//overload calcComparison (this one is for the non baseline case comparing all groups) PairwiseCompairsons for each pair of peptides and every pair of groups
private List <PairwiseCompairison> calcComparison(List <Peptide> PepsInProt, List <string> groups, int minNumStoichiometries)
{
List <PairwiseCompairison> comparePeps = new List <PairwiseCompairison>();
//loop over all peptide, peptide, group, group permutations
for (int p1 = 0; p1 < this.PeptidesInProtein.Count(); ++p1)
{
for (int p2 = (p1 + 1); p2 < this.PeptidesInProtein.Count(); ++p2)
{
for (int g1 = 0; g1 < groups.Count(); ++g1)
{
for (int g2 = (g1 + 1); g2 < groups.Count(); ++g2)
{
PairwiseCompairison temp = new PairwiseCompairison(PepsInProt[p1], PepsInProt[p2], groups[g1], groups[g2], minNumStoichiometries);
if (temp.PeptideStoichiometriesGroupOne.Count() >= minNumStoichiometries &&
temp.PeptideStoichiometriesGroupTwo.Count() >= minNumStoichiometries)
{
comparePeps.Add(temp);
}
}
}
}
}
return(comparePeps);
}
//overload calcComparison (baseline averaged comparing against only one group) function to compare all modified peptides in protein against baseline using PairwiseCompairison
private List <PairwiseCompairison> calcComparison(List <Peptide> PepsInProt, List <string> groups, Boolean compareUnmod, int minNumStoichiometries, string groupToCompare)
{
List <PairwiseCompairison> comparePeps = new List <PairwiseCompairison>();
List <Peptide> PeptidesToCompare = PepsInProt;
//if not considering unmod peptides -> remove
if (!compareUnmod)
{
PeptidesToCompare = PeptidesToCompare.Where(p => p.Mod).ToList();
}
groups.Remove(groupToCompare);
//loop over all peptide, group, groupToCompare permutations
for (int p1 = 0; p1 < PeptidesToCompare.Count(); ++p1)
{
for (int g1 = 0; g1 < groups.Count(); ++g1)
{
PairwiseCompairison temp = new PairwiseCompairison(PeptidesToCompare[p1], getBaselineIntensities(), groups[g1], groupToCompare, minNumStoichiometries);
if (temp.PeptideStoichiometriesGroupOne.Count() >= minNumStoichiometries && temp.PeptideStoichiometriesGroupTwo.Count() >= minNumStoichiometries)
{
comparePeps.Add(temp);
}
}
}
groups.Add(groupToCompare);
return(comparePeps);
}
