public PrecursorIon(Sample sample, IEnumerable <Query> queries, double mz, int charge)
{
this.MZ = mz;
this.Charge = charge;
this.Queries = new Queries();
foreach (Query query in queries)
{
if (query.sample == sample)
{
this.Queries.Add(query);
}
}
this.Queries.Sort(Query.AscendingRetentionTimeComparison);
Dictionary <double, double> dicOfTimeInMsVsIntensityPerMs = new Dictionary <double, double>();
Dictionary <double, double> dicOfTimeInMsVsIntensityCount = new Dictionary <double, double>();
PeakTopIntensity = 0.0;
foreach (Query query in this.Queries)
{
double time = query.spectrum.RetentionTimeInMin * 60.0 * 1000.0;
dicOfTimeInMsVsIntensityPerMs.Add(time, query.spectrum.PrecursorIntensityPerMilliSecond);
dicOfTimeInMsVsIntensityCount.Add(time, query.spectrum.PrecursorIntensity);
if (query.spectrum.PrecursorIntensity > PeakTopIntensity)
{
PeakTopIntensity = query.spectrum.PrecursorIntensity;
}
}
this.eCurveIntensityCount = ElutionCurve.Create(dicOfTimeInMsVsIntensityCount);//dicOfTimeInMsVsIntensityPerMs);
this.eCurveIntensityPerMS = ElutionCurve.Create(dicOfTimeInMsVsIntensityPerMs);
this.Sample = sample;
}
/// <summary>
/// Computes a curve [precursor observed intensity ; correction so that precursor computed intensity from fragments matches observed intensity]
/// </summary>
/// <param name="dbOptions"></param>
/// <param name="nbProductsToKeep"></param>
/// <returns></returns>
private ElutionCurve GetNormalizingCurve(DBOptions dbOptions, int nbProductsToKeep)
{
List <CharacterizedPrecursor> Isomers = new List <CharacterizedPrecursor>();
Isomers.Add(this);
ElutionCurve curve = new ElutionCurve();
foreach (Query query in this.Queries)
{
double timeInMilliSeconds = query.spectrum.RetentionTimeInMin * 60.0 * 1000.0;
double underFlow = 0;
double percentError = 0;
double intInTrap = query.spectrum.PrecursorIntensityPerMilliSecond * query.spectrum.InjectionTime;
Dictionary <CharacterizedPrecursor, PositionnalIsomerSolver.SolvedResult> finalRatios = PositionnalIsomerSolver.SolveFromSpectrum(Isomers, nbProductsToKeep, query.spectrum.Peaks, dbOptions.productMassTolerance,
intInTrap, query.spectrum.PrecursorIntensity,
out underFlow, out percentError, dbOptions.ConSole);
if (percentError < 0.5 && finalRatios[this].NbFitTimes > 0)
{
double ratio = intInTrap / finalRatios[this].NbFitTimes;
if (ratio > 0.5 && ratio < 2)
{
curve.AddPoint(intInTrap, intInTrap / finalRatios[this].NbFitTimes);
}
}
}
curve.Compute(CurveType.LINEAR, true);
return(curve);
}
private double GetNbTimesFit(DBOptions dbOptions, int nbProductsToKeep, double precision, out double area)
{
long nbRatios = 0;
double nbTimes = 0;
area = 0.0;
List <CharacterizedPrecursor> Isomers = new List <CharacterizedPrecursor>();
Isomers.Add(this);
ElutionCurve curve = new ElutionCurve();
foreach (Query query in this.Queries)
{
//double overFlow = 0;
double underFlow = 0;
double percentError = 0;
Dictionary <CharacterizedPrecursor, PositionnalIsomerSolver.SolvedResult> finalRatios = PositionnalIsomerSolver.SolveFromSpectrum(Isomers, nbProductsToKeep, precision, query.spectrum.Peaks, dbOptions.productMassTolerance,
query.spectrum.PrecursorIntensityPerMilliSecond * query.spectrum.InjectionTime, out underFlow, out percentError, dbOptions.ConSole);
if (percentError < 0.5)
{
curve.AddPoint(query.spectrum.RetentionTimeInMin * 1000.0 * 60.0, finalRatios[this].Ratio * query.spectrum.PrecursorIntensityPerMilliSecond);
nbTimes += finalRatios[this].NbFitTimes;
nbRatios++;
}
}
if (nbRatios > 2 && curve.GetNbPoints() > this.Queries.Count * 0.5)
{
curve.Compute();
if (curve.Area > 0)
{
area = curve.Area;
}
}
return(nbTimes / (double)nbRatios);
}
