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F

f - Variable in class de.jstacs.algorithms.optimization.NumericalDifferentiableFunction
The function to be differentiated numerically
factors - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.MEManager
The independent maximum entropy models.
FALSE - Static variable in class de.jstacs.results.StorableResult
The model/classifier has not been trained.
FalsePositiveRateForFixedSensitivity - Class in de.jstacs.classifiers.performanceMeasures
This class implements the false positive rate for a fixed sensitivity.
FalsePositiveRateForFixedSensitivity() - Constructor for class de.jstacs.classifiers.performanceMeasures.FalsePositiveRateForFixedSensitivity
Constructs a new instance of the performance measure FalsePositiveRateForFixedSensitivity with empty parameter values.
FalsePositiveRateForFixedSensitivity(double) - Constructor for class de.jstacs.classifiers.performanceMeasures.FalsePositiveRateForFixedSensitivity
Constructs a new instance of the performance measure FalsePositiveRateForFixedSensitivity with given sensitivity.
FalsePositiveRateForFixedSensitivity(StringBuffer) - Constructor for class de.jstacs.classifiers.performanceMeasures.FalsePositiveRateForFixedSensitivity
The standard constructor for the interface Storable.
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.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM
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.
filereader - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM
Reading component probabilities from a file.
FileRepresentation(String, String) - Constructor for class de.jstacs.parameters.FileParameter.FileRepresentation
Creates a FileParameter.FileRepresentation out of the filename and the file's contents.
FileRepresentation(String) - Constructor for class de.jstacs.parameters.FileParameter.FileRepresentation
Creates a new FileParameter.FileRepresentation from a filename.
FileRepresentation(StringBuffer) - Constructor for class de.jstacs.parameters.FileParameter.FileRepresentation
The standard constructor for the interface Storable .
FileResult(String, String, String) - Constructor for class de.jstacs.tools.ui.galaxy.GalaxyAdaptor.FileResult
Creates a new GalaxyAdaptor.FileResult with name, comment, and path to the file.
FileResult(String, String, String, String, String) - Constructor for class de.jstacs.tools.ui.galaxy.GalaxyAdaptor.FileResult
Creates a new GalaxyAdaptor.FileResult with name, comment, path to the file, filename and extension.
FileResult(StringBuffer) - Constructor for class de.jstacs.tools.ui.galaxy.GalaxyAdaptor.FileResult
Creates a new TextResult from its XML-representation
filewriter - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM
Saving component probabilities in a file.
fill(FileParameter) - Method in class de.jstacs.results.TextResult
Fills the supplied FileParameter with a clone of the contents of this TextResult.
fill(double[], double[][][][]) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree
Fills all parameters with the probabilities given in distribution.
fillBwdMatrix(int, int, Sequence) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM
This method fills the backward-matrix for a given sequence.
fillBwdMatrix(int, int, Sequence) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.HigherOrderHMM
 
fillBwdOrViterbiMatrix(HigherOrderHMM.Type, int, int, double, Sequence) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.HigherOrderHMM
This method computes the entries of the backward or the viterbi matrix.
fillComponentScoreOf(int, Sequence, int) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.ExtendedZOOPSDiffSM
This method fills an internal array with the partial scores.
fillComponentScores(Sequence, int) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.AbstractMixtureDiffSM
Fills the internal array AbstractMixtureDiffSM.componentScore with the logarithmic scores of the components given a Sequence.
fillComponentScores(Sequence, int) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.MixtureDiffSM
 
fillComponentScores(Sequence, int) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.ExtendedZOOPSDiffSM
 
fillComponentScores(Sequence, int) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.StrandDiffSM
 
fillContainer(float[], int) - Method in class de.jstacs.data.sequences.ArbitraryFloatSequence
 
fillContainer(double[], int) - Method in class de.jstacs.data.sequences.ArbitrarySequence
 
fillContainer(T, int) - Method in class de.jstacs.data.sequences.CyclicSequenceAdaptor
 
fillContainer(int[], int) - Method in class de.jstacs.data.sequences.MappedDiscreteSequence
 
fillContainer(double[], int) - Method in class de.jstacs.data.sequences.MultiDimensionalArbitrarySequence
 
fillContainer(int[], int) - Method in class de.jstacs.data.sequences.MultiDimensionalDiscreteSequence
 
fillContainer(T, int) - Method in class de.jstacs.data.sequences.Sequence
The method fills the content of a specific position in to the container.
fillContainer(T, int) - Method in class de.jstacs.data.sequences.Sequence.RecursiveSequence
 
fillContainer(int[], int) - Method in class de.jstacs.data.sequences.SimpleDiscreteSequence
 
fillCurrentParameter(double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.GaussianEmission
 
