tree/common_tree/functions.cpp File Reference

Detailed Description

Implementation of Common Tree functions.

Definition in file tree/common_tree/functions.cpp.

#include "genesis/tree/common_tree/functions.hpp"
#include "genesis/tree/common_tree/distances.hpp"
#include "genesis/tree/common_tree/tree.hpp"
#include "genesis/tree/function/functions.hpp"
#include "genesis/tree/function/operators.hpp"
#include "genesis/tree/function/tree_set.hpp"
#include "genesis/tree/iterator/preorder.hpp"
#include "genesis/tree/tree_set.hpp"
#include "genesis/utils/text/string.hpp"
#include <algorithm>
#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::tree

Functions
Tree	average_branch_length_tree (std::vector< Tree > const &tset)
	Return a Tree where the branch lengths are the average of the Trees in the given vector of Trees or TreeSet, given that they all have the same topology. More...
std::vector< double >	branch_lengths (Tree const &tree)
	Get a vector of all branch lengths of a Tree, index by the edge index. More...
double	diameter (Tree const &tree)
	Get the diameter of the tree, i.e., the longest distance between any two nodes, measured using the branch_length. More...
TreeNode *	find_node (Tree &tree, std::string const &name, bool throw_on_failure=false, bool replace_underscores=false)
	Finds a Node, given its name. If not found, nullptr is returned. More...
TreeNode const *	find_node (Tree const &tree, std::string const &name, bool throw_on_failure=false, bool replace_underscores=false)
	Finds a Node, given its name. More...
std::vector< TreeNode * >	find_nodes (Tree &tree, std::vector< std::string > const &node_names, bool throw_on_failure=false, bool replace_underscores=false)
	Find TreeNodes in a Tree, given their name. More...
std::vector< TreeNode const * >	find_nodes (Tree const &tree, std::vector< std::string > const &node_names, bool throw_on_failure=false, bool replace_underscores=false)
	Find TreeNodes in a Tree, given their name. More...
double	height (Tree const &tree)
	Get the height of the tree, i.e., the longest distance from the root to a leaf, measured using the branch_length. More...
double	length (Tree const &tree)
	Get the length of the tree, i.e., the sum of all branch lengths. More...
std::vector< std::string >	node_names (std::vector< Tree > const &tree_set, bool leaves_only=false)
	Returns a set of all TreeNode names of a vector of Trees or a TreeSet. More...
std::vector< std::string >	node_names (Tree const &tree, bool leaves_only=false)
	Returns a list of all TreeNode names of a Tree. More...
void	scale_all_branch_lengths (Tree &tree, double factor=1.0)
	Scale all branch lengths of a Tree by a given factor. More...
void	set_all_branch_lengths (Tree &tree, double length=1.0)
	Set all branch lengths of a Tree to a given value. More...