private PeptideModificationState[] ApplyVariableModificationFixedNumber(PeptideModificationState peptide,
Modification mod, int n,
out bool incomplete)
{
incomplete = false;
if (n == 0)
{
return(new PeptideModificationState[0]);
}
if (mod.GetPosition() == ModificationPosition.anyNterm)
{
if (n > 1)
{
return(new PeptideModificationState[0]);
}
if (peptide.GetNTermModification() == ushort.MaxValue)
{
PeptideModificationState q = peptide.Clone();
q.SetNTermModification(mod.Index);
return(new PeptideModificationState[] { q });
}
return(new PeptideModificationState[0]);
}
if (mod.GetPosition() == ModificationPosition.anyCterm)
{
if (n > 1)
{
return(new PeptideModificationState[0]);
}
if (peptide.GetCTermModification() == ushort.MaxValue)
{
PeptideModificationState q = peptide.Clone();
q.SetCTermModification(mod.Index);
return(new PeptideModificationState[] { q });
}
return(new PeptideModificationState[0]);
}
if (mod.GetPosition() == ModificationPosition.proteinNterm)
{
if (n > 1)
{
return(new PeptideModificationState[0]);
}
if (peptide.GetNTermModification() == ushort.MaxValue)
{
PeptideModificationState q = peptide.Clone();
q.SetNTermModification(mod.Index);
return(new PeptideModificationState[] { q });
}
return(new PeptideModificationState[0]);
}
if (mod.GetPosition() == ModificationPosition.proteinCterm)
{
if (n > 1)
{
return(new PeptideModificationState[0]);
}
if (peptide.GetCTermModification() == ushort.MaxValue)
{
PeptideModificationState q = peptide.Clone();
q.SetCTermModification(mod.Index);
return(new PeptideModificationState[] { q });
}
return(new PeptideModificationState[0]);
}
string s = Sequence;
switch (mod.GetTermType(0))
{
case ModificationSiteType.aa: {
HashSet <int> ind = new HashSet <int>();
for (int j = 0; j < s.Length; j++)
{
for (int i = 0; i < mod.AaCount; i++)
{
if (s[j] == mod.GetAaAt(i) && peptide.GetModificationAt(j) == ushort.MaxValue)
{
ind.Add(j);
}
}
}
int[] indices = ind.ToArray();
if (indices.Length < n)
{
return(new PeptideModificationState[0]);
}
List <PeptideModificationState> result = new List <PeptideModificationState>();
bool incompl;
int[][] comb = NumUtil.GetCombinations(indices.Length, n, 10000, out incompl);
if (incompl)
{
incomplete = incompl;
}
for (int j = 0; j < comb.Length; j++)
{
int[] iind = ArrayUtil.SubArray(indices, comb[j]);
PeptideModificationState q = peptide.Clone();
for (int k = 0; k < iind.Length; k++)
{
q.SetModificationAt(iind[k], mod.Index);
}
result.Add(q);
}
return(result.ToArray());
}
case ModificationSiteType.nterm: {
if (n > 1)
{
return(new PeptideModificationState[0]);
}
for (int i = 0; i < mod.AaCount; i++)
{
List <PeptideModificationState> toBeAdded = new List <PeptideModificationState>();
if (s[0] == mod.GetAaAt(i) && peptide.GetNTermModification() == ushort.MaxValue)
{
PeptideModificationState q = peptide.Clone();
q.SetNTermModification(mod.Index);
toBeAdded.Add(q);
}
if (toBeAdded.Count > 0)
{
return(toBeAdded.ToArray());
}
}
return(new PeptideModificationState[0]);
}
case ModificationSiteType.cterm: {
if (n > 1)
{
return(new PeptideModificationState[0]);
}
for (int i = 0; i < mod.AaCount; i++)
{
List <PeptideModificationState> toBeAdded = new List <PeptideModificationState>();
if (s[s.Length - 1] == mod.GetAaAt(i) && peptide.GetCTermModification() == ushort.MaxValue)
{
PeptideModificationState q = peptide.Clone();
q.SetCTermModification(mod.Index);
toBeAdded.Add(q);
}
if (toBeAdded.Count > 0)
{
return(toBeAdded.ToArray());
}
}
return(new PeptideModificationState[0]);
}
}
throw new Exception("Never get here.");
}
