ExitCodes main_(int, const char**)
{
// parsing parameters
String in(getStringOption_("in"));
String feature_in(getStringOption_("feature_in"));
String out(getStringOption_("out"));
double precursor_mass_tolerance(getDoubleOption_("precursor_mass_tolerance"));
// reading input
FileHandler fh;
FileTypes::Type in_type = fh.getType(in);
PeakMap exp;
fh.loadExperiment(in, exp, in_type, log_type_, false, false);
exp.sortSpectra();
FeatureMap feature_map;
if (feature_in != "")
{
FeatureXMLFile().load(feature_in, feature_map);
}
// calculations
FeatureFinderAlgorithmIsotopeWavelet iso_ff;
Param ff_param(iso_ff.getParameters());
ff_param.setValue("max_charge", getIntOption_("max_charge"));
ff_param.setValue("intensity_threshold", getDoubleOption_("intensity_threshold"));
iso_ff.setParameters(ff_param);
FeatureFinder ff;
ff.setLogType(ProgressLogger::NONE);
PeakMap exp2 = exp;
exp2.clear(false);
for (PeakMap::ConstIterator it = exp.begin(); it != exp.end(); ++it)
{
if (it->size() != 0)
{
exp2.addSpectrum(*it);
}
}
exp = exp2;
exp.updateRanges();
// TODO check MS2 and MS1 counts
ProgressLogger progresslogger;
progresslogger.setLogType(log_type_);
progresslogger.startProgress(0, exp.size(), "Correcting precursor masses");
for (PeakMap::Iterator it = exp.begin(); it != exp.end(); ++it)
{
progresslogger.setProgress(exp.end() - it);
if (it->getMSLevel() != 2)
{
continue;
}
// find first MS1 scan of the MS/MS scan
PeakMap::Iterator ms1_it = it;
while (ms1_it != exp.begin() && ms1_it->getMSLevel() != 1)
{
--ms1_it;
}
if (ms1_it == exp.begin() && ms1_it->getMSLevel() != 1)
{
writeLog_("Did not find a MS1 scan to the MS/MS scan at RT=" + String(it->getRT()));
continue;
}
if (ms1_it->size() == 0)
{
writeDebug_("No peaks in scan at RT=" + String(ms1_it->getRT()) + String(", skipping"), 1);
continue;
}
PeakMap::Iterator ms2_it = ms1_it;
++ms2_it;
while (ms2_it != exp.end() && ms2_it->getMSLevel() == 2)
{
// first: error checks
if (ms2_it->getPrecursors().empty())
{
writeDebug_("Warning: found no precursors of spectrum RT=" + String(ms2_it->getRT()) + ", skipping it.", 1);
++ms2_it;
continue;
}
else if (ms2_it->getPrecursors().size() > 1)
{
writeLog_("Warning: found more than one precursor of spectrum RT=" + String(ms2_it->getRT()) + ", using first one.");
}
Precursor prec = *ms2_it->getPrecursors().begin();
double prec_pos = prec.getMZ();
PeakMap new_exp;
// now excise small region from the MS1 spec for the feature finder (isotope pattern must be covered...)
PeakSpectrum zoom_spec;
for (PeakSpectrum::ConstIterator pit = ms1_it->begin(); pit != ms1_it->end(); ++pit)
{
if (pit->getMZ() > prec_pos - 3 && pit->getMZ() < prec_pos + 3)
{
zoom_spec.push_back(*pit);
}
}
new_exp.addSpectrum(zoom_spec);
new_exp.updateRanges();
FeatureMap features, seeds;
ff.run("isotope_wavelet", new_exp, features, ff_param, seeds);
if (features.empty())
{
writeDebug_("No features found for scan RT=" + String(ms1_it->getRT()), 1);
++ms2_it;
continue;
}
double max_int(numeric_limits<double>::min());
double min_dist(numeric_limits<double>::max());
Size max_int_feat_idx(0);
for (Size i = 0; i != features.size(); ++i)
{
if (fabs(features[i].getMZ() - prec_pos) < precursor_mass_tolerance &&
features[i].getIntensity() > max_int)
{
max_int_feat_idx = i;
max_int = features[i].getIntensity();
min_dist = fabs(features[i].getMZ() - prec_pos);
}
}
writeDebug_(" max_int=" + String(max_int) + " mz=" + String(features[max_int_feat_idx].getMZ()) + " charge=" + String(features[max_int_feat_idx].getCharge()), 5);
if (min_dist < precursor_mass_tolerance)
{
prec.setMZ(features[max_int_feat_idx].getMZ());
prec.setCharge(features[max_int_feat_idx].getCharge());
vector<Precursor> precs;
precs.push_back(prec);
ms2_it->setPrecursors(precs);
writeDebug_("Correcting precursor mass of spectrum RT=" + String(ms2_it->getRT()) + " from " + String(prec_pos) + " to " + String(prec.getMZ()) + " (z=" + String(prec.getCharge()) + ")", 1);
}
++ms2_it;
}
it = --ms2_it;
}
progresslogger.endProgress();
// writing output
fh.storeExperiment(out, exp, log_type_);
return EXECUTION_OK;
}
