placement/function/distances.hpp

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#ifndef GENESIS_PLACEMENT_FUNCTION_DISTANCES_H_
#define GENESIS_PLACEMENT_FUNCTION_DISTANCES_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 "genesis/placement/placement_tree.hpp"
#include "genesis/utils/containers/matrix.hpp"

#include <vector>

namespace genesis {

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

namespace tree {

    class Tree;

    class TreeEdge;
    class TreeNode;

    class CommonNodeData;
    class CommonEdgeData;

    using CommonTree = Tree;
}

namespace placement {

    class Pquery;
    class PqueryPlacement;
    struct PqueryPlain;

    class PlacementEdgeData;
    class PlacementNodeData;

    class Sample;
    class SampleSet;
}

namespace placement {

// =================================================================================================
//     Pquery to Pquery Distances
// =================================================================================================

double pquery_distance(
    PqueryPlain const&           pquery_a,
    PqueryPlain const&           pquery_b,
    utils::Matrix<double> const& node_distances,
    bool                         with_pendant_length = false
);

double pquery_distance(
    Pquery const&                pquery_a,
    Pquery const&                pquery_b,
    utils::Matrix<double> const& node_distances,
    bool                         with_pendant_length = false
);

double placement_distance(
    PqueryPlacement const&       place_a,
    PqueryPlacement const&       place_b,
    utils::Matrix<double> const& node_distances
);

double pquery_path_length_distance(
    Pquery const&                pquery_a,
    Pquery const&                pquery_b,
    utils::Matrix<size_t> const& node_path_lengths
);

size_t placement_path_length_distance(
    PqueryPlacement const&       place_a,
    PqueryPlacement const&       place_b,
    utils::Matrix<size_t> const& node_path_lengths
);

// =================================================================================================
//     Pquery to Tree Element Distances
// =================================================================================================

double pquery_distance(
    Pquery const&                pquery,
    tree::TreeNode const&        node,
    utils::Matrix<double> const& node_distances
);

double placement_distance(
    PqueryPlacement const&       placement,
    tree::TreeNode const&        node,
    utils::Matrix<double> const& node_distances
);

// /**
//  * @brief Calculate the weighted discrete distance between the PqueryPlacement%s of a Pquery and a
//  * tree::TreeNode, in number of nodes, using the `like_weight_ratio` of the PqueryPlacement%s
//  * for weighing.
//  *
//  * The Matrix @p node_path_lengths has to come from tree::node_path_length_matrix().
//  */
// double pquery_path_length_distance(
//     Pquery const&                pquery,
//     tree::TreeNode const&        node,
//     utils::Matrix<size_t> const& node_path_lengths
// );
//
// /**
//  * @brief
//  *
//  * The Matrix @p node_path_lengths has to come from tree::node_path_length_matrix().
//  */
// size_t placement_path_length_distance(
//     PqueryPlacement const&       placement,
//     tree::TreeNode const&        node,
//     utils::Matrix<size_t> const& node_path_lengths
// );

double pquery_path_length_distance(
    Pquery const&                pquery,
    tree::TreeEdge const&        edge,
    utils::Matrix<size_t> const& edge_path_lengths
);

size_t placement_path_length_distance(
    PqueryPlacement const&       placement,
    tree::TreeEdge const&        edge,
    utils::Matrix<size_t> const& edge_path_lengths
);

} // namespace placement
} // namespace genesis

#endif // include guard