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SafeOutputStream.
true if for test respectively train dataset the
sequences of the non-reference classes have the same length as the
corresponding sequence of the reference class.
Sample from a StringExtractor
using the given AlphabetContainer.
Sample from a StringExtractor
using the given AlphabetContainer and all overlapping windows of
subsequenceLength.
Sample from a StringExtractor
using the given AlphabetContainer and delimiter.
Sample from a StringExtractor
using the given AlphabetContainer, the given delimiter and all
overlapping windows of subsequenceLength.
Model.emitSample(int, int...).
Sample.ElementEnumerator on the given
data.
Sample.WeightedSampleFactory on the given
Sample(s).
Sample.WeightedSampleFactory on the given
Sample and weights.
Sample.WeightedSampleFactory on the given
Sample and weights.
Sample.WeightedSampleFactory on the given
array of Samples and weights.
enum defines the different types of sort operations
that can be performed while creating a Sample.WeightedSampleFactory.ClassifierAssessmentAssessParameterSet that
must be used to call method assess( ... ) of a
Sampled_RepeatedHoldOutExperiment.Sampled_RepeatedHoldOutAssessParameterSet with
empty parameter values.
Sampled_RepeatedHoldOutAssessParameterSet out of an
XML representation.
Sampled_RepeatedHoldOutAssessParameterSet with
given parameter values.
ClassifierAssessment that partitions the data
of a user-specified reference class (typically the smallest class) and samples
non-overlapping for all other classes, so that one gets the same number of
sequences (and the same lengths of the sequences) in each train and test data
set.Sampled_RepeatedHoldOutExperiment from an array of
AbstractClassifiers and a two-dimensional array of Model
s, which are combined to additional classifiers.
Sampled_RepeatedHoldOutExperiment from a set of
AbstractClassifiers.
Sampled_RepeatedHoldOutExperiment from a set of
Models.
AbstractClassifiers and those constructed using the given
AbstractModels by a Sampled_RepeatedHoldOutExperiment.
Sample.SampleResult from a Sample with the annotation name and comment.
SampleResult from its XML-representation as returned by SampleResult.toXML().
SequenceIterator from sample preserving as
much annotation as possible.
initModelForSampling.
GibbsSamplingComponent.extendSampling(int, boolean).
start.
sequence
msg and the sample to a file
f.
Storable.
Parameters for any ScoreClassifier.Storable.
LogPrior that defines a Gaussian prior on the parameters
of a set of NormalizableScoringFunctions and a set of class
parameters.SeparateGaussianLogPrior from a set of base
variances vars, a set of class variances
classVars, and a set of class means classMus.
SeparateGaussianLogPrior from its XML representation
as returned by SeparateLogPrior.toXML().
LogPrior that defines a Laplace prior on the parameters
of a set of NormalizableScoringFunctions and a set of class
parameters.SeparateLaplaceLogPrior from a set of base
variances vars, a set of class variances
classVars, and a set of class means classMus.
SeparateLaplaceLogPrior from its XML representation
as returned by SeparateLogPrior.toXML().
SeparateLogPrior using the class-specific base
variances vars, the variances classVars and the
means classMus for the class parameters.
SeparateLogPrior from its XML representation as
returned by SeparateLogPrior.toXML().
Sequence.SequenceAnnotation of type type, with
identifier identifier, and additional annotation (that does
not fit the SequenceAnnotation definitions) result.
SequenceAnnotation of type type, with
identifier identifier, and additional annotation (that does
not fit the SequenceAnnotation definitions) results.
SequenceAnnotation of type type, with
identifier identifier, and additional annotation (that does
not fit the SequenceAnnotation definitions)
additionalAnnotation.
SequenceAnnotation of type type, with
identifier identifier, and additional annotation (that does
not fit the SequenceAnnotation definitions) results.
SequenceAnnotation from its XML representation as
returned by SequenceAnnotation.toXML().
length.
Sample from a SequenceIterator.
ParameterSet containing all parameters necessary to construct an
Object that implements InstantiableFromParameterSet.InstanceParameterSet having empty parameter values.
InstanceParameterSet having empty parameter values.
InstanceParameterSet from its XML-representation.
InstanceParameterSet from the alphabet and the length.
InstanceParameterSet for an object that can handle sequences of variable length and with the alphabet.
ScoringFunctions funs.
setNewAlphabetContainerInstance( AlphabetContainer ) and not be made public.
train to init the gammas.
defaultValue
AbstractBurnInTest.
