private void AddGeneralProcessor(CompositeProcessor <PeakList <Peak> > result)
{
result.Add(new PeakListMassRangeProcessor <Peak>(PrecursorMassRange.From, PrecursorMassRange.To, new int[] { 2, 3 }));
result.Add(new PeakListMinIonIntensityProcessor <Peak>(MinimumIonIntensity));
result.Add(new PeakListMinIonCountProcessor <Peak>(MinimumIonCount));
result.Add(new PeakListMinTotalIonIntensityProcessor <Peak>(MinimumTotalIonIntensity));
}
public Raw2MgfProcessor GetRaw2MgfProcessor()
{
PeakListMassRangeProcessor <Peak> p1 = new PeakListMassRangeProcessor <Peak>(MinimumMass, MaximumMass, new int[] { 2, 3 });
PeakListMinIonIntensityProcessor <Peak> p2 = new PeakListMinIonIntensityProcessor <Peak>(MinimumIonIntensity);
PeakListMinIonCountProcessor <Peak> p3 = new PeakListMinIonCountProcessor <Peak>(MinIonCount);
PeakListMinTotalIonIntensityProcessor <Peak> p4 = new PeakListMinTotalIonIntensityProcessor <Peak>(MinimumTotalIonCount);
CompositeProcessor <PeakList <Peak> > p = new CompositeProcessor <PeakList <Peak> >();
p.Add(p1);
p.Add(p2);
p.Add(p3);
p.Add(p4);
return(new Raw2MgfProcessor(null, GetMascotGenericFormatWriter(), GetRetentionTime(), PrecursorTolerance, PeakTolerance, p, new DirectoryInfo(TargetDirectory), GroupByScanMode));
}
public CompositeProcessor <PeakList <Peak> > GetProcessor(string fileName, IProgressCallback callBack)
{
CompositeProcessor <PeakList <Peak> > result = new CompositeProcessor <PeakList <Peak> >();
if (!this.OutputMzXmlFormat)
{
AddGeneralProcessor(result);
}
if (RemoveIons)
{
if (RemoveIsobaricIons)
{
result.Add(GetIsobaricProcessor());
}
if (RemoveSpecialIons)
{
var ranges = ParseRemoveMassRange();
foreach (var range in ranges)
{
result.Add(new PeakListRemoveMassRangeProcessor <Peak>(range.From, range.To));
}
}
}
if (Deisotopic)
{
result.Add(new PeakListDeisotopicByChargeProcessor <Peak>(ProductIonPPM));
}
if (PrecursorOptions.RemovePrecursor)
{
result.Add(new PeakListRemovePrecursorProcessor <Peak>(this.PrecursorOptions));
}
if (ChargeDeconvolution)
{
result.Add(new PeakListDeconvolutionByChargeProcessor <Peak>(ProductIonPPM));
if (Deisotopic)
{
result.Add(new PeakListDeisotopicByChargeProcessor <Peak>(ProductIonPPM));
}
}
if (KeepTopX)
{
result.Add(new PeakListTopXProcessor <Peak>(TopX));
}
return(result);
}
public SimpleProteinGroupBuilder(string[] perferReferenceRegexString)
{
processor = new CompositeProcessor <IIdentifiedProteinGroup>();
processor.Add(new ProteinNameProcessor(perferReferenceRegexString));
processor.Add(new ProteinLengthProcessor(false));
}