See: Description
Interface  Description 

ProgressUpdater  Deprecated 
Class  Description 

ComparableElement<E,C extends Comparable> 
This class is a container for any objects that have to be compared.

Compression 
Class for compressing and decompressing
String s
using ZIP. 
DefaultProgressUpdater 
Simple class that implements
ProgressUpdater and prints the
percentage of iterations that is already done on the screen. 
DiscreteInhomogenousDataSetEmitter 
Emits
DataSet s 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 . 
LargeSequenceReader 
Class for reading large DNA sequences (e.g.

NiceScale 
Class for creating nive tick marks on axes given a minimum and maximum value.

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 KullbackLeiblerdivergence.

PFMComparator.UniformBorderWrapper 
Wraps a given
PFMComparator.PFMDistance and pads the considered PFMs with uniformly distributed positions. 
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  
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 . 
SeqLogoPlotter.SeqLogoPlotGenerator 
PlotGeneratorResult.PlotGenerator for plotting sequence logos. 
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 
Utilityclass with static methods to
find all subclasses of a certain class (or interface) within the scope
of the current classloader
find all subclasses of a certain class (or interface) within the scope
of the current classloader 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  Description 

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