//Calculate score based on All possible Products Masses for inter- or intra- crosslinks and deadend.
public static void XlLocalizationForLoopCrosslink(Ms2ScanWithSpecificMass theScan, PsmCross psmCross, double modMass, CrosslinkerTypeClass crosslinker, List <ProductType> lp, Tolerance fragmentTolerance, List <int> linkPos)
{
var pmmhList = PsmCross.XlCalculateTotalProductMassesForLoopCrosslink(psmCross, modMass, crosslinker, lp, linkPos);
List <double> scoreList = new List <double>();
List <MatchedIonInfo> miil = new List <MatchedIonInfo>();
foreach (var pmm in pmmhList)
{
var matchedIonMassesListPositiveIsMatch = new MatchedIonInfo(pmm.ProductMz.Length);
double pmmScore = PsmCross.XlMatchIons(theScan.TheScan, fragmentTolerance, pmm.ProductMz, pmm.ProductName, matchedIonMassesListPositiveIsMatch);
miil.Add(matchedIonMassesListPositiveIsMatch);
scoreList.Add(pmmScore);
}
psmCross.XLBestScore = scoreList.Max();
psmCross.MatchedIonInfo = miil[scoreList.IndexOf(scoreList.Max())];
psmCross.XlPos = pmmhList[scoreList.IndexOf(scoreList.Max())].XlPos + 1;
psmCross.XlPos2 = pmmhList[scoreList.IndexOf(scoreList.Max())].XlPos2 + 1;
}
//Calculate score based on All possible Products Masses for inter- or intra- crosslinks and deadend.
public static void XlLocalization(Ms2ScanWithSpecificMass theScan, PsmCross psmCross, double modMass,
CrosslinkerTypeClass crosslinker, List <ProductType> lp, Tolerance fragmentTolerance, bool Charge_2_3, bool Charge_2_3_PrimeFragment, List <int> linkPos)
{
var pmmhList = PsmCross.XlCalculateTotalProductMasses(psmCross, modMass, crosslinker, lp, Charge_2_3, Charge_2_3_PrimeFragment, linkPos);
List <double> scoreList = new List <double>();
List <MatchedIonInfo> miil = new List <MatchedIonInfo>();
foreach (var pmm in pmmhList)
{
var matchedIonMassesListPositiveIsMatch = new MatchedIonInfo(pmm.ProductMz.Length);
double pmmScore = PsmCross.XlMatchIons(theScan.TheScan, fragmentTolerance, pmm.ProductMz, pmm.ProductName, matchedIonMassesListPositiveIsMatch);
miil.Add(matchedIonMassesListPositiveIsMatch);
scoreList.Add(pmmScore);
}
psmCross.XLBestScore = scoreList.Max();
psmCross.MatchedIonInfo = miil[scoreList.IndexOf(scoreList.Max())];
psmCross.XlPos = pmmhList[scoreList.IndexOf(scoreList.Max())].XlPos + 1;
if (crosslinker.Cleavable)
{
psmCross.ParentIonMaxIntensityRanks = new List <int>();
if (psmCross.MatchedIonInfo.MatchedIonName.Any(p => p != null && p.Contains("PepS")))
{
psmCross.ParentIonExist += "PepS";
psmCross.ParentIonExistNum += 1;
}
if (psmCross.MatchedIonInfo.MatchedIonName.Any(p => p != null && p.Contains("PepL")))
{
psmCross.ParentIonExist += "PepL";
psmCross.ParentIonExistNum += 1;
}
//if (psmCross.MatchedIonInfo.MatchedIonName.Any(p => p != null && p.Equals("PepS2")))
//{
// psmCross.ParentIonExist += "PepS2";
// psmCross.ParentIonExistNum += 1;
//}
//if (psmCross.MatchedIonInfo.MatchedIonName.Any(p => p != null && p.Equals("PepL2")))
//{
// psmCross.ParentIonExist += "PepL2";
// psmCross.ParentIonExistNum += 1;
//}
for (int i = 0; i < psmCross.MatchedIonInfo.MatchedIonName.Length; i++)
{
if (psmCross.MatchedIonInfo.MatchedIonName[i] != null)
{
if (psmCross.MatchedIonInfo.MatchedIonName[i].Contains("Pep"))
{
psmCross.ParentIonMaxIntensityRanks.Add(psmCross.MatchedIonInfo.MatchedIonIntensityRank[i]);
}
}
}
}
if (Charge_2_3 || Charge_2_3_PrimeFragment)
{
int Charge2IonExist = 0;
for (int i = 0; i < psmCross.MatchedIonInfo.MatchedIonName.Length; i++)
{
if (psmCross.MatchedIonInfo.MatchedIonName[i] != null && (psmCross.MatchedIonInfo.MatchedIonName[i].Contains("t2") || psmCross.MatchedIonInfo.MatchedIonName[i].Contains("t3")))
{
Charge2IonExist++;
}
}
psmCross.Charge2IonExist = Charge2IonExist;
}
}