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A library for working with phylogenetic and population genetic data.
v0.32.0 |
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A library for working with phylogenetic and population genetic data.
v0.32.0 |
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CommonTree functions.
Definition in file tree/common_tree/functions.hpp.
#include <set>#include <string>#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 | |
| 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... | |
1.8.17