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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`.
rc - Variable in class de.jstacs.data.Sequence
  The pointer to the reverse complement of the `Sequence.CompositeSequence`.
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.
RecursiveSequence - Class in de.jstacs.data.sequences
  This is the main class for subsequences, composite sequences, ... .
RecursiveSequence(AlphabetContainer, SequenceAnnotation[], Sequence) - Constructor for class de.jstacs.data.sequences.RecursiveSequence
  Creates a new `RecursiveSequence` on the `Sequence` `seq` with the `AlphabetContainer` `alphabet` and the annotation `annotation`.
RecursiveSequence(AlphabetContainer, Sequence) - Constructor for class de.jstacs.data.sequences.RecursiveSequence
  Creates a new `RecursiveSequence` on the `Sequence` `seq` with the `AlphabetContainer` `alphabet` using the annotation of the given `Sequence`.
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`.
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 class 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
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`.
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.CompositeSequence` containing the reverse current `Sequence.CompositeSequence`.
reverse(int, int) - Method in class de.jstacs.data.Sequence
  This method returns a new instance of `Sequence.CompositeSequence` containing a part of the reverse current `Sequence.CompositeSequence`.
reverse(int, int) - Method in class de.jstacs.data.sequences.SparseSequence
reverseComplement() - Method in class de.jstacs.data.Sequence
  This method returns a new instance of `Sequence.CompositeSequence` containing the reverse complementary current `Sequence.CompositeSequence`.
reverseComplement(int, int) - Method in class de.jstacs.data.Sequence
  This method returns a new instance of `Sequence.CompositeSequence` containing a reverse part of the complementary current `Sequence.CompositeSequence`.
reverseComplement(int, int) - Method in class de.jstacs.data.Sequence.SubSequence
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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