functions/taxonomy.cpp File Reference

#include "genesis/taxonomy/functions/taxonomy.hpp"
#include "genesis/taxonomy/iterator/preorder.hpp"
#include "genesis/taxonomy/printers/nested.hpp"
#include "genesis/utils/core/logging.hpp"
#include "genesis/utils/text/string.hpp"
#include <algorithm>
#include <cassert>
#include <ostream>
#include <stdexcept>
#include <string>
#include <unordered_set>
#include <vector>

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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::taxonomy

Functions
Taxon *	find_taxon_by_id (Taxonomy &tax, std::string const &id)
	Alias for find_taxon_by_id(..., DepthFirstSearch{}). More...
Taxon const *	find_taxon_by_id (Taxonomy const &tax, std::string const &id)
	Alias for find_taxon_by_id(..., DepthFirstSearch{}). More...
Taxon *	find_taxon_by_name (Taxonomy &tax, std::string const &name)
	Alias for find_taxon_by_name(..., DepthFirstSearch{}). More...
Taxon const *	find_taxon_by_name (Taxonomy const &tax, std::string const &name)
	Alias for find_taxon_by_name(..., DepthFirstSearch{}). More...
bool	has_unique_ids (Taxonomy const &tax)
	Return true iff all IDs of the Taxa in the Taxonomy are unique. More...
std::ostream &	operator<< (std::ostream &out, Taxonomy const &tax)
	Print the contents of a Taxonomy, i.e., all nested taxa, up to a limit of 10. More...
void	remove_taxa_at_level (Taxonomy &tax, size_t level)
	Remove all Taxa at a given level of depth in the Taxonomy hierarchy, and all their children. More...
void	sort_by_name (Taxonomy &tax, bool recursive=true, bool case_sensitive=false)
	Sort the Taxa of a Taxonomy by their name. More...
size_t	taxa_count_at_level (Taxonomy const &tax, size_t level)
	Count the number of Taxa at a certain level of depth in the Taxonomy. More...
std::vector< size_t >	taxa_count_levels (Taxonomy const &tax)
	Count the number of Taxa at each level of depth in the Taxonomy. More...
size_t	taxa_count_lowest_levels (Taxonomy const &tax)
	Return the number of lowest level Taxa (i.e., taxa without sub-taxa) in the Taxonomy. More...
std::unordered_map< std::string, size_t >	taxa_count_ranks (Taxonomy const &tax, bool case_sensitive=false)
	Count the number of Taxa in a Taxonomy per rank. More...
size_t	taxa_count_with_rank (Taxonomy const &tax, std::string const &rank, bool case_sensitive=false)
	Count the number of Taxa in a Taxonomy that have a certain rank assigned to them. More...
size_t	taxon_level (Taxon const &taxon)
	Return the level of depth of a given Taxon. More...
size_t	total_taxa_count (Taxonomy const &tax)
	Return the total number of taxa contained in the Taxomony, i.e., the number of (non-unique) names of all children (recursively). More...
bool	validate (Taxonomy const &taxonomy, bool stop_at_first_error=false)
	Validate the internal data structures of a Taxonomy and its child Taxa Taxa. More...