IsotopeDistribution EmpiricalFormula::getIsotopeDistribution(UInt max_depth) const
{
IsotopeDistribution result(max_depth);
Map<const Element *, SignedSize>::ConstIterator it = formula_.begin();
for (; it != formula_.end(); ++it)
{
IsotopeDistribution tmp = it->first->getIsotopeDistribution();
tmp.setMaxIsotope(max_depth);
result += tmp * it->second;
}
result.renormalize();
return result;
}
void TheoreticalSpectrumGenerator::addIsotopeCluster_(RichPeakSpectrum & spectrum, const AASequence & ion, Residue::ResidueType res_type, Int charge, double intensity) const
{
double pos = ion.getMonoWeight(res_type, charge) / (double)charge;
RichPeak1D p;
IsotopeDistribution dist = ion.getFormula(res_type, charge).getIsotopeDistribution(max_isotope_);
UInt j(0);
for (IsotopeDistribution::ConstIterator it = dist.begin(); it != dist.end(); ++it, ++j)
{
// TODO: this is usually dominated by 13C-12C mass shift which deviates a bit from neutron mass
p.setMZ((double)(pos + (double)j * Constants::NEUTRON_MASS_U) / (double)charge);
p.setIntensity(intensity * it->second);
if (add_metainfo_ && j == 0)
{
String ion_name = String(residueTypeToIonLetter_(res_type)) + String(ion.size()) + String(charge, '+');
p.setMetaValue("IonName", ion_name);
}
spectrum.push_back(p);
}
}
void getAveragineIsotopeDistribution(double product_mz,
std::vector<std::pair<double, double> >& isotopesSpec, double charge,
int nr_isotopes, double mannmass)
{
typedef OpenMS::FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern TheoreticalIsotopePattern;
// create the theoretical distribution
IsotopeDistribution d;
TheoreticalIsotopePattern isotopes;
d.setMaxIsotope(nr_isotopes);
//std::cout << product_mz * charge << std::endl;
d.estimateFromPeptideWeight(product_mz * charge);
double mass = product_mz;
for (IsotopeDistribution::Iterator it = d.begin(); it != d.end(); ++it)
{
isotopesSpec.push_back(std::make_pair(mass, it->second));
mass += mannmass;
}
} //end of dia_isotope_corr_sub
int main( int argc, char * argv[] )
{
ProRataConfig::setFilename( "ProRataConfig.xml" );
vector< Isotopologue * > vpIsotopologue;
residueMap mAtomicComposition;
ProRataConfig::getResidueAtomicComposition( mAtomicComposition );
residueMap::const_iterator iterResidueMap;
for( iterResidueMap = mAtomicComposition.begin(); iterResidueMap != mAtomicComposition.end(); ++iterResidueMap )
{
vpIsotopologue.push_back( new Isotopologue( iterResidueMap->first, iterResidueMap->second ) );
}
string sSequence;
cout << "Enter the query amino acid sequence: ";
cin >> sSequence;
int iChargeState;
cout << "Enter the charge state: ";
cin >> iChargeState;
int i;
string sAtom = "CHONPSCHONPS";
vector< int > tempAtomicComposition;
IsotopeDistribution tempIsotopeDistribution;
MZwindows mzWin;
vector< double > vdYion;
vector< double > vdBion;
for( int n = 0; n < vpIsotopologue.size(); n++ )
