A B C D E F G H I J 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 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 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 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 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 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 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 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.KeyEntryComparator() - Constructor for class de.jstacs.parameters.ParameterSetTagger.KeyEntryComparator
Creates a Comparator that only compares the keys of Map.Entrys.
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.Entrys 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 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
 
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 Integers.
partition(double, Sample.PartitionMethod, int) - Method in class de.jstacs.data.Sample
This method partitions the elements, i.e. the Sequences, 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 Sequences, of the Sample 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 Sequences, 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
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.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(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 Parameters 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
 

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