Uses of Class
de.jstacs.parameters.ParameterSet

Packages that use ParameterSet

Package	Description
de.jstacs.algorithms.optimization.termination	Provides classes for termination conditions that can be used in algorithms.
de.jstacs.classifiers.assessment	This package allows to assess classifiers. It contains the class ClassifierAssessment that is used as a super-class of all implemented methodologies of an assessment to assess classifiers.
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.classifiers.performanceMeasures	This package provides the implementations of performance measures that can be used to assess any classifier.
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.sequenceScores.statisticalModels.trainable.hmm.training	The package provides all classes used to determine the training algorithm of a hidden Markov model.
de.jstacs.tools
de.jstacs.tools.ui.galaxy
de.jstacs.utils	This package contains a bundle of useful classes and interfaces like ...

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

Subclasses of ParameterSet 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 ParameterSet in de.jstacs.classifiers.assessment

Subclasses of ParameterSet in de.jstacs.classifiers.assessment

Modifier and Type	Class and Description
class	ClassifierAssessmentAssessParameterSet This class is the superclass used by all ClassifierAssessmentAssessParameterSets.
class	KFoldCrossValidationAssessParameterSet This class implements a ClassifierAssessmentAssessParameterSet that must be used to call method assess( ...
class	RepeatedHoldOutAssessParameterSet This class implements a ClassifierAssessmentAssessParameterSet that must be used to call method assess( ...
class	RepeatedSubSamplingAssessParameterSet This class implements a ClassifierAssessmentAssessParameterSet that must be used to call method assess( ...
class	Sampled_RepeatedHoldOutAssessParameterSet This class implements a ClassifierAssessmentAssessParameterSet that must be used to call the method assess( ...

Uses of ParameterSet in de.jstacs.classifiers.differentiableSequenceScoreBased

Subclasses of ParameterSet in de.jstacs.classifiers.differentiableSequenceScoreBased

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

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

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

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

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

Subclasses of ParameterSet 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 ParameterSet in de.jstacs.classifiers.performanceMeasures

Subclasses of ParameterSet in de.jstacs.classifiers.performanceMeasures

Modifier and Type	Class and Description
class	AbstractNumericalTwoClassPerformanceMeasure This class is the abstract super class of any performance measure that can only be computed for binary classifiers.
class	AbstractPerformanceMeasure This class is the abstract super class of any performance measure used to evaluate an AbstractClassifier.
class	AbstractPerformanceMeasureParameterSet<T extends PerformanceMeasure> This class implements a container of PerformanceMeasures that can be used in AbstractClassifier.evaluate(AbstractPerformanceMeasureParameterSet, boolean, de.jstacs.data.DataSet...).
class	AbstractTwoClassPerformanceMeasure This class is the abstract super class of any performance measure that can only be computed for binary classifiers.
class	AucPR This class implements the area under curve of the precision-recall curve.
class	AucROC This class implements the area under curve of the Receiver Operating Characteristics curve.
class	ClassificationRate This class implements the classification rate, i.e.
class	ConfusionMatrix This class implements the performance measure confusion matrix.
class	CorrelationCoefficient PerformanceMeasure using Pearson or Spearman correlation between prediction scores and weighted class labels.
class	FalsePositiveRateForFixedSensitivity This class implements the false positive rate for a fixed sensitivity.
class	MaximumCorrelationCoefficient This class implements the maximum of the correlation coefficient .
class	MaximumFMeasure Computes the maximum of the general F-measure given a positive real parameter .
class	MaximumNumericalTwoClassMeasure This class prepares everything for an easy implementation of a maximum of any numerical performance measure.
class	NumericalPerformanceMeasureParameterSet This class implements a container for NumericalPerformanceMeasures that can be used, for instance, in an repeated assessment, (cf.
class	PerformanceMeasureParameterSet This class implements a container of AbstractPerformanceMeasures that can be used in AbstractClassifier.evaluate(AbstractPerformanceMeasureParameterSet, boolean, de.jstacs.data.DataSet...).
class	PositivePredictiveValueForFixedSensitivity This class implements the positive predictive value for a fixed sensitivity.
class	PRCurve This class implements the precision-recall curve and its area under the curve.
class	ROCCurve This class implements the Receiver Operating Characteristics curve and the area under the curve.
class	SensitivityForFixedSpecificity This class implements the sensitivity for a fixed specificity.

Uses of ParameterSet in de.jstacs.data

Subclasses of ParameterSet 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.
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

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.

Uses of ParameterSet in de.jstacs.io

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

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

Uses of ParameterSet in de.jstacs.parameters

Subclasses of ParameterSet in de.jstacs.parameters

Modifier and Type	Class and Description
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<T extends InstantiableFromParameterSet> Container class for a set of Parameters that can be used to instantiate another class.
class	SequenceScoringParameterSet<T extends InstantiableFromParameterSet> 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.