ProgressUpdater.setValue(int), so a value of max indicates the
end of the supervised method call.
ParameterSet whose validity depends on
the value of this Parameter.
AlphabetContainer
for the current model.
NullProgressUpdater.setOffset() is called the current value
will be added to every value set by
NullProgressUpdater.setValue(int).
OutputStream that is used e.g. for writing information
while training.
symbol and context context to parameter par.
params between start and
start + this.getNumberOfParameters() - 1
ParameterSet of this
Parameter to parent.
ParameterSetContainer of this ParameterSet
to parent.
data using weights.
isRangeable() to rangeable
isRangeable() to rangeable
val for the root node child.
sel depending on
b.
key to the value of selected
RangeParameter to one of
LIST, RANGE, or NO.
ParameterValidator for this SimpleParameter.
parents[0],...
- setValue(double) -
Method in class de.jstacs.models.mixture.gibbssampling.AbstractBurnInTest
-
- setValue(double) -
Method in class de.jstacs.models.mixture.gibbssampling.BurnInTest
- This method can be used to fill the internal memory with the values that
will be used to determine the length of the burn-in phase.
- setValue(double) -
Method in class de.jstacs.models.mixture.gibbssampling.SimpleBurnInTest
-
- setValue(Object) -
Method in class de.jstacs.parameters.CollectionParameter
- Sets the selected value to the one that is specified by the key
value
- setValue(Object) -
Method in class de.jstacs.parameters.EnumParameter
-
- setValue(Object) -
Method in class de.jstacs.parameters.FileParameter
-
- setValue(Object) -
Method in class de.jstacs.parameters.MultiSelectionCollectionParameter
-
- setValue(Object) -
Method in class de.jstacs.parameters.Parameter
- Sets the value of this parameter to
value.
- setValue(Object) -
Method in class de.jstacs.parameters.ParameterSetContainer
-
- setValue(Object) -
Method in class de.jstacs.parameters.RangeParameter
-
- setValue(Object) -
Method in class de.jstacs.parameters.SimpleParameter
-
- setValue(double) -
Method in class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
- Sets the current value of this parameter.
- setValue(int) -
Method in class de.jstacs.utils.DefaultProgressUpdater
-
- setValue(int) -
Method in class de.jstacs.utils.GUIProgressUpdater
-
- setValue(int) -
Method in class de.jstacs.utils.NullProgressUpdater
-
- setValue(int) -
Method in interface de.jstacs.utils.ProgressUpdater
- Sets the current value the supervised process has reached.
- setValue(int) -
Method in class de.jstacs.utils.TimeLimitedProgressUpdater
-
- setValues(String) -
Method in class de.jstacs.parameters.RangeParameter
- Sets a list of values from a
String containing a space separated list of values.
- setValues(Object, int, Object, RangeParameter.Scale) -
Method in class de.jstacs.parameters.RangeParameter
- Sets the values of this
RangeParameter as a range of values, specified by a start values,
a last value, a number of steps between these values (without the last value), and a scale in that
the values between the first and the last value are chosen.
- setValuesInLogScale(boolean, double, Object, int, Object) -
Method in class de.jstacs.parameters.RangeParameter
- This method enables you to set a list of values in an easy manner.
- setWeights(double...) -
Method in class de.jstacs.models.mixture.AbstractMixtureModel
- Sets the weights.
- shallBeRanged() -
Method in class de.jstacs.parameters.RangeParameter
- Returns one of
LIST, RANGE, or NO
depending on the input used to specify this RangeParameter
- SharedStructureClassifier - Class in de.jstacs.models.discrete.inhomogeneous.shared
- This class enables you to learn the structure on all classes together.
- SharedStructureClassifier(int, StructureLearner.ModelType, byte, StructureLearner.LearningType, FSDAGModel...) -
Constructor for class de.jstacs.models.discrete.inhomogeneous.shared.SharedStructureClassifier
- The main constructor.
- SharedStructureClassifier(StringBuffer) -
Constructor for class de.jstacs.models.discrete.inhomogeneous.shared.SharedStructureClassifier
- The constructor for the
Storable interface.
- SharedStructureMixture - Class in de.jstacs.models.discrete.inhomogeneous.shared
- This class handles a mixture of models with the same structure that are learned via EM.
