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## F

FALSE - Static variable in class de.jstacs.results.StorableResult
  The model/classifier has not 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 `File`s.
FileParameter - Class in de.jstacs.parameters
  Class for a `Parameter` that represents a local file.
FileParameter(StringBuffer) - Constructor for class de.jstacs.parameters.FileParameter
  The standard constructor for the interface `Storable`.
FileParameter(String, String, String, boolean) - Constructor for class de.jstacs.parameters.FileParameter
  Creates a `FileParameter`.
FileParameter(String, String, String, boolean, ParameterValidator) - Constructor for class de.jstacs.parameters.FileParameter
  Constructs a `FileParameter`.
FileParameter.FileRepresentation - Class in de.jstacs.parameters
  Class that represents a file.
FileParameter.FileRepresentation(String, String) - Constructor for class de.jstacs.parameters.FileParameter.FileRepresentation
  Creates a `FileParameter.FileRepresentation` out of the filename and the file's contents.
FileParameter.FileRepresentation(StringBuffer) - Constructor for class de.jstacs.parameters.FileParameter.FileRepresentation
  The standard constructor for the interface `Storable` .
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[], double[][][][]) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree
  Fills all parameters with the probabilities given in `distribution`.
fillComponentScoreOf(int, Sequence, int) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.HiddenMotifsMixture
  This method fills an internal array with the partial scores.
fillComponentScores(Sequence, int) - Method in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
  Fills the internal array `AbstractMixtureScoringFunction.componentScore` with the logarithmic scores of the components given a `Sequence`.
fillComponentScores(Sequence, int) - Method in class de.jstacs.scoringFunctions.mix.MixtureScoringFunction
fillComponentScores(Sequence, int) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.HiddenMotifsMixture
fillComponentScores(Sequence, int) - Method in class de.jstacs.scoringFunctions.mix.StrandScoringFunction
fillParameters(String, String...) - Method in class de.jstacs.parameters.ParameterSetTagger
fillTensor(Tensor, double[][]) - Static method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.Measure
  Fills a `Tensor` `t` with the weights defined in `weights`.
fillTensor(Tensor, double[][][]) - Static method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.Measure
  Fills a `Tensor` `t` with the weights defined in `weights`.
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 the content of a `File` using a given `AlphabetContainer` 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 the 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.
findMax() - Method in class de.jstacs.algorithms.optimization.QuadraticFunction
  This method returns the maximum of the `QuadraticFunction`.
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 of the `QuadraticFunction`.
findModification(int, int, MutableMotifDiscoverer, ScoringFunction[], Sample[], SFBasedOptimizableFunction, DifferentiableFunction, byte, double, StartDistanceForecaster, SafeOutputStream, History, int, boolean) - Static method in class de.jstacs.motifDiscovery.MutableMotifDiscovererToolbox
  This method tries to find a modification, i.e. shifting, shrinking, or expanding a motif, that is promising.
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.
findSignificantMotifOccurrences(int, Sequence, int) - Method in class de.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder
  This method finds the significant motif occurrences in the sequence.
findSignificantMotifOccurrences(int, Sequence, int, int) - Method in class de.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder
  This method finds the significant motif occurrences in the sequence.
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
  Indicates whether only the free parameters or all should be used.
freeParams - Variable in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
  This `boolean` indicates whether free parameterization or all parameters are 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
  Recreates an array of `ParameterTree`s 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 a `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.NormalizableScoringFunctionModel
fromXML(StringBuffer) - Method in class de.jstacs.models.UniformModel
fromXML(StringBuffer) - Method in class de.jstacs.models.VariableLengthWrapperModel
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 a 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 for the `Storable` interface to create a scoring function from a `StringBuffer`.
fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.CMMScoringFunction
fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.MutableMarkovModelScoringFunction
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.mix.motifSearch.DurationScoringFunction
fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.MixtureDuration
fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.PositionScoringFunction
fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.SkewNormalLikeScoringFunction
fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.MRFScoringFunction
fromXML(StringBuffer) - Method in class de.jstacs.scoringFunctions.NormalizedScoringFunction
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 directed acyclic graphical 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
  The standard constructor for the interface `Storable`.
FSDAGModelForGibbsSampling - Class in de.jstacs.models.mixture.gibbssampling
  This is the class for a fixed structure directed acyclic graphical model (see `FSDAGModel`) 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 `Storable` interface.
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` (fixed structure directed acyclic graphical model).
FSDAGMParameterSet(StringBuffer) - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.FSDAGMParameterSet
  The standard constructor for the interface `Storable`.
FSDAGMParameterSet() - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.FSDAGMParameterSet
  This constructor creates an empty `FSDAGMParameterSet` set for a `FSDAGModel`.
FSDAGMParameterSet(AlphabetContainer, int, double, String, String) - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.FSDAGMParameterSet
  This constructor creates an `FSDAGMParameterSet` instance.
FSDAGMParameterSet(Class<? extends FSDAGModel>) - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.FSDAGMParameterSet
  This the constructor creates an empty `FSDAGMParameterSet` from the class that can be instantiated using this `FSDAGMParameterSet`.
FSDAGMParameterSet(Class<? extends FSDAGModel>, AlphabetContainer, int, double, String, String) - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.FSDAGMParameterSet
  This constructor creates an `FSDAGMParameterSet` instance for the specified class.
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.classifier.scoringFunctionBased.gendismix.GenDisMixClassifier
  The function that is optimized in this classifier.
function - Variable in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
  This array contains the internal `ScoringFunction`s that are used to determine the score.
funs - Variable in class de.jstacs.classifier.scoringFunctionBased.logPrior.SeparateLogPrior
  The `ScoringFunction`s using the parameters that shall be penalized.

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