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

R

r - Static variable in class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

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.

This class was written by Sundar Dorai-Raj and was downloaded from http://www.stat.vt.edu/~sundar/java/.

RandomNumberGenerator() - Constructor for class de.jstacs.utils.random.RandomNumberGenerator

RandomNumberGenerator(long) - Constructor for class de.jstacs.utils.random.RandomNumberGenerator

RandomSequenceScoreDistance - Class in de.jstacs.clustering.distances

Class for a distance metric between StatisticalModels based on the correlation of score profiles on random sequences.

RandomSequenceScoreDistance(DiscreteAlphabet, int, boolean) - Constructor for class de.jstacs.clustering.distances.RandomSequenceScoreDistance

Creates a distance using a random sequence of length .

Rangeable - Interface in de.jstacs.parameters

Interface for Parameters that potentially can be varied over a certain interval or a list of values.

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.
These values may be given either as a list of values separated by spaces, as a range between a first and a last value with a given number of steps between these values, or a single value.

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.

rank(double[], ToolBox.TiedRanks) - Static method in class de.jstacs.utils.ToolBox

Ranks the values in values, where the greatest value obtains the lowest rank.

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.

RasterizedAdaptor - Class in de.jstacs.utils.graphics

GraphicsAdaptor for rasterized formats, namely PNG or JPEG.

RasterizedAdaptor(String) - Constructor for class de.jstacs.utils.graphics.RasterizedAdaptor

Creates a new RasterizedAdaptor for different formats.

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

The pointer to the reverse complement of the Sequence.

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.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGModelForGibbsSampling

The reader for the paramsFile after a sampling.

reader - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission

The reader for the paramsFile after a sampling.

reader - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.HigherOrderTransition

The reader for the paramsFile after a sampling.

readFile(String) - Static method in class de.jstacs.io.FileManager

This method reads a StringBuffer from a file with the given filen name.

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.

readNextSequences(BufferedReader, StringBuffer, int) - Static method in class de.jstacs.utils.LargeSequenceReader

Returns the next chunk of input sequences.

readPFMFromUniprobe(String, File) - Static method in class de.jstacs.utils.PFMComparator

Reads a PFM from the UniProbe format.

readPFMsFromEMBL(String, int) - Static method in class de.jstacs.utils.PFMComparator

This method reads a number of PFMs from a file and return them in an ArrayList together with some annotation.

readPFMsFromJasparFastA(String) - Static method in class de.jstacs.utils.PFMComparator

This method reads a number of PFMs from a file in the Jaspar FastA-like format and returns them in an ArrayList together with some annotation.

readPFMsFromJasparFastA(BufferedReader) - Static method in class de.jstacs.utils.PFMComparator

Reads a list of PFMs from the Jaspar format

readPFMsFromTransfac(String, int) - Static method in class de.jstacs.utils.PFMComparator

Reads a set of PFM from the Transfac format

readPFMsFromUniprobe(String) - Static method in class de.jstacs.utils.PFMComparator

This method reads a number of PFMs from a directory as downloaded from the Uniprobe data base and returns them in an ArrayList together with some annotation.

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

RecursiveSequence(AlphabetContainer, SequenceAnnotation[], Sequence<T>) - Constructor for class de.jstacs.data.sequences.Sequence.RecursiveSequence

Creates a new Sequence.RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet and the annotation annotation.

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

Creates a new Sequence.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.sequenceScores.statisticalModels.trainable.discrete.ConstraintManager

This method tries to find and remove subconstraints that are already fulfilled by a bigger one.

ReferenceBasedTransitionElement - Class in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements

This class implements transition elements that utilize a reference sequence to determine the transition probability.

ReferenceBasedTransitionElement(int[], int[], double, double[], String) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.ReferenceBasedTransitionElement

Creates an ReferenceBasedTransitionElement representing a conditional transition probability distribution of a Hidden Markov TrainableStatisticalModel for the given context.

ReferenceBasedTransitionElement(int[], int[], double, double[], String, double[]) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.ReferenceBasedTransitionElement

Creates an ReferenceBasedTransitionElement representing a conditional transition probability distribution of a Hidden Markov TrainableStatisticalModel for the given context.

ReferenceBasedTransitionElement(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.ReferenceBasedTransitionElement

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, String) - Constructor for class de.jstacs.data.sequences.annotation.ReferenceSequenceAnnotationParser

Creates a new ReferenceSequenceAnnotationParser with user-specified delimiters.

