taxonomy/functions/taxonomy.hpp File Reference

#include "genesis/taxonomy/taxon.hpp"
#include "genesis/taxonomy/taxonomy.hpp"
#include <functional>
#include <iosfwd>
#include <string>
#include <unordered_map>
#include <vector>
#include <queue>

Go to the source code of this file.

Classes
struct	BreadthFirstSearch
	Tag used for find_taxon(). More...
struct	DepthFirstSearch
	Tag used for find_taxon(). More...

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

Typedefs
using	BFS = BreadthFirstSearch
	Alias for BreadthFirstSearch. More...
using	DFS = DepthFirstSearch
	Alias for DepthFirstSearch. More...

Functions
template<class UnaryPredicate >
Taxon *	find_taxon (Taxonomy &tax, UnaryPredicate p)
	Alias for find_taxon(..., DepthFirstSearch{}) More...
template<class SearchStrategy , class UnaryPredicate >
Taxon *	find_taxon (Taxonomy &tax, UnaryPredicate p, SearchStrategy strat)
	Find a Taxon based on a given predicate by recursively searching the Taxonomy according to a search strategy. More...
template<class UnaryPredicate >
Taxon const *	find_taxon (Taxonomy const &tax, UnaryPredicate p)
	Alias for find_taxon(..., DepthFirstSearch{}) More...
template<class UnaryPredicate >
Taxon const *	find_taxon (Taxonomy const &tax, UnaryPredicate p, BreadthFirstSearch)
	Find a Taxon based on a given predicate by recursively searching the Taxonomy in a breadth first manner. More...
template<class UnaryPredicate >
Taxon const *	find_taxon (Taxonomy const &tax, UnaryPredicate p, DepthFirstSearch)
	Find a Taxon based on a given predicate by recursively searching the Taxonomy in a depth first manner. More...
Taxon *	find_taxon_by_id (Taxonomy &tax, std::string const &id)
	Alias for find_taxon_by_id(..., DepthFirstSearch{}). More...
template<class SearchStrategy >
Taxon *	find_taxon_by_id (Taxonomy &tax, std::string const &id, SearchStrategy strat)
	Find a Taxon with a given ID by recursively searching the Taxonomy according to a search strategy. More...
Taxon const *	find_taxon_by_id (Taxonomy const &tax, std::string const &id)
	Alias for find_taxon_by_id(..., DepthFirstSearch{}). More...
template<class SearchStrategy >
Taxon const *	find_taxon_by_id (Taxonomy const &tax, std::string const &id, SearchStrategy strat)
	Find a Taxon with a given ID by recursively searching the Taxonomy according to a search strategy. More...
Taxon *	find_taxon_by_name (Taxonomy &tax, std::string const &name)
	Alias for find_taxon_by_name(..., DepthFirstSearch{}). More...
template<class SearchStrategy >
Taxon *	find_taxon_by_name (Taxonomy &tax, std::string const &name, SearchStrategy strat)
	Find a Taxon with a given name by recursively searching the Taxonomy according to a search strategy. More...
Taxon const *	find_taxon_by_name (Taxonomy const &tax, std::string const &name)
	Alias for find_taxon_by_name(..., DepthFirstSearch{}). More...
template<class SearchStrategy >
Taxon const *	find_taxon_by_name (Taxonomy const &tax, std::string const &name, SearchStrategy strat)
	Find a Taxon with a given name by recursively searching the Taxonomy according to a search strategy. 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...