public LcMsPeakMatrix(LcMsRun run, LcMsFeatureLikelihood scorer = null, int minScanCharge = 1, int maxScanCharge = 60, int maxThreadCount = 0)
{
Run = run;
_maxThreadCount = maxThreadCount;
_ms1PeakList = new List<Ms1Peak>();
Ms1Spectra = new List<Ms1Spectrum>();
var ms1ScanNums = run.GetMs1ScanVector();
NColumns = ms1ScanNums.Length;
MinSearchCharge = minScanCharge;
MaxSearchCharge = maxScanCharge;
NRows = Math.Min(MaxSearchCharge - MinSearchCharge + 1, 35);
for (var i = 0; i < Math.Min(ms1ScanNums.Length, ushort.MaxValue); i++)
{
var ms1Spec = run.GetMs1Spectrum(ms1ScanNums[i]);
Ms1Spectra.Add(ms1Spec);
foreach (var peak in ms1Spec.Peaks) _ms1PeakList.Add(peak as Ms1Peak);
}
_ms1PeakList.Sort();
_distProfileAcrossCharge = new double[NRows];
_corrProfileAcrossCharge = new double[NRows];
_intensityAcrossCharge = new double[NRows];
_summedEnvelopeColRange = new int[NRows, 2];
_featureMatrix = null;
Comparer = new MzComparerWithBinning(27); // 16ppm
_scorer = scorer;
_seedEnvelopes = new List<KeyValuePair<double, ObservedIsotopeEnvelope>>();
_ms1Filter = null;
}
private Tuple<int, int> GetMinMaxMs1ScanNum(LcMsRun run, double minTime, double maxTime)
{
var ms1ScanNums = run.GetMs1ScanVector();
var minScanNum = -1;
var maxScanNum = -1;
for(var i = 1; i < ms1ScanNums.Length; i++)
{
var time = run.GetElutionTime(ms1ScanNums[i]);
if (minScanNum < 0 && time > minTime)
{
minScanNum = ms1ScanNums[i - 1];
}
if (maxScanNum < 0 && time > maxTime)
{
maxScanNum = ms1ScanNums[i];
break;
}
}
return new Tuple<int, int>(minScanNum, maxScanNum);
}