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Parameters that potentially can be varied over a
certain interval or a list of values.Parameters of this ParameterSet that
implement Rangeable and return true shall be
replaced by their ranged instances
Parameter or ParameterSet that can have
multiple values at the same time.SimpleParameters 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.Sequence.CompositeSequence.
paramsFile after a sampling.
StringBuffer from a given File.
Tensor.writeTensorToFile(String, OutputStream).
Time.Parameter.neededReferenceIds in the hierarchy
below this ParameterSet and sets the corresponding
Parameter.neededReferences.
RecursiveSequence on the Sequence
seq with the AlphabetContainer alphabet
and the annotation annotation.
RecursiveSequence on the Sequence
seq with the AlphabetContainer alphabet
using the annotation of the given Sequence.
Constraint that defines a condition on one
Parameter (the one containing the ConstraintValidator) with
respect to another Parameter.ReferenceConstraint with respect to the
Parameter constraintParameter.
Storable.
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( ... ) of a
RepeatedHoldOutExperiment.RepeatedHoldOutAssessParameterSet with empty
parameter values.
Storable.
RepeatedHoldOutAssessParameterSet with given
parameter values.
RepeatedHoldOutExperiment from an array of
AbstractClassifiers and a two-dimensional array of Model
s, which are combined to additional classifiers.
RepeatedHoldOutExperiment from a set of
AbstractClassifiers.
RepeatedHoldOutExperiment from a set of
Models.
AbstractClassifiers and those constructed using the given
AbstractModels by a
RepeatedHoldOutExperiment.
ClassifierAssessmentAssessParameterSet that
must be used to call method assess( ... ) of a
RepeatedSubSamplingExperiment.RepeatedSubSamplingAssessParameterSet with empty
parameter values.
Storable.
RepeatedSubSamplingAssessParameterSet with given
parameter values.
RepeatedSubSamplingExperiment from an array of
AbstractClassifiers and a two-dimensional array of Model
s, which are combined to additional classifiers.
RepeatedSubSamplingExperiment from a set of
AbstractClassifiers.
RepeatedSubSamplingExperiment from a set of
Models.
AbstractClassifiers and those constructed using the given
AbstractModels by a
RepeatedSubSamplingExperiment.
ParameterSetContainers and
afterwards adds all given ParameterSets (in the given order)
enclosed in new ParameterSetContainers.
Parameters in this ParameterSet by their
equivalents implementing the Rangeable interface.
ScoringFunctions and all pre-computed values.
FileParameter to its original state.
null if no defaults are given.
Parameters in this ParameterSet to their
default values or null if not default value was provided.
0.
parents -> child to
Double.NEGATIVE_INFTINITY.
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
-
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