public WorkflowParameters(ArgumentParser.QcOptions qcOptions)
{
QcParams = new QcWorkflowParameters();
Enum.TryParse(qcOptions.SearchAlgorithm, true, out QcParams.SearchAlgorithm);
ExpType = ExperimentType.DDA;
MgfIntensityCutoff = qcOptions.IntensityCutoff;
MgfMassCutoff = qcOptions.MassCutOff;
RawFileDirectory = qcOptions.DirectoryToQc;
RefineMassCharge = qcOptions.RefineMassCharge;
QcParams.FastaDatabase = qcOptions.FastaDatabase;
QcParams.FixedMods = qcOptions.FixedMods;
QcParams.FixedScans = qcOptions.FixedScans;
QcParams.IdentipyScript = qcOptions.IdentipyScript;
QcParams.KMod = qcOptions.VariableKMod;
QcParams.NMod = qcOptions.VariableNMod;
QcParams.XMod = qcOptions.VariableXMod;
QcParams.NumberSpectra = qcOptions.NumberSpectra;
QcParams.PythonExecutable = qcOptions.PythonExecutable;
QcParams.QcDirectory = qcOptions.QcDirectory;
QcParams.XTandemDirectory = qcOptions.XTandemDirectory;
if (QcParams.SearchAlgorithm != SearchAlgorithm.None)
{
QcParams.PerformSearch = true;
}
if (QcParams.FastaDatabase != null)
{
if (!Path.IsPathRooted(QcParams.FastaDatabase))
{
QcParams.FastaDatabase = Path.Combine(Directory.GetCurrentDirectory(), QcParams.FastaDatabase);
}
}
if (QcParams.QcDirectory != null)
{
if (!Path.IsPathRooted(QcParams.QcDirectory))
{
QcParams.QcDirectory = Path.Combine(Directory.GetCurrentDirectory(), QcParams.QcDirectory);
}
}
if (QcParams.XTandemDirectory != null)
{
if (!Path.IsPathRooted(QcParams.XTandemDirectory))
{
QcParams.XTandemDirectory = Path.Combine(Directory.GetCurrentDirectory(), QcParams.XTandemDirectory);
}
}
}
public WorkflowParameters()
{
QcParams = new QcWorkflowParameters();
ParseParams = new ParseWorkflowParameters();
}
