de.jstacs.data

Class DeBruijnSequenceGenerator

java.lang.Object

de.jstacs.data.DeBruijnSequenceGenerator

public class DeBruijnSequenceGenerator
extends Object

Generates De Buijn sequences using the algorithm from Frank Ruskey's Combinatorial Generation.

Author:

Jan Grau

Constructor Summary

Constructors

Constructor and Description
DeBruijnSequenceGenerator()

Method Summary

Methods

Modifier and Type	Method and Description
static CyclicSequenceAdaptor[]	generate(DiscreteAlphabet alphabet, int n) Generates a De Bruijn sequence of length , where A denotes the alphabet.
static CyclicSequenceAdaptor	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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DeBruijnSequenceGenerator

public DeBruijnSequenceGenerator()

Method Detail

generate

public static CyclicSequenceAdaptor[] generate(DiscreteAlphabet alphabet,
                               int n)
                                        throws WrongAlphabetException,
                                               WrongSequenceTypeException

Generates a De Bruijn sequence of length , where A denotes the alphabet.

Parameters:

alphabet - the alphabet

n - the exponent of length length, corresponds to the length of n-mers covered exactly once

Returns:

the sequence (wrapped in an array)

Throws:

WrongAlphabetException - forwarded from IntSequence, should not happen

WrongSequenceTypeException - forwarded from IntSequence, should not happen

generate

public static CyclicSequenceAdaptor generate(DiscreteAlphabet alphabet,
                             int n,
                             int alphabetShift)
                                      throws WrongAlphabetException,
                                             WrongSequenceTypeException

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.

Parameters:

alphabet - the alphabet

n - the length of the covered n-mers

alphabetShift - the alphabet shift (0 equals no shift)

Returns:

the De Bruijn sequence

Throws:

WrongAlphabetException - forwarded from IntSequence, should not happen

WrongSequenceTypeException - forwarded from IntSequence, should not happen