void MSDataSqlConsumer::consumeSpectrum(SpectrumType & s)
{
spectra_.push_back(s);
s.clear(false);
if (full_meta_) peak_meta_.addSpectrum(s);
if (spectra_.size() >= flush_after_) {flush();}
}
static void deisotopeAndSingleChargeMSSpectrum_(SpectrumType& in, Int min_charge, Int max_charge, double fragment_tolerance, bool fragment_unit_ppm, bool keep_only_deisotoped = false, Size min_isopeaks = 3, Size max_isopeaks = 10, bool make_single_charged = true)
{
if (in.empty())
{
return;
}
SpectrumType old_spectrum = in;
// determine charge seeds and extend them
vector<Size> mono_isotopic_peak(old_spectrum.size(), 0);
vector<Int> features(old_spectrum.size(), -1);
Int feature_number = 0;
for (Size current_peak = 0; current_peak != old_spectrum.size(); ++current_peak)
{
double current_mz = old_spectrum[current_peak].getPosition()[0];
for (Int q = max_charge; q >= min_charge; --q) // important: test charge hypothesis from high to low
{
// try to extend isotopes from mono-isotopic peak
// if extension larger then min_isopeaks possible:
// - save charge q in mono_isotopic_peak[]
// - annotate all isotopic peaks with feature number
if (features[current_peak] == -1) // only process peaks which have no assigned feature number
{
bool has_min_isopeaks = true;
vector<Size> extensions;
for (Size i = 0; i < max_isopeaks; ++i)
{
double expected_mz = current_mz + i * Constants::C13C12_MASSDIFF_U / q;
Size p = old_spectrum.findNearest(expected_mz);
double tolerance_dalton = fragment_unit_ppm ? fragment_tolerance * old_spectrum[p].getPosition()[0] * 1e-6 : fragment_tolerance;
if (fabs(old_spectrum[p].getPosition()[0] - expected_mz) > tolerance_dalton) // test for missing peak
{
if (i < min_isopeaks)
{
has_min_isopeaks = false;
}
break;
}
else
{
// TODO: include proper averagine model filtering. for now start at the second peak to test hypothesis
Size n_extensions = extensions.size();
if (n_extensions != 0)
{
if (old_spectrum[p].getIntensity() > old_spectrum[extensions[n_extensions - 1]].getIntensity())
{
if (i < min_isopeaks)
{
has_min_isopeaks = false;
}
break;
}
}
// averagine check passed
extensions.push_back(p);
}
}
if (has_min_isopeaks)
{
//cout << "min peaks at " << current_mz << " " << " extensions: " << extensions.size() << endl;
mono_isotopic_peak[current_peak] = q;
for (Size i = 0; i != extensions.size(); ++i)
{
features[extensions[i]] = feature_number;
}
feature_number++;
}
}
}
}
in.clear(false);
for (Size i = 0; i != old_spectrum.size(); ++i)
{
Int z = mono_isotopic_peak[i];
if (keep_only_deisotoped)
{
if (z == 0)
{
continue;
}
// if already single charged or no decharging selected keep peak as it is
if (!make_single_charged)
{
in.push_back(old_spectrum[i]);
}
else
{
RichPeak1D p = old_spectrum[i];
p.setMZ(p.getMZ() * z - (z - 1) * Constants::PROTON_MASS_U);
in.push_back(p);
}
}
else
{
// keep all unassigned peaks
if (features[i] < 0)
{
in.push_back(old_spectrum[i]);
continue;
}
// convert mono-isotopic peak with charge assigned by deisotoping
if (z != 0)
{
if (!make_single_charged)
{
in.push_back(old_spectrum[i]);
}
else
{
RichPeak1D p = old_spectrum[i];
p.setMZ(p.getMZ() * z - (z - 1) * Constants::PROTON_MASS_U);
in.push_back(p);
}
}
}
}
in.sortByPosition();
}