Uses of Package
de.jstacs.parameters

Packages that use de.jstacs.parameters

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.assessment	This package allows to assess classifiers.
de.jstacs.classifiers.differentiableSequenceScoreBased	Provides the classes for Classifiers that are based on SequenceScores.
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.
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.parameters.validation	Provides classes for the validation of Parameter values
de.jstacs.results	This package provides classes for results and sets of results.
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.utils	This package contains a bundle of useful classes and interfaces like ...
de.jstacs.utils.galaxy

Classes in de.jstacs.parameters used by de.jstacs

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

Classes in de.jstacs.parameters used by de.jstacs.algorithms.optimization.termination

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter.

ParameterSet
(Container) class for a set of Parameters.

SimpleParameter.DatatypeNotValidException
Class for an Exception that can be thrown if the provided int-value that represents a data type is not one of the values defined in DataType.

SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.classifiers.assessment

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter.

ParameterSet
(Container) class for a set of Parameters.

SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.

SimpleParameterSet
Class for a ParameterSet that is constructed from an array of Parameters.

Classes in de.jstacs.parameters used by de.jstacs.classifiers.differentiableSequenceScoreBased

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterSet
(Container) class for a set of Parameters.

SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary to construct an Object that implements InstantiableFromParameterSet.

Classes in de.jstacs.parameters used by de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterSet
(Container) class for a set of Parameters.

SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary to construct an Object that implements InstantiableFromParameterSet.

SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.classifiers.differentiableSequenceScoreBased.sampling

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterSet
(Container) class for a set of Parameters.

SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary to construct an Object that implements InstantiableFromParameterSet.

SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.classifiers.performanceMeasures

ExpandableParameterSet
A class for a ParameterSet that can be expanded by additional Parameters at runtime.

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

ParameterSet
(Container) class for a set of Parameters.

SelectionParameter
Class for a collection parameter, i.e. a parameter that provides some collection of possible values the user can choose from.

SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.data

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.

ExpandableParameterSet
A class for a ParameterSet that can be expanded by additional Parameters at runtime.

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterSet
(Container) class for a set of Parameters.

Classes in de.jstacs.parameters used by de.jstacs.data.alphabets

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter.

ParameterSet
(Container) class for a set of Parameters.

Classes in de.jstacs.parameters used by de.jstacs.io

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

Parameter
Abstract class for a parameter that shall be used as the parameter of some method, constructor, etc.

ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter.

ParameterSet
(Container) class for a set of Parameters.

Classes in de.jstacs.parameters used by de.jstacs.parameters

AbstractSelectionParameter
Class for a collection parameter, i.e. a parameter that provides some collection of possible values the user can choose from.

AbstractSelectionParameter.InconsistentCollectionException
This exception is thrown if the AbstractSelectionParameter is inconsistent for some reason.

EnumParameter
This class implements a SelectionParameter based on an Enum.

ExpandableParameterSet
A class for a ParameterSet that can be expanded by additional Parameters at runtime.

FileParameter
Class for a Parameter that represents a local file.

FileParameter.FileRepresentation
Class that represents a file.

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

MultiSelectionParameter
Class for a Parameter that provides a collection of possible values.

Parameter
Abstract class for a parameter that shall be used as the parameter of some method, constructor, etc.

ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter.

ParameterSet
(Container) class for a set of Parameters.

ParameterSet.ParameterList
Class for a AnnotatedEntityList that automatically sets the Parameter.parent field to the enclosing ParameterSet.

ParameterSetContainer
Class for a ParameterSetContainer that contains a ParameterSet as value.

Rangeable
Interface for Parameters that potentially can be varied over a certain interval or a list of values.

RangeIterator
Interface for a Parameter or ParameterSet that can have multiple values at the same time.

RangeParameter
Class for a parameter wrapper that allows SimpleParameters to be set to a set of values.

RangeParameter.RangeType
The possible types of defining ranges for a RangeParameter.

RangeParameter.Scale
This enum defines possible scales, if RangeParameter.RangeType is RangeParameter.RangeType.RANGE.

SelectionParameter
Class for a collection parameter, i.e. a parameter that provides some collection of possible values the user can choose from.

SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary to construct an Object that implements InstantiableFromParameterSet.

SimpleParameter
Class for a "simple" parameter.

SimpleParameter.DatatypeNotValidException
Class for an Exception that can be thrown if the provided int-value that represents a data type is not one of the values defined in DataType.

SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.

SimpleParameterSet
Class for a ParameterSet that is constructed from an array of Parameters.

Classes in de.jstacs.parameters used by de.jstacs.parameters.validation

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

Classes in de.jstacs.parameters used by de.jstacs.results

SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.sampling

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterSet
(Container) class for a set of Parameters.

SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterSet
(Container) class for a set of Parameters.

SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary to construct an Object that implements InstantiableFromParameterSet.

Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterSet
(Container) class for a set of Parameters.

SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter.

ParameterSet
(Container) class for a set of Parameters.

SimpleParameter.DatatypeNotValidException
Class for an Exception that can be thrown if the provided int-value that represents a data type is not one of the values defined in DataType.

Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter.

ParameterSet
(Container) class for a set of Parameters.

SimpleParameter.DatatypeNotValidException
Class for an Exception that can be thrown if the provided int-value that represents a data type is not one of the values defined in DataType.

Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterSet
(Container) class for a set of Parameters.

SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary to construct an Object that implements InstantiableFromParameterSet.

SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterSet
(Container) class for a set of Parameters.

SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary to construct an Object that implements InstantiableFromParameterSet.

Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterSet
(Container) class for a set of Parameters.

SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary to construct an Object that implements InstantiableFromParameterSet.

SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training

GalaxyConvertible
Interface for Parameters that can be converted to and extracted from Galaxy representations.

ParameterSet
(Container) class for a set of Parameters.

SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.utils

InstanceParameterSet
Container class for a set of Parameters that can be used to instantiate another class.

ParameterSet
(Container) class for a set of Parameters.

SelectionParameter
Class for a collection parameter, i.e. a parameter that provides some collection of possible values the user can choose from.

Classes in de.jstacs.parameters used by de.jstacs.utils.galaxy

ParameterSet
(Container) class for a set of Parameters.