public static void LoadOmssaModifications(Stream stream, bool userMod = true)
{
XmlDocument mods_xml = new XmlDocument();
mods_xml.Load(stream);
XmlNamespaceManager mods_xml_ns = new XmlNamespaceManager(mods_xml.NameTable);
mods_xml_ns.AddNamespace("omssa", mods_xml.ChildNodes[1].Attributes["xmlns"].Value);
foreach (XmlNode mod_node in mods_xml.SelectNodes("/omssa:MSModSpecSet/omssa:MSModSpec", mods_xml_ns))
{
string name = mod_node.SelectSingleNode("./omssa:MSModSpec_name", mods_xml_ns).FirstChild.Value;
int id = int.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_mod/omssa:MSMod", mods_xml_ns).FirstChild.Value);
double mono = double.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_monomass", mods_xml_ns).FirstChild.Value);
double average = double.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_averagemass", mods_xml_ns).FirstChild.Value);
ModificationSites sites = ModificationSites.None;
foreach (
XmlNode node in
mod_node.SelectNodes("./omssa:MSModSpec_residues/omssa:MSModSpec_residues_E", mods_xml_ns))
{
string aa = node.FirstChild.Value;
sites = sites.Set(aa[0]);
}
OmssaModification mod = new OmssaModification(name, id, mono, average, userMod, sites);
Modifications.Add(name, mod);
_modificationKeyDicitonary[id] = name;
}
}
public static bool TryGetModification(int id, out OmssaModification modification)
{
string name;
modification = null;
return(_modificationKeyDicitonary.TryGetValue(id, out name) && TryGetModification(name, out modification));
}
/// <summary>
/// Parse and apply an omssa modification line to this current amino acid polymer
/// </summary>
/// <param name="aap"></param>
/// <param name="omssaModificationLine"></param>
/// <returns></returns>
public static AminoAcidPolymer SetModifications(this AminoAcidPolymer aap, string omssaModificationLine)
{
if (string.IsNullOrEmpty(omssaModificationLine))
{
return(aap);
}
foreach (Tuple <Modification, int> modPosition in OmssaModification.ParseModificationLine(omssaModificationLine))
{
int pos = modPosition.Item2;
if (pos == 0)
{
aap.NTerminusModification = modPosition.Item1;
}
else if (pos == aap.Length + 1)
{
aap.CTerminusModification = modPosition.Item1;
}
else
{
aap.SetModification(modPosition.Item1, pos);
}
}
return(aap);
}
public static void LoadOmssaModifications(string file, bool userMod = true)
{
XmlDocument mods_xml = new XmlDocument();
mods_xml.Load(file);
XmlNamespaceManager mods_xml_ns = new XmlNamespaceManager(mods_xml.NameTable);
mods_xml_ns.AddNamespace("omssa", mods_xml.ChildNodes[1].Attributes["xmlns"].Value);
foreach (XmlNode mod_node in mods_xml.SelectNodes("/omssa:MSModSpecSet/omssa:MSModSpec", mods_xml_ns))
{
string name = mod_node.SelectSingleNode("./omssa:MSModSpec_name", mods_xml_ns).FirstChild.Value;
int id = int.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_mod/omssa:MSMod", mods_xml_ns).FirstChild.Value);
double mono = double.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_monomass", mods_xml_ns).FirstChild.Value);
double average = double.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_averagemass", mods_xml_ns).FirstChild.Value);
int modType = int.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_type/omssa:MSModType", mods_xml_ns).FirstChild.Value);
ModificationSites sites = ModificationSites.None;
switch (modType)
{
case 0:
foreach (
XmlNode node in
mod_node.SelectNodes("./omssa:MSModSpec_residues/omssa:MSModSpec_residues_E", mods_xml_ns))
{
string aa = node.FirstChild.Value;
sites = sites.Set(aa[0]);
}
break;
case 1:
sites |= ModificationSites.NProt;
break;
case 3:
sites |= ModificationSites.ProtC;
break;
case 5:
sites |= ModificationSites.NPep;
break;
case 6:
sites |= ModificationSites.PepC;
break;
}
OmssaModification mod = new OmssaModification(name, id, mono, average, userMod, sites);
