internal ModifiedPeptide Clone()
{
ModifiedPeptide p = new ModifiedPeptide();
p.peptideIndex = peptideIndex;
p.modifications = modifications.Clone();
p.mass = mass;
return(p);
}
public ModifiedPeptide[] ApplyVariableModifications(Modification[] modifications, int index)
{
ModifiedPeptide[] result = new ModifiedPeptide[] { CreateNonmodifiedVersion(index) };
for (int i = 0; i < modifications.Length; i++)
{
result = ApplyVariableModification(result, modifications[i]);
}
result = FilterEqualMasses(result);
return(result);
}
private static ModifiedPeptide[] ApplyLabelModifications(ModifiedPeptide peptide, Modification[][] mod,
string sequence)
{
ModifiedPeptide[] result = new ModifiedPeptide[mod.Length + 1];
result[0] = peptide;
for (int i = 0; i < mod.Length; i++)
{
result[i + 1] = ApplyLabelModifications(peptide, mod[i], sequence);
}
return(result);
}
public ModifiedPeptide SetVariableModifications(PeptideModificationState varMods, int index)
{
ModifiedPeptide result = CreateNonmodifiedVersion(index);
result.modifications = varMods;
if (varMods != null)
{
result.mass += varMods.GetDeltaMass();
}
return(result);
}
public static ModifiedPeptide Read(BinaryReader reader)
{
try {
ModifiedPeptide result = new ModifiedPeptide();
result.peptideIndex = reader.ReadInt32();
result.modifications = PeptideModificationState.Read(reader);
result.mass = reader.ReadDouble();
return(result);
} catch (EndOfStreamException) {
return(null);
}
}
public DatabaseModifiedPeptide[] ApplyVariableModifications(Modification[] modifications, Modification[][] lMods,
int index, IProteinSet proteinSet)
{
string sequence = GetSequence(proteinSet);
ModifiedPeptide[] result = new ModifiedPeptide[] { CreateNonmodifiedVersion(index, sequence) };
result = ApplyLabelModifications(result, lMods, sequence);
for (int i = 0; i < modifications.Length; i++)
{
result = ApplyVariableModification(result, modifications[i], sequence, proteinSet);
}
result = FilterEqualMods(result);
return(ConvertToDatabasePeptides(result));
}
private static ModifiedPeptide[] FilterEqualMasses(IEnumerable <ModifiedPeptide> peptides)
{
Dictionary <double, ModifiedPeptide> x = new Dictionary <double, ModifiedPeptide>();
foreach (ModifiedPeptide p in peptides)
{
if (!x.ContainsKey(p.mass))
{
x.Add(p.mass, p);
}
}
ModifiedPeptide[] result = new ModifiedPeptide[x.Count];
x.Values.CopyTo(result, 0);
return(result);
}
private static ModifiedPeptide ApplyLabelModifications(ModifiedPeptide peptide, Modification[] mod,
string s)
{
ModifiedPeptide result = peptide.Clone();
for (int i = 0; i < mod.Length; i++)
{
for (int j = 0; j < mod[i].AaCount; j++)
{
for (int k = 0; k < s.Length; k++)
{
if (s[k] == mod[i].GetAaAt(j) && result.modifications.GetModificationAt(k) == ushort.MaxValue)
{
result.mass += mod[i].DeltaMass;
result.modifications.SetModificationAt(k, mod[i].Index);
}
}
}
}
return(result);
}
private ModifiedPeptide[] ApplyVariableModification(ModifiedPeptide peptide, Modification mod, string s, IProteinSet proteinSet)
{
help.Clear();
help.Add(peptide);
for (int i = 0; i < mod.AaCount; i++)
{
switch (mod.GetTermType(i))
{
case ModificationSiteType.aa: {
toBeAdded.Clear();
foreach (ModifiedPeptide w in help)
{
List <int> indices = new List <int>();
for (int j = 0; j < s.Length; j++)
{
if (s[j] == mod.GetAaAt(i) && w.modifications.GetModificationAt(j) == ushort.MaxValue)
{
indices.Add(j);
}
}
for (int j = 1; j <= indices.Count; j++)
{
ModifiedPeptide q = w.Clone();
q.mass += j * mod.DeltaMass;
for (int k = 0; k < j; k++)
{
q.modifications.SetModificationAt(indices[k], mod.Index);
}
toBeAdded.Add(q);
}
}
foreach (ModifiedPeptide a in toBeAdded)
{
help.Add(a);
}
break;
}
case ModificationSiteType.nterm: {
toBeAdded.Clear();
foreach (ModifiedPeptide w in help)
{
if (s[0] == mod.GetAaAt(i) && w.modifications.GetNTermModification() == ushort.MaxValue)
{
ModifiedPeptide q = w.Clone();
q.mass += mod.DeltaMass;
q.modifications.SetNTermModification(mod.Index);
toBeAdded.Add(q);
}
}
foreach (ModifiedPeptide a in toBeAdded)
{
help.Add(a);
}
break;
}
case ModificationSiteType.cterm: {
toBeAdded.Clear();
foreach (ModifiedPeptide w in help)
{
if (s[s.Length - 1] == mod.GetAaAt(i) && w.modifications.GetCTermModification() == ushort.MaxValue)
{
ModifiedPeptide q = w.Clone();
q.mass += mod.DeltaMass;
q.modifications.SetCTermModification(mod.Index);
toBeAdded.Add(q);
}
}
foreach (ModifiedPeptide a in toBeAdded)
{
help.Add(a);
}
break;
}
}
}
if (mod.GetPosition() == ModificationPosition.anyNterm)
{
toBeAdded.Clear();
foreach (ModifiedPeptide w in help)
{
if (w.modifications.GetNTermModification() == ushort.MaxValue)
{
ModifiedPeptide q = w.Clone();
q.mass += mod.DeltaMass;
q.modifications.SetNTermModification(mod.Index);
toBeAdded.Add(q);
}
}
foreach (ModifiedPeptide a in toBeAdded)
{
help.Add(a);
}
}
if (mod.GetPosition() == ModificationPosition.anyCterm)
{
toBeAdded.Clear();
foreach (ModifiedPeptide w in help)
{
if (w.modifications.GetCTermModification() == ushort.MaxValue)
{
ModifiedPeptide q = w.Clone();
q.mass += mod.DeltaMass;
q.modifications.SetCTermModification(mod.Index);
toBeAdded.Add(q);
}
}
foreach (ModifiedPeptide a in toBeAdded)
{
help.Add(a);
}
}
if (mod.GetPosition() == ModificationPosition.proteinNterm && IsNterm())
{
toBeAdded.Clear();
foreach (ModifiedPeptide w in help)
{
if (w.modifications.GetNTermModification() == ushort.MaxValue)
{
ModifiedPeptide q = w.Clone();
q.mass += mod.DeltaMass;
q.modifications.SetNTermModification(mod.Index);
toBeAdded.Add(q);
}
}
foreach (ModifiedPeptide a in toBeAdded)
{
help.Add(a);
}
}
if (mod.GetPosition() == ModificationPosition.proteinCterm && IsCterm(proteinSet))
{
toBeAdded.Clear();
foreach (ModifiedPeptide w in help)
{
if (w.modifications.GetCTermModification() == ushort.MaxValue)
{
ModifiedPeptide q = w.Clone();
q.mass += mod.DeltaMass;
q.modifications.SetCTermModification(mod.Index);
toBeAdded.Add(q);
}
}
foreach (ModifiedPeptide a in toBeAdded)
{
help.Add(a);
}
}
return(help.ToArray());
}
