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## R

r - Static variable in class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
  This object can be used for drawing initial parameters.
RandomNumberGenerator - Class in de.jstacs.utils.random
  Class for generating random numbers of many different distributions.
RandomNumberGenerator() - Constructor for class de.jstacs.utils.random.RandomNumberGenerator
RandomNumberGenerator(long) - Constructor for class de.jstacs.utils.random.RandomNumberGenerator
Rangeable - Interface in de.jstacs.parameters
  Interface for `Parameter`s that potentially can be varied over a certain interval or a list of values.
ranged - Variable in class de.jstacs.parameters.ParameterSet
  Indicates if the `Parameter`s of this `ParameterSet` that implement `Rangeable` and return `true` shall be replaced by their ranged instances
RangeIterator - Interface in de.jstacs.parameters
  Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.
RangeParameter - Class in de.jstacs.parameters
  Class for a parameter wrapper that allows `SimpleParameter`s to be set to a set of values.
RangeParameter(SimpleParameter) - Constructor for class de.jstacs.parameters.RangeParameter
  Constructs a `RangeParameter` from a `SimpleParameter` that is rangeable.
RangeParameter(StringBuffer) - Constructor for class de.jstacs.parameters.RangeParameter
  The standard constructor for the interface `Storable`.
RangeParameter.RangeType - Enum in de.jstacs.parameters
  The possible types of defining ranges for a `RangeParameter`.
RangeParameter.Scale - Enum in de.jstacs.parameters
  This `enum` defines possible scales, if `RangeParameter.RangeType` is `RangeParameter.RangeType.RANGE`.
rank(double[], boolean) - Static method in class de.jstacs.utils.ToolBox
  Ranks the values in `values`, where the greatest value obtains the lowest rank.
rc - Variable in class de.jstacs.data.Sequence
  The pointer to the reverse complement of the `Sequence.RecursiveSequence`.
read(Reader) - Static method in class de.jstacs.io.FileManager
  This method reads a `StringBuffer` from a given `Reader`.
reader - Variable in class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSampling
  The reader for the `paramsFile` after a sampling.
readFile(File) - Static method in class de.jstacs.io.FileManager
  This method reads a `StringBuffer` from a given `File`.
readInputStream(InputStream) - Static method in class de.jstacs.io.FileManager
  This method reads a `StringBuffer` from a given `InputStream`.
readTensorFromFile(String, boolean) - Static method in class de.jstacs.algorithms.graphs.tensor.Tensor
  The opposite of the method `Tensor.writeTensorToFile(String, OutputStream)`.
RealTime - Class in de.jstacs.utils
  This is a very simple implementation of `Time`.
RealTime() - Constructor for class de.jstacs.utils.RealTime
recieveId() - Method in class de.jstacs.parameters.ParameterSet
  Searches for all `Parameter.neededReferenceId`s in the hierarchy below this `ParameterSet` and sets the corresponding `Parameter.neededReference`s.
RecyclableSequenceEnumerator - Interface in de.jstacs.data
  This interface extends `Enumeration` of `Sequence`s by declaring an additional method that allows to reuse the Enumeration.
reduce(AbstractList<int[]>) - Static method in class de.jstacs.models.discrete.ConstraintManager
  This method tries to find and remove subconstraints that are already fulfilled by a bigger one.
ReferenceConstraint - Class in de.jstacs.parameters.validation
  Class for a `Constraint` that defines a condition on one `Parameter` (the one containing the `ConstraintValidator`) with respect to another `Parameter`.
ReferenceConstraint(Parameter) - Constructor for class de.jstacs.parameters.validation.ReferenceConstraint
  Creates a new `ReferenceConstraint` with respect to the `Parameter` `constraintParameter`.
ReferenceConstraint(StringBuffer) - Constructor for class de.jstacs.parameters.validation.ReferenceConstraint
  The standard constructor for the interface `Storable`.
ReferenceSequenceAnnotation - Class in de.jstacs.data.sequences.annotation
  This class implements a `SequenceAnnotation` that contains a reference sequence.
ReferenceSequenceAnnotation(String, Sequence, Result...) - Constructor for class de.jstacs.data.sequences.annotation.ReferenceSequenceAnnotation
  Creates a new `ReferenceSequenceAnnotation` with identifier `identifier`, reference sequence `ref`, and additional annotation (that does not fit the `SequenceAnnotation` definitions) given as a `Result` `result`.
