A B C D E F G H I J 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
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.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
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 Sequences 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 Files that accepts Files 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 Files 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 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
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 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 ParameterSetContainers 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
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 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 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 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 two-dimensional array of Results.
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
 

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