void FeatureFinder::run(const String& algorithm_name, PeakMap& input_map, FeatureMap& features, const Param& param, const FeatureMap& seeds)
{
// Nothing to do if there is no data
if ((algorithm_name != "mrm" && input_map.empty()) || (algorithm_name == "mrm" && input_map.getChromatograms().empty()))
{
features.clear(true);
return;
}
// check input
{
// We need updated ranges => check number of peaks
if (algorithm_name != "mrm" && input_map.getSize() == 0)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "FeatureFinder needs updated ranges on input map. Aborting.");
}
// We need MS1 data only => check levels
if (algorithm_name != "mrm" && (input_map.getMSLevels().size() != 1 || input_map.getMSLevels()[0] != 1))
{
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "FeatureFinder can only operate on MS level 1 data. Please do not use MS/MS data. Aborting.");
}
//Check if the peaks are sorted according to m/z
if (!input_map.isSorted(true))
{
LOG_WARN << "Input map is not sorted by RT and m/z! This is done now, before applying the algorithm!" << std::endl;
input_map.sortSpectra(true);
input_map.sortChromatograms(true);
}
for (Size s = 0; s < input_map.size(); ++s)
{
if (input_map[s].empty())
continue;
if (input_map[s][0].getMZ() < 0)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "FeatureFinder can only operate on spectra that contain peaks with positive m/z values. Filter the data accordingly beforehand! Aborting.");
}
}
}
// initialize
if (algorithm_name != "mrm" && algorithm_name != "centroided")
{
// Resize peak flag vector
flags_.resize(input_map.size());
for (Size i = 0; i < input_map.size(); ++i)
{
flags_[i].assign(input_map[i].size(), UNUSED);
}
}
// do the work
if (algorithm_name != "none")
{
FeatureFinderAlgorithm* algorithm = Factory<FeatureFinderAlgorithm>::create(algorithm_name);
algorithm->setParameters(param);
algorithm->setData(input_map, features, *this);
algorithm->setSeeds(seeds);
algorithm->run();
delete(algorithm);
}
if (algorithm_name != "mrm") // mrm works on chromatograms; the next section is only for conventional data
{
//report RT apex spectrum index and native ID for each feature
for (Size i = 0; i < features.size(); ++i)
{
//index
Size spectrum_index = input_map.RTBegin(features[i].getRT()) - input_map.begin();
features[i].setMetaValue("spectrum_index", spectrum_index);
//native id
if (spectrum_index < input_map.size())
{
String native_id = input_map[spectrum_index].getNativeID();
features[i].setMetaValue("spectrum_native_id", native_id);
}
else
{
/// @todo that happens sometimes using IsotopeWaveletFeatureFinder (Rene, Marc, Andreas, Clemens)
std::cerr << "FeatureFinderAlgorithm_impl, line=" << __LINE__ << "; FixMe this cannot be, but happens" << std::endl;
}
}
}
}
set<Size> correctToNearestMS1Peak(PeakMap & exp, double mz_tolerance, bool ppm, vector<double> & deltaMZs, vector<double> & mzs, vector<double> & rts)
{
set<Size> corrected_precursors;
// load experiment and extract precursors
vector<Precursor> precursors; // precursor
vector<double> precursors_rt; // RT of precursor MS2 spectrum
vector<Size> precursor_scan_index;
getPrecursors_(exp, precursors, precursors_rt, precursor_scan_index);
for (Size i = 0; i != precursors_rt.size(); ++i)
{
// get precursor rt
double rt = precursors_rt[i];
// get precursor MZ
double mz = precursors[i].getMZ();
//cout << rt << " " << mz << endl;
// get precursor spectrum
