measures.hpp

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#ifndef GENESIS_PLACEMENT_FUNCTION_MEASURES_H_
#define GENESIS_PLACEMENT_FUNCTION_MEASURES_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 <cstddef>
#include <utility>
#include <vector>

namespace genesis {

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

namespace placement {

    class Sample;
    class SampleSet;
    class PlacementTreeEdgeData;
    class PlacementTreeNodeData;
    class Pquery;
    class PqueryPlacement;
    struct PqueryPlain;

}

namespace utils {

    template<typename T>
    class Matrix;

    class Histogram;

}

namespace placement {

// =================================================================================================
//     Expected Distance between Placement Locations
// =================================================================================================

double edpl( Pquery const& pquery, utils::Matrix<double> const& node_distances );

std::vector<double> edpl( Sample const& sample, utils::Matrix<double> const& node_distances );

double edpl( Sample const& sample, Pquery const& pquery );

std::vector<double> edpl( Sample const& sample );

// =================================================================================================
//     Pairwise Distance
// =================================================================================================

double pairwise_distance (
    const Sample& smp_a,
    const Sample& smp_b,
    bool          with_pendant_length = false
);

// double closest_pair_distance (
//     const Sample& smp_a,
//     const Sample& smp_b,
//     bool                with_pendant_length = false
// );

// =================================================================================================
//     Variance
// =================================================================================================

double variance (
    const Sample& smp,
    bool          with_pendant_length = false
);

} // namespace placement
} // namespace genesis

#endif // include guard