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); } } }