rf.cpp File Reference

#include "genesis/tree/bipartition/rf.hpp"
#include "genesis/tree/common_tree/tree.hpp"
#include "genesis/tree/function/functions.hpp"
#include "genesis/tree/iterator/postorder.hpp"
#include "genesis/utils/core/algorithm.hpp"
#include <cstdint>
#include <algorithm>
#include <cassert>
#include <stdexcept>
#include <limits>

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::tree

Functions
size_t	rf_distance_absolute (Tree const &lhs, Tree const &rhs)
	Compute the absolute RF (Robinson-Foulds) distance metric between two Trees. More...
std::vector< size_t >	rf_distance_absolute (Tree const &lhs, TreeSet const &rhs)
	Compute the absolute RF (Robinson-Foulds) distance metric between a given lhs Tree and all of the trees in the rhs TreeSet. More...
utils::Matrix< size_t >	rf_distance_absolute (TreeSet const &trees)
	Compute the pairwise absolute RF (Robinson-Foulds) distance metric between a set of trees. More...
double	rf_distance_relative (Tree const &lhs, Tree const &rhs)
	Compute the relative RF (Robinson-Foulds) distance metric between two Trees. More...
std::vector< double >	rf_distance_relative (Tree const &lhs, TreeSet const &rhs)
	Compute the relative RF (Robinson-Foulds) distance metric between a given lhs Tree and all of the trees in the rhs TreeSet. More...
utils::Matrix< double >	rf_distance_relative (TreeSet const &trees)
	Compute the pairwise relative RF (Robinson-Foulds) distance metric between a set of trees. More...
std::vector< utils::Bitvector >	rf_get_bitvectors (Tree const &tree, std::unordered_map< std::string, size_t > const &names)
	Get all split Bitvectors for a given Tree. More...
template<typename BitvectorProcessor >
void	rf_get_bitvectors_template (Tree const &tree, std::unordered_map< std::string, size_t > const &names, BitvectorProcessor const &process_bitvector)
	Local helper function template that constructs all bitvectors for the splits of a tree, but allows to customize what to do with them once constructed. More...
std::unordered_map< utils::Bitvector, utils::Bitvector >	rf_get_occurrences (Tree const &lhs, Tree const &rhs)
	Get an occurrence map for each split found in two trees. More...
std::unordered_map< utils::Bitvector, utils::Bitvector >	rf_get_occurrences (Tree const &lhs, TreeSet const &rhs)
	Get an occurrence map for each split found in some Trees. More...
std::unordered_map< utils::Bitvector, utils::Bitvector >	rf_get_occurrences (TreeSet const &trees)
	Get an occurrence map for each split found in the given TreeSet. More...
std::unordered_map< std::string, size_t >	rf_taxon_name_map (Tree const &tree)
	Get a mapping from taxon names to unique IDs. More...