public static Protease AddProtease(string name, Terminus terminus, string cut, string noCut = "")
{
Protease protease = new Protease(name, terminus, cut, noCut);
Proteases[name] = protease;
OnProteasesChanged();
return(protease);
}
public Protease GetSampleProtease()
{
var node = _root.SelectSingleNode("//pepxml:sample_enzyme", _nsmgr);
var name = node.Attributes["name"].Value;
Protease protease;
var specificityNode = node.FirstChild;
string sense = specificityNode.Attributes["sense"].Value;
string cut = specificityNode.Attributes["cut"].Value;
string nocut = specificityNode.Attributes["no_cut"].Value;
protease = new Protease(name, (sense.Equals("C")) ? Terminus.C : Terminus.N, cut, nocut);
//Protease protease = new Protease(name, (sense.Equals("C")) ? Terminus.C : Terminus.N, cut, nocut);
return protease;
}
public void WriteSearchProtease(Protease protease, int maxMissedClevages, bool semiDigested = false)
{
if (CurrentStage != Stage.SearchSummary)
throw new ArgumentException("You must be in the Search Summary stage to write modifications");
_writer.WriteStartElement("enzymatic_search_constraint");
_writer.WriteAttributeString("enzyme", protease.Name);
_writer.WriteAttributeString("max_num_internal_clevages", maxMissedClevages.ToString());
_writer.WriteAttributeString("min_number_termini", (semiDigested) ? "1" : "2");
_writer.WriteEndElement();
}
public void WriteSampleProtease(Protease protease)
{
if (CurrentStage != Stage.RunSummary)
throw new ArgumentException("You must be in the Run Summary stage to write proteases");
_writer.WriteStartElement("sample_enzyme");
_writer.WriteAttributeString("name", protease.Name);
_writer.WriteStartElement("specificity");
_writer.WriteAttributeString("sense", Enum.GetName(typeof(Terminus), protease.Terminal));
//_writer.WriteAttributeString("pattern", protease.CleavagePattern); // not part of the schema
_writer.WriteAttributeString("cut", protease.Cut);
_writer.WriteAttributeString("no_cut", protease.NoCut);
_writer.WriteEndElement(); // specificity
_writer.WriteEndElement(); // sample_enzyme
}
public static bool RemoveProtease(Protease protease)
{
return(RemoveProtease(protease.Name));
}
public static bool TryGetProtease(string name, out Protease protease)
{
return(Proteases.TryGetValue(name, out protease));
}
public static bool TryGetProtease(string name, out Protease protease)
{
return Proteases.TryGetValue(name, out protease);
}
public static bool RemoveProtease(Protease protease)
{
return RemoveProtease(protease.Name);
}
public static Protease AddProtease(string name, Terminus terminus, string cut, string noCut = "")
{
Protease protease = new Protease(name, terminus, cut, noCut);
Proteases[name] = protease;
OnProteasesChanged();
return protease;
}
public static Protease AddProtease(string name, Terminus terminus, string cut, string noCut = "")
{
Protease protease = new Protease(name, terminus, cut, noCut);
Proteases.Add(protease.Name, protease);
return protease;
}