Fields in de.jstacs.parameters declared as ParameterSet

Modifier and Type	Field and Description
protected ParameterSet	AbstractSelectionParameter.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

Modifier and Type	Method and Description
ParameterSet	ParameterSet.clone() Creates a full clone (deep copy) of this ParameterSet.
ParameterSet	AbstractSelectionParameter.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

Modifier and Type	Method and Description
static String	ParameterSet.getComment(ParameterSet p) Returns a comment for the ParameterSet.
static String	ParameterSet.getName(ParameterSet p) Returns a name for the ParameterSet.
boolean	ParameterSet.isComparable(ParameterSet p) This method checks whether the given ParameterSet is comparable to the current instance, i.e.
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	Parameter.setParent(ParameterSet parent) Sets the reference of the enclosing ParameterSet of this Parameter to parent.

Method parameters in de.jstacs.parameters with type arguments of type ParameterSet

Modifier and Type	Method and Description
static String	ParameterSet.getComment(Class<? extends ParameterSet> c) Returns a comment for the class.
static String	ParameterSet.getName(Class<? extends ParameterSet> c) Returns a name for the class.

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

Constructor and Description
AbstractSelectionParameter(String name, String comment, boolean required, ParameterSet... values) Constructor for a AbstractSelectionParameter from an array of ParameterSets.
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.
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.
MultiSelectionParameter(String name, String comment, boolean required, ParameterSet... values) Creates a new MultiSelectionParameter from an array of ParameterSets.
ParameterSetContainer(ParameterSet p) Creates an new ParameterSetContainer out of a ParameterSet.
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.
SelectionParameter(String name, String comment, boolean required, ParameterSet... values) Constructor for a SelectionParameter from an array of ParameterSets.

Constructor parameters in de.jstacs.parameters with type arguments of type ParameterSet

Constructor and Description
ParameterSetContainer(Class<? extends ParameterSet> contentClazz) Creates an new ParameterSetContainer out of the class of a ParameterSet.
ParameterSetContainer(String name, String comment, Class<? extends ParameterSet> contentClazz) Creates an new ParameterSetContainer out of the class of a ParameterSet.

Uses of ParameterSet in de.jstacs.sampling

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

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

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

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

Subclasses of ParameterSet 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.

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

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

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

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

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

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

Modifier and Type	Class and Description
class	BayesianNetworkTrainSMParameterSet The ParameterSet for the class BayesianNetworkTrainSM.
class	ConstraintParameterSet This class enables you to input your own structure defined by some constraints.
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 ParameterSet in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training

Subclasses of ParameterSet in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training

Modifier and Type	Class and Description
class	BaumWelchParameterSet This class implements an HMMTrainingParameterSet for the Baum-Welch training of an AbstractHMM.
class	HMMTrainingParameterSet This class implements an abstract ParameterSet that is used for the 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	MultiThreadedTrainingParameterSet This class is the super class for any MaxHMMTrainingParameterSet that is used for a multi-threaded 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.tools

Methods in de.jstacs.tools that return ParameterSet

Modifier and Type	Method and Description
ParameterSet	ToolResult.getToolParameters() Returns the tool's parameters that have been used to create the results stored in this ToolResult.
ParameterSet	JstacsTool.getToolParameters() Returns the input parameters of this tool.

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

Modifier and Type	Method and Description
static FileParameter	DataColumnParameter.find(ParameterSet top, String dataRef) Finds the parameter for the given ID in a ParameterSet.
ToolResult	JstacsTool.run(ParameterSet parameters, Protocol protocol, ProgressUpdater progress, int threads) Runs the tool using the provided (now filled) parameters, which are in structure identical to those returned by JstacsTool.getToolParameters().
void	ToolResult.setFromStoredParameters(ParameterSet other) Sets the values of all parameters in other to those stored in the internal parameters that have been supplied upon construction.

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

Constructor and Description
ToolResult(String name, String comment, ResultSet annotation, ResultSet result, ParameterSet toolParameters, String toolName, Date finished) Creates a new ToolResult with most arguments identical to those of a ListResult.

Uses of ParameterSet in de.jstacs.tools.ui.galaxy

Constructors in de.jstacs.tools.ui.galaxy with parameters of type ParameterSet

Constructor and Description
GalaxyAdaptor(ParameterSet parameters, JstacsTool.ResultEntry[] defaultResults, boolean[] addLine, String toolname, String description, String version, String command, String labelName) 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.

Uses of ParameterSet in de.jstacs.utils

Method parameters in de.jstacs.utils with type arguments of type ParameterSet

Modifier and Type	Method and Description
static <T> SelectionParameter	SubclassFinder.getSelectionParameter(Class<? extends ParameterSet> clazz, String startPackage, String name, String comment, boolean required) This method creates an SelectionParameter that contains InstanceParameterSet for each possible class.