MassDistribution multiply(const MassDistribution& m, const MassDistribution& n)
{
MassDistribution result;
for (MassDistribution::const_iterator i=m.begin(); i!=m.end(); ++i)
for (MassDistribution::const_iterator j=n.begin(); j!=n.end(); ++j)
result.push_back(MassAbundance(i->mass + j->mass, i->abundance * j->abundance));
return result;
}
void printEnvelope(const MassDistribution& md, int charge)
{
using namespace pwiz::calibration; // for Ion
for (MassDistribution::const_iterator it=md.begin(); it!=md.end(); ++it)
{
if (it->abundance < .0001) continue;
cout << Ion::mz(it->mass, charge) << " " << it->abundance << endl;
}
}
void testNormalization(const IsotopeCalculator& calc)
{
if (os_) *os_ << "mass normalized:\n"
<< calc.distribution(Formula("C100"), 0,
IsotopeCalculator::NormalizeMass) << endl;
if (os_) *os_ << "abundance normalized:\n"
<< calc.distribution(Formula("C100"), 0,
IsotopeCalculator::NormalizeAbundance) << endl;
MassDistribution md = calc.distribution(Formula("C100"), 0,
IsotopeCalculator::NormalizeMass |
IsotopeCalculator::NormalizeAbundance);
if (os_) *os_ << "both normalized:\n" << md << endl;
double sumSquares = 0;
for (MassDistribution::iterator it=md.begin(); it!=md.end(); ++it)
sumSquares += it->abundance * it->abundance;
if (os_) *os_ << "sumSquares: " << sumSquares << endl;
unit_assert_equal(sumSquares, 1, 1e-12);
unit_assert(md[0].mass == 0);
}
void test()
{
using namespace Peptide;
cout.precision(12);
initializeIsotopes();
for (Element e=ElementBegin; e!=ElementEnd; ++e)
{
cout << e << ":\n";
copy(isotopes[e].begin(), isotopes[e].end(), ostream_iterator<MassAbundance>(cout, "\n"));
}
cout << endl;
for (Element e=ElementBegin; e!=ElementEnd; ++e)
{
if (isotopes[e].size() != 2) continue;
MassDistribution test = calculateDistributionFor2Isotopes(isotopes[e], 100);
cout << e << ":\n";
copy(test.begin(), test.end(), ostream_iterator<MassAbundance>(cout, "\n"));
cout << endl;
}
}
void calculateIsotopeEnvelope(const PepDatum& peptide)
{
using namespace Peptide;
const string& name = peptide.first;
const Peptide::Formula f = peptide.second;
cout << name << endl << endl;
MassDistribution c = calculateDistributionFor2Isotopes(isotopes[C], f[C]);
cout << "C envelope:\n";
copy(c.begin(), c.end(), ostream_iterator<MassAbundance>(cout, "\n"));
cout << endl;
MassDistribution n = calculateDistributionFor2Isotopes(isotopes[N], f[N]);
cout << "N envelope:\n";
copy(n.begin(), n.end(), ostream_iterator<MassAbundance>(cout, "\n"));
cout << endl;
// calculate product of C and N envelopes
MassDistribution cn = multiply(c,n);
sort(cn.begin(), cn.end(), isMoreAbundant);
cout << "C*N envelope:\n";
copy(cn.begin(), cn.begin()+5, ostream_iterator<MassAbundance>(cout, "\n"));
cout << endl;
// hack to add back in H, O, S
Peptide::Formula hack(0, f[H], 0, f[O], f[S]);
double hackMass = hack.monoisotopicMass();
for (MassDistribution::iterator it=cn.begin(); it!=cn.end(); ++it)
it->mass += hackMass;
// print envelopes by charge state
for (int i=1; i<5; i++)
{
cout << "charge state " << i << endl;
printEnvelope(cn, i);
cout << endl;
}
}
