public static void TestLocalization()
{
var protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
Protein parentProteinForMatch = new Protein("MEK", null);
DigestionParams digestionParams = new DigestionParams
{
MinPeptideLength = 1,
};
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
List <ModificationWithMass> variableModifications = new List <ModificationWithMass> {
new ModificationWithMass("21", null, motif, TerminusLocalization.Any, 21.981943)
};
List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
Assert.AreEqual(4, allPeptidesWithSetModifications.Count());
PeptideWithSetModifications ps = allPeptidesWithSetModifications.First();
List <ProductType> lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1];
IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetModsForSpectrum
});
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.Last() as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >, pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null);
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps.CompactPeptide(TerminusType.None), 0, 0, 2, scan);
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ ps.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
ps
} }
};
newPsm.MatchToProteinLinkedPeptides(matching);
LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> {
newPsm
}, lp, myMsDataFile, fragmentTolerance, new List <string>(), false);
f.Run();
// Was single peak!!!
Assert.AreEqual(0, newPsm.MatchedIonDictOnlyMatches[ProductType.BnoB1ions].Count(b => b > 0));
Assert.AreEqual(1, newPsm.MatchedIonDictOnlyMatches[ProductType.Y].Count(b => b > 0));
// If localizing, three match!!!
Assert.IsTrue(newPsm.LocalizedScores[1] > 3 && newPsm.LocalizedScores[1] < 4);
}
public static void TestLocalization()
{
Protein parentProteinForMatch = new Protein("MEK", null);
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
List <ModificationWithMass> variableModifications = new List <ModificationWithMass> {
new ModificationWithMass("21", null, motif, TerminusLocalization.Any, 21.981943)
};
List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
Assert.AreEqual(4, allPeptidesWithSetModifications.Count());
PeptideWithSetModifications ps = allPeptidesWithSetModifications.First();
List <ProductType> lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1];
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetModsForSpectrum
});
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.GetAllScansList().Last(), pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null);
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps.CompactPeptide(TerminusType.None), 0, 0, 2, scan, digestionParams);
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ ps.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
ps
} }
};
newPsm.MatchToProteinLinkedPeptides(matching);
CommonParameters commonParameters = new CommonParameters(productMassTolerance: fragmentTolerance);
LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> {
newPsm
}, lp, myMsDataFile, commonParameters, new List <string>());
f.Run();
// Was single peak!!!
Assert.AreEqual(0, newPsm.MatchedIonMassToChargeRatioDict[ProductType.BnoB1ions].Count(b => b > 0));
Assert.AreEqual(1, newPsm.MatchedIonMassToChargeRatioDict[ProductType.Y].Count(b => b > 0));
Assert.AreEqual(0, newPsm.MatchedIonIntensitiesDict[ProductType.BnoB1ions].Count(b => b > 0));
Assert.AreEqual(1, newPsm.MatchedIonIntensitiesDict[ProductType.Y].Count(b => b > 0));
// If localizing, three match!!!
Assert.IsTrue(newPsm.LocalizedScores[1] > 3 && newPsm.LocalizedScores[1] < 4);
}
public static void TestCompactPeptideSerialization()
{
// purpose of this test is to serialize/deserialize a CompactPeptide and make sure the deserialized peptide
// has the same properties as before it was serialized. This peptide is unmodified
string sequence = "PEPTIDE";
PeptideWithSetModifications p = new PeptideWithSetModifications(sequence, new Dictionary <string, Modification>(), 0, null, null, 0, 7, 0, null);
