Coalesce.hpp

#ifndef __SEQUENCE_COALESCENT_COALESCE_HPP__
#define __SEQUENCE_COALESCENT_COALESCE_HPP__

#include <Sequence/Coalescent/SimTypes.hpp>
#include <utility>
#include <functional>

namespace Sequence
{
  namespace coalsim {
    template<typename uniform_generator>
    std::pair<int,int> pick2_in_deme( uniform_generator & uni, 
                                      const std::vector<Sequence::coalsim::chromosome> & sample,
                                      const int & ttl_nsam,
                                      const int & deme_nsam,
                                      const int & deme );

    template<typename uniform_generator>
    std::pair<int,int> pick2_in_deme( const uniform_generator & uni, 
                                      const std::vector<Sequence::coalsim::chromosome> & sample,
                                      const int & ttl_nsam,
                                      const int & deme_nsam,
                                      const int & deme );

    template<typename uniform_generator>
    std::pair<int,int> pick2( uniform_generator & uni, const int & nsam);

    template<typename uniform_generator>
    std::pair<int,int> pick2( const uniform_generator & uni, const int & nsam);

    bool isseg( chromosome::const_iterator seg, const unsigned & nsegs,
                const int & pos, unsigned * offset );

    int coalesce(const double & time,
                 const int & ttl_nsam,
                 const int & current_nsam,
                 const int & c1,
                 const int & c2,
                 const int & nsites,
                 int * nlinks,
                 std::vector<chromosome> * sample,
                 arg * sample_history);
  }
}
#endif
#include <Sequence/Coalescent/bits/Coalesce.tcc>