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 interval [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 interval [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() - 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 and 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 ParameterSetParser.NotInstantiableException from an error-message.

ParameterSetParser.WrongParameterTypeException - Exception in de.jstacs.io

An Exception 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 ParameterSetParser.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 during 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

Parses 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(MotifDiscoverer, int, int, Sequence, int, REnvironment, int, int, MotifDiscoverer.KindOfProfile) - Static method in class de.jstacs.motifDiscovery.MotifDiscovererToolBox

This method creates a simple plot of the profile of scores for a sequence and a start position.

plot(String) - Method in class de.jstacs.utils.REnvironment

Creates a buffered image from a given plot command.

plot(String, double, double) - Method in class de.jstacs.utils.REnvironment

Creates a buffered image with given dimension from a given plot command.

plotAndAnnotate(MotifDiscoverer, int, int, Sequence, int, REnvironment, int, int, double, double, double, MotifDiscoverer.KindOfProfile) - Static method in class de.jstacs.motifDiscovery.MotifDiscovererToolBox

This method creates a plot of the profile of scores for a sequence and a start position and annotates bindings sites in the plot.

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 from a given plot command.

plotToPDF(String, double, double, String, boolean) - Method in class de.jstacs.utils.REnvironment

Creates a pdf file with given dimension from a given plot command.

plotToTexFile(String, String, boolean) - Method in class de.jstacs.utils.REnvironment

Creates a tex file from a given plot command.

plotToTexFile(String, double, double, String, boolean) - Method in class de.jstacs.utils.REnvironment

Creates a tex file with given dimension from 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.

PMMExplainingAwayResidual(PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMExplainingAwayResidual

Creates a new PMMExplainingAwayResidual from the corresponding InstanceParameterSet parameters/code>.

PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures

Class for the parameters of a PMMExplainingAwayResidual structure Measure.

PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet() - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet

Creates a new PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet with empty parameter values.

PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet(byte, double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet

Creates a new PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet with the parameter for the order set to order and the parameter for the ess set to ess.

PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet

Creates a new PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet from its XML-representation as defined by the Storable interface.

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, BTMutualInformation.DataSource, double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation

Creates a new PMMMutualInformation of order order.

PMMMutualInformation(PMMMutualInformation.PMMMutualInformationParameterSet) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation

Creates a new PMMMutualInformation from the corresponding InstanceParameterSet parameters/code>.

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().

PMMMutualInformation.PMMMutualInformationParameterSet - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures

Class for the parameters of a PMMMutualInformation structure Measure.

PMMMutualInformation.PMMMutualInformationParameterSet() - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation.PMMMutualInformationParameterSet

Creates a new PMMMutualInformation.PMMMutualInformationParameterSet with empty parameter values.

PMMMutualInformation.PMMMutualInformationParameterSet(byte, BTMutualInformation.DataSource, double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation.PMMMutualInformationParameterSet

Creates a new PMMMutualInformation.PMMMutualInformationParameterSet with the parameter for the order set to order, the parameter for the BTMutualInformation.DataSource set to clazz, and the parameter for the ess set to ess.

PMMMutualInformation.PMMMutualInformationParameterSet(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation.PMMMutualInformationParameterSet

Creates a new PMMMutualInformation.PMMMutualInformationParameterSet from its XML-representation as defined by the Storable interface.

position - Variable in class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter

The position of symbol this parameter is responsible for.

PositionPrior - Class in de.jstacs.models.mixture.motif.positionprior

This is the main class for any position prior that can be used in a motif discovery.

PositionPrior() - Constructor for class de.jstacs.models.mixture.motif.positionprior.PositionPrior

This empty constructor creates an instance with motif length -1.

PositionPrior(StringBuffer) - Constructor for class de.jstacs.models.mixture.motif.positionprior.PositionPrior

The standard constructor for the interface Storable.

posPrior - Variable in class de.jstacs.models.mixture.motif.HiddenMotifMixture

The prior for the positions.

powers - Variable in class de.jstacs.algorithms.graphs.tensor.Tensor

powers - Variable in class de.jstacs.models.discrete.homogeneous.HomogeneousModel

The powers of the alphabet length.

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.

probFor(Sequence, int, int) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousMM

probFor(Sequence, int, int) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousModel

This method computes the probability of the given sequence in the given interval.

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