public static void RunSearch(WorkflowParameters parameters, MethodDataContainer methodData, string rawFileName)
{
string mgfFile = Path.Combine(parameters.QcParams.QcSearchDataDirectory, Path.GetFileName(rawFileName) + ".mgf");
string outputFile = Path.Combine(parameters.QcParams.QcSearchDataDirectory, Path.GetFileName(rawFileName) + ".pep.xml");
if (parameters.QcParams.SearchAlgorithm == SearchAlgorithm.XTandem)
{
XTandem.RunXTandem(parameters, methodData, mgfFile, outputFile, genDecoy: true);
}
}
public static void RunSearch(QcParameters qcParameters, RawDataCollection rawData, IRawDataPlus rawFile)
{
string mgfFile = Path.Combine(qcParameters.QcSearchDataDirectory, Path.GetFileName(rawData.rawFileName) + ".mgf");
string outputFile = Path.Combine(qcParameters.QcSearchDataDirectory, Path.GetFileName(rawData.rawFileName) + ".pep.xml");
if (qcParameters.searchParameters.SearchAlgorithm == SearchAlgorithm.XTandem)
{
XTandem.RunXTandem(rawData, qcParameters.searchParameters, mgfFile, outputFile, genDecoy: true);
}
if (qcParameters.searchParameters.SearchAlgorithm == SearchAlgorithm.IdentiPy)
{
var pars = qcParameters.searchParameters;
Identipy.RunIdentipy(rawData, rawFile, qcParameters.QcSearchDataDirectory, pars, writeMGF: false);
}
}