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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 | Provides classes for termination conditions that can be used in algorithms
de.jstacs.classifiers | This package provides the framework for any classifier.
de.jstacs.classifiers.assessment | This package allows to assess classifiers.
de.jstacs.classifiers.differentiableSequenceScoreBased | Provides the classes for `Classifier`s that are based on `SequenceScore`s.
de.jstacs.classifiers.utils | Provides some useful classes for working with classifiers
de.jstacs.data | Provides classes for the representation of data.
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.sampling | This package contains many classes that can be used while a sampling.
de.jstacs.sequenceScores.differentiable |
de.jstacs.sequenceScores.differentiable.logistic |
de.jstacs.sequenceScores.statisticalModels.differentiable | Provides all `DifferentiableStatisticalModel`s, which can compute the gradient with respect to their parameters for a given input `Sequence`.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels | Provides `DifferentiableStatisticalModel`s that are directed graphical models.
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous | Provides `DifferentiableStatisticalModel`s that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture | Provides `DifferentiableSequenceScore`s that are mixtures of other `DifferentiableSequenceScore`s.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous | This package contains various inhomogeneous models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm | The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models | The package provides different implementations of hidden Markov models based on `AbstractHMM`
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states | The package provides all interfaces and classes for states used in hidden Markov models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions | The package provides all interfaces and classes for transitions used in hidden Markov models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements |
de.jstacs.sequenceScores.statisticalModels.trainable.mixture | This package is the super package for any mixture model.
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.classifiers
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.classifiers.assessment
ProgressUpdater Interface for supervising the progress of long time processes like cross validation.

Classes in de.jstacs.utils used by de.jstacs.classifiers.differentiableSequenceScoreBased
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.classifiers.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.
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.motifDiscovery
ComparableElement This class is a container for any objects that have to be compared.
IntList A simple list of primitive type `int`.
Pair A very simple container.
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.sampling
DoubleList A simple list of primitive type `double`.

Classes in de.jstacs.utils used by de.jstacs.sequenceScores.differentiable
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.sequenceScores.differentiable.logistic
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.sequenceScores.statisticalModels.differentiable
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.sequenceScores.statisticalModels.differentiable.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.sequenceScores.statisticalModels.differentiable.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.sequenceScores.statisticalModels.differentiable.mixture
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.sequenceScores.statisticalModels.differentiable.mixture.motif
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.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous
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.sequenceScores.statisticalModels.trainable.hmm
IntList A simple list of primitive type `int`.
Pair A very simple container.
SafeOutputStream This class is for any output.

Classes in de.jstacs.utils used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models
DoubleList A simple list of primitive type `double`.
IntList A simple list of primitive type `int`.
Pair A very simple container.

Classes in de.jstacs.utils used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states
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.sequenceScores.statisticalModels.trainable.hmm.states.emissions
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.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous
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.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete
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.sequenceScores.statisticalModels.trainable.hmm.transitions
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.sequenceScores.statisticalModels.trainable.hmm.transitions.elements
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.sequenceScores.statisticalModels.trainable.mixture
SafeOutputStream This class is for any output.

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.
DoubleList A simple list of primitive type `double`.
IntList A simple list of primitive type `int`.
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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