public TopDownScorer(Composition proteinComposition, LcMsRun run, Tolerance tolernace, SubScoreFactory factory)
{
_run = run;
_proteinCompositionPlusWater = proteinComposition + Composition.H2O;
_tolerance = tolernace;
_factory = factory;
_maxIntensityIsotopeIndex = _proteinCompositionPlusWater.GetMostAbundantIsotopeZeroBasedIndex();
var thorethicalIsotopeEnvelope = _proteinCompositionPlusWater.GetIsotopomerEnvelopeRelativeIntensities();
_minIsotopeIndex = 0;
for (var i = 0; i < thorethicalIsotopeEnvelope.Length; i++)
{
if (!(thorethicalIsotopeEnvelope[i] > MinIsotopeIntensity)) continue;
_minIsotopeIndex = i;
break;
}
_isotopeEnvelope = new double[Math.Min(_maxIntensityIsotopeIndex + NumberAfterMaxIsotopeIndex, thorethicalIsotopeEnvelope.Length) - _minIsotopeIndex];
for (var k = 0; k < _isotopeEnvelope.Length; k++)
{
_isotopeEnvelope[k] = thorethicalIsotopeEnvelope[k + _minIsotopeIndex];
}
/*foreach (var iso in thorethicalIsotopeEnvelope)
{
Console.WriteLine(iso);
}
Console.WriteLine();
foreach (var iso in _isotopeEnvelope)
{
Console.WriteLine(iso);
}
System.Environment.Exit(1);
*/
_xicArray = GetXicArray();
_smoothedXicArray = GetSmoothedXicArray();
}
public void TestIsotopemerProfileByKyowon() // is faster and more accurate than IsotopicDistributionCalculator
{
var methodName = MethodBase.GetCurrentMethod().Name;
ShowStarting(methodName);
//C78H120N22O28S3 C150H120N220O28S30
//var additionalElements = new[]
// {
// new Tuple<Atom, short>(Atom.Get("P"), 1),
// new Tuple<Atom, short>(Atom.Get("13C"), 3),
// new Tuple<Atom, short>(Atom.Get("15N"), 1),
// };
//var composition = new Composition(149, 244, 44, 57, 0, additionalElements);
// var composition = new Composition(83, 136, 22, 24, 1);
//var composition = new Composition(210, 323, 54, 61, 0);
var composition = new Composition(419, 699, 119, 129, 1);
const int charge = 14;
var ion = new Ion(composition + Composition.H2O, charge);
var ff = composition.GetIsotopomerEnvelopeRelativeIntensities();
var isotopeIndex = -1;
foreach (var ii in ff)
{
++isotopeIndex;
Console.WriteLine("{0}: {1}\t{2}", isotopeIndex, ion.GetIsotopeMz(isotopeIndex), ii);
}
}