Uses of Class
de.jstacs.parameters.InstanceParameterSet

Packages that use InstanceParameterSet

Package	Description
de.jstacs	This package is the root package for the most and important packages.
de.jstacs.algorithms.optimization.termination	Provides classes for termination conditions that can be used in algorithms.
de.jstacs.classifiers.differentiableSequenceScoreBased	Provides the classes for Classifiers that are based on SequenceScores. It includes a sub-package for discriminative objective functions, namely conditional likelihood and supervised posterior, and a separate sub-package for the parameter priors, that can be used for the supervised posterior.
de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix	Provides an implementation of a classifier that allows to train the parameters of a set of DifferentiableStatisticalModels by a unified generative-discriminative learning principle.
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling	Provides the classes for AbstractScoreBasedClassifiers that are based on SamplingDifferentiableStatisticalModels and that sample parameters using the Metropolis-Hastings algorithm.
de.jstacs.data	Provides classes for the representation of data. The base classes to represent data are Alphabet and AlphabetContainer for representing alphabets, Sequence and its sub-classes to represent continuous and discrete sequences, and DataSet to represent data sets comprising a set of sequences.
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.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.sequenceScores.statisticalModels.differentiable.directedGraphicalModels	Provides DifferentiableStatisticalModels that are directed graphical models.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures	Provides the facilities to learn the structure of a BayesianNetworkDiffSM.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures	Provides the facilities to learn the structure of a BayesianNetworkDiffSM as a Bayesian tree using a number of measures to define a rating of structures.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures	Provides the facilities to learn the structure of a BayesianNetworkDiffSM as a permuted Markov model using a number of measures to define a rating of structures.
de.jstacs.sequenceScores.statisticalModels.trainable.discrete
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters
de.jstacs.utils	This package contains a bundle of useful classes and interfaces like ...

Uses of InstanceParameterSet in de.jstacs

Methods in de.jstacs that return InstanceParameterSet

Modifier and Type	Method and Description
InstanceParameterSet<? extends InstantiableFromParameterSet>	InstantiableFromParameterSet.getCurrentParameterSet() Returns the InstanceParameterSet that has been used to instantiate the current instance of the implementing class.

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

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

Modifier and Type	Class and Description
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	MultipleIterationsCondition.MultipleIterationsConditionParameterSet This class implements the parameter set for a MultipleIterationsCondition.
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 InstanceParameterSet in de.jstacs.classifiers.differentiableSequenceScoreBased

Subclasses of InstanceParameterSet in de.jstacs.classifiers.differentiableSequenceScoreBased

Modifier and Type	Class and Description
class	ScoreClassifierParameterSet A set of Parameters for any ScoreClassifier.

Uses of InstanceParameterSet in de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix

Subclasses of InstanceParameterSet in de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix

Modifier and Type	Class and Description
class	GenDisMixClassifierParameterSet This class contains the parameters for the GenDisMixClassifier.

Uses of InstanceParameterSet in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling

Subclasses of InstanceParameterSet in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling

Modifier and Type	Class and Description
class	SamplingGenDisMixClassifierParameterSet ParameterSet to instantiate a SamplingGenDisMixClassifier.
class	SamplingScoreBasedClassifierParameterSet ParameterSet to instantiate a SamplingScoreBasedClassifier.

Uses of InstanceParameterSet in de.jstacs.data

Subclasses of InstanceParameterSet in de.jstacs.data

Modifier and Type	Class and Description
static class	AlphabetContainer.AbstractAlphabetContainerParameterSet<T extends AlphabetContainer> This class is the super class of any InstanceParameterSet for AlphabetContainer.
class	AlphabetContainerParameterSet Class for the ParameterSet of an AlphabetContainer.

Methods in de.jstacs.data that return types with arguments of type InstanceParameterSet

Modifier and Type	Method and Description
LinkedList<InstanceParameterSet>	AlphabetContainer.AlphabetContainerType.getInstanceParameterSets() This method returns a LinkedList of InstanceParameterSets which can be used to create Alphabets that can be used in a AlphabetContainer of the given AlphabetContainer.AlphabetContainerType.

Uses of InstanceParameterSet in de.jstacs.data.alphabets

Subclasses of InstanceParameterSet in de.jstacs.data.alphabets

Modifier and Type	Class and Description
static class	Alphabet.AlphabetParameterSet<T extends Alphabet> The super class for the InstanceParameterSet of any Alphabet.
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	DNAAlphabetContainer.DNAAlphabetContainerParameterSet This class implements a singleton for the ParameterSet of a DNAAlphabetContainer.
static class	GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet This class is used as container for the parameters of a GenericComplementableDiscreteAlphabet.
static class	IUPACDNAAlphabet.IUPACDNAAlphabetParameterSet The parameter set for a IUPACDNAAlphabet.
static class	ProteinAlphabet.ProteinAlphabetParameterSet The parameter set for a ProteinAlphabet.

