A toolkit for working with phylogenetic data.
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tree/default/distances.hpp
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1 #ifndef GENESIS_TREE_DEFAULT_DISTANCES_H_
2 #define GENESIS_TREE_DEFAULT_DISTANCES_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 <vector>
35 
38 
39 namespace genesis {
40 namespace tree {
41 
42 // =================================================================================================
43 // Branch Distance Measures
44 // =================================================================================================
45 
52 utils::Matrix<double> node_branch_length_distance_matrix(
53  Tree const& tree
54 );
55 
66 std::vector<double> node_branch_length_distance_vector(
67  Tree const& tree,
68  TreeNode const* node = nullptr
69 );
70 
71 utils::Matrix<double> edge_branch_length_distance_matrix(
72  Tree const& tree
73 );
74 
75 std::vector<double> edge_branch_length_distance_vector(
76  Tree const& tree,
77  TreeEdge const* edge = nullptr
78 );
79 
80 // =================================================================================================
81 // Complex Distance Methods
82 // =================================================================================================
83 
87 double deepest_distance( Tree const& tree );
88 
100 std::vector<std::pair< TreeNode const*, double>> closest_leaf_distance_vector(
101  Tree const& tree
102 );
103 
104 std::vector<std::pair< TreeNode const*, double>> closest_leaf_distance_vector(
105  Tree const& tree,
106  utils::Matrix<double> const& node_branch_length_distance_mat
107 );
108 
112 std::vector<std::pair< TreeNode const*, double>> furthest_leaf_distance_vector(
113  Tree const& tree
114 );
115 
116 std::vector<std::pair< TreeNode const*, double>> furthest_leaf_distance_vector(
117  Tree const& tree,
118  utils::Matrix<double> const& node_branch_length_distance_mat
119 );
120 
121 } // namespace tree
122 } // namespace genesis
123 
124 #endif // include guard
utils::Matrix< double > edge_branch_length_distance_matrix(Tree const &tree)
utils::Matrix< double > node_branch_length_distance_matrix(Tree const &tree)
Return a distance matrix containing pairwise distances between all Nodes, using the branch_length of ...
std::vector< double > edge_branch_length_distance_vector(Tree const &tree, TreeEdge const *edge)
std::vector< std::pair< TreeNode const *, double > > furthest_leaf_distance_vector(Tree const &tree)
Opposite of closest_leaf_distance_vector().
double deepest_distance(Tree const &tree)
Return the longest distance from any point in the tree (on the edges) to any leaf.
std::vector< std::pair< TreeNode const *, double > > closest_leaf_distance_vector(Tree const &tree)
Return a vector containing the closest leaf node for each node, using the branch_length as distance m...
std::vector< double > node_branch_length_distance_vector(Tree const &tree, TreeNode const *node)
Return a vector containing the distance of all nodes with respect to the given start node...