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 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 TopDownScorer(Composition proteinComposition, LcMsRun run, Tolerance tolerance, SubScoreFactory factory) : this(proteinComposition, run, tolerance)
{
}