fillCurrentParameter(double[]) - Method in interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.DifferentiableEmission
Fills the current parameters in the global params array using the internal offset.
fillCurrentParameter(double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission
 
fillCurrentParameter(double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.SilentEmission
 
fillCurrentParameter(double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.UniformEmission
 
fillFwdMatrix(int, int, Sequence) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM
This method fills the forward-matrix for a given sequence.
fillFwdMatrix(int, int, Sequence) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.HigherOrderHMM
 
fillInfixScore(int[], int, int, double[]) - Method in interface de.jstacs.sequenceScores.QuickScanningSequenceScore
Computes the position-wise scores of an infix of the sequence seq (which must be encoded by the same alphabet as this QuickScanningSequenceScore) beginning at start and extending for length positions.
fillInfixScore(int[], int, int, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BayesianNetworkDiffSM
 
fillInfixScore(int[], int, int, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.localMixture.LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder
 
fillLogStatePosteriorMatrix(double[][], int, int, Sequence, boolean) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM
This method fills the log state posterior of Sequence seq in a given matrix.
fillLogStatePosteriorMatrix(double[][], int, int, Sequence, boolean) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.HigherOrderHMM
 
fillParameters(String, String...) - Method in class de.jstacs.parameters.ParameterSetTagger
 
fillParameters(double[]) - Method in interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition
This method allows to fill the parameters of the transition in a given array.
fillParameters(double[], int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.TransitionElement
This method fills the current parameters of this TransitionElement into the given array params starting at position offset.
fillParameters(double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.HigherOrderTransition
 
fillParameters(double[], int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.HigherOrderTransition
This method allows to fill the current parameters using a specific offset.
fillSamplingGroups(int, LinkedList<int[]>) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.GaussianEmission
 
fillSamplingGroups(int, LinkedList<int[]>) - Method in interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.DifferentiableEmission
Adds the groups of indexes of those parameters of this emission that should be sampled together in one step of a grouped sampling procedure, each as an int[], into list.
fillSamplingGroups(int, LinkedList<int[]>) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission
 
fillSamplingGroups(int, LinkedList<int[]>) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.SilentEmission
 
fillSamplingGroups(int, LinkedList<int[]>) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.UniformEmission
 
fillSamplingGroups(int, LinkedList<int[]>) - Method in interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition
Adds the groups of indexes of those parameters of this transition that should be sampled together in one step of a grouped sampling procedure, each as an int[], into list.
fillSamplingGroups(int, LinkedList<int[]>) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.HigherOrderTransition
 
fillTensor(Tensor, double[][]) - Static method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure
Fills a Tensor t with the weights defined in weights.
fillTensor(Tensor, double[][][]) - Static method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure
Fills a Tensor t with the weights defined in weights.
fillTransitionInformation(int, int, int, int[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition
 
fillTransitionInformation(int, int, int, int[]) - Method in interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.Transition
This method fills all relevant information for a specific edge in a given container.
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.
filterProperties(String, Boolean, DinucleotideProperty.HowCreated, DinucleotideProperty.Type, String) - Static method in enum de.jstacs.data.DinucleotideProperty
Filters all DinucleotidePropertys by some of their annotations.
finalize() - Method in class de.jstacs.io.SparseStringExtractor
 
finalize() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGModelForGibbsSampling
 
finalize() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM
 
finalize() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.HigherOrderHMM
 
finalize() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission
 
finalize() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.HigherOrderTransition
 
finalize() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM
 
finalize() - Method in class de.jstacs.utils.GUIProgressUpdater
 
finalize() - Method in class de.jstacs.utils.REnvironment
 
finalize() - Method in class de.jstacs.utils.SafeOutputStream
 
finalState - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM
An array of switches that contains for each state whether is is a final state or not (cf.
find(int) - Method in class de.jstacs.algorithms.graphs.UnionFind
Finds the root of the tree with node n and does path contraction.
find(ParameterSet, String) - Static method in class de.jstacs.tools.DataColumnParameter
Finds the parameter for the given ID in a ParameterSet.
find(ComplementableDiscreteAlphabet, double[][], ArrayList<AbstractMap.SimpleEntry<String, double[][]>>, PFMComparator.PFMDistance, int, int, boolean, double) - Static method in class de.jstacs.utils.PFMComparator
This methods finds for a user specified PFM pfm similar PFMs in a list of known PFMs.
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, DifferentiableSequenceScore[], DataSet[], double[][], DiffSSBasedOptimizableFunction, 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.
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.
findSplitIndex(double[], double) - Static method in class de.jstacs.classifiers.performanceMeasures.AbstractPerformanceMeasure
Returns the index in sortedScores with value greater or equal to t.
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.
findThreshold(double[], double[], double[], double, boolean) - Static method in class de.jstacs.classifiers.performanceMeasures.AbstractPerformanceMeasure
Determines the threshold for a given percentage on the reference weights using the scores in sortedReferenceScores and sortedMeasureScores.
flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.ArbitraryFloatSequence
 
