rf.hpp

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#ifndef GENESIS_TREE_BIPARTITION_RF_H_
#define GENESIS_TREE_BIPARTITION_RF_H_

/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2019 Lucas Czech

    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/tree_set.hpp"
#include "genesis/utils/containers/matrix.hpp"
#include "genesis/utils/math/bitvector.hpp"

#include <string>
#include <unordered_map>
#include <unordered_set>
#include <vector>
#include <utility>

namespace genesis {
namespace tree {

// =================================================================================================
//     Helper Functions
// =================================================================================================

std::unordered_map<std::string, size_t> rf_taxon_name_map( Tree const& tree );

std::vector<utils::Bitvector> rf_get_bitvectors(
    Tree const& tree,
    std::unordered_map<std::string, size_t> const& names
);

std::unordered_map<utils::Bitvector, utils::Bitvector> rf_get_occurrences(
    TreeSet const& trees
);

std::unordered_map<utils::Bitvector, utils::Bitvector> rf_get_occurrences(
    Tree const& lhs,
    TreeSet const& rhs
);

std::unordered_map<utils::Bitvector, utils::Bitvector> rf_get_occurrences(
    Tree const& lhs,
    Tree const& rhs
);

// =================================================================================================
//     Absolute RF Distance Functions
// =================================================================================================

utils::Matrix<size_t> rf_distance_absolute( TreeSet const& trees );

std::vector<size_t> rf_distance_absolute( Tree const& lhs, TreeSet const& rhs );

size_t rf_distance_absolute( Tree const& lhs, Tree const& rhs );

// =================================================================================================
//     Relative RF Distance Functions
// =================================================================================================

utils::Matrix<double> rf_distance_relative( TreeSet const& trees );

std::vector<double> rf_distance_relative( Tree const& lhs, TreeSet const& rhs );

double rf_distance_relative( Tree const& lhs, Tree const& rhs );

} // namespace tree
} // namespace genesis

#endif // include guard