public IEnumerable <ComplexFragmentIon> PermuteFragmentIons(SrmSettings settings, int maxFragmentationCount, bool useFilter,
ModificationSite modificationSite, IEnumerable <ComplexFragmentIon> startingFragmentIons)
{
var linkedFragmentIonList = ImmutableList.ValueOf(ListComplexFragmentIons(settings, maxFragmentationCount, useFilter));
return(startingFragmentIons.SelectMany(cfi =>
PermuteFragmentIon(settings, maxFragmentationCount, cfi, modificationSite, linkedFragmentIonList)));
}
public ComplexFragmentIonName AddChild(ModificationSite modificationSite, ComplexFragmentIonName child)
{
if (IsOrphan)
{
if (Children.Count > 0)
{
throw new InvalidOperationException();
}
}
return(ChangeProp(ImClone(this),
im => { im.Children = ToChildList(Children.Append(Tuple.Create(modificationSite, child))); }));
}
private CrosslinkBuilder GetChildBuilder(ModificationSite modificationSite)
{
CrosslinkBuilder childBuilder;
if (!_childBuilders.TryGetValue(modificationSite, out childBuilder))
{
LinkedPeptide linkedPeptide;
ExplicitMods.Crosslinks.TryGetValue(modificationSite, out linkedPeptide);
childBuilder = new CrosslinkBuilder(Settings, linkedPeptide.Peptide, linkedPeptide.ExplicitMods, LabelType);
_childBuilders.Add(modificationSite, childBuilder);
}
return(childBuilder);
}
private IEnumerable <ComplexFragmentIon> PermuteFragmentIon(SrmSettings settings,
int maxFragmentationCount,
ComplexFragmentIon fragmentIon,
ModificationSite modificationSite,
IList <ComplexFragmentIon> linkedFragmentIons)
{
if (fragmentIon.IsOrphan && !fragmentIon.IsEmptyOrphan ||
!fragmentIon.IncludesAaIndex(modificationSite.IndexAa))
{
yield return(fragmentIon);
yield break;
}
int fragmentCountRemaining = maxFragmentationCount - fragmentIon.GetFragmentationEventCount();
foreach (var linkedFragmentIon in linkedFragmentIons)
{
if (linkedFragmentIon.GetFragmentationEventCount() > fragmentCountRemaining)
{
continue;
}
if (fragmentIon.IsOrphan)
{
if (linkedFragmentIon.IncludesAaIndex(IndexAa))
{
continue;
}
}
else
{
if (!linkedFragmentIon.IncludesAaIndex(IndexAa))
{
continue;
}
}
yield return(fragmentIon.AddChild(modificationSite, linkedFragmentIon));
}
}
public ComplexFragmentIon AddChild(ModificationSite modificationSite, ComplexFragmentIon child)
{
if (IsOrphan && !IsEmptyOrphan)
{
throw new InvalidOperationException(string.Format(@"Cannot add {0} to {1}.", child, this));
}
if (child.Transition.MassIndex != 0)
{
throw new InvalidOperationException(string.Format(@"{0} cannot be a child fragment ion transition.", child.Transition));
}
var newLosses = TransitionLosses;
if (child.TransitionLosses != null)
{
if (newLosses == null)
{
newLosses = child.TransitionLosses;
}
else
{
newLosses = new TransitionLosses(newLosses.Losses.Concat(child.TransitionLosses.Losses).ToList(), newLosses.MassType);
}
child = child.ChangeLosses(null);
}
return(ChangeProp(ImClone(this), im =>
{
im.Children =
ImmutableSortedList.FromValues(Children.Append(
new KeyValuePair <ModificationSite, ComplexFragmentIon>(
modificationSite, child)));
im.TransitionLosses = newLosses;
}));
}
