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))); }));
}
public static ComplexFragmentIonName FromLinkedIonProto(SkylineDocumentProto.Types.LinkedIon linkedIon)
{
ComplexFragmentIonName child;
if (linkedIon.Orphan)
{
child = ORPHAN;
}
else
{
child = new ComplexFragmentIonName(DataValues.FromIonType(linkedIon.IonType), linkedIon.Ordinal);
}
child = child.AddLinkedIonProtos(linkedIon.Children);
return(child);
}
/// <summary>
/// Returns a ComplexFragmentIonName object representing this ComplexFragmentIon
/// </summary>
public ComplexFragmentIonName GetName()
{
ComplexFragmentIonName name;
if (IsOrphan)
{
name = ComplexFragmentIonName.ORPHAN;
}
else
{
name = new ComplexFragmentIonName(Transition.IonType, Transition.Ordinal);
}
foreach (var child in Children)
{
name = name.AddChild(child.Key, child.Value.GetName());
}
return(name);
}
public ComplexFragmentIonName AddLinkedIonProtos(IEnumerable <SkylineDocumentProto.Types.LinkedIon> linkedIons)
{
var result = this;
foreach (var linkedIon in linkedIons)
{
ComplexFragmentIonName child;
if (linkedIon.Orphan)
{
child = ORPHAN;
}
else
{
child = new ComplexFragmentIonName(DataValues.FromIonType(linkedIon.IonType), linkedIon.Ordinal);
}
child = child.AddLinkedIonProtos(linkedIon.Children);
result = result.AddChild(new ModificationSite(linkedIon.ModificationIndex, linkedIon.ModificationName),
child);
}
return(result);
}
public ComplexFragmentIon MakeComplexFragmentIon(SrmSettings settings, IsotopeLabelType labelType, ComplexFragmentIonName complexFragmentIonName)
{
var transitionGroup = GetTransitionGroup(labelType, Adduct.SINGLY_PROTONATED);
Transition transition;
if (complexFragmentIonName.IonType == IonType.precursor || complexFragmentIonName.IonType == IonType.custom)
{
transition = new Transition(transitionGroup, IonType.precursor, Peptide.Length - 1, 0, Adduct.SINGLY_PROTONATED);
}
else
{
transition = new Transition(transitionGroup, complexFragmentIonName.IonType,
Transition.OrdinalToOffset(complexFragmentIonName.IonType, complexFragmentIonName.Ordinal, Peptide.Length),
0, Adduct.SINGLY_PROTONATED);
}
var result = new ComplexFragmentIon(transition, null, CrosslinkStructure, complexFragmentIonName.IsOrphan);
if (ExplicitMods != null)
{
foreach (var child in complexFragmentIonName.Children)
{
LinkedPeptide linkedPeptide;
if (!ExplicitMods.Crosslinks.TryGetValue(child.Item1, out linkedPeptide))
{
throw new InvalidOperationException(@"No crosslink at " + child.Item1);
}
result = result.AddChild(child.Item1,
linkedPeptide.MakeComplexFragmentIon(settings, labelType, child.Item2));
}
}
return(result);
}
protected bool Equals(ComplexFragmentIonName other)
{
return(IonType == other.IonType && Ordinal == other.Ordinal && Children.Equals(other.Children) && IsOrphan == other.IsOrphan);
}