- SharedStructureMixture(FSDAGModel[], StructureLearner.ModelType, byte, int, double, double) -
Constructor for class de.jstacs.models.discrete.inhomogeneous.shared.SharedStructureMixture
- This main constructor creates an instance which estimates the component probabilities.
- SharedStructureMixture(FSDAGModel[], StructureLearner.ModelType, byte, int, double[], double, double) -
Constructor for class de.jstacs.models.discrete.inhomogeneous.shared.SharedStructureMixture
- This main constructor creates an instance with fixed component weights.
- SharedStructureMixture(FSDAGModel[], StructureLearner.ModelType, byte, int, boolean, double[], double, double) -
Constructor for class de.jstacs.models.discrete.inhomogeneous.shared.SharedStructureMixture
- This constructor is used from the other main constructors.
- SharedStructureMixture(StringBuffer) -
Constructor for class de.jstacs.models.discrete.inhomogeneous.shared.SharedStructureMixture
- The constructor for the
Storable interface.
- shortcut -
Variable in class de.jstacs.classifier.scoringFunctionBased.AbstractOptimizableFunction
- These shortcuts indicate the beginning of a new part in the parameter
vector.
- ShortSequence - Class in de.jstacs.data.sequences
- This class can be used for discrete
AlphabetContainers with alphabets
that use many different symbols. - ShortSequence(AlphabetContainer, short[]) -
Constructor for class de.jstacs.data.sequences.ShortSequence
- This constructor is designed for the method
AbstractModel.emitSample(int, int...).
- ShortSequence(AlphabetContainer, String) -
Constructor for class de.jstacs.data.sequences.ShortSequence
- Creates a new sequence from a string representation using the default
delimiter.
- ShortSequence(AlphabetContainer, SequenceAnnotation[], String, String) -
Constructor for class de.jstacs.data.sequences.ShortSequence
- Creates a new sequence from a string representation using the delimiter
delim.
- ShortSequence(AlphabetContainer, SequenceAnnotation[], SymbolExtractor) -
Constructor for class de.jstacs.data.sequences.ShortSequence
- Creates a new sequence from a
SymbolExtractor.
- shouldBeNormalized() -
Method in class de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifierParameterSet
- This method returns
true if a normalization shall be used
while optimization.
- showImage(String, BufferedImage) -
Static method in class de.jstacs.utils.REnvironment
- Enables you to show an image.
- showImage(String, BufferedImage, int) -
Static method in class de.jstacs.utils.REnvironment
- Enables you to show an image.
- SimpleBurnInTest - Class in de.jstacs.models.mixture.gibbssampling
- This is a very simple test for the length of the burn-in phase.
- SimpleBurnInTest(int) -
Constructor for class de.jstacs.models.mixture.gibbssampling.SimpleBurnInTest
- This is the main constructor that creates an instance of fixed burn-in
length.
- SimpleBurnInTest(StringBuffer) -
Constructor for class de.jstacs.models.mixture.gibbssampling.SimpleBurnInTest
- The standard constructor for the interface
Storable.
- SimpleGaussianSumLogPrior - Class in de.jstacs.classifier.scoringFunctionBased.logPrior
- This class implements a prior that is a product of Gaussian distributions
with mean 0 and equal variance for each parameter.
- SimpleGaussianSumLogPrior(double) -
Constructor for class de.jstacs.classifier.scoringFunctionBased.logPrior.SimpleGaussianSumLogPrior
- Creates a new
SimpleGaussianSumLogPrior with mean 0 and variance
sigma for all parameters, including the class parameters.
- SimpleGaussianSumLogPrior(StringBuffer) -
Constructor for class de.jstacs.classifier.scoringFunctionBased.logPrior.SimpleGaussianSumLogPrior
- Recreates a
SimpleGaussianSumLogPrior from its XML representation
as returned by SimpleGaussianSumLogPrior.toXML().
- SimpleParameter - Class in de.jstacs.parameters
- Class for a "simple" parameter.
- SimpleParameter(StringBuffer) -
Constructor for class de.jstacs.parameters.SimpleParameter
- Constructs a
SimpleParameter out of an XML representation
- SimpleParameter(DataType, String, String, boolean) -
Constructor for class de.jstacs.parameters.SimpleParameter
- Constructor for a
SimpleParameter without validator
- SimpleParameter(DataType, String, String, boolean, Object) -
Constructor for class de.jstacs.parameters.SimpleParameter
- Constructor for a
SimpleParameter without ParameterValidator but with a default value
- SimpleParameter(DataType, String, String, boolean, ParameterValidator) -
Constructor for class de.jstacs.parameters.SimpleParameter
- Constructor for a
SimpleParameter with a ParameterValidator.