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.CyclicSequenceAdaptor
 
flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.IntSequence
 
flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.MappedDiscreteSequence
 
flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.MultiDimensionalSequence
 
flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.PermutedSequence
 
flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.Sequence.CompositeSequence
 
flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.Sequence
Works in analogy to Object.clone(), but does not clone the annotation.
flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.Sequence.SubSequence
 
flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.ShortSequence
 
flatCloneWithoutAnnotation() - Method in class de.jstacs.data.sequences.SparseSequence
 
flush() - Method in class de.jstacs.tools.ui.cli.CLI.SysProtocol
 
flush() - Method in class de.jstacs.tools.ui.galaxy.GalaxyAdaptor.Protocol
 
flush() - Method in class de.jstacs.utils.SafeOutputStream
 
forward(BNDiffSMParameterTree[]) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree
Computes the forward-part of the normalization constant starting from this BNDiffSMParameterTree.
forward - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM
An array of switches that contains for each state whether the emission is forward or the reverse strand.
forward - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleState
A switch that decides whether to use the forward or the reverse complementary strand of a sequence.
freeParameters - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.SeparateLogPrior
Indicates, if only free parameters shall be used and hence penalized.
freeParams - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.AbstractOptimizableFunction
Indicates whether only the free parameters or all should be used.
freeParams - Variable in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.AbstractMixtureDiffSM
This boolean indicates whether free parameterization or all parameters are used.
freq - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint
The frequencies estimated from the counts.
fromGalaxy(String, StringBuffer) - Method in class de.jstacs.parameters.ExpandableParameterSet
 
fromGalaxy(String, StringBuffer) - Method in class de.jstacs.parameters.FileParameter
 
fromGalaxy(String, StringBuffer) - Method in interface de.jstacs.parameters.GalaxyConvertible
Parses the contents of command in the format defined by configBuffer of GalaxyConvertible.toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) and sets the values of the Parameter or ParameterSet accordingly.
fromGalaxy(String, StringBuffer) - Method in class de.jstacs.parameters.MultiSelectionParameter
 
fromGalaxy(String, StringBuffer) - Method in class de.jstacs.parameters.ParameterSet
 
fromGalaxy(String, StringBuffer) - Method in class de.jstacs.parameters.ParameterSetContainer
 
fromGalaxy(String, StringBuffer) - Method in class de.jstacs.parameters.RangeParameter
 
fromGalaxy(String, StringBuffer) - Method in class de.jstacs.parameters.SelectionParameter
 
fromGalaxy(String, StringBuffer) - Method in class de.jstacs.parameters.SimpleParameter
 
fromGalaxy(String, StringBuffer) - Method in class de.jstacs.parameters.validation.NumberValidator
 
fromGalaxy(String, StringBuffer) - Method in class de.jstacs.parameters.validation.RegExpValidator
 
fromGalaxy(String, StringBuffer) - Method in class de.jstacs.tools.DataColumnParameter
 
fromGalaxy(String, StringBuffer) - Method in class de.jstacs.tools.ui.galaxy.MultilineSimpleParameter
 
fromGalaxyConfig(String) - Method in class de.jstacs.tools.ui.galaxy.GalaxyAdaptor
Parses the values of the parameters from a galaxy script file
fromXML(StringBuffer) - Method in class de.jstacs.algorithms.alignment.PairwiseStringAlignment
 
fromXML(StringBuffer) - Method in class de.jstacs.algorithms.alignment.StringAlignment
Parses the XML representation.
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.parameters.ArrayParameterSet
 
fromXML(StringBuffer) - Method in class de.jstacs.parameters.ExpandableParameterSet
 
fromXML(StringBuffer) - Method in class de.jstacs.parameters.InstanceParameterSet
 
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.SequenceScoringParameterSet
 
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.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.MeanResultSet
 