ReferenceSequenceAnnotationParser(String, AlphabetContainer, String, String) - Constructor for class de.jstacs.data.sequences.annotation.ReferenceSequenceAnnotationParser

Creates a new ReferenceSequenceAnnotationParser with user-specified delimiters.

ReferenceSequenceDiscreteEmission - Class in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete

This class implements a discrete emission that depends on some ReferenceSequenceAnnotation at a certain reference position.

ReferenceSequenceDiscreteEmission(AlphabetContainer, AlphabetContainer, int, double) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.ReferenceSequenceDiscreteEmission

This is a simple constructor for a ReferenceSequenceDiscreteEmission based on the equivalent sample size.

ReferenceSequenceDiscreteEmission(AlphabetContainer, AlphabetContainer, int, double, double[][]) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.ReferenceSequenceDiscreteEmission

This is a simple constructor for a ReferenceSequenceDiscreteEmission based on the equivalent sample size.

ReferenceSequenceDiscreteEmission(AlphabetContainer, AlphabetContainer, int, double[][]) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.ReferenceSequenceDiscreteEmission

This constructor creates a ReferenceSequenceDiscreteEmission defining the individual hyper parameters.

ReferenceSequenceDiscreteEmission(AlphabetContainer, AlphabetContainer, int, double[][], double[][]) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.ReferenceSequenceDiscreteEmission

This constructor creates a ReferenceSequenceDiscreteEmission defining the individual hyper parameters.

ReferenceSequenceDiscreteEmission(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.ReferenceSequenceDiscreteEmission

Creates a ReferenceSequenceDiscreteEmission from its XML representation.

refIdx - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.ReferenceSequenceDiscreteEmission

The index in the reference sequence

RegExFilenameFilter - Class in de.jstacs.io

A simple filter on Files that accepts Files with a specific regular expression in the filename.

RegExFilenameFilter(String, RegExFilenameFilter.Directory, 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.

RegExFilenameFilter.Directory - Enum in de.jstacs.io

A switch to decide whether the results of a RegExFilenameFilter are forbidden, allowed or required to be a directory.

RegExFilterOutputStream - Class in de.jstacs.utils

This class allows to filter individual lines that are then passed to an internal OutputStream.

RegExFilterOutputStream(OutputStream, String) - Constructor for class de.jstacs.utils.RegExFilterOutputStream

Creates a new RegExFilterOutputStream.

RegExpValidator - Class in de.jstacs.parameters.validation

ParameterValidator that checks if a given input String matches a regular expression.

RegExpValidator(String) - Constructor for class de.jstacs.parameters.validation.RegExpValidator

Creates a validator for the given regular expression.

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

Creates a RegExpValidator from its XML representation.

register() - Static method in class de.jstacs.results.savers.DataSetResultSaver

Registers this ResultSaver in the ResultSaverLibrary

register() - Static method in class de.jstacs.results.savers.ListResultSaver

Registers this ResultSaver in the ResultSaverLibrary

register() - Static method in class de.jstacs.results.savers.PlotGeneratorResultSaver

Registers this ResultSaver in the ResultSaverLibrary

register(Class<? extends T>, ResultSaver<T>) - Static method in class de.jstacs.results.savers.ResultSaverLibrary

Registers the supplied ResultSaver for the given class in the library.

register() - Static method in class de.jstacs.results.savers.ResultSetResultSaver

Registers this ResultSaver in the ResultSaverLibrary

register() - Static method in class de.jstacs.results.savers.StorableResultSaver

Registers this ResultSaver in the ResultSaverLibrary

register() - Static method in class de.jstacs.results.savers.TextResultSaver

Registers this ResultSaver in the ResultSaverLibrary

remove(int) - Method in class de.jstacs.AnnotatedEntityList

Removes and returns the AnnotatedEntity at index idx.

remove() - Method in class de.jstacs.data.DataSet.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.

removeMeasure(int) - Method in class de.jstacs.classifiers.performanceMeasures.AbstractPerformanceMeasureParameterSet

Removes the measure with index index from the set and returns this measure.

removeMeasures(Class<? extends AbstractPerformanceMeasure>) - Method in class de.jstacs.classifiers.performanceMeasures.AbstractPerformanceMeasureParameterSet

Removes all measures of a specific class from the set.

removeMeasures(String) - Method in class de.jstacs.classifiers.performanceMeasures.AbstractPerformanceMeasureParameterSet

Removes all measures with a specific name.

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

Removes the last Parameter from set.

rename(String) - Method in class de.jstacs.results.Result

Renames this Result.

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() - Constructor for class de.jstacs.utils.REnvironment

This constructor creates a connection to an R instance on the "localhost" with empty login and password.

