void IDMapper::getIDDetails_(const PeptideIdentification & id, DoubleReal & rt_pep, DoubleList & mz_values, IntList & charges, bool use_avg_mass) const
{
mz_values.clear();
charges.clear();
rt_pep = id.getMetaValue("RT");
// collect m/z values of pepId
if (param_.getValue("mz_reference") == "precursor") // use precursor m/z of pepId
{
mz_values.push_back(id.getMetaValue("MZ"));
}
for (vector<PeptideHit>::const_iterator hit_it = id.getHits().begin();
hit_it != id.getHits().end(); ++hit_it)
{
Int charge = hit_it->getCharge();
charges.push_back(charge);
if (param_.getValue("mz_reference") == "peptide") // use mass of each pepHit (assuming H+ adducts)
{
DoubleReal mass = use_avg_mass ?
hit_it->getSequence().getAverageWeight(Residue::Full, charge) :
hit_it->getSequence().getMonoWeight(Residue::Full, charge);
mz_values.push_back( mass / (DoubleReal) charge);
}
}
}
void IDFilter::filterIdentificationsByMzError(const PeptideIdentification& identification, DoubleReal mass_error, bool unit_ppm, PeptideIdentification& filtered_identification)
{
vector<PeptideHit> hits;
filtered_identification = identification;
vector<PeptideHit> temp_hits = identification.getHits();
for (vector<PeptideHit>::iterator it = temp_hits.begin(); it != temp_hits.end(); ++it)
{
Int charge = it->getCharge();
if (charge == 0)
{
charge = 1;
}
DoubleReal exp_mz = (DoubleReal)identification.getMetaValue("MZ");
DoubleReal theo_mz = (it->getSequence().getMonoWeight() + (DoubleReal)charge * Constants::PROTON_MASS_U) / (DoubleReal)charge;
DoubleReal error(exp_mz - theo_mz);
if (unit_ppm)
{
error = error / theo_mz * (DoubleReal)1e6;
}
if (fabs(error) <= mass_error)
{
hits.push_back(*it);
}
}
filtered_identification.setHits(hits);
}
bool IDFilter::filterIdentificationsByMetaValueRange(const PeptideIdentification& identification, const String& key, DoubleReal low, DoubleReal high, bool missing)
{
if (!identification.metaValueExists(key)) return missing;
DoubleReal value = identification.getMetaValue(key);
return (value >= low) && (value <= high);
}