void pr_int(t_conv *conv)
{
int signoffset;
char fillchar;
pre_int(conv);
if (conv->precision_on || conv->minus)
conv->zero = 0;
fillchar = conv->zero && !conv->minus ? '0' : ' ';
signoffset = fillchar == '0' && (conv->str[0] == '-' || \
conv->plus || conv->space) ? 1 : 0;
while (conv->precision_on && (int)ft_strlen(conv->str) < \
conv->precision + (conv->str[0] == '-'))
conv->str = insert_at(conv->str, '0', (conv->str[0] == '-'));
if (conv->plus)
conv->str = insert_at(conv->str, '+', 0);
else if (conv->space)
conv->str = insert_at(conv->str, ' ', 0);
if ((conv->specifier == 'x' || conv->specifier == 'X') \
&& conv->hash && fillchar == '0')
signoffset = 2;
while ((int)ft_strlen(conv->str) < conv->width)
conv->str = insert_at(conv->str, fillchar, \
signoffset + conv->minus * ft_strlen(conv->str));
}
void TheoreticalSpectrumGenerator::addPrecursorPeaks(RichPeakSpectrum & spec, const AASequence & peptide, Int charge)
{
bool add_metainfo(param_.getValue("add_metainfo").toBool());
DoubleReal pre_int((DoubleReal)param_.getValue("precursor_intensity"));
DoubleReal pre_int_H2O((DoubleReal)param_.getValue("precursor_H2O_intensity"));
DoubleReal pre_int_NH3((DoubleReal)param_.getValue("precursor_NH3_intensity"));
bool add_isotopes(param_.getValue("add_isotopes").toBool());
int max_isotope((int)param_.getValue("max_isotope"));
// precursor peak
DoubleReal mono_pos = peptide.getMonoWeight(Residue::Full, charge) / DoubleReal(charge);
if (add_isotopes)
{
IsotopeDistribution dist = peptide.getFormula(Residue::Full, charge).getIsotopeDistribution(max_isotope);
UInt j(0);
for (IsotopeDistribution::ConstIterator it = dist.begin(); it != dist.end(); ++it, ++j)
{
p_.setMZ((DoubleReal)(mono_pos + j * Constants::NEUTRON_MASS_U) / (DoubleReal)charge);
p_.setIntensity(pre_int * it->second);
if (add_metainfo)
{
String name("[M+H]+");
if (charge == 2)
{
name = "[M+2H]++";
}
p_.setMetaValue("IonName", name);
}
spec.push_back(p_);
}
}
else
{
p_.setMZ(mono_pos);
p_.setIntensity(pre_int);
if (add_metainfo)
{
String name("[M+H]+");
if (charge == 2)
{
name = "[M+2H]++";
}
p_.setMetaValue("IonName", name);
}
spec.push_back(p_);
}
// loss peaks of the precursor
//loss of water
EmpiricalFormula ion = peptide.getFormula(Residue::Full, charge) - EmpiricalFormula("H2O");
mono_pos = ion.getMonoWeight() / DoubleReal(charge);
if (add_isotopes)
{
IsotopeDistribution dist = ion.getIsotopeDistribution(max_isotope);
UInt j(0);
for (IsotopeDistribution::ConstIterator it = dist.begin(); it != dist.end(); ++it, ++j)
{
p_.setMZ((DoubleReal)(mono_pos + j * Constants::NEUTRON_MASS_U) / (DoubleReal)charge);
p_.setIntensity(pre_int_H2O * it->second);
if (add_metainfo)
{
String name("[M+H]-H2O+");
if (charge == 2)
{
name = "[M+2H]-H2O++";
}
p_.setMetaValue("IonName", name);
}
spec.push_back(p_);
}
}
else
{
p_.setMZ(mono_pos);
p_.setIntensity(pre_int_H2O);
if (add_metainfo)
{
String name("[M+H]-H2O+");
if (charge == 2)
{
name = "[M+2H]-H2O++";
}
p_.setMetaValue("IonName", name);
}
spec.push_back(p_);
}
//loss of ammonia
ion = peptide.getFormula(Residue::Full, charge) - EmpiricalFormula("NH3");
mono_pos = ion.getMonoWeight() / DoubleReal(charge);
if (add_isotopes)
{
IsotopeDistribution dist = ion.getIsotopeDistribution(max_isotope);
UInt j(0);
for (IsotopeDistribution::ConstIterator it = dist.begin(); it != dist.end(); ++it, ++j)
{
p_.setMZ((DoubleReal)(mono_pos + j * Constants::NEUTRON_MASS_U) / (DoubleReal)charge);
p_.setIntensity(pre_int_NH3 * it->second);
if (add_metainfo)
{
String name("[M+H]-NH3+");
if (charge == 2)
{
name = "[M+2H]-NH3++";
}
p_.setMetaValue("IonName", name);
}
spec.push_back(p_);
}
}
else
{
p_.setMZ(mono_pos);
p_.setIntensity(pre_int_NH3);
if (add_metainfo)
{
String name("[M+H]-NH3+");
if (charge == 2)
{
name = "[M+2H]-NH3++";
}
p_.setMetaValue("IonName", name);
}
spec.push_back(p_);
}
spec.sortByPosition();
}