/// <summary>
/// MaxEnt deconvolution algorithm constructor
/// </summary>
/// <param name="tolerance">tolerance</param>
/// <param name="massBinning">mass binning interface</param>
/// <param name="minCharge">maximum charge to be considered</param>
/// <param name="maxCharge">minimum charge to be considered</param>
/// <param name="minMass">minimum mass to be considered</param>
/// <param name="maxMass">maximum mass to be considered</param>
public MaxEntDeconvoluter(Spectrum spec, Tolerance tolerance, MzComparerWithBinning massBinning, int minCharge = 1, int maxCharge = 100, double minMass = 10000, double maxMass = 100000)
{
_minCharge = minCharge;
_maxCharge = maxCharge;
_minMass = minMass;
_maxMass = maxMass;
_tolerance = tolerance;
_massBinning = massBinning;
_spectrum = spec;
_deconvolutedSpectrum = null;
}
public LcMsChargeMap(LcMsRun run, Tolerance tolerance, int maxNumMs2ScansPerMass = MaxNumMs2ScansPerFeature)
{
_run = run;
_scanToIsolationWindow = new Dictionary <int, IsolationWindow>();
_maxNumMs2ScansPerMass = maxNumMs2ScansPerMass;
foreach (var ms2ScanNum in _run.GetScanNumbers(2))
{
var isoWindow = _run.GetIsolationWindow(ms2ScanNum);
if (isoWindow != null)
{
_scanToIsolationWindow.Add(ms2ScanNum, isoWindow);
}
}
_tolerance = tolerance;
_map = new Dictionary <int, BitArray>();
_comparer = new MzComparerWithBinning(30); // 2 ppm binning
_sequenceMassBinToScanNumsMap = new Dictionary <int, IEnumerable <int> >();
_scanNumToMassBin = new Dictionary <int, List <int> >();
}