phylo_factor.hpp

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#ifndef GENESIS_TREE_MASS_TREE_PHYLO_FACTOR_H_
#define GENESIS_TREE_MASS_TREE_PHYLO_FACTOR_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2024 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/mass_tree/balances.hpp"
#include "genesis/utils/containers/matrix.hpp"
 
#include <functional>
#include <unordered_set>
#include <vector>
 
namespace genesis {
namespace tree {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
class Subtree;
class Tree;
using MassTree = Tree;
 
// =================================================================================================
//     Phylogenetic Factorization
// =================================================================================================
 
using PhyloFactorObjectiveFunction = std::function<
    double( size_t iteration, size_t edge_index, std::vector<double> const& balances )
>;
 
struct PhyloFactor
{
    size_t                     edge_index;
 
    std::unordered_set<size_t> edge_indices_primary;
 
    std::unordered_set<size_t> edge_indices_secondary;
 
    std::vector<double>        balances;
 
    double                     objective_value;
 
    std::vector<double>        all_objective_values;
};
 
std::unordered_set<size_t> phylo_factor_subtree_indices(
    Subtree const& subtree,
    std::unordered_set<size_t> const& candidate_edges
);
 
PhyloFactor phylo_factor_find_best_edge(
    size_t iteration,
    BalanceData const& data,
    std::unordered_set<size_t> const& candidate_edges,
    PhyloFactorObjectiveFunction objective
);
 
std::vector<PhyloFactor> phylogenetic_factorization(
    BalanceData const& data,
    std::function<double( std::vector<double> const& balances )> objective,
    size_t max_iterations = 0,
    std::function<void( size_t iteration, size_t max_iterations )> log_progress = {}
);
 
std::vector<PhyloFactor> phylogenetic_factorization(
    BalanceData const& data,
    PhyloFactorObjectiveFunction objective,
    size_t max_iterations = 0,
    std::function<void( size_t iteration, size_t max_iterations )> log_progress = {}
);
 
} // namespace tree
} // namespace genesis
 
#endif // include guard