private void InitializeEngine(CancellationTokenSource token, string spectrumFileName)
{
_outputParameters = new OutputParameters();
_outputParameters.FastaFiles = FastaFileNames.ToList();
_outputParameters.DBFile = FastaFileNames[0];
//2 == mzid
_outputParameters.SetOutputFileFormat(2);
_outputParameters.IsPercolatorOutput = true;
_outputParameters.SpectraFiles = new List <string>()
{
spectrumFileName
};
Settings.GenerateDecoyDb = true;
Settings.ConsideredCharges.Clear();
Settings.ConsideredCharges.Add(2);
Settings.ConsideredCharges.Add(3);
Settings.ChemicalData.UseMonoisotopicMass = true;
Settings.ReportBothBestHitsForTD = false;
mzID.Settings = Settings;
SearchEngine = new MSAmandaSearch(helper, _baseDir.DirPath, _outputParameters, Settings, token);
SearchEngine.InitializeOutputMZ(mzID);
Settings.LoadedProteinsAtOnce = (int)AdditionalSettings[MAX_LOADED_PROTEINS_AT_ONCE].Value;
Settings.LoadedSpectraAtOnce = (int)AdditionalSettings[MAX_LOADED_SPECTRA_AT_ONCE].Value;
}