de.jstacs.data

Class DeBruijnGraphSequenceGenerator

java.lang.Object

de.jstacs.data.DeBruijnGraphSequenceGenerator

public class DeBruijnGraphSequenceGenerator
extends Object

Class for creating De Bruin sequences using explicit De Bruijn graphs.

Author:

Jan Grau

Constructor Summary

Constructors

Constructor and Description
DeBruijnGraphSequenceGenerator()

Method Summary

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

DeBruijnGraphSequenceGenerator

public DeBruijnGraphSequenceGenerator()

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 - if the sequence for this alphabet could not be created

WrongSequenceTypeException - if the sequence could not be created

generate

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

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 - if the sequence for this alphabet could not be created