void
add_fixations(sample_t &sample, const vec_mutation_t &fixations,
const unsigned nsam, const sugar::treat_neutral treat,
const std::pair<double, double> &boundary)
{
for (const auto &f : fixations)
{
if (f.pos >= boundary.first && f.pos < boundary.second)
{
if (treat == sugar::treat_neutral::ALL)
{
sample.emplace_back(f.pos,
std::string(nsam, '1'));
}
else if (treat == sugar::treat_neutral::NEUTRAL
&& f.neutral)
{ // only add neutral mutations
sample.emplace_back(f.pos,
std::string(nsam, '1'));
}
else if (treat == sugar::treat_neutral::SELECTED
&& !f.neutral)
{ // only add selected mutations
sample.emplace_back(f.pos,
std::string(nsam, '1'));
}
}
}
}
void update_sample_block(sample_t & block,
const gamete_mcont_t & variants,
const mcont_t & mutations,
const size_t & i,
const size_t & n,
const pos_finder & pf,
const size_t & offset = 0,
const size_t & scalar = 2)
{
for( const auto & m : variants )
{
auto mutpos = mutations[m].pos;
auto itr = std::find_if(block.begin(),block.end(),std::bind(pf,std::placeholders::_1,mutpos));
if( itr == block.end() )
{
block.push_back( std::make_pair(mutpos,std::string(n,'0')) );
block[block.size()-1].second[scalar*i+offset] = '1';
}
else
{
itr->second[scalar*i+offset]='1';
}
}
}
void
finish_sample(sample_t &sample, const vec_mutation_t &fixations,
const unsigned nsam, const bool removeFixed,
const sugar::treat_neutral treat)
{
if (!removeFixed)
{
add_fixations(sample, fixations, nsam, treat);
}
std::sort(sample.begin(), sample.end(),
[](const sample_site_t &a, const sample_site_t &b) noexcept {
return a.first < b.first;
});
if (!removeFixed)
{
sample.erase(std::unique(sample.begin(), sample.end()),
sample.end());
}
}