A toolkit for working with phylogenetic data.
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tree/function/functions.hpp File Reference
#include "genesis/utils/containers/matrix.hpp"
#include <cstddef>
#include <vector>

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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 degree (TreeNode const &node)
 Return the degree of the node, i.e. how many neighbouring nodes it has. More...
 
size_t edge_count (Tree const &tree)
 Return the number of Edges of a Tree. Same as Tree::edge_count(). More...
 
utils::Matrix< signed char > edge_sides (Tree const &tree)
 Create a Matrix that indiciaces the relative position of the Edges of a Tree, i.e., whether they are on the root side or non-root side. More...
 
size_t inner_edge_count (Tree const &tree)
 Return the number of Edges of a Tree that do not lead to a leaf Node. More...
 
std::vector< size_t > inner_edge_indices (Tree const &tree)
 Get a list of the edge indices of all inner edges, that is, all TreeEdges that do not lead to a leaf TreeNode. More...
 
size_t inner_node_count (Tree const &tree)
 Count the number of inner Nodes. More...
 
std::vector< size_t > inner_node_indices (Tree const &tree)
 Get a list of the node indices of all inner TreeNodes. More...
 
bool is_bifurcating (Tree const &tree, bool strict=false)
 Return whether the Tree is bifurcating. More...
 
bool is_inner (TreeLink const &link)
 Return true iff the node of the given link is an inner node. More...
 
bool is_inner (TreeEdge const &edge)
 Return true iff the secondary node (outwards) of the given edge is an inner node. More...
 
bool is_inner (TreeNode const &node)
 Return whether the node is an inner node. More...
 
bool is_leaf (TreeLink const &link)
 Return true iff the node of the given link is a leaf node. More...
 
bool is_leaf (TreeEdge const &edge)
 Return true iff the secondary node (outwards) of the given edge is a leaf node. More...
 
bool is_leaf (TreeNode const &node)
 Return whether the node is a leaf/tip. More...
 
bool is_root (TreeNode const &node)
 Return whether the node is the root of its Tree. More...
 
bool is_rooted (Tree const &tree)
 Return whether the Tree is rooted, that is, whether the root node has two neighbors. More...
 
size_t leaf_edge_count (Tree const &tree)
 Return the number of Edges of a Tree that lead to a leaf Node. More...
 
std::vector< size_t > leaf_edge_indices (Tree const &tree)
 Get a list of the edge indices of all leaf edges, that is, all TreeEdges that lead to a leaf TreeNode. More...
 
size_t leaf_node_count (Tree const &tree)
 Count the number of leaf Nodes of a Tree. More...
 
std::vector< size_t > leaf_node_indices (Tree const &tree)
 Get a list of the node indices of all leaf TreeNodes. More...
 
TreeNode const & lowest_common_ancestor (TreeNode const &node_a, TreeNode const &node_b)
 Return the lowest common ancestor of two TreeNodes. More...
 
TreeNode & lowest_common_ancestor (TreeNode &node_a, TreeNode &node_b)
 Return the lowest common ancestor of two TreeNodes. More...
 
utils::Matrix< size_t > lowest_common_ancestors (Tree const &tree)
 Return the lowest common ancestor of each pair of TreeNodes for a given tree, in form of a Matrix of their indices. More...
 
size_t max_degree (Tree const &tree)
 Return the highest degree of the Nodes of a Tree. More...
 
size_t node_count (Tree const &tree)
 Return the number of Nodes of a Tree. Same as Tree::node_count(). More...
 
utils::Matrix< signed char > node_root_direction_matrix (Tree const &tree)
 Calculate a Matrix that indicates the nodes on the root side of a given node. More...
 
std::vector< TreeLink const * > path_to_root (TreeNode const &node)
 Helper function that finds all TreeLinks between a given TreeNode and the root of the Tree. More...
 
size_t subtree_max_path_height (Tree const &tree, TreeLink const &link)
 Calculate the height of a subtree, that is, the maximum path length to a leaf of that subtree, measured in edges between the link and the leaf. More...
 
std::vector< size_t > subtree_max_path_heights (Tree const &tree, TreeNode const &node)
 
std::vector< size_t > subtree_max_path_heights (Tree const &tree)
 
size_t subtree_size (Tree const &tree, TreeLink const &link)
 Return the size of the subtree defined by the given TreeLink, measured in number of nodes. More...
 
std::vector< size_t > subtree_sizes (Tree const &tree, TreeNode const &node)
 Calculate the sizes of all subtrees as seen from the given TreeNode. More...
 
std::vector< size_t > subtree_sizes (Tree const &tree)
 Calculate the sizes of all subtrees as seen from the root of the tree. More...