sequence/functions/stats.cpp File Reference

#include "genesis/sequence/functions/stats.hpp"
#include "genesis/sequence/counts.hpp"
#include "genesis/sequence/functions/functions.hpp"
#include "genesis/sequence/sequence_set.hpp"
#include "genesis/sequence/sequence.hpp"
#include "genesis/utils/tools/char_lookup.hpp"
#include <array>
#include <cassert>

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

Functions
std::map< char, double >	base_frequencies (Sequence const &seq, std::string const &plain_chars)
	Get the base frequencies of the sites in a Sequence given the base chars. More...
std::map< char, double >	base_frequencies (SequenceSet const &set, std::string const &plain_chars)
	Get the base frequencies of the sites in a SequenceSet given the base chars. More...
static std::map< char, double >	base_frequencies_accumulator (std::map< char, size_t > const &sitehistogram, std::string const &plain_chars)
	Local helper function that turns a site histogram into base frequencies. More...
size_t	count_chars (SequenceSet const &set, std::string const &chars)
	Count the number of occurrences of the given chars within the sites of the SequenceSet. More...
size_t	gap_site_count (SiteCounts const &counts)
double	gapyness (SequenceSet const &set, std::string const &gap_chars)
	Return the "gapyness" of the Sequences, i.e., the proportion of gap chars and other completely undetermined chars to the total length of all sequences. More...
std::map< char, size_t >	site_histogram (Sequence const &seq)
	Get a histogram of the occurrences of particular sites, given a Sequence. More...
std::map< char, size_t >	site_histogram (SequenceSet const &set)
	Get a histogram of the occurrences of particular sites, given a SequenceSet. More...