virtual void
w(const dipvector_t &diploids, gcont_t &gametes,
const mcont_t &mutations)
{
auto N_curr = diploids.size();
if (fitnesses.size() < N_curr)
fitnesses.resize(N_curr);
wbar = 0.;
for (size_t i = 0; i < N_curr; ++i)
{
gametes[diploids[i].first].n
= gametes[diploids[i].second].n = 0;
fitnesses[i] = diploids[i].w;
wbar += diploids[i].w;
}
wbar /= double(N_curr);
lookup = KTfwd::fwdpp_internal::gsl_ran_discrete_t_ptr(
gsl_ran_discrete_preproc(N_curr, &fitnesses[0]));
}
sep_sample_t
ms_sample_separate_single_deme( const mcont_t & mutations,
const gcont_t & gametes,
const dipvector_t & diploids,
const std::vector<unsigned> & diplist,
const unsigned & n,
const bool & remove_fixed )
{
sep_sample_t rv;
sample_t::iterator itr;
std::function<bool(const sample_site_t &, const double &)> sitefinder = [](const sample_site_t & site,
const double & d )
{
return std::fabs(site.first-d) <= std::numeric_limits<double>::epsilon();
};
for( size_t i = 0 ; i < diplist.size() ; ++i )
{
typename dipvector_t::difference_type ind = diplist[i];
assert(ind>=0);
assert( unsigned(ind) < diploids.size() );
fwdpp_internal::update_sample_block( rv.first,gametes[diploids[ind].first].mutations,mutations,i,2*diplist.size(),sitefinder);
fwdpp_internal::update_sample_block( rv.first,gametes[diploids[ind].second].mutations,mutations,i,2*diplist.size(),sitefinder,1);
fwdpp_internal::update_sample_block( rv.second,gametes[diploids[ind].first].smutations,mutations,i,2*diplist.size(),sitefinder);
fwdpp_internal::update_sample_block( rv.second,gametes[diploids[ind].second].smutations,mutations,i,2*diplist.size(),sitefinder,1);
}
if(remove_fixed&&!rv.first.empty())
{
remove_fixed_variants_from_sample(rv.first,2*diplist.size());
}
if(!rv.first.empty())
{
std::sort(rv.first.begin(),rv.first.end(),
[](const sample_site_t & lhs,
const sample_site_t & rhs) { return lhs.first < rhs.first; });
}
if(remove_fixed&&!rv.second.empty())
{
remove_fixed_variants_from_sample(rv.second,2*diplist.size());
}
if(!rv.second.empty())
{
std::sort(rv.second.begin(),rv.second.end(),
[](const sample_site_t & lhs,
const sample_site_t & rhs) { return lhs.first < rhs.first; });
}
//Deal w/odd sample sizes
if(n%2 != 0.)
{
trim_last(&rv.first);
trim_last(&rv.second);
}
assert(std::is_sorted(rv.first.begin(),rv.first.end(),
[](const sample_site_t & a,
const sample_site_t & b) noexcept {
return a.first<b.first;
}));
assert(std::is_sorted(rv.second.begin(),rv.second.end(),
[](const sample_site_t & a,
const sample_site_t & b) noexcept {
return a.first<b.first;
}));
return rv;
}
std::vector<sep_sample_t >
ms_sample_separate_mlocus( const mcont_t & mutations,
const gcont_t & gametes,
const dipvector_t & diploids,
const std::vector<unsigned> & diplist,
const unsigned & n,
const bool & remove_fixed)
{
using rvtype = std::vector<sep_sample_t>;
//using genotype = typename dipvector_t::value_type;
rvtype rv( diploids.size() );
std::function<bool(const sample_site_t &, const double &)> sitefinder = [](const sample_site_t & site,
const double & d )
{
return std::fabs(site.first-d) <= std::numeric_limits<double>::epsilon();
};
//Go over each indidivual's mutations and update the return value
//typename dipvector_t::const_iterator dbegin = diploids->begin();
for( unsigned ind = 0 ; ind < diplist.size() ; ++ind )
{
unsigned rv_count=0;
for (const auto & locus : diploids[diplist[ind]] )
{
//finally, we can go over mutations
fwdpp_internal::update_sample_block(rv[rv_count].first,gametes[locus.first].mutations,mutations,ind,2*diplist.size(),sitefinder);
fwdpp_internal::update_sample_block(rv[rv_count].second,gametes[locus.first].smutations,mutations,ind,2*diplist.size(),sitefinder);
fwdpp_internal::update_sample_block(rv[rv_count].first,gametes[locus.second].mutations,mutations,ind,2*diplist.size(),sitefinder,1);
fwdpp_internal::update_sample_block(rv[rv_count].second,gametes[locus.second].smutations,mutations,ind,2*diplist.size(),sitefinder,1);
++rv_count;
}
}
if( remove_fixed )
{
for( unsigned i = 0 ; i < rv.size() ; ++i )
{
remove_fixed_variants_from_sample(rv[i].first,2*diplist.size());
remove_fixed_variants_from_sample(rv[i].second,2*diplist.size());
}
}
//sort on position
for( unsigned i = 0 ; i < rv.size() ; ++i )
{
std::sort(rv[i].first.begin(),rv[i].first.end(),
[](const sample_site_t & lhs,
const sample_site_t & rhs) { return lhs.first < rhs.first; });
std::sort(rv[i].second.begin(),rv[i].second.end(),
[](const sample_site_t & lhs,
const sample_site_t & rhs) { return lhs.first < rhs.first; });
//Deal w/odd sample sizes
if(n%2!=0.)
{
trim_last(&rv[i].first);
trim_last(&rv[i].second);
}
}
#ifndef NDEBUG
for(const auto & rvi : rv )
{
assert(std::is_sorted(rvi.first.begin(),rvi.first.end(),
[](const sample_site_t & a,
const sample_site_t & b) noexcept {
return a.first<b.first;
}));
assert(std::is_sorted(rvi.second.begin(),rvi.second.end(),
[](const sample_site_t & a,
const sample_site_t & b) noexcept {
return a.first<b.first;
}));
}
#endif
return rv;
}