public PeptideModificationState GetTrueModifications(HashSet <string> labelModificationSet)
{
PeptideModificationState result = GetFreshCopy(Length);
result.SetNTermModification(GetNTermModification());
result.SetCTermModification(GetCTermModification());
for (int i = 0; i < Length; i++)
{
ushort m = GetModificationAt(i);
if (m == ushort.MaxValue || labelModificationSet.Contains(Tables.modificationList[m].Title))
{
result.SetModificationAt(i, ushort.MaxValue);
}
else
{
result.SetModificationAt(i, GetModificationAt(i));
}
}
return(result);
}
public PeptideModificationState GetLabelModifications(ushort[] fixedMods, string sequence,
HashSet <string> labelModificationSet)
{
PeptideModificationState result = GetFreshCopy(Length);
for (int i = 0; i < Length; i++)
{
ushort m = GetModificationAt(i);
if (m != ushort.MaxValue && labelModificationSet.Contains(Tables.modificationList[m].Title))
{
result.SetModificationAt(i, GetModificationAt(i));
}
else
{
result.SetModificationAt(i, ushort.MaxValue);
}
}
foreach (ushort fixMod in fixedMods)
{
if (labelModificationSet.Contains(Tables.modificationList[fixMod].Title))
{
Modification mod = Tables.modificationList[fixMod];
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);
}
}
}
}
}
return(result);
}