public bool Equals(MSDataScan <TSpectrum> other)
{
if (ReferenceEquals(this, other))
{
return(true);
}
return(SpectrumNumber.Equals(other.SpectrumNumber) && ParentFile.Equals(other.ParentFile));
}
protected virtual MSDataScan <TSpectrum> GetMSDataScan(int spectrumNumber)
{
int msn = GetMsnOrder(spectrumNumber);
MSDataScan <TSpectrum> scan = msn > 1 ? new MsnDataScan <TSpectrum>(spectrumNumber, msn, this) : new MSDataScan <TSpectrum>(spectrumNumber, msn, this);
return(scan);
}
public virtual IEnumerable <MSDataScan <TSpectrum> > GetMsScans(double firstRT, double lastRT)
{
int spectrumNumber = GetSpectrumNumber(firstRT - 0.0000001);
while (spectrumNumber <= LastSpectrumNumber)
{
MSDataScan <TSpectrum> scan = GetMsScan(spectrumNumber++);
double rt = scan.RetentionTime;
if (rt < firstRT)
{
continue;
}
if (rt > lastRT)
{
yield break;
}
yield return(scan);
}
}
public IEnumerable <Feature> ExtractFeatures(IList <int> scans, double ppmTolerance, int minConsecutiveScans = 5)
{
List <Feature> activeFeatures = new List <Feature>();
List <ThermoMzPeak> outPeaks = new List <ThermoMzPeak>();
rawFile.GetLabeledSpectrum(scans[0]).TryGetPeaks(0, 1000, out outPeaks);
double currRT = rawFile.GetRetentionTime(scans[0]);
//MZPeak[] currentPeaks = currentScan.MassSpectrum.GetPeaks(0, 1000).ToArray();
MZPeak[] currentPeaks = outPeaks.ToArray();
activeFeatures.AddRange(currentPeaks.Select(p => new Feature(p, currRT)));
int counter = 0;
int percent = (scans.Count) / 100;
for (int i = 1; i < scans.Count; i++)
{
rawFile.ClearCachedScans();
if (i % percent == 0)
{
counter++;
if (counter < 100)
{
OnProgressUpdate(0.01);
}
}
MSDataScan <ThermoSpectrum> currentScan = rawFile.GetMsScan(scans[i]);
//currentScan = scans[i];
// outPeaks = new List<ThermoMzPeak>();
// double[,] peakArray = currentScan.MassSpectrum.ToArray();
//for (int j = 0; j < peakArray.Length / 2; j++)
//{
// outPeaks.Add(new MZPeak(peakArray[0, j], peakArray[1, j]));
//}
rawFile.GetLabeledSpectrum(currentScan.SpectrumNumber).TryGetPeaks(0, 1000, out outPeaks);
outPeaks = outPeaks.OrderBy(x => x.MZ).ToList();
//currentPeaks = currentScan.MassSpectrum.GetPeaks(0, 1000).ToArray();
currentPeaks = outPeaks.ToArray();
double rt = currentScan.RetentionTime;
// Order features based on their average m/z which may change each round as new peaks are added
activeFeatures = activeFeatures.OrderBy(feat => feat.AverageMZ).ToList();
// Match all the active features to the current spectrum at a given ppm tolerance
MatchPeaks(activeFeatures, currentPeaks, ppmTolerance, rt);
// Find features that are finished and return them if they pass the filters
int f = 0;
while (f < activeFeatures.Count)
{
var feature = activeFeatures[f];
//DJB
//if (feature.LastAddedTime < rt || feature.CurrentState == PeakState.Tailing)
//NWK
if (feature.MaxRT < rt)
{
//DJB
//if (feature.Count >= minConsecutiveScans && (feature.TotalStates & PeakState.Tailing) == PeakState.Tailing)
//NWK
if (feature.Count >= minConsecutiveScans && CheckPeakRise(feature))
{
yield return(feature);
}
activeFeatures.RemoveAt(f);
}
else
{
f++;
}
}
}
//DJB
//foreach (var feature in activeFeatures.Where(f => f.Count > minConsecutiveScans && f.CurrentState != PeakState.Random))
//NWK
foreach (var feature in activeFeatures.Where(f => f.Count > minConsecutiveScans))
{
if (CheckPeakRise(feature))
{
yield return(feature);
}
}
}
