public void UpdateWithDecoyScore(List <Ms1Spectrum> ms1Spectra, int targetMinCharge, int targetMaxCharge)
{
var ms1ScanNumToIndex = _run.GetMs1ScanNumToIndex();
var ms1ScanNums = _run.GetMs1ScanVector();
var minCol = ms1ScanNumToIndex[MinScanNum];
var maxCol = ms1ScanNumToIndex[MaxScanNum];
MinCharge = targetMinCharge;
MaxCharge = targetMaxCharge;
var rnd = new Random();
var comparer = new MzComparerWithBinning(28);
var mostAbuInternalIndex = TheoreticalEnvelope.IndexOrderByRanking[0];
var nRows = MaxCharge - MinCharge + 1;
var nCols = maxCol - minCol + 1;
Envelopes = new ObservedIsotopeEnvelope[nRows][];
for (var i = 0; i < nRows; i++)
{
Envelopes[i] = new ObservedIsotopeEnvelope[nCols];
}
for (var charge = targetMinCharge; charge <= targetMaxCharge; charge++)
{
var mostAbuMz = TheoreticalEnvelope.GetIsotopeMz(charge, mostAbuInternalIndex);
if (_run.MaxMs1Mz < mostAbuMz || mostAbuMz < _run.MinMs1Mz)
{
continue;
}
for (var col = minCol; col <= maxCol; col++)
{
var localWin = ms1Spectra[col].GetLocalMzWindow(mostAbuMz);
var numMzBins = comparer.GetBinNumber(localWin.MaxMz) - comparer.GetBinNumber(localWin.MinMz) + 1;
var peakSet = new Ms1Peak[TheoreticalEnvelope.Size];
for (var k = 0; k < peakSet.Length; k++)
{
var r = rnd.Next(0, numMzBins);
if (r < localWin.PeakCount)
{
peakSet[k] = (Ms1Peak)ms1Spectra[col].Peaks[r + localWin.PeakStartIndex];
}
}
var env = new ObservedIsotopeEnvelope(Mass, charge, ms1ScanNums[col], peakSet, TheoreticalEnvelope);
//AddObservedEnvelope(env);
Envelopes[charge - MinCharge][col - minCol] = env;
}
}
UpdateScore(ms1Spectra, false);
}
public override Isotope GetMostAbundantIsotope()
{
return(TheoreticalEnvelope.GetMostAbundantIsotope());
}
public void UpdateScore(List <Ms1Spectrum> ms1Spectra, bool pValueCheck = true)
{
var nRows = MaxCharge - MinCharge + 1;
var ms1ScanNumToIndex = _run.GetMs1ScanNumToIndex();
var minCol = ms1ScanNumToIndex[MinScanNum];
var maxCol = ms1ScanNumToIndex[MaxScanNum];
var nCols = maxCol - minCol + 1;
var mostAbuIdx = TheoreticalEnvelope.IndexOrderByRanking[0];
ClearScore();
var bestChargeDist = new double[] { 10.0d, 10.0d };
// sum envelopes at each charge
var summedIntensity = new double[TheoreticalEnvelope.Size];
var xicLen = nCols + 18;
var xicStartIdx = 9;
/*
* if (nCols < 13)
* {
* xicLen = 13;
* xicStartIdx = (int) Math.Floor((xicLen - nCols)*0.5);
* }*/
var xic2 = new double[2][];
xic2[0] = new double[xicLen];
xic2[1] = new double[xicLen];
var chargeXic = new double[nRows][];
var tempBestBcDist = 10.0d;
var repEnvelopeBcDist = 10.0d;
ObservedIsotopeEnvelope repEnvelope = null;
var repEnvelopeBcDist2 = 10.0d;
ObservedIsotopeEnvelope repEnvelope2 = null;
var tempBestDistanceScoreAcrossCharge = new double[2] {
10, 10
};
var tempBestIntensityScoreAcrossCharge = new double[2];