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.classifiers.assessment

This class implements a ClassifierAssessmentAssessParameterSet that must be used to call method assess( ...

RepeatedHoldOutAssessParameterSet() - Constructor for class de.jstacs.classifiers.assessment.RepeatedHoldOutAssessParameterSet

Constructs a new RepeatedHoldOutAssessParameterSet with empty parameter values.

RepeatedHoldOutAssessParameterSet(StringBuffer) - Constructor for class de.jstacs.classifiers.assessment.RepeatedHoldOutAssessParameterSet

The standard constructor for the interface Storable.

RepeatedHoldOutAssessParameterSet(DataSet.PartitionMethod, int, boolean, int, double[]) - Constructor for class de.jstacs.classifiers.assessment.RepeatedHoldOutAssessParameterSet

Constructs a new RepeatedHoldOutAssessParameterSet with given parameter values.

RepeatedHoldOutExperiment - Class in de.jstacs.classifiers.assessment

This class implements a repeated hold-out experiment for assessing classifiers.

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

Creates a new RepeatedHoldOutExperiment from an array of AbstractClassifiers and a two-dimensional array of TrainableStatisticalModel s, which are combined to additional classifiers.

RepeatedHoldOutExperiment(AbstractClassifier...) - Constructor for class de.jstacs.classifiers.assessment.RepeatedHoldOutExperiment

Creates a new RepeatedHoldOutExperiment from a set of AbstractClassifiers.

RepeatedHoldOutExperiment(boolean, TrainableStatisticalModel[]...) - Constructor for class de.jstacs.classifiers.assessment.RepeatedHoldOutExperiment

Creates a new RepeatedHoldOutExperiment from a set of TrainableStatisticalModels.

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

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

RepeatedSubSamplingAssessParameterSet - Class in de.jstacs.classifiers.assessment

This class implements a ClassifierAssessmentAssessParameterSet that must be used to call method assess( ...

RepeatedSubSamplingAssessParameterSet() - Constructor for class de.jstacs.classifiers.assessment.RepeatedSubSamplingAssessParameterSet

Constructs a new RepeatedSubSamplingAssessParameterSet with empty parameter values.

RepeatedSubSamplingAssessParameterSet(StringBuffer) - Constructor for class de.jstacs.classifiers.assessment.RepeatedSubSamplingAssessParameterSet

The standard constructor for the interface Storable.

RepeatedSubSamplingAssessParameterSet(int, boolean, int, double[], double[]) - Constructor for class de.jstacs.classifiers.assessment.RepeatedSubSamplingAssessParameterSet

Constructs a new RepeatedSubSamplingAssessParameterSet with given parameter values.

RepeatedSubSamplingExperiment - Class in de.jstacs.classifiers.assessment

This class implements a repeated subsampling experiment.

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

Creates a new RepeatedSubSamplingExperiment from an array of AbstractClassifiers and a two-dimensional array of TrainableStatisticalModel s, which are combined to additional classifiers.

RepeatedSubSamplingExperiment(AbstractClassifier...) - Constructor for class de.jstacs.classifiers.assessment.RepeatedSubSamplingExperiment

Creates a new RepeatedSubSamplingExperiment from a set of AbstractClassifiers.

RepeatedSubSamplingExperiment(boolean, TrainableStatisticalModel[]...) - Constructor for class de.jstacs.classifiers.assessment.RepeatedSubSamplingExperiment

Creates a new RepeatedSubSamplingExperiment from a set of TrainableStatisticalModels.

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

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

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(DifferentiableSequenceScore[]) - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.DiffSSBasedOptimizableFunction

This method allows to reset the internally used functions and the corresponding objects.

reset() - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.DiffSSBasedOptimizableFunction

reset(DifferentiableSequenceScore[]) - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.LogGenDisMixFunction

reset() - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.OptimizableFunction

Resets the all objects and pre-computed values.

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.DataSet.ElementEnumerator

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

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.SequenceEnumeration

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

Resets the FileParameter to its original state.

