private ChromatogramRequestDocumentChromatogramGroup MakeChromatogramRequestDocumentChromatogramGroup(
ChromSource chromSource, bool calculateMassErrors, IEnumerable <ChromatogramRequestDocumentChromatogramGroupChromatogram> chromatograms)
{
ChromatogramRequestDocumentChromatogramGroup docFilterPair = new ChromatogramRequestDocumentChromatogramGroup
{
ModifiedSequence = ModifiedSequence != null?ModifiedSequence.ToString() : null,
PrecursorMz = Q1.RawValue, // A negative ion mode precursor will be serialized as a negative mz value
MassErrors = calculateMassErrors,
};
switch (Extractor)
{
case ChromExtractor.base_peak:
docFilterPair.Extractor = RemoteApi.GeneratedCode.ChromExtractor.BasePeak;
break;
case ChromExtractor.summed:
docFilterPair.Extractor = RemoteApi.GeneratedCode.ChromExtractor.Summed;
break;
}
if (MinTime.HasValue)
{
docFilterPair.MinTime = MinTime.Value;
docFilterPair.MinTimeSpecified = true;
}
if (MaxTime.HasValue)
{
docFilterPair.MaxTime = MaxTime.Value;
docFilterPair.MaxTimeSpecified = true;
}
if (MinIonMobilityValue.HasValue && MaxIonMobilityValue.HasValue)
{
docFilterPair.DriftTime = (MinIonMobilityValue.Value + MaxIonMobilityValue.Value) / 2;
if (ChromSource.fragment == chromSource) // Use high energy offset for fragments
{
docFilterPair.DriftTime += HighEnergyIonMobilityValueOffset;
}
docFilterPair.DriftTimeSpecified = true;
docFilterPair.DriftTimeWindow = MaxIonMobilityValue.Value - MinIonMobilityValue.Value;
docFilterPair.DriftTimeWindowSpecified = true;
}
switch (chromSource)
{
case ChromSource.ms1:
docFilterPair.Source = RemoteApi.GeneratedCode.ChromSource.Ms1;
break;
case ChromSource.fragment:
docFilterPair.Source = RemoteApi.GeneratedCode.ChromSource.Ms2;
break;
case ChromSource.sim:
docFilterPair.Source = RemoteApi.GeneratedCode.ChromSource.Sim;
break;
}
docFilterPair.Chromatogram = chromatograms.ToArray();
return(docFilterPair);
}
private ChromatogramRequestDocumentChromatogramGroup MakeChromatogramRequestDocumentChromatogramGroup(
ChromSource chromSource, bool calculateMassErrors, IEnumerable <ChromatogramRequestDocumentChromatogramGroupChromatogram> chromatograms)
{
ChromatogramRequestDocumentChromatogramGroup docFilterPair = new ChromatogramRequestDocumentChromatogramGroup
{
ModifiedSequence = ModifiedSequence,
PrecursorMz = Q1,
MassErrors = calculateMassErrors,
};
switch (Extractor)
{
case ChromExtractor.base_peak:
docFilterPair.Extractor = RemoteApi.GeneratedCode.ChromExtractor.BasePeak;
break;
case ChromExtractor.summed:
docFilterPair.Extractor = RemoteApi.GeneratedCode.ChromExtractor.Summed;
break;
}
if (MinTime.HasValue)
{
docFilterPair.MinTime = MinTime.Value;
docFilterPair.MinTimeSpecified = true;
}
if (MaxTime.HasValue)
{
docFilterPair.MaxTime = MaxTime.Value;
docFilterPair.MaxTimeSpecified = true;
}
if (MinDriftTimeMsec.HasValue && MaxDriftTimeMsec.HasValue)
{
docFilterPair.DriftTime = (MinDriftTimeMsec.Value + MaxDriftTimeMsec.Value) / 2;
if (ChromSource.fragment == chromSource && HighEnergyDriftTimeOffsetMsec.HasValue)
{
docFilterPair.DriftTime += HighEnergyDriftTimeOffsetMsec.Value;
}
docFilterPair.DriftTimeSpecified = true;
docFilterPair.DriftTimeWindow = MaxDriftTimeMsec.Value - MinDriftTimeMsec.Value;
docFilterPair.DriftTimeWindowSpecified = true;
}
switch (chromSource)
{
case ChromSource.ms1:
docFilterPair.Source = RemoteApi.GeneratedCode.ChromSource.Ms1;
break;
case ChromSource.fragment:
docFilterPair.Source = RemoteApi.GeneratedCode.ChromSource.Ms2;
break;
case ChromSource.sim:
docFilterPair.Source = RemoteApi.GeneratedCode.ChromSource.Sim;
break;
}
docFilterPair.Chromatogram = chromatograms.ToArray();
return(docFilterPair);
}
public SpectrumFilterPair(ChromatogramRequestDocumentChromatogramGroup requestGroup)
{
Q1 = new SignedMz(requestGroup.PrecursorMz);
ModifiedSequence = new Target(requestGroup.ModifiedSequence);
switch (requestGroup.Extractor)
{
case RemoteApi.GeneratedCode.ChromExtractor.BasePeak:
Extractor = ChromExtractor.base_peak;
break;
case RemoteApi.GeneratedCode.ChromExtractor.Summed:
Extractor = ChromExtractor.summed;
break;
}
if (requestGroup.MinTimeSpecified)
{
MinTime = requestGroup.MinTime;
}
if (requestGroup.MaxTimeSpecified)
{
MaxTime = requestGroup.MaxTime;
}
switch (requestGroup.Source)
{
case RemoteApi.GeneratedCode.ChromSource.Ms1:
Ms1ProductFilters = requestGroup.Chromatogram.Select(
product => new SpectrumProductFilter(product.ProductMz, product.MzWindow)).ToArray();
HighAccQ1 = requestGroup.MassErrors;
break;
case RemoteApi.GeneratedCode.ChromSource.Ms2:
Ms2ProductFilters = requestGroup.Chromatogram.Select(
product => new SpectrumProductFilter(product.ProductMz, product.MzWindow)).ToArray();
HighAccQ3 = requestGroup.MassErrors;
break;
}
}
