public TransitionDocNode MakeTransitionDocNode(SrmSettings settings, ExplicitMods explicitMods,
IsotopeDistInfo isotopeDist,
Annotations annotations,
TransitionDocNode.TransitionQuantInfo transitionQuantInfo,
ExplicitTransitionValues explicitTransitionValues,
Results <TransitionChromInfo> results)
{
return(GetCrosslinkBuilder(settings, explicitMods).MakeTransitionDocNode(this, isotopeDist, annotations, transitionQuantInfo, explicitTransitionValues, results));
}
public TransitionDocNode MakeTransitionDocNode(ComplexFragmentIon complexFragmentIon,
IsotopeDistInfo isotopeDist,
Annotations annotations,
TransitionDocNode.TransitionQuantInfo transitionQuantInfo,
ExplicitTransitionValues explicitTransitionValues,
Results <TransitionChromInfo> results)
{
var neutralFormula = GetNeutralFormula(complexFragmentIon);
var productMass = GetFragmentMassFromFormula(Settings, neutralFormula);
if (complexFragmentIon.Children.Count > 0)
{
complexFragmentIon = complexFragmentIon.CloneTransition();
}
if (complexFragmentIon.IsMs1 && Settings.TransitionSettings.FullScan.IsHighResPrecursor)
{
isotopeDist = isotopeDist ?? GetPrecursorIsotopeDistInfo(complexFragmentIon.Transition.Adduct, 0);
productMass = isotopeDist.GetMassI(complexFragmentIon.Transition.MassIndex, complexFragmentIon.Transition.DecoyMassShift);
transitionQuantInfo = transitionQuantInfo.ChangeIsotopeDistInfo(new TransitionIsotopeDistInfo(
isotopeDist.GetRankI(complexFragmentIon.Transition.MassIndex), isotopeDist.GetProportionI(complexFragmentIon.Transition.MassIndex)));
}
return(new TransitionDocNode(complexFragmentIon, annotations, productMass, transitionQuantInfo, explicitTransitionValues, results));
}