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

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.SelectionParameter

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.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter

Resets the counts to the pseudocounts and the value to 0.

reset() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.DurationDiffSM

reset() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.PositionDiffSM

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.sequenceScores.statisticalModels.trainable.discrete.Constraint

This method resets all member variables that are in some way counters, frequencies, ...

reset() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.CombinationIterator

This method resets the internal combination.

reset() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.MEMConstraint

reset() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.SequenceIterator

Resets the internal sequence representation.

reset() - Method in class de.jstacs.tools.ui.galaxy.GalaxyAdaptor.LineBasedResult

Resets the line counter to the beginning

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.sampling.AbstractBurnInTest

resetAllValues() - Method in interface de.jstacs.sampling.BurnInTest

This method can be used to remove all values from the internal memory.

resetAllValues() - Method in class de.jstacs.sampling.SimpleBurnInTest

Deprecated.

resetCounts() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint

This method allows to reset the internal field Constraint.counts that is used for estimating the probabilities.

resetStatistic() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.GaussianEmission

resetStatistic() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.MultivariateGaussianEmission

resetStatistic() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission

resetStatistic() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.PhyloDiscreteEmission

resetStatistic() - Method in interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.Emission

This method resets the internal sufficient statistic.

resetStatistic() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.MixtureEmission

resetStatistic() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.SilentEmission

resetStatistic() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.UniformEmission

resetStatistic() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

This method resets the sufficient statistic for the parameters.

resetStatistic() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition

resetStatistic() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.DistanceBasedScaledTransitionElement

resetStatistic() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.ScaledTransitionElement

resetStatistic() - Method in interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TransitionWithSufficientStatistic

This method reset the internal sufficient statistics that can be used for estimating the parameters.

resetStatistics() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.HigherOrderHMM

This method resets all sufficient statistics of all emissions and the transition.

resetToFirst() - Method in class de.jstacs.parameters.MultiSelectionParameter

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],...,parents[k-1] -> child to Double.NEGATIVE_INFINITY.

resize(double[], int) - Method in class de.jstacs.data.DataSet

Returns modified version of this data set with adjusted subsequence length.

RestrictedRepeatHistory - Class in de.jstacs.motifDiscovery.history

This class implements a history that allows operations (i.e.

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.

reStructure(int[][], int) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure

Helper method that converts the structure returned by MST.kruskal(double[][]) to that returned by the Measure.getParents(DataSet, DataSet, double[], double[], int) method

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.

ResultEntry(Class<? extends Result>, String, String) - Constructor for class de.jstacs.tools.JstacsTool.ResultEntry

Creates a new default result entry.

results - Variable in class de.jstacs.results.ResultSet

The internally stores results.

ResultSaver<T extends Result> - Interface in de.jstacs.results.savers

Interface for saving Results to a file.

ResultSaverLibrary - Class in de.jstacs.results.savers

Library of all registered ResultSavers.

ResultSaverLibrary() - Constructor for class de.jstacs.results.savers.ResultSaverLibrary

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.

ResultSetResult - Class in de.jstacs.results

Class for a Result that contains a single ResultSet.

ResultSetResult(String, String, ResultSet, ResultSet) - Constructor for class de.jstacs.results.ResultSetResult

Creates a new ResultSetResult with given name, comment, annotation, and content.

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

Creates a ResultSetResult from its XML representation.

ResultSetResultSaver - Class in de.jstacs.results.savers

ResultSaver for a ResultSetResult.

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

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

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

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

reverse - Variable in class de.jstacs.sequenceScores.differentiable.IndependentProductDiffSS

This array specifies whether the sequence or its reverse complement is used in the specific parts.

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.sequences.CyclicSequenceAdaptor

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

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

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

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

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

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

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

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

reverseOrder() - Method in class de.jstacs.clustering.hierachical.ClusterTree

Reverses the order of the child trees of this cluster tree root node.

ROCCurve - Class in de.jstacs.classifiers.performanceMeasures

This class implements the Receiver Operating Characteristics curve and the area under the curve.

ROCCurve() - Constructor for class de.jstacs.classifiers.performanceMeasures.ROCCurve

Constructs a new instance of the performance measure ROCCurve.

ROCCurve(StringBuffer) - Constructor for class de.jstacs.classifiers.performanceMeasures.ROCCurve

The standard constructor for the interface Storable.

run(ParameterSet, Protocol, ProgressUpdater, int) - Method in interface de.jstacs.tools.JstacsTool

Runs the tool using the provided (now filled) parameters, which are in structure identical to those returned by JstacsTool.getToolParameters().

run(String[]) - Method in class de.jstacs.tools.ui.cli.CLI

Runs this command line application with the specified arguments in args.

run(String[]) - Method in class de.jstacs.tools.ui.galaxy.Galaxy

Runs this Galaxy interface with the supplied arguments.

RUtils - Class in de.jstacs.utils

This is a collection of various silly things you can do when accessing Rserve.

This class is based on an implementation of Andreas Stephanik and was further developed by Jens Keilwagen.

RUtils() - Constructor for class de.jstacs.utils.RUtils

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