Spec
D2Star AFSScoreD2Star computes the inner product of the standardised kmer count vectors.
D2Star computes the inner product of the standardised kmer count vectors.
Extends | AFScore |
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All Extended | AFScore |
Defined in | <seqan/alignment_free.h> |
Signature |
template <>
struct AFScore<D2Star>;
|
Member Function Overview
Member Variable Overview
-
unsigned D2StarAFScore::bgModelOrder
Order of the background model. -
unsigned D2StarAFScore::kmerSize
Size of the kmers. -
CharString D2StarAFScore::outputFile
When specified, all kmerWeights will be written to this file, for every sequence, and for every sequence comparison.
Detailed Description
D2Star can be used for alignment-free sequence comparison, this version calculates the background model on the concatenation of both sequences
References
Reinert, G.; Chew, D.; Sun, F., Waterman, M. S. Alignment-Free Sequence Comparison (I): Statistics and Power. J Comput Biol, 2009.
See Also
Member Functions Detail
AFScore::AFScore(kmerSize, bgModelOrder, verbose);
Constructor
Parameters
kmerSize
|
Size of kmer, unsigned. |
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bgModelOrder
|
Order of the background Markov model, unsigned. |
verbose
|
This option will report progress to standard output, bool. |
Data Races
Thread safety unknown!
Member Variables Detail
unsigned D2StarAFScore::bgModelOrder
Order of the background model.
unsigned D2StarAFScore::kmerSize
Size of the kmers.
CharString D2StarAFScore::outputFile
When specified, all kmerWeights will be written to this file, for every sequence, and for every sequence
comparison.