1 #ifndef __SEQUENCE_COALESCENT_MUTATION_HPP__ 2 #define __SEQUENCE_COALESCENT_MUTATION_HPP__ 14 typedef std::vector<std::string>::size_type MAX_SEG_T;
41 typedef std::pair< std::vector<double>,
44 template<
typename uniform_generator>
45 void add_S_inf_sites ( uniform_generator & uni ,
46 marginal::const_iterator history,
48 const int & beg,
const int & end,
52 const int & first_snp_index,
53 gamete_storage_type * gametes );
55 template<
typename uniform_generator>
56 void add_S_inf_sites (
const uniform_generator & uni,
57 marginal::const_iterator history,
59 const int & beg,
const int & end,
63 const int & first_snp_index,
64 gamete_storage_type * gametes );
66 template<
typename poisson_generator,
67 typename uniform_generator>
68 int infinite_sites( poisson_generator & poiss,
69 uniform_generator & uni,
70 gamete_storage_type * gametes,
73 const double & theta );
75 template<
typename poisson_generator,
76 typename uniform_generator>
77 int infinite_sites(
const poisson_generator & poiss,
78 const uniform_generator & uni,
79 gamete_storage_type * gametes,
82 const double & theta );
84 template<
typename uniform_generator>
85 int infinite_sites( uniform_generator & uni,
86 gamete_storage_type * gametes,
89 const double * total_times,
90 const unsigned * segsites );
92 template<
typename uniform_generator>
93 int infinite_sites(
const uniform_generator & uni,
94 gamete_storage_type * gametes,
97 const double * total_times,
98 const unsigned * segsites );
100 template<
typename poisson_generator,
101 typename uniform_generator>
102 SimData infinite_sites_sim_data( poisson_generator & poiss,
103 uniform_generator & uni,
106 const double & theta)__attribute((deprecated));
108 template<
typename poisson_generator,
109 typename uniform_generator>
110 SimData infinite_sites_sim_data(
const poisson_generator & poiss,
111 const uniform_generator & uni,
116 template<
typename uniform_generator>
117 SimData infinite_sites_sim_data( uniform_generator & uni,
120 const double * total_times,
123 template<
typename uniform_generator>
124 SimData infinite_sites_sim_data(
const uniform_generator & uni,
127 const double * total_times,
131 const unsigned & nsam,
132 const gamete_storage_type & gametes);
136 #include <Sequence/Coalescent/bits/Mutation.tcc> std::list< marginal > arg
Ancestral Recombination Graph.
MAX_SEG_T MAX_SEGS_INC
controls (re)allocation of simulated gametes You must define this in namespace Sequence in your progr...
The namespace in which this library resides.
declaration of types for coalescent simulation
std::pair< std::vector< double >, std::vector< std::string > > gamete_storage_type
an object to store simulated gametes An object of this type will tend to exist in the calling environ...
class __attribute__((deprecated)) FST
Functor to count the number of states, excluding gaps and missing data, in a range of characters...
void output_gametes(FILE *fp, const unsigned &segsites, const unsigned &nsam, const gamete_storage_type &gametes)
Write an object of type gamete_storage type to a C-style file stream This function is used when you n...
MAX_SEG_T MAX_SEGSITES
controls allocation of simulated gametes You must define this in namespace Sequence in your program...
Declaration of Sequence::SimData, a class representing polymorphism data from coalescent simulations ...
Data from coalescent simulations.