protected bool Equals(LinkedPeptide other)
{
return(Equals(Peptide, other.Peptide) && IndexAa == other.IndexAa &&
Equals(ExplicitMods, other.ExplicitMods));
}
public IEnumerable <TransitionDocNode> GetAllComplexTransitions(
TransitionGroup transitionGroup,
IsotopeDistInfo isotopeDist,
IEnumerable <TransitionDocNode> simpleTransitions,
bool useFilter)
{
var startingFragmentIons = new List <ComplexFragmentIon>();
var productAdducts = Settings.TransitionSettings.Filter.PeptideProductCharges.ToHashSet();
var precursorLosses = new HashSet <TransitionLosses>();
foreach (var simpleTransition in simpleTransitions)
{
var startingFragmentIon = simpleTransition.ComplexFragmentIon
.ChangeCrosslinkStructure(ExplicitMods.Crosslinks);
startingFragmentIons.Add(startingFragmentIon);
if (startingFragmentIon.IsIonTypePrecursor)
{
precursorLosses.Add(startingFragmentIon.TransitionLosses);
}
}
bool excludePrecursors = false;
IEnumerable <Adduct> allProductAdducts;
if (useFilter)
{
allProductAdducts = Settings.TransitionSettings.Filter.PeptideProductCharges;
excludePrecursors = !Settings.TransitionSettings.Filter.PeptideIonTypes.Contains(IonType.precursor);
}
else
{
allProductAdducts = Settings.TransitionSettings.Filter.PeptideProductCharges
.Concat(Transition.DEFAULT_PEPTIDE_CHARGES);
}
allProductAdducts = allProductAdducts.Append(transitionGroup.PrecursorAdduct);
// Add ions representing the precursor waiting to be joined with a crosslinked peptide
foreach (var productAdduct in allProductAdducts.Distinct())
{
foreach (var transitionLosses in precursorLosses)
{
if (productAdduct.IsValidProductAdduct(transitionGroup.PrecursorAdduct, null))
{
var precursorTransition = new Transition(transitionGroup, IonType.precursor,
Peptide.Sequence.Length - 1, 0, productAdduct);
startingFragmentIons.Add(new ComplexFragmentIon(precursorTransition, transitionLosses, ExplicitMods.Crosslinks, true));
startingFragmentIons.Add(new ComplexFragmentIon(precursorTransition, transitionLosses, ExplicitMods.Crosslinks));
}
}
}
foreach (var complexFragmentIon in LinkedPeptide.PermuteComplexFragmentIons(ExplicitMods, Settings,
Settings.PeptideSettings.Modifications.MaxNeutralLosses, useFilter, startingFragmentIons.Distinct()).Distinct())
{
bool isPrecursor = complexFragmentIon.IsIonTypePrecursor;
if (isPrecursor)
{
if (excludePrecursors)
{
continue;
}
var expectedCharge = transitionGroup.PrecursorAdduct.AdductCharge;
if (complexFragmentIon.TransitionLosses != null)
{
if (complexFragmentIon.Transition.MassIndex != 0)
{
continue;
}
expectedCharge -= complexFragmentIon.TransitionLosses.TotalCharge;
}
if (expectedCharge != complexFragmentIon.Transition.Adduct.AdductCharge)
{
continue;
}
}
else
{
if (complexFragmentIon.Transition.MassIndex != 0)
{
continue;
}
if (useFilter)
{
if (!productAdducts.Contains(complexFragmentIon.Transition.Adduct))
{
continue;
}
}
}
if (!complexFragmentIon.Transition.Adduct.IsValidProductAdduct(transitionGroup.PrecursorAdduct,
complexFragmentIon.TransitionLosses))
{
continue;
}
var complexTransitionDocNode = MakeTransitionDocNode(complexFragmentIon, isotopeDist);
yield return(complexTransitionDocNode);
}
}
