permutations_iterator<T>& permutations_iterator<T>::operator++()
{
if(_size!=pool.size())
{
// Slow path, the iterator is a "view" of a prefix smaller
// than the the pool size
// FIXME a better implementation would be to avoid
// std::next_permutation, but only in the slow path
types::list<int> prev_permut(curr_permut.begin(), curr_permut.begin()+_size);
types::list<int> new_permut;
while((end = std::next_permutation(curr_permut.begin(), curr_permut.end())))
{
// Check if the prefix of the new permutation is
// different of the previous one
types::list<int> new_permut(curr_permut.begin(), curr_permut.begin()+_size);
if(!(prev_permut==new_permut))
break;
}
} else
end = std::next_permutation(curr_permut.begin(), curr_permut.end());
return *this;
}
void CompNovoIdentificationCID::reducePermuts_(set<String> & permuts, const PeakSpectrum & CID_spec, double prefix, double suffix)
{
if (permuts.size() < max_subscore_number_)
{
return;
}
vector<Permut> score_permuts;
Size i(0);
for (set<String>::const_iterator it = permuts.begin(); it != permuts.end(); ++it, ++i)
{
#ifdef REDUCE_PERMUTS_DEBUG
if (i % 1000 == 0)
{
cerr << (double)i / permuts.size() * 100 << "%" << endl;
}
#endif
PeakSpectrum CID_sim_spec;
getCIDSpectrumLight_(CID_sim_spec, *it, prefix, suffix);
//getCIDSpectrum_(CID_sim_spec, *it, 1, prefix, suffix);
double score = zhang_(CID_sim_spec, CID_spec);
if (boost::math::isnan(score))
{
score = 0;
}
score /= it->size();
if (boost::math::isnan(score))
{
score = 0;
}
#ifdef REDUCE_PERMUTS_DEBUG
cerr << "Subscoring: " << *it << " " << cid_score << " (CID=";
/* for (PeakSpectrum::ConstIterator pit = CID_sim_spec.begin(); pit != CID_sim_spec.end(); ++pit)
{
cerr << pit->getPosition()[0] << "|" << pit->getIntensity() << "; ";
}*/
cerr << endl;
#endif
Permut new_permut(it, score);
score_permuts.push_back(new_permut);
}
sort(score_permuts.begin(), score_permuts.end(), Internal::PermutScoreComparator);
set<String> new_permuts;
Size count(0);
for (vector<Permut>::const_iterator it = score_permuts.begin(); it != score_permuts.end() && count < max_subscore_number_; ++it, ++count)
{
new_permuts.insert(*it->getPermut());
#ifdef REDUCE_PERMUTS_DEBUG
cerr << "Subscore winner: " << it->getPermut() << " " << it->getScore() << endl;
#endif
}
permuts = new_permuts;
return;
}