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

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.

PairwiseStringAlignment - Class in de.jstacs.algorithms.alignment

Class for the representation of an alignment of two Strings.

PairwiseStringAlignment(String, String, double, int, int, int) - Constructor for class de.jstacs.algorithms.alignment.PairwiseStringAlignment

Creates the instance for the two (extended) Strings and the edit-costs.

PairwiseStringAlignment(StringBuffer) - Constructor for class de.jstacs.algorithms.alignment.PairwiseStringAlignment

The standard constructor for the interface Storable.

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 - Variable in class de.jstacs.algorithms.optimization.termination.AbstractTerminationCondition

The internally used parameters.

Parameter - Class in de.jstacs.parameters

Abstract class for a parameter that shall be used as the parameter of some method, constructor, etc.

Parameter(String, String, DataType) - Constructor for class de.jstacs.parameters.Parameter

The main constructor which takes the main information of a Parameter.

Parameter(StringBuffer) - Constructor for class de.jstacs.parameters.Parameter

The standard constructor for the interface Storable.

parameter - Variable in class de.jstacs.sequenceScores.differentiable.logistic.LogisticDiffSS

the parameters of the logistic regression

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.

ParameterList() - Constructor for class de.jstacs.parameters.ParameterSet.ParameterList

ParameterList(int) - Constructor for class de.jstacs.parameters.ParameterSet.ParameterList

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.AlphabetContainer

The parameters for this instance.

parameters - Variable in class de.jstacs.data.alphabets.DiscreteAlphabet

The parameter set describing this DiscreteAlphabet .

parameters - Variable in class de.jstacs.parameters.AbstractSelectionParameter

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.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BayesianNetworkDiffSM

The parameters of the scoring function.

parameters - Variable in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure

The parameters of this measure

parameters - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

The parameters defining the distribution over all states that can be visited.

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

The standard constructor for the interface Storable.

ParameterSet.ParameterList - Class in de.jstacs.parameters

Class for a AnnotatedEntityList that automatically sets the Parameter.parent field to the enclosing ParameterSet.

ParameterSetContainer - Class in de.jstacs.parameters

Class for a ParameterSetContainer that contains a ParameterSet as value.

ParameterSetContainer(ParameterSet) - Constructor for class de.jstacs.parameters.ParameterSetContainer

Creates an new ParameterSetContainer out of a ParameterSet.

ParameterSetContainer(String, String, ParameterSet) - Constructor for class de.jstacs.parameters.ParameterSetContainer

Creates an new ParameterSetContainer out of a ParameterSet.

ParameterSetContainer(Class<? extends ParameterSet>) - Constructor for class de.jstacs.parameters.ParameterSetContainer

Creates an new ParameterSetContainer out of the class of a ParameterSet.

ParameterSetContainer(String, String, Class<? extends ParameterSet>) - Constructor for class de.jstacs.parameters.ParameterSetContainer

Creates an new ParameterSetContainer out of the class 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 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.WrongParameterTypeException - Exception in de.jstacs.io

An Exception that is thrown if the DataType of a Parameter is not appropriate for some purpose.

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 ParameterSets.

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.RankEntryComparator<K,V> - Class in de.jstacs.parameters

This class implements a comparator on Map.Entry where value is a ComparableElement with weight Integer.

parametersLoaded() - Method in class de.jstacs.parameters.ParameterSet

Returns true if the parameters of this ParameterSet have been loaded.

ParameterValidator - Interface in de.jstacs.parameters.validation

Interface for a parameter validator, i.e.

paramRef - Variable in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.AbstractMixtureDiffSM

This array contains the references/indices for the parameters.

params - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.AbstractMultiThreadedOptimizableFunction

This is a pointer for the current parameters.

params - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.SamplingScoreBasedClassifier

Parameters

params - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.ScoreClassifier

The parameter set for the classifier.

params - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DiscreteGraphicalTrainSM

The current parameter set of the model.

params - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission

The parameters of the emission

paramsFile - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGModelForGibbsSampling

The files for saving the parameters during the sampling.

