void SeedListGenerator::generateSeedList(vector<PeptideIdentification>&
peptides, SeedList& seeds,
bool use_peptide_mass)
{
seeds.clear();
for (vector<PeptideIdentification>::iterator pep_it = peptides.begin();
pep_it != peptides.end(); ++pep_it)
{
double mz;
if (!pep_it->getHits().empty() && use_peptide_mass)
{
pep_it->sort();
const PeptideHit& hit = pep_it->getHits().front();
Int charge = hit.getCharge();
mz = hit.getSequence().getMonoWeight(Residue::Full, charge) /
double(charge);
}
else
{
mz = pep_it->getMZ();
}
DPosition<2> point(pep_it->getRT(), mz);
seeds.push_back(point);
}
}
void SeedListGenerator::convertSeedList(const FeatureMap& features,
SeedList& seeds)
{
seeds.clear();
for (FeatureMap::ConstIterator feat_it = features.begin();
feat_it != features.end(); ++feat_it)
{
DPosition<2> point(feat_it->getRT(), feat_it->getMZ());
seeds.push_back(point);
}
}
void SeedListGenerator::generateSeedList(const MSExperiment<>& experiment,
SeedList& seeds)
{
seeds.clear();
for (MSExperiment<>::ConstIterator exp_it = experiment.begin();
exp_it != experiment.end(); ++exp_it)
{
if (exp_it->getMSLevel() == 2) // MS2 spectrum -> look for precursor
{
MSExperiment<>::ConstIterator prec_it =
experiment.getPrecursorSpectrum(exp_it);
const vector<Precursor>& precursors = exp_it->getPrecursors();
DPosition<2> point(prec_it->getRT(), precursors[0].getMZ());
seeds.push_back(point);
}
}
}
