private void InitializeUserDefinedTypedMods(SrmDocument document)
{
var mods = document.Settings.PeptideSettings.Modifications;
foreach (var type in mods.GetModificationTypes())
{
// Set the default heavy type to the first heavy type encountered.
if (!ReferenceEquals(type, IsotopeLabelType.light) && DefaultHeavyLabelType == null)
{
DefaultHeavyLabelType = type;
}
foreach (var mod in mods.GetModificationsByName(type.Name).Modifications.Where(m => !m.IsUserSet))
{
UserDefinedTypedMods.Add(mod);
}
}
var staticMods = new TypedModifications(IsotopeLabelType.light, mods.StaticModifications);
var heavyMods = new TypedModifications(DefaultHeavyLabelType, mods.GetModifications(DefaultHeavyLabelType));
foreach (var mod in staticMods.Modifications.Union(heavyMods.Modifications))
{
UserDefinedTypedMods.Add(mod);
}
}
private void InitUserDefTypedModDict(TypedModifications typedModifications, bool includeExplicit)
{
var type = typedModifications.LabelType;
foreach (StaticMod mod in typedModifications.Modifications
.Where(mod => includeExplicit || !mod.IsUserSet))
{
var modName = mod.Name;
if (!UserDefinedTypedMods.Keys.Contains(key => Equals(key.Name, modName)))
{
var newMod = mod;
// TODO: This appears to be problematic
if (includeExplicit && !mod.IsVariable)
{
newMod = mod.ChangeExplicit(true);
}
UserDefinedTypedMods.Add(newMod, type);
}
}
}
