TreeOperations.hpp

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#ifndef __SEQUENCE_COALESCENT_TREE_OPERATIONS_HPP__
#define __SEQUENCE_COALESCENT_TREE_OPERATIONS_HPP__

#include <Sequence/Coalescent/SimTypes.hpp>
#include <vector>
#include <memory>
namespace Sequence
{
  namespace coalsim {
    double total_time( const marginal::const_iterator beg,
                       const int & nsam );
  
    int pick_branch( marginal::const_iterator beg,
                     const int & nsam,
                     const double & rtime);
  
    std::vector<int> get_all_descendants (marginal::const_iterator beg,
                                          const int & nsam,
                                          const int & branch);

    bool is_descendant( marginal::const_iterator beg,
                        const int & ind,
                        const int & branch );

    double total_time_on_arg( const Sequence::coalsim::arg & sample_history,
                              const int & total_number_of_sites );

    void minimize_arg( arg * sample_history );

    class sfs_times_impl;
    class sfs_times
    {
    private:
      std::unique_ptr<sfs_times_impl> impl;
    public:
      sfs_times();
      sfs_times(arg::const_iterator sample_history_beg,
                const arg::size_type & nsegs,
                const int & total_nsites_simulated,
                bool folded = false);
      sfs_times(const sfs_times &);
      ~sfs_times();
    
      double operator[]( std::vector<double>::size_type const & ) const;
      sfs_times & operator=(const sfs_times &);
      bool operator==(const sfs_times & rhs) const;
      double ttime() const;
      size_t size() const;
      typedef std::vector<double>::const_iterator const_iterator;
      const_iterator begin() const;
      const_iterator end() const;
    };
  }
}
#endif