A toolkit for working with phylogenetic data.
v0.20.0
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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...