paramsFile - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission

The files for saving the parameters during the sampling.

paramsFile - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.HigherOrderTransition

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 Parameter, this variable holds a reference to that Parameter.

parse(String[], boolean) - Method in class de.jstacs.tools.ui.galaxy.GalaxyAdaptor

Parses the command line.

parseAnnotationToComment(char, SequenceAnnotation...) - Method in class de.jstacs.data.sequences.annotation.MotifAnnotationParser

parseAnnotationToComment(char, SequenceAnnotation...) - Method in class de.jstacs.data.sequences.annotation.NullSequenceAnnotationParser

parseAnnotationToComment(char, SequenceAnnotation...) - Method in class de.jstacs.data.sequences.annotation.ReferenceSequenceAnnotationParser

parseAnnotationToComment(char, SequenceAnnotation...) - Method in interface de.jstacs.data.sequences.annotation.SequenceAnnotationParser

This method returns a String representation of the given SequenceAnnotations 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

parseAttributes(Map<String, String>) - Static method in class de.jstacs.io.XMLParser

This method parses a map of attribute, i.e.

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.classifiers.differentiableSequenceScoreBased.sampling.SamplingScoreBasedClassifier.DiffSMSamplingComponent

parseNextParameterSet() - Method in interface de.jstacs.sampling.SamplingComponent

This method allows the user to parse the next set of parameters (from a file).

parseNextParameterSet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGModelForGibbsSampling

parseNextParameterSet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.SamplingHigherOrderHMM

This method parse a parameter set stored in file during sampling

parseNextParameterSet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission

parseNextParameterSet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.SilentEmission

parseNextParameterSet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleSamplingState

parseNextParameterSet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.HigherOrderTransition

parseNextParameterSet() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM

This method allows the user to parse the next set of parameters (from a file).

parseParameterSet(int, int) - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.SamplingScoreBasedClassifier.DiffSMSamplingComponent

parseParameterSet(int, int) - Method in interface de.jstacs.sampling.SamplingComponent

This method allows the user to parse the set of parameters with index n of a certain sampling (from a file).

parseParameterSet(int, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGModelForGibbsSampling

parseParameterSet(int, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.SamplingHigherOrderHMM

This method allows the user to parse the set of parameters with index idx of a certain sampling (from a file).

parseParameterSet(int, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission

parseParameterSet(int, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.SilentEmission

parseParameterSet(int, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleSamplingState

parseParameterSet(int, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.HigherOrderTransition

parseParameterSet(int, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM

This method allows the user to parse the set of parameters with index burnInIteration of a specific sampling (from a file).

parseProfileHMMFromHMMer(Reader, StringBuffer, LinkedList<Integer>, LinkedList<Integer>) - Static method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.HMMFactory

Parses a profile HMM from the textual HMMer representation.

parseSections(String) - Static method in class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet

Parses the sections as defined in sections to a LinkedList of Integers.

parseString(String) - Static method in class de.jstacs.io.XMLParser

This method parses the original String to null if original equals "null".

partDerState - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.DifferentiableHigherOrderHMM

Help array for the derivatives of the parameters of the states

partDerTransition - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.DifferentiableHigherOrderHMM

Help array for the derivatives of the parameters of the transition

partialLength - Variable in class de.jstacs.sequenceScores.differentiable.IndependentProductDiffSS

This array specifies the lengths of the specific parts.

partition(DataSet.PartitionMethod, double...) - Method in class de.jstacs.data.DataSet

This method partitions the elements, i.e.

partition(double[], DataSet.PartitionMethod, double...) - Method in class de.jstacs.data.DataSet

This method partitions the elements, i.e.

partition(DataSet.PartitionMethod, int) - Method in class de.jstacs.data.DataSet

This method partitions the elements, i.e.

partition(double[], DataSet.PartitionMethod, int) - Method in class de.jstacs.data.DataSet

This method partitions the elements, i.e.

partNorm - Variable in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.AbstractMixtureDiffSM

This array contains the partial normalization constants, i.e.

