public LcMsPeakScorer(Ms1Spectrum spec, int numBits4WinSize = 19) // 19 bits -> 4096 ppm, 20 bits -> 2048
{
Spectrum = spec;
var peaks = spec.Peaks;
_windowComparer = new MzComparerWithBinning(numBits4WinSize);
_minBinNum = _windowComparer.GetBinNumber(peaks[0].Mz);
_maxBinNum = _windowComparer.GetBinNumber(peaks[peaks.Length - 1].Mz);
var numberOfbins = _maxBinNum - _minBinNum + 1;
_peakStartIndex = new int[2][];
_peakRanking = new int[2][][];
var intensities = new List<double>[2][];
for (var i = 0; i < 2; i++)
{
_peakStartIndex[i] = new int[numberOfbins];
_peakRanking[i] = new int[numberOfbins][];
intensities[i] = new List<double>[numberOfbins];
for (var j = 0; j < numberOfbins; j++)
{
_peakStartIndex[i][j] = peaks.Length - 1;
intensities[i][j] = new List<double>();
}
}
for (var i = 0; i < peaks.Length; i++)
{
var binNum = _windowComparer.GetBinNumber(peaks[i].Mz);
var binMzAverage = _windowComparer.GetMzAverage(binNum);
var binIdx = binNum - _minBinNum;
intensities[0][binIdx].Add(peaks[i].Intensity);
if (i < _peakStartIndex[0][binIdx]) _peakStartIndex[0][binIdx] = i;
if (peaks[i].Mz < binMzAverage)
{
intensities[1][binIdx].Add(peaks[i].Intensity);
if (i < _peakStartIndex[1][binIdx]) _peakStartIndex[1][binIdx] = i;
}
else if (binNum < _maxBinNum) // skip this at the rightmost bin
{
intensities[1][binIdx + 1].Add(peaks[i].Intensity);
if (i < _peakStartIndex[1][binIdx + 1]) _peakStartIndex[1][binIdx + 1] = i;
}
}
for (var i = 0; i < 2; i++)
{
for (var binIdx = 0; binIdx < numberOfbins; binIdx++)
{
if (intensities[i][binIdx].Count < 1) continue;
double medianIntensity;
_peakRanking[i][binIdx] = GetRankings(intensities[i][binIdx].ToArray(), out medianIntensity);
}
}
}
private bool CorrectChargeState(ObservedIsotopeEnvelope envelope, Ms1Spectrum spectrum)
{
if (envelope.Charge > 20) return true; //high charge (> +20), just pass
var peaks = spectrum.Peaks;
var peakStartIndex = envelope.MinMzPeak.IndexInSpectrum;
var peakEndIndex = envelope.MaxMzPeak.IndexInSpectrum;
var intensityThreshold = envelope.HighestIntensity * 0.15;
var nPeaks = 0;
for (var i = peakStartIndex; i <= peakEndIndex; i++)
{
if (peaks[i].Intensity > intensityThreshold) nPeaks++;
}
if (envelope.NumberOfPeaks > nPeaks * 0.7) return true;
//var tolerance = new Tolerance(5);
var tolerance = new Tolerance(Comparer.Ppm * 0.5);
var threshold = nPeaks * 0.5;
var threshold2 = envelope.NumberOfPeaks + (envelope.TheoreticalEnvelope.Size - 1) * 0.7;
var mzTol = tolerance.GetToleranceAsTh(peaks[peakStartIndex].Mz);
var minCheckCharge = Math.Max(envelope.Charge * 2 - 1, 4);
var maxCheckCharge = Math.Min(envelope.Charge * 5 + 1, 60);
var maxDeltaMz = Constants.C13MinusC12 / minCheckCharge + mzTol;
var nChargeGaps = new int[maxCheckCharge - minCheckCharge + 1];
for (var i = peakStartIndex; i <= peakEndIndex; i++)
{
if (!(peaks[i].Intensity > intensityThreshold)) continue;
for (var j = i + 1; j <= peakEndIndex; j++)
{
if (!(peaks[j].Intensity > intensityThreshold)) continue;
var deltaMz = peaks[j].Mz - peaks[i].Mz;
if (deltaMz > maxDeltaMz) break;
if (Math.Abs(deltaMz - mzTol) < float.Epsilon)
{
// Peaks are too close together; continue
continue;
}
for (var c = Math.Round(1 / (deltaMz + mzTol)); c <= Math.Round(1 / (deltaMz - mzTol)); c++)
{
if (c < minCheckCharge)
continue;
if (c > maxCheckCharge)
break;
var k = (int)c - minCheckCharge;
nChargeGaps[k]++;
if (nChargeGaps[k] + 1 > threshold && nChargeGaps[k] + 1 > threshold2) return false;
}
}
}
return true;
}
public LcMsPeakScorer(Ms1Spectrum spec, int numBits4WinSize = 19) // 19 bits -> 4096 ppm, 20 bits -> 2048
{
Spectrum = spec;
var peaks = spec.Peaks;
_windowComparer = new MzComparerWithBinning(numBits4WinSize);
_minBinNum = _windowComparer.GetBinNumber(peaks[0].Mz);
_maxBinNum = _windowComparer.GetBinNumber(peaks[peaks.Length - 1].Mz);
var numberOfbins = _maxBinNum - _minBinNum + 1;
_peakStartIndex = new int[2][];
_peakRanking = new int[2][][];
var intensities = new List <double> [2][];
for (var i = 0; i < 2; i++)
{
_peakStartIndex[i] = new int[numberOfbins];
_peakRanking[i] = new int[numberOfbins][];
intensities[i] = new List <double> [numberOfbins];
for (var j = 0; j < numberOfbins; j++)
{
_peakStartIndex[i][j] = peaks.Length - 1;
intensities[i][j] = new List <double>();
}
}
for (var i = 0; i < peaks.Length; i++)
{
var binNum = _windowComparer.GetBinNumber(peaks[i].Mz);
var binMzAverage = _windowComparer.GetMzAverage(binNum);
var binIdx = binNum - _minBinNum;
intensities[0][binIdx].Add(peaks[i].Intensity);
if (i < _peakStartIndex[0][binIdx])
{
_peakStartIndex[0][binIdx] = i;
}
if (peaks[i].Mz < binMzAverage)
{
intensities[1][binIdx].Add(peaks[i].Intensity);
if (i < _peakStartIndex[1][binIdx])
{
_peakStartIndex[1][binIdx] = i;
}
}
else if (binNum < _maxBinNum) // skip this at the rightmost bin
{
intensities[1][binIdx + 1].Add(peaks[i].Intensity);
if (i < _peakStartIndex[1][binIdx + 1])
{
_peakStartIndex[1][binIdx + 1] = i;
}
}
}
for (var i = 0; i < 2; i++)
{
for (var binIdx = 0; binIdx < numberOfbins; binIdx++)
{
if (intensities[i][binIdx].Count < 1)
{
continue;
}
double medianIntensity;
_peakRanking[i][binIdx] = GetRankings(intensities[i][binIdx].ToArray(), out medianIntensity);
}
}
}
