public static void SingleAbsoluteAroundZeroSearchMode()
{
var result = new SingleAbsoluteAroundZeroSearchMode(2.0);
Assert.That(result.Accepts(2.0, 2.0) == 0);
result.GetAllowedPrecursorMassIntervalsFromTheoreticalMass(2.0);
result.GetAllowedPrecursorMassIntervalsFromObservedMass(2.0);
result.ToString();
result.ToProseString();
}
private static MassDiffAcceptor ParseSearchMode(string text)
{
MassDiffAcceptor massDiffAcceptor = null;
try
{
var split = text.Split(' ');
switch (split[1])
{
case "dot":
double[] massShifts = split[4].Split(',').Select(p => double.Parse(p, CultureInfo.InvariantCulture)).ToArray();
string newString = split[2].Replace("�", "");
double toleranceValue = double.Parse(newString, CultureInfo.InvariantCulture);
if (split[3].ToUpperInvariant().Equals("PPM"))
{
massDiffAcceptor = new DotMassDiffAcceptor(split[0], massShifts, new PpmTolerance(toleranceValue));
}
else if (split[3].ToUpperInvariant().Equals("DA"))
{
massDiffAcceptor = new DotMassDiffAcceptor(split[0], massShifts, new AbsoluteTolerance(toleranceValue));
}
break;
case "interval":
IEnumerable <DoubleRange> doubleRanges = Array.ConvertAll(split[2].Split(';'), b => new DoubleRange(double.Parse(b.Trim(new char[] { '[', ']' }).Split(',')[0],
CultureInfo.InvariantCulture), double.Parse(b.Trim(new char[] { '[', ']' }).Split(',')[1], CultureInfo.InvariantCulture)));
massDiffAcceptor = new IntervalMassDiffAcceptor(split[0], doubleRanges);
break;
case "OpenSearch":
massDiffAcceptor = new OpenSearchMode();
break;
case "daltonsAroundZero":
massDiffAcceptor = new SingleAbsoluteAroundZeroSearchMode(double.Parse(split[2], CultureInfo.InvariantCulture));
break;
case "ppmAroundZero":
massDiffAcceptor = new SinglePpmAroundZeroSearchMode(double.Parse(split[2], CultureInfo.InvariantCulture));
break;
default:
throw new MetaMorpheusException("Unrecognized search mode type: " + split[1]);
}
}
catch (Exception e)
{
throw new MetaMorpheusException("Could not parse search mode string: " + e.Message);
}
return(massDiffAcceptor);
}
private static MassDiffAcceptor ParseSearchMode(string text)
{
MassDiffAcceptor ye = null;
var split = text.Split(' ');
switch (split[1])
{
case "dot":
var massShifts = Array.ConvertAll(split[4].Split(','), Double.Parse);
var newString = split[2].Replace("�", "");
var toleranceValue = double.Parse(newString, CultureInfo.InvariantCulture);
if (split[3].ToUpperInvariant().Equals("PPM"))
{
ye = new DotMassDiffAcceptor(split[0], massShifts, new PpmTolerance(toleranceValue));
}
else if (split[3].ToUpperInvariant().Equals("DA"))
{
ye = new DotMassDiffAcceptor(split[0], massShifts, new AbsoluteTolerance(toleranceValue));
}
break;
case "interval":
IEnumerable <DoubleRange> doubleRanges = Array.ConvertAll(split[2].Split(','), b => new DoubleRange(double.Parse(b.Trim(new char[] { '[', ']' }).Split(';')[0], CultureInfo.InvariantCulture), double.Parse(b.Trim(new char[] { '[', ']' }).Split(';')[1], CultureInfo.InvariantCulture)));
ye = new IntervalMassDiffAcceptor(split[0], doubleRanges);
break;
case "OpenSearch":
ye = new OpenSearchMode();
break;
case "daltonsAroundZero":
ye = new SingleAbsoluteAroundZeroSearchMode(double.Parse(split[2], CultureInfo.InvariantCulture));
break;
case "ppmAroundZero":
ye = new SinglePpmAroundZeroSearchMode(double.Parse(split[2], CultureInfo.InvariantCulture));
break;
default:
throw new MetaMorpheusException("Could not parse search mode string");
}
return(ye);
}
private (List <PeptideSpectralMatch>, DataPointAquisitionResults) GetDataAcquisitionResults(IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile, string currentDataFile, List <ModificationWithMass> variableModifications, List <ModificationWithMass> fixedModifications, List <Protein> proteinList, string taskId, ICommonParameters combinedParameters, Tolerance initPrecTol, Tolerance initProdTol)
{
var fileNameWithoutExtension = Path.GetFileNameWithoutExtension(currentDataFile);
MassDiffAcceptor searchMode;
if (initPrecTol is PpmTolerance)
{
searchMode = new SinglePpmAroundZeroSearchMode(initPrecTol.Value);
}
else
{