PDFAdaptor - Class in de.jstacs.utils.graphics

GraphicsAdaptor for the PDF format.

PDFAdaptor() - Constructor for class de.jstacs.utils.graphics.PDFAdaptor

Creates a new adaptor for plotting to a PDF device.

pearsonCorrelation(double[], double[]) - Static method in class de.jstacs.utils.ToolBox

The method computes the Pearson correlation of two vectors.

pearsonCorrelation(double[], double[], double[]) - Static method in class de.jstacs.utils.ToolBox

Computes the Pearson correlation of two vectors with weights on the individual entries.

pearsonCorrelation(double[], double[], int, int) - Static method in class de.jstacs.utils.ToolBox

The method computes the Pearson correlation of two vectors beginning at specific offsets.

pearsonCorrelation(double[], double[], int, int, int) - Static method in class de.jstacs.utils.ToolBox

The method computes the Pearson correlation of two vectors beginning at specific offsets and using a given number of entries.

PearsonCorrelationDistanceMetric - Class in de.jstacs.clustering.distances

Implements a distance metric based on the Pearson correlation of two double vectors.

PearsonCorrelationDistanceMetric(boolean) - Constructor for class de.jstacs.clustering.distances.PearsonCorrelationDistanceMetric

Creates a new distance based on the Pearson correlation.

percentile(double[], double) - Static method in class de.jstacs.utils.ToolBox

Returns the percent percentile of the array, i.e., returns the element at percent*(array.length) of the sorted array.

percentile(int, int, double[], double) - Static method in class de.jstacs.utils.ToolBox

Returns the percent percentile of the array between start and end, i.e., returns the element at percent*(end-start) of the sorted sub-array.

PerformanceMeasure - Interface in de.jstacs.classifiers.performanceMeasures

Interface of any performance measure used to evaluate an AbstractClassifier.

PerformanceMeasureParameterSet - Class in de.jstacs.classifiers.performanceMeasures

This class implements a container of AbstractPerformanceMeasures that can be used in AbstractClassifier.evaluate(AbstractPerformanceMeasureParameterSet, boolean, de.jstacs.data.DataSet...).

PerformanceMeasureParameterSet(StringBuffer) - Constructor for class de.jstacs.classifiers.performanceMeasures.PerformanceMeasureParameterSet

The standard constructor for the interface Storable.

PerformanceMeasureParameterSet(int) - Constructor for class de.jstacs.classifiers.performanceMeasures.PerformanceMeasureParameterSet

Constructs a new PerformanceMeasureParameterSet that can be used for classifiers that handle the given number of classes.

PerformanceMeasureParameterSet(PerformanceMeasure...) - Constructor for class de.jstacs.classifiers.performanceMeasures.PerformanceMeasureParameterSet

Constructs a new PerformanceMeasureParameterSet with the given performance measures.

permute(double[]) - Static method in class de.jstacs.utils.ToolBox

Creates and returns a permutation of the values in values.

permute(double[], double[]) - Static method in class de.jstacs.utils.ToolBox

Creates a new permutation of the values in values.

PermutedSequence<T> - Class in de.jstacs.data.sequences

This class is for permuted sequences.

PermutedSequence(Sequence<T>) - Constructor for class de.jstacs.data.sequences.PermutedSequence

Creates a new PermutedSequence by shuffling the symbols of a given Sequence.

PermutedSequence(Sequence<T>, int[]) - Constructor for class de.jstacs.data.sequences.PermutedSequence

Creates a new PermutedSequence for a given permutation

PFMComparator - Class in de.jstacs.utils

This class implements a number of methods for the comparison of position frequency matrices (PFMs) as described in the Amadeus paper

PFMComparator() - Constructor for class de.jstacs.utils.PFMComparator

PFMComparator.NormalizedEuclideanDistance - Class in de.jstacs.utils

This class implements the normalized Euclidean distance.

PFMComparator.OneMinusPearsonCorrelationCoefficient - Class in de.jstacs.utils

This class implements the Pearson correlation coefficient.