CompactPeptide cp = p.CompactPeptide(FragmentationTerminus.Both);
CompactPeptide deserializedCp = null;
string dir = System.IO.Path.Combine(TestContext.CurrentContext.TestDirectory, "TestCompactPeptideSerialization");
System.IO.Directory.CreateDirectory(dir);
string path = System.IO.Path.Combine(dir, "myCompactPeptideIndex.ind");
var messageTypes = typeof(CompactPeptide);
var ser = new NetSerializer.Serializer(new List <Type> {
messageTypes
});
using (var file = System.IO.File.Create(path))
{
ser.Serialize(file, cp);
}
using (var file = System.IO.File.OpenRead(path))
{
deserializedCp = (CompactPeptide)ser.Deserialize(file);
}
Assert.That(cp.Equals(deserializedCp));
}
public TestDataFile(PeptideWithSetModifications pepWithSetMods, int charge, double intensity, double rt) : base(2, new SourceFile(null, null, null, null, null))
{
var mz1 = new double[] { pepWithSetMods.MonoisotopicMass.ToMz(charge), (pepWithSetMods.MonoisotopicMass + 1.003).ToMz(charge), (pepWithSetMods.MonoisotopicMass + 2.005).ToMz(charge) };
var intensities1 = new double[] { intensity, intensity * 10, intensity / 10 };
var MassSpectrum1 = new MzSpectrum(mz1, intensities1, false);
var ScansHere = new List <MsDataScan> {
new MsDataScan(MassSpectrum1, 1, 1, true, Polarity.Positive, rt, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, null, "scan=1")
};
List <double> mz2 = new List <double>();
List <double> intensities2 = new List <double>();
foreach (var aok in pepWithSetMods.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
}))
{
mz2.Add(aok.ToMz(1));
mz2.Add((aok + 1.003).ToMz(1));
intensities2.Add(intensity);
intensities2.Add(intensity);
}
var MassSpectrum2 = new MzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false);
var scan2 = new MsDataScan(MassSpectrum2, 2, 2, true, Polarity.Positive, rt + 0.01, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, 1, null, "scan=2", pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2));
scan2.ComputeSelectedPeakIntensity(MassSpectrum1);
scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1);
ScansHere.Add(scan2);
Scans = ScansHere.ToArray();
}
public TestDataFile(PeptideWithSetModifications pepWithSetMods, string v) : base(2, new SourceFile(null, null, null, null, null))
{
if (v.Equals("quadratic"))
{
// Add three ms1 peaks with charge 2, exact
var MassSpectrum1 = new MzSpectrum(new double[] { pepWithSetMods.MonoisotopicMass.ToMz(2), (pepWithSetMods.MonoisotopicMass + 1.003).ToMz(2), (pepWithSetMods.MonoisotopicMass + 2.005).ToMz(2) }, new double[] { 1, 1, 1 }, false);
List <double> mz2 = new List <double>();
List <double> intensities2 = new List <double>();
foreach (var aok in pepWithSetMods.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
}))
{
var t1 = aok.ToMz(1);
var c = 0.0000001;
mz2.Add(t1 + c * Math.Pow(t1, 2));
var t2 = (aok + 1.003).ToMz(1);
mz2.Add(t2 + c * Math.Pow(t2, 2));
intensities2.Add(1);
intensities2.Add(1);
}
var MassSpectrum2 = new MzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false);
var scan2 = new MsDataScan(MassSpectrum2, 2, 2, true, Polarity.Positive, 2, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, 1, null, "scan=2", pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2));
scan2.ComputeSelectedPeakIntensity(MassSpectrum1);
scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1);
var ScansHere = new List <MsDataScan> {
new MsDataScan(MassSpectrum1, 1, 1, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, null, "scan=1"),
scan2
};
Scans = ScansHere.ToArray();
}
}
public TestDataFile(PeptideWithSetModifications pepWithSetMods) : base(2, new SourceFile(@"no nativeID format", "mzML format", null, "SHA-1", @"C:\fake.mzML", null))
{
var mz1 = new double[] { pepWithSetMods.MonoisotopicMass.ToMz(2), (pepWithSetMods.MonoisotopicMass + 1.003).ToMz(2), (pepWithSetMods.MonoisotopicMass + 2.005).ToMz(2) };
var intensities1 = new double[] { 1, 1, 1 };
var MassSpectrum1 = new MzmlMzSpectrum(mz1, intensities1, false);
var ScansHere = new List <IMzmlScan> {
