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 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 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
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[][][]) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree
Fills all parameters with the probabilities given in fillEmptyWith.
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
 
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.
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.
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 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 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.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 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.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.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.scoringFunctions.mix.AbstractMixtureScoringFunction
This array contains the internal ScoringFunctions 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