Methods in de.jstacs.data.alphabets that return InstanceParameterSet

Modifier and Type	Method and Description
abstract InstanceParameterSet<? extends Alphabet>	Alphabet.getCurrentParameterSet()

Uses of InstanceParameterSet in de.jstacs.io

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

Modifier and Type	Method and Description
static <T extends InstantiableFromParameterSet> T	ParameterSetParser.getInstanceFromParameterSet(InstanceParameterSet<T> pars) Returns an instance of a subclass of InstantiableFromParameterSet that can be instantiated by the InstanceParameterSet pars.

Uses of InstanceParameterSet in de.jstacs.parameters

Subclasses of InstanceParameterSet in de.jstacs.parameters

Modifier and Type	Class and Description
class	SequenceScoringParameterSet<T extends InstantiableFromParameterSet> Abstract class for a ParameterSet containing all parameters necessary to construct an Object that implements InstantiableFromParameterSet.

Uses of InstanceParameterSet in de.jstacs.sampling

Subclasses of InstanceParameterSet in de.jstacs.sampling

Modifier and Type	Class and Description
class	AbstractBurnInTestParameterSet Class for the parameters of a AbstractBurnInTest.
class	VarianceRatioBurnInTestParameterSet Class for the parameters of a VarianceRatioBurnInTest.

Uses of InstanceParameterSet in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels

Subclasses of InstanceParameterSet in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels

Modifier and Type	Class and Description
class	BayesianNetworkDiffSMParameterSet Class for the parameters of a BayesianNetworkDiffSM.

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels that return InstanceParameterSet

Modifier and Type	Method and Description
InstanceParameterSet	BayesianNetworkDiffSM.getCurrentParameterSet()

Uses of InstanceParameterSet in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures

Subclasses of InstanceParameterSet in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures

Modifier and Type	Class and Description
static class	InhomogeneousMarkov.InhomogeneousMarkovParameterSet Class for an InstanceParameterSet that defines the parameters of an InhomogeneousMarkov structure Measure.
static class	Measure.MeasureParameterSet This class is the super class of any ParameterSet that can be used to instantiate a Measure.

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures that return InstanceParameterSet

Modifier and Type	Method and Description
InstanceParameterSet<Measure>	Measure.getCurrentParameterSet()

Uses of InstanceParameterSet in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures

Subclasses of InstanceParameterSet in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures

Modifier and Type	Class and Description
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 InstanceParameterSet in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures

Subclasses of InstanceParameterSet in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures

Modifier and Type	Class and Description
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 InstanceParameterSet in de.jstacs.sequenceScores.statisticalModels.trainable.discrete

Subclasses of InstanceParameterSet in de.jstacs.sequenceScores.statisticalModels.trainable.discrete

Modifier and Type	Class and Description
class	DGTrainSMParameterSet<T extends DiscreteGraphicalTrainSM> The super ParameterSet for any parameter set of a DiscreteGraphicalTrainSM.

Uses of InstanceParameterSet in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters

Subclasses of InstanceParameterSet in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters

Modifier and Type	Class and Description
class	HomMMParameterSet This class implements a container for all parameters of a homogeneous Markov model.
class	HomogeneousTrainSMParameterSet This class implements a container for all parameters of any homogeneous model.

Uses of InstanceParameterSet in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters

Subclasses of InstanceParameterSet in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters

Modifier and Type	Class and Description
class	BayesianNetworkTrainSMParameterSet The ParameterSet for the class BayesianNetworkTrainSM.
class	FSDAGModelForGibbsSamplingParameterSet The class for the parameters of a FSDAGModelForGibbsSampling.
class	FSDAGTrainSMParameterSet The class for the parameters of a FSDAGTrainSM (fixed structure directed acyclic graphical model).
class	FSMEMParameterSet The ParameterSet for a FSMEManager.
class	IDGTrainSMParameterSet This is the abstract container of parameters that is a root container for all inhomogeneous discrete graphical model parameter containers.
class	MEManagerParameterSet The ParameterSet for any MEManager.

Uses of InstanceParameterSet in de.jstacs.utils

Methods in de.jstacs.utils that return types with arguments of type InstanceParameterSet

Modifier and Type	Method and Description
static <T> LinkedList<InstanceParameterSet<? extends T>>	SubclassFinder.getInstanceParameterSets(Class<T> clazz, String startPackage) This method returns a list of InstanceParameterSets that can be used to create a subclass of clazz.
static LinkedList<Class<? extends InstanceParameterSet>>	SubclassFinder.getParameterSetFor(Class<? extends InstantiableFromParameterSet> clazz) Returns a LinkedList of the classes of the InstanceParameterSets that can be used to instantiate the sub-class of InstantiableFromParameterSet that is given by clazz