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

P

parabolicInterpolation(OneDimensionalFunction, double, double, double, double, double, double, double) - Static method in class de.jstacs.algorithms.optimization.Optimizer
Approximates a minimum (not necessary the global) in the intervall [lower,upper].
parabolicInterpolation(OneDimensionalFunction, double, double, double, double) - Static method in class de.jstacs.algorithms.optimization.Optimizer
Approximates a minimum (not necessary the global) in the intervall [lower,upper].
Parameter - Class in de.jstacs.parameters
Abstract class for a parameter that shall be used as the parameter of some method, constructor, etc.
Parameter() - Constructor for class de.jstacs.parameters.Parameter
Creates a new Parameter and generates the internal id.
Parameter - Class in de.jstacs.scoringFunctions.directedGraphicalModels
Class for the parameters of a BayesianNetworkScoringFunction.
Parameter(int, byte, int, double, boolean) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
Creates a new parameter, that is parameter no index in the list of parameters of the BayesianNetworkScoringFunction and responsible for symbol at position position and pseudo count pseudoCount.
Parameter(int, byte, int, int[][], double, boolean) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
Creates a new parameter, that is parameter no index in the list of parameters of the BayesianNetworkScoringFunction and responsible for symbol at position position having context context and pseudo count pseudoCount.
Parameter(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
Re-creates a parameter from its XML-representation as returned by the Parameter.toXML()} method.
ParameterException - Exception in de.jstacs.parameters
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter.
ParameterException(String) - Constructor for exception de.jstacs.parameters.ParameterException
Constructor for a ParameterException with the specified error message.
ParameterException() - Constructor for exception de.jstacs.parameters.ParameterException
Constructor for a ParameterException without specific message
parameterRemovable() - Method in class de.jstacs.parameters.ExpandableParameterSet
Returns true if there is still a Parameter that can be removed from the set.
parameters - Variable in class de.jstacs.data.alphabets.DiscreteAlphabet
The ParameterSet describing this DiscreteAlphabet
parameters - Variable in class de.jstacs.parameters.CollectionParameter
The internal ParameterSet that holds the possible values
parameters - Variable in class de.jstacs.parameters.ParameterSet
The set of parameters
parameters - Variable in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
The parameters of the scoring function.
ParameterSet - Class in de.jstacs.parameters
(Container) class for a set of Parameters.
ParameterSet(Class) - Constructor for class de.jstacs.parameters.ParameterSet
Constructs a ParameterSet from the class that can be instantiated using this ParameterSet.
ParameterSet() - Constructor for class de.jstacs.parameters.ParameterSet
Constructs a new ParameterSet with empty parameter values.
ParameterSet(Parameter[]) - Constructor for class de.jstacs.parameters.ParameterSet
Constructs a ParameterSet out of an array of parameters.
ParameterSet(ArrayList<Parameter>) - Constructor for class de.jstacs.parameters.ParameterSet
Constructs a ParameterSet out of an ArrayList of parameters.
ParameterSet(StringBuffer) - Constructor for class de.jstacs.parameters.ParameterSet
Constructs a ParameterSet out of an XML representation
ParameterSet.ParameterList - Class in de.jstacs.parameters
Class for a List of Parameters that basically has the same functionality as ArrayList, but additionally takes care of the references Parameter.parent.
ParameterSet.ParameterList() - Constructor for class de.jstacs.parameters.ParameterSet.ParameterList
Creates a new, empty ParameterSet.ParameterList.
ParameterSet.ParameterList(Collection<? extends Parameter>) - Constructor for class de.jstacs.parameters.ParameterSet.ParameterList
Creates a new ParameterSet.ParameterList from an existing Collection of Parameters.
ParameterSet.ParameterList(int) - Constructor for class de.jstacs.parameters.ParameterSet.ParameterList
Creates a new, empty ParameterSet.ParameterList with a defined initial capacity.
ParameterSetContainer - Class in de.jstacs.parameters
Class for a Parameter that contains a ParameterSet as value.
ParameterSetContainer(String, String, ParameterSet) - Constructor for class de.jstacs.parameters.ParameterSetContainer
Creates an new ParameterSetContainer out of a ParameterSet.
ParameterSetContainer(StringBuffer) - Constructor for class de.jstacs.parameters.ParameterSetContainer
Creates a new ParameterSetContainer from its XML-representation.
ParameterSetParser - Class in de.jstacs.io
Class that extracts values from Parameters und creates instances of InstantiableFromParameterSets from a ParameterSet.
ParameterSetParser() - Constructor for class de.jstacs.io.ParameterSetParser
 
