Package de.jstacs.utils

This package contains a bundle of useful classes and interfaces like ...

See:
Description

Interface Summary

ProgressUpdater

Interface for supervising the progress of long time processes like cross validation.

Class Summary

ComparableElement<E,C extends Comparable>	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.
DiscreteInhomogenousDataSetEmitter	Emits DataSets for discrete inhomogeneous models by a naive implementation.
DoubleArrayComparator	This class implements a Comparator of double arrays.
DoubleList	A simple list of primitive type double.
GUIProgressUpdater	This class implements a ProgressUpdater with a GUI.
IntList	A simple list of primitive type int.
Normalisation	This class can be used for normalisation of any double array or a part of a double array.
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<E1,E2>	A very simple container.
PFMComparator	This class implements a number of methods for the comparison of position frequency matrices (PFMs) as described in the Amadeus paper
PFMComparator.NormalizedEuclideanDistance	This class implements the normalized Euclidean distance.
PFMComparator.OneMinusPearsonCorrelationCoefficient	This class implements the Pearson correlation coefficient.
PFMComparator.PFMDistance	This interface declares a method for comparing different PFMs.
PFMComparator.SymmetricKullbackLeiblerDivergence	This class implements the symmetric Kullback-Leibler-divergence.
RealTime	This is a very simple implementation of Time.
RegExFilterOutputStream	This class allows to filter individual lines that are then passed to an internal OutputStream.
REnvironment	This is an environment class for R and Rserve that helps you to handle all things in a more gentle way.
RUtils	This is a collection of various silly things you can do when accessing Rserve. This class is based on an implementation of Andreas Stephanik and was further developed by Jens Keilwagen.
SafeOutputStream	This class is for any output.
SeqLogoPlotter	Class with static methods for plotting sequence logos of DNA motifs, i.e., position weight matrices defined over a DNAAlphabet.
StationaryDistribution	This class can be used to determine the stationary distribution.
StatisticalModelTester	This class is useful for some test for any (discrete) models.
StatisticalTest	This class enables the user to compute some divergences.
SubclassFinder	Utility-class with static methods to find all sub-classes of a certain class (or interface) within the scope of the current class-loader find all sub-classes of a certain class (or interface) within the scope of the current class-loader that can be instantiated, i.e.
Time	This interface is the framework for stopping the time of anything.
TimeLimitedProgressUpdater	This class is an extension of DefaultProgressUpdater.
ToolBox	This class is a collection of methods which might be useful for the programmer.
UserTime	This is an implementation of Time that uses a native method.

Enum Summary

ToolBox.TiedRanks

Handling of tied ranks in ToolBox.rank(double[], TiedRanks).

Package de.jstacs.utils Description

This package contains a bundle of useful classes and interfaces like ...

• ProgressUpdater: an interface that allows the user to monitor the progress of a process,
• REnvironment: a class that helps to handle a connection to R in a gentle way,
• SafeOutputStream: a class that enables the user to determine whether some output should be written or not
• Time: the abstract class for measuring the time,
• ...