PFMComparator.PFMDistance - Class in de.jstacs.utils

This interface declares a method for comparing different PFMs.

PFMComparator.SymmetricKullbackLeiblerDivergence - Class in de.jstacs.utils

This class implements the symmetric Kullback-Leibler-divergence.

PFMComparator.UniformBorderWrapper - Class in de.jstacs.utils

Wraps a given PFMComparator.PFMDistance and pads the considered PFMs with uniformly distributed positions.

PFMDistance() - Constructor for class de.jstacs.utils.PFMComparator.PFMDistance

PFMWrapperTrainSM - Class in de.jstacs.sequenceScores.statisticalModels.trainable

A wrapper class for representing position weight matrices or position frequency matrices from databases as TrainableStatisticalModels.

PFMWrapperTrainSM(AlphabetContainer, String, double[][], double) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.PFMWrapperTrainSM

Creates a new wrapper for a given position frequency matrix.

PFMWrapperTrainSM(AlphabetContainer, String, double[][]) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.PFMWrapperTrainSM

Creates a new wrapper for a given position frequency matrix.

PFMWrapperTrainSM(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.PFMWrapperTrainSM

Creates a wrapper from its XML representation

PhyloDiscreteEmission - Class in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete

Phylogenetic discrete emission This class uses a phylogenetic tree to describe multidimensional data It implements Felsensteins model for nucleotide substitution (F81)

PhyloDiscreteEmission(AlphabetContainer, double, PhyloTree) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.PhyloDiscreteEmission

This is a simple constructor for a PhyloDiscreteEmission based on the equivalent sample size.

PhyloDiscreteEmission(AlphabetContainer, double[], PhyloTree) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.PhyloDiscreteEmission

This is a simple constructor for a DiscreteEmission defining the individual hyper parameters.

PhyloNode - Class in de.jstacs.sequenceScores.statisticalModels.trainable.phylo

This class implements a node in a PhyloTree A PhyloNode contains some basic informations of itself and the incoming edge Furthermore it contains a list of PhyloNodes that represent the children nodes

PhyloNode() - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.phylo.PhyloNode

Basic constructor

PhyloNode(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.phylo.PhyloNode

The standard constructor for the interface Storable.

PhyloTree - Class in de.jstacs.sequenceScores.statisticalModels.trainable.phylo

This class implements a simple (phylogenetic) tree.

PhyloTree(String, PhyloNode) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.phylo.PhyloTree

Construct an instance of the class PhyloTree

PhyloTree(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.phylo.PhyloTree

The standard constructor for the interface Storable.

plot(REnvironment, AbstractScoreBasedClassifier.DoubleTableResult...) - Static method in class de.jstacs.classifiers.AbstractScoreBasedClassifier.DoubleTableResult

This method plots an array of AbstractScoreBasedClassifier.DoubleTableResults 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(CharSequence) - Method in class de.jstacs.utils.REnvironment

Creates a buffered image from a given plot command.

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

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

plot(CharSequence, 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.

plotDefaultDependencyLogoToBufferedImage(DataSet, double[], int) - Static method in class de.jstacs.utils.SeqLogoPlotter

Plots a dependency logo using default parameters to a BufferedImage.

plotDefaultDependencyLogoToGraphicsAdaptor(GraphicsAdaptor, DataSet, double[], int) - Static method in class de.jstacs.utils.SeqLogoPlotter

Plots a dependency logo using default parameters to a GraphicsAdaptor.

plotDependencyLogo(DataSet, Object[], int, double[][], double[], Graphics2D, int, int, int, int[], int[], double, int, boolean, int, boolean, boolean, boolean, double) - Static method in class de.jstacs.utils.SeqLogoPlotter

Plots a dependency logo using the supplied parameters.

PlotGeneratorResult - Class in de.jstacs.results

Class for a Result that may be used to generate plots for different output formats using GraphicsAdaptor sub-classes.

