Uses of Class
de.jstacs.parameters.ParameterSet

Packages that use ParameterSet

de.jstacs.algorithms.optimization.termination
de.jstacs.classifier.assessment	This package allows to assess classifiers.
de.jstacs.classifier.scoringFunctionBased	Provides the classes for Classifiers that are based on ScoringFunctions.
de.jstacs.classifier.scoringFunctionBased.gendismix	Provides an implementation of a classifier that allows to train the parameters of a set of NormalizableScoringFunctions by a unified generative-discriminative learning principle
de.jstacs.classifier.scoringFunctionBased.sampling	Provides the classes for AbstractScoreBasedClassifiers that are based on SamplingScoringFunctions and that sample parameters using the Metropolis-Hastings algorithm.
de.jstacs.data	Provides classes for the representation of data.
de.jstacs.data.alphabets	Provides classes for the representation of discrete and continuous alphabets, including a DNAAlphabet for the most common case of DNA-sequences
de.jstacs.io	Provides classes for reading data from and writing to a file and storing a number of datatypes, including all primitives, arrays of primitives, and Storables to an XML-representation
de.jstacs.models.discrete
de.jstacs.models.discrete.homogeneous.parameters
de.jstacs.models.discrete.inhomogeneous.parameters
de.jstacs.models.hmm	The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.models.hmm.training	The package provides all classes used to determine the training algorithm of a hidden Markov model
de.jstacs.parameters	This package provides classes for parameters that establish a general convention for the description of parameters as defined in the Parameter-interface.
de.jstacs.sampling	This package contains many classes that can be used while a sampling.
de.jstacs.scoringFunctions.directedGraphicalModels	Provides ScoringFunctions that are equivalent to directed graphical models.
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures	Provides the facilities to learn the structure of a BayesianNetworkScoringFunction.
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures	Provides the facilities to learn the structure of a BayesianNetworkScoringFunction as a Bayesian tree using a number of measures to define a rating of structures
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures	Provides the facilities to learn the structure of a BayesianNetworkScoringFunction as a permuted Markov model using a number of measures to define a rating of structures
de.jstacs.utils.galaxy

Uses of ParameterSet in de.jstacs.algorithms.optimization.termination

Subclasses of ParameterSet in de.jstacs.algorithms.optimization.termination

static class	AbsoluteValueCondition.AbsoluteValueConditionParameterSet Deprecated. This class implements the parameter set for a AbsoluteValueCondition.
static class	AbstractTerminationCondition.AbstractTerminationConditionParameterSet This class implements the super class of all parameter sets of instances from AbstractTerminationCondition.
static class	CombinedCondition.CombinedConditionParameterSet This class implements the parameter set for a CombinedCondition.
static class	IterationCondition.IterationConditionParameterSet This class implements the parameter set for a IterationCondition.
static class	SmallDifferenceOfFunctionEvaluationsCondition.SmallDifferenceOfFunctionEvaluationsConditionParameterSet This class implements the parameter set for a SmallDifferenceOfFunctionEvaluationsCondition.
static class	SmallGradientConditon.SmallGradientConditonParameterSet This class implements the parameter set for a SmallStepCondition.
static class	SmallStepCondition.SmallStepConditionParameterSet This class implements the parameter set for a SmallStepCondition.
static class	TimeCondition.TimeConditionParameterSet This class implements the parameter set for a TimeCondition.

Uses of ParameterSet in de.jstacs.classifier.assessment

Subclasses of ParameterSet in de.jstacs.classifier.assessment

class	ClassifierAssessmentAssessParameterSet This class is the superclass used by all ClassifierAssessmentAssessParameterSets.
class	KFoldCVAssessParameterSet This class implements a ClassifierAssessmentAssessParameterSet that must be used to call method assess( ... ) of a KFoldCrossValidation.
class	RepeatedHoldOutAssessParameterSet This class implements a ClassifierAssessmentAssessParameterSet that must be used to call method assess( ... ) of a RepeatedHoldOutExperiment.
class	RepeatedSubSamplingAssessParameterSet This class implements a ClassifierAssessmentAssessParameterSet that must be used to call method assess( ... ) of a RepeatedSubSamplingExperiment.
class	Sampled_RepeatedHoldOutAssessParameterSet This class implements a ClassifierAssessmentAssessParameterSet that must be used to call the method assess( ... ) of a Sampled_RepeatedHoldOutExperiment.

