tree/mass_tree/functions.hpp

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#ifndef GENESIS_TREE_MASS_TREE_FUNCTIONS_H_
#define GENESIS_TREE_MASS_TREE_FUNCTIONS_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 <cstddef>
#include <utility>
#include <vector>

namespace genesis {

// =================================================================================================
//     Forward Declarations
// =================================================================================================

namespace utils {

    template<typename T>
    class Matrix;

}

namespace tree {

    class Tree;
    class TreeSet;
    class TreeNode;
    class TreeEdge;

    using MassTree = Tree;

}

namespace tree {

// =================================================================================================
//     Manipulate Masses
// =================================================================================================

MassTree mass_tree_merge_trees(
    MassTree const& lhs,
    MassTree const& rhs,
    double const scaler_lhs = 1.0,
    double const scaler_rhs = 1.0
);

void mass_tree_merge_trees_inplace(
    MassTree& lhs,
    MassTree const& rhs,
    double const scaler_lhs = 1.0,
    double const scaler_rhs = 1.0
);

void mass_tree_clear_masses( MassTree& tree );

void mass_tree_reverse_signs( MassTree& tree );

void mass_tree_scale_masses( MassTree& tree, double factor );

void mass_tree_normalize_masses( MassTree& tree );

void mass_tree_transform_to_unit_branch_lengths( MassTree& tree );

double mass_tree_center_masses_on_branches( MassTree& tree );

double mass_tree_center_masses_on_branches_averaged( MassTree& tree );

double mass_tree_binify_masses( MassTree& tree, size_t number_of_bins );

// =================================================================================================
//     Others
// =================================================================================================

void mass_trees_make_average_branch_lengths( std::vector<MassTree>& mass_trees );

std::vector<double> mass_tree_mass_per_edge( MassTree const& tree );

utils::Matrix<double> mass_tree_mass_per_edge( std::vector<MassTree> const& mass_trees );

std::vector<std::pair<double, double>> mass_tree_mass_per_edge_averaged( MassTree const& tree );

double mass_tree_sum_of_masses( MassTree const& tree );

bool mass_tree_validate( MassTree const& tree, double valid_total_mass_difference = -1.0);

} // namespace tree
} // namespace genesis

#endif // include guard