{
cout << vpIsotopologue[n]->getName() << endl;
vpIsotopologue[n]->computeAtomicComposition(sSequence, tempAtomicComposition);
for( i = 0; i < 6; i++ )
cout << sAtom[i] << " " << tempAtomicComposition[i] << "\t";
cout << endl;
for( i = 6; i < tempAtomicComposition.size(); i++ )
cout << sAtom[i] << " " << tempAtomicComposition[i] << "\t";
cout << endl;
vpIsotopologue[n]->computeIsotopicDistribution( sSequence, tempIsotopeDistribution );
tempIsotopeDistribution.print();
vpIsotopologue[n]->computeMZwindows( sSequence , iChargeState, mzWin );
for( i = 0; i < mzWin.vfLowerMZ.size() ; i++ )
{
cout << mzWin.vfLowerMZ[i] << " --- " << mzWin.vfUpperMZ[i] << endl;
}
cout << "Num Yion Bion" << endl;
if( !vpIsotopologue[n]->computeProductIonMass( sSequence, vdYion, vdBion ) )
cout << "failed product ion calculation " << endl;
cout << vdBion.size() << endl;
for( i = 0 ; i < vdYion.size(); ++i )
{
cout << ( i+1 ) << '\t' << vdYion[i] << '\t' << vdBion[i] << endl;
}
}
return 0;
}
void ElementDB::readFromFile_(const String& file_name)
{
String file = File::find(file_name);
// load elements into param object
Param param;
ParamXMLFile paramFile;
paramFile.load(file, param);
UInt an(0);
String name, symbol;
// determine prefix
vector<String> split;
param.begin().getName().split(':', split);
String prefix("");
for (Size i = 0; i < split.size() - 1; ++i)
{
prefix += split[i] + ":";
}
//cout << "first element prefix=" << prefix << endl;
Map<UInt, double> Z_to_abundancy;
Map<UInt, double> Z_to_mass;
for (Param::ParamIterator it = param.begin(); it != param.end(); ++it)
{
// new element started?
if (!it.getName().hasPrefix(prefix))
{
// update prefix
it.getName().split(':', split);
prefix = "";
for (Size i = 0; i < split.size() - 1; ++i)
{
prefix += split[i] + ":";
}
// cout << "new element prefix=" << prefix << endl;
// Parsing of previous element is finished. Now store data in Element object
IsotopeDistribution isotopes = parseIsotopeDistribution_(Z_to_abundancy);
double avg_weight = calculateAvgWeight_(Z_to_abundancy, Z_to_mass);
double mono_weight = calculateMonoWeight_(Z_to_mass);
/*
// print information about elements
cout << "Name: " << name << " AtomicNumber: " << an << " Symbol: " << symbol << " AvgWeight: " << avg_weight
<< " MonoWeight: " << mono_weight << " NIsotopes: " << isotopes.size() << endl;
*/
Element* e = new Element(name, symbol, an, avg_weight, mono_weight, isotopes);
names_[name] = e;
symbols_[symbol] = e;
atomic_numbers_[an] = e;
// add all the individual isotopes as separat elements
for (IsotopeDistribution::ConstIterator iit = isotopes.begin(); iit != isotopes.end(); ++iit)
{
String iso_name = "(" + String(iit->first) + ")" + name;
String iso_symbol = "(" + String(iit->first) + ")" + symbol;
// set avg and mono to same value for isotopes (old hack...)