- SimpleParameter(DataType, String, String, boolean, ParameterValidator, Object) -
Constructor for class de.jstacs.parameters.SimpleParameter
- Constructor for a
SimpleParameter with validator and default value.
- SimpleParameter.DatatypeNotValidException - Exception in de.jstacs.parameters
- Class for an
Exception that can be thrown if the provided int-value
that represents a datatype is not one of the values defined in the Parameter-interface. - SimpleParameter.DatatypeNotValidException(String) -
Constructor for exception de.jstacs.parameters.SimpleParameter.DatatypeNotValidException
- Creates a new
DatatypeNotValidException from an error-message.
- SimpleParameter.IllegalValueException - Exception in de.jstacs.parameters
- This exception is thrown if a parameter is not valid.
- SimpleParameter.IllegalValueException(String) -
Constructor for exception de.jstacs.parameters.SimpleParameter.IllegalValueException
- Creates a new
IllegalValueException with the reason of the exception reason
- SimpleParameterSet - Class in de.jstacs.parameters
- Class for a
ParameterSet that is constructed from an array of Parameters
and thus does nothing in the loadParameters()-method. - SimpleParameterSet(Parameter[]) -
Constructor for class de.jstacs.parameters.SimpleParameterSet
- Creates a new
SimpleParameterSet from an array of Parameters.
- SimpleParameterSet(StringBuffer) -
Constructor for class de.jstacs.parameters.SimpleParameterSet
- Constructs a
SimpleParameterSet from its XML-representation
- SimpleReferenceConstraint - Class in de.jstacs.parameters.validation
- Class for a
ReferenceConstraint that checks for "simple" conditions as defined
in the Constraint-interface. - SimpleReferenceConstraint(SimpleParameter, int) -
Constructor for class de.jstacs.parameters.validation.SimpleReferenceConstraint
- Creates a new
SimpleReferenceConstraint from a reference SimpleParameter
and a comparison operator, which is one of the values defined in the Constraint-interface.
- SimpleReferenceConstraint(StringBuffer) -
Constructor for class de.jstacs.parameters.validation.SimpleReferenceConstraint
- Creates a new
SimpleReferenceConstraint from its XML-representation.
- SimpleResult - Class in de.jstacs.results
- Abstract class for a
Result with a value of a primitive data type or String. - SimpleResult(String, String, DataType) -
Constructor for class de.jstacs.results.SimpleResult
- The main constructor which takes the main information of a result.
- SimpleResult(StringBuffer) -
Constructor for class de.jstacs.results.SimpleResult
- This is the constructor for
Storable.
- SimpleSequenceIterator - Class in de.jstacs.data.bioJava
- Class that implements the
SequenceIterator interface of BioJava in a
simple way, backed by an array of Sequences. - SimpleSequenceIterator(Sequence...) -
Constructor for class de.jstacs.data.bioJava.SimpleSequenceIterator
- Creates a new
SimpleSequenceIterator from an array of
Sequences.
- SimpleStaticConstraint - Class in de.jstacs.parameters.validation
- Class for a
Constraint that checks values against static values using the comparison operators
defined in the Constraint-interface. - SimpleStaticConstraint(Number, int) -
Constructor for class de.jstacs.parameters.validation.SimpleStaticConstraint
- Creates a new
SimpleStaticConstraint from a Number-reference and
a comparisonOperator as defined in Constraint.
- SimpleStaticConstraint(String, int) -
Constructor for class de.jstacs.parameters.validation.SimpleStaticConstraint
- Creates a new
SimpleStaticConstraint from a String-reference and
a comparisonOperator as defined in Constraint.
- SimpleStaticConstraint(StringBuffer) -
Constructor for class de.jstacs.parameters.validation.SimpleStaticConstraint
- Creates a new
SimpleStaticConstraint from its XML-representation
- simplify() -
Method in class de.jstacs.parameters.CollectionParameter
-
- simplify() -
Method in class de.jstacs.parameters.FileParameter
-
- simplify() -
Method in class de.jstacs.parameters.MultiSelectionCollectionParameter
-
- simplify() -
Method in class de.jstacs.parameters.Parameter
- Simplifies the Parameter and its contents to the relevant information.
