public PepXmlModifications ParseModifications(XElement searchSummary)
{
PepXmlModifications result = new PepXmlModifications();
var aminoacid_modifications = searchSummary.FindDescendants("aminoacid_modification");
foreach (var am in aminoacid_modifications)
{
PepXmlModificationItem item = new PepXmlModificationItem();
item.IsVariable = am.Attribute("variable").Value.Equals("Y");
item.IsAminoacid = true;
item.IsProteinTerminal = false;
item.IsTerminalN = false;
item.Aminoacid = am.Attribute("aminoacid").Value;
item.Mass = MyConvert.ToDouble(am.Attribute("mass").Value);
item.MassDiff = MyConvert.ToDouble(am.Attribute("massdiff").Value);
result.Add(item);
}
var terminal_modifications = searchSummary.FindDescendants("terminal_modification");
foreach (var am in terminal_modifications)
{
PepXmlModificationItem item = new PepXmlModificationItem();
item.IsVariable = am.Attribute("variable").Value.Equals("Y");
item.IsAminoacid = false;
item.IsProteinTerminal = am.Attribute("protein_terminus").Value.Equals("Y");
item.IsTerminalN = am.Attribute("terminus").Value.Equals("n");;
item.Mass = MyConvert.ToDouble(am.Attribute("mass").Value);
item.MassDiff = MyConvert.ToDouble(am.Attribute("massdiff").Value);
result.Add(item);
}
result.AssignModificationChar();
return(result);
}
private void ParseSearchHit(IIdentifiedSpectrum sph, XElement searchHit, PepXmlModifications ppmods)
{
var sp = new IdentifiedPeptide(sph);
var mod_info = searchHit.FindFirstDescendant("modification_info");
string seq = searchHit.Attribute("peptide").Value;
if (mod_info != null)
{
var modified_peptide = mod_info.Attribute("modified_peptide");
if (modified_peptide != null && !modReg.Match(modified_peptide.Value).Success)
{
seq = modified_peptide.Value;
}
else
{
var pureSeq = seq;
var modaas = PeptideProphetUtils.ParseModificationAminoacidMass(mod_info);
if (modaas != null && modaas.Count > 0)
{
modaas.Reverse();
foreach (var modaa in modaas)
{
string modchar = FindModificationChar(ppmods, modaa, pureSeq);
seq = seq.Insert(modaa.Position, modchar);
}
}
}
}
if (searchHit.Attribute("peptide_prev_aa") != null)
{
sp.Sequence = searchHit.Attribute("peptide_prev_aa").Value + "." +
seq + "." +
searchHit.Attribute("peptide_next_aa").Value;
}
else
{
sp.Sequence = seq;
}
sph.NumMissedCleavages = GetAttributeValue(searchHit, "num_missed_cleavages", 0);
sph.NumProteaseTermini = GetAttributeValue(searchHit, "num_tol_term", 2);
sp.AddProtein(searchHit.Attribute("protein").Value);
var NumTotalProteins = int.Parse(searchHit.Attribute("num_tot_proteins").Value);
if (NumTotalProteins > 1)
{
var alternative_proteins = searchHit.FindDescendants("alternative_protein");
foreach (var alternative_protein in alternative_proteins)
{
sp.AddProtein(alternative_protein.Attribute("protein").Value);
}
}
ParseScoreAndOtherInformation(sph, searchHit);
}
private void WriteModifications(StreamWriter sw, PepXmlModifications sp)
{
var aas = new Aminoacids();
foreach (var ssm in sp)
{
if (ssm.MassDiff != 0.0)
{
if (ssm.IsAminoacid)
{
sw.Write(" <aminoacid_modification aminoacid=\"{0}\" massdiff=\"{1:0.0000}\" mass=\"{2:0.0000}\" variable=\"{3}\"",
ssm.Aminoacid,
ssm.MassDiff,
ssm.Mass,
ssm.IsVariable ? "Y" : "N");
}
else
{
sw.Write(" <terminal_modification terminus=\"{0}\" massdiff=\"{1:0.0000}\" mass=\"{2:0.0000}\" variable=\"{3}\" protein_terminus=\"{4}\"",
ssm.IsTerminalN ? "n" : "c",
ssm.MassDiff,
ssm.Mass,
ssm.IsVariable ? "Y" : "N",
ssm.IsProteinTerminal ? (ssm.IsTerminalN ? "n" : "c") : "");
}
if (string.IsNullOrEmpty(ssm.Symbol))
{
sw.WriteLine("/>");
}
else
{
sw.WriteLine(" symbol=\"{0}\"/>", ssm.Symbol);
}
}
}
}
protected virtual string FindModificationChar(PepXmlModifications ppmods, ModificationAminoacidMass modaa, string pureSeq)
{
return(ppmods.FindModificationChar(modaa.Mass));
}
