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## 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 |
de.jstacs.classifier | This package provides the framework for any classifier.
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.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.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 | 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 `Parameter`s that can be used to instantiate another class.

Classes in de.jstacs.parameters used by de.jstacs.algorithms.optimization.termination
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.
SimpleParameter.IllegalValueException This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.classifier
CollectionParameter Class for a collection parameter, i.e. a parameter that provides some collection of possible values the user can choose from.
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
MultiSelectionCollectionParameter 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.
Rangeable Interface for `Parameter`s 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 `SimpleParameter`s to be set to a set of values.
RangeParameter.Scale This `enum` defines possible scales, if `RangeParameter.RangeType` is `RangeParameter.RangeType.RANGE`.

Classes in de.jstacs.parameters used by de.jstacs.classifier.assessment
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.
SimpleParameter.IllegalValueException This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.classifier.scoringFunctionBased
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.
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.classifier.scoringFunctionBased.gendismix
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.
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.classifier.scoringFunctionBased.sampling
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.
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.data
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.
ExpandableParameterSet A class for a `ParameterSet` that can be expanded by additional `Parameter`s at runtime.
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.

Classes in de.jstacs.parameters used by de.jstacs.data.alphabets
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.

Classes in de.jstacs.parameters used by de.jstacs.io
InstanceParameterSet Container class for a set of `Parameter`s 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 `Parameter`s.

Classes in de.jstacs.parameters used by de.jstacs.models.discrete
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.
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.models.discrete.homogeneous.parameters
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.
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.models.discrete.inhomogeneous.parameters
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.
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.models.hmm
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.
SimpleParameter.IllegalValueException This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.models.hmm.training
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.
SimpleParameter.IllegalValueException This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.parameters
CollectionParameter Class for a collection parameter, i.e. a parameter that provides some collection of possible values the user can choose from.
CollectionParameter.InconsistentCollectionException This exception is thrown if the `CollectionParameter` is inconsistent for some reason.
ExpandableParameterSet A class for a `ParameterSet` that can be expanded by additional `Parameter`s at runtime.
FileParameter Class for a `Parameter` that represents a local file.
FileParameter.FileRepresentation Class that represents a file.
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
MultiSelectionCollectionParameter 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 `Parameter`s.
ParameterSet.ParameterList Class for a `List` of `Parameter`s that basically has the same functionality as `ArrayList`, but additionally takes care of the references `Parameter.parent`.
ParameterSetContainer Class for a `ParameterSetContainer` that contains a `ParameterSet` as value.
Rangeable Interface for `Parameter`s 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 `SimpleParameter`s 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`.
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 `Parameter`s and thus does nothing in the method `SimpleParameterSet.loadParameters()`.

Classes in de.jstacs.parameters used by de.jstacs.parameters.validation
GalaxyConvertible Interface for `Parameter`s 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.
SimpleParameter Class for a "simple" parameter.

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 `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.
SimpleParameter.IllegalValueException This exception is thrown if a parameter is not valid.

Classes in de.jstacs.parameters used by de.jstacs.scoringFunctions.directedGraphicalModels
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.
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.scoringFunctions.directedGraphicalModels.structureLearning.measures
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.

Classes in de.jstacs.parameters used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.

Classes in de.jstacs.parameters used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures
GalaxyConvertible Interface for `Parameter`s that can be converted to and extracted from Galaxy representations.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.
ParameterSet (Container) class for a set of `Parameter`s.
RangeIterator Interface for a `Parameter` or `ParameterSet` that can have multiple values at the same time.

Classes in de.jstacs.parameters used by de.jstacs.utils
CollectionParameter Class for a collection parameter, i.e. a parameter that provides some collection of possible values the user can choose from.
InstanceParameterSet Container class for a set of `Parameter`s that can be used to instantiate another class.

Classes in de.jstacs.parameters used by de.jstacs.utils.galaxy
ParameterSet (Container) class for a set of `Parameter`s.

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