void TheoreticalSpectrumGenerator::addLosses_(RichPeakSpectrum & spectrum, const AASequence & ion, double intensity, Residue::ResidueType res_type, int charge) const
{
RichPeak1D p;
set<String> losses;
for (AASequence::ConstIterator it = ion.begin(); it != ion.end(); ++it)
{
if (it->hasNeutralLoss())
{
vector<EmpiricalFormula> loss_formulas = it->getLossFormulas();
for (Size i = 0; i != loss_formulas.size(); ++i)
{
losses.insert(loss_formulas[i].toString());
}
}
}
if (!add_isotopes_)
{
p.setIntensity(intensity * rel_loss_intensity_);
}
for (set<String>::const_iterator it = losses.begin(); it != losses.end(); ++it)
{
EmpiricalFormula loss_ion = ion.getFormula(res_type, charge) - EmpiricalFormula(*it);
// thanks to Chris and Sandro
// check for negative element frequencies (might happen if losses are not allowed for specific ions)
bool negative_elements(false);
for (EmpiricalFormula::ConstIterator eit = loss_ion.begin(); eit != loss_ion.end(); ++eit)
{
if (eit->second < 0)
{
negative_elements = true;
break;
}
}
if (negative_elements)
{
continue;
}
double loss_pos = loss_ion.getMonoWeight() / (double)charge;
const String& loss_name = *it;
if (add_isotopes_)
{
IsotopeDistribution dist = loss_ion.getIsotopeDistribution(max_isotope_);
UInt j(0);
for (IsotopeDistribution::ConstIterator iso = dist.begin(); iso != dist.end(); ++iso)
{
p.setMZ((double)(loss_pos + j) / (double)charge);
p.setIntensity(intensity * rel_loss_intensity_ * iso->second);
if (add_metainfo_ && j == 0)
{
// note: important to construct a string from char. If omitted it will perform pointer arithmetics on the "-" string literal
String ion_name = String(residueTypeToIonLetter_(res_type)) + String(ion.size()) + "-" + loss_name + String(charge, '+');
p.setMetaValue("IonName", ion_name);
}
spectrum.push_back(p);
}
}
else
{
p.setMZ(loss_pos);
if (add_metainfo_)
{
// note: important to construct a string from char. If omitted it will perform pointer arithmetics on the "-" string literal
String ion_name = String(residueTypeToIonLetter_(res_type)) + String(ion.size()) + "-" + loss_name + String(charge, '+');
p.setMetaValue("IonName", ion_name);
}
spectrum.push_back(p);
}
}
}
void TheoreticalSpectrumGenerator::addPeaks(RichPeakSpectrum & spectrum, const AASequence & peptide, Residue::ResidueType res_type, Int charge)
{
if (peptide.empty())
{
return;
}
Map<DoubleReal, AASequence> ions;
Map<DoubleReal, String> names;
AASequence ion;
DoubleReal intensity(0);
bool add_first_prefix_ion(param_.getValue("add_first_prefix_ion").toBool());
// generate the ion peaks
switch (res_type)
{
case Residue::AIon:
{
Size i = 1;
if (!add_first_prefix_ion)
{
i = 2;
}
for (; i < peptide.size(); ++i)
{
ion = peptide.getPrefix(i);
DoubleReal pos = ion.getMonoWeight(Residue::AIon, charge) / (DoubleReal)charge;
ions[pos] = ion;
names[pos] = "a" + String(i) + String(charge, '+');
}
intensity = (DoubleReal)param_.getValue("a_intensity");
break;
}
case Residue::BIon:
{
Size i = 1;
if (!add_first_prefix_ion)
{
i = 2;
}
for (; i < peptide.size(); ++i)
{
ion = peptide.getPrefix(i);
DoubleReal pos = ion.getMonoWeight(Residue::BIon, charge) / (DoubleReal)charge;
ions[pos] = ion;
names[pos] = "b" + String(i) + String(charge, '+');
}
intensity = (DoubleReal)param_.getValue("b_intensity");
break;
}
case Residue::CIon:
{
Size i = 1;
if (!add_first_prefix_ion)
{
i = 2;
}
for (; i < peptide.size(); ++i)
{
ion = peptide.getPrefix(i);
DoubleReal pos = ion.getMonoWeight(Residue::CIon, charge) / (DoubleReal)charge;
ions[pos] = ion;
names[pos] = "c" + String(i) + String(charge, '+');
}
intensity = (DoubleReal)param_.getValue("c_intensity");
break;
}
case Residue::XIon:
{
for (Size i = 1; i < peptide.size(); ++i)
{
