tree/common_tree/distances.hpp

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#ifndef GENESIS_TREE_COMMON_TREE_DISTANCES_H_
#define GENESIS_TREE_COMMON_TREE_DISTANCES_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2018 Lucas Czech and HITS gGmbH
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lucas.czech@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/
 
#include <vector>
 
#include "genesis/tree/common_tree/tree.hpp"
#include "genesis/utils/containers/matrix.hpp"
 
namespace genesis {
namespace tree {
 
// =================================================================================================
//     Branch Distance Measures
// =================================================================================================
 
utils::Matrix<double> node_branch_length_distance_matrix(
    Tree const& tree
);
 
std::vector<double> node_branch_length_distance_vector(
    Tree const& tree,
    TreeNode const* node = nullptr
);
 
utils::Matrix<double> edge_branch_length_distance_matrix(
    Tree const& tree
);
 
std::vector<double> edge_branch_length_distance_vector(
    Tree const& tree,
    TreeEdge const* edge = nullptr
);
 
// =================================================================================================
//     Complex Distance Methods
// =================================================================================================
 
double deepest_distance( Tree const& tree );
 
std::vector<std::pair< TreeNode const*, double>> closest_leaf_distance_vector(
    Tree const& tree
);
 
std::vector<std::pair< TreeNode const*, double>> closest_leaf_distance_vector(
    Tree const& tree,
    utils::Matrix<double> const& node_branch_length_distance_mat
);
 
std::vector<std::pair< TreeNode const*, double>> furthest_leaf_distance_vector(
    Tree const& tree
);
 
std::vector<std::pair< TreeNode const*, double>> furthest_leaf_distance_vector(
    Tree const& tree,
    utils::Matrix<double> const& node_branch_length_distance_mat
);
 
} // namespace tree
} // namespace genesis
 
#endif // include guard