new MzmlScan(1, MassSpectrum1, 1, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, "scan=1")
};
List <double> mz2 = new List <double>();
List <double> intensities2 = new List <double>();
foreach (var aok in pepWithSetMods.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
}))
{
mz2.Add(aok.ToMz(1));
mz2.Add((aok + 1.003).ToMz(1));
intensities2.Add(1);
intensities2.Add(1);
}
var MassSpectrum2 = new MzmlMzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false);
var scan2 = new MzmlScanWithPrecursor(2, MassSpectrum2, 2, true, Polarity.Positive, 2, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 1, "scan=2");
scan2.ComputeSelectedPeakIntensity(MassSpectrum1);
scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1);
ScansHere.Add(scan2);
Scans = ScansHere.ToArray();
}
protected override MetaMorpheusEngineResults RunSpecific()
{
TerminusType terminusType = ProductTypeMethod.IdentifyTerminusType(lp);
foreach (var ok in allResultingIdentifications)
{
ok.MatchedIonDictOnlyMatches = new Dictionary <ProductType, double[]>();
ok.ProductMassErrorDa = new Dictionary <ProductType, double[]>();
ok.ProductMassErrorPpm = new Dictionary <ProductType, double[]>();
var theScan = myMsDataFile.GetOneBasedScan(ok.ScanNumber);
double thePrecursorMass = ok.ScanPrecursorMass;
foreach (var huh in lp)
{
var ionMasses = ok.CompactPeptides.First().Key.ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
huh
});
Array.Sort(ionMasses);
List <double> matchedIonMassesList = new List <double>();
List <double> productMassErrorDaList = new List <double>();
List <double> productMassErrorPpmList = new List <double>();
MatchIons(theScan, fragmentTolerance, ionMasses, matchedIonMassesList, productMassErrorDaList, productMassErrorPpmList, thePrecursorMass, dissociationTypes, addCompIons);
double[] matchedIonMassesOnlyMatches = matchedIonMassesList.ToArray();
ok.MatchedIonDictOnlyMatches.Add(huh, matchedIonMassesOnlyMatches);
ok.ProductMassErrorDa.Add(huh, productMassErrorDaList.ToArray());
ok.ProductMassErrorPpm.Add(huh, productMassErrorPpmList.ToArray());
}
}
foreach (var ok in allResultingIdentifications.Where(b => b.NumDifferentCompactPeptides == 1))
{
var theScan = myMsDataFile.GetOneBasedScan(ok.ScanNumber);
double thePrecursorMass = ok.ScanPrecursorMass;
if (ok.FullSequence == null)
{
continue;
}
var representative = ok.CompactPeptides.First().Value.Item2.First();
var localizedScores = new List <double>();
for (int indexToLocalize = 0; indexToLocalize < representative.Length; indexToLocalize++)
{
PeptideWithSetModifications localizedPeptide = representative.Localize(indexToLocalize, ok.ScanPrecursorMass - representative.MonoisotopicMass);
var gg = localizedPeptide.CompactPeptide(terminusType).ProductMassesMightHaveDuplicatesAndNaNs(lp);
Array.Sort(gg);
var score = CalculatePeptideScore(theScan, fragmentTolerance, gg, thePrecursorMass, dissociationTypes, addCompIons, 0);
localizedScores.Add(score);
}
ok.LocalizedScores = localizedScores;
}
return(new LocalizationEngineResults(this));
}
public static void TestLastPeaks()
{
IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
var prot = new Protein("MMMM", null, null, null, mods);
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
PeptideWithSetModifications thePep = prot.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First();
var massArray = thePep.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
});
Array.Sort(massArray);
double[] intensities = new double[] { 1, 1, 1 };
double[] mz = new double[] { 1, 2, massArray[4].ToMz(1) };
MzSpectrum massSpectrum = new MzSpectrum(mz, intensities, false);
MsDataScan scan = new MsDataScan(massSpectrum, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, null, null, "scan=1", 0, null, null, 0, null, DissociationType.Unknown, 1, null);
PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1];
Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 0, 0, null) };
CommonParameters CommonParameters = new CommonParameters(
scoreCutoff: 1,
productMassTolerance: new PpmTolerance(5),
digestionParams: new DigestionParams(