var tempBestCorrelationScoreAcrossCharge = new double[2];
for (var i = 0; i < nRows; i++)
{
var charge = i + MinCharge;
var mostAbuMz = TheoreticalEnvelope.GetIsotopeMz(charge, mostAbuIdx);
Array.Clear(summedIntensity, 0, summedIntensity.Length);
chargeXic[i] = new double[xicLen];
var chargeIdx = (charge % 2 == 0) ? EvenCharge : OddCharge;
var summedMostAbuIsotopeIntensity = 0d;
var summedReferenceIntensity = 0d;
for (var j = 0; j < nCols; j++)
{
var envelope = Envelopes[i][j];
var col = minCol + j;
var localWin = ms1Spectra[col].GetLocalMzWindow(mostAbuMz);
if (envelope == null)
{
continue;
}
envelope.Peaks.SumEnvelopeTo(summedIntensity);
var mostAbuPeak = envelope.Peaks[mostAbuIdx];
if (mostAbuPeak != null && mostAbuPeak.Active)
{
summedMostAbuIsotopeIntensity += mostAbuPeak.Intensity;
summedReferenceIntensity += localWin.HighestIntensity;
}
AbundanceDistributionAcrossCharge[chargeIdx] += envelope.Abundance;
var newBcDist = TheoreticalEnvelope.GetBhattacharyyaDistance(envelope.Peaks);
var newCorr = TheoreticalEnvelope.GetPearsonCorrelation(envelope.Peaks);
var goodEnvelope = (newBcDist <0.07 || newCorr> 0.7);
if (goodEnvelope)
{
xic2[chargeIdx][xicStartIdx + j] += envelope.Abundance;
chargeXic[i][xicStartIdx + j] = envelope.Abundance;
}
var levelOneEnvelope = true;
var levelTwoEnvelope = true;
if (pValueCheck)
{
var poissonPvalue = localWin.GetPoissonTestPvalue(envelope.Peaks, TheoreticalEnvelope.Size);
var rankSumPvalue = localWin.GetRankSumTestPvalue(envelope.Peaks, TheoreticalEnvelope.Size);
levelOneEnvelope = (rankSumPvalue < 0.01 && poissonPvalue < 0.01);
//levelTwoEnvelope = (rankSumPvalue < 0.05 || poissonPvalue < 0.05);
}
if (levelOneEnvelope)
{
if (newBcDist < BestDistanceScoreAcrossCharge[chargeIdx])
{
BestDistanceScoreAcrossCharge[chargeIdx] = newBcDist;
if (localWin.MedianIntensity > 0)
{
BestIntensityScoreAcrossCharge[chargeIdx] = envelope.HighestIntensity / localWin.HighestIntensity;
}
else
{
BestIntensityScoreAcrossCharge[chargeIdx] = 1.0d;
}
}
BestCorrelationScoreAcrossCharge[chargeIdx] = Math.Max(BestCorrelationScoreAcrossCharge[chargeIdx], newCorr);
if (newBcDist < repEnvelopeBcDist)
{
repEnvelopeBcDist = newBcDist;
repEnvelope = envelope;
}
// in the initial scoring, classify major and minor envelopes
if (!_initScore && goodEnvelope)
{
envelope.GoodEnough = true;
}
}
if (levelTwoEnvelope)
{
if (newBcDist < tempBestDistanceScoreAcrossCharge[chargeIdx])
{
tempBestDistanceScoreAcrossCharge[chargeIdx] = newBcDist;
if (localWin.MedianIntensity > 0)
{
tempBestIntensityScoreAcrossCharge[chargeIdx] = envelope.HighestIntensity / localWin.HighestIntensity;
}
else
{
tempBestIntensityScoreAcrossCharge[chargeIdx] = 1.0d;
}
}
tempBestCorrelationScoreAcrossCharge[chargeIdx] = Math.Max(tempBestCorrelationScoreAcrossCharge[chargeIdx], newCorr);
if (newBcDist < repEnvelopeBcDist2)
{