ion = peptide.getSuffix(i);
DoubleReal pos = ion.getMonoWeight(Residue::XIon, charge) / (DoubleReal)charge;
ions[pos] = ion;
names[pos] = "x" + String(i) + String(charge, '+');
}
intensity = (DoubleReal)param_.getValue("x_intensity");
break;
}
case Residue::YIon:
{
for (Size i = 1; i < peptide.size(); ++i)
{
ion = peptide.getSuffix(i);
DoubleReal pos = ion.getMonoWeight(Residue::YIon, charge) / (DoubleReal)charge;
ions[pos] = ion;
names[pos] = "y" + String(i) + String(charge, '+');
}
intensity = (DoubleReal)param_.getValue("y_intensity");
break;
}
case Residue::ZIon:
{
for (Size i = 1; i < peptide.size(); ++i)
{
ion = peptide.getSuffix(i);
DoubleReal pos = ion.getMonoWeight(Residue::ZIon, charge) / (DoubleReal)charge;
ions[pos] = ion;
names[pos] = "z" + String(i) + String(charge, '+');
}
intensity = (DoubleReal)param_.getValue("z_intensity");
break;
}
default:
cerr << "Cannot create peaks of that ion type" << endl;
}
// get the params
bool add_losses(param_.getValue("add_losses").toBool());
bool add_metainfo(param_.getValue("add_metainfo").toBool());
bool add_isotopes(param_.getValue("add_isotopes").toBool());
Int max_isotope((Int)param_.getValue("max_isotope"));
DoubleReal rel_loss_intensity((DoubleReal)param_.getValue("relative_loss_intensity"));
for (Map<DoubleReal, AASequence>::ConstIterator cit = ions.begin(); cit != ions.end(); ++cit)
{
ion = cit->second;
DoubleReal pos = cit->first;
String ion_name = names[pos];
if (add_isotopes)
{
IsotopeDistribution dist = ion.getFormula(res_type, charge).getIsotopeDistribution(max_isotope);
UInt j(0);
for (IsotopeDistribution::ConstIterator it = dist.begin(); it != dist.end(); ++it, ++j)
{
p_.setMZ((DoubleReal)(pos + (DoubleReal)j * Constants::NEUTRON_MASS_U) / (DoubleReal)charge);
p_.setIntensity(intensity * it->second);
if (add_metainfo && j == 0)
{
p_.setMetaValue("IonName", ion_name);
}
spectrum.push_back(p_);
}
}
else
{
p_.setMZ(pos);
p_.setIntensity(intensity);
if (add_metainfo)
{
p_.setMetaValue("IonName", ion_name);
}
spectrum.push_back(p_);
}
if (add_losses)
{
set<String> losses;
for (AASequence::ConstIterator it = cit->second.begin(); it != cit->second.end(); ++it)
{
if (it->hasNeutralLoss())
{
vector<EmpiricalFormula> loss_formulas = it->getLossFormulas();
for (Size i = 0; i != loss_formulas.size(); ++i)
{
losses.insert(loss_formulas[i].toString());
}
}
}
if (!add_isotopes)
{
p_.setIntensity(intensity * rel_loss_intensity);
}
for (set<String>::const_iterator it = losses.begin(); it != losses.end(); ++it)
{
EmpiricalFormula loss_ion = ion.getFormula(res_type, charge) - EmpiricalFormula(*it);
// thanks to Chris and Sandro
// check for negative element frequencies (might happen if losses are not allowed for specific ions)
bool negative_elements(false);
for (EmpiricalFormula::ConstIterator eit = loss_ion.begin(); eit != loss_ion.end(); ++eit)
{
if (eit->second < 0)
{
negative_elements = true;
break;
}
}
if (negative_elements)
{
continue;
}
DoubleReal loss_pos = loss_ion.getMonoWeight() / (DoubleReal)charge;
String loss_name = *it;
if (add_isotopes)
{
IsotopeDistribution dist = loss_ion.getIsotopeDistribution(max_isotope);
UInt j(0);
for (IsotopeDistribution::ConstIterator iso = dist.begin(); iso != dist.end(); ++iso)
{
p_.setMZ((DoubleReal)(loss_pos + j) / (DoubleReal)charge);
p_.setIntensity(intensity * rel_loss_intensity * iso->second);
if (add_metainfo && j == 0)
{
p_.setMetaValue("IonName", ion_name + "-" + loss_name);
}
spectrum.push_back(p_);
}
}
else
{
p_.setMZ(loss_pos);
if (add_metainfo)
{
p_.setMetaValue("IonName", ion_name + "-" + loss_name);
}
spectrum.push_back(p_);
}
}
}
}
if (add_metainfo)
{
p_.setMetaValue("IonName", String(""));
}
spectrum.sortByPosition();
return;
}
