringBuffer) - Method in class de.jstacs.parameters.validation.ReferenceConstraint

Parses a ReferenceConstraint from the XML-representation as returned by ReferenceConstraint.toXML().

fromXML(StringBuffer) - Method in class de.jstacs.parameters.validation.SimpleReferenceConstraint

fromXML(StringBuffer) - Method in class de.jstacs.parameters.validation.SimpleStaticConstraint

Parses a SimpleStaticConstraint from the XML-representation as returned by SimpleStaticConstraint.toXML().

fromXML(StringBuffer) - Method in class de.jstacs.parameters.validation.StorableValidator

Parses a StorableValidator from the XML-representation as returned by StorableValidator.toXML().

fromXML(StringBuffer) - Method in class de.jstacs.results.CategoricalResult

fromXML(StringBuffer) - Method in class de.jstacs.results.ImageResult

fromXML(StringBuffer) - Method in class de.jstacs.results.ListResult

fromXML(StringBuffer) - Method in class de.jstacs.results.MeanResultSet

fromXML(StringBuffer) - Method in class de.jstacs.results.NumericalResult

fromXML(StringBuffer) - Method in class de.jstacs.results.Result

This method is used in Result.Result(StringBuffer) to extract the information.

fromXML(StringBuffer) - Method in class de.jstacs.results.ResultSet

Parses the contents of a ResultSet from its XML-representation as returned by ResultSet.toXML().

fromXML(StringBuffer) - Method in class de.jstacs.results.SampleResult

fromXML(StringBuffer) - Method in class de.jstacs.results.SimpleResult

fromXML(StringBuffer) - Method in class de.jstacs.results.StorableResult

fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction

This method is called in the constructor to create a scoring function from a StringBuffer

fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction

fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.homogeneous.HMM0ScoringFunction

fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.homogeneous.HMMScoringFunction

fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.homogeneous.UniformHomogeneousScoringFunction

fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.IndependentProductScoringFunction

fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction

fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.MRFScoringFunction

fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.UniformScoringFunction

FSDAGModel - Class in de.jstacs.models.discrete.inhomogeneous

This class can be used for any discrete fixed structure DAG model (FSDAGModel).

FSDAGModel(FSDAGMParameterSet) - Constructor for class de.jstacs.models.discrete.inhomogeneous.FSDAGModel

This is the main constructor.

FSDAGModel(StringBuffer) - Constructor for class de.jstacs.models.discrete.inhomogeneous.FSDAGModel

This is the constructor for Storable.

FSDAGModelForGibbsSampling - Class in de.jstacs.models.mixture.gibbssampling

This is the class for a fixed structure directed acyclic graphical model that can be used in a Gibbs sampling.

FSDAGModelForGibbsSampling(FSDAGModelForGibbsSamplingParameterSet) - Constructor for class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSampling

The default constructor.

FSDAGModelForGibbsSampling(StringBuffer) - Constructor for class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSampling

This is the constructor for the interface Storable.

FSDAGModelForGibbsSamplingParameterSet - Class in de.jstacs.models.mixture.gibbssampling

The class for the parameters of a FSDAGModelForGibbsSampling.

FSDAGModelForGibbsSamplingParameterSet(StringBuffer) - Constructor for class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSamplingParameterSet

The constructor for the Storable interface.

FSDAGModelForGibbsSamplingParameterSet() - Constructor for class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSamplingParameterSet

This is the constructor that creates an empty parameter set for a FSDAGModelForGibbsSampling.

FSDAGModelForGibbsSamplingParameterSet(AlphabetContainer, int, double, String, String) - Constructor for class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSamplingParameterSet

This is the constructor that creates a filled parameter set.

FSDAGMParameterSet - Class in de.jstacs.models.discrete.inhomogeneous.parameters

The class for the parameters of a FSDAGModel.

FSDAGMParameterSet(StringBuffer) - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.FSDAGMParameterSet

The constructor for the Storable interface.

FSDAGMParameterSet() - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.FSDAGMParameterSet

This is the constructor that creates an empty parameter set for a FSDAGModel.

FSDAGMParameterSet(AlphabetContainer, int, double, String, String) - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.FSDAGMParameterSet

This is the constructor that creates a filled parameter set.

FSDAGMParameterSet(Class<? extends FSDAGModel>) - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.FSDAGMParameterSet

This is the constructor that creates an empty parameter set.

FSDAGMParameterSet(Class<? extends FSDAGModel>, AlphabetContainer, int, double, String, String) - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.FSDAGMParameterSet

This is the constructor that creates a filled parameter set.

Function - Interface in de.jstacs.algorithms.optimization

This interface is the framework for any mathematical function f: R^n -> R.

function - Variable in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction

This array contains the internal functions that are used to determine the score.

funs - Variable in class de.jstacs.classifier.scoringFunctionBased.logPrior.SeparateLogPrior

The ScoringFunctions using the parameters that shall be penalized