/// <summary>
/// Makes the call to generate the ion masses adjusts for etd fragmentation
/// </summary>
/// <param name="charge">charge, do i need this?</param>
/// <param name="aParams">ascore parameters</param>
private void Calculate(int charge, AScoreParameters aParams)
{
chargeState = charge;
// First thing to do is generate the base ion masses
GenerateIonMasses(aParams.StaticMods, aParams.TerminiMods);
// If the fragment type is ETD, we need to convert the B and Y ions
// into C and Z ions
if (aParams.FragmentType == FragmentType.ETD)
{
for (int i = 0; i < yIonsMonoisotopicMass.Count; ++i)
{
MolecularWeights.MassType = MassType.Monoisotopic;
if (i < bIonsMonoisotopicMass.Count)
{
bIonsMonoisotopicMass[i] += MolecularWeights.Ammonia;
}
yIonsMonoisotopicMass[i] -= MolecularWeights.NH2;
}
}
}
public TheoreticalSpectra(string fht, AScoreParameters aparam, int chargeS, List <Mod.DynamicModification> moveMod)
{
chargeState = chargeS;
this.fht = fht;
Calculate(chargeState, aparam);
}
/// <summary>
/// Parses the parameter file for ascore
/// </summary>
/// <param name="inputFile">name of the xml file</param>
/// <returns>ascore parameters object</returns>
public static AScoreParameters ParseXml(string inputFile)
{
XmlDocument parameterFile = new XmlDocument();
parameterFile.Load(new XmlTextReader(inputFile));
XmlNodeList staticMod = parameterFile.SelectNodes("/Run/Modifications/StaticSeqModifications");
XmlNodeList terminiMod = parameterFile.SelectNodes("/Run/Modifications/TerminiModifications");
XmlNodeList dynamicMod = parameterFile.SelectNodes("/Run/Modifications/DynamicModifications");
XmlNode massTolerance = parameterFile.SelectSingleNode("/Run/MassTolerance");
XmlNode fragmentType = parameterFile.SelectSingleNode("/Run/FragmentType");
FragmentType f = GetFragmentType(fragmentType);
double massTol = double.Parse(massTolerance.InnerText);
List <Modification> stat = new List <Modification>();
List <TerminiModification> termMod = new List <TerminiModification>();
List <DynamicModification> dynam = new List <DynamicModification>();
foreach (XmlNode mod in staticMod)
{
foreach (XmlNode mod2 in mod.ChildNodes)
{
double massMonoIsotopic = 0.0;
char modSymbol = ' ';
List <char> possibleModSites = new List <char>();
int uniqueID = 0;
foreach (XmlNode item in mod2.ChildNodes)
{
if (item.Name == "MassMonoIsotopic")
{
massMonoIsotopic = double.Parse(item.InnerText);
}
else if (item.Name == "PossibleModSites")
{
foreach (XmlNode item2 in item.ChildNodes)
{
possibleModSites.Add(item2.InnerText[0]);
}
}
else if (item.Name == "UniqueID")
{
uniqueID = int.Parse(item.InnerText);
}
}
Modification m = new Modification();
m.MassMonoisotopic = massMonoIsotopic;
m.ModSymbol = modSymbol;
m.PossibleModSites = possibleModSites;
m.UniqueID = uniqueID;
stat.Add(m);
}
}
foreach (XmlNode mod in terminiMod)
{
foreach (XmlNode mod2 in mod.ChildNodes)
{
double massMonoIsotopic = 0.0;
char modSymbol = ' ';
List <char> possibleModSites = new List <char>();
int uniqueID = 0;
bool nTerm = false;
bool cTerm = false;
foreach (XmlNode item in mod2.ChildNodes)
{
if (item.Name == "MassMonoIsotopic")
{
massMonoIsotopic = double.Parse(item.InnerText);
}
else if (item.Name == "UniqueID")
{
uniqueID = int.Parse(item.InnerText);
}
else if (item.Name == "Nterm")
{
nTerm = bool.Parse(item.InnerText);
}
else if (item.Name == "Cterm")
{
cTerm = bool.Parse(item.InnerText);
}
}
TerminiModification m = new TerminiModification();
m.MassMonoisotopic = massMonoIsotopic;
m.ModSymbol = modSymbol;
m.PossibleModSites = possibleModSites;
m.UniqueID = uniqueID;
m.nTerminus = nTerm;
m.cTerminus = cTerm;
termMod.Add(m);
}
}
foreach (XmlNode mod in dynamicMod)
{
foreach (XmlNode mod2 in mod.ChildNodes)
{
double massMonoIsotopic = 0.0;
char modSymbol = ' ';
List <char> possibleModSites = new List <char>();
int uniqueID = 0;
foreach (XmlNode item in mod2.ChildNodes)
{
if (item.Name == "MassMonoIsotopic")
{
massMonoIsotopic = double.Parse(item.InnerText);
}
else if (item.Name == "ModificationSymbol")
{
modSymbol = item.InnerText[0];
}
else if (item.Name == "PossibleModSites")
{
foreach (XmlNode item2 in item.ChildNodes)
{
possibleModSites.Add(item2.InnerText[0]);
}
}
else if (item.Name == "UniqueID")
{
uniqueID = int.Parse(item.InnerText);
}
else if (item.Name == "MaxPerSite")
{
}
}
DynamicModification m = new DynamicModification();
m.MassMonoisotopic = massMonoIsotopic;
m.ModSymbol = modSymbol;
m.PossibleModSites = possibleModSites;
m.UniqueID = uniqueID;
dynam.Add(m);
}
}
AScoreParameters aParams = new AScoreParameters(stat, termMod, dynam, f, massTol);
return(aParams);
}