PlotGeneratorResult(String, String, PlotGeneratorResult.PlotGenerator, boolean) - Constructor for class de.jstacs.results.PlotGeneratorResult

Creates a new PlotGeneratorResult with the given name, comment, PlotGeneratorResult.PlotGenerator.

PlotGeneratorResult(StringBuffer) - Constructor for class de.jstacs.results.PlotGeneratorResult

Creates a new PlotGeneratorResult from its XML representation.

PlotGeneratorResult.PlotGenerator - Interface in de.jstacs.results

Interface for a class that may generate a plot using the specified GraphicsAdaptor.

PlotGeneratorResultSaver - Class in de.jstacs.results.savers

ResultSaver for PlotGeneratorResults.

plotLogo(Graphics2D, int, double[][]) - Static method in class de.jstacs.utils.SeqLogoPlotter

Plots the sequence logo for the position weight matrix given in ps.

plotLogo(Graphics2D, int, double[][], String[], String, String) - Static method in class de.jstacs.utils.SeqLogoPlotter

Plots the sequence logo for the position weight matrix given in ps.

plotLogo(Graphics2D, int, int, double[][], String[], String, String) - Static method in class de.jstacs.utils.SeqLogoPlotter

Plots the sequence logo for the position weight matrix given in ps.

plotLogo(Graphics2D, int, int, int, int, double[][], String[], String, String) - Static method in class de.jstacs.utils.SeqLogoPlotter

Plots the sequence logo for the position weight matrix given in ps.

plotLogo(Graphics2D, double, double, double, double, double[]) - Static method in class de.jstacs.utils.SeqLogoPlotter

Plots a sequence logo for a single position to a graphics object.

plotLogoToBufferedImage(int, double[][]) - Static method in class de.jstacs.utils.SeqLogoPlotter

Plots the sequence logo for the position weight matrix given in ps.

plotLogoToPNG(String, int, double[][]) - Static method in class de.jstacs.utils.SeqLogoPlotter

Plots the sequence logo for the position weight matrix given in ps.

plotScores(AbstractScoreBasedClassifier, DataSet, DataSet, REnvironment, int, double, String) - Static method in class de.jstacs.classifiers.utils.ClassificationVisualizer

This method returns an ImageResult containing a plot of the histograms of the scores.

plotScores(AbstractScoreBasedClassifier, DataSet, DataSet, REnvironment, int, double, String, String) - Static method in class de.jstacs.classifiers.utils.ClassificationVisualizer

This method creates a pdf containing a plot of the histograms of the scores.

plotTALgetterLogo(Graphics2D, int, int, int, int, double[][], double[], String[], String, String, String) - Static method in class de.jstacs.utils.SeqLogoPlotter

Plots the TALgetter logo for the binding specificities given in ps.

plotTALgetterLogoToBufferedImage(int, double[][], double[], String[]) - Static method in class de.jstacs.utils.SeqLogoPlotter

Plots the TALgetter logo for the binding specificities given in ps.

plotTALgetterLogoToPNG(String, int, double[][], double[], String[]) - Static method in class de.jstacs.utils.SeqLogoPlotter

Plots the TALgetter logo for the binding specificities given in ps.

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

Creates a pdf file from a given plot command.

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

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

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

Creates a tex file from a given plot command.

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

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

PluginGaussianEmission - Class in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous

Basic Gaussian emission distribution without random initialization of parameters.

PluginGaussianEmission(double, double, double, double, double, double) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.PluginGaussianEmission

Creates a Gaussian emission density with mean mean and standard deviation sd.

PluginGaussianEmission(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.PluginGaussianEmission

Creates a PluginGaussianEmission from its XML representation.

plugInParameters - Variable in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BayesianNetworkDiffSM

Indicates if plug-in parameters, i.e.

PMMExplainingAwayResidual - Class in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures

Class for the network structure of a BayesianNetworkDiffSM that is a permuted Markov model based on the explaining away residual.

PMMExplainingAwayResidual(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMExplainingAwayResidual

The standard constructor for the interface Storable.

PMMExplainingAwayResidual(byte, double[]) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMExplainingAwayResidual

Creates a new PMMExplainingAwayResidual of order order.

