private TransitionDocNode GetMatchingTransition(SrmSettings settings,
TransitionGroupDocNode nodeGroupMatching,
TransitionDocNode nodeTran,
IFragmentMassCalc calc)
{
var transition = nodeTran.Transition;
var losses = nodeTran.Losses;
var libInfo = nodeTran.LibInfo;
int?decoyMassShift = transition.IsPrecursor() ? DecoyMassShift : transition.DecoyMassShift;
var tranNew = new Transition(this,
transition.IonType,
transition.CleavageOffset,
transition.MassIndex,
transition.Charge,
decoyMassShift,
transition.CustomIon ?? CustomIon); // Handle reporter ions as well as small molecules
var isotopeDist = nodeGroupMatching.IsotopeDist;
double massH;
if (tranNew.IsCustom())
{
massH = tranNew.CustomIon.GetMass(settings.TransitionSettings.Prediction.FragmentMassType);
}
else
{
massH = calc.GetFragmentMass(tranNew, isotopeDist);
}
var isotopeDistInfo = TransitionDocNode.GetIsotopeDistInfo(tranNew, losses, isotopeDist);
var nodeTranMatching = new TransitionDocNode(tranNew, losses, massH, isotopeDistInfo, libInfo);
return(nodeTranMatching);
}
private TransitionDocNode GetMatchingTransition(SrmSettings settings,
TransitionGroupDocNode nodeGroupMatching,
TransitionDocNode nodeTran,
IFragmentMassCalc calc)
{
var transition = nodeTran.Transition;
var losses = nodeTran.Losses;
var libInfo = nodeTran.LibInfo;
int?decoyMassShift = transition.IsPrecursor() ? DecoyMassShift : transition.DecoyMassShift;
var tranNew = new Transition(this,
transition.IonType,
transition.CleavageOffset,
transition.MassIndex,
transition.Adduct,
decoyMassShift,
transition.CustomIon ?? CustomMolecule); // Handle reporter ions as well as small molecules
var isotopeDist = nodeGroupMatching.IsotopeDist;
TypedMass massH;
var massType = calc.MassType;
if (tranNew.IsCustom())
{
massH = tranNew.CustomIon.GetMass(massType);
}
else
{
massH = calc.GetFragmentMass(tranNew, isotopeDist);
}
var isotopeDistInfo = TransitionDocNode.GetIsotopeDistInfo(tranNew, losses, isotopeDist);
var nodeTranMatching = new TransitionDocNode(tranNew, losses, massH, new TransitionDocNode.TransitionQuantInfo(isotopeDistInfo, libInfo, nodeTran.IsQuantitative(settings)), nodeTran.ExplicitValues);
return(nodeTranMatching);
}