Snn.hpp

/*

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 __SEQUENCE_SNN_HPP__
#define __SEQUENCE_SNN_HPP__

#include <Sequence/Comparisons.hpp>
#include <Sequence/PolyTable.hpp>
#include <vector>
#include <utility>
#include <cassert>

namespace Sequence
{
  double Snn_statistic( const unsigned individuals[],
                        const std::vector< std::vector<double> > & dkj,
                        const unsigned config[],
                        const size_t & npop,
                        const unsigned & nsam )__attribute__ ((deprecated));
  
  template< typename shuffler >
  std::pair<double,double>
  Snn_test(const PolyTable & snpTable,
           const unsigned config[],
           const size_t & npop,
           shuffler & s,
           const unsigned & nperms = 10000)__attribute__ ((deprecated));

  template< typename shuffler >
  std::vector< std::vector<double> >
  Snn_test_pairwise(const PolyTable & snpTable,
                    const unsigned config[],
                    const size_t & npop,
                    shuffler & s,
                    const unsigned & nperms = 10000)__attribute__ ((deprecated));
}
#endif
#include <Sequence/bits/Snn.tcc>