public void ComputeMonoisotopicPeakIntensity(IMzSpectrum <IMzPeak> precursorSpectrum)
{
var thePeak = precursorSpectrum.GetClosestPeak(SelectedIonMonoisotopicGuessMz.Value);
SelectedIonMonoisotopicGuessIntensity = thePeak.Intensity;
SelectedIonMonoisotopicGuessMz = thePeak.Mz;
}
public void ComputeSelectedPeakIntensity(IMzSpectrum <IMzPeak> precursorSpectrum)
{
var thePeak = precursorSpectrum.GetClosestPeak(SelectedIonMZ);
SelectedIonIntensity = thePeak.Intensity;
SelectedIonMZ = thePeak.Mz;
}
public void RefineSelectedMzAndIntensity(IMzSpectrum <IMzPeak> precursorSpectrum)
{
var thePeak = precursorSpectrum.GetClosestPeak(IsolationMz);
SelectedIonIntensity = thePeak.Intensity;
SelectedIonMZ = thePeak.Mz;
}
public override IMsDataScan <IMzSpectrum <IMzPeak> > GetOneBasedScan(int oneBasedScanNumber)
{
if (Scans[oneBasedScanNumber - 1] == null)
{
var representativeScanNumber = oneBasedScanNumber + (numScansToAverage - 1) / 2;
var representative = raw.GetOneBasedScan(representativeScanNumber);
if (representative.MsnOrder != 1)
{
throw new MzLibException("Scan " + representativeScanNumber + " is not MS1 scan");
}
int msnOrder = 1;
Polarity polarity = representative.Polarity;
if (!representative.IsCentroid)
{
throw new MzLibException("Scan " + representativeScanNumber + " is not centroid scan");
}
bool isCentroid = true;
double retentionTime = representative.RetentionTime;
MZAnalyzerType mzAnalyzer = representative.MzAnalyzer;
IMzSpectrum <IMzPeak> peaks = CombinePeaks(raw.Where(b => b.OneBasedScanNumber >= oneBasedScanNumber && b.OneBasedScanNumber <= oneBasedScanNumber + numScansToAverage - 1).Select(b => b.MassSpectrum).ToList(), ppmToleranceForPeakCombination);
MzRange scanWindowRange = representative.ScanWindowRange;
double totalIonCurrent = peaks.SumOfAllY;
double injectionTime = double.NaN;
double[,] noiseData = null;
Scans[oneBasedScanNumber - 1] = new MsDataScan <IMzSpectrum <IMzPeak> >(peaks, oneBasedScanNumber, msnOrder, isCentroid, polarity, retentionTime, scanWindowRange, null, mzAnalyzer, totalIonCurrent, injectionTime, noiseData, "scan=" + oneBasedScanNumber);
}
return(Scans[oneBasedScanNumber - 1]);
}
public void ComputeMonoisotopicPeakIntensity(IMzSpectrum <IMzPeak> precursorSpectrum)
{
if (precursorSpectrum.Size == 0)
{
throw new MzLibException("Could not compute monoisotopic peak intensity because precursorSpectrum.Size == 0");
}
var thePeak = precursorSpectrum.GetClosestPeakIndex(SelectedIonMonoisotopicGuessMz.Value);
SelectedIonMonoisotopicGuessIntensity = precursorSpectrum.YArray[thePeak.Value];
SelectedIonMonoisotopicGuessMz = precursorSpectrum.XArray[thePeak.Value];
}
public void ComputeSelectedPeakIntensity(IMzSpectrum <IMzPeak> precursorSpectrum)
{
if (precursorSpectrum.Size == 0)
{
throw new MzLibException("Could not compute selected peak intensity because precursorSpectrum.Size == 0");
}
var thePeak = precursorSpectrum.GetClosestPeakIndex(SelectedIonMZ);
SelectedIonIntensity = precursorSpectrum.YArray[thePeak.Value];
SelectedIonMZ = precursorSpectrum.XArray[thePeak.Value];
}
public IEnumerable <IsotopicEnvelope> GetIsolatedMassesAndCharges(IMzSpectrum <IMzPeak> precursorSpectrum, int minAssumedChargeState, int maxAssumedChargeState, double deconvolutionTolerancePpm, double intensityRatio)
{
if (IsolationRange == null)
{
yield break;
}
foreach (var haha in precursorSpectrum.Deconvolute(new MzRange(IsolationRange.Minimum - 8.5, IsolationRange.Maximum + 8.5), minAssumedChargeState, maxAssumedChargeState, deconvolutionTolerancePpm, intensityRatio)
.Where(b => b.peaks.Any(cc => isolationRange.Contains(cc.mz))))
{
yield return(haha);
}
}
public void RefineSelectedMzAndIntensity(IMzSpectrum <IMzPeak> precursorSpectrum)
{
if (!IsolationMz.HasValue)
{
throw new MzLibException("Could not refine selected m/z and intensity because !IsolationMz.HasValue");
}
if (precursorSpectrum.Size == 0)
{
throw new MzLibException("Could not refine selected m/z and intensity because precursorSpectrum.Size == 0");
}
var thePeak = precursorSpectrum.GetClosestPeakIndex(IsolationMz.Value);
SelectedIonIntensity = precursorSpectrum.YArray[thePeak.Value];
SelectedIonMZ = precursorSpectrum.XArray[thePeak.Value];
}
public IEnumerable <Tuple <List <IMzPeak>, int> > GetIsolatedMassesAndCharges(IMzSpectrum <IMzPeak> precursorSpectrum, int maxAssumedChargeState, Tolerance massTolerance, double intensityRatio)
{
if (IsolationRange == null)
{
yield break;
}
foreach (var haha in precursorSpectrum.Deconvolute(new MzRange(IsolationRange.Minimum - 8.5, IsolationRange.Maximum + 8.5), maxAssumedChargeState, massTolerance, intensityRatio)
.Where(b => b.Item1.Any(cc => isolationRange.Contains(cc.Mz))))
{
yield return(haha);
}
}
