|
||||||||||
| PREV LETTER NEXT LETTER | FRAMES NO FRAMES All Classes | |||||||||
Parameters 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.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.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.
Tensor.writeTensorToFile(String, OutputStream).
Time.Enumeration of Sequences 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.
Files that accepts Files with a specific regular expression
in the filename.RegExFilenameFilter with given
regular expressions regex to be found in the
file name of the Files to be filtered.
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( ... ) 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 TrainableStatisticalModel
s, which are combined to additional classifiers.
RepeatedHoldOutExperiment from a set of
AbstractClassifiers.
RepeatedHoldOutExperiment from a set of
TrainableStatisticalModels.
AbstractClassifiers and those constructed using the given
TrainableStatisticalModels 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 TrainableStatisticalModel
s, which are combined to additional classifiers.
RepeatedSubSamplingExperiment from a set of
AbstractClassifiers.
RepeatedSubSamplingExperiment from a set of
TrainableStatisticalModels.
AbstractClassifiers and those constructed using the given
TrainableStatisticalModels by a
RepeatedSubSamplingExperiment.
ParameterSetContainers and
afterwards adds all given ParameterSets (in the given order)
enclosed in new ParameterSetContainers.
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.
Constraint.counts that is used for estimating the probabilities.
parents -> child to
Double.NEGATIVE_INFTINITY.
parents[0],...
RestrictedRepeatHistory - Class in de.jstacs.motifDiscovery.historyThis 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.
RestrictedRepeatHistory(StringBuffer) -
Constructor for class de.jstacs.motifDiscovery.history.RestrictedRepeatHistory
This is the constructor for the interface Storable.
Result - Class in de.jstacs.resultsThe 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.resultsClass 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.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.performanceMeasuresThis 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.utilsThis is a collection of various silly things you can do when accessing
Rserve.RUtils() -
Constructor for class de.jstacs.utils.RUtils
Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
NO FRAMES
All Classes
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