}//*/
public IEnumerable <ProductMatch> GetProductMZs(DBOptions options, GraphML_List <MsMsPeak> peaks)//, List<double> theoretical_product_mzs = null)
{
// speed optimizations
//double[] experimental_masses = Query.spectrum.Masses;
//GraphML_List<MSPeak> peaks = Query.spectrum.Peaks;
int num_experimental_peaks = peaks.Count;
TotalTheoreticalProducts = 0;
TotalWeightedProducts = 0;
//New version that should include charged ions
//foreach (ProductMatch matchTheo in AllFragmentSearch.ComputeAllFragments(Peptide, Query.precursor.Charge, options))
foreach (ProductMatch matchTheo in options.fragments.ComputeFragmentsFast(Peptide.GetMasses(), Query.precursor.Charge, options))
//foreach (ProductMatch matchTheo in options.fragments.ComputeFragments(Peptide, Query.precursor.Charge, options))
{
TotalTheoreticalProducts++;
TotalWeightedProducts += matchTheo.weight;//++;
//TODO test what is most common between charged ions, and uncharged ions
//for (int charge = 1; charge <= Query.precursor.Charge; charge++)
//for (int charge = Query.precursor.Charge; charge >= 1; charge--)
//{
double massDiff = options.productMassTolerance.Value;
double bestMz = -1;
double bestInt = 0;
foreach (int index in Query.spectrum.GetIndexOfMZInRange(matchTheo.theoMz, options.productMassTolerance))
{
if (peaks[index].Charge <= 0 || peaks[index].Charge == matchTheo.charge)
{
double diff = Numerics.CalculateMassError(peaks[index].MZ, matchTheo.theoMz, options.productMassTolerance.Units);
//double diff = matchTheo.theoMz - peaks[index].MZ;// experimental_masses[index];//TODO DALTON ONLY : add product mass tolerance unit test
if (Math.Abs(diff) < options.productMassTolerance.Value)
{
if (Math.Abs(diff) < Math.Abs(massDiff))//TODO Priority to intensity, or precision?
{
massDiff = diff;
bestMz = peaks[index].MZ;
}
//if (peaks[index].Intensity > bestInt)
bestInt += peaks[index].Intensity;
}
}
}
if (bestMz >= 0)
{
ProductMatch pMatch = new ProductMatch();
pMatch.weight = matchTheo.weight;
pMatch.theoMz = matchTheo.theoMz; // Utilities.MZFromMzSingleCharge(theoMass, charge);
pMatch.obsMz = bestMz; // experimental_masses[bestIndex];
pMatch.mass_diff = massDiff;
pMatch.obsIntensity = bestInt; // Intensities[bestIndex];
pMatch.charge = matchTheo.charge; // peaks[bestIndex].Charge;
pMatch.Fragment = matchTheo.Fragment;
pMatch.fragmentPos = matchTheo.fragmentPos;
pMatch.normalizedIntensity = pMatch.obsIntensity / (Query.spectrum.InjectionTime * Query.spectrum.PrecursorIntensityPerMilliSecond);
yield return(pMatch);
//break;
}
}
}
}//*/
/*
* private static IEnumerable<double> fragmentsTypesCTerm(double cTermCumul)
* {
* yield return cTermCumul + Constants.OXYGEN_MASS * 2 + Constants.HYDROGEN_MASS + Constants.CARBON_MASS;//X
* yield return cTermCumul + Constants.OXYGEN_MASS + Constants.HYDROGEN_MASS * 3;//Y
* yield return cTermCumul + Constants.OXYGEN_MASS + Constants.HYDROGEN_MASS - Constants.NITROGEN_MASS - Constants.HYDROGEN_MASS;//Z
* } //*/
public static IEnumerable <ProductMatch> ComputeAllFragments(Peptide peptide, int precursorKnownCharge, DBOptions dbOptions)
{
int maxCharge;
if (precursorKnownCharge > 1)
{
maxCharge = precursorKnownCharge - 1;
}
else
{
maxCharge = 1;
}
FragmentA fragNTerm = new FragmentA();
FragmentX fragCTerm = new FragmentX();
double[] masses = peptide.GetMasses();
ProductMatch match = new ProductMatch();
match.weight = 1;
double cumulN = 0.0; // Constants.WATER_MONOISOTOPIC_MASS;
double cumulC = 0.0; // Constants.WATER_MONOISOTOPIC_MASS;
for (int r = 0; r < masses.Length; r++)
{
cumulN += masses[r];
cumulC += masses[masses.Length - r - 1];
foreach (double product_mass in fragmentsTypesCTerm(cumulC))
{
match.fragmentPos = masses.Length - r;
match.Fragment = fragCTerm;
for (int c = maxCharge; c > 0; c--)
{
match.theoMz = Numerics.MZFromMass(product_mass, c);
match.charge = c;
yield return(match);
//match.theoMz = Numerics.MZFromMass(product_mass - Constants.WATER_MONOISOTOPIC_MASS, c);
//yield return match;
}
}
foreach (double product_mass in fragmentsTypesNTerm(cumulN))
{
match.fragmentPos = r + 1;
match.Fragment = fragNTerm;
for (int c = maxCharge; c > 0; c--)
{
match.theoMz = Numerics.MZFromMass(product_mass, c);
match.charge = c;
yield return(match);
match.theoMz = Numerics.MZFromMass(product_mass - Constants.WATER_MONOISOTOPIC_MASS, c);
yield return(match);
match.theoMz = Numerics.MZFromMass(product_mass - Constants.AMONIA_MASS, c);
yield return(match);
}
}
}
//Single charge immonium ions
//Water Loss
//Amonia Loss
//Internal fragments
//Fragment types
}