searchMode = new SingleAbsoluteAroundZeroSearchMode(initPrecTol.Value);
}
FragmentTypes fragmentTypesForCalibration = FragmentTypes.None;
if (combinedParameters.BIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.b;
}
if (combinedParameters.YIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.y;
}
if (combinedParameters.CIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.c;
}
if (combinedParameters.ZdotIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.zdot;
}
var listOfSortedms2Scans = GetMs2Scans(myMsDataFile, currentDataFile, combinedParameters.DoPrecursorDeconvolution, combinedParameters.UseProvidedPrecursorInfo, combinedParameters.DeconvolutionIntensityRatio, combinedParameters.DeconvolutionMaxAssumedChargeState, combinedParameters.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
List <ProductType> lp = new List <ProductType>();
if (combinedParameters.BIons)
{
lp.Add(ProductType.B);
}
if (combinedParameters.YIons)
{
lp.Add(ProductType.Y);
}
if (combinedParameters.CIons)
{
lp.Add(ProductType.C);
}
if (combinedParameters.ZdotIons)
{
lp.Add(ProductType.Zdot);
}
Log("Searching with searchMode: " + searchMode, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
});
Log("Searching with productMassTolerance: " + initProdTol, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
});
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, proteinList, lp, searchMode, false, combinedParameters, initProdTol, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
List <PeptideSpectralMatch> allPsms = allPsmsArray.ToList();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > compactPeptideToProteinPeptideMatching = ((SequencesToActualProteinPeptidesEngineResults) new SequencesToActualProteinPeptidesEngine(allPsms, proteinList, fixedModifications, variableModifications, lp, new List <IDigestionParams> {
combinedParameters.DigestionParams
}, combinedParameters.ReportAllAmbiguity, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run()).CompactPeptideToProteinPeptideMatching;
foreach (var huh in allPsms)
{
if (huh != null)
{
huh.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching);
}
}
allPsms = allPsms.Where(b => b != null).OrderByDescending(b => b.Score).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).GroupBy(b => (b.FullFilePath, b.ScanNumber, b.PeptideMonisotopicMass)).Select(b => b.First()).ToList();
new FdrAnalysisEngine(allPsms, searchMode.NumNotches, false, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
List <PeptideSpectralMatch> goodIdentifications = allPsms.Where(b => b.FdrInfo.QValueNotch < 0.01 && !b.IsDecoy && b.FullSequence != null).ToList();
if (!goodIdentifications.Any())
{
Warn("No PSMs below 1% FDR observed!");
return(new List <PeptideSpectralMatch>(), null);
}
var dissociationTypes = MetaMorpheusEngine.DetermineDissociationType(lp);
foreach (var psm in allPsms)
{
var theScan = myMsDataFile.GetOneBasedScan(psm.ScanNumber);
double thePrecursorMass = psm.ScanPrecursorMass;
foreach (var huh in lp)
{
var ionMasses = psm.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>();
LocalizationEngine.MatchIons(theScan, initProdTol, ionMasses, matchedIonMassesList, productMassErrorDaList, productMassErrorPpmList, thePrecursorMass, dissociationTypes, false);
double[] matchedIonMassesOnlyMatches = matchedIonMassesList.ToArray();
psm.MatchedIonDictOnlyMatches.Add(huh, matchedIonMassesOnlyMatches);
psm.ProductMassErrorDa.Add(huh, productMassErrorDaList.ToArray());
psm.ProductMassErrorPpm.Add(huh, productMassErrorPpmList.ToArray());
}
}
DataPointAquisitionResults currentResult = (DataPointAquisitionResults) new DataPointAcquisitionEngine(
goodIdentifications,
myMsDataFile,
initPrecTol,
initProdTol,
CalibrationParameters.NumFragmentsNeededForEveryIdentification,
CalibrationParameters.MinMS1IsotopicPeaksNeededForConfirmedIdentification,
CalibrationParameters.MinMS2IsotopicPeaksNeededForConfirmedIdentification,
fragmentTypesForCalibration,
new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
return(goodIdentifications, currentResult);
}