public IsotopeDistribution estimateForFragmentFromWeightsAndSulfur(double monoPeptideMass, double monoFragmentMass,
int minIsotope, int maxIsotope, int precursorSulfur, int fragmentSulfur)
{
IsotopeDistribution fragment = estimateFromPeptideWeightAndSulfur(monoFragmentMass, maxIsotope, precursorSulfur);
IsotopeDistribution compFragment = estimateFromPeptideWeightAndSulfur(monoPeptideMass - monoFragmentMass, maxIsotope, fragmentSulfur);
return(calcFragmentIsotopeDistribution(fragment, compFragment, minIsotope, maxIsotope));
}
private IsotopeDistribution calcFragmentIsotopeDistribution(IsotopeDistribution fragment, IsotopeDistribution compFragment,
int minIsotope, int maxIsotope)
{
IsotopeDistribution result = new IsotopeDistribution(maxIsotope);
for (int i = 0; i < fragment.size(); ++i)
{
for (int isotope = minIsotope; isotope <= maxIsotope; ++isotope)
{
if (isotope >= i && (isotope - i) < compFragment.size())
{
result.setIntensity(i, (float)(result.getIntensity(i) + compFragment.getIntensity(isotope - i)));
}
}
result.setIntensity(i, (float)(result.getIntensity(i) * fragment.getIntensity(i)));
result.setMass(i, fragment.getMass(0) + (i * C13C12_MASSDIFF_U));
}
return(result);
}
IsotopeDistribution estimateFromPeptideWeightAndSulfur(double monoMass, int maxIsotope, int numSulfur)
{
IsotopeDistribution result;
if (inModelBounds(monoMass, maxIsotope, numSulfur))
{
result = new IsotopeDistribution(maxIsotope);
for (int isotope = 0; isotope <= maxIsotope; ++isotope)
{
//double probability = numSulfur2models_.get(numSulfur).get(isotope).eval(monoMass);
double probability = numSulfur2models_[numSulfur][isotope].eval(monoMass);
result.setMass(isotope, monoMass + (isotope * C13C12_MASSDIFF_U));
result.setIntensity(isotope, (float)probability);
}
}
else
{
throw new Exception("Request out of range.");
}
return(result);
}