Modifications[name] = mod;
_modificationKeyDicitonary[id] = name;
}
}
public static AminoAcidPolymer SetModifications(this AminoAcidPolymer aap, string mods)
{
if (string.IsNullOrEmpty(mods))
{
return(aap);
}
foreach (Tuple <Modification, int> modPosition in OmssaModification.ParseModificationLine(mods))
{
aap.SetModification(modPosition.Item1, modPosition.Item2);
}
return(aap);
}
public static bool TryGetModification(string name, out OmssaModification modification)
{
return(Modifications.TryGetValue(name, out modification));
}
public static void LoadOmssaModifications(Stream stream, bool userMod = true)
{
XmlDocument mods_xml = new XmlDocument();
mods_xml.Load(stream);
XmlNamespaceManager mods_xml_ns = new XmlNamespaceManager(mods_xml.NameTable);
mods_xml_ns.AddNamespace("omssa", mods_xml.ChildNodes[1].Attributes["xmlns"].Value);
foreach (XmlNode mod_node in mods_xml.SelectNodes("/omssa:MSModSpecSet/omssa:MSModSpec", mods_xml_ns))
{
string name = mod_node.SelectSingleNode("./omssa:MSModSpec_name", mods_xml_ns).FirstChild.Value;
int id = int.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_mod/omssa:MSMod", mods_xml_ns).FirstChild.Value);
double mono = double.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_monomass", mods_xml_ns).FirstChild.Value);
double average = double.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_averagemass", mods_xml_ns).FirstChild.Value);
ModificationSites sites = ModificationSites.None;
foreach (
XmlNode node in
mod_node.SelectNodes("./omssa:MSModSpec_residues/omssa:MSModSpec_residues_E", mods_xml_ns))
{
string aa = node.FirstChild.Value;
sites = sites.Set(aa[0]);
}
OmssaModification mod = new OmssaModification(name, id, mono, average, userMod, sites);
Modifications.Add(name, mod);
_modificationKeyDicitonary[id] = name;
}
}
public static bool TryGetModification(string name, out OmssaModification modification)
{
return Modifications.TryGetValue(name, out modification);
}
public static bool TryGetModification(int id, out OmssaModification modification)
{
string name;
modification = null;
return _modificationKeyDicitonary.TryGetValue(id, out name) && TryGetModification(name, out modification);
}
public static void LoadOmssaModifications(string file, bool userMod = true)
{
XmlDocument mods_xml = new XmlDocument();
mods_xml.Load(file);
XmlNamespaceManager mods_xml_ns = new XmlNamespaceManager(mods_xml.NameTable);
mods_xml_ns.AddNamespace("omssa", mods_xml.ChildNodes[1].Attributes["xmlns"].Value);
foreach (XmlNode mod_node in mods_xml.SelectNodes("/omssa:MSModSpecSet/omssa:MSModSpec", mods_xml_ns))
{
string name = mod_node.SelectSingleNode("./omssa:MSModSpec_name", mods_xml_ns).FirstChild.Value;
int id = int.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_mod/omssa:MSMod", mods_xml_ns).FirstChild.Value);
double mono = double.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_monomass", mods_xml_ns).FirstChild.Value);
double average = double.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_averagemass", mods_xml_ns).FirstChild.Value);
int modType = int.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_type/omssa:MSModType", mods_xml_ns).FirstChild.Value);
ModificationSites sites = ModificationSites.None;
switch (modType)
{
case 0:
foreach (
XmlNode node in
mod_node.SelectNodes("./omssa:MSModSpec_residues/omssa:MSModSpec_residues_E", mods_xml_ns))
{
string aa = node.FirstChild.Value;
sites = sites.Set(aa[0]);
}
break;
case 1:
sites |= ModificationSites.NProt;
break;
case 3:
sites |= ModificationSites.ProtC;
break;
case 5:
sites |= ModificationSites.NPep;
break;
case 6:
sites |= ModificationSites.PepC;
break;
}
OmssaModification mod = new OmssaModification(name, id, mono, average, userMod, sites);
Modifications[name] = mod;
_modificationKeyDicitonary[id] = name;
}
}
