Package | Description |
---|---|
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. |
Modifier and Type | Class and Description |
---|---|
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. |
Modifier and Type | Field and Description |
---|---|
static DinucleotideProperty.Smoothing |
DinucleotideProperty.NO_SMOOTHING |
Modifier and Type | Method and Description |
---|---|
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 DinucleotideProperty s 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. |
ArbitrarySequence |
DinucleotideProperty.getPropertyAsSequence(Sequence original,
DinucleotideProperty.Smoothing smoothing)
Computes this dinucleotide property for all overlapping dimers 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) |