- simplify() -
Method in class de.jstacs.parameters.ParameterSet
- Simplifies all parameters in this
ParameterSet
- simplify() -
Method in class de.jstacs.parameters.ParameterSetContainer
-
- simplify() -
Method in class de.jstacs.parameters.RangeParameter
-
- simplify() -
Method in class de.jstacs.parameters.SimpleParameter
-
- SingleHiddenMotifMixture - Class in de.jstacs.models.mixture.motif
- This class enables the user to search for a single motif in a sequence.
- SingleHiddenMotifMixture(Model, Model, boolean, int, double[], double[], PositionPrior, AbstractMixtureModel.Algorithm, double, double, AbstractMixtureModel.Parameterization, int, int, BurnInTest) -
Constructor for class de.jstacs.models.mixture.motif.SingleHiddenMotifMixture
- Creates a new SingleHiddenMotifMixture.
- SingleHiddenMotifMixture(Model, Model, boolean, int, double[], PositionPrior, double, double, AbstractMixtureModel.Parameterization) -
Constructor for class de.jstacs.models.mixture.motif.SingleHiddenMotifMixture
- Creates a single hidden motif mixture using EM and estimating the probability for finding a motif.
- SingleHiddenMotifMixture(Model, Model, boolean, int, double, PositionPrior, double, double, AbstractMixtureModel.Parameterization) -
Constructor for class de.jstacs.models.mixture.motif.SingleHiddenMotifMixture
- Creates a single hidden motif mixture using EM and fixed probability for finding a motif.
- SingleHiddenMotifMixture(StringBuffer) -
Constructor for class de.jstacs.models.mixture.motif.SingleHiddenMotifMixture
- The standard constructor for the interface
Storable.
- SinglePositionSequenceAnnotation - Class in de.jstacs.data.sequences.annotation
- Class for some annotations that consist mainly of one position on a sequence.
- SinglePositionSequenceAnnotation(SinglePositionSequenceAnnotation.Type, String, int) -
Constructor for class de.jstacs.data.sequences.annotation.SinglePositionSequenceAnnotation
- Creates a new
SinglePositionSequenceAnnotation of type
type, with identifier identifier and position
position.
- SinglePositionSequenceAnnotation(SinglePositionSequenceAnnotation.Type, String, int, Result...) -
Constructor for class de.jstacs.data.sequences.annotation.SinglePositionSequenceAnnotation
- Creates a new
SinglePositionSequenceAnnotation of type
type, with identifier identifier, position
position, and additional annotations
additionalAnnotation.
- SinglePositionSequenceAnnotation(StringBuffer) -
Constructor for class de.jstacs.data.sequences.annotation.SinglePositionSequenceAnnotation
- Re-creates a
SinglePositionSequenceAnnotation from its XML
representation as returned by
LocatedSequenceAnnotation.toXML().
- SinglePositionSequenceAnnotation.Type - Enum in de.jstacs.data.sequences.annotation
- The possible types of a
SinglePositionSequenceAnnotation. - skip(int) -
Method in class de.jstacs.models.discrete.inhomogeneous.SequenceIterator
- This method skips some position.
- skipLastClassifiersDuringClassifierTraining -
Variable in class de.jstacs.classifier.assessment.ClassifierAssessment
- Skip last classifier.
- SoftOneOfN - Class in de.jstacs.utils.random
- This random generator returns
1-epsilon for one and equal parts
for the rest of a random vector. - SoftOneOfN(double) -
Constructor for class de.jstacs.utils.random.SoftOneOfN
- This constructor can be used for (soft) sampling one of n.
- SoftOneOfN() -
Constructor for class de.jstacs.utils.random.SoftOneOfN
- This constructor can be used for (hard) sampling one of n.
- sort(String) -
Method in class de.jstacs.results.ListResult
- This method enables you to sort the entrys of this container by a specified column.
- sostream -
Variable in class de.jstacs.classifier.scoringFunctionBased.ScoreClassifier
- This stream is used for comments, ... while the training, ... .
- sostream -
Variable in class de.jstacs.models.discrete.inhomogeneous.InhomogeneousDGM
- This stream is used for comments, ... while the training, ... .
- sostream -
Variable in class de.jstacs.models.mixture.AbstractMixtureModel
- This is the stream for writing information while training.
