FragmentsRescaling.hpp

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#ifndef __SEQUENCE_COALESCENT_FRAGMENTS_RESCALING_HPP__
#define __SEQUENCE_COALESCENT_FRAGMENTS_RESCALING_HPP__

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

namespace Sequence
{
  int sample_length( const std::vector< std::pair<int,int> > & fragments );
  int total_length( const std::vector< std::pair<int,int> > & fragments );
  void calculate_scales(const std::vector< std::pair<int,int> > & fragments,
                        std::vector< std::pair<double,double> > * sample_scale,
                        std::vector< std::pair<double,double> > * mutation_scale );
  class SimData; //forward declaration
  void rescale_mutation_positions(SimData * d,
                                  const std::vector< std::pair<double,double> > & sample_scale, 
                                  const std::vector< std::pair<double,double> > & mutation_scale );
  void rescale_arg( arg * sample_history,
                    const std::vector< std::pair<int,int> > & fragments );
  double integrate_genetic_map( const std::vector<chromosome> & sample,
                                const int & current_nsam,
                                const std::vector<double> & genetic_map,
                                std::vector<double> * reclens);
}

#endif

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