public LabelAmountAlgorithm(
IEventAggregator eventAggregator,
IXicSelection xicSelection,
IChromatographicPeakDetection chromatographicPeakDetection,
XicPeakPicker xicPeakPicker,
ISpectrumSelection spectrumSelection,
ISpectralPeakDetection spectralPeakDetection,
IsotopicProfileFinder isotopicProfileFinder,
LabelAmountCalculator labelAmountCalculator,
ISmoothing xicSmoothing,
ISmoothing spectrumSmoothing,
DeuterationResultGenerator deuterationResultGenerator,
IServiceLocator serviceLocator)
: base()
{
_eventAggregator = eventAggregator;
_xicSelection = xicSelection;
_chromatographicPeakDetection = chromatographicPeakDetection;
_spectrumSelection = spectrumSelection;
_spectralPeakDetection = spectralPeakDetection;
_xicPeakPicker = xicPeakPicker;
_isotopicProfileFinder = isotopicProfileFinder;
_labelAmountCalculator = labelAmountCalculator;
_xicSmoothing = xicSmoothing;
_spectrumSmoothing = spectrumSmoothing;
_deuterationResultGenerator = deuterationResultGenerator;
_serviceLocator = serviceLocator;
ProcessingSteps.Add(_xicSelection);
ProcessingSteps.Add(_xicSmoothing);
ProcessingSteps.Add(_chromatographicPeakDetection);
ProcessingSteps.Add(_xicPeakPicker);
ProcessingSteps.Add(_spectrumSelection);
ProcessingSteps.Add(_spectrumSmoothing);
ProcessingSteps.Add(_spectralPeakDetection);
ProcessingSteps.Add(_isotopicProfileFinder);
ProcessingSteps.Add(_labelAmountCalculator);
}
public void MyTestInitialize()
{
mockEventAggregator = new Mock<IEventAggregator>();
outputEvent = new OutputEvent();
mockEventAggregator.Setup(mock => mock.GetEvent<OutputEvent>()).Returns(outputEvent);
isotopicProfileFinder = new IsotopicProfileFinder(mockEventAggregator.Object);
isotopicProfileFinder.PeakWidthMaximum = 0.5;
isotopicProfileFinder.MSPeakSelectionOption = Hydra.Core.MSPeakSelectionOption.MostIntenseWithinMzVariation;
}
public void Execute(RunResult result, IXYData msmsSpectrum)
{
output.Publish(" MSMS Fragment Analyzer");
PeptideUtility pu = new PeptideUtility();
if (result.IsResultBasedOnFragment)
{
pu.GetIsotopicProfileForFragmentIon(result, 20);
}
else
{
result.TheoreticalIsotopicPeakList = pu.GetIsotopicProfile(result.Peptide.Sequence, result.Peptide.ChargeState, true, 20, true, true, string.Empty);
}
Peptide peptide = new Peptide(result.FragmentIon.Sequence);
peptide.MonoIsotopicMass = result.FragmentIon.MZ;
peptide.ChargeState = result.FragmentIon.ChargeState;
peptide.PeaksInCalculation = result.FragmentIon.PeaksInCalculation;
peptide.MsThreshold = result.FragmentIon.MsThreshold;
peptide.DeuteriumDistributionRightPadding = result.FragmentIon.DeutDistRightPadding;
peptide.DeuteriumDistributionThreshold = result.FragmentIon.DeutDistThreshold;
RunResult rr = new RunResult(peptide, result.Run);
rr.IsResultBasedOnFragment = true;
rr.FragmentIon = result.FragmentIon;
rr.TheoreticalIsotopicPeakList = result.TheoreticalIsotopicPeakList;
try
{
output.Publish(" Executing Spectral Peak Detection");
SpectralPeakDetection mspeakDetector = new SpectralPeakDetection(eventAggregator);
mspeakDetector.PeakToBackgroundRatio = _peakToBackgroundRatio;
mspeakDetector.SignalToNoiseThreshold = _signalToNoiseThreshold;
IList<MSPeak> peakList = mspeakDetector.Execute(msmsSpectrum);
output.Publish(" Executing Isotopic Profile Finder");
IsotopicProfileFinder profileFinder = new IsotopicProfileFinder(eventAggregator);
profileFinder.IntensityThreshold = intensityThreshold;
profileFinder.MassVariability = massVariability;
profileFinder.MSPeakSelectionOption = _msPeakSelectionOption;
profileFinder.PeakNumberMaximum = peakNumberMaximum;
profileFinder.PeakWidthMaximum = peakWidthMaximum;
profileFinder.PeakWidthMinimum = peakWidthMinimum;
profileFinder.Execute(rr, peakList);
output.Publish(" Executing Label Amount Calculator");
LabelAmountCalculator labelAmountCalc = new LabelAmountCalculator(eventAggregator);
labelAmountCalc.PeaksInCalcMode = PeaksInLabelCalculationMode.Manual;
labelAmountCalc.Mode = Mode.CalculatedMassAndExperimentalIntensity;
labelAmountCalc.Execute(rr);
}
catch (Exception ex)
{
throw ex;
}
result.IsotopicPeakList = rr.IsotopicPeakList;
output.Publish(" IsotopicPeakList Count=" + result.IsotopicPeakList.Count);
result.AverageMass = rr.AverageMass;
output.Publish(" AverageMass=" + result.AverageMass);
result.TheoreticalAverageMass = MSUtility.GetAverageMassFromPeakList(result.TheoreticalIsotopicPeakList, result.ActualPeaksInCalculation); // TODO: this is a bandaid solution
output.Publish(" TheoreticalAverageMass=" + result.TheoreticalAverageMass);
result.AmountDeut = rr.AmountDeut;
output.Publish(" AmountDeut=" + result.AmountDeut);
result.IsUsedInCalculations = rr.IsUsedInCalculations;
output.Publish(" IsUsedInCalculations=" + result.IsUsedInCalculations);
result.AmountDeutFromDeutDist = rr.AmountDeutFromDeutDist;
output.Publish(" AmountDeutFromDeutDist=" + result.AmountDeutFromDeutDist);
}
public void MyTestInitialize()
{
Initialize();
IsotopicProfileFinder finder = new IsotopicProfileFinder(MockEventAggregator.Object);
finder.PeakWidthMaximum = 0.5;
finder.MSPeakSelectionOption = Hydra.Core.MSPeakSelectionOption.MostIntenseWithinMzVariation;
labelAmountCalculator = new LabelAmountAlgorithm(
MockEventAggregator.Object,
new XicSelection(MockEventAggregator.Object, MockRegionManager.Object),
new ChromatographicPeakDetection(MockEventAggregator.Object),
new XicPeakPicker(MockEventAggregator.Object),
new SpectrumSelection(MockEventAggregator.Object, MockRegionManager.Object),
new SpectralPeakDetection(MockEventAggregator.Object),
finder,
new LabelAmountCalculator(MockEventAggregator.Object),
new SavitzkyGolaySmoothing(MockEventAggregator.Object, MockRegionManager.Object),
new SavitzkyGolaySmoothing(MockEventAggregator.Object, MockRegionManager.Object),
new DeuterationResultGenerator(MockEventAggregator.Object),
MockServiceLocator.Object);
}