public ObservedIsotopeEnvelope(double monoMass, int charge, int scanNum, Ms1Peak[] peaks, TheoreticalIsotopeEnvelope theoreticalEnvelope)
{
MonoMass = monoMass;
Charge = charge;
ScanNum = scanNum;
TheoreticalEnvelope = theoreticalEnvelope;
Peaks = new Ms1Peak[theoreticalEnvelope.Size];
Array.Copy(peaks, Peaks, theoreticalEnvelope.Size);
GoodEnough = false;
}
public Ms1Spectrum(int scanNum, int index, Peak[] peaks) : base(scanNum)
{
Index = index;
MsLevel = 1;
Peaks = new Peak[peaks.Length];
var sIndex = (ushort)index;
for (var i = 0; i < Peaks.Length; i++)
{
Peaks[i] = new Ms1Peak(peaks[i].Mz, peaks[i].Intensity, i)
{
Ms1SpecIndex = sIndex
}
}
;
MedianIntensity = Peaks.Select(p => p.Intensity).Median();
PreArrangeLocalMzWindows();
}
public double GetBhattacharyyaDistance(Ms1Peak[] isotopePeaks)
{
var s2 = 0d;
for (var i = 0; i < Size; i++)
{
if (isotopePeaks[i] != null && isotopePeaks[i].Active)
s2 += isotopePeaks[i].Intensity;
}
if (!(s2 > 0)) return MaxBhattacharyyaDistance;
var bc = 0d;
for (var i = 0; i < Size; i++)
{
var p = Probability[i];
var q = (isotopePeaks[i] != null && isotopePeaks[i].Active) ? isotopePeaks[i].Intensity / s2 : 0;
bc += Math.Sqrt(p * q);
}
if (!(bc > 0)) return MaxBhattacharyyaDistance;
return -Math.Log(bc);
}
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 Ms1Peak[] GetAllIsotopePeaks(double monoIsotopeMass, int charge, TheoreticalIsotopeEnvelope isotopeList, Tolerance tolerance)
{
var observedPeaks = new Ms1Peak[isotopeList.Size];
var mz = isotopeList.GetIsotopeMz(charge, 0);
var tolTh = tolerance.GetToleranceAsTh(mz);
var minMz = mz - tolTh;
var maxMz = mz + tolTh;
var index = Array.BinarySearch(Peaks, new Ms1Peak(minMz, 0, 0));
if (index < 0)
{
index = ~index;
}
var bestPeakIndex = -1;
var bestIntensity = 0.0;
// go up
var i = index;
while (i >= 0 && i < Peaks.Length)
{
if (Peaks[i].Mz >= maxMz)
{
break;
}
if (Peaks[i].Intensity > bestIntensity)
{
bestIntensity = Peaks[i].Intensity;
bestPeakIndex = i;
observedPeaks[0] = (Ms1Peak)Peaks[bestPeakIndex];
}
++i;
}
var peakIndex = (bestPeakIndex >= 0) ? bestPeakIndex + 1 : index;
// go up
for (var j = 1; j < isotopeList.Size; j++)
{
var isotopeMz = isotopeList.GetIsotopeMz(charge, j);
tolTh = tolerance.GetToleranceAsTh(isotopeMz);
minMz = isotopeMz - tolTh;
maxMz = isotopeMz + tolTh;
for (i = peakIndex; i < Peaks.Length; i++)
{
var peakMz = Peaks[i].Mz;
if (peakMz > maxMz)
{
peakIndex = i;
break;
}
if (peakMz >= minMz) // find match, move to prev isotope
{
var peak = Peaks[i];
if (observedPeaks[j] == null ||
peak.Intensity > observedPeaks[j].Intensity)
{
observedPeaks[j] = (Ms1Peak)peak;
}
}
}
}
return(observedPeaks);
}
public double GetPearsonCorrelation(Ms1Peak[] isotopePeaks)
{
var m1 = 1.0/Size;
var m2 = 0.0;
for (var i = 0; i < Size; i++)
{
if (isotopePeaks[i] != null && isotopePeaks[i].Active) m2 += isotopePeaks[i].Intensity;
}
m2 /= Size;
// compute Pearson correlation
var cov = 0.0;
var s1 = 0.0;
var s2 = 0.0;
for (var i = 0; i < Size; i++)
{
var d1 = Probability[i] - m1;
var d2 = (isotopePeaks[i] != null && isotopePeaks[i].Active) ? isotopePeaks[i].Intensity - m2 : -m2;
cov += d1 * d2;
s1 += d1 * d1;
s2 += d2 * d2;
}
if (s1 <= 0 || s2 <= 0) return 0;
return cov < 0 ? 0d : cov / Math.Sqrt(s1 * s2);
}
