taxonomy/functions/tree.cpp File Reference

#include "genesis/taxonomy/functions/tree.hpp"
#include "genesis/taxonomy/taxon.hpp"
#include "genesis/taxonomy/taxonomy.hpp"
#include "genesis/taxonomy/taxopath.hpp"
#include "genesis/taxonomy/formats/taxopath_generator.hpp"
#include "genesis/taxonomy/functions/taxonomy.hpp"
#include "genesis/taxonomy/functions/taxopath.hpp"
#include "genesis/taxonomy/iterator/preorder.hpp"
#include "genesis/tree/tree.hpp"
#include "genesis/tree/formats/newick/broker.hpp"
#include "genesis/tree/formats/newick/element.hpp"
#include "genesis/tree/formats/newick/reader.hpp"
#include "genesis/tree/common_tree/newick_reader.hpp"
#include <cassert>
#include <stdexcept>

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::taxonomy

Functions
static void	add_subtaxonomy_ (Taxonomy const &taxonomy, bool keep_singleton_inner_nodes, bool keep_inner_node_names, int max_level, int parent_level, tree::NewickBroker &broker)
	Recursive local helper function to add taxa to the tree broker. More...
tree::Tree	taxonomy_to_tree (std::unordered_map< std::string, Taxopath > const &taxon_map, bool keep_singleton_inner_nodes=false, bool keep_inner_node_names=false, int max_level=-1)
	Turn a list of Taxa into a (possibly multifurcating) Tree. More...
tree::Tree	taxonomy_to_tree (Taxonomy const &taxonomy, bool keep_singleton_inner_nodes=false, bool keep_inner_node_names=false, int max_level=-1)
	Turn a Taxonomy into a (possibly multifurcating) Tree. More...
tree::Tree	taxonomy_to_tree (Taxonomy const &taxonomy, std::unordered_map< std::string, Taxopath > const &extra_taxa, bool keep_singleton_inner_nodes=false, bool keep_inner_node_names=false, int max_level=-1, bool add_extra_taxa_parents=true)
	Turn a Taxonomy into a (possibly multifurcating) Tree, and allow to add extra tips to it. More...