taxonomy/functions/tree.hpp

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#ifndef GENESIS_TAXONOMY_FUNCTIONS_TREE_H_
#define GENESIS_TAXONOMY_FUNCTIONS_TREE_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2019 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 <string>
#include <unordered_map>
 
namespace genesis {
namespace taxonomy {
 
// =================================================================================================
//     Forwad Declarations
// =================================================================================================
 
class Taxon;
class Taxonomy;
class Taxopath;
 
// =================================================================================================
//     Tree
// =================================================================================================
 
tree::Tree taxonomy_to_tree(
    Taxonomy const& taxonomy,
    bool keep_singleton_inner_nodes = false,
    bool keep_inner_node_names = false,
    int  max_level = -1
);
 
tree::Tree taxonomy_to_tree(
    Taxonomy const& taxonomy,
    std::unordered_map<std::string, Taxopath> const& extra_taxa,
    bool keep_singleton_inner_nodes = false,
    bool keep_inner_node_names = false,
    int  max_level = -1,
    bool add_extra_taxa_parents = true
);
 
tree::Tree taxonomy_to_tree(
    std::unordered_map<std::string, Taxopath> const& taxon_map,
    bool keep_singleton_inner_nodes = false,
    bool keep_inner_node_names = false,
    int  max_level = -1
);
 
} // namespace taxonomy
} // namespace genesis
 
#endif // include guard