ParameterSetParser.NotInstantiableException - Exception in de.jstacs.io
An Exception that is thrown if an instance of some class could not be created.
ParameterSetParser.NotInstantiableException(String) - Constructor for exception de.jstacs.io.ParameterSetParser.NotInstantiableException
Creates a new instance of a NotInstantiableException from an error-message.
ParameterSetParser.WrongParameterTypeException - Exception in de.jstacs.io
An that is thrown if the datatype of a Parameter is not appropriate for some purpose.
ParameterSetParser.WrongParameterTypeException(String) - Constructor for exception de.jstacs.io.ParameterSetParser.WrongParameterTypeException
Creates a new instance of a WrongParameterTypeException from an error-message
parametersLoaded() - Method in class de.jstacs.parameters.ParameterSet
Returns true if the parameters of this ParameterSet have already been loaded using the loadParameters()-method
ParameterTree - Class in de.jstacs.scoringFunctions.directedGraphicalModels
Class for the tree that represents the context of a Parameter in a BayesianNetworkScoringFunction.
ParameterTree(int, int[], AlphabetContainer, int, int[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree
Creates a new ParameterTree for the parameters at position pos using the parent positions in contextPoss.
ParameterTree(StringBuffer, AlphabetContainer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree
Re-creates a ParameterTree from its XML-representation as returned by ParameterTree.toXML().
ParameterValidator - Interface in de.jstacs.parameters.validation
Interface for a parameter validator, i.e. a class that can validate some possible parameter value.
paramRef - Variable in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
This array contains the references/indices for the parameters.
params - Variable in class de.jstacs.classifier.scoringFunctionBased.ScoreClassifier
The parameter set for the classifier.
params - Variable in class de.jstacs.models.discrete.DiscreteGraphicalModel
The current parameter set of the model
paramsFile - Variable in class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSampling
The files for saving the parameters while the sampling.
parent - Variable in class de.jstacs.parameters.Parameter
If this Parameter is enclosed in a ParameterSet, this variable holds a reference to that ParameterSet.
parent - Variable in class de.jstacs.parameters.ParameterSet
Is this ParameterSet is contained in a ParameterSetContainer, this variable holds a reference to that ParameterSetContainer.
parseNextParameterSet() - Method in class de.jstacs.models.mixture.AbstractMixtureModel
This method allows the user to parse the next set of parameters (from a file).
parseNextParameterSet() - Method in class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSampling
 
parseNextParameterSet() - Method in interface de.jstacs.models.mixture.gibbssampling.GibbsSamplingComponent
This method allows the user to parse the next set of parameters (from a file).
parseParameterSet(int, int) - Method in class de.jstacs.models.mixture.AbstractMixtureModel
This method allows the user to parse the set of parameters with index burnInIteration of a specific sampling (from a file).
parseParameterSet(int, int) - Method in class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSampling
 