repEnvelopeBcDist2 = newBcDist;
repEnvelope2 = envelope;
}
}
}
var bcDist = TheoreticalEnvelope.GetBhattacharyyaDistance(summedIntensity);
EnvelopeDistanceScoreAcrossCharge[chargeIdx] = Math.Min(bcDist, EnvelopeDistanceScoreAcrossCharge[chargeIdx]);
EnvelopeCorrelationScoreAcrossCharge[chargeIdx] = Math.Max(TheoreticalEnvelope.GetPearsonCorrelation(summedIntensity), EnvelopeCorrelationScoreAcrossCharge[chargeIdx]);
if (BestCharge[chargeIdx] < 1 || bcDist < bestChargeDist[chargeIdx])
{
BestCharge[chargeIdx] = charge;
bestChargeDist[chargeIdx] = bcDist;
if (summedReferenceIntensity > 0)
{
EnvelopeIntensityScoreAcrossCharge[chargeIdx] = summedMostAbuIsotopeIntensity / summedReferenceIntensity;
}
//if (summedMedianIntensity > 0) EnvelopeIntensityScoreAcrossCharge[chargeIdx] = Math.Min(1.0, 0.1*(summedMostAbuIsotopeIntensity / summedMedianIntensity));
}
if (bcDist < tempBestBcDist)
{
tempBestBcDist = bcDist;
Array.Copy(summedIntensity, RepresentativeSummedEnvelop, RepresentativeSummedEnvelop.Length);
}
}
// when good envellope is observed at only either even or odd charge...
if (BestCorrelationScoreAcrossCharge[0] > 0.7 && BestCorrelationScoreAcrossCharge[1] < 0.5)
{
const int i = 1;
BestCorrelationScoreAcrossCharge[i] = tempBestCorrelationScoreAcrossCharge[i];
BestIntensityScoreAcrossCharge[i] = tempBestIntensityScoreAcrossCharge[i];
BestDistanceScoreAcrossCharge[i] = tempBestDistanceScoreAcrossCharge[i];
}
if (BestCorrelationScoreAcrossCharge[1] > 0.7 && BestCorrelationScoreAcrossCharge[0] < 0.5)
{
const int i = 0;
BestCorrelationScoreAcrossCharge[i] = tempBestCorrelationScoreAcrossCharge[i];
BestIntensityScoreAcrossCharge[i] = tempBestIntensityScoreAcrossCharge[i];
BestDistanceScoreAcrossCharge[i] = tempBestDistanceScoreAcrossCharge[i];
}
// normalize abudnace across charges
var s = AbundanceDistributionAcrossCharge[0] + AbundanceDistributionAcrossCharge[1];
if (s > 0)
{
for (var chargeIdx = 0; chargeIdx < 2; chargeIdx++)
{
AbundanceDistributionAcrossCharge[chargeIdx] = AbundanceDistributionAcrossCharge[chargeIdx] / s;
}
}
if (nCols > 1)
{
var evenChargeIdx = BestCharge[EvenCharge] - MinCharge;
var oddChargeIdx = BestCharge[OddCharge] - MinCharge;
XicCorrelationBetweenBestCharges[0] = FitScoreCalculator.GetPearsonCorrelation(Smoother.Smooth(chargeXic[evenChargeIdx]), Smoother.Smooth(chargeXic[oddChargeIdx]));
XicCorrelationBetweenBestCharges[1] = FitScoreCalculator.GetPearsonCorrelation(Smoother.Smooth(xic2[EvenCharge]), Smoother.Smooth(xic2[OddCharge]));
}
if (repEnvelope == null && repEnvelope2 != null)
{
repEnvelope = repEnvelope2;
}
if (repEnvelope != null)
{
// set representative charge, mz and scanNum
RepresentativeCharge = repEnvelope.Charge;
RepresentativeMz = repEnvelope.RepresentativePeak.Mz;
RepresentativeScanNum = repEnvelope.ScanNum;
}
_initScore = true;
}
