Uses of Package
de.jstacs.utils

Packages that use de.jstacs.utils

Package	Description
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. 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.utils	Provides some useful classes for working with classifiers.
de.jstacs.clustering.distances
de.jstacs.clustering.hierachical
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.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 DifferentiableStatisticalModels, which can compute the gradient with respect to their parameters for a given input Sequence.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels	Provides DifferentiableStatisticalModels that are directed graphical models.
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous	Provides DifferentiableStatisticalModels that are homogeneous, i.e.
de.jstacs.sequenceScores.statisticalModels.differentiable.localMixture
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture	Provides DifferentiableSequenceScores that are mixtures of other DifferentiableSequenceScores.
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

Class and Description
Time This interface is the framework for stopping the time of anything.

Classes in de.jstacs.utils used by de.jstacs.algorithms.optimization.termination

Class and Description
Time This interface is the framework for stopping the time of anything.

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

Class and Description
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

Class and Description
ProgressUpdater Deprecated.

Classes in de.jstacs.utils used by de.jstacs.classifiers.differentiableSequenceScoreBased

Class and Description
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

Class and Description
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.clustering.distances

Class and Description
Pair A very simple container.

Classes in de.jstacs.utils used by de.jstacs.clustering.hierachical

Class and Description
IntList A simple list of primitive type int.

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

Class and Description
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

Class and Description
ComparableElement This class is a container for any objects that have to be compared.
DoubleList A simple list of primitive type double.
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

Class and Description
ComparableElement This class is a container for any objects that have to be compared.

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

Class and Description
DoubleList A simple list of primitive type double.

Classes in de.jstacs.utils used by de.jstacs.sequenceScores.differentiable

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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.localMixture

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
SafeOutputStream This class is for any output.

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

Class and Description
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.
Pair A very simple container.
PFMComparator.PFMDistance This interface declares a method for comparing different PFMs.
ProgressUpdater Deprecated.
SafeOutputStream This class is for any output.
Time This interface is the framework for stopping the time of anything.
ToolBox.TiedRanks Handling of tied ranks in ToolBox.rank(double[], TiedRanks).