placement/function/emd.hpp

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#ifndef GENESIS_PLACEMENT_FUNCTION_EMD_H_
#define GENESIS_PLACEMENT_FUNCTION_EMD_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2017 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 <utility>
#include <vector>
 
namespace genesis {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
namespace placement {
 
    class Sample;
    class SampleSet;
 
}
 
namespace utils {
 
    template<typename T>
    class Matrix;
 
}
 
namespace placement {
 
// =================================================================================================
//     Earth Movers Distance
// =================================================================================================
 
double earth_movers_distance (
    Sample const& lhs,
    Sample const& rhs,
    double const  p = 1.0,
    bool const    with_pendant_length = false
);
 
utils::Matrix<double> earth_movers_distance(
    SampleSet const& sample_set,
    double const     p = 1.0,
    bool const       with_pendant_length = false
);
 
} // namespace placement
} // namespace genesis
 
#endif // include guard