protected FindCpdsMassHunterParameters GetMFEParams()
{
var findParams = new FindCpdsMassHunterParameters();
findParams.ProcessingParameters = m_AppManager[QualDAMethod.ParamKeyMFEProcessing] as PSetMassHunterProcessing;
// Results filters are not shown in the wizard
// however the pset contains parameters for Mass Filters hence we require it
findParams.ResultFilters = m_AppManager[QualDAMethod.ParamKeyMFEResultFilters] as PSetMassHunterResultFilters;
findParams.TimeRangeFilters = new PSetTimeRangeCollection();
findParams.TimeRangeFilters.UseRanges = false;
findParams.MassDefectFilters = m_AppManager[QualDAMethod.ParamKeyMassDefectFilter] as IPSetMassDefectFilter;
findParams.ChargeStateAssignment = m_AppManager[QualDAMethod.GetUsageKey(QualFunctionality.ChargeStateAssignment, QualDataType.MS)] as IPSetChargeStateAssignment;
// TT 147479: MFE Mass Filter throws error about invalid DB path, even when filter is disabled
// TT #147535: MFE: Invalid Mass Filters Database location when disabled should not prevent MFE from running - Added the LimitedMassRange condition for
// The IPSetCpdDatabase should be retireved only if both the "Filter Mass List" option is anabled and "Database" option
// is selected in the MFE UI
if (findParams.ResultFilters.MassSourceIsDatabase && findParams.ResultFilters.LimitedMassRange)
{
findParams.CpdDbAccessor =
CpdDatabase.GetQualifiedAccessor(m_AppManager[QualDAMethod.ParamKeyMFEDBLocation] as IPSetCpdDatabase);
// MFE has its own instance of PSetDBLocation
}
else
{
findParams.CpdDbAccessor = null;
}
findParams.IdentityScoring = m_AppManager[QualDAMethod.ParamKeyIdScoring] as IPSetIdentityScoring;
findParams.MSMSPeakFilter = m_AppManager[QualDAMethod.GetUsageKey(QualFunctionality.SpectrumPeakFilters, QualDataType.MSMS)]
as IPSetPeakFilter; //Using the one for Spectrum(MSMS), shared with MFE tab
findParams.TofPkFinder = m_AppManager[QualDAMethod.GetUsageKey(QualFunctionality.SpectrumPeakFinder, QualDataType.MSMS)] as
IPSetTofPeakFinder; //Using the one for Spectrum(MSMS)
//Abhijit:-there was a check for factory only key in Qual's MFE which I have removed.
findParams.SaturationThresholdPct = 10.0;
// disable extraction of all graphics/plots
findParams.ProcessingParameters.ExrtactMSMSSpectrum = false;
findParams.ProcessingParameters.ExtractECC = false;
findParams.ProcessingParameters.ExtractEIC = false;
findParams.ProcessingParameters.ExtractMFESpectrum = false;
findParams.ProcessingParameters.ExtractRawSpectra = false;
findParams.ProcessingParameters.PreferProfileRawSpectra = false;
// add MFEGC filter
if (AppFeatureConfig.Configuration.IsApplicable(AppFeatureConfig.Key_GcSep))
{
IPSetPeakFilter mfeGCpeakFilter = m_AppManager[QualDAMethod.ParamKeyMSPeakFilters] as IPSetPeakFilter;
findParams.MFEGCPeakFilter = mfeGCpeakFilter;
}
return(findParams);
}
public static IPSetChargeStateAssignment GetChargeStateParameters(ProfinderLogic AppLogic)
{
IPSetChargeStateAssignment chargeStateInfo = AppLogic[QualDAMethod.GetUsageKey(QualFunctionality.ChargeStateAssignment, QualDataType.MS)] as IPSetChargeStateAssignment;
return(chargeStateInfo);
}
