private void UpdateModel(int x)
{
Ms2ScanWithSpecificMass msScanForDraw = arrayOfMs2ScansSortedByMass.Where(p => p.OneBasedScanNumber == x).First();
//mainViewModel.UpdateScanModel(msScanForDraw);
PsmCross psmCross = PSMs.Where(p => p.ScanNumber == x).First();
var lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
Tolerance productMassTolerance = new PpmTolerance(20);
var pmm = PsmCross.XlCalculateTotalProductMassesForSingle(psmCross, lp, false);
var matchedIonMassesListPositiveIsMatch = new MatchedIonInfo(pmm.ProductMz.Length);
double pmmScore = PsmCross.XlMatchIons(msScanForDraw.TheScan, productMassTolerance, pmm.ProductMz, pmm.ProductName, matchedIonMassesListPositiveIsMatch);
matchedIonMassesListPositiveIsMatch.PredictedIonName = psmCross.ProductMassesMightHaveDuplicatesAndNaNs(lp).ProductName;
matchedIonMassesListPositiveIsMatch.PredictedIonMZ = psmCross.ProductMassesMightHaveDuplicatesAndNaNs(lp).ProductMz;
matchedIonMassesListPositiveIsMatch.PredictedIonIntensity = predictedIntensities[psmCross.ScanNumber];
psmCross.MatchedIonInfo = matchedIonMassesListPositiveIsMatch;
mainViewModel.UpdateCrosslinkModelForSingle(msScanForDraw, psmCross);
pdeepModelView.UpdataModelForPdeep(psmCross);
}
public void TestMods()
{
PsmCross PSM = new PsmCross();
PSM.BaseSequence = "DMHGDSEYNIMFGPDICGPGTK";
PSM.FullSequence = "DM[Common Variable:Oxidation of M]HGDSEYNIM[Common Variable:Oxidation of M]FGPDIC[Common Fixed:Carbamidomethyl of C]GPGTK";
PSM.PeptideMonisotopicMass = 2472.0032;
var mods = TsvResultReader.GetMods(PSM);
Dictionary <int, ModificationWithMass> allModsOneIsNterminus = new Dictionary <int, ModificationWithMass>();
foreach (var item in mods)
{
ModificationMotif.TryGetMotif(item.Value, out ModificationMotif modificationMotif);
ModificationWithMass mod = new ModificationWithMass("mod", null, modificationMotif, TerminusLocalization.Any, 10);
allModsOneIsNterminus.Add(item.Key, mod);
}
PepWithSetModForCompactPep pepWithSetModForCompactPep = new PepWithSetModForCompactPep();
pepWithSetModForCompactPep.allModsOneIsNterminus = allModsOneIsNterminus;
pepWithSetModForCompactPep.BaseSequence = PSM.BaseSequence;
pepWithSetModForCompactPep.Length = PSM.BaseSequence.Length;
pepWithSetModForCompactPep.MonoisotopicMass = (double)PSM.PeptideMonisotopicMass;
var compactPeptide = new CompactPeptide(pepWithSetModForCompactPep, TerminusType.None);
PSM.CompactPeptide = compactPeptide;
var lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
Tolerance productMassTolerance = new PpmTolerance(10);
var pmm = PsmCross.XlCalculateTotalProductMassesForSingle(PSM, lp, false);
var matchedIonMassesListPositiveIsMatch = new MatchedIonInfo(pmm.ProductMz.Length);
//double pmmScore = PsmCross.XlMatchIons(theScan.TheScan, productMassTolerance, pmm.ProductMz, pmm.ProductName, matchedIonMassesListPositiveIsMatch);
}