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## P

Pair<E1,E2> - Class in de.jstacs.utils
  A very simple container.
Pair(E1, E2) - Constructor for class de.jstacs.utils.Pair
  This constructor creates a pair of `element1` and `element2`.
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 `Parameter`s 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 `Parameter`s of the `BayesianNetworkScoringFunction` and responsible for `symbol` at position `position` having context `context` and pseudocount `pseudoCount`.
Parameter(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
  The standard constructor for the interface `Storable`.
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 a 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 parameter set 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 `Parameter`s.
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 `Parameter`s.
ParameterSet(ArrayList<Parameter>) - Constructor for class de.jstacs.parameters.ParameterSet
  Constructs a `ParameterSet` out of an `ArrayList` of `Parameter`s.
ParameterSet(StringBuffer) - Constructor for class de.jstacs.parameters.ParameterSet
  The standard constructor for the interface `Storable`.
ParameterSet.ParameterList - Class in de.jstacs.parameters
  Class for a `List` of `Parameter`s 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 `Parameter`s.
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 `ParameterSetContainer` 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
  The standard constructor for the interface `Storable`.
ParameterSetParser - Class in de.jstacs.io
  This class extracts values from `Parameter`s and creates instances of `InstantiableFromParameterSet`s 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` with a given 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` with a given error message.
ParameterSetTagger - Class in de.jstacs.parameters
  This class implements a tagger for `Parameter` of `ParameterSet`.
ParameterSetTagger(String[], ParameterSet...) - Constructor for class de.jstacs.parameters.ParameterSetTagger
  The constructor creates an new instance by collecting and tagging all parameters of the `ParameterSet`s.
ParameterSetTagger.KeyEntryComparator<K extends Comparable<K>,V> - Class in de.jstacs.parameters
  This class implements a comparator on `Map.Entry` that sorts by the key of the `Map.Entry`.
ParameterSetTagger.KeyEntryComparator() - Constructor for class de.jstacs.parameters.ParameterSetTagger.KeyEntryComparator
  Creates a `Comparator` that only compares the keys of `Map.Entry`s.
ParameterSetTagger.RankEntryComparator<K,V> - Class in de.jstacs.parameters
  This class implements a comparator on `Map.Entry` where value is a `ComparableElement` with weight `Integer`.
ParameterSetTagger.RankEntryComparator() - Constructor for class de.jstacs.parameters.ParameterSetTagger.RankEntryComparator
  Creates a `Comparator` that only compares the ranks of `Map.Entry`s where the rank is determined by the `ParameterSet.parameters`.
parametersLoaded() - Method in class de.jstacs.parameters.ParameterSet
  Returns `true` if the parameters of this `ParameterSet` have already been loaded using `ParameterSet.loadParameters()`.
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
  Recreates 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 values.
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.AbstractMultiThreadedOptimizableFunction
  This is a pointer for the current 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
  If this `ParameterSet` is contained in a `ParameterSetContainer`, this variable holds a reference to that `ParameterSetContainer`.
parseAnnotationToComment(char, SequenceAnnotation...) - Method in class de.jstacs.data.sequences.annotation.NullSequenceAnnotationParser
parseAnnotationToComment(char, SequenceAnnotation...) - Method in interface de.jstacs.data.sequences.annotation.SequenceAnnotationParser
  This method returns a `String` representation of the given `SequenceAnnotation`s that can be used as comment line in a file.
parseAnnotationToComment(char, SequenceAnnotation...) - Method in class de.jstacs.data.sequences.annotation.SimpleSequenceAnnotationParser
parseAnnotationToComment(char, SequenceAnnotation...) - Method in class de.jstacs.data.sequences.annotation.SplitSequenceAnnotationParser
parseHashSet2IndexHashtable(HashSet<K>) - Static method in class de.jstacs.utils.ToolBox
  This method converts a `HashSet` in a `Hashtable` with unique indices starting at 0.
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 `LinkedList` of `Integer`s.
partition(double, Sample.PartitionMethod, int) - Method in class de.jstacs.data.Sample
  This method partitions the elements, i.e. the `Sequence`s, of the `Sample` in two distinct parts.
partition(Sample.PartitionMethod, double...) - Method in class de.jstacs.data.Sample
  This method partitions the elements, i.e. the `Sequence`s, of the `Sample` in distinct parts where each part holds the corresponding percentage given in the array `percentage`.
partition(double[], Sample.PartitionMethod, double...) - Method in class de.jstacs.data.Sample
  This method partitions the elements, i.e. the `Sequence`s, of the `Sample` and the corresponding weights in distinct parts where each part holds the corresponding percentage given in the array `percentage`.
partition(int, Sample.PartitionMethod) - Method in class de.jstacs.data.Sample
  This method partitions the elements, i.e. the `Sequence`s, of the `Sample` in `k` distinct parts.
partition(double[], int, Sample.PartitionMethod) - Method in class de.jstacs.data.Sample
  This method partitions the elements, i.e. the `Sequence`s, of the `Sample` and the corresponding weights 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
  This class is for permuted sequences.
PermutedSequence(Sequence) - Constructor for class de.jstacs.data.sequences.PermutedSequence
  Creates a new `PermutedSequence` by shuffling the symbols of a given `Sequence`.
plot(REnvironment, AbstractScoreBasedClassifier.DoubleTableResult...) - Static method in class de.jstacs.classifier.AbstractScoreBasedClassifier.DoubleTableResult
  This method plots an array of `AbstractScoreBasedClassifier.DoubleTableResult`s 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.
plot(String, double, double, String, OutputStream) - Method in class de.jstacs.utils.REnvironment
  This method creates an image with given dimension from a given plot command and pipes it to the output stream.
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 that have a higher score than `threshold`.
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.
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
  The standard constructor for the interface `Storable`.
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 equivalent sample sizes (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`.
PMMMutualInformation(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation
  The standard constructor for the interface `Storable`.
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 equivalent sample sizes (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`.
PositionScoringFunction - Class in de.jstacs.scoringFunctions.mix.motifSearch
  This class implements a position scoring function that enables the user to get a score without using a Sequence object.
PositionScoringFunction(AlphabetContainer, int) - Constructor for class de.jstacs.scoringFunctions.mix.motifSearch.PositionScoringFunction
  This constructor allows create instance with more than one dimension.
PositionScoringFunction(int, int) - Constructor for class de.jstacs.scoringFunctions.mix.motifSearch.PositionScoringFunction
  This is the main constructor that creates the `AlphabetContainer` internally.
PositionScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.mix.motifSearch.PositionScoringFunction
  This is the constructor for `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
  An array containing the powers for the number of nodes.
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
  Pre-computes the normalization constant.
precomputeNormalization() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
  Pre-computes all normalization constants.
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.gendismix.GenDisMixClassifier
  The prior that is used in this classifier.
prior - Variable in class de.jstacs.classifier.scoringFunctionBased.SFBasedOptimizableFunction
  The prior that is used in this function.
PRIOR_INDEX - Static variable in enum de.jstacs.classifier.scoringFunctionBased.gendismix.LearningPrinciple
  This constant is the array index of the weighting factor for the prior.
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 `Parameter`s above and below in the hierarchy.
pseudoCount - Variable in class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
  The pseudocount 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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