Uses of Class
de.jstacs.data.sequences.CyclicSequenceAdaptor

Packages that use CyclicSequenceAdaptor

Package	Description
de.jstacs.clustering.distances
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 DiscreteSequences prepared for alphabets of different sizes, and ArbitrarySequences that may contain continuous values as well. As sub-package provides the facilities to annotate Sequences.

Uses of CyclicSequenceAdaptor in de.jstacs.clustering.distances

Fields in de.jstacs.clustering.distances declared as CyclicSequenceAdaptor

Modifier and Type	Field and Description
protected CyclicSequenceAdaptor[]	SequenceScoreDistance.seqs The De Bruijn sequences

Methods in de.jstacs.clustering.distances that return CyclicSequenceAdaptor

Modifier and Type	Method and Description
static CyclicSequenceAdaptor[]	RandomSequenceScoreDistance.createSequences(DiscreteAlphabet alphabet, int n) Creates a new random sequence of the given length and alphabet.

Methods in de.jstacs.clustering.distances with parameters of type CyclicSequenceAdaptor

Modifier and Type	Method and Description
static double[][]	DeBruijnMotifComparison.getProfilesForMotif(CyclicSequenceAdaptor[] ad, StatisticalModel model, boolean revcom, boolean exp) Returns the score profile on a De Bruin sequence for a De Bruijn sequence.

Constructors in de.jstacs.clustering.distances with parameters of type CyclicSequenceAdaptor

Constructor and Description
SequenceScoreDistance(CyclicSequenceAdaptor[] seqs, boolean exp) Creates a new distance for a given set of sequences.

Uses of CyclicSequenceAdaptor in de.jstacs.data

Methods in de.jstacs.data that return CyclicSequenceAdaptor

Modifier and Type	Method and Description
static CyclicSequenceAdaptor[]	DeBruijnSequenceGenerator.generate(DiscreteAlphabet alphabet, int n) Generates a De Bruijn sequence of length , where A denotes the alphabet.
static CyclicSequenceAdaptor[]	DeBruijnGraphSequenceGenerator.generate(DiscreteAlphabet alphabet, int n) Generates a De Bruijn sequence of length , where A denotes the alphabet.
static CyclicSequenceAdaptor	DeBruijnSequenceGenerator.generate(DiscreteAlphabet alphabet, int n, int alphabetShift) Generates a De Bruijn sequence using the supplied alphabet and the given alphabet shift, i.e., for a cyclic shift of the symbols of the alphabet.
static CyclicSequenceAdaptor	DeBruijnGraphSequenceGenerator.generate(DiscreteAlphabet alphabet, int n, int alphabetShift) Generates a De Bruijn sequence using the supplied alphabet and the given alphabet shift, i.e., for a cyclic shift of the symbols of the alphabet.

Uses of CyclicSequenceAdaptor in de.jstacs.data.sequences

Methods in de.jstacs.data.sequences that return CyclicSequenceAdaptor

Modifier and Type	Method and Description
CyclicSequenceAdaptor<T>	CyclicSequenceAdaptor.complement()
CyclicSequenceAdaptor<T>	CyclicSequenceAdaptor.complement(int start, int end)
protected CyclicSequenceAdaptor<T>	CyclicSequenceAdaptor.flatCloneWithoutAnnotation()
CyclicSequenceAdaptor<T>	CyclicSequenceAdaptor.getSuperSequence(int length) Returns a new cyclic sequence using the internal sequence of this CyclicSequenceAdaptor but with the supplied virtual length
CyclicSequenceAdaptor<T>	CyclicSequenceAdaptor.reverse(int start, int end)
CyclicSequenceAdaptor<T>	CyclicSequenceAdaptor.reverseComplement()
CyclicSequenceAdaptor<T>	CyclicSequenceAdaptor.reverseComplement(int start, int end)