protected override string FindModificationChar(PepXmlModifications ppmods, ModificationAminoacidMass modaa, string pureSeq)
{
if (!ppmods.HasModification(modaa.Mass))
{
var newmod = new PepXmlModificationItem()
{
Mass = modaa.Mass,
IsVariable = true,
};
var aa = pureSeq[modaa.Position - 1];
newmod.Aminoacid = aa.ToString();
newmod.MassDiff = Math.Round(modaa.Mass - new Aminoacids()[aa].MonoMass);
if (modaa.Position == 1)
{
newmod.IsTerminalN = true;
}
ppmods.Add(newmod);
ppmods.AssignModificationChar();
}
return(ppmods.FindModificationChar(modaa.Mass));
}
private void UpdateModifications(List <IIdentifiedSpectrum> result)
{
PepXmlModifications mods = new PepXmlModifications();
var map = new Dictionary <string, PepXmlModificationItem>();
foreach (var pep in result)
{
var curMods = pep.Modifications.Split(';');
foreach (var curMod in curMods)
{
var m = modReg2.Match(curMod);
if (m.Success)
{
var modname = m.Groups[2].Value;
if (!map.ContainsKey(modname))
{
var item = new PepXmlModificationItem();
item.Aminoacid = modname;
item.IsVariable = curMod.Contains("variable");
map[modname] = item;
}
}
}
}
map.OrderBy(m => m.Key).ToList().ForEach(m => mods.Add(m.Value));
mods.AssignModificationChar();
foreach (var spectrum in result)
{
if (string.IsNullOrEmpty(spectrum.Modifications))
{
continue;
}
Stack <Tuple <int, string> > vmods = new Stack <Tuple <int, string> >();
var curMods = spectrum.Modifications.Split(';');
foreach (var curMod in curMods)
{
if (!curMod.Contains("variable"))
{
continue;
}
var m = modReg2.Match(curMod);
if (m.Success)
{
var modname = m.Groups[2].Value;
var modchar = map[modname].Symbol;
var modpos = int.Parse(m.Groups[1].Value);
vmods.Push(new Tuple <int, string>(modpos, modchar));
}
}
foreach (var pep in spectrum.Peptides)
{
pep.Sequence = pep.Sequence.ToUpper();
}
while (vmods.Count > 0)
{
var vmod = vmods.Pop();
foreach (var pep in spectrum.Peptides)
{
pep.Sequence = pep.Sequence.Insert(vmod.Item1, vmod.Item2);
}
}
}
}
