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 de-compressing
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 Kullback-Leibler-divergence.
|
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 |
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 | Description |
---|---|
ToolBox.TiedRanks |
Handling of tied ranks in
ToolBox.rank(double[], TiedRanks) . |