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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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#include "genesis/tree/function/manipulation.hpp"#include "genesis/tree/function/functions.hpp"#include "genesis/tree/function/operators.hpp"#include "genesis/tree/iterator/node_links.hpp"#include "genesis/tree/iterator/preorder.hpp"#include "genesis/tree/tree.hpp"#include "genesis/tree/tree/subtree.hpp"#include "genesis/utils/core/algorithm.hpp"#include "genesis/utils/core/logging.hpp"#include "genesis/utils/core/std.hpp"#include <algorithm>#include <cassert>#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 | |
| TreeNode & | add_new_leaf_node (Tree &tree, TreeEdge &target_edge, std::function< void(TreeEdge &target_edge, TreeEdge &new_edge)> adjust_edges={}) |
| Add a new Node as a leaf to an existing Edge, by also adding a new Node in the middle of that Edge. More... | |
| TreeNode & | add_new_node (Tree &tree, TreeEdge &target_edge, std::function< void(TreeEdge &target_edge, TreeEdge &new_edge)> adjust_edges={}) |
| Add a new Node that splits an existing Edge. More... | |
| TreeNode & | add_new_node (Tree &tree, TreeNode &target_node) |
| Add a new Node as a leaf to an existing Node. More... | |
| void | change_rooting (Tree &tree, TreeLink &at_link) |
| "Reroot" the Tree at the given TreeLink. More... | |
| void | change_rooting (Tree &tree, TreeNode &at_node) |
| Reroot the Tree at the given TreeNode. More... | |
| void | delete_edge (Tree &tree, TreeEdge &target_edge, std::function< void(TreeNode &remaining_node, TreeNode &deleted_node)> adjust_nodes={}) |
| Delete a TreeEdge from a Tree, that is, contract the two TreeNodes at its ends into one TreeNode. More... | |
| template<class T > | |
| static void | delete_from_tree_container_ (T &old_elems, std::vector< size_t > &del_elems) |
| Local helper function template that takes one of the tree element containers and deletes all elements at given indices from it. More... | |
| void | delete_leaf_node (Tree &tree, TreeNode &target_node) |
| Delete a leaf TreeNode. More... | |
| void | delete_linear_node (Tree &tree, TreeNode &target_node, std::function< void(TreeEdge &remaining_edge, TreeEdge &deleted_edge)> adjust_edges={}) |
| Delete a "linear" TreeNode from a Tree, that is, a node with two neighbours. More... | |
| void | delete_node (Tree &tree, TreeNode &target_node) |
| Delete a TreeNode from a Tree. More... | |
| void | delete_subtree (Tree &tree, Subtree const &subtree) |
| Delete a complete Subtree from a Tree. More... | |
| void | delete_zero_branch_length_edges (Tree &tree, bool include_leaf_edges=false) |
| Delete (contract) all branches of a CommonTree that have branch length zero. More... | |
| void | ladderize (Tree &tree, LadderizeOrder order=LadderizeOrder::kSmallFirst) |
| Ladderize a Tree, that is, order its subtrees by size. More... | |
| TreeNode & | make_rooted (Tree &tree, std::function< void(TreeEdge &target_edge, TreeEdge &new_edge)> adjust_edges={}) |
| Root a Tree on the first TreeEdge of its current top level TreeNode. More... | |
| TreeNode & | make_rooted (Tree &tree, TreeEdge &target_edge, std::function< void(TreeEdge &target_edge, TreeEdge &new_edge)> adjust_edges={}) |
| Root a Tree at a given TreeEdge. More... | |
| void | make_unrooted (Tree &tree, std::function< void(TreeEdge &remaining_edge, TreeEdge &deleted_edge)> adjust_edges={}) |
| Unroot a Tree. More... | |
| Tree | minimal_tree_topology () |
| Create a minimal Tree that can be used with manipulation functions such as add_new_node() or add_new_leaf_node() to build a custom tree. More... | |
1.8.17