Recombination.hpp

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/*

Copyright (C) 2003-2009 Kevin Thornton, krthornt[]@[]uci.edu

Remove the brackets to email me.

This file is part of libsequence.

libsequence 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.

libsequence 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
long with libsequence.  If not, see <http://www.gnu.org/licenses/>.

*/

#ifndef RECOMBINATION_H
#define RECOMBINATION_H

#include <vector>
#include <limits>

namespace Sequence
{
  class PolyTable;
  namespace Recombination
  {
    double HudsonsC (const Sequence::PolyTable * data, const bool & haveOutgroup,
                     const unsigned & outgroup);
    std::vector < std::vector<double> > Disequilibrium (const Sequence::PolyTable * data,
                                                        const bool & haveOutgroup=false,
                                                        const unsigned & outgroup=0,
                                                        const unsigned & mincount = 1,
                                                        const double max_distance = std::numeric_limits<double>::max());

    bool Disequilibrium (const Sequence::PolyTable *data,
                         std::vector<double> & return_values,
                         unsigned * i , unsigned * j,
                         const bool & haveOutgroup = false,
                         const unsigned & outgroup = 0,
                         const unsigned & mincount = 1,
                         const double max_distance = std::numeric_limits<double>::max());

  }
}
#endif

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