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.StringExtractor
The comment-character for FastA-formatted files is '>'.
FastDirichletMRGParams - Class in de.jstacs.utils.random
The container for parameter of a Dirichlet random generator that used the same hyperparameter at all positions.
FastDirichletMRGParams(double) - Constructor for class de.jstacs.utils.random.FastDirichletMRGParams
 
FG - Static variable in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation
Compute mutual information only from foreground data
FG - Static variable in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation
Compute mutual information only from foreground data
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.
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
This method does not close the internal stream.
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.
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 onedimensional subfunction.
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
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.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(FSDAGMParameterSet) - 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 Storable.
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(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

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