Uses of ParameterSet in de.jstacs.classifier.scoringFunctionBased

Subclasses of ParameterSet in de.jstacs.classifier.scoringFunctionBased

class

ScoreClassifierParameterSet A set of Parameters for any ScoreClassifier.

Uses of ParameterSet in de.jstacs.classifier.scoringFunctionBased.gendismix

Subclasses of ParameterSet in de.jstacs.classifier.scoringFunctionBased.gendismix

class

GenDisMixClassifierParameterSet This class contains the parameters for the GenDisMixClassifier.

Uses of ParameterSet in de.jstacs.classifier.scoringFunctionBased.sampling

Subclasses of ParameterSet in de.jstacs.classifier.scoringFunctionBased.sampling

class	SamplingGenDisMixClassifierParameterSet ParameterSet to instantiate a SamplingGenDisMixClassifier.
class	SamplingScoreBasedClassifierParameterSet ParameterSet to instantiate a SamplingScoreBasedClassifier.

Uses of ParameterSet in de.jstacs.data

Subclasses of ParameterSet in de.jstacs.data

static class	Alphabet.AlphabetParameterSet The super class for the InstanceParameterSet of any Alphabet.
class	AlphabetContainerParameterSet Class for the AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet of an AlphabetContainer.
static class	AlphabetContainerParameterSet.AlphabetArrayParameterSet Class for the parameters of an array of Alphabets of defined length.
static class	AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet Class for the parameter set of an array of Alphabets where each Alphabet may be used for one or more sections of positions.

Uses of ParameterSet in de.jstacs.data.alphabets

Subclasses of ParameterSet in de.jstacs.data.alphabets

static class	ContinuousAlphabet.ContinuousAlphabetParameterSet Class for the ParameterSet of a ContinuousAlphabet.
static class	DiscreteAlphabet.DiscreteAlphabetParameterSet Class for the ParameterSet of a DiscreteAlphabet.
static class	DNAAlphabet.DNAAlphabetParameterSet The parameter set for a DNAAlphabet.
static class	GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet This class is used as container for the parameters of a GenericComplementableDiscreteAlphabet.

Uses of ParameterSet in de.jstacs.io

Methods in de.jstacs.io with parameters of type ParameterSet

static InstantiableFromParameterSet

ParameterSetParser.getInstanceFromParameterSet(ParameterSet pars, Class instanceClass) Returns an instance of a subclass of InstantiableFromParameterSet that can be instantiated by the ParameterSet pars.

Uses of ParameterSet in de.jstacs.models.discrete

Subclasses of ParameterSet in de.jstacs.models.discrete

class

DGMParameterSet The super ParameterSet for any parameter set of a DiscreteGraphicalModel.

Uses of ParameterSet in de.jstacs.models.discrete.homogeneous.parameters

Subclasses of ParameterSet in de.jstacs.models.discrete.homogeneous.parameters

class	HomMMParameterSet This class implements a container for all parameters of a homogeneous Markov model.
class	HomogeneousModelParameterSet This class implements a container for all parameters of any homogeneous model.

Uses of ParameterSet in de.jstacs.models.discrete.inhomogeneous.parameters

Subclasses of ParameterSet in de.jstacs.models.discrete.inhomogeneous.parameters

class	BayesianNetworkModelParameterSet The ParameterSet for the class BayesianNetworkModel.
class	FSDAGModelForGibbsSamplingParameterSet The class for the parameters of a FSDAGModelForGibbsSampling.
class	FSDAGMParameterSet The class for the parameters of a FSDAGModel (fixed structure directed acyclic graphical model).
class	IDGMParameterSet This is the abstract container of parameters that is a root container for all inhomogeneous discrete graphical model parameter containers.