parseParameterSet(int, int) - Method in interface de.jstacs.models.mixture.gibbssampling.GibbsSamplingComponent
This method allows the user to parse the set of parameters with index n of a certain sampling (from a file).
parseSections(String) - Static method in class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
Parsed the sections as defined in sections to a list of Integers.
partition(double, Sample.PartitionMethod, int) - Method in class de.jstacs.data.Sample
This method partitions the elements of the sample in 2 distinct parts.
partition(Sample.PartitionMethod, double...) - Method in class de.jstacs.data.Sample
This method partitions the elements of the sample in distinct parts.
partition(int, Sample.PartitionMethod) - Method in class de.jstacs.data.Sample
This method partitions the elements of the sample in k distinct parts.
partNorm - Variable in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
This array contains the partial normalization constants, i.e. the normalization constant for each component.
PermutedSequence - Class in de.jstacs.data.sequences
Class for a permuted sequence.
PermutedSequence(Sequence) - Constructor for class de.jstacs.data.sequences.PermutedSequence
This constructor creates an instance by shuffling the symbols.
plot(REnvironment, AbstractScoreBasedClassifier.DoubleTableResult...) - Static method in class de.jstacs.classifier.AbstractScoreBasedClassifier.DoubleTableResult
This method plots an array of DoubleTableResult in one image
plot(String) - Method in class de.jstacs.utils.REnvironment
Creates a buffered image form a given plot command.
plot(String, double, double) - Method in class de.jstacs.utils.REnvironment
Creates a buffered image with given dimension form a given plot command.
plotScores(AbstractScoreBasedClassifier, Sample, Sample, REnvironment, int, double, String) - Static method in class de.jstacs.classifier.utils.ClassificationVisualizer
This method returns an ImageResult containing a plot of the histograms of the scores.
plotScores(AbstractScoreBasedClassifier, Sample, Sample, REnvironment, int, double, String, String) - Static method in class de.jstacs.classifier.utils.ClassificationVisualizer
This method creates a pdf containing a plot of the histograms of the scores.
plotToPDF(String, String, boolean) - Method in class de.jstacs.utils.REnvironment
Creates a pdf file form a given plot command.
plotToPDF(String, double, double, String, boolean) - Method in class de.jstacs.utils.REnvironment
Creates a pdf file with given dimension form a given plot command.
plotToTexFile(String, String, boolean) - Method in class de.jstacs.utils.REnvironment
Creates a tex file form a given plot command.
plotToTexFile(String, double, double, String, boolean) - Method in class de.jstacs.utils.REnvironment
Creates a tex file with given dimension form a given plot command.
plugIn - Variable in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
This boolean indicates whether to use a plug-in strategy to initialize the instance.
plugInParameters - Variable in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
Indicates if plug-in parameters, i.e. generative (MAP) parameters shall be used upon initialization
PMMExplainingAwayResidual - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures
Class for the network structure of a BayesianNetworkScoringFunction that is a permuted Markov model based on the explaining away residual.
PMMExplainingAwayResidual(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMExplainingAwayResidual
Re-creates a PMMExplainingAwayResidual from its XML-representation as returned by PMMExplainingAwayResidual.toXML().
PMMExplainingAwayResidual(byte, double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMExplainingAwayResidual
Creates a new PMMExplainingAwayResidual of order order.
PMMMutualInformation - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures
Class for the network structure of a BayesianNetworkScoringFunction that is a permuted Markov model based on mutual information.
PMMMutualInformation(byte, int, double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation
Creates a new PMMMutualInformation of order order.
PMMMutualInformation(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation
Re-creates a PMMMutualInformation from its XML-representation as returned by PMMMutualInformation.toXML().
position - Variable in class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
The position of symbol this parameter is responsible for.
powers - Variable in class de.jstacs.algorithms.graphs.tensor.Tensor
 
precomputeNorm() - Method in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
Precomutes the normalisation constant.
precomputeNormalization() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
Precomputes all normalization constants and saves the global normalization constant to BayesianNetworkScoringFunction.normalizationConstant.
prepareAssessment(Sample...) - Method in class de.jstacs.classifier.assessment.ClassifierAssessment
Prepares an assessment.
print(PrintWriter) - Method in class de.jstacs.results.ListResult
Prints the information of this ListResult to the provided PrintWriter.
print() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
Prints the counts and the value of this parameter to System.out.
print() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree
Prints the structure of this tree.
prior - Variable in class de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifier
The prior that is used in this instance.
ProgressUpdater - Interface in de.jstacs.utils
Interface for supervising the progress of long time processes like cross validation.
propagateId() - Method in class de.jstacs.parameters.ParameterSet
Propagates the id of this ParameterSet to all Parameters above and below in the hierarchy.
pseudoCount - Variable in class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
The pseudo count for this parameter.
PValueComputation - Class in de.jstacs.classifier.utils
This class can be used to compute any p-value from a given statistic.
PValueComputation() - Constructor for class de.jstacs.classifier.utils.PValueComputation
 

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