IsotopeDistribution EmpiricalFormula::getIsotopeDistribution(UInt max_depth) const
{
IsotopeDistribution result(max_depth);
Map<const Element *, SignedSize>::ConstIterator it = formula_.begin();
for (; it != formula_.end(); ++it)
{
IsotopeDistribution tmp = it->first->getIsotopeDistribution();
tmp.setMaxIsotope(max_depth);
result += tmp * it->second;
}
result.renormalize();
return result;
}
void getAveragineIsotopeDistribution(double product_mz,
std::vector<std::pair<double, double> >& isotopesSpec, double charge,
int nr_isotopes, double mannmass)
{
typedef OpenMS::FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern TheoreticalIsotopePattern;
// create the theoretical distribution
IsotopeDistribution d;
TheoreticalIsotopePattern isotopes;
d.setMaxIsotope(nr_isotopes);
//std::cout << product_mz * charge << std::endl;
d.estimateFromPeptideWeight(product_mz * charge);
double mass = product_mz;
for (IsotopeDistribution::Iterator it = d.begin(); it != d.end(); ++it)
{
isotopesSpec.push_back(std::make_pair(mass, it->second));
mass += mannmass;
}
} //end of dia_isotope_corr_sub
IsotopeDistributionCache::IsotopeDistributionCache(DoubleReal max_mass, DoubleReal mass_window_width, DoubleReal intensity_percentage, DoubleReal intensity_percentage_optional) :
mass_window_width_(mass_window_width)
{
Size num_isotopes = std::ceil(max_mass / mass_window_width) + 1;
//reserve enough space
isotope_distributions_.resize(num_isotopes);
//calculate distribution if necessary
for (Size index = 0; index < num_isotopes; ++index)
{
//log_ << "Calculating iso dist for mass: " << 0.5*mass_window_width_ + index * mass_window_width_ << std::endl;
IsotopeDistribution d;
d.setMaxIsotope(20);
d.estimateFromPeptideWeight(0.5 * mass_window_width + index * mass_window_width);
//trim left and right. And store the number of isotopes on the left, to reconstruct the monoisotopic peak
Size size_before = d.size();
d.trimLeft(intensity_percentage_optional);
isotope_distributions_[index].trimmed_left = size_before - d.size();
d.trimRight(intensity_percentage_optional);
for (IsotopeDistribution::Iterator it = d.begin(); it != d.end(); ++it)
{
isotope_distributions_[index].intensity.push_back(it->second);
//log_ << " - " << it->second << std::endl;
}
//determine the number of optional peaks at the beginning/end
Size begin = 0;
Size end = 0;
bool is_begin = true;
bool is_end = false;
for (Size i = 0; i < isotope_distributions_[index].intensity.size(); ++i)
{
if (isotope_distributions_[index].intensity[i] < intensity_percentage)
{
if (!is_end && !is_begin)
is_end = true;
if (is_begin)
++begin;
else if (is_end)
++end;
}
else if (is_begin)
{
is_begin = false;
}
}
isotope_distributions_[index].optional_begin = begin;
isotope_distributions_[index].optional_end = end;
//scale the distibution to a maximum of 1
DoubleReal max = 0.0;
for (Size i = 0; i < isotope_distributions_[index].intensity.size(); ++i)
{
if (isotope_distributions_[index].intensity[i] > max)
{
max = isotope_distributions_[index].intensity[i];
}
}
isotope_distributions_[index].max = max;
for (Size i = 0; i < isotope_distributions_[index].intensity.size(); ++i)
{
isotope_distributions_[index].intensity[i] /= max;
}
}
}
