tree/common_tree/distances.cpp File Reference

Detailed Description

Implementation of CommonTree distance methods.

Definition in file tree/common_tree/distances.cpp.

#include "genesis/tree/common_tree/distances.hpp"
#include "genesis/tree/function/functions.hpp"
#include "genesis/tree/function/lca_lookup.hpp"
#include "genesis/tree/iterator/levelorder.hpp"
#include "genesis/tree/iterator/preorder.hpp"
#include "genesis/tree/tree.hpp"
#include "genesis/utils/containers/matrix/operators.hpp"
#include <algorithm>
#include <cassert>
#include <stdexcept>
#include <vector>

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
std::vector< std::pair< TreeNode const *, double > >	closest_leaf_distance_vector (Tree const &tree)
	Return a vector containing the closest leaf node for each node, using the branch_length as distance measure. More...
std::vector< std::pair< TreeNode const *, double > >	closest_leaf_distance_vector (Tree const &tree, utils::Matrix< double > const &node_distances)
double	deepest_distance (Tree const &tree)
	Return the longest distance from any point in the tree (on the edges) to any leaf. More...
utils::Matrix< double >	edge_branch_length_distance_matrix (Tree const &tree)
std::vector< double >	edge_branch_length_distance_vector (Tree const &tree, TreeEdge const *edge)
std::vector< std::pair< TreeNode const *, double > >	furthest_leaf_distance_vector (Tree const &tree)
	Opposite of closest_leaf_distance_vector(). More...
std::vector< std::pair< TreeNode const *, double > >	furthest_leaf_distance_vector (Tree const &tree, utils::Matrix< double > const &node_distances)
template<class Comparator >
std::vector< std::pair< TreeNode const *, double > >	leaf_distance_vector (Tree const &tree, utils::Matrix< double > const &node_distances, Comparator comp)
	Local helper function to calculate either closest_leaf_distance_vector() or furthest_leaf_distance_vector(). More...
utils::Matrix< double >	node_branch_length_distance_matrix (Tree const &tree)
	Return a distance matrix containing pairwise distances between all Nodes, using the branch_length of the Edges as distance measurement. More...
std::vector< double >	node_branch_length_distance_vector (Tree const &tree, TreeNode const *node=nullptr)
	Return a vector containing the distance of all nodes with respect to the given start node, where distance is measured in the sum of branch lengths between the nodes. More...