libsequence  1.9.5
Mutation.hpp
1 #ifndef __SEQUENCE_COALESCENT_MUTATION_HPP__
2 #define __SEQUENCE_COALESCENT_MUTATION_HPP__
3 
4 #include <Sequence/Coalescent/SimTypes.hpp>
5 #include <Sequence/SimData.hpp>
6 #include <vector>
7 #include <string>
8 #include <utility>
9 #include <cstdio>
10 
11 namespace Sequence
12 {
13  namespace coalsim {
14  typedef std::vector<std::string>::size_type MAX_SEG_T;
21  extern MAX_SEG_T MAX_SEGSITES;
28  extern MAX_SEG_T MAX_SEGS_INC;
29 
41  typedef std::pair< std::vector<double>,
42  std::vector<std::string> > gamete_storage_type;
43 
44  template<typename uniform_generator>
45  void add_S_inf_sites ( uniform_generator & uni ,
46  marginal::const_iterator history,
47  const double & tt,
48  const int & beg, const int & end,
49  const int & nsam,
50  const int & nsites,
51  const int & S ,
52  const int & first_snp_index,
53  gamete_storage_type * gametes );
54 
55  template<typename uniform_generator>
56  void add_S_inf_sites ( const uniform_generator & uni,
57  marginal::const_iterator history,
58  const double & tt,
59  const int & beg, const int & end,
60  const int & nsam,
61  const int & nsites,
62  const int & S ,
63  const int & first_snp_index,
64  gamete_storage_type * gametes );
65 
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,
71  const int & nsites,
72  const arg & history,
73  const double & theta );
74 
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,
80  const int & nsites,
81  const arg & history,
82  const double & theta );
83 
84  template<typename uniform_generator>
85  int infinite_sites( uniform_generator & uni,
86  gamete_storage_type * gametes,
87  const int & nsites,
88  const arg & history,
89  const double * total_times,
90  const unsigned * segsites );
91 
92  template<typename uniform_generator>
93  int infinite_sites( const uniform_generator & uni,
94  gamete_storage_type * gametes,
95  const int & nsites,
96  const arg & history,
97  const double * total_times,
98  const unsigned * segsites );
99 
100  template<typename poisson_generator,
101  typename uniform_generator>
102  SimData infinite_sites_sim_data( poisson_generator & poiss,
103  uniform_generator & uni,
104  const int & nsites,
105  const arg & history,
106  const double & theta)__attribute((deprecated));
107 
108  template<typename poisson_generator,
109  typename uniform_generator>
110  SimData infinite_sites_sim_data( const poisson_generator & poiss,
111  const uniform_generator & uni,
112  const int & nsites,
113  const arg & history,
114  const double & theta)__attribute__((deprecated));
115 
116  template<typename uniform_generator>
117  SimData infinite_sites_sim_data( uniform_generator & uni,
118  const int & nsites,
119  const arg & history,
120  const double * total_times,
121  const unsigned * segsites)__attribute__((deprecated));
122 
123  template<typename uniform_generator>
124  SimData infinite_sites_sim_data( const uniform_generator & uni,
125  const int & nsites,
126  const arg & history,
127  const double * total_times,
128  const unsigned * segsites)__attribute__((deprecated));
129 
130  void output_gametes(FILE * fp,const unsigned & segsites,
131  const unsigned & nsam,
132  const gamete_storage_type & gametes);
133  }
134 }
135 #endif
136 #include <Sequence/Coalescent/bits/Mutation.tcc>
Sequence::coalsim::arg
std::list< marginal > arg
Ancestral Recombination Graph.
Definition: SimTypes.hpp:217
Sequence::coalsim::MAX_SEGS_INC
MAX_SEG_T MAX_SEGS_INC
controls (re)allocation of simulated gametes You must define this in namespace Sequence in your progr...
Sequence
The namespace in which this library resides.
SimTypes.hpp
declaration of types for coalescent simulation
Sequence::coalsim::gamete_storage_type
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...
Definition: Mutation.hpp:42
Sequence::__attribute__
class __attribute__((deprecated)) FST
Functor to count the number of states, excluding gaps and missing data, in a range of characters...
Definition: FST.hpp:41
Sequence::coalsim::output_gametes
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...
Definition: CoalescentMutation.cc:29
Sequence::coalsim::MAX_SEGSITES
MAX_SEG_T MAX_SEGSITES
controls allocation of simulated gametes You must define this in namespace Sequence in your program...
SimData.hpp
Declaration of Sequence::SimData, a class representing polymorphism data from coalescent simulations ...
Sequence::SimData
Data from coalescent simulations.