public XicSelectionView(IXYData xyData)
{
InitializeComponent();
graphView.LoadGraph("Time", "XIC", xyData.XValues, xyData.YValues);
listView.ItemsSource = xyData.GetXYPairs();
}
public SpectrumSelectionView(IXYData xyData)
{
InitializeComponent();
graphView.LoadGraph("m/z", "Spectrum", xyData.XValues, xyData.YValues);
listView.ItemsSource = xyData.GetXYPairs();
}
public static void AssertChromatogram(IXYData tic, int expectedDataPoints, Stopwatch timer, int minimumMillisecondsGenerationShouldTake, int maximumMillisecondsGenerationShouldTake)
{
Assert.AreEqual(expectedDataPoints, tic.XValues.Count);
Assert.IsTrue(
timer.ElapsedMilliseconds >= minimumMillisecondsGenerationShouldTake &&
timer.ElapsedMilliseconds <= maximumMillisecondsGenerationShouldTake,
"The TIC took " + timer.ElapsedMilliseconds + " which is outside of the acceptable performance range of (" + minimumMillisecondsGenerationShouldTake + " - " + maximumMillisecondsGenerationShouldTake + ")");
}
public static void AssertXYData(IXYData xyData, double[] expectedXValues, double[] expectedYValues)
{
Assert.AreEqual(expectedXValues.Length, xyData.XValues.Count);
Assert.AreEqual(expectedYValues.Length, xyData.YValues.Count);
for (int i = 0; i < xyData.XValues.Count; i++)
{
Assert.AreEqual(expectedXValues[i], xyData.XValues[i]);
Assert.AreEqual(expectedYValues[i], xyData.YValues[i]);
}
}
private void OnViewXIC(IXYData value)
{
ManagedContent view = _regionManager.FindExistingView("DocumentRegion", typeof(XicSelectionView), value.Title);
if (view == null)
{
view = new XicSelectionView(value);
view.Title = value.Title;
_regionManager.AddToRegion("DocumentRegion", view);
}
view.Show();
view.Activate();
}
public IList<ChromatographicPeak> Execute(IXYData xyData)
{
_output.Publish(" Chromatographic Peak Detection Started (PeakToBackgroundRatio=" + PeakToBackgroundRatio + ", SignalToNoiseThreshold=" + SignalToNoiseThreshold + ")");
Decon2LS.Peaks.clsPeak[] peakList = GetDeconToolsPeaks(xyData);
IList<ChromatographicPeak> peaks = new List<ChromatographicPeak>();
foreach (Decon2LS.Peaks.clsPeak peak in peakList)
{
peaks.Add(ConvertDeconPeakToChromatographicPeak(peak));
_output.Publish(" Peak Found: RT=" + peak.mdbl_mz + ", PeakHeight=" + peak.mdbl_intensity + ", PeakWidth=" + peak.mdbl_FWHM + ")");
}
_output.Publish(" " + peaks.Count + " peaks found.");
return peaks;
}
protected Decon2LS.Peaks.clsPeak[] GetDeconToolsPeaks(IXYData xyData)
{
float[] xData = ConvertDoubleArrayToFloat(xyData.XValues);
float[] yData = ConvertDoubleArrayToFloat(xyData.YValues);
Decon2LS.Peaks.clsPeakProcessor peakProcessor = new Decon2LS.Peaks.clsPeakProcessor();
Decon2LS.Peaks.clsPeakProcessorParameters parameters = new Decon2LS.Peaks.clsPeakProcessorParameters();
parameters.PeakBackgroundRatio = PeakToBackgroundRatio;
parameters.SignalToNoiseThreshold = SignalToNoiseThreshold;
parameters.PeakFitType = Decon2LS.Peaks.PEAK_FIT_TYPE.QUADRATIC;
peakProcessor.SetOptions(parameters);
Decon2LS.Peaks.clsPeak[] peakList = new Decon2LS.Peaks.clsPeak[1];
peakProcessor.DiscoverPeaks(ref xData, ref yData, ref peakList, 0, float.MaxValue);
return peakList;
}
private void OnViewXIC(IXYData value)
{
if (value.Title.ToLower().Contains(" xic"))
{
XicSelectionView view = new XicSelectionView(value);
view.Title = value.Title;
_regionManager.AddToRegion("DocumentRegion", view);
view.Activate();
}
else
{
SpectrumSelectionView view = new SpectrumSelectionView(value);
view.Title = value.Title;
_regionManager.AddToRegion("DocumentRegion", view);
view.Activate();
}
}
public IXYData Execute(IXYData xyData)
{
if (Enabled && !executeDisabled)
{
_output.Publish(" Savitzky Golay Smoothing Started (LeftParam=" + LeftParam + ", RightParam=" + RightParam + ", Order=" + order + ")");
float[] xvals = new float[xyData.XValues.Count];
float[] yvals = new float[xyData.YValues.Count];
xvals = xyData.XValues.Select(item => (float)item).ToArray();
yvals = xyData.YValues.Select(item => (float)item).ToArray();
DeconEngine.Utils.SavitzkyGolaySmooth(this.leftParam, this.rightParam, this.order, ref xvals, ref yvals);
IXYData smoothedXYData = new XYData(xvals.Select(item => (double)item).ToList(), yvals.Select(item => (double)item).ToList());
smoothedXYData.Title = "Smoothed " + xyData.Title;
_clickableOutput.Publish(new ClickableOutputEvent()
{
Parameter = smoothedXYData,
Text = " Smoothing completed",
Click = new DelegateCommand<IXYData>(OnViewXIC)
});
return smoothedXYData;
}
return xyData;
}
public static void AssertValue(IXYData xyData, int index, double expectedXValue, double expectedYValue)
{
Assert.AreEqual(expectedXValue, Math.Round(xyData.XValues[index], 10));
Assert.AreEqual(expectedYValue, Math.Round(xyData.YValues[index], 10));
}
public void Constructor()
{
xyData = new XYData(XYDataHelper.XValueTestSet2, XYDataHelper.YValueTestSet2);
XYDataHelper.AssertXYData(xyData, XYDataHelper.XValueTestSet2, XYDataHelper.YValueTestSet2);
}
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);
}
private void LoadXic()
{
_xyData = _run.GetExtractedIonChromatogram(_xicMass, _xicMass, _mzTolerance, TimeUnit.Seconds);
_xyData.Title = "XIC (" + _xicMass.ToString("N4") + " mzTol=" + _mzTolerance + ") - " + Path.GetFileName(_run.FileName);
}
private void LoadTic()
{
_xyData = _run.GetTotalIonChromatogram();
_xyData.Title = "TIC - " + Path.GetFileName(_run.FileName);
}
private void LoadSpectrum()
{
_xyData = _run.GetSpectrum(_startTime, _stopTime, _monoIsotopicMass - _mzLowerOffset, _monoIsotopicMass + _mzUpperOffset, 0);
_xyData.Title = "MS (RT=" + _startTime.ToString("N2") + "-" + _stopTime.ToString("N2") + " Mass=" + _monoIsotopicMass.ToString("N4") + ") - " + Path.GetFileName(_run.FileName);
}
public void MyTestInitialize()
{
xyData = new XYData(XYDataHelper.XValueTestSet1, XYDataHelper.YValueTestSet1);
}
private void OnViewXIC(IXYData value)
{
throw new NotImplementedException();
}
public void Set(IXYData tic)
{
cache = tic;
}
