public static void AddMods(IEnumerable <Modification> modifications, bool modsAreFromTheTopOfProteinXml)
{
foreach (var mod in modifications)
{
if (string.IsNullOrEmpty(mod.ModificationType) || string.IsNullOrEmpty(mod.IdWithMotif))
{
ErrorsReadingMods.Add(mod.ToString() + Environment.NewLine + " has null or empty modification type");
continue;
}
if (AllModsKnown.Any(b => b.IdWithMotif.Equals(mod.IdWithMotif) && b.ModificationType.Equals(mod.ModificationType) && !b.Equals(mod)))
{
if (modsAreFromTheTopOfProteinXml)
{
_AllModsKnown.RemoveAll(p => p.IdWithMotif.Equals(mod.IdWithMotif) && p.ModificationType.Equals(mod.ModificationType) && !p.Equals(mod));
_AllModsKnown.Add(mod);
_AllModTypesKnown.Add(mod.ModificationType);
}
else
{
ErrorsReadingMods.Add("Modification id and type are equal, but some fields are not! " +
"The following mod was not read in: " + Environment.NewLine + mod.ToString());
}
continue;
}
else if (AllModsKnown.Any(b => b.IdWithMotif.Equals(mod.IdWithMotif) && b.ModificationType.Equals(mod.ModificationType)))
{
// same ID, same mod type, and same mod properties; continue and don't output an error message
// this could result from reading in an XML database with mods annotated at the top
// that are already loaded in MetaMorpheus
continue;
}
else if (AllModsKnown.Any(m => m.IdWithMotif == mod.IdWithMotif))
{
// same ID but different mod types. This can happen if the user names a mod the same as a UniProt mod
// this is problematic because if a mod is annotated in the database, all we have to go on is an ID ("description" tag).
// so we don't know which mod to use, causing unnecessary ambiguity
if (modsAreFromTheTopOfProteinXml)
{
_AllModsKnown.RemoveAll(p => p.IdWithMotif.Equals(mod.IdWithMotif) && !p.Equals(mod));
_AllModsKnown.Add(mod);
_AllModTypesKnown.Add(mod.ModificationType);
}
else if (!mod.ModificationType.Equals("Unimod"))
{
ErrorsReadingMods.Add("Duplicate mod IDs! Skipping " + mod.ModificationType + ":" + mod.IdWithMotif);
}
continue;
}
else
{
// no errors! add the mod
_AllModsKnown.Add(mod);
_AllModTypesKnown.Add(mod.ModificationType);
}
}
}
public static void AddMods(IEnumerable <Modification> enumerable)
{
foreach (var ye in enumerable)
{
if (string.IsNullOrEmpty(ye.modificationType) || string.IsNullOrEmpty(ye.id))
{
throw new MetaMorpheusException(ye.ToString() + Environment.NewLine + " has null or empty modification type");
}
if (AllModsKnown.Any(b => b.id.Equals(ye.id) && b.modificationType.Equals(ye.modificationType) && !b.Equals(ye)))
{
throw new MetaMorpheusException("Modification id and type are equal, but some fields are not! Please modify/remove one of the modifications: " + Environment.NewLine + Environment.NewLine + ye.ToString() + Environment.NewLine + Environment.NewLine + " has same and id and modification type as " + Environment.NewLine + Environment.NewLine + AllModsKnown.First(b => b.id.Equals(ye.id) && b.modificationType.Equals(ye.modificationType)) + Environment.NewLine + Environment.NewLine);
}
else if (AllModsKnown.Any(b => b.id.Equals(ye.id) && b.modificationType.Equals(ye.modificationType)))
{
continue;
}
else
{
allModsKnown.Add(ye);
allModTypesKnown.Add(ye.modificationType);
}
}
}
