Spec D2Star AFSScore

D2Star computes the inner product of the standardised kmer count vectors.

/*!
 * @class D2StarAFScore D2Star AFSScore
 * 
 * @extends AFScore
 * 
 * @headerfile <seqan/alignment_free.h>
 * 
 * @brief D2Star computes the inner product of the standardised kmer count
 *        vectors.
 * 
 * @signature template <> struct AFScore<D2Star>;
 * 
 * D2Star can be used for alignment-free sequence comparison, this version
 * calculates the background model on the concatenation of both sequences
 * 
 * @section References
 * 
 * Reinert, G.; Chew, D.; Sun, F., Waterman, M. S. Alignment-Free Sequence
 * Comparison (I): Statistics and Power. J Comput Biol, 2009.
 * 
 * @see alignmentFreeComparison
 * 
 * @fn D2StarAFScore::AFScore
 * 
 * @brief Constructor
 * 
 * @signature AFScore::AFScore(kmerSize, bgModelOrder, verbose);
 * 
 * @param[in] kmerSize Size of kmer, <tt>unsigned</tt>.
 * @param[in] bgModelOrder Order of the background Markov model,
 *                         <tt>unsigned</tt>.
 * @param[in] verbose This option will report progress to standard output,
 *                    <tt>bool</tt>.
 * 
 * @var unsigned D2StarAFScore::kmerSize;
 * 
 * @brief Size of the kmers.
 * 
 * @var CharString D2StarAFScore::outputFile;
 * 
 * @brief When specified, all kmerWeights will be written to this file, for
 *        every sequence, and for every sequence comparison.
 * 
 * @var unsigned D2StarAFScore::bgModelOrder;
 * 
 * @brief Order of the background model.
 */