PMMExplainingAwayResidual(PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMExplainingAwayResidual

Creates a new PMMExplainingAwayResidual from the corresponding InstanceParameterSet parameters.

PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet - Class in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures

Class for the parameters of a PMMExplainingAwayResidual structure Measure.

PMMExplainingAwayResidualParameterSet() - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet

Creates a new PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet with empty parameter values.

PMMExplainingAwayResidualParameterSet(byte, double[]) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.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.

PMMExplainingAwayResidualParameterSet(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.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.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures

Class for the network structure of a BayesianNetworkDiffSM that is a permuted Markov model based on mutual information.

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

Creates a new PMMMutualInformation of order order.

PMMMutualInformation(PMMMutualInformation.PMMMutualInformationParameterSet) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation

Creates a new PMMMutualInformation from the corresponding InstanceParameterSet parameters.

PMMMutualInformation(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation

The standard constructor for the interface Storable.

PMMMutualInformation.PMMMutualInformationParameterSet - Class in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures

Class for the parameters of a PMMMutualInformation structure Measure.

PMMMutualInformationParameterSet() - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation.PMMMutualInformationParameterSet

Creates a new PMMMutualInformation.PMMMutualInformationParameterSet with empty parameter values.

PMMMutualInformationParameterSet(byte, BTMutualInformation.DataSource, double[]) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.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.

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

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

pop() - Method in class de.jstacs.utils.IntList

Returns the last element and removes it from the list.

position - Variable in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter

The position of symbol this parameter is responsible for.

PositionDiffSM - Class in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

This class implements a position scoring function that enables the user to get a score without using a Sequence object.

PositionDiffSM(AlphabetContainer, int) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.PositionDiffSM

This constructor allows create instance with more than one dimension.

PositionDiffSM(int, int) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.PositionDiffSM

This is the main constructor that creates the AlphabetContainer internally.

PositionDiffSM(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.PositionDiffSM

This is the constructor for Storable.

PositionPrior - Class in de.jstacs.sequenceScores.statisticalModels.trainable.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.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior.PositionPrior

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

PositionPrior(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior.PositionPrior

The standard constructor for the interface Storable.

PositivePredictiveValueForFixedSensitivity - Class in de.jstacs.classifiers.performanceMeasures

This class implements the positive predictive value for a fixed sensitivity.

PositivePredictiveValueForFixedSensitivity() - Constructor for class de.jstacs.classifiers.performanceMeasures.PositivePredictiveValueForFixedSensitivity

Constructs a new instance of the performance measure PositivePredictiveValueForFixedSensitivity with empty parameter values.

PositivePredictiveValueForFixedSensitivity(double) - Constructor for class de.jstacs.classifiers.performanceMeasures.PositivePredictiveValueForFixedSensitivity

Constructs a new instance of the performance measure PositivePredictiveValueForFixedSensitivity with given sensitivity.

PositivePredictiveValueForFixedSensitivity(StringBuffer) - Constructor for class de.jstacs.classifiers.performanceMeasures.PositivePredictiveValueForFixedSensitivity

The standard constructor for the interface Storable.

posPrior - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.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.sequenceScores.statisticalModels.trainable.discrete.homogeneous.HomogeneousTrainSM

The powers of the alphabet length.

PRCurve - Class in de.jstacs.classifiers.performanceMeasures

This class implements the precision-recall curve and its area under the curve.

PRCurve() - Constructor for class de.jstacs.classifiers.performanceMeasures.PRCurve

Constructs a new instance of the performance measure PRCurve.

