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);
}
public static List <PsmCross> ReadTsv(string filePath)
{
List <PsmCross> PSMs = new List <PsmCross>();
Dictionary <string, int> ids = new Dictionary <string, int>();
//Empty array. Is this correct?
string[][] resultArray = new string[][] { };
try
{
resultArray = File.ReadLines(filePath).Select(p => p.Split('\t')).ToArray();
}
catch (Exception)
{
MessageBox.Show("Please check the file.");
return(null);
}
for (int i = 0; i < resultArray[0].Length; i++)
{
ids.Add(resultArray[0][i], i);
}
for (int i = 1; i < resultArray.Length; i++)
{
PsmCross PSM = new PsmCross();
PSM.ScanNumber = Convert.ToInt32(resultArray[i][ids["Scan Number"]]);
var baseSeq = resultArray[i][ids["Base Sequence"]];
var chargeState = resultArray[i][ids["Precursor Charge"]];
var fullSeq = resultArray[i][ids["Full Sequence"]];
if (baseSeq.Contains("|"))
{
baseSeq = baseSeq.Split('|').First();
fullSeq = fullSeq.Split('|').First();
}
PSM.BaseSequence = baseSeq;
PSM.ScanPrecursorCharge = Convert.ToInt32(chargeState);
PSM.FullSequence = fullSeq;
PSM.IsDecoy = (resultArray[i][ids["Decoy"]] == "N" ? false :true);
PSM.PeptideMonisotopicMass = Convert.ToDouble(resultArray[i][ids["Precursor Mass"]]);
var mods = GetMods(PSM);
Dictionary <int, ModificationWithMass> allModsOneIsNterminus = new Dictionary <int, ModificationWithMass>();
foreach (var item in mods)
{
//I don't really know why use as here.
var theMod = GlobalVariables.AllModsKnown.Where(p => p.id == item.Value).First() as ModificationWithMass;
allModsOneIsNterminus.Add(item.Key, theMod);
}
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;
PSMs.Add(PSM);
}
return(PSMs);
}