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

## 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 `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 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 `ScoringFunction`s using the parameters that shall be penalized

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