signatures.hpp File Reference

#include <iosfwd>
#include <string>
#include <vector>

Go to the source code of this file.

Namespaces
	genesis
	Container namespace for all symbols of genesis in order to keep them separate when used as a library.
	genesis::sequence

Functions
std::string	kmer_string_overlapping (Sequence const &sequence, SignatureSpecifications const &settings)
	Return the sequence spitted into overlapping k-mers. More...
void	kmer_string_overlapping (Sequence const &sequence, SignatureSpecifications const &settings, std::ostream &out)
	Print the sequence spitted into overlapping k-mers. More...
std::vector< std::string >	kmer_strings_non_overlapping (Sequence const &sequence, SignatureSpecifications const &settings)
	Return the sequence spitted into a set of non-overlapping k-mers. More...
void	kmer_strings_non_overlapping (Sequence const &sequence, SignatureSpecifications const &settings, std::ostream &out)
	Print the sequence spitted into non-overlapping k-mers. More...
std::vector< size_t >	signature_counts (Sequence const &sequence, SignatureSpecifications const &settings)
	Count the occurences of k-mers in the sequence according to the settings. More...
std::vector< double >	signature_frequencies (Sequence const &sequence, SignatureSpecifications const &settings)
	Calculate the frequencies of occurences of k-mers in the sequence according to the settings. More...
std::vector< double >	signature_frequency_ratios_1 (Sequence const &sequence, SignatureSpecifications const &settings)
	Calculate the ratio 1 signature of a sequence. More...
std::vector< double >	signature_frequency_ratios_2 (Sequence const &sequence, SignatureSpecifications const &settings)
	Calculate the ratio 2 signature of a sequence. More...
std::vector< double >	signature_jensen_shannon (Sequence const &sequence, SignatureSpecifications const &settings)
	Calculate the Jensen-Shannon (JS) signature of a sequence. More...
std::vector< double >	signature_maximal_complementarity_frequencies (Sequence const &sequence, SignatureSpecifications const &settings)
	Calculate the signature of a sequence that uses the maximum frequency of reverse complement k-mers. More...
std::vector< double >	signature_minimal_complementarity_frequencies (Sequence const &sequence, SignatureSpecifications const &settings)
	Calculate the signature of a sequence that uses the minimum frequency of reverse complement k-mers. More...
std::vector< size_t >	signature_ranks (Sequence const &sequence, SignatureSpecifications const &settings)
	Calcuate the rank signature of a sequence according to the settings. More...
std::vector< double >	signature_reverse_identity_frequencies (Sequence const &sequence, SignatureSpecifications const &settings)
	Calculate the signature of a sequence that uses only the frequencies of k-mers whose reverse complement is the k-mer itself. More...
std::vector< size_t >	signature_symmetrized_counts (Sequence const &sequence, SignatureSpecifications const &settings)
	Calcuate the symmetrized counts of the sequence according to the settings. More...
std::vector< double >	signature_symmetrized_frequencies (Sequence const &sequence, SignatureSpecifications const &settings)
	Calcuate the symmetrized counts of the sequence according to the settings. More...
std::vector< size_t >	signature_symmetrized_ranks (Sequence const &sequence, SignatureSpecifications const &settings)
	Calcuate the symmetrized rank signature of a sequence according to the settings. More...