nhd.hpp

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#ifndef GENESIS_PLACEMENT_FUNCTION_NHD_H_
#define GENESIS_PLACEMENT_FUNCTION_NHD_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 <vector>
 
namespace genesis {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
namespace placement {
 
    class Sample;
    class SampleSet;
 
}
 
namespace tree {
 
    class Tree;
 
}
 
namespace utils {
 
    template<typename T>
    class Matrix;
 
}
 
namespace placement {
 
// =================================================================================================
//     Node Distance Histogram
// =================================================================================================
 
struct NodeDistanceHistogram
{
    double min;
    double max;
    std::vector<double> bins;
};
 
struct NodeDistanceHistogramSet
{
    std::vector<NodeDistanceHistogram> histograms;
};
 
// =================================================================================================
//     Basic Functions
// =================================================================================================
 
NodeDistanceHistogramSet node_distance_histogram_set(
    Sample const& sample,
    utils::Matrix<double> const& node_distances,
    utils::Matrix<signed char> const& node_sides,
    size_t const  histogram_bins
);
 
double node_histogram_distance(
    NodeDistanceHistogramSet const& lhs,
    NodeDistanceHistogramSet const& rhs
);
 
utils::Matrix<double> node_histogram_distance(
    std::vector<NodeDistanceHistogramSet> const& histogram_sets
);
 
// =================================================================================================
//     High Level Functions
// =================================================================================================
 
double node_histogram_distance(
    Sample const& sample_a,
    Sample const& sample_b,
    size_t const  histogram_bins = 25
);
 
utils::Matrix<double> node_histogram_distance(
    SampleSet const& sample_set,
    size_t const     histogram_bins = 25
);
 
} // namespace placement
} // namespace genesis
 
#endif // include guard