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## Uses of Package
de.jstacs.utils

Packages that use de.jstacs.utils
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.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.utils | Provides some useful classes for working with classifiers
de.jstacs.data | Provides classes for the representation of data.
de.jstacs.models.discrete.inhomogeneous | This package contains various inhomogeneous models.
de.jstacs.models.mixture | This package is the super package for any mixture model.
de.jstacs.models.mixture.gibbssampling | This package contains many classes that can be used while a Gibbs sampling.
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer
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.scoringFunctions | Provides `ScoringFunction`s that can be used in a `ScoreClassifier`.
de.jstacs.scoringFunctions.directedGraphicalModels | Provides `ScoringFunction`s that are equivalent to directed graphical models.
de.jstacs.scoringFunctions.homogeneous | Provides `ScoringFunction`s that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.scoringFunctions.mix | Provides `ScoringFunction`s that are mixtures of other `ScoringFunction`s.
de.jstacs.scoringFunctions.mix.motifSearch |
de.jstacs.utils | This package contains a bundle of useful classes and interfaces like ...

Classes in de.jstacs.utils used by de.jstacs.algorithms.optimization
Time This interface is the framework for stopping the time of anything.

Classes in de.jstacs.utils used by de.jstacs.algorithms.optimization.termination
Time This interface is the framework for stopping the time of anything.

Classes in de.jstacs.utils used by de.jstacs.classifier
REnvironment This is an environment class for R and Rserve that helps you to handle all things in a more gentle way.

Classes in de.jstacs.utils used by de.jstacs.classifier.assessment
ProgressUpdater Interface for supervising the progress of long time processes like cross validation.

Classes in de.jstacs.utils used by de.jstacs.classifier.scoringFunctionBased
DoubleList A simple list of primitive type `double`.
IntList A simple list of primitive type `int`.
SafeOutputStream This class is for any output.

Classes in de.jstacs.utils used by de.jstacs.classifier.utils
REnvironment This is an environment class for R and Rserve that helps you to handle all things in a more gentle way.

Classes in de.jstacs.utils used by de.jstacs.data
Pair A very simple container.

Classes in de.jstacs.utils used by de.jstacs.models.discrete.inhomogeneous
REnvironment This is an environment class for R and Rserve that helps you to handle all things in a more gentle way.
SafeOutputStream This class is for any output.

Classes in de.jstacs.utils used by de.jstacs.models.mixture
SafeOutputStream This class is for any output.

Classes in de.jstacs.utils used by de.jstacs.models.mixture.gibbssampling
DoubleList A simple list of primitive type `double`.

Classes in de.jstacs.utils used by de.jstacs.motifDiscovery
ComparableElement This class is a container for any objects that have to be compared.
IntList A simple list of primitive type `int`.
REnvironment This is an environment class for R and Rserve that helps you to handle all things in a more gentle way.
SafeOutputStream This class is for any output.

Classes in de.jstacs.utils used by de.jstacs.parameters
ComparableElement This class is a container for any objects that have to be compared.

Classes in de.jstacs.utils used by de.jstacs.scoringFunctions
DoubleList A simple list of primitive type `double`.
IntList A simple list of primitive type `int`.

Classes in de.jstacs.utils used by de.jstacs.scoringFunctions.directedGraphicalModels
DoubleList A simple list of primitive type `double`.
IntList A simple list of primitive type `int`.

Classes in de.jstacs.utils used by de.jstacs.scoringFunctions.homogeneous
DoubleList A simple list of primitive type `double`.
IntList A simple list of primitive type `int`.

Classes in de.jstacs.utils used by de.jstacs.scoringFunctions.mix
DoubleList A simple list of primitive type `double`.
IntList A simple list of primitive type `int`.

Classes in de.jstacs.utils used by de.jstacs.scoringFunctions.mix.motifSearch
DoubleList A simple list of primitive type `double`.
IntList A simple list of primitive type `int`.

Classes in de.jstacs.utils used by de.jstacs.utils
ComparableElement This class is a container for any objects that have to be compared.
DefaultProgressUpdater Simple class that implements `ProgressUpdater` and prints the percentage of iterations that is already done on the screen.
NullProgressUpdater This class implements a `ProgressUpdater` doing nothing but forces a crossvalidation that is used with an instance of this class to continue to its end.
ProgressUpdater Interface for supervising the progress of long time processes like cross validation.
SafeOutputStream This class is for any output.
Time This interface is the framework for stopping the time of anything.

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