maxMissedCleavages: 0,
minPeptideLength: 1,
maxModificationIsoforms: int.MaxValue,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain));
ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <ModificationWithMass>(), new List <ModificationWithMass>(), new List <Protein> {
prot
}, new List <ProductType> {
ProductType.B, ProductType.Y
}, new OpenSearchMode(), CommonParameters, new List <string>());
cse.Run();
Assert.Less(globalPsms[0].Score, 2);
Assert.Greater(globalPsms[0].Score, 1);
}
public static void TryFailSequenceCoverage()
{
var prot1 = new Protein("MMKMMK", "prot1");
ModificationMotif.TryGetMotif("M", out ModificationMotif motifM);
ModificationWithMass mod1 = new ModificationWithMass("mod1", "mt", motifM, TerminusLocalization.NProt, 10);
ModificationWithMass mod2 = new ModificationWithMass("mod2", "mt", motifM, TerminusLocalization.NPep, 10);
ModificationWithMass mod3 = new ModificationWithMass("mod3", "mt", motifM, TerminusLocalization.Any, 10);
ModificationMotif.TryGetMotif("K", out ModificationMotif motifK);
ModificationWithMass mod4 = new ModificationWithMass("mod4", "mt", motifK, TerminusLocalization.PepC, 10);
ModificationWithMass mod5 = new ModificationWithMass("mod5", "mt", motifK, TerminusLocalization.ProtC, 10);
Dictionary <int, ModificationWithMass> modsFor1 = new Dictionary <int, ModificationWithMass>
{
{ 1, mod1 },
{ 3, mod3 },
{ 5, mod4 },
};
Dictionary <int, ModificationWithMass> modsFor2 = new Dictionary <int, ModificationWithMass>
{
{ 1, mod2 },
{ 5, mod5 },
};
Dictionary <int, ModificationWithMass> modsFor3 = new Dictionary <int, ModificationWithMass>
{
{ 1, mod1 },
{ 5, mod3 },
{ 8, mod5 }
};
DigestionParams digestionParams = new DigestionParams();
var pwsm1 = new PeptideWithSetModifications(protein: prot1, digestionParams: digestionParams, oneBasedStartResidueInProtein: 1, oneBasedEndResidueInProtein: 3, peptideDescription: "", missedCleavages: 0, allModsOneIsNterminus: modsFor1, numFixedMods: 0);
var pwsm2 = new PeptideWithSetModifications(protein: prot1, digestionParams: digestionParams, oneBasedStartResidueInProtein: 4, oneBasedEndResidueInProtein: 6, peptideDescription: "", missedCleavages: 0, allModsOneIsNterminus: modsFor2, numFixedMods: 0);
var pwsm3 = new PeptideWithSetModifications(protein: prot1, digestionParams: digestionParams, oneBasedStartResidueInProtein: 1, oneBasedEndResidueInProtein: 6, peptideDescription: "", missedCleavages: 0, allModsOneIsNterminus: modsFor3, numFixedMods: 0);
HashSet <PeptideWithSetModifications> peptides = new HashSet <PeptideWithSetModifications>
{
pwsm1,
pwsm2,
pwsm3,
};
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ pwsm1.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
pwsm1
} },
{ pwsm2.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
pwsm2
} },
{ pwsm3.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
pwsm3
} },
};
IScan scan = new ThisTestScan();
var psm1 = new PeptideSpectralMatch(pwsm1.CompactPeptide(TerminusType.None), 0, 1, 0, scan, digestionParams);
psm1.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
psm1.MatchToProteinLinkedPeptides(matching);
var psm2 = new PeptideSpectralMatch(pwsm2.CompactPeptide(TerminusType.None), 0, 1, 0, scan, digestionParams);
psm2.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
psm2.MatchToProteinLinkedPeptides(matching);
var psm3 = new PeptideSpectralMatch(pwsm3.CompactPeptide(TerminusType.None), 0, 1, 0, scan, digestionParams);
psm3.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
psm3.MatchToProteinLinkedPeptides(matching);
List <PeptideSpectralMatch> newPsms = new List <PeptideSpectralMatch>
{
psm1,
psm2,
psm3,
};
ProteinParsimonyEngine ppe = new ProteinParsimonyEngine(matching, true, new CommonParameters(), new List <string>());
ProteinParsimonyResults fjkd = (ProteinParsimonyResults)ppe.Run();
ProteinScoringAndFdrEngine psafe = new ProteinScoringAndFdrEngine(fjkd.ProteinGroups, newPsms, true, true, true, new CommonParameters(), new List <string>());
psafe.Run();