PRCurve(StringBuffer) - Constructor for class de.jstacs.classifiers.performanceMeasures.PRCurve

The standard constructor for the interface Storable.

precompute() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.GaussianEmission

This method precomputes some normalization constant.

precompute() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission

This method precomputes some normalization constant and probabilities.

precompute() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

This method precomputes internal fields as for instance the normalization constant.

precompute() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.ReferenceBasedTransitionElement

precompute() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.TransitionElement

precomputeBurnInLength(SamplingScoreBasedClassifier.DiffSMSamplingComponent) - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.SamplingScoreBasedClassifier

Precomputes the length of the burn-in phase, e.g.

precomputeNorm() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.AbstractMixtureDiffSM

Pre-computes the normalization constant.

precomputeNormalization() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BayesianNetworkDiffSM

Pre-computes all normalization constants.

preoptimize(OptimizableFunction) - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.ScoreClassifier

This method allows to pre-optimize the parameter before the real optimization.

prepareAssessment(boolean, DataSet...) - Method in class de.jstacs.classifiers.assessment.ClassifierAssessment

Prepares an assessment.

prepareThreads() - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.AbstractMultiThreadedOptimizableFunction

Assigns parts of the data to the threads

previousParameters - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.SamplingScoreBasedClassifier

The previously accepted parameters, backup for rollbacks

prGrad - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.LogGenDisMixFunction

Array for the gradient of the prior

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.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter

Prints the counts and the value of this parameter to System.out.

print() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree

Prints the structure of this tree.

prior - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.DiffSSBasedOptimizableFunction

The prior that is used in this function.

prior - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.GenDisMixClassifier

The prior that is used in this classifier.

PRIOR_INDEX - Static variable in enum de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.LearningPrinciple

This constant is the array index of the weighting factor for the prior.

probabilities - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.ReferenceBasedTransitionElement

Represents the initial the transition probabilities.

probs - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission

The parameters transformed to probabilites

probs - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.TransitionElement

The precomputed probabilities for each possible transition.

ProductConstraint - Class in de.jstacs.sequenceScores.differentiable.logistic

This class implements product constraints, i.e., the method ProductConstraint.getValue(Sequence,int) returns the product of the values for the positions defined in the constructor.

ProductConstraint(int...) - Constructor for class de.jstacs.sequenceScores.differentiable.logistic.ProductConstraint

This is the main constructor creating an instance from a given set of positions.

ProductConstraint(StringBuffer) - Constructor for class de.jstacs.sequenceScores.differentiable.logistic.ProductConstraint

This is the constructor for Storable.

ProgressUpdater - Class in de.jstacs.tools

Interface for a progress bar (or similar) indicating a tool's progress.

ProgressUpdater() - Constructor for class de.jstacs.tools.ProgressUpdater

Creates a new ProgressUpdater.

ProgressUpdater - Interface in de.jstacs.utils

Deprecated.

propagateESS(double, ArrayList<HMMFactory.PseudoTransitionElement>) - Static method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.HMMFactory

Propagates the ess for an HMM with absorbing states.

ProteinAlphabet - Class in de.jstacs.data.alphabets

This class implements the discrete alphabet that is used for proteins (one letter code).

ProteinAlphabet.ProteinAlphabetParameterSet - Class in de.jstacs.data.alphabets

The parameter set for a ProteinAlphabet.

Protocol - Interface in de.jstacs.tools

Interface for the protocol of the run of a JstacsTool.

Protocol() - Constructor for class de.jstacs.tools.ui.galaxy.GalaxyAdaptor.Protocol

Creates a new Protocol

provideMatrix(int, int) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM

This method invokes the method AbstractHMM.createHelperVariables() and provides the matrix with given type.

pseudoCount - Variable in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter

The pseudocount for this parameter.

PseudoTransitionElement(int[], int[], double[]) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.HMMFactory.PseudoTransitionElement

This constructor creates an new HMMFactory.PseudoTransitionElement without edge weights.

PseudoTransitionElement(int[], int[], double[], double[]) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.HMMFactory.PseudoTransitionElement

This constructor creates an new HMMFactory.PseudoTransitionElement with specific edge weights.

PValueComputation - Class in de.jstacs.classifiers.utils

This class can be used to compute any p-value from a given statistic.

PValueComputation() - Constructor for class de.jstacs.classifiers.utils.PValueComputation

PWMSupplier - Interface in de.jstacs.clustering.hierachical

Interface for classes that may provide a position weight matrix

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