private LcMsPeakCluster CollectLcMsPeaks(double targetMass, int minRow, int maxRow, int minCol, int maxCol, bool reCollectAllPeaks = false)
{
var ms1ScanNums = Run.GetMs1ScanVector();
var envelopes = new List<ObservedIsotopeEnvelope>();
var bestBcDist = 100d;
ObservedIsotopeEnvelope bestEnvelope = null;
var mostAbuInternalIndex = _theoreticalEnvelope.IndexOrderByRanking[0];
var tolerance = new Tolerance(Comparer.Ppm * 0.5);
var massTol = tolerance.GetToleranceAsTh(targetMass);
var nPeaksCutoff = NumberOfPeaksCutoff;
var bcCutoff = GetSeedBcDistThreshold();
var corrCutoff = GetSeedCorrThreshold();
for (var i = minRow; i <= maxRow; i++)
{
for (var j = minCol; j <= maxCol; j++)
{
if (reCollectAllPeaks) _featureMatrix[i][j].Init();
if (reCollectAllPeaks || !_featureMatrix[i][j].Exist || Math.Abs(_featureMatrix[i][j].AccurateMass - targetMass) > massTol)
{
var peaks = Ms1Spectra[j].GetAllIsotopePeaks(targetMass, i + _targetMinCharge, _theoreticalEnvelope, tolerance);
if (peaks.Count(p => p != null) > 0)
{
_featureMatrix[i][j].DivergenceDist = _theoreticalEnvelope.GetBhattacharyyaDistance(peaks); ;
_featureMatrix[i][j].AccurateMass = targetMass;
_featureMatrix[i][j].CorrelationCoeff = _theoreticalEnvelope.GetPearsonCorrelation(peaks); ;
Array.Copy(peaks, _featureMatrix[i][j].EnvelopePeaks, peaks.Length);
}
}
if (!_featureMatrix[i][j].Exist) continue;
if (_featureMatrix[i][j].CountActivePeaks < nPeaksCutoff) continue;
if (_featureMatrix[i][j].DivergenceDist > bcCutoff && _featureMatrix[i][j].CorrelationCoeff < corrCutoff) continue; // exclude outliers
var envelope = new ObservedIsotopeEnvelope(_featureMatrix[i][j].AccurateMass, i + _targetMinCharge, ms1ScanNums[j], _featureMatrix[i][j].EnvelopePeaks, _theoreticalEnvelope);
envelopes.Add(envelope);
if (_featureMatrix[i][j].EnvelopePeaks[mostAbuInternalIndex] != null && _featureMatrix[i][j].DivergenceDist < bestBcDist)
{
bestBcDist = _featureMatrix[i][j].DivergenceDist;
bestEnvelope = envelope;
}
}
}
if (bestEnvelope == null) return null;
var cluster = new LcMsPeakCluster(Run, bestEnvelope);
cluster.AddEnvelopes(minRow + _targetMinCharge, maxRow + _targetMinCharge, ms1ScanNums[minCol], ms1ScanNums[maxCol], envelopes);
return cluster;
}
public LcMsPeakCluster GetLcMsPeaksFromNoisePeaks(double targetMass, int targetCharge, int targetMinScanNum, int targetMaxScanNum, int targetMinCharge, int targetMaxCharge)
{
SetTargetMass(targetMass);
var ms1ScanNums = Run.GetMs1ScanVector();
var ms1ScanNumToIndex = Run.GetMs1ScanNumToIndex();
if (Run.GetMsLevel(targetMinScanNum) > 1) targetMinScanNum = Run.GetPrevScanNum(targetMinScanNum, 1);
if (Run.GetMsLevel(targetMaxScanNum) > 1) targetMaxScanNum = Run.GetNextScanNum(targetMaxScanNum, 1);
var minCol = ms1ScanNumToIndex[targetMinScanNum];
var maxCol = ms1ScanNumToIndex[targetMaxScanNum];
var minRow = targetMinCharge - _targetMinCharge;
var maxRow = targetMaxCharge - _targetMinCharge;
var abundance = 0d;
for (var j = minCol; j <= maxCol; j++)
{
abundance += Ms1Spectra[j].MedianIntensity;
}
var repScanNum = ms1ScanNums[(int)((minCol + maxCol) * 0.5)];
var repMz = 0;
var cluster = new LcMsPeakCluster(Run, _theoreticalEnvelope, targetMass, targetCharge, repMz, repScanNum, abundance);
cluster.AddEnvelopes(minRow + _targetMinCharge, maxRow + _targetMinCharge, ms1ScanNums[minCol], ms1ScanNums[maxCol]);
cluster.Score = float.MinValue;
return cluster;
}