void add_new_mutation( const std::size_t idx,
const mcont_t & mutations,
gamete_type & new_gamete )
{
assert(idx<mutations.size());
if(mutations[idx].neutral)
{
assert(std::find(new_gamete.mutations.begin(),
new_gamete.mutations.end(),idx)==new_gamete.mutations.end());
new_gamete.mutations.emplace(std::upper_bound(new_gamete.mutations.begin(),
new_gamete.mutations.end(),mutations[idx].pos,
[&mutations](const double & __value,const std::size_t __mut) noexcept {
assert(__mut<mutations.size());
return __value < mutations[__mut].pos;}),
idx );
assert(gamete_is_sorted_n(new_gamete,mutations));
}
else
{
assert(std::find(new_gamete.smutations.begin(),
new_gamete.smutations.end(),idx)==new_gamete.smutations.end());
new_gamete.smutations.emplace(std::upper_bound(new_gamete.smutations.begin(),
new_gamete.smutations.end(),mutations[idx].pos,
[&mutations](const double & __value,const std::size_t __mut) noexcept {
assert(__mut<mutations.size());
return __value < mutations[__mut].pos;}),
idx );
assert(gamete_is_sorted_s(new_gamete,mutations));
}
}
inline void process_gametes( const gcont_t & gametes,
const mcont_t & mutations,
std::vector<uint_t> & mcounts)
/*!
For every non-extinct gamete, increment the count of its mutations
using the frequency of the gamete.
This is usually the most expensive function call in a simulation.
*/
{
if(mutations.size()>mcounts.size())
{
mcounts.resize(mutations.size(),0);
}
//zero out mcounts
for(auto & mc : mcounts) mc=0;
//update mutation counts
for(const auto & g : gametes)
{
if(g.n) //only do this for extant gametes
{
for(const auto & m : g.mutations) mcounts[m]+=g.n;
for(const auto & m : g.smutations) mcounts[m]+=g.n;
}
}
}
//! Empty all the containers
void
clear_containers()
{
mutations.clear();
mcounts.clear();
mcounts_from_preserved_nodes.clear();
gametes.clear();
mut_lookup.clear();
fixations.clear();
fixation_times.clear();
}
inline itr_type rec_update_itr( itr_type __first,
itr_type __last,
const mcont_t & mutations,
const double & val)
{
if(__first==__last) return __first;
return std::upper_bound(__first,__last,
std::cref(val),
[&mutations](const double __val,const std::size_t __mut) noexcept {
assert(__mut < mutations.size());
return __val < mutations[__mut].pos;
});
}
inline void process_gametes( const gcont_t & gametes,
const mcont_t & mutations,
std::vector<uint_t> & mcounts)
/*!
For every non-extinct gamete, increment the counts of its mutations
via a call to KTfwd::fwdpp_internal::adjust_mutation_counts.
*/
{
if(mutations.size()>mcounts.size())
{
mcounts.resize(mutations.size(),0);
}
//zero out mcounts
for(auto & mc : mcounts) mc=0;
//update mutation counts
for(const auto & g : gametes)
{
if(g.n) //only do this for extant gametes
{
for(const auto & m : g.mutations) mcounts[m]+=g.n;
for(const auto & m : g.smutations) mcounts[m]+=g.n;
}
}
}