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## Uses of Package
de.jstacs.algorithms.optimization

Packages that use de.jstacs.algorithms.optimization
de.jstacs.algorithms.optimization | Provides classes for different types of algorithms that are not directly linked to the modelling components of Jstacs: Algorithms on graphs, algorithms for numerical optimization, and a basic alignment algorithm.
de.jstacs.classifier.scoringFunctionBased | Provides the classes for `Classifier`s that are based on `ScoringFunction`s.
de.jstacs.classifier.scoringFunctionBased.cll | Provides the implementation of the log conditional likelihood as an `OptimizableFunction` and a classifier that uses log conditional likelihood or supervised posterior to learn the parameters of a set of `ScoringFunctions`
de.jstacs.classifier.scoringFunctionBased.logPrior | Provides a general definition of a parameter log-prior and a number of implementations of Laplace and Gaussian priors
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer

Classes in de.jstacs.algorithms.optimization used by de.jstacs.algorithms.optimization
DifferentiableFunction This class is the framework for any (at least) one time differentiable function `f: R^n -> R`.
DimensionException This class is for `Exception`s depending on wrong dimensions of vectors for a given function.
EvaluationException This class indicates that there was a problem to evaluate a function or the gradient of the function.
Function This interface is the framework for any mathematical function `f: R^n -> R`.
OneDimensionalFunction This class implements the interface `Function` for an one-dimensional function.
Optimizer.TerminationCondition This `enum` defines all kinds of termination conditions for the `Optimizer`.
StartDistanceForecaster This interface is used to determine the next start distance that will be used in a line search.
TerminationException This class is for an `Exception` that is thrown if something with a termination was not correct.

Classes in de.jstacs.algorithms.optimization used by de.jstacs.classifier.scoringFunctionBased
DifferentiableFunction This class is the framework for any (at least) one time differentiable function `f: R^n -> R`.
DimensionException This class is for `Exception`s depending on wrong dimensions of vectors for a given function.
Function This interface is the framework for any mathematical function `f: R^n -> R`.

Classes in de.jstacs.algorithms.optimization used by de.jstacs.classifier.scoringFunctionBased.cll
DifferentiableFunction This class is the framework for any (at least) one time differentiable function `f: R^n -> R`.
DimensionException This class is for `Exception`s depending on wrong dimensions of vectors for a given function.
EvaluationException This class indicates that there was a problem to evaluate a function or the gradient of the function.
Function This interface is the framework for any mathematical function `f: R^n -> R`.

Classes in de.jstacs.algorithms.optimization used by de.jstacs.classifier.scoringFunctionBased.logPrior
DifferentiableFunction This class is the framework for any (at least) one time differentiable function `f: R^n -> R`.
DimensionException This class is for `Exception`s depending on wrong dimensions of vectors for a given function.
EvaluationException This class indicates that there was a problem to evaluate a function or the gradient of the function.
Function This interface is the framework for any mathematical function `f: R^n -> R`.

Classes in de.jstacs.algorithms.optimization used by de.jstacs.motifDiscovery
StartDistanceForecaster This interface is used to determine the next start distance that will be used in a line search.

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