public DtaGenerator(IList<string> rawFilepaths,
int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
bool cleanPrecursor, bool enableEtdPreProcessing,
bool cleanTmtDuplex, bool cleanItraq4Plex, bool cleanTmt6Plex, bool cleanItraq8Plex,
bool groupByActivationEnergyTime,
bool sequestDtaOutput, bool omssaTxtOutput, bool mascotMgfOutput,
string outputFolder,
List<double> neutralLosses,
List<MzRange> rangesToRemove,
bool includeLog = true,
double clnPrecursorLowMz = LOW_PRECURSOR_CLEANING_WINDOW_MZ,
double clnPrecursorHighMz = HIGH_PRECURSOR_CLEANING_WINDOW_MZ,
double etdLowDa = LOW_NEUTRAL_LOSS_CLEANING_WINDOW_DA,
double etdHighDa = HIGH_PRECURSOR_CLEANING_WINDOW_MZ)
{
this.rawFilepaths = rawFilepaths;
this.minimumAssumedPrecursorChargeState = minimumAssumedPrecursorChargeState;
this.maximumAssumedPrecursorChargeState = maximumAssumedPrecursorChargeState;
this.cleanPrecursor = cleanPrecursor;
this.enableEtdPreProcessing = enableEtdPreProcessing;
this.cleanTmtDuplex = cleanTmtDuplex;
this.cleanItraq4Plex = cleanItraq4Plex;
this.cleanTmt6Plex = cleanTmt6Plex;
this.cleanItraq8Plex = cleanItraq8Plex;
this.groupByActivationEnergyTime = groupByActivationEnergyTime;
this.sequestDtaOutput = sequestDtaOutput;
this.omssaTxtOutput = omssaTxtOutput;
this.mascotMgfOutput = mascotMgfOutput;
this.outputFolder = outputFolder;
this.neutralLosses = neutralLosses;
IncludeLog = includeLog;
RangesToRemove = rangesToRemove;
CleanPrecursorLowMz = clnPrecursorLowMz;
CleanPrecursorHighMz = clnPrecursorHighMz;
EtdLowDa = etdLowDa;
EtdHighDa = etdHighDa;
LogFolder = Path.Combine(outputFolder, "log");
NeutralLossesIncluded = (neutralLosses != null && neutralLosses.Count > 0);
}