- source -
Variable in class de.jstacs.algorithms.graphs.Edge
- The source node.
- SparseSequence - Class in de.jstacs.data.sequences
- This class is an implementation for sequences on one alphabet with length 4.
- SparseSequence(AlphabetContainer, String) -
Constructor for class de.jstacs.data.sequences.SparseSequence
- This constructor creates an instance from a
String.
- SparseSequence(AlphabetContainer, SymbolExtractor) -
Constructor for class de.jstacs.data.sequences.SparseSequence
- This constructor creates an instance from a
SymbolExtractor.
- SparseStringExtractor - Class in de.jstacs.io
- This StringExtractor reads the Strings from a
File as the user asks
for the String. - SparseStringExtractor(File) -
Constructor for class de.jstacs.io.SparseStringExtractor
- A constructor that reads the lines from
file.
- SparseStringExtractor(File, char) -
Constructor for class de.jstacs.io.SparseStringExtractor
- A constructor that reads the lines from
file and ignores
those starting with ignore.
- SparseStringExtractor(File, String) -
Constructor for class de.jstacs.io.SparseStringExtractor
- A constructor that reads the lines from
file .
- SparseStringExtractor(File, char, String) -
Constructor for class de.jstacs.io.SparseStringExtractor
- A constructor that reads the lines from
file and ignores
those starting with ignore.
- StartDistanceForecaster - Interface in de.jstacs.algorithms.optimization
- This interface is used to determine the next start distance that will be used
in a line search.
- starts -
Variable in class de.jstacs.models.CompositeModel
- The start indices.
- starts -
Variable in class de.jstacs.models.mixture.AbstractMixtureModel
- The number of starts
- StationaryDistribution - Class in de.jstacs.models.utils
- This class can be used to determine the stationary distribution.
- StationaryDistribution() -
Constructor for class de.jstacs.models.utils.StationaryDistribution
-
- stationaryIteration -
Variable in class de.jstacs.models.mixture.AbstractMixtureModel
- The number of iterations of the Gibbs Sampler
- StatisticalTest - Class in de.jstacs.models.utils
- This class enables the user to compute some divergences.
- StatisticalTest() -
Constructor for class de.jstacs.models.utils.StatisticalTest
-
- STEEPEST_DESCENT -
Static variable in class de.jstacs.algorithms.optimization.Optimizer
- This constant can be used to specify that steepest descent should be used
in the
optimize-method.
- steepestDescent(DifferentiableFunction, double[], Optimizer.TerminationCondition, double, double, StartDistanceForecaster, SafeOutputStream, Time) -
Static method in class de.jstacs.algorithms.optimization.Optimizer
- The steepest descent.
- Storable - Interface in de.jstacs
- This is the root interface for all immutable objects that must be stored in e.g. a file
or a database.
- StorableArrayWithTags(Storable[]) -
Static method in class de.jstacs.io.XMLParser
- Encodes a Storable array.
- StorableResult - Class in de.jstacs.results
- Class for results that are
Storables. - StorableResult(String, String, Storable) -
Constructor for class de.jstacs.results.StorableResult
- Creates a result for an XML-representation of an object.
- StorableResult(StringBuffer) -
Constructor for class de.jstacs.results.StorableResult
- Constructs a new
ObjectResult from its XML-representation
- StorableValidator - Class in de.jstacs.parameters.validation
- Class for a validator that validates instances and XML-representations for the correct class types (e.g.
- StorableValidator(Class<? extends Storable>, boolean) -
Constructor for class de.jstacs.parameters.validation.StorableValidator
- Creates a new
ObjectValidator for a subclass of AbstractModel
or AbstractClassifier.
- StorableValidator(Class<? extends Storable>) -
Constructor for class de.jstacs.parameters.validation.StorableValidator
- Creates a new
ObjectValidator for a subclass of Storable.
- StorableValidator(StringBuffer) -
Constructor for class de.jstacs.parameters.validation.StorableValidator
- Constructs an
ObjectValidator from its XML-representation
- StrandedLocatedSequenceAnnotationWithLength - Class in de.jstacs.data.sequences.annotation
- Class for a
SequenceAnnotation that has a position, a length, and an
orientation on the strand of a Sequence. - StrandedLocatedSequenceAnnotationWithLength(int, int, StrandedLocatedSequenceAnnotationWithLength.Strand, String, String, Result...) -
Constructor for class de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength
- Creates a new
StrandedLocatedSequenceAnnotationWithLength of type
type, with identifier identifier, and
additional annotation (that does not fit the SequenceAnnotation
definitions) result.
