private double GetFragmentMass(string seq,
IonType type,
int ordinal,
int? decoyMassShift,
int massIndex,
IsotopeDistInfo isotopeDists,
ExplicitSequenceMods mods)
{
if (Transition.IsPrecursor(type))
{
if (isotopeDists != null)
{
int i = isotopeDists.MassIndexToPeakIndex(massIndex);
if (0 > i || i >= isotopeDists.CountPeaks)
{
throw new IndexOutOfRangeException(
string.Format(Resources.SequenceMassCalc_GetFragmentMass_Precursor_isotope__0__is_outside_the_isotope_distribution__1__to__2__,
GetMassIDescripion(massIndex), isotopeDists.PeakIndexToMassIndex(0),
isotopeDists.PeakIndexToMassIndex(isotopeDists.CountPeaks - 1)));
}
return isotopeDists.GetMassI(massIndex, decoyMassShift);
}
return GetPrecursorMass(seq, mods);
}
int len = seq.Length - 1;
bool nterm = Transition.IsNTerminal(type);
double mass = GetTermMass(nterm ? IonType.b : IonType.y, mods) + BioMassCalc.MassProton;
int iA = (nterm ? 0 : len);
int inc = (nterm ? 1 : -1);
var modMasses = GetModMasses(mods);
mass += (nterm ? modMasses._aminoNTermModMasses[seq[iA]] : modMasses._aminoCTermModMasses[seq[iA]]);
for (int i = 0; i < ordinal; i++)
{
char aa = seq[iA];
mass += _aminoMasses[aa] + modMasses._aminoModMasses[aa];
if (mods != null && iA < mods.ModMasses.Count)
mass += mods.ModMasses[iA];
iA += inc;
}
mass += GetTermDeltaMass(type); // Exactly match GetFragmentIonMasses()
return mass;
}
public double GetFragmentMass(Transition transition, IsotopeDistInfo isotopeDist, ExplicitSequenceMods mods)
{
if (transition.IsCustom())
{
var type = transition.IonType;
var massIndex = transition.MassIndex;
if (Transition.IsPrecursor(type) && (isotopeDist != null))
{
var i = isotopeDist.MassIndexToPeakIndex(massIndex);
if (0 > i || i >= isotopeDist.CountPeaks)
{
throw new IndexOutOfRangeException(
string.Format(Resources.SequenceMassCalc_GetFragmentMass_Precursor_isotope__0__is_outside_the_isotope_distribution__1__to__2__,
GetMassIDescripion(massIndex), isotopeDist.PeakIndexToMassIndex(0),
isotopeDist.PeakIndexToMassIndex(isotopeDist.CountPeaks - 1)));
}
return isotopeDist.GetMassI(massIndex);
}
return (MassType == MassType.Average)
? transition.CustomIon.AverageMass
: transition.CustomIon.MonoisotopicMass;
}
return GetFragmentMass(transition.Group.Peptide.Sequence,
transition.IonType,
transition.Ordinal,
transition.DecoyMassShift,
transition.MassIndex,
isotopeDist,
mods);
}