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);
}
}
}
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);
}
}
}
