protected void CopyFrom(DynamicModification itemToCopy)
{
base.CopyFrom(itemToCopy);
this.MaxPerSite = itemToCopy.MaxPerSite;
this.Position = itemToCopy.Position;
this.Count = itemToCopy.Count;
}
/// <summary>
/// Constructor whose source is a dynamic mod entry
/// </summary>
// ReSharper disable once UnusedMember.Global
public DynamicModification(DynamicModification itemToCopy)
{
this.CopyFrom(itemToCopy);
}
/// <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);
}
