public PeptideModificationState GetTrueModifications()
{
PeptideModificationState result = GetFreshCopy(Length);
if (NTermModification != ushort.MaxValue && Modification.IsStandardVarMod(NTermModification))
{
result.NTermModification = NTermModification;
}
if (CTermModification != ushort.MaxValue && Modification.IsStandardVarMod(CTermModification))
{
result.CTermModification = CTermModification;
}
for (int i = 0; i < Length; i++)
{
ushort m = GetModificationAt(i);
if (m == ushort.MaxValue || !Modification.IsStandardVarMod(m))
{
result.SetModificationAt(i, ushort.MaxValue);
}
else
{
result.SetModificationAt(i, GetModificationAt(i));
}
}
return(result);
}
public PeptideModificationState GetLabelModifications(ushort[] labelMods, string sequence)
{
PeptideModificationState result = GetFreshCopy(Length);
if (NTermModification != ushort.MaxValue && !Modification.IsStandardVarMod(NTermModification))
{
result.NTermModification = NTermModification;
}
if (CTermModification != ushort.MaxValue && !Modification.IsStandardVarMod(CTermModification))
{
result.CTermModification = CTermModification;
}
for (int i = 0; i < Length; i++)
{
ushort m = GetModificationAt(i);
if (m != ushort.MaxValue && !Modification.IsStandardVarMod(m))
{
result.SetModificationAt(i, m);
}
else
{
result.SetModificationAt(i, ushort.MaxValue);
}
}
foreach (ushort labelMod in labelMods)
{
if (!Modification.IsStandardVarMod(labelMod))
{
Modification mod = Tables.ModificationList[labelMod];
if (mod.IsInternal)
{
for (int j = 0; j < mod.AaCount; j++)
{
char c = mod.GetAaAt(j);
for (int i = 0; i < Length; i++)
{
if (sequence[i] == c)
{
result.SetModificationAt(i, mod.Index);
}
}
}
}
else
{
if (mod.IsNterminal)
{
result.NTermModification = mod.Index;
}
else
{
result.CTermModification = mod.Index;
}
}
}
}
return(result);
}