Uses of ParameterSet in de.jstacs.models.hmm

Subclasses of ParameterSet in de.jstacs.models.hmm

class

HMMTrainingParameterSet This class implements an abstract ParameterSet that is used for the training of an AbstractHMM.

Uses of ParameterSet in de.jstacs.models.hmm.training

Subclasses of ParameterSet in de.jstacs.models.hmm.training

class	BaumWelchParameterSet This class implements an HMMTrainingParameterSet for the Baum-Welch training of an AbstractHMM.
class	MaxHMMTrainingParameterSet This class is the super class for any HMMTrainingParameterSet that is used for a maximizing training algorithm of a hidden Markov model.
class	NumericalHMMTrainingParameterSet This class implements an ParameterSet for numerical training of an AbstractHMM.
class	SamplingHMMTrainingParameterSet This class contains the parameters for training training an AbstractHMM using a sampling strategy.
class	ViterbiParameterSet This class implements an ParameterSet for the viterbi training of an AbstractHMM.

Uses of ParameterSet in de.jstacs.parameters

Subclasses of ParameterSet in de.jstacs.parameters

class	ArrayParameterSet Class for a ParameterSet that consists of a length-Parameter that defines the length of the array and an array of ParameterSetContainers of this length.
class	ExpandableParameterSet A class for a ParameterSet that can be expanded by additional Parameters at runtime.
class	InstanceParameterSet Container class for a set of Parameters that can be used to instantiate another class.
class	SequenceScoringParameterSet Abstract class for a ParameterSet containing all parameters necessary to construct an Object that implements InstantiableFromParameterSet.
class	SimpleParameterSet Class for a ParameterSet that is constructed from an array of Parameters and thus does nothing in the method SimpleParameterSet.loadParameters().

Fields in de.jstacs.parameters declared as ParameterSet

protected ParameterSet	Parameter.neededReference In cases, when the validity of some ParameterSet depends on the value of this Parameter, this variable holds a reference to that ParameterSet.
protected ParameterSet	CollectionParameter.parameters The internal ParameterSet that holds the possible values
protected ParameterSet	Parameter.parent If this Parameter is enclosed in a ParameterSet, this variable holds a reference to that ParameterSet.
protected ParameterSet	ExpandableParameterSet.template The template for each ParameterSet

Methods in de.jstacs.parameters that return ParameterSet

ParameterSet	ParameterSet.clone() Creates a full clone (deep copy) of this ParameterSet.
ParameterSet	RangeParameter.getNeededReference()
ParameterSet	Parameter.getNeededReference() Returns a reference to a ParameterSet whose hasDefaultOrIsSet()-method depends on the value of this Parameter.
ParameterSet	CollectionParameter.getParametersInCollection() Returns the possible values in this collection.
ParameterSet	Parameter.getParent() Returns a reference to the ParameterSet enclosing this Parameter.
ParameterSet	ParameterSetContainer.getValue()

Methods in de.jstacs.parameters with parameters of type ParameterSet

boolean	ExpandableParameterSet.replaceContentWith(ParameterSet[] paramSetArray) First removes all previous added ParameterSetContainers and afterwards adds all given ParameterSets (in the given order) enclosed in new ParameterSetContainers.
void	RangeParameter.setNeededReference(ParameterSet reference)
void	Parameter.setNeededReference(ParameterSet reference) Sets an internal reference to a ParameterSet whose validity depends on the value of this Parameter.
void	Parameter.setParent(ParameterSet parent) Sets the reference of the enclosing ParameterSet of this Parameter to parent.

Constructors in de.jstacs.parameters with parameters of type ParameterSet

ArrayParameterSet(ParameterSet template, String nameTemplate, String commentTemplate)
Creates a new ArrayParameterSet from a Class that can be instantiated using this ArrayParameterSet and templates for the ParameterSet in each element of the array, the name and the comment that are displayed for the ParameterSetContainers enclosing the ParameterSets.

ArrayParameterSet(ParameterSet template, String nameTemplate, String commentTemplate, String lengthName, String lengthComment, NumberValidator<Integer> allowedLengths)
Creates a new ArrayParameterSet from a Class that can be instantiated using this ArrayParameterSet and templates for the ParameterSet in each element of the array, the name and the comment that are displayed for the ParameterSetContainers enclosing the ParameterSets.

CollectionParameter(ParameterSet[] values, String[] keys, String[] comments, String name, String comment, boolean required)
Constructor for a CollectionParameter from an array of ParameterSets.

CollectionParameter(ParameterSet options, int selected, int defaultSelected, boolean userSelected, String name, String comment, boolean required, DataType datatype, String errorMessage, boolean rangeable)
Creates a new CollectionParameter from the necessary field.

ExpandableParameterSet(ParameterSet[] templateAndContent, String nameTemplate, String commentTemplate)
Creates a new ExpandableParameterSet from a ParameterSet -array.

ExpandableParameterSet(ParameterSet template, String nameTemplate, String commentTemplate)
Creates a new ExpandableParameterSet from a Class that can be instantiated using this ExpandableParameterSet and templates for the ParameterSet in each element of the array, the name and the comment that are displayed for the ParameterSetContainers enclosing the ParameterSets.

ExpandableParameterSet(ParameterSet template, String nameTemplate, String commentTemplate, int initCount)
Creates a new ExpandableParameterSet from a Class that can be instantiated using this ExpandableParameterSet and templates for the ParameterSet in each element of the array, the name and the comment that are displayed for the ParameterSetContainers enclosing the ParameterSets.

MultiSelectionCollectionParameter(ParameterSet[] values, String[] keys, String[] comments, String name, String comment, boolean required)
Creates a new MultiSelectionCollectionParameter from an array of ParameterSets.

MultiSelectionCollectionParameter(ParameterSet options, boolean[] selected, boolean[] defaultSelected, boolean userSelected, String name, String comment, boolean required, DataType datatype, String errorMessage, int current, boolean makeRanged)
Creates a new MultiSelectionCollectionParameter from the necessary field.

ParameterSetContainer(String name, String comment, ParameterSet content)
Creates an new ParameterSetContainer out of a ParameterSet.

ParameterSetTagger(String[] tags, ParameterSet... sets)
The constructor creates an new instance by collecting and tagging all parameters of the ParameterSets.

Uses of ParameterSet in de.jstacs.sampling

Subclasses of ParameterSet in de.jstacs.sampling

class	AbstractBurnInTestParameterSet Class for the parameters of a AbstractBurnInTest.
class	VarianceRatioBurnInTestParameterSet Class for the parameters of a VarianceRatioBurnInTest.

Uses of ParameterSet in de.jstacs.scoringFunctions.directedGraphicalModels

Subclasses of ParameterSet in de.jstacs.scoringFunctions.directedGraphicalModels

class

BayesianNetworkScoringFunctionParameterSet Class for the parameters of a BayesianNetworkScoringFunction.

Uses of ParameterSet in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures

Subclasses of ParameterSet in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures

static class

InhomogeneousMarkov.InhomogeneousMarkovParameterSet Class for an InstanceParameterSet that defines the parameters of an InhomogeneousMarkov structure Measure.

Uses of ParameterSet in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures

Subclasses of ParameterSet in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures

static class	BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet Class for the parameters of a BTExplainingAwayResidual structure Measure.
static class	BTMutualInformation.BTMutualInformationParameterSet Class for the parameters of a BTMutualInformation structure Measure.

Uses of ParameterSet in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures

Subclasses of ParameterSet in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures

static class	PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet Class for the parameters of a PMMExplainingAwayResidual structure Measure.
static class	PMMMutualInformation.PMMMutualInformationParameterSet Class for the parameters of a PMMMutualInformation structure Measure.

Uses of ParameterSet in de.jstacs.utils.galaxy

Constructors in de.jstacs.utils.galaxy with parameters of type ParameterSet

GalaxyAdaptor(ParameterSet parameters, String toolname, String description, String version, String command)
Creates a new GalaxyAdaptor from a given ParameterSet containing all parameters that are necessary for a program is shall be included in a Galaxy installation.