A toolkit for working with phylogenetic data.
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manipulation.hpp
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1 #ifndef GENESIS_TREE_FUNCTION_MANIPULATION_H_
2 #define GENESIS_TREE_FUNCTION_MANIPULATION_H_
3 
4 /*
5  Genesis - A toolkit for working with phylogenetic data.
6  Copyright (C) 2014-2018 Lucas Czech and HITS gGmbH
7 
8  This program is free software: you can redistribute it and/or modify
9  it under the terms of the GNU General Public License as published by
10  the Free Software Foundation, either version 3 of the License, or
11  (at your option) any later version.
12 
13  This program is distributed in the hope that it will be useful,
14  but WITHOUT ANY WARRANTY; without even the implied warranty of
15  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16  GNU General Public License for more details.
17 
18  You should have received a copy of the GNU General Public License
19  along with this program. If not, see <http://www.gnu.org/licenses/>.
20 
21  Contact:
22  Lucas Czech <lucas.czech@h-its.org>
23  Exelixis Lab, Heidelberg Institute for Theoretical Studies
24  Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
25 */
26 
34 #include <cstddef> // size_t
35 
36 namespace genesis {
37 namespace tree {
38 
39 // =================================================================================================
40 // Forward Declarations
41 // =================================================================================================
42 
43 class Tree;
44 class TreeNode;
45 class TreeEdge;
46 class TreeLink;
47 
48 // =================================================================================================
49 // Add single Nodes
50 // =================================================================================================
51 
84 TreeEdge& add_new_node( Tree& tree, TreeNode& target_node );
85 
106 TreeNode& add_new_node( Tree& tree, TreeEdge& target_edge );
107 
132 TreeEdge& add_new_leaf_node( Tree& tree, TreeEdge& target_edge );
133 
140 TreeNode& add_root_node( Tree& tree, TreeEdge& target_edge );
141 
142 // =================================================================================================
143 // Rerooting
144 // =================================================================================================
145 
174 void reroot( Tree& tree, TreeLink& at_link );
175 
183 void reroot( Tree& tree, TreeNode& at_node );
184 
192 void reroot_at_node( Tree& tree, size_t node_index );
193 
194 // =================================================================================================
195 // Ladderize
196 // =================================================================================================
197 
198 enum class LadderizeOrder
199 {
200  kSmallFirst,
202 };
203 
204 void ladderize( Tree& tree, LadderizeOrder order = LadderizeOrder::kSmallFirst );
205 
206 } // namespace tree
207 } // namespace genesis
208 
209 #endif // include guard
TreeEdge & add_new_node(Tree &tree, TreeNode &target_node)
Add a new Node as a leaf to an existing Node.
TreeEdge & add_new_leaf_node(Tree &tree, TreeEdge &target_edge)
Add a new Node as a leaf to an existing Edge, by also adding a new Node in the middle of that Edge...
void reroot(Tree &tree, TreeLink &at_link)
Reroot the Tree at the given TreeLink.
void reroot_at_node(Tree &tree, size_t node_index)
Reroot the Tree at the TreeNode with the given index.
void ladderize(Tree &tree, LadderizeOrder order)
TreeNode & add_root_node(Tree &tree, TreeEdge &target_edge)
Add a new Node that splits an existing Edge, and root the tree on that new Node.