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Optimize MS2 value peak extraction #775

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Optimize MS2 value peak extraction #775

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24 changes: 3 additions & 21 deletions src/MSDIAL5/MsdialCore/Utility/DataAccess.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -332,10 +332,7 @@ public static List<ValuePeak[]> GetMs2ValuePeaks(IDataProvider provider, double
int startScanID, int endScanID, IReadOnlyList<double> pMzValues, ParameterBase param, AcquisitionType acquisitionType,
double targetCE = -1, ChromXType type = ChromXType.RT, ChromXUnit unit = ChromXUnit.Min) {

var counter = 0;
var arrayLength = GetTargetArrayLength(provider, startScanID, endScanID, precursorMz, targetCE, param, acquisitionType);
var valuePeakArrayList = new List<ValuePeak[]>(pMzValues.Count);
valuePeakArrayList.AddRange(pMzValues.Select(_ => new ValuePeak[arrayLength]));
var valuePeakLists = pMzValues.Select(_ => new List<ValuePeak>()).ToArray();

for (int i = startScanID; i <= endScanID; i++) {
var spec = provider.LoadMsSpectrumFromIndex(i);
Expand All @@ -348,27 +345,12 @@ public static List<ValuePeak[]> GetMs2ValuePeaks(IDataProvider provider, double
var intensities = RetrieveIntensitiesFromMzValues(pMzValues, spec.Spectrum, param.CentroidMs2Tolerance);

for (int j = 0; j < pMzValues.Count; j++) {
valuePeakArrayList[j][counter] = new ValuePeak(id, chromX, pMzValues[j], intensities[j]);
valuePeakLists[j].Add(new ValuePeak(id, chromX, pMzValues[j], intensities[j]));
}
counter++;
}
}
}
return valuePeakArrayList;
}

private static int GetTargetArrayLength(IDataProvider provider, int startScanID, int endScanID, double precursorMz, double targetCE, ParameterBase param, AcquisitionType type) {
var counter = 0;
for (int i = startScanID; i <= endScanID; i++) {
var spec = provider.LoadMsSpectrumFromIndex(i);
if (spec.MsLevel == 2 && spec.Precursor != null) {
if (targetCE >= 0 && spec.CollisionEnergy >= 0 && Math.Abs(targetCE - spec.CollisionEnergy) > 1) continue; // for AIF mode
if (IsInMassWindow(precursorMz, spec, param.CentroidMs1Tolerance, type)) {
counter++;
}
}
}
return counter;
return valuePeakLists.Select(peaks => peaks.ToArray()).ToList();
}

public static double[] RetrieveIntensitiesFromMzValues(
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