public static ModifiedSequence GetFragmentSequence(ModifiedSequence modifiedSequence, IonType ionType,
int ordinal)
{
string unmodifiedSequence = modifiedSequence.GetUnmodifiedSequence();
switch (ionType)
{
case IonType.a:
case IonType.b:
case IonType.c:
return(new ModifiedSequence(unmodifiedSequence.Substring(0, ordinal),
modifiedSequence.GetModifications().Where(mod => mod.IndexAA < ordinal),
MassType.Monoisotopic));
}
int offset = unmodifiedSequence.Length - ordinal;
string fragmentSequence = unmodifiedSequence.Substring(offset);
var newModifications = modifiedSequence.GetModifications()
.Where(mod => mod.IndexAA >= offset)
.Select(mod => mod.ChangeIndexAa(mod.IndexAA - offset));
return(new ModifiedSequence(fragmentSequence, newModifications, MassType.Monoisotopic));
}
private static Molecule GetSequenceFormula(ModifiedSequence modifiedSequence, MassType massType, out double unexplainedMassShift)
{
unexplainedMassShift = 0;
var molecule = new Dictionary <string, int>();
string unmodifiedSequence = modifiedSequence.GetUnmodifiedSequence();
var modifications = modifiedSequence.GetModifications().ToLookup(mod => mod.IndexAA);
for (int i = 0; i < unmodifiedSequence.Length; i++)
{
char aminoAcid = unmodifiedSequence[i];
AddAminoAcidFormula(massType, aminoAcid, molecule, ref unexplainedMassShift);
foreach (var mod in modifications[i])
{
string formula = mod.Formula;
if (formula == null)
{
var staticMod = mod.StaticMod;
var aa = unmodifiedSequence[i];
if ((staticMod.LabelAtoms & LabelAtoms.LabelsAA) != LabelAtoms.None && AminoAcid.IsAA(aa))
{
formula = SequenceMassCalc.GetHeavyFormula(aa, staticMod.LabelAtoms);
}
}
if (formula != null)
{
var modFormula = Molecule.ParseExpression(formula);
Add(molecule, modFormula);
}
else
{
unexplainedMassShift += massType.IsMonoisotopic() ? mod.MonoisotopicMass : mod.AverageMass;
}
}
}
return(Molecule.FromDict(molecule));
}