Uses of Class
de.jstacs.data.DinucleotideProperty.Smoothing

Packages that use DinucleotideProperty.Smoothing

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.

Uses of DinucleotideProperty.Smoothing in de.jstacs.data

Subclasses of DinucleotideProperty.Smoothing in de.jstacs.data

static class	DinucleotideProperty.MeanSmoothing Smoothing by mean using a pre-defined window width.
static class	DinucleotideProperty.MedianSmoothing Smoothing by median using a pre-defined window width.
static class	DinucleotideProperty.NoSmoothing Implementation of DinucleotideProperty.Smoothing that conducts no smoothing.

Fields in de.jstacs.data declared as DinucleotideProperty.Smoothing

static DinucleotideProperty.Smoothing

DinucleotideProperty.NO_SMOOTHING

Methods in de.jstacs.data with parameters of type DinucleotideProperty.Smoothing

static DataSet	DinucleotideProperty.getDataSetForProperty(DataSet original, DinucleotideProperty.Smoothing smoothing, boolean addToAnnotation, DinucleotideProperty... properties) Creates a new DataSet by converting each Sequence in original to the DinucleotidePropertys properties and adding or setting these as ReferenceSequenceAnnotation of each original sequence.
static DataSet	DinucleotideProperty.getDataSetForProperty(DataSet original, DinucleotideProperty.Smoothing smoothing, boolean originalAsAnnotation, DinucleotideProperty property) Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty property using the DinucleotideProperty.Smoothing smoothing.
double[]	DinucleotideProperty.getProperty(Sequence original, DinucleotideProperty.Smoothing smoothing) Computes this dinucleotide property for all overlapping twomers in original, smoothes the result using smoothing, and returns the smoothed property as a double array.
Sequence	DinucleotideProperty.getPropertyAsSequence(Sequence original, DinucleotideProperty.Smoothing smoothing) Computes this dinucleotide property for all overlapping twomers in original, smoothes the result using smoothing, and returns the smoothed property as a Sequence.
static ImageResult	DinucleotideProperty.getPropertyImage(DataSet original, DinucleotideProperty prop, DinucleotideProperty.Smoothing smoothing, REnvironment re, int xLeft, String pltOptions, int width, int height)
static ImageResult	DinucleotideProperty.getPropertyImage(Sequence original, DinucleotideProperty prop, DinucleotideProperty.Smoothing smoothing, REnvironment re, int xLeft, String pltOptions, int width, int height)