public PeptideFileAnalysisData SetChromatogramSet(ChromatