tree/bipartition/functions.hpp

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#ifndef GENESIS_TREE_BIPARTITION_FUNCTIONS_H_
#define GENESIS_TREE_BIPARTITION_FUNCTIONS_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2020 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 "genesis/tree/tree.hpp"
#include "genesis/tree/bipartition/bipartition.hpp"
#include "genesis/utils/math/bitvector.hpp"
 
#include <string>
#include <vector>
 
namespace genesis {
namespace tree {
 
// =================================================================================================
//     Bipartition Helper Functions
// =================================================================================================
 
std::vector<Bipartition> bipartition_set( Tree const& tree );
 
std::vector<size_t> node_to_leaf_map( Tree const& tree );
 
utils::Bitvector leaf_node_bitvector( Tree const& tree, std::vector<TreeNode const*> leaf_nodes );
 
std::vector<size_t> get_subtree_edges( TreeLink const& subtree );
 
Bipartition find_smallest_subtree(
    Tree const& tree,
    std::vector<Bipartition> const& bipartitions,
    std::vector<TreeNode const*> const& nodes
);
 
// =================================================================================================
//     Monophyletic Subtree Functions
// =================================================================================================
 
std::vector<size_t> find_monophyletic_subtree_edges(
    Tree const& tree,
    std::vector<Bipartition> const& bipartitions,
    std::vector<TreeNode const*> const& nodes,
    bool include_splitting_edges = true,
    bool include_leaf_edges = true
);
 
std::vector<size_t> find_monophyletic_subtree_edges(
    Tree const& tree,
    std::vector<TreeNode const*> const& nodes,
    bool include_splitting_edges = true,
    bool include_leaf_edges = true
);
 
std::vector<size_t> find_monophyletic_subtree_edges(
    Tree const& tree,
    std::vector< std::string > const& node_names,
    bool include_splitting_edges = true,
    bool include_leaf_edges = true
);
 
// =================================================================================================
//     Whole Clade Functions
// =================================================================================================
 
std::vector<size_t> get_clade_edges(
    Tree const& tree,
    std::vector< tree::TreeNode const* > const& nodes
);
 
std::vector<size_t> get_clade_edges(
    Tree const& tree,
    std::vector< std::string > const& node_names
);
 
} // namespace tree
} // namespace genesis
 
#endif // include guard