public List <MZPeak> GetPeaksFromNearestSpectrum(FeatureGroup group, ThermoRawFile rawFile)
{
int scanNum = rawFile.GetSpectrumNumber(group.ApexTime);
List <MZPeak> returnPeaks = new List <MZPeak>();
ThermoSpectrum spectrum = rawFile.GetLabeledSpectrum(scanNum);
HashSet <double> peakMZs = new HashSet <double>();
foreach (Feature feature in group.allFeatures)
{
MZPeak outPeak = spectrum.GetClosestPeak(MassRange.FromPPM(feature.AverageMZ, 10));
if (outPeak != null)
{
if (!peakMZs.Contains(outPeak.Intensity))
{
returnPeaks.Add(new MZPeak(feature.AverageMZ, outPeak.Intensity));
peakMZs.Add(outPeak.Intensity);
}
}
}
returnPeaks = returnPeaks.OrderBy(x => x.MZ).ToList();
return(returnPeaks);
}
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);
}
}
}
