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 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);
}
