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. |
de.jstacs.data.sequences |
Provides classes for representing sequences.
The implementations of sequences currently include DiscreteSequence s prepared for alphabets of different sizes, and ArbitrarySequence s that may
contain continuous values as well.As sub-package provides the facilities to annotate Sequence s. |
Modifier and Type | Method and Description |
---|---|
ArbitrarySequence |
DinucleotideProperty.getPropertyAsSequence(Sequence original)
Computes this dinucleotide property for all overlapping dimers in
original
and returns the result as a Sequence of length original.getLength()-1 |
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 . |
Modifier and Type | Method and Description |
---|---|
protected ArbitrarySequence |
ArbitrarySequence.flatCloneWithoutAnnotation() |
Constructor and Description |
---|
MultiDimensionalArbitrarySequence(SequenceAnnotation[] seqAn,
ArbitrarySequence... sequence)
This constructor creates an
MultiDimensionalDiscreteSequence from a set of individual Sequence s. |