Uses of Package
de.jstacs.parameters

Packages that use de.jstacs.parameters

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.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.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.tools
de.jstacs.tools.ui.galaxy
de.jstacs.utils	This package contains a bundle of useful classes and interfaces like ...

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

Class and Description
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

Class and Description
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.IllegalValueException This exception is thrown if a parameter is not valid.

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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

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

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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
AbstractSelectionParameter Class for a collection parameter, i.e.
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. These values may be given either as a list of values separated by spaces, as a range between a first and a last value with a given number of steps between these values, or a single value.
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.
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

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

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

Class and Description
FileParameter Class for a Parameter that represents a local file.
FileParameter.FileRepresentation Class that represents a file.
SimpleParameter.IllegalValueException This exception is thrown if a parameter is not valid.

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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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.tools

Class and Description
FileParameter Class for a Parameter that represents a local file.
GalaxyConvertible Interface for Parameters that can be converted to and extracted from Galaxy representations.
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.
Rangeable Interface for Parameters that potentially can be varied over a certain interval or a list of values.
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.

Classes in de.jstacs.parameters used by de.jstacs.tools.ui.galaxy

Class and Description
GalaxyConvertible Interface for Parameters that can be converted to and extracted from Galaxy representations.
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.
Rangeable Interface for Parameters that potentially can be varied over a certain interval or a list of values.
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.

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

Class and Description
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.