public NonSpecificEnzymeSearchEngine(PeptideSpectralMatch[][] globalPsms, Ms2ScanWithSpecificMass[] listOfSortedms2Scans,
List <PeptideWithSetModifications> peptideIndex, List <int>[] fragmentIndex, List <int>[] precursorIndex, int currentPartition,
CommonParameters commonParameters, List <Modification> variableModifications, MassDiffAcceptor massDiffAcceptor, double maximumMassThatFragmentIonScoreIsDoubled, List <string> nestedIds)
: base(null, listOfSortedms2Scans, peptideIndex, fragmentIndex, currentPartition, commonParameters, massDiffAcceptor, maximumMassThatFragmentIonScoreIsDoubled, nestedIds)
{
PrecursorIndex = precursorIndex;
MinimumPeptideLength = commonParameters.DigestionParams.MinPeptideLength;
GlobalCategorySpecificPsms = globalPsms;
ModifiedParametersNoComp = commonParameters.CloneWithNewTerminus(addCompIons: false);
ProductTypesToSearch = DissociationTypeCollection.ProductsFromDissociationType[commonParameters.DissociationType].Intersect(TerminusSpecificProductTypes.ProductIonTypesFromSpecifiedTerminus[commonParameters.DigestionParams.FragmentationTerminus]).ToList();
VariableTerminalModifications = GetVariableTerminalMods(commonParameters.DigestionParams.FragmentationTerminus, variableModifications);
}