- StrandedLocatedSequenceAnnotationWithLength(int, int, StrandedLocatedSequenceAnnotationWithLength.Strand, String, String, Collection<Result>) -
Constructor for class de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength
- Creates a new
StrandedLocatedSequenceAnnotationWithLength of type
type, with identifier identifier, and
additional annotation (that does not fit the SequenceAnnotation
definitions) result.
- StrandedLocatedSequenceAnnotationWithLength(int, int, StrandedLocatedSequenceAnnotationWithLength.Strand, String, String, SequenceAnnotation[], Result...) -
Constructor for class de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength
- Creates a new
StrandedLocatedSequenceAnnotationWithLength of type
type, with identifier identifier, and
additional annotation (that does not fit the SequenceAnnotation
definitions) additionalAnnotations, and sub-annotations.
- StrandedLocatedSequenceAnnotationWithLength(String, String, StrandedLocatedSequenceAnnotationWithLength.Strand, LocatedSequenceAnnotation[], Result...) -
Constructor for class de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength
- Creates a new
StrandedLocatedSequenceAnnotationWithLength of type
type, with identifier identifier, and
additional annotation (that does not fit the SequenceAnnotation
definitions) additionalAnnotations, and sub-annotations.
- StrandedLocatedSequenceAnnotationWithLength(StringBuffer) -
Constructor for class de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength
- Re-creates a
StrandedLocatedSequenceAnnotationWithLength from its
XML representation as returned by
StrandedLocatedSequenceAnnotationWithLength.toXML().
- StrandedLocatedSequenceAnnotationWithLength.Strand - Enum in de.jstacs.data.sequences.annotation
- The possible orientations on the strands.
- strandedness() -
Method in enum de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength.Strand
- Returns the strandedness as a
String.
- StrandModel - Class in de.jstacs.models.mixture
- This model handles sequences that can either lie on the forward strand or on the backward strand.
- StrandModel(Model, int, boolean, double[], double, AbstractMixtureModel.Algorithm, double, double, AbstractMixtureModel.Parameterization, int, int, BurnInTest) -
Constructor for class de.jstacs.models.mixture.StrandModel
- Creates a new StrandModel.
- StrandModel(Model, int, double[], double, double, AbstractMixtureModel.Parameterization) -
Constructor for class de.jstacs.models.mixture.StrandModel
- Creates an instance using EM and estimating the component probabilities.
- StrandModel(Model, int, double, double, double, AbstractMixtureModel.Parameterization) -
Constructor for class de.jstacs.models.mixture.StrandModel
- Creates an instance using EM and fixed component probabilities.
- StrandModel(Model, int, double[], int, int, BurnInTest) -
Constructor for class de.jstacs.models.mixture.StrandModel
- Creates an instance using Gibbs Sampling and sampling the component probabilities.
- StrandModel(Model, int, double, int, int, BurnInTest) -
Constructor for class de.jstacs.models.mixture.StrandModel
- Creates an instance using Gibbs Sampling and fixed component probabilities.
- StrandModel(StringBuffer) -
Constructor for class de.jstacs.models.mixture.StrandModel
- This constructor can be used for loading a
StrandModel form a StringBuffer;
- StringArrayWithTags(String[]) -
Static method in class de.jstacs.io.XMLParser
- Encodes a String array.
- StringExtractor - Class in de.jstacs.io
- This class implements the reader that extracts strings from either a file or
a string.
- StringExtractor(File, int) -
Constructor for class de.jstacs.io.StringExtractor
- A constructor that reads the lines from
file.
- StringExtractor(File, int, char) -
Constructor for class de.jstacs.io.StringExtractor
- A constructor that reads the lines from
file and ignores
those starting with ignore.
- StringExtractor(File, int, String) -
Constructor for class de.jstacs.io.StringExtractor
- A constructor that reads the lines from
file .
- StringExtractor(File, int, char, String) -
Constructor for class de.jstacs.io.StringExtractor
- A constructor that reads the lines from
file and ignores
those starting with ignore.
- StringExtractor(String, int, String) -
Constructor for class de.jstacs.io.StringExtractor
- A constructor that reads the lines from a String
content.
