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) 2014-2017 Lucas Czech
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 
110 TreeEdge& add_new_node( Tree& tree, TreeEdge& target_edge );
111 
112 // =================================================================================================
113 // Rerooting
114 // =================================================================================================
115 
144 void reroot( Tree& tree, TreeLink& at_link );
145 
153 void reroot( Tree& tree, TreeNode& at_node );
154 
162 void reroot_at_node( Tree& tree, size_t node_index );
163 
164 // =================================================================================================
165 // Ladderize
166 // =================================================================================================
167 
168 enum class LadderizeOrder
169 {
170  kSmallFirst,
172 };
173 
174 void ladderize( Tree& tree, LadderizeOrder order = LadderizeOrder::kSmallFirst );
175 
176 } // namespace tree
177 } // namespace genesis
178 
179 #endif // include guard
TreeEdge & add_new_node(Tree &tree, TreeNode &target_node)
Add a new Node as a leaf to an existing Node.
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)