//overload: peptide to peptide case
private List <Stoichiometry> calcStoichiometry(Peptide pep1, Peptide pep2, string group)
{
List <Stoichiometry> stoich = new List <Stoichiometry>();
List <Intensity> Pep1Intensity = pep1.Intensities.Where(p => p.GroupID == group).ToList();
List <Intensity> Pep2Intensity = pep2.Intensities.Where(p => p.GroupID == group).ToList();
foreach (Intensity i1 in Pep1Intensity)
{
Intensity i2 = Pep2Intensity.Where(p => p.FileName == i1.FileName).ToList()[0];
Stoichiometry calcStoich = new Stoichiometry(i1, i2);
if (i1.IntensityVal > 0 || i2.IntensityVal > 0)
{
stoich.Add(calcStoich);
}
}
return(stoich);
}
//calculate stoichiometries for all intensities
private List <Stoichiometry> calcStoichiometry(Peptide pep, string group, List <Intensity> baselineIntensity)
{
List <Stoichiometry> stoich = new List <Stoichiometry>();
List <Intensity> PepIntensity = pep.Intensities.Where(p => p.GroupID == group).ToList(); //intensities pep1 for group of interest
List <Intensity> baselineGroupIntensity = baselineIntensity.Where(p => p.GroupID == group).ToList();
double baseline = baselineGroupIntensity.Select(p => p.IntensityVal).Median();
foreach (Intensity i1 in PepIntensity)
{
Stoichiometry calcStoich = new Stoichiometry(i1, baseline);
//if (calcStoich.usefulStoichiometry)
//{
stoich.Add(new Stoichiometry(i1, baseline));
//}
}
return(stoich);
}