- StringExtractor(String, int, char, String) -
Constructor for class de.jstacs.io.StringExtractor
- A constructor that reads the lines from a String
content and
ignores those starting with ignore
- StructureLearner - Class in de.jstacs.models.discrete.inhomogeneous
- This class can be used to learn the structure of any discrete model.
- StructureLearner(AlphabetContainer, int, double) -
Constructor for class de.jstacs.models.discrete.inhomogeneous.StructureLearner
- Creates a StructureLearner
- StructureLearner(AlphabetContainer, int) -
Constructor for class de.jstacs.models.discrete.inhomogeneous.StructureLearner
- Creates a StructureLearner with ess = 0.
- StructureLearner.LearningType - Enum in de.jstacs.models.discrete.inhomogeneous
- This enum defines the different types of learning that are possible with the
StructureLearner. - StructureLearner.ModelType - Enum in de.jstacs.models.discrete.inhomogeneous
- This enum defines the different types of models that can be learned with the
StructureLearner. - structureMeasure -
Variable in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
Measure that defines the network structure
- SubclassFinder - Class in de.jstacs.utils
- Utility-class with static methods to
find all sub-classes of a certain class (or interface) within the scope of the current class-loader
find all sub-classes of a certain class (or interface) within the scope of the current class-loader that
can be instantiated, i.e. that are neither interfaces nor abstract
filter a set of classes by inheritance from a super-class
obtain the class of an
InstanceParameterSet that can be used to instantiate a sub-class of InstantiableFromParameterSet. - SubclassFinder() -
Constructor for class de.jstacs.utils.SubclassFinder
-
- subSampling(int) -
Method in class de.jstacs.data.Sample
- Randomly samples elements (sequences) from the set of all elements
(sequences) contained in this
Sample.
- SubstringFilenameFilter - Class in de.jstacs.io
- A simple filter on files.
- SubstringFilenameFilter(SubstringFilenameFilter.PartOfName, String, boolean, boolean, String...) -
Constructor for class de.jstacs.io.SubstringFilenameFilter
- A simple constructor.
- SubstringFilenameFilter.PartOfName - Enum in de.jstacs.io
- This enum defines the different types a string can be part of a other string.
- sum -
Variable in class de.jstacs.classifier.scoringFunctionBased.AbstractOptimizableFunction
- The sums of the weighted data per class and additional the total weight
sum.
- sum(double[]) -
Static method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.Measure
- Computes the sum of all elements in
ar.
- sumNormalisation(double[]) -
Static method in class de.jstacs.utils.Normalisation
- The method does a sum-normalisation on
d and returns the the
sum of the values.
- sumNormalisation(double[], double[], int) -
Static method in class de.jstacs.utils.Normalisation
- The method does a sum-normalisation on
d.
- swap() -
Method in class de.jstacs.models.mixture.AbstractMixtureModel
- This method swaps the current component models with the alternative model.
- symbol -
Variable in class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
- The symbol (out of some
Alphabet) this parameter is responsible for.
- SymbolExtractor - Class in de.jstacs.io
- This class enables you to extract elements form a given string similar to an StringTokenizer.
- SymbolExtractor(String) -
Constructor for class de.jstacs.io.SymbolExtractor
- Creates a new instance using
delim as delimiter.
- SymbolExtractor(String, String) -
Constructor for class de.jstacs.io.SymbolExtractor
- Creates a new instance using
delim as delimiter and string as string to be parsed.
- SymmetricTensor - Class in de.jstacs.algorithms.graphs.tensor
- This class can be used for
Tensors with a special symmetry property. - SymmetricTensor(int, byte) -
Constructor for class de.jstacs.algorithms.graphs.tensor.SymmetricTensor
- This constructor creates an empty symmetric tensor with given dimension.
- SymmetricTensor(SymmetricTensor[], double[]) -
Constructor for class de.jstacs.algorithms.graphs.tensor.SymmetricTensor
- The constructor can be used creating a new
SymmetricTensor as
weighted sum of SymmetricTensors.
- SymmetricTensor(AsymmetricTensor) -
Constructor for class de.jstacs.algorithms.graphs.tensor.SymmetricTensor
- This constructor creates and checks a filled asymmetric tensor from an
AsymmetricTensor instance.
- SymmetricTensor(double[][][], int, byte) -
Constructor for class de.jstacs.algorithms.graphs.tensor.SymmetricTensor
- This constructor creates and checks a filled asymmetric tensor with given
dimension.
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