MSSpectrum::Iterator
MSSpectrum::MZEnd(MSSpectrum::Iterator begin, MSSpectrum::CoordinateType mz, MSSpectrum::Iterator end)
{
PeakType p;
p.setPosition(mz);
return upper_bound(begin, end, p, PeakType::PositionLess());
}
MSSpectrum::ConstIterator MSSpectrum::MZBegin(MSSpectrum::ConstIterator begin, MSSpectrum::CoordinateType mz,
MSSpectrum::ConstIterator end) const
{
PeakType p;
p.setPosition(mz);
return lower_bound(begin, end, p, PeakType::PositionLess());
}
PeakType fillPeak(double rt, double mz, double it)
{
PeakType p;
p.setIntensity((OpenMS::Peak2D::IntensityType)it);
p.setMZ(mz);
p.setRT((rt));
return p;
}
void updateWeightedSDEstimate(PeakType p, const double& mean_t1, double& sd_t, double& last_weights_sum)
{
double denom = last_weights_sum * sd_t * sd_t + p.getIntensity() * (p.getMZ() - mean_t1) * (p.getMZ() - mean_t1);
double weights_sum = last_weights_sum + p.getIntensity();
double tmp_sd = std::sqrt(denom / weights_sum);
if (tmp_sd > std::numeric_limits<double>::epsilon())
{
sd_t = tmp_sd;
}
last_weights_sum = weights_sum;
}
void updateWeightedSDEstimateRobust(PeakType p, const double& mean_t1, double& sd_t, double& last_weights_sum)
{
double denom1 = std::log(last_weights_sum) + 2 * std::log(sd_t);
double denom2 = std::log(p.getIntensity()) + 2 * std::log(std::abs(p.getMZ() - mean_t1));
double denom = std::sqrt(std::exp(denom1) + std::exp(denom2));
double weights_sum = last_weights_sum + p.getIntensity();
double tmp_sd = denom / std::sqrt(weights_sum);
if (tmp_sd > std::numeric_limits<double>::epsilon())
{
sd_t = tmp_sd;
}
last_weights_sum = weights_sum;
}
MSSpectrum<FeatureFinderAlgorithmIsotopeWavelet::PeakType>* FeatureFinderAlgorithmIsotopeWavelet::createHRData(const UInt i)
{
MSSpectrum<PeakType> spec((*this->map_)[i]);
const MSSpectrum<PeakType>& specr((*this->map_)[i]);
for (UInt j = 0; j < spec.size() - 1; ++j)
{
spec[j].setMZ(-1 * (specr[j + 1].getMZ() - specr[j].getMZ()));
spec[j].setIntensity((specr[j].getIntensity() + specr[j + 1].getIntensity()));
}
spec[spec.size() - 1].setMZ(-1); spec[spec.size() - 1].setIntensity(-1);
ConstRefVector<MSSpectrum<PeakType> > c_sorted_spec(spec.begin(), spec.end());
//Sort in ascending order according to the intensities present in the transform
c_sorted_spec.sortByPosition();
#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET
std::ofstream ofilex("spacings.trans");
for (UInt j = 0; j < spec.size() - 1; ++j)
{
ofilex << ::std::setprecision(12) << std::fixed << spec[j].getMZ() << "\t" << spec[j].getIntensity() << std::endl;
}
ofilex.close();
#endif
UInt pos = 0;
while (c_sorted_spec[pos].getIntensity() <= 0)
{
if (++pos >= c_sorted_spec.size())
{
std::cout << "Detected empty scan or a scan that cannot be interpolated with zeros in HR mode. " << std::endl;
std::cout << "Please check scan # " << i << " of your data set." << std::endl;
exit(-1);
}
}
double bound = -1 * c_sorted_spec[pos].getMZ();
if (bound > (1. / max_charge_) / 2.)
{
//that might be case for simulated spectra,
//which might show a very artificial spacing
bound = (1. / max_charge_) / 2. / 4.;
}
MSSpectrum<PeakType>* new_spec = new MSSpectrum<PeakType>;
new_spec->reserve(200000);
new_spec->setRT(((*this->map_)[i]).getRT());
PeakType p; p.setMZ(specr[0].getMZ()); p.setIntensity(specr[0].getIntensity());
new_spec->push_back(p);
UInt count;
for (UInt j = 0; j < spec.size() - 1; ++j)
{
count = 0;
while (-spec[j].getMZ() - count * bound > bound)
{
++count;
p.setMZ(specr[j].getMZ() + count * bound); p.setIntensity(0);
new_spec->push_back(p);
}
p.setMZ(specr[j + 1].getMZ()); p.setIntensity(specr[j + 1].getIntensity());
new_spec->push_back(p);
}
#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET
std::ofstream ofiley("new_spec.trans");
for (UInt j = 0; j < new_spec->size(); ++j)
{
ofiley << ::std::setprecision(12) << std::fixed << (*new_spec)[j].getMZ() << "\t" << (*new_spec)[j].getIntensity() << std::endl;
}
ofiley.close();
#endif
return new_spec;
}
void TOFPeakTest<PeakType>::testGetSetTOF() {
PeakType peak;
peak.setTOF(23.42);
CPPUNIT_ASSERT_EQUAL(23.42, peak.getTOF());
}
void fillIntensity(PeakType& peak) const
{
peak.setIntensity(getIntensity(peak.getPosition()));
}
MSSpectrum::ConstIterator MSSpectrum::MZBegin(MSSpectrum::CoordinateType mz) const
{
PeakType p;
p.setPosition(mz);
return lower_bound(ContainerType::begin(), ContainerType::end(), p, PeakType::PositionLess());
}
MSSpectrum::Iterator MSSpectrum::MZEnd(MSSpectrum::CoordinateType mz)
{
PeakType p;
p.setPosition(mz);
return upper_bound(ContainerType::begin(), ContainerType::end(), p, PeakType::PositionLess());
}
