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

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 Parameters 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 Parameters 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 SimpleParameters 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

Restores a RangeParameter from its XML-representation.

RangeParameter.RangeType - Enum in de.jstacs.parameters

The possible types of defining ranges for a RangeParameter

RangeParameter.Scale - Enum in de.jstacs.parameters

The possible scales, if RangeParameter.RangeType is RangeParameter.RangeType.RANGE.

rc - Variable in class de.jstacs.data.Sequence

The pointer to the reverse complement

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.

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.neededReferenceIds in the hierarchy below this ParameterSet and sets the corresponding Parameter.neededReferences.

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

This constructor creates a recursive sequence.

RecursiveSequence(AlphabetContainer, Sequence) - Constructor for class de.jstacs.data.sequences.RecursiveSequence

This constructor creates a recursive sequence using the annotation of the given sequence.

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 ReferenceCoinstraint with respect to the Parameter constraintParameter.

ReferenceConstraint(StringBuffer) - Constructor for class de.jstacs.parameters.validation.ReferenceConstraint

Creates a new ReferenceConstraint from its XML-representation.

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 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

Constructs a RepeatedHoldOutAssessParameterSet out of an XML representation.

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 AbstractClassifiers 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 AbstractClassifiers.

RepeatedHoldOutExperiment(boolean, Model[]...) - Constructor for class de.jstacs.classifier.assessment.RepeatedHoldOutExperiment

Creates a new RepeatedHoldOutExperiment from a set of Models.

RepeatedHoldOutExperiment(AbstractClassifier[], boolean, Model[]...) - Constructor for class de.jstacs.classifier.assessment.RepeatedHoldOutExperiment

This constructor allows to assess a collection of given AbstractClassifiers and those constructed using the given AbstractModels 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

Constructs a RepeatedSubSamplingAssessParameterSet out of an XML representation.

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 AbstractClassifiers 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 AbstractClassifiers.

RepeatedSubSamplingExperiment(boolean, Model[]...) - Constructor for class de.jstacs.classifier.assessment.RepeatedSubSamplingExperiment

Creates a new RepeatedSubSamplingExperiment from a set of Models.

RepeatedSubSamplingExperiment(AbstractClassifier[], boolean, Model[]...) - Constructor for class de.jstacs.classifier.assessment.RepeatedSubSamplingExperiment

This constructor allows to assess a collection of given AbstractClassifiers and those constructed using the given AbstractModels by a RepeatedSubSamplingExperiment.

replaceContentWith(ParameterSet[]) - Method in class de.jstacs.parameters.ExpandableParameterSet

First removes all previous added ParameterSetContainer and afterwards adds all given ParameterSets (in the given order) enclosed in new ParameterSetContainers.

replaceParametersWithRangedInstance() - Method in class de.jstacs.parameters.ExpandableParameterSet

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

Replaces all Parameters 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

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.cll.NormConditionalLogLikelihood

reset(ScoringFunction[]) - Method in class de.jstacs.classifier.scoringFunctionBased.OptimizableFunction

Resets the ScoringFunctions and all pre-computed values.

reset() - Method in class de.jstacs.data.bioJava.SimpleSequenceIterator

Provides the possibility to reset and afterwards re-use this iterator.

reset() - Method in class de.jstacs.data.DiscreteSequenceEnumerator

This method enables the user to reuse this enumerator.

reset() - Method in class de.jstacs.data.Sample.ElementEnumerator

Restarts the enumeration.

reset() - Method in class de.jstacs.models.discrete.Constraint

This method resets all member variables the are in someway counters, frequencies, ...

reset() - Method in class de.jstacs.models.discrete.inhomogeneous.CombinationIterator

This method reset 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 file parameter 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 not defaults are given.

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

Resets all parameters 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 pseudo counts and the value to 0.

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.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],...

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 constructor for the Storable interface.

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 Results

ResultSet - Class in de.jstacs.results

Class for a set of Results, which provides methods to access single Results in the set, to retrieve the number of Results in the set, to get a String representation or an XML-representation of all the Results 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 2-dimensional array of Results.

ResultSet(Collection<? extends Result>) - Constructor for class de.jstacs.results.ResultSet

Constructs a new ResultSet from a Collection of type Results.

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

Constructs a ResultSet from its XML-representation.

reverse() - Method in class de.jstacs.data.Sequence

This method returns a new instance of sequence containing the reverse current sequence.

reverse(int, int) - Method in class de.jstacs.data.Sequence

This method returns a new instance of sequence containing a part of the reverse current sequence.

reverse(int, int) - Method in class de.jstacs.data.sequences.SparseSequence

reverseComplement() - Method in class de.jstacs.data.Sequence

This method returns a new sequence instance containing the complementary current sequence.

reverseComplement(int, int) - Method in class de.jstacs.data.Sequence

This method returns a new sequence instance containing a part of the complementary current sequence.

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