static private List <FragmentFeatureNode> GetTargetNodes(FragmentFeatureNode primeNode, IEnumerable <FragmentFeatureNode> nodes, bool diffTerminal, bool diffCharge) // if diffCharge is true, diffTerminal is ignored
{
var targetNodes = new List <FragmentFeatureNode>();
//var primeNterm = primeNode.FragmentIonClassBase is IonType.NtermIonType;
var primeNterm = primeNode.FragmentIonClassBase.IsPrefixIon; // Modified by Sangtae
foreach (var node in nodes)
{
//Console.WriteLine(node.FragmentIonClassBase);
if (node.Equals(primeNode))
{
continue;
}
if (diffCharge)
{
if (node.FragmentIonClassBase.Charge != primeNode.FragmentIonClassBase.Charge)
{
targetNodes.Add(node);
}
}
else
{
if (node.FragmentIonClassBase.Charge != primeNode.FragmentIonClassBase.Charge)
{
continue;
}
if (diffTerminal && primeNterm || !diffTerminal && !primeNterm)
{
if (!node.FragmentIonClassBase.IsPrefixIon)
{
targetNodes.Add(node);
}
}
else
{
if (node.FragmentIonClassBase.IsPrefixIon)
{
targetNodes.Add(node);
}
}
}
}
return(targetNodes);
}
private List <FragmentFeatureNode> GetFragmentNodes(ImsDataCached imsData, Feature precursorFeature, Composition cutComposition, Ion precursorIon, GroupParameter parameter)
{
var ionTypes = _scoringParams.GetIonTypes(parameter);
var nodes = new List <FragmentFeatureNode>();
var suffixComposition = precursorIon.Composition - Composition.H2O - cutComposition;
//Console.WriteLine(cutComposition.GetMass() + " " + suffixComposition.GetMass());
foreach (var ionType in ionTypes)
{
var composition = ionType.IsPrefixIon ? cutComposition : suffixComposition;
//Console.WriteLine("FragFeatureGraph\t" + ionType.Name + "\t" + composition.GetMass() + "\t" + ionType.GetIon(composition).GetMonoIsotopicMz());
var node = new FragmentFeatureNode(IsotopomerFeatures.GetFramentIsotopomerFeatures(imsData, composition, ionType, precursorFeature), ionType, precursorFeature, parameter, _scoringParams);
//if(node.Feature != null)
// if (20 * node.Feature.IntensityMax < precursorFeature.IntensityMax || node.Feature.IntensityMax > 20 * precursorFeature.IntensityMax) continue; //
nodes.Add(node);
}
return(nodes);
}