public RankScore(ActivationMethod activationMethod, Ms2DetectorType ms2DetectorType, Enzyme enzyme, Protocol protocol)
{
if (activationMethod == ActivationMethod.HCD && enzyme == Enzyme.Trypsin)
{
var paramFile = Properties.Resources.HCD_Trypsin;
var stream = new MemoryStream();
var writer = new StreamWriter(stream);
writer.Write(paramFile);
writer.Flush();
stream.Position = 0;
_trainingParameters = new TrainingParameters(stream);
}
else
{
throw new ArgumentException("No parameter file available for selected arguments.");
}
}
public int GetActivationMethodIndex(ActivationMethod actMethod)
{
return (actMethod != ActivationMethod.ETD) ? 0 : 1;
}
public double GetEdgeScore(ActivationMethod activationMethod, int charge1, double mass1, int charge2, double mass2)
{
var mzErrorPpm = (Math.Abs(mass1 - mass2)/mass1)*1e6;
return GetEdgeScore(activationMethod, Math.Abs(charge1 - charge2), mzErrorPpm);
}
public double GetEdgeScore(ActivationMethod activationMethod, int chargeDiff, double massErrorPpm)
{
return 0d;
}
public double GetNodeScore(ActivationMethod activationMethod, bool isPrefix, double fragmentIonMass, int fragmentIonCharge,
double corrScore, double distScore, double intensityScore, double massErrorPpm)
{
var score = GetNodeScoreWithoutMassError(activationMethod, isPrefix, fragmentIonMass, fragmentIonCharge, corrScore,
distScore, intensityScore);
score += GetMassErrorScore(massErrorPpm);
return score;
}
public double GetNodeScore(ActivationMethod activationMethod, bool isPrefix, double fragmentIonMass, DeconvolutedPeak matchedPeak, double refIntensity)
{
var massErrorPpm = 1e6 * ((matchedPeak.Mass - fragmentIonMass) / fragmentIonMass);
return GetNodeScore(activationMethod, isPrefix, fragmentIonMass, matchedPeak.Charge, matchedPeak.Corr, matchedPeak.Dist, matchedPeak.Intensity / refIntensity, massErrorPpm);
}
// minScanNum, maxScanNum, minCharge, maxCharge: inclusive
public ProductSpectrum GetSummedMs2Spectrum(double monoIsotopicMass,
int minScanNum, int maxScanNum, int minCharge, int maxCharge, ActivationMethod activationMethod = ActivationMethod.Unknown)
{
var isoEnv = Averagine.GetIsotopomerEnvelope(monoIsotopicMass);
var ms2ScanNums = new List<int>();
for (var charge = minCharge; charge <= maxCharge; charge++)
{
var mostAbundantIsotopeMz = Ion.GetIsotopeMz(monoIsotopicMass, charge, isoEnv.MostAbundantIsotopeIndex);
ms2ScanNums.AddRange(GetFragmentationSpectraScanNums(mostAbundantIsotopeMz)
.Where(ms2ScanNum => ms2ScanNum >= minScanNum && ms2ScanNum <= maxScanNum &&
(activationMethod == ActivationMethod.Unknown ||
((ProductSpectrum) GetSpectrum(ms2ScanNum)).ActivationMethod == activationMethod)))
;
}
var summedSpec = GetSummedSpectrum(ms2ScanNums);
return new ProductSpectrum(summedSpec.Peaks, 0) {ActivationMethod = activationMethod};
}
public ChoEtl(ActivationMethod activationMethod)
{
_activationMethod = activationMethod;
}
/// <summary>
/// Get the scorer by scan number.