MSExperiment<Peak1D>::ConstIterator rt_it = exp.RTBegin(rt - 1e-8);
// store index of MS2 spectrum
UInt precursor_spectrum_idx = rt_it - exp.begin();
// get parent (MS1) of precursor spectrum
rt_it = exp.getPrecursorSpectrum(rt_it);
if (rt_it->getMSLevel() != 1)
{
LOG_WARN << "Error: no MS1 spectrum for this precursor" << endl;
}
//cout << rt_it->getRT() << " " << rt_it->size() << endl;
// find peak (index) closest to expected position
Size nearest_peak_idx = rt_it->findNearest(mz);
// get actual position of closest peak
double nearest_peak_mz = (*rt_it)[nearest_peak_idx].getMZ();
// calculate error between expected and actual position
double nearestPeakError = ppm ? abs(nearest_peak_mz - mz)/mz * 1e6 : abs(nearest_peak_mz - mz);
// check if error is small enough
if (nearestPeakError < mz_tolerance)
{
// sanity check: do we really have the same precursor in the original and the picked spectrum
if (fabs(exp[precursor_spectrum_idx].getPrecursors()[0].getMZ() - mz) > 0.0001)
{
LOG_WARN << "Error: index is referencing different precursors in original and picked spectrum." << endl;
}
// cout << mz << " -> " << nearest_peak_mz << endl;
double deltaMZ = nearest_peak_mz - mz;
deltaMZs.push_back(deltaMZ);
mzs.push_back(mz);
rts.push_back(rt);
// correct entries
Precursor corrected_prec = precursors[i];
corrected_prec.setMZ(nearest_peak_mz);
exp[precursor_spectrum_idx].getPrecursors()[0] = corrected_prec;
corrected_precursors.insert(precursor_spectrum_idx);
}
}
return corrected_precursors;
}
void correct(PeakMap & exp, vector<DoubleReal> & deltaMZs, vector<DoubleReal> & mzs, vector<DoubleReal> & rts)
{
// load experiment and extract precursors
vector<Precursor> precursors; // precursor
vector<double> precursors_rt; // RT of precursor MS2 spectrum
getPrecursors_(exp, precursors, precursors_rt);
for (Size i = 0; i != precursors_rt.size(); ++i)
{
// get precursor rt
DoubleReal rt = precursors_rt[i];
// get precursor MZ
DoubleReal mz = precursors[i].getMZ();
//cout << rt << " " << mz << endl;
// get precursor spectrum
MSExperiment<Peak1D>::ConstIterator rt_it = exp.RTBegin(rt);
// store index of MS2 spectrum
UInt precursor_spectrum_idx = rt_it - exp.begin();
// get parent (MS1) of precursor spectrum
rt_it = exp.getPrecursorSpectrum(rt_it);
if (rt_it->getMSLevel() != 1)
{
cout << "Error: no MS1 spectrum for this precursor" << endl;
}
//cout << rt_it->getRT() << " " << rt_it->size() << endl;
// find peak (index) closest to expected position
Size nearest_peak_idx = rt_it->findNearest(mz);
// get actual position of closest peak
DoubleReal nearest_peak_mz = (*rt_it)[nearest_peak_idx].getMZ();
// calculate error between expected and actual position
DoubleReal nearestPeakError = abs(nearest_peak_mz - mz);
// check if error is small enough
if (nearestPeakError < 0.1)
{
// sanity check: do we really have the same precursor in the original and the picked spectrum
if (fabs(exp[precursor_spectrum_idx].getPrecursors()[0].getMZ() - mz) > 0.0001)
{
cout << "Error: index is referencing different precursors in original and picked spectrum." << endl;
}
// cout << mz << " -> " << nearest_peak_mz << endl;
DoubleReal deltaMZ = nearest_peak_mz - mz;
deltaMZs.push_back(deltaMZ);
mzs.push_back(mz);
rts.push_back(rt);
// correct entries
Precursor corrected_prec = precursors[i];
corrected_prec.setMZ(nearest_peak_mz);
exp[precursor_spectrum_idx].getPrecursors()[0] = corrected_prec;
}
}
}