public void Parse(XmlDocument data)
{
#region Parameter Initialization
foreach (XmlNode mod in data.SelectNodes(".//parameters/const_mod"))
{
MSDigestModification constMod = MSDigestModification.FromURI(mod.InnerText);
Parameters.ConstantModifications.Add(constMod);
}
foreach (XmlNode mod in data.SelectNodes(".//parameters/mod_AA"))
{
Parameters.VariableModifications.Add(MSDigestModification.FromURI(mod.InnerText));
}
Parameters.Enzyme = data.SelectSingleNode(".//parameters/enzyme").InnerText;
Parameters.MissedCleavages = Convert.ToInt32(data.SelectSingleNode(".//parameters/missed_cleavages").InnerText);
Parameters.UserProteinSequence = data.SelectSingleNode(".//parameters/user_protein_sequence").InnerText;
#endregion
//No Database extractions for now
#region Peptide Extraction
foreach (XmlNode peptideNode in data.SelectNodes(".//peptide"))
{
//Console.WriteLine("------------------------------");
MSDigestPeptide peptideObj = new MSDigestPeptide();
peptideObj.PeptideIndex = Convert.ToInt32(peptideNode.SelectSingleNode(".//protein_index").InnerText);
peptideObj.Charge = Convert.ToInt32(peptideNode.SelectSingleNode(".//charge").InnerText);
peptideObj.Mass = Convert.ToDouble(peptideNode.SelectSingleNode(".//mi_m_over_z").InnerText);
String modStr = "";
foreach (XmlNode mod in peptideNode.SelectNodes(".//modification"))
{
//Console.WriteLine(mod.InnerText);
modStr += mod.InnerText + " ";
}
peptideObj.Modifications = modStr;
peptideObj.StartAA = Convert.ToInt32(peptideNode.SelectSingleNode(".//start_aa").InnerText);
peptideObj.EndAA = Convert.ToInt32(peptideNode.SelectSingleNode(".//end_aa").InnerText);
peptideObj.NextAA = (peptideNode.SelectSingleNode(".//next_aa").InnerText);
peptideObj.PreviousAA = (peptideNode.SelectSingleNode(".//previous_aa").InnerText);
peptideObj.MissedCleavages = Convert.ToInt32(peptideNode.SelectSingleNode(".//missed_cleavages").InnerText);
peptideObj.Sequence = (peptideNode.SelectSingleNode(".//database_sequence").InnerText);
peptideObj.ProteinID = Parameters.UserProteinSequence;
peptideObj.NumGlycosylations = PeptideUtilities.CountNGlycanSequons(peptideObj);
//Console.WriteLine(peptideObj);
Peptides.Add(peptideObj);
}
#endregion
}
public MSDigestPeptide ConvertToMSDigestPeptide()
{
MSDigestPeptide peptide = new MSDigestPeptide();
peptide.Charge = Charge;
peptide.Selected = Selected;
peptide.PeptideIndex = PeptideIndex;
peptide.Mass = Mass;
peptide.Modifications = Modifications;
peptide.StartAA = StartAA;
peptide.EndAA = EndAA;
peptide.MissedCleavages = MissedCleavages;
peptide.PreviousAA = PreviousAA;
peptide.StartAA = StartAA;
peptide.NextAA = NextAA;
peptide.NumGlycosylations = NumGlycosylations;
peptide.Sequence = Sequence;
peptide.ProteinID = ProteinID;
return peptide;
}
public Peptide(MSDigestPeptide other)
: base()
{
this.Selected = other.Selected;
this.PeptideIndex = other.PeptideIndex;
this.Mass = other.Mass;
this.Charge = other.Charge;
this.Modifications = other.Modifications;
this.StartAA = other.StartAA;
this.EndAA = other.EndAA;
this.MissedCleavages = other.MissedCleavages;
this.PreviousAA = other.PreviousAA;
this.Sequence = other.Sequence;
this.NextAA = other.NextAA;
this.NumGlycosylations = other.NumGlycosylations;
this.ProteinID = other.ProteinID;
}
public static int CountNGlycanSequons(MSDigestPeptide sequence)
{
return CountNGlycanSequons(sequence.Sequence);
}
/// <summary>
/// Combination Cosntructor
/// </summary>
/// <param name="glycanComposition"></param>
/// <param name="peptide"></param>
public GlycopeptideComposition(GlycanComposition glycanComposition, MSDigestPeptide peptide)
: base(glycanComposition)
{
this.PeptideSequence = peptide.Sequence;
this.PeptideModification = peptide.Modifications;
this.StartAA = peptide.StartAA;
this.EndAA = peptide.EndAA;
this.GlycosylationCount = peptide.NumGlycosylations;
this.MassWeight += peptide.Mass - WaterMass - glycanComposition.AdductMass;
MolecularComposition["Water"] -= 1;
if (ElementalComposition.ContainsKey("O"))
{
ElementalComposition["O"] -= 1;
ElementalComposition["H"] -= 2;
}
this.ProteinID = peptide.ProteinID;
AdductAmount = 0;
AdductReplaces = "";
}
/// <summary>
/// Peptide-Only Constructor
/// </summary>
/// <param name="peptide"></param>
public GlycopeptideComposition(MSDigestPeptide peptide)
: base()
{
this.PeptideSequence = peptide.Sequence;
this.PeptideModification = peptide.Modifications;
this.StartAA = peptide.StartAA;
this.EndAA = peptide.EndAA;
this.GlycosylationCount = peptide.NumGlycosylations;
this.MassWeight += peptide.Mass;
this.ProteinID = peptide.ProteinID;
}