fjkd.ProteinGroups.First().CalculateSequenceCoverage();
var firstSequenceCoverageDisplayList = fjkd.ProteinGroups.First().SequenceCoverageDisplayList.First();
Assert.AreEqual("MMKMMK", firstSequenceCoverageDisplayList);
var firstSequenceCoverageDisplayListWithMods = fjkd.ProteinGroups.First().SequenceCoverageDisplayListWithMods.First();
Assert.AreEqual("[mod1]-MM[mod3]KM[mod3]MK-[mod5]", firstSequenceCoverageDisplayListWithMods);
var firstModInfo = fjkd.ProteinGroups.First().ModsInfo.First();
Assert.IsTrue(firstModInfo.Contains(@"#aa1[mod1,info:occupancy=1.00(2/2)]"));
Assert.IsTrue(firstModInfo.Contains(@"#aa2[mod3,info:occupancy=0.50(1/2)]"));
Assert.IsFalse(firstModInfo.Contains(@"#aa3"));
Assert.IsTrue(firstModInfo.Contains(@"#aa4[mod3,info:occupancy=0.50(1/2)]"));
Assert.IsFalse(firstModInfo.Contains(@"#aa5"));
Assert.IsTrue(firstModInfo.Contains(@"#aa6[mod5,info:occupancy=1.00(2/2)]"));
}
protected override MetaMorpheusEngineResults RunSpecific()
{
TerminusType terminusType = ProductTypeMethods.IdentifyTerminusType(ProductTypes);
foreach (PeptideSpectralMatch psm in AllResultingIdentifications)
{
// Stop loop if canceled
if (GlobalVariables.StopLoops)
{
break;
}
psm.MatchedIonSeriesDict = new Dictionary <ProductType, int[]>();
psm.MatchedIonMassToChargeRatioDict = new Dictionary <ProductType, double[]>();
psm.ProductMassErrorDa = new Dictionary <ProductType, double[]>();
psm.ProductMassErrorPpm = new Dictionary <ProductType, double[]>();
psm.MatchedIonIntensitiesDict = new Dictionary <ProductType, double[]>();
var theScan = MyMsDataFile.GetOneBasedScan(psm.ScanNumber);
double thePrecursorMass = psm.ScanPrecursorMass;
foreach (ProductType productType in ProductTypes)
{
var sortedTheoreticalProductMasses = psm.CompactPeptides.First().Key.ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
productType
});
Array.Sort(sortedTheoreticalProductMasses);
List <int> matchedIonSeriesList = new List <int>();
List <double> matchedIonMassToChargeRatioList = new List <double>();
List <double> productMassErrorDaList = new List <double>();
List <double> productMassErrorPpmList = new List <double>();
List <double> matchedIonIntensityList = new List <double>();
//populate the above lists
MatchIonsOld(theScan, commonParameters.ProductMassTolerance, sortedTheoreticalProductMasses, matchedIonSeriesList, matchedIonMassToChargeRatioList, productMassErrorDaList, productMassErrorPpmList, matchedIonIntensityList, thePrecursorMass, productType, commonParameters.AddCompIons);
psm.MatchedIonSeriesDict.Add(productType, matchedIonSeriesList.ToArray());
psm.MatchedIonMassToChargeRatioDict.Add(productType, matchedIonMassToChargeRatioList.ToArray());
psm.ProductMassErrorDa.Add(productType, productMassErrorDaList.ToArray());
psm.ProductMassErrorPpm.Add(productType, productMassErrorPpmList.ToArray());
psm.MatchedIonIntensitiesDict.Add(productType, matchedIonIntensityList.ToArray());
}
}
foreach (PeptideSpectralMatch psm in AllResultingIdentifications.Where(b => b.NumDifferentCompactPeptides == 1))
{
// Stop loop if canceled
if (GlobalVariables.StopLoops)
{
break;
}
var theScan = MyMsDataFile.GetOneBasedScan(psm.ScanNumber);
double thePrecursorMass = psm.ScanPrecursorMass;
if (psm.FullSequence == null)
{
continue;
}
PeptideWithSetModifications representative = psm.CompactPeptides.First().Value.Item2.First();
var localizedScores = new List <double>();
for (int indexToLocalize = 0; indexToLocalize < representative.Length; indexToLocalize++)
{
PeptideWithSetModifications localizedPeptide = representative.Localize(indexToLocalize, psm.ScanPrecursorMass - representative.MonoisotopicMass);
var gg = localizedPeptide.CompactPeptide(terminusType).ProductMassesMightHaveDuplicatesAndNaNs(ProductTypes);
Array.Sort(gg);
var score = CalculatePeptideScoreOld(theScan, commonParameters.ProductMassTolerance, gg, thePrecursorMass, DissociationTypes, commonParameters.AddCompIons, 0);
localizedScores.Add(score);
}
psm.LocalizedScores = localizedScores;
}
return(new LocalizationEngineResults(this));
}