public DatabaseSearcher(IList<string> dataFilepaths,
int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, bool deisotope,
string proteomeDatabaseFilepath, bool onTheFlyDecoys,
Protease protease, int maximumMissedCleavages, InitiatorMethionineBehavior initiatorMethionineBehavior,
IEnumerable<Modification> fixedModifications, IEnumerable<Modification> variableModifications, int maximumVariableModificationIsoforms,
MassTolerance precursorMassTolerance, MassType precursorMassType,
IEnumerable<double> acceptedPrecursorMassErrors,
MassTolerance productMassTolerance, MassType productMassType,
double maximumFalseDiscoveryRate, bool considerModifiedFormsAsUniquePeptides,
int maximumThreads, bool minimizeMemoryUsage,
string outputFolder)
{
this.dataFilepaths = dataFilepaths;
this.assignChargeStates = assignChargeStates;
this.deisotope = deisotope;
this.proteomeDatabaseFilepath = proteomeDatabaseFilepath;
this.onTheFlyDecoys = onTheFlyDecoys;
this.protease = protease;
this.maximumMissedCleavages = maximumMissedCleavages;
this.initiatorMethionineBehavior = initiatorMethionineBehavior;
this.fixedModifications = fixedModifications;
this.variableModifications = variableModifications;
this.maximumVariableModificationIsoforms = maximumVariableModificationIsoforms;
this.minimumAssumedPrecursorChargeState = minimumAssumedPrecursorChargeState;
this.maximumAssumedPrecursorChargeState = maximumAssumedPrecursorChargeState;
this.absoluteThreshold = absoluteThreshold;
this.relativeThresholdPercent = relativeThresholdPercent;
this.maximumNumberOfPeaks = maximumNumberOfPeaks;
this.precursorMassTolerance = precursorMassTolerance;
this.precursorMassType = precursorMassType;
this.acceptedPrecursorMassErrors = acceptedPrecursorMassErrors;
this.productMassTolerance = productMassTolerance;
this.productMassType = productMassType;
this.maximumFalseDiscoveryRate = maximumFalseDiscoveryRate;
this.considerModifiedFormsAsUniquePeptides = considerModifiedFormsAsUniquePeptides;
this.maximumThreads = maximumThreads;
this.minimizeMemoryUsage = minimizeMemoryUsage;
this.outputFolder = outputFolder;
}