DoubleReal iso_avg_weight = Z_to_mass[(UInt) iit->first];
DoubleReal iso_mono_weight = iso_avg_weight;
IsotopeDistribution iso_isotopes;
vector<pair<Size, double> > iso_container;
iso_container.push_back(make_pair(iit->first, 1.0));
iso_isotopes.set(iso_container);
/*
// print name, symbal and atomic mass of the current isotope
cout << "Isotope Name: " << iso_name << " Symbol: " << iso_symbol << " AtomicMass: " << iso_mono_weight << endl;
*/
Element* iso_e = new Element(iso_name, iso_symbol, an, iso_avg_weight, iso_mono_weight, iso_isotopes);
names_[iso_name] = iso_e;
names_[iso_symbol] = iso_e;
}
Z_to_abundancy.clear();
Z_to_mass.clear();
}
// top level: read the contents of the element section
it.getName().split(':', split);
String key = split[2];
String value = it->value;
value.trim();
// cout << "Key=" << key << endl;
if (key == "AtomicNumber")
{
an = (UInt)value.toInt();
}
else
{
if (key == "Isotopes")
{
UInt Z = UInt(split[3].toInt());
String item = split[4];
if (item == "RelativeAbundance")
{
Z_to_abundancy[Z] = double(value.toDouble() / 100.0);
}
else if (item == "AtomicMass")
{
Z_to_mass[Z] = double(value.toDouble());
}
else
{
cerr << "read unknown item in Isotopes: " << item << endl;
}
}
else
{
if (key == "Name")
{
name = value;
}
else
{
if (key == "Symbol")
{
symbol = value;
}
else
{
cerr << "read unknown tag: " << key << endl;
}
}
}
}
}
// build last element
double avg_weight(0), mono_weight(0);
IsotopeDistribution isotopes = parseIsotopeDistribution_(Z_to_abundancy);
Element* e = new Element(name, symbol, an, avg_weight, mono_weight, isotopes);
names_[name] = e;
symbols_[symbol] = e;
atomic_numbers_[an] = e;
}
void TheoreticalSpectrumGenerator::addPrecursorPeaks(RichPeakSpectrum & spec, const AASequence & peptide, Int charge) const
{
RichPeak1D p;
// precursor peak
double mono_pos = peptide.getMonoWeight(Residue::Full, charge) / double(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((double)(mono_pos + j * Constants::NEUTRON_MASS_U) / (double)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() / double(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((double)(mono_pos + j * Constants::NEUTRON_MASS_U) / (double)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() / double(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((double)(mono_pos + j * Constants::NEUTRON_MASS_U) / (double)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();
}
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::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();
}
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;
}
IsotopeDistributionCache::IsotopeDistributionCache(DoubleReal max_mass, DoubleReal mass_window_width, DoubleReal intensity_percentage, DoubleReal intensity_percentage_optional) :
mass_window_width_(mass_window_width)
{
Size num_isotopes = std::ceil(max_mass / mass_window_width) + 1;
//reserve enough space
isotope_distributions_.resize(num_isotopes);
//calculate distribution if necessary
for (Size index = 0; index < num_isotopes; ++index)
{
//log_ << "Calculating iso dist for mass: " << 0.5*mass_window_width_ + index * mass_window_width_ << std::endl;
IsotopeDistribution d;
d.setMaxIsotope(20);
d.estimateFromPeptideWeight(0.5 * mass_window_width + index * mass_window_width);
//trim left and right. And store the number of isotopes on the left, to reconstruct the monoisotopic peak
Size size_before = d.size();
d.trimLeft(intensity_percentage_optional);
isotope_distributions_[index].trimmed_left = size_before - d.size();
d.trimRight(intensity_percentage_optional);
for (IsotopeDistribution::Iterator it = d.begin(); it != d.end(); ++it)
{
isotope_distributions_[index].intensity.push_back(it->second);
//log_ << " - " << it->second << std::endl;
}
//determine the number of optional peaks at the beginning/end
Size begin = 0;
Size end = 0;
bool is_begin = true;
bool is_end = false;
for (Size i = 0; i < isotope_distributions_[index].intensity.size(); ++i)
{
if (isotope_distributions_[index].intensity[i] < intensity_percentage)
{
if (!is_end && !is_begin)
is_end = true;
if (is_begin)
++begin;
else if (is_end)
++end;
}
else if (is_begin)
{
is_begin = false;
}
}
isotope_distributions_[index].optional_begin = begin;
isotope_distributions_[index].optional_end = end;
//scale the distibution to a maximum of 1
DoubleReal max = 0.0;
for (Size i = 0; i < isotope_distributions_[index].intensity.size(); ++i)
{
if (isotope_distributions_[index].intensity[i] > max)
{
max = isotope_distributions_[index].intensity[i];
}
}
isotope_distributions_[index].max = max;
for (Size i = 0; i < isotope_distributions_[index].intensity.size(); ++i)
{
isotope_distributions_[index].intensity[i] /= max;
}
}
}
