void IScanConsumer <Scan, Run <Scan> > .Notify(Scan scan, float[] mzs, float[] intensities, Run <Scan> run)
{
scan.IsolationWindowLowerBoundary = scan.IsolationWindowTargetMz - scan.IsolationWindowLowerOffset;
scan.IsolationWindowUpperBoundary = scan.IsolationWindowTargetMz + scan.IsolationWindowUpperOffset;
if (intensities.Count() == 0)
{
intensities = FillZeroArray(intensities);
mzs = FillZeroArray(mzs);
logger.Debug("Empty binary array for a MS{0} scan in cycle number: {1}. The empty scans have been filled with zero values.", scan.MsLevel, scan.Cycle);
run.MissingScans++;
}
var spectrum = intensities.Select((x, i) => new SpectrumPoint(x, mzs[i], (float)scan.ScanStartTime)).Where(x => x.Intensity >= run.AnalysisSettings.MinimumIntensity).ToList();
//Predicted singly charged proportion:
//The theory is that an M and M+1 pair are singly charged so we are very simply just looking for occurences where two ions are 1 mz apart (+-massTolerance)
//We therefore create an array cusums that accumulates the difference between ions, so for every ion we calculate the distance between that ion
//and the previous and add that to each of the previous ions' cusum of differences. If the cusum of an ion overshoots 1 +massTolerance, we stop adding to it, if it reaches our mark we count it and stop adding to it
List <int> indexes = new List <int>();
float[] cusums = new float[mzs.Length];
int movingPoint = 0;
double minimum = 1 - 0.001;
double maximum = 1 + 0.001;
for (int i = 1; i < mzs.Length; i++)
{
float distance = mzs[i] - mzs[i - 1];
bool matchedWithLower = false;
for (int ii = movingPoint; ii < i; ii++)
{
cusums[ii] += distance;
if (cusums[ii] < minimum)
{
continue;
}
else if (cusums[ii] > minimum && cusums[ii] < maximum)
{
if (!matchedWithLower)//This is to try and minimise false positives where for example if you have an array: 351.14, 351.15, 352.14 all three get chosen.
{
indexes.Add(i);
indexes.Add(movingPoint);
}
movingPoint += 1;
matchedWithLower = true;
continue;
}
else if (cusums[ii] > maximum)
{
movingPoint += 1;
}
}
}
int distinct = indexes.Distinct().Count();
int len = mzs.Length;
scan.ProportionChargeStateOne = distinct / (double)len;
if (scan.TotalIonCurrent == 0)
{
scan.TotalIonCurrent = intensities.Sum();
TicNotFound = true;
}
scan.Spectrum = new Spectrum()
{
SpectrumPoints = spectrum
};
scan.IsolationWindowLowerBoundary = scan.IsolationWindowTargetMz - scan.IsolationWindowLowerOffset;
scan.IsolationWindowUpperBoundary = scan.IsolationWindowTargetMz + scan.IsolationWindowUpperOffset;
scan.Density = spectrum.Count();
scan.BasePeakIntensity = intensities.Max();
scan.BasePeakMz = mzs[Array.IndexOf(intensities, intensities.Max())];
float basepeakIntensity;
if (intensities.Count() > 0)
{
// TODO: This approach requires two scans across intensities plus converting intensities to a List; is there a simpler approach involving a single scan in a for-next loop?
basepeakIntensity = intensities.Max();
int maxIndex = intensities.ToList().IndexOf(basepeakIntensity);
double mz = mzs[maxIndex];
AtomicallyRecordBasePeakAndRT(new DoubleSpectrumPoint(basepeakIntensity, mz, scan.ScanStartTime), run);
}
else
{
basepeakIntensity = 0;
}
//Extract info for Basepeak chromatograms
bool irt = run.AnalysisSettings.IrtLibrary != null;
if (irt)
{
FindIrtPeptideCandidates(scan, run, spectrum);
}
}
private void FindMs2IsolationWindows(Run <Scan> run)
{
run.IsolationWindows = run.Ms2Scans.Select(x => (x.IsolationWindowTargetMz - x.IsolationWindowLowerOffset, x.IsolationWindowTargetMz + x.IsolationWindowUpperOffset)).Distinct().ToList();
logger.Debug("{0} isolation windows detected: min {1} max {2}", run.IsolationWindows.Count, run.IsolationWindows.Min(x => x.Item2 - x.Item1), run.IsolationWindows.Max(x => x.Item2 - x.Item1));
}
