libsequence: DemographicModels.hpp Source File

00001 #ifndef __SEQUENCE_COALESCENT_DEMOGRAPHICMODELS_HPP__
00002 #define __SEQUENCE_COALESCENT_DEMOGRAPHICMODELS_HPP__
00003 
00004 #include <Sequence/Coalescent/SimTypes.hpp>
00005 
00006 namespace Sequence
00007 {
00008   template<typename uniform_generator,
00009            typename uniform01_generator,
00010            typename exponential_generator>
00011   arg bottleneck( uniform_generator & uni,
00012                   uniform01_generator & uni01,
00013                   exponential_generator & expo,
00014                   const std::vector<chromosome> & initialized_sample, 
00015                   const marginal & initialized_marginal,
00016                   const double & tr,
00017                   const double & d,
00018                   const double & f,
00019                   const double & rho = 0.,
00020                   const bool & exponential_recovery = false,
00021                   const double & recovered_size = 1. );
00022 
00023   template<typename uniform_generator,
00024            typename uniform01_generator,
00025            typename exponential_generator>
00026   arg bottleneck( const uniform_generator & uni,
00027                   const uniform01_generator & uni01,
00028                   const exponential_generator & expo,
00029                   const std::vector<chromosome> & initialized_sample, 
00030                   const marginal & initialized_marginal,
00031                   const double & tr,
00032                   const double & d,
00033                   const double & f,
00034                   const double & rho = 0.,
00035                   const bool & exponential_recovery = false,
00036                   const double & recovered_size = 1. );
00037 
00038   template<typename uniform_generator,
00039            typename uniform01_generator,
00040            typename exponential_generator>
00041   arg exponential_change( uniform_generator & uni,
00042                           uniform01_generator & uni01,
00043                           exponential_generator & expo,
00044                           const std::vector<chromosome> & initialized_sample, 
00045                           const marginal & initialized_marginal,
00046                           const double & G,
00047                           const double & t_begin,
00048                           const double & t_end,
00049                           const double & rho = 0.,
00050                           const double & size_at_end = -1);
00051 
00052   template<typename uniform_generator,
00053            typename uniform01_generator,
00054            typename exponential_generator>
00055   arg exponential_change( const uniform_generator & uni,
00056                           const uniform01_generator & uni01,
00057                           const exponential_generator & expo,
00058                           const std::vector<chromosome> & initialized_sample, 
00059                           const marginal & initialized_marginal,
00060                           const double & G,
00061                           const double & t_begin,
00062                           const double & t_end,
00063                           const double & rho = 0.,
00064                           const double & size_at_end = -1);
00065 
00066   template<typename uniform_generator,
00067            typename uniform01_generator,
00068            typename exponential_generator>
00069   arg snm( uniform_generator & uni,
00070            uniform01_generator & uni01,
00071            exponential_generator & expo,
00072            const std::vector<chromosome> & initialized_sample, 
00073            const marginal & initialized_marginal,
00074            const double & rho);
00075 
00076   template<typename uniform_generator,
00077            typename uniform01_generator,
00078            typename exponential_generator>
00079   arg snm( const uniform_generator & uni,
00080            const uniform01_generator & uni01,
00081            const exponential_generator & expo,
00082            const std::vector<chromosome> & initialized_sample, 
00083            const marginal & initialized_marginal,
00084            const double & rho);
00085 
00086 } //namespace Sequence
00087 #endif
00088 #include <Sequence/Coalescent/bits/DemographicModels.tcc>