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.sequenceScores.differentiable.AbstractDifferentiableSequenceScore
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.sequenceScores.differentiable.IndependentProductDiffSS
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.differentiable.logistic.LogisticDiffSS
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.differentiable.MultiDimensionalSequenceWrapperDiffSS
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.differentiable.UniformDiffSS
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.CyclicMarkovModelDiffSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BayesianNetworkDiffSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.MarkovModelDiffSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure
Parses this Measure from its XML representation.
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.HomogeneousMM0DiffSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.HomogeneousMMDiffSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.UniformHomogeneousDiffSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.localMixture.LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.MappingDiffSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.MarkovRandomFieldDiffSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.AbstractMixtureDiffSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.DurationDiffSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.MixtureDurationDiffSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.PositionDiffSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.SkewNormalLikeDurationDiffSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.NormalizedDiffSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel
This method should only be used by the constructor that works on a StringBuffer.
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.CompositeTrainSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.DifferentiableStatisticalModelWrapperTrainSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DiscreteGraphicalTrainSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared.SharedStructureMixture
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM
This method is used by the AbstractHMM.AbstractHMM(StringBuffer) constructor for creating an instance from an XML representation.
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.GaussianEmission
This method is internally used by the constructor GaussianEmission.GaussianEmission(StringBuffer).
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.MultivariateGaussianEmission
Parses the XML representation.
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.PluginGaussianEmission
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.PFMWrapperTrainSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.UniformTrainSM
 
fromXML(StringBuffer) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.VariableLengthWrapperTrainSM
 
FSDAGModelForGibbsSampling - Class in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous
This is the class for a fixed structure directed acyclic graphical model (see FSDAGTrainSM) that can be used in a Gibbs sampling.
FSDAGModelForGibbsSampling(FSDAGModelForGibbsSamplingParameterSet) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGModelForGibbsSampling
The default constructor.
FSDAGModelForGibbsSampling(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGModelForGibbsSampling
This is the constructor for the Storable interface.
FSDAGModelForGibbsSamplingParameterSet - Class in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters
The class for the parameters of a FSDAGModelForGibbsSampling.
FSDAGModelForGibbsSamplingParameterSet(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.FSDAGModelForGibbsSamplingParameterSet
The constructor for the Storable interface.
FSDAGModelForGibbsSamplingParameterSet() - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.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.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.FSDAGModelForGibbsSamplingParameterSet
This is the constructor that creates a filled parameter set.
FSDAGTrainSM - Class in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous
This class can be used for any discrete fixed structure directed acyclic graphical model ( FSDAGTrainSM).
FSDAGTrainSM(FSDAGTrainSMParameterSet) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGTrainSM
This is the main constructor.
FSDAGTrainSM(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGTrainSM
The standard constructor for the interface Storable.
FSDAGTrainSMParameterSet - Class in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters
The class for the parameters of a FSDAGTrainSM (fixed structure directed acyclic graphical model).
FSDAGTrainSMParameterSet(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.FSDAGTrainSMParameterSet
The standard constructor for the interface Storable.
FSDAGTrainSMParameterSet() - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.FSDAGTrainSMParameterSet
This constructor creates an empty FSDAGTrainSMParameterSet set for a FSDAGTrainSM.
FSDAGTrainSMParameterSet(AlphabetContainer, int, double, String, String) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.FSDAGTrainSMParameterSet
This constructor creates an FSDAGTrainSMParameterSet instance.
FSDAGTrainSMParameterSet(Class<? extends FSDAGTrainSM>) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.FSDAGTrainSMParameterSet
This the constructor creates an empty FSDAGTrainSMParameterSet from the class that can be instantiated using this FSDAGTrainSMParameterSet.
FSDAGTrainSMParameterSet(Class<? extends FSDAGTrainSM>, AlphabetContainer, int, double, String, String) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.FSDAGTrainSMParameterSet
This constructor creates an FSDAGTrainSMParameterSet instance for the specified class.
FSMEManager - Class in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous
This class can be used for any discrete fixed structure maximum entropy model (FSMEM).
FSMEManager(FSMEMParameterSet) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSMEManager
Creates a new MEManager from a given MEManagerParameterSet.
FSMEManager(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSMEManager
The standard constructor for the interface Storable.
FSMEMParameterSet - Class in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters
The ParameterSet for a FSMEManager.
FSMEMParameterSet() - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.FSMEMParameterSet
The simple constructor.
FSMEMParameterSet(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.FSMEMParameterSet
The constructor for the Storable interface.
FSMEMParameterSet(AlphabetContainer, int, double, String, ConstraintManager.Decomposition, boolean, byte, double, String) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.FSMEMParameterSet
The fast constructor.
Function - Interface in de.jstacs.algorithms.optimization
This interface is the framework for any mathematical function $f: \mathbb{R}^n \to \mathbb{R}$.
function - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.GenDisMixClassifier
The function that is optimized in this classifier.
function - Variable in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.AbstractMixtureDiffSM
This array contains the internal DifferentiableStatisticalModels that are used to determine the score.
funs - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.SeparateLogPrior
The DifferentiableSequenceScores using the parameters that shall be penalized.
furtherInits(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.SamplingHigherOrderHMM
This method allows the implementation of further initializations
fwdMatrix - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM
matrix for all forward-computed variables; fwdMatrix[l][c] = log P(x_1,...,x_l,(s_{l-order+1},...,s_l)=c | parameter)
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