ReferenceSequenceAnnotation(StringBuffer) - Constructor for class de.jstacs.data.sequences.annotation.ReferenceSequenceAnnotation
  The standard constructor for the interface `Storable`.
ReferenceSequenceAnnotationParser - Class in de.jstacs.data.sequences.annotation
  This class implements an `SequenceAnnotationParser` that parses a `ReferenceSequenceAnnotation` from the comment lines of a sequence.
ReferenceSequenceAnnotationParser(String, AlphabetContainer, String, String) - Constructor for class de.jstacs.data.sequences.annotation.ReferenceSequenceAnnotationParser
  Creates a new `ReferenceSequenceAnnotationParser` with user-specified delimiters.
RegExFilenameFilter - Class in de.jstacs.io
  A simple filter on `File`s that accepts `File`s with a specific regular expression in the filename.
RegExFilenameFilter(String, boolean, boolean, String...) - Constructor for class de.jstacs.io.RegExFilenameFilter
  Creates a new `RegExFilenameFilter` with given regular expressions `regex` to be found in the file name of the `File`s to be filtered.
remove() - Method in class de.jstacs.data.Sample.ElementEnumerator
removeBackground(Hashtable<Sequence, BitSet[]>, int, int, double, double) - Static method in class de.jstacs.motifDiscovery.KMereStatistic
  This method allows to remove those entries from the statistic that have a lower weighted foreground cardinality than the weighted background cardinality.
removeParameterFromSet() - Method in class de.jstacs.parameters.ExpandableParameterSet
  Removes the last `Parameter` from set.
REnvironment - Class in de.jstacs.utils
  This is an environment class for R and Rserve that helps you to handle all things in a more gentle way.
REnvironment(String, String, String, int) - Constructor for class de.jstacs.utils.REnvironment
  Creates a new `REnvironment` using the default port.
REnvironment(String, String, String) - Constructor for class de.jstacs.utils.REnvironment
  Creates a new `REnvironment` with initial size 10 using the default port.
REnvironment(String, int, String, String, int) - Constructor for class de.jstacs.utils.REnvironment
  Creates a new `REnvironment` using the given port.
REnvironment(String, int, String, String) - Constructor for class de.jstacs.utils.REnvironment
  Creates a new `REnvironment` with initial size 10 using the given port.
RepeatedHoldOutAssessParameterSet - Class in de.jstacs.classifier.assessment
  This class implements a `ClassifierAssessmentAssessParameterSet` that must be used to call method `assess( ... )` of a `RepeatedHoldOutExperiment`.
RepeatedHoldOutAssessParameterSet() - Constructor for class de.jstacs.classifier.assessment.RepeatedHoldOutAssessParameterSet
  Constructs a new `RepeatedHoldOutAssessParameterSet` with empty parameter values.
RepeatedHoldOutAssessParameterSet(StringBuffer) - Constructor for class de.jstacs.classifier.assessment.RepeatedHoldOutAssessParameterSet
  The standard constructor for the interface `Storable`.
RepeatedHoldOutAssessParameterSet(Sample.PartitionMethod, int, boolean, int, double[]) - Constructor for class de.jstacs.classifier.assessment.RepeatedHoldOutAssessParameterSet
  Constructs a new `RepeatedHoldOutAssessParameterSet` with given parameter values.
RepeatedHoldOutExperiment - Class in de.jstacs.classifier.assessment
  This class implements a repeated hold-out experiment for assessing classifiers.
RepeatedHoldOutExperiment(AbstractClassifier[], Model[][], boolean, boolean) - Constructor for class de.jstacs.classifier.assessment.RepeatedHoldOutExperiment
  Creates a new `RepeatedHoldOutExperiment` from an array of `AbstractClassifier`s and a two-dimensional array of `Model` s, which are combined to additional classifiers.
RepeatedHoldOutExperiment(AbstractClassifier...) - Constructor for class de.jstacs.classifier.assessment.RepeatedHoldOutExperiment
  Creates a new `RepeatedHoldOutExperiment` from a set of `AbstractClassifier`s.
RepeatedHoldOutExperiment(boolean, Model[]...) - Constructor for class de.jstacs.classifier.assessment.RepeatedHoldOutExperiment
  Creates a new `RepeatedHoldOutExperiment` from a set of `Model`s.
