/// <summary>
/// Get the weighted score of the ion without including mass error in the score.
/// </summary>
/// <param name="peak">The peak for the ion to calculate the score for.</param>
/// <returns>The score.</returns>
public double GetMatchedIonPeakScoreWithoutError(DeconvolutedPeak peak)
{
double score = 0.0;
score += this.SummedIntensityWeight * peak.Intensity;
score += this.SummedPearsonCorrelationWeight * peak.Corr;
score += this.SummedCosineWeight * peak.Dist;
return(score);
}
private double GetMatchedIonPeakScore(bool isPrefixIon, DeconvolutedPeak peak)
{
var param = (isPrefixIon) ? ScoreParam.Prefix : ScoreParam.Suffix;
var score = param.Count;
score += param.Intensity * Math.Min(peak.Intensity / ReferencePeakIntensity, 1.0d);
score += param.Corr * peak.Corr;
score += param.Dist * peak.Dist;
return(score);
}
/// <summary>
/// Get the weighted score of the ion including mass error in the score.
/// </summary>
/// <param name="baseIonType">The base ion type to use the feature vector for.</param>
/// <param name="peak">The peak for the ion to calculate the score for.</param>
/// <returns>The score.</returns>
public double GetMatchedIonPeakScoreWithError(BaseIonType baseIonType, DeconvolutedPeak peak, double theoMass)
{
var featureVector = this.IonWeights[baseIonType];
double score = featureVector.GetMatchedIonPeakScoreWithoutError(peak);
var ppmError = Math.Abs(peak.Mass - theoMass) / theoMass * 1e6;
score += this.MassErrorWeight * ppmError;
return(score);
}
private void UpdateDeconvPeak(int binNum, DeconvolutedPeak newPeak)
{
if (newPeak == null)
{
return;
}
if (_massBinToPeakMap.TryGetValue(binNum, out var existingPeak))
{
if (existingPeak.Intensity < newPeak.Intensity)
{
_massBinToPeakMap[binNum] = newPeak;
}
}
else
{
_massBinToPeakMap[binNum] = newPeak;
}
}
/// <summary>
/// Gets the score for a single deconvoluted peak.
/// Does not include Mass error score.
/// </summary>
/// <param name="deconvolutedPeak">The peak to score.</param>
/// <param name="ionType">The type of ion to score against.</param>
/// <returns>The score of the peak.</returns>
public double GetFragmentScore(DeconvolutedPeak deconvolutedPeak, BaseIonType ionType)
{
IonWeights featureVector = this.scoringParameters.FeatureWeights.IonWeights[ionType];
return(featureVector.GetMatchedIonPeakScoreWithoutError(deconvolutedPeak));
}
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 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));
}
/// <summary>
/// Read a spectrum from the current position in <paramref name="reader"/>, with the option to only read the metadata.
/// </summary>
/// <param name="reader"></param>
/// <param name="includePeaks"></param>
/// <returns></returns>
protected internal override Spectrum ReadSpectrum(BinaryReader reader, bool includePeaks = true)
{
// Must reflect all changes to WriteSpectrum
var scanNum = reader.ReadInt32();
var c = new char[NativeIdLength];
reader.Read(c, 0, NativeIdLength);
var nativeId = (new string(c)).Trim();
var msLevel = reader.ReadByte();
var elutionTime = reader.ReadDouble();
var tic = reader.ReadSingle();
double?precursorMass = reader.ReadDouble();
if (Math.Abs(precursorMass.Value) < float.Epsilon)
{
precursorMass = null;
}
int?precursorCharge = reader.ReadInt32();
if (precursorCharge == 0)
{
precursorCharge = null;
}
var activationMethod = (ActivationMethod)reader.ReadByte();
var isolationWindowTargetMz = reader.ReadDouble();
var isolationWindowLowerOffset = reader.ReadDouble();
var isolationWindowUpperOffset = reader.ReadDouble();
var peakList = new List <DeconvolutedPeak>();
var numPeaks = reader.ReadInt32();
for (var i = 0; i < numPeaks; i++)
{
var mz = reader.ReadDouble();
var intensity = reader.ReadSingle();
var charge = reader.ReadInt32();
var corr = reader.ReadSingle();
var dist = reader.ReadSingle();
var peak = new DeconvolutedPeak(mz, intensity, charge, corr, dist);
var isoPeakCount = (int)reader.ReadByte();
peak.ObservedPeakIndices.Capacity = isoPeakCount;
for (var j = 0; j < isoPeakCount; j++)
{
peak.ObservedPeakIndices.Add(reader.ReadUInt16());
}
peakList.Add(peak);
}
var spec = new DeconvolutedSpectrum(peakList, scanNum)
{
ActivationMethod = activationMethod,
IsolationWindow = new IsolationWindow(
isolationWindowTargetMz,
isolationWindowLowerOffset,
isolationWindowUpperOffset,
precursorMass,
precursorCharge
),
MsLevel = msLevel,
ElutionTime = elutionTime,
NativeId = nativeId,
TotalIonCurrent = tic
};
return(spec);
}
