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); }