/// <summary>
/// Illustrate how to make calls to deisotope a spectrum.
/// </summary>
/// <param name="dataAccess"></param>
private void DeisotopeTest(IMsdrDataReader dataAccess)
{
IMsdrPeakFilter filter1 = new MsdrPeakFilter();
filter1.AbsoluteThreshold = 10;
filter1.RelativeThreshold = 0.1;
filter1.MaxNumPeaks = 0;//no limit on max number of peaks
IMsdrChargeStateAssignmentFilter csaFilter = new MsdrChargeStateAssignmentFilter();
IBDASpecFilter f = new BDASpecFilter();
f.SpectrumType = SpecType.MassSpectrum;
IBDAMSScanFileInformation msscanFileInfo = dataAccess.MSScanFileInformation;
int numSpectra = (int)msscanFileInfo.TotalScansPresent;
int nNonEmptyCount = 0; // just deisotope the first 10 non-empty spectra
for (int i = 0; i < numSpectra; i++)
{
IBDASpecData spec = dataAccess.GetSpectrum(i, filter1, filter1);//same peak filter used for both MS and MS2 spectra (you can pass in 2 different filters)
println("Original spectrum has " + spec.TotalDataPoints + " points");
if (spec.XArray.Length > 0)
{
++nNonEmptyCount;
}
if (nNonEmptyCount > 10)
{
break;
}
dataAccess.Deisotope(spec, csaFilter);
println(" Deisotoped spectrum has " + spec.TotalDataPoints + " points");
}
}
