public PeptideDocNode EnsureMods(PeptideModifications source, PeptideModifications target,
MappedList<string, StaticMod> defSetStat, MappedList<string, StaticMod> defSetHeavy)
{
// Create explicit mods matching the implicit mods on this peptide for each document.
var sourceImplicitMods = new ExplicitMods(this, source.StaticModifications, defSetStat, source.GetHeavyModifications(), defSetHeavy);
var targetImplicitMods = new ExplicitMods(this, target.StaticModifications, defSetStat, target.GetHeavyModifications(), defSetHeavy);
// If modifications match, no need to create explicit modifications for the peptide.
if (sourceImplicitMods.Equals(targetImplicitMods))
return this;
// Add explicit mods if static mods not implicit in the target document.
IList<ExplicitMod> newExplicitStaticMods = null;
bool preserveVariable = HasVariableMods;
// Preserve non-variable explicit modifications
if (!preserveVariable && HasExplicitMods && ExplicitMods.StaticModifications != null)
{
// If they are not the same as the implicit modifications in the new document
if (!ArrayUtil.EqualsDeep(ExplicitMods.StaticModifications, targetImplicitMods.StaticModifications))
newExplicitStaticMods = ExplicitMods.StaticModifications;
}
else if (!ArrayUtil.EqualsDeep(sourceImplicitMods.StaticModifications, targetImplicitMods.StaticModifications))
{
preserveVariable = false;
newExplicitStaticMods = sourceImplicitMods.StaticModifications;
}
else if (preserveVariable)
{
newExplicitStaticMods = ExplicitMods.StaticModifications;
}
// Drop explicit mods if matching implicit mods are found in the target document.
IList<TypedExplicitModifications> newExplicitHeavyMods = new List<TypedExplicitModifications>();
// For each heavy label type, add explicit mods if static mods not found in the target document.
var newTypedStaticMods = newExplicitStaticMods != null
? new TypedExplicitModifications(Peptide, IsotopeLabelType.light, newExplicitStaticMods)
: null;
foreach (TypedExplicitModifications targetDocMod in targetImplicitMods.GetHeavyModifications())
{
// Use explicit modifications when available. Otherwise, compare against new implicit modifications
IList<ExplicitMod> heavyMods = (HasExplicitMods ? ExplicitMods.GetModifications(targetDocMod.LabelType) : null) ??
sourceImplicitMods.GetModifications(targetDocMod.LabelType);
if (heavyMods != null && !ArrayUtil.EqualsDeep(heavyMods, targetDocMod.Modifications) && heavyMods.Count > 0)
{
var newTypedHeavyMods = new TypedExplicitModifications(Peptide, targetDocMod.LabelType, heavyMods);
newTypedHeavyMods = newTypedHeavyMods.AddModMasses(newTypedStaticMods);
newExplicitHeavyMods.Add(newTypedHeavyMods);
}
}
if (newExplicitStaticMods != null || newExplicitHeavyMods.Count > 0)
return ChangeExplicitMods(new ExplicitMods(Peptide, newExplicitStaticMods, newExplicitHeavyMods, preserveVariable));
return ChangeExplicitMods(null);
}