RepeatedHoldOutExperiment(AbstractClassifier[], boolean, Model[]...) - Constructor for class de.jstacs.classifier.assessment.RepeatedHoldOutExperiment
  This constructor allows to assess a collection of given `AbstractClassifier`s and those constructed using the given `AbstractModel`s by a `RepeatedHoldOutExperiment`.
RepeatedSubSamplingAssessParameterSet - Class in de.jstacs.classifier.assessment
  This class implements a `ClassifierAssessmentAssessParameterSet` that must be used to call method `assess( ... )` of a `RepeatedSubSamplingExperiment`.
RepeatedSubSamplingAssessParameterSet() - Constructor for class de.jstacs.classifier.assessment.RepeatedSubSamplingAssessParameterSet
  Constructs a new `RepeatedSubSamplingAssessParameterSet` with empty parameter values.
RepeatedSubSamplingAssessParameterSet(StringBuffer) - Constructor for class de.jstacs.classifier.assessment.RepeatedSubSamplingAssessParameterSet
  The standard constructor for the interface `Storable`.
RepeatedSubSamplingAssessParameterSet(int, boolean, int, int[], int[]) - Constructor for class de.jstacs.classifier.assessment.RepeatedSubSamplingAssessParameterSet
  Constructs a new `RepeatedSubSamplingAssessParameterSet` with given parameter values.
RepeatedSubSamplingExperiment - Class in de.jstacs.classifier.assessment
  This class implements a repeated subsampling experiment.
RepeatedSubSamplingExperiment(AbstractClassifier[], Model[][], boolean, boolean) - Constructor for class de.jstacs.classifier.assessment.RepeatedSubSamplingExperiment
  Creates a new `RepeatedSubSamplingExperiment` from an array of `AbstractClassifier`s and a two-dimensional array of `Model` s, which are combined to additional classifiers.
RepeatedSubSamplingExperiment(AbstractClassifier...) - Constructor for class de.jstacs.classifier.assessment.RepeatedSubSamplingExperiment
  Creates a new `RepeatedSubSamplingExperiment` from a set of `AbstractClassifier`s.
RepeatedSubSamplingExperiment(boolean, Model[]...) - Constructor for class de.jstacs.classifier.assessment.RepeatedSubSamplingExperiment
  Creates a new `RepeatedSubSamplingExperiment` from a set of `Model`s.
RepeatedSubSamplingExperiment(AbstractClassifier[], boolean, Model[]...) - Constructor for class de.jstacs.classifier.assessment.RepeatedSubSamplingExperiment
  This constructor allows to assess a collection of given `AbstractClassifier`s and those constructed using the given `AbstractModel`s by a `RepeatedSubSamplingExperiment`.
replaceContentWith(ParameterSet[]) - Method in class de.jstacs.parameters.ExpandableParameterSet
  First removes all previous added `ParameterSetContainer`s and afterwards adds all given `ParameterSet`s (in the given order) enclosed in new `ParameterSetContainer`s.
replaceParametersWithRangedInstance() - Method in class de.jstacs.parameters.ExpandableParameterSet
replaceParametersWithRangedInstance() - Method in class de.jstacs.parameters.ParameterSet
  Replaces all `Parameter`s in this `ParameterSet` by their equivalents implementing the `Rangeable` interface.
replaceParametersWithRangedInstance() - Method in class de.jstacs.parameters.SequenceScoringParameterSet
required - Variable in class de.jstacs.parameters.SimpleParameter
  Determines if the parameter is required
reset() - Method in class de.jstacs.algorithms.optimization.ConstantStartDistance
reset() - Method in class de.jstacs.algorithms.optimization.LimitedMedianStartDistance
reset() - Method in interface de.jstacs.algorithms.optimization.StartDistanceForecaster
  Resets the object to the initial state.
reset(ScoringFunction[]) - Method in class de.jstacs.classifier.scoringFunctionBased.gendismix.LogGenDisMixFunction
reset() - Method in class de.jstacs.classifier.scoringFunctionBased.OptimizableFunction
  Resets the all objects and pre-computed values.
reset(ScoringFunction[]) - Method in class de.jstacs.classifier.scoringFunctionBased.SFBasedOptimizableFunction
  This method allows to reset the internally used functions and the corresponding objects.
