public static TransitionLosses FromLossProtos(SrmSettings settings,
IEnumerable <SkylineDocumentProto.Types.TransitionLoss> lossProtos)
{
var staticMods = settings.PeptideSettings.Modifications.StaticModifications;
MassType massType = settings.TransitionSettings.Prediction.FragmentMassType;
var listLosses = new List <TransitionLoss>();
foreach (var loss in lossProtos)
{
String nameMod = loss.ModificationName;
if (string.IsNullOrEmpty(nameMod))
{
listLosses.Add(new TransitionLoss(null,
new FragmentLoss(loss.Formula, loss.MonoisotopicMass,
loss.AverageMass, DataValues.FromLossInclusion(loss.LossInclusion)),
massType));
}
else
{
int indexLoss = loss.LossIndex;
int indexMod = staticMods.IndexOf(mod => Equals(nameMod, mod.Name));
if (indexMod == -1)
{
throw new InvalidDataException(
string.Format(Resources.TransitionInfo_ReadTransitionLosses_No_modification_named__0__was_found_in_this_document,
nameMod));
}
StaticMod modLoss = staticMods[indexMod];
if (!modLoss.HasLoss || indexLoss >= modLoss.Losses.Count)
{
throw new InvalidDataException(
string.Format(Resources.TransitionInfo_ReadTransitionLosses_Invalid_loss_index__0__for_modification__1__,
indexLoss, nameMod));
}
listLosses.Add(new TransitionLoss(modLoss, modLoss.Losses[indexLoss], massType));
}
}
if (listLosses.Any())
{
return(new TransitionLosses(listLosses, massType));
}
return(null);
}