/// </summary>
/// <param name="scanNum">The scan number to get the scorer for.</param>
/// <param name="precursorMass">The precursor mass to get the scorer for.</param>
/// <param name="precursorCharge">The precursor charge to get the scorer for.</param>
/// <param name="activationMethod">The activation method to get the scorer for.</param>
/// <returns>The scorer selected based on the arguments.</returns>
public IScorer GetScorer(int scanNum, double precursorMass = 0, int precursorCharge = 1, ActivationMethod activationMethod = ActivationMethod.Unknown)
{
IScorer scorer;
if (this.scorerHash.ContainsKey(scanNum))
{
scorer = this.scorerHash[scanNum];
}
else
{
var parameters = this.scoringParameterSet.GetScoringParameters(activationMethod, precursorMass);
scorer = new FlipScorer <DeconvolutedSpectrum>(parameters, this.lcmsRun.GetSpectrum(scanNum) as DeconvolutedSpectrum);
this.scorerHash.Add(scanNum, scorer);
}
return(scorer);
}
/// <summary>
/// Get a summed MS2 spectrum from the dataset, with the provided limits
/// </summary>
/// <param name="monoIsotopicMass"></param>
/// <param name="minScanNum">min scan number, inclusive</param>
/// <param name="maxScanNum">max scan number, inclusive</param>
/// <param name="minCharge">min charge, inclusive</param>
/// <param name="maxCharge">max charge, inclusive</param>
/// <param name="activationMethod"></param>
/// <returns></returns>
public ProductSpectrum GetSummedMs2Spectrum(double monoIsotopicMass,
int minScanNum, int maxScanNum, int minCharge, int maxCharge, ActivationMethod activationMethod = ActivationMethod.Unknown)
{
var isoEnv = Averagine.GetIsotopomerEnvelope(monoIsotopicMass);
var ms2ScanNums = new List <int>();
for (var charge = minCharge; charge <= maxCharge; charge++)
{
var mostAbundantIsotopeMz = Ion.GetIsotopeMz(monoIsotopicMass, charge, isoEnv.MostAbundantIsotopeIndex);
ms2ScanNums.AddRange(GetFragmentationSpectraScanNums(mostAbundantIsotopeMz)
.Where(ms2ScanNum => ms2ScanNum >= minScanNum && ms2ScanNum <= maxScanNum &&
(activationMethod == ActivationMethod.Unknown ||
((ProductSpectrum)GetSpectrum(ms2ScanNum)).ActivationMethod == activationMethod)))
;
}
var summedSpec = GetSummedSpectrum(ms2ScanNums);
return(new ProductSpectrum(summedSpec.Peaks, 0)
{
ActivationMethod = activationMethod
});
}
/// <summary>
/// Get the scorer by spectrum.
/// This creates the scorer directly for that spectrum. It bypasses the scorer cache.
/// </summary>
/// <param name="spectrum">The spectrum number to get the scorer for.</param>
/// <param name="precursorMass">The precursor mass to get the scorer for.</param>
/// <param name="precursorCharge">The precursor charge to get the scorer for.</param>
/// <returns>The scorer selected based on the arguments.</returns>
public IScorer GetScorer(ProductSpectrum spectrum, double precursorMass, int precursorCharge, ActivationMethod activationMethod = ActivationMethod.Unknown)
{
var parameters = this.scoringParameterSet.GetScoringParameters(spectrum.ActivationMethod, precursorMass);
var targetedDeconvolutedSpectrum = new TargetedDeconvolutedSpectrum(spectrum, 1, precursorCharge - 1);
return(new FlipScorer <TargetedDeconvolutedSpectrum>(parameters, targetedDeconvolutedSpectrum));
}
public FastCsvParser(ActivationMethod activationMethod)
{
_activationMethod = activationMethod;
}
public TxtCsvHelper(ActivationMethod activationMethod)
{
_activationMethod = activationMethod;
}
public double GetNodeScoreWithoutMassError(ActivationMethod activationMethod, bool isPrefix, DeconvolutedPeak matchedPeak, double refIntensity)
{
return GetNodeScoreWithoutMassError(activationMethod, isPrefix, matchedPeak.Mass, matchedPeak.Charge, matchedPeak.Corr, matchedPeak.Dist, matchedPeak.Intensity / refIntensity);
}
public Precursor()
{
Ions = new List<SelectedIon>();
IsolationWindowTargetMz = 0.0;
IsolationWindowLowerOffset = 0.0;
IsolationWindowUpperOffset = 0.0;
Activation = ActivationMethod.Unknown;
}
public double GetNodeScoreWithoutMassError(ActivationMethod activationMethod, bool isPrefix, double fragmentIonMass, int fragmentIonCharge,
double corrScore, double distScore, double intensityScore)
{
var m = MassBinning.GetBinIndex(fragmentIonMass);
var c = GetChargeIndex(fragmentIonCharge);
var a = GetActivationMethodIndex(activationMethod);
var t = GetIonTypeIndex(isPrefix);
var ci = CorrBinning.GetBinIndex(corrScore);
var di = DistBinning.GetBinIndex(distScore);
var ii = IntensityBinning.GetBinIndex(intensityScore);
var score = IonTypeScoreTable[a][t];
score += MassScoreTable[a][t][m];
score += ChargeScoreTable[m][c];
score += CorrScoreTable[c][m][ci];
score += DistScoreTable[c][m][di];
score += IntensityScoreTable[c][m][ii];
return score;
}
public CommonLibrary_NET(ActivationMethod activationMethod)
{
_activationMethod = activationMethod;
}
