public CompactPeptide(PepWithSetModForCompactPep peptideWithSetModifications, TerminusType terminusType)
{
NTerminalMasses = null;
CTerminalMasses = null;
if (terminusType == TerminusType.None || terminusType == TerminusType.N)
{
NTerminalMasses = ComputeFollowingFragmentMassesByPepCom(peptideWithSetModifications, 0, 0, 1).ToArray();
}
if (terminusType == TerminusType.None || terminusType == TerminusType.C)
{
CTerminalMasses = ComputeFollowingFragmentMassesByPepCom(peptideWithSetModifications, 0, peptideWithSetModifications.Length + 1, -1).ToArray();
}
MonoisotopicMassIncludingFixedMods = peptideWithSetModifications.MonoisotopicMass;
}
protected static IEnumerable <double> ComputeFollowingFragmentMassesByPepCom(PepWithSetModForCompactPep yyy, double prevMass, int oneBasedIndexToLookAt, int direction)
{
ModificationWithMass currentModification = null;
do
{
if (oneBasedIndexToLookAt != 0 && oneBasedIndexToLookAt != yyy.Length + 1)
{
prevMass += Residue.ResidueMonoisotopicMass[yyy.BaseSequence[oneBasedIndexToLookAt - 1]];
}
// If modification exists
if (yyy.allModsOneIsNterminus.TryGetValue(oneBasedIndexToLookAt + 1, out currentModification))
{
if (currentModification.neutralLosses.Count == 1 && oneBasedIndexToLookAt != 0 && oneBasedIndexToLookAt != yyy.Length + 1)
{
prevMass += currentModification.monoisotopicMass - currentModification.neutralLosses.First();
yield return(Math.Round(prevMass, digitsForRoundingMasses));
}
else
{
foreach (double nl in currentModification.neutralLosses)
{
var theMass = prevMass + currentModification.monoisotopicMass - nl;
if (oneBasedIndexToLookAt != 0 && oneBasedIndexToLookAt != yyy.Length + 1)
{
yield return(Math.Round(theMass, digitsForRoundingMasses));
}
if ((direction == 1 && oneBasedIndexToLookAt + direction < yyy.Length) ||
(direction == -1 && oneBasedIndexToLookAt + direction > 1))
{
foreach (var nextMass in ComputeFollowingFragmentMassesByPepCom(yyy, theMass, oneBasedIndexToLookAt + direction, direction))
{
yield return(Math.Round(nextMass, digitsForRoundingMasses));
}
}
}
break;
}
}
else if (oneBasedIndexToLookAt != 0 && oneBasedIndexToLookAt != yyy.Length + 1) // No modification exists
{
yield return(Math.Round(prevMass, digitsForRoundingMasses));
}
oneBasedIndexToLookAt += direction;
} while ((oneBasedIndexToLookAt > 1 && direction == -1) || (oneBasedIndexToLookAt < yyy.Length && direction == 1));
}
