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