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.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 Classifiers that are based on ScoringFunctions. 
de.jstacs.classifier.utils Provides some useful classes for working with classifiers 
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.scoringFunctions Provides ScoringFunctions that can be used in a ScoreClassifier
de.jstacs.scoringFunctions.directedGraphicalModels Provides ScoringFunctions that are equivalent to directed graphical models. 
de.jstacs.scoringFunctions.homogeneous Provides ScoringFunctions that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence 
de.jstacs.scoringFunctions.mix Provides ScoringFunctions that are mixtures of other ScoringFunctions. 
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
SafeOutputStream
          This class is for any output.
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 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
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 that helps you to handle all things in a more gentle way.
 

Classes in de.jstacs.utils used by de.jstacs.models.discrete.inhomogeneous
REnvironment
          This is an environment class for R 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.
REnvironment
          This is an environment class for R 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.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.
Time
          This interface is the framework for stopping the time of anything.