reset() - Method in class de.jstacs.classifier.scoringFunctionBased.SFBasedOptimizableFunction
reset() - Method in class de.jstacs.data.bioJava.SimpleSequenceIterator
  Provides the possibility to reset and afterwards reuse this iterator.
reset() - Method in class de.jstacs.data.DiscreteSequenceEnumerator
reset() - Method in interface de.jstacs.data.RecyclableSequenceEnumerator
  This method enables the user to reuse this enumerator.
reset() - Method in class de.jstacs.data.Sample.ElementEnumerator
reset() - Method in class de.jstacs.data.SampleKMerEnumerator
reset() - Method in class de.jstacs.data.SequenceEnumeration
reset() - Method in class de.jstacs.models.discrete.Constraint
  This method resets all member variables that are in some way counters, frequencies, ...
reset() - Method in class de.jstacs.models.discrete.inhomogeneous.CombinationIterator
  This method resets the internal combination.
reset() - Method in class de.jstacs.models.discrete.inhomogeneous.MEMConstraint
reset() - Method in class de.jstacs.models.discrete.inhomogeneous.SequenceIterator
  Resets the internal sequence representation.
reset() - Method in class de.jstacs.parameters.CollectionParameter
reset() - Method in class de.jstacs.parameters.FileParameter
  Resets the `FileParameter` to its original state.
reset() - Method in class de.jstacs.parameters.MultiSelectionCollectionParameter
reset() - Method in class de.jstacs.parameters.Parameter
  Resets the parameter and its contents to the default values or `null` if no defaults are given.
reset() - Method in class de.jstacs.parameters.ParameterSet
  Resets all `Parameter`s in this `ParameterSet` to their default values or `null` if not default value was provided.
reset() - Method in class de.jstacs.parameters.ParameterSetContainer
reset() - Method in class de.jstacs.parameters.RangeParameter
reset() - Method in class de.jstacs.parameters.SequenceScoringParameterSet
reset() - Method in class de.jstacs.parameters.SimpleParameter
reset() - Method in class de.jstacs.parameters.SimpleParameterSet
reset() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
  Resets the counts to the pseudocounts and the value to `0`.
reset() - Method in class de.jstacs.scoringFunctions.mix.motifSearch.DurationScoringFunction
reset() - Method in class de.jstacs.scoringFunctions.mix.motifSearch.PositionScoringFunction
  This method resets the iterator to the initial state (first reasonable output) so that it can be used again.
reset() - Method in class de.jstacs.utils.RealTime
reset() - Method in class de.jstacs.utils.Time
  Restarts the time stopping.
reset() - Method in class de.jstacs.utils.UserTime
resetAllValues() - Method in class de.jstacs.models.mixture.gibbssampling.AbstractBurnInTest
resetAllValues() - Method in interface de.jstacs.models.mixture.gibbssampling.BurnInTest
  This method can be used to remove all values from the internal memory.
resetAllValues() - Method in class de.jstacs.models.mixture.gibbssampling.SimpleBurnInTest
  Deprecated.
resetCounts() - Method in class de.jstacs.models.discrete.Constraint
  This method allows to reset the internal field `Constraint.counts` that is used for estimating the probabilities.
resetToFirst() - Method in class de.jstacs.parameters.MultiSelectionCollectionParameter
resetToFirst() - Method in class de.jstacs.parameters.ParameterSet
resetToFirst() - Method in class de.jstacs.parameters.ParameterSetContainer
resetToFirst() - Method in interface de.jstacs.parameters.RangeIterator
  Resets the current value in the collection to the first value.
resetToFirst() - Method in class de.jstacs.parameters.RangeParameter
resetValue(byte, int, int...) - Method in class de.jstacs.algorithms.graphs.tensor.AsymmetricTensor
resetValue(byte, int, int...) - Method in class de.jstacs.algorithms.graphs.tensor.SubTensor
resetValue(byte, int, int...) - Method in class de.jstacs.algorithms.graphs.tensor.SymmetricTensor
  Sets the value for the edge `parents -> child` to `Double.NEGATIVE_INFTINITY`.
resetValue(byte, int, int...) - Method in class de.jstacs.algorithms.graphs.tensor.Tensor
  Sets the value for the edge `parents[0],...`
RestrictedRepeatHistory - Class in de.jstacs.motifDiscovery.history
  This class implements a history that allows operations (i.e. a pair of `int`), that are not a priorily forbidden and that are done before less than a specified threshold.
