protected virtual void InitializeProcessingTasks()
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType);
PeakDetector = PeakDetectorFactory.CreatePeakDetector(NewDeconToolsParameters);
Deconvolutor = DeconvolutorFactory.CreateDeconvolutor(NewDeconToolsParameters);
//the new iThrash imports the _peaks.txt file
if (Deconvolutor is DeconTools.Backend.ProcessingTasks.Deconvoluters.InformedThrashDeconvolutor)
{
_deconvolutorRequiresPeaksFile = true;
}
//Will initialize these but whether or not they are used are determined elsewhere
ZeroFiller = new DeconToolsZeroFiller(NewDeconToolsParameters.MiscMSProcessingParameters.ZeroFillingNumZerosToFill);
Smoother = new SavitzkyGolaySmoother(NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayNumPointsInSmooth,
NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayOrder);
FitScoreCalculator = new DeconToolsFitScoreCalculator();
ScanResultUpdater = new ScanResultUpdater(NewDeconToolsParameters.ScanBasedWorkflowParameters.ProcessMS2);
ResultValidator = new ResultValidatorTask();
IsosResultExporter = IsosExporterFactory.CreateIsosExporter(Run.ResultCollection.ResultType, ExporterType,
IsosOutputFileName);
ScanResultExporter = ScansExporterFactory.CreateScansExporter(Run.MSFileType, ExporterType,
ScansOutputFileName);
if (!_deconvolutorRequiresPeaksFile)
{
PeakListExporter = PeakListExporterFactory.Create(ExporterType, Run.MSFileType, PeakListExporterTriggerValue,
PeakListOutputFileName);
}
PeakToMSFeatureAssociator = new PeakToMSFeatureAssociator();
}
protected override void InitializeProcessingTasks()
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType);
PeakDetector = PeakDetectorFactory.CreatePeakDetector(NewDeconToolsParameters);
var moreSensitivePeakToBackgroundRatio = NewDeconToolsParameters.PeakDetectorParameters.PeakToBackgroundRatio / 2;
var moreSensitiveSigNoiseThresh = NewDeconToolsParameters.PeakDetectorParameters.SignalToNoiseThreshold;
_moreSensitiveMS1PeakDetector = new DeconToolsPeakDetectorV2(moreSensitivePeakToBackgroundRatio,
moreSensitiveSigNoiseThresh, NewDeconToolsParameters.PeakDetectorParameters.PeakFitType,
NewDeconToolsParameters.PeakDetectorParameters.IsDataThresholded);
_superSensitiveMS1PeakDetector = new DeconToolsPeakDetectorV2(0, 0, NewDeconToolsParameters.PeakDetectorParameters.PeakFitType,
NewDeconToolsParameters.PeakDetectorParameters.IsDataThresholded);
Deconvolutor = DeconvolutorFactory.CreateDeconvolutor(NewDeconToolsParameters);
//Will initialize these but whether or not they are used are determined elsewhere
ZeroFiller = new DeconToolsZeroFiller(NewDeconToolsParameters.MiscMSProcessingParameters.ZeroFillingNumZerosToFill);
Smoother = new SavitzkyGolaySmoother(NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayNumPointsInSmooth,
NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayOrder);
FitScoreCalculator = new DeconToolsFitScoreCalculator();
ResultValidator = new ResultValidatorTask();
PeakToMSFeatureAssociator = new PeakToMSFeatureAssociator();
_ms2PeakDetectorForCentroidData = new DeconToolsPeakDetectorV2(0, 0, Globals.PeakFitType.QUADRATIC, true)
{
RawDataType = Globals.RawDataType.Centroided
};
_ms2PeakDetectorForProfileData = new DeconToolsPeakDetectorV2(NewDeconToolsParameters.PeakDetectorParameters.PeakToBackgroundRatio,
NewDeconToolsParameters.PeakDetectorParameters.SignalToNoiseThreshold,
NewDeconToolsParameters.PeakDetectorParameters.PeakFitType,
NewDeconToolsParameters.PeakDetectorParameters.IsDataThresholded);
Check.Ensure(Deconvolutor is ThrashDeconvolutorV2, "Error. Currently the DeconMSn workflow only works with the ThrashV2 deconvolutor. Selected deconvolutor= " + Deconvolutor);
}