Package | Description |
---|---|
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 | Class and Description |
---|---|
class |
MultiDimensionalArbitrarySequence
This class is for multidimensional arbitrary sequences.
|
class |
MultiDimensionalDiscreteSequence
This class is for multidimensional discrete sequences that can be used, for instance, for phylogenetic footprinting.
|
Modifier and Type | Method and Description |
---|---|
MultiDimensionalSequence<T> |
MultiDimensionalSequence.complement(int start,
int end) |
protected MultiDimensionalSequence<T> |
MultiDimensionalSequence.flatCloneWithoutAnnotation() |
protected abstract MultiDimensionalSequence<T> |
MultiDimensionalSequence.getInstance(SequenceAnnotation[] seqAn,
Sequence... seqs)
Returns a new instance of a
MultiDimensionalSequence with given SequenceAnnotation s and given Sequence s. |
MultiDimensionalSequence<T> |
MultiDimensionalSequence.reverseComplement(int start,
int end) |