RestrictedRepeatHistory() - Constructor for class de.jstacs.motifDiscovery.history.RestrictedRepeatHistory
  This constructor creates an instance that allows to shift, shrink, and expand the motif, to do the reverse operation, and to do each operation at most once.
RestrictedRepeatHistory(boolean) - Constructor for class de.jstacs.motifDiscovery.history.RestrictedRepeatHistory
  This constructor creates an instance that allows to shift, shrink, and expand the motif, and allows to do each operation at most once.
RestrictedRepeatHistory(int) - Constructor for class de.jstacs.motifDiscovery.history.RestrictedRepeatHistory
  This constructor creates an instance that allows to shift shrink and expand the motif.
RestrictedRepeatHistory(boolean, boolean, boolean) - Constructor for class de.jstacs.motifDiscovery.history.RestrictedRepeatHistory
  This constructor creates an instance that allows to do each operation at most once.
RestrictedRepeatHistory(boolean, boolean, boolean, boolean, int) - Constructor for class de.jstacs.motifDiscovery.history.RestrictedRepeatHistory
  This constructor creates an instance with user specified allowed operations and `threshold`.
RestrictedRepeatHistory(StringBuffer) - Constructor for class de.jstacs.motifDiscovery.history.RestrictedRepeatHistory
  This is the constructor for the interface `Storable`.
Result - Class in de.jstacs.results
  The abstract class for any result.
Result(String, String, DataType) - Constructor for class de.jstacs.results.Result
  The main constructor which takes the main information of a result.
Result(StringBuffer) - Constructor for class de.jstacs.results.Result
  The standard constructor for the interface `Storable`.
result - Variable in class de.jstacs.results.SimpleResult
  The result.
results - Variable in class de.jstacs.results.ResultSet
  The set of results as an array of `Result`s.
ResultSet - Class in de.jstacs.results
  Class for a set of `Result`s which provides methods to access single `Result`s in the set, to retrieve the number of `Result`s in the set, to get a `String` representation or an XML representation of all the `Result`s in the set.
ResultSet(Result) - Constructor for class de.jstacs.results.ResultSet
  Constructs a new `ResultSet` containing one `Result`.
ResultSet(Result[]...) - Constructor for class de.jstacs.results.ResultSet
  Constructs a new `ResultSet` from a two-dimensional array of `Result`s.
ResultSet(Collection<? extends Result>) - Constructor for class de.jstacs.results.ResultSet
  Constructs a new `ResultSet` from a `Collection` of type `Result`.
ResultSet(StringBuffer) - Constructor for class de.jstacs.results.ResultSet
  The standard constructor for the interface `Storable`.
reverse() - Method in class de.jstacs.data.Sequence
  This method returns a new instance of `Sequence.RecursiveSequence` containing the reverse current `Sequence.RecursiveSequence`.
reverse(int, int) - Method in class de.jstacs.data.Sequence
  This method returns a new instance of `Sequence.RecursiveSequence` containing a part of the reverse current `Sequence.RecursiveSequence`.
reverse(int, int) - Method in class de.jstacs.data.sequences.SparseSequence
reverse() - Method in class de.jstacs.utils.IntList
  This method reverses the list, i.e., after invoking this method the formerly first element is than the last, the formerly second element is than the last but one, ...
reverseComplement() - Method in class de.jstacs.data.Sequence
  This method returns a new instance of `Sequence.RecursiveSequence` containing the reverse complementary current `Sequence.RecursiveSequence`.
reverseComplement(int, int) - Method in class de.jstacs.data.Sequence
  This method returns a new instance of `Sequence.RecursiveSequence` containing a reverse part of the complementary current `Sequence.RecursiveSequence`.
reverseComplement(int, int) - Method in class de.jstacs.data.Sequence.SubSequence
reverseComplement(int, int) - Method in class de.jstacs.data.sequences.MultiDimensionalDiscreteSequence
reverseComplement(int, int) - Method in class de.jstacs.data.sequences.SparseSequence
RUtils - Class in de.jstacs.utils
  This is a collection of various silly things you can do when accessing Rserve.
RUtils() - Constructor for class de.jstacs.utils.RUtils

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