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Parameter
s that potentially can be varied over a
certain interval or a list of values.Parameter
or ParameterSet
that can have
multiple values at the same time.SimpleParameter
s to be set
to a set of values.RangeParameter
from a SimpleParameter
that
is rangeable.
Storable
.
RangeParameter
.enum
defines possible scales, if RangeParameter.RangeType
is
RangeParameter.RangeType.RANGE
.values
, where the greatest value obtains the lowest rank.
values
, where the greatest value obtains the lowest rank.
Sequence
.
StringBuffer
from a given Reader
.
paramsFile
after a sampling.
paramsFile
after a sampling.
paramsFile
after a sampling.
StringBuffer
from a file with the given filen name.
StringBuffer
from a given File
.
StringBuffer
from a given InputStream
.
ArrayList
together with some annotation.
ArrayList
together with some annotation.
ArrayList
together with some annotation.
Tensor.writeTensorToFile(String, OutputStream)
.
Time
.Enumeration
of Sequence
s by declaring an additional method that allows to reuse the Enumeration.ReferenceBasedTransitionElement
representing a conditional transition probability distribution of a Hidden Markov TrainableStatisticalModel for the given context.
ReferenceBasedTransitionElement
representing a conditional transition probability distribution of a Hidden Markov TrainableStatisticalModel for the given context.
Storable
.
SequenceAnnotation
that contains a reference
sequence.ReferenceSequenceAnnotation
with identifier
identifier
, reference sequence ref
, and
additional annotation (that does not fit the SequenceAnnotation
definitions) given as a Result
result
.
Storable
.
SequenceAnnotationParser
that parses a ReferenceSequenceAnnotation
from the comment lines of a sequence.ReferenceSequenceAnnotationParser
with user-specified delimiters.
ReferenceSequenceAnnotationParser
with user-specified delimiters.
ReferenceSequenceAnnotation
at a certain reference position.ReferenceSequenceDiscreteEmission
based on the equivalent sample size.
ReferenceSequenceDiscreteEmission
based on the equivalent sample size.
ReferenceSequenceDiscreteEmission
defining the individual hyper parameters.
ReferenceSequenceDiscreteEmission
defining the individual hyper parameters.
ReferenceSequenceDiscreteEmission
from its XML representation.
File
s that accepts File
s with a specific regular expression
in the filename.RegExFilenameFilter
with given
regular expressions regex
to be found in the
file name of the File
s to be filtered.
RegExFilenameFilter
are forbidden, allowed or required to be a directory.OutputStream
.RegExFilterOutputStream
.
AnnotatedEntity
at index idx
.
index
from the set and returns this measure.
Parameter
from set.
REnvironment
using the default port.
REnvironment
with initial size 10 using the default
port.
REnvironment
using the given port.
REnvironment
with initial size 10 using the given
port.
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
AbstractClassifier
s 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
AbstractClassifier
s.
- RepeatedHoldOutExperiment(boolean, TrainableStatisticalModel[]...) -
Constructor for class de.jstacs.classifiers.assessment.RepeatedHoldOutExperiment
- Creates a new
RepeatedHoldOutExperiment
from a set of
TrainableStatisticalModel
s.
- RepeatedHoldOutExperiment(AbstractClassifier[], boolean, TrainableStatisticalModel[]...) -
Constructor for class de.jstacs.classifiers.assessment.RepeatedHoldOutExperiment
- This constructor allows to assess a collection of given
AbstractClassifier
s and those constructed using the given
TrainableStatisticalModel
s 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
AbstractClassifier
s 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
AbstractClassifier
s.
- RepeatedSubSamplingExperiment(boolean, TrainableStatisticalModel[]...) -
Constructor for class de.jstacs.classifiers.assessment.RepeatedSubSamplingExperiment
- Creates a new
RepeatedSubSamplingExperiment
from a set of
TrainableStatisticalModel
s.
- RepeatedSubSamplingExperiment(AbstractClassifier[], boolean, TrainableStatisticalModel[]...) -
Constructor for class de.jstacs.classifiers.assessment.RepeatedSubSamplingExperiment
- This constructor allows to assess a collection of given
AbstractClassifier
s and those constructed using the given
TrainableStatisticalModel
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.
- 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
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.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.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
-
- 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
.
- 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 internally stores results.
- 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.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(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
-
- 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
.
- 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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