Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES

## 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 `Classifier`s that are based on `ScoringFunction`s.
de.jstacs.classifier.scoringFunctionBased.gendismix | Provides an implementation of a classifier that allows to train the parameters of a set of `NormalizableScoringFunction`s by a unified generative-discriminative learning principle
de.jstacs.classifier.scoringFunctionBased.sampling | Provides the classes for `AbstractScoreBasedClassifier`s that are based on `SamplingScoringFunction`s 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 `Storable`s 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 `ScoringFunction`s 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 `ClassifierAssessmentAssessParameterSet`s.
`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 `Parameter`s 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 `Alphabet`s of defined length.
`static class` | `AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet` Class for the parameter set of an array of `Alphabet`s 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 `ParameterSetContainer`s of this length.
`class` | `ExpandableParameterSet` A class for a `ParameterSet` that can be expanded by additional `Parameter`s at runtime.
`class` | `InstanceParameterSet` Container class for a set of `Parameter`s 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 `Parameter`s 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 `ParameterSetContainer`s and afterwards adds all given `ParameterSet`s (in the given order) enclosed in new `ParameterSetContainer`s.
`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 `ParameterSetContainer`s enclosing the `ParameterSet`s.
`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 `ParameterSetContainer`s enclosing the `ParameterSet`s.
`CollectionParameter(ParameterSet[] values, String[] keys, String[] comments, String name, String comment, boolean required)` Constructor for a `CollectionParameter` from an array of `ParameterSet`s.
`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 `ParameterSetContainer`s enclosing the `ParameterSet`s.
`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 `ParameterSetContainer`s enclosing the `ParameterSet`s.
`MultiSelectionCollectionParameter(ParameterSet[] values, String[] keys, String[] comments, String name, String comment, boolean required)` Creates a new `MultiSelectionCollectionParameter` from an array of `ParameterSet`s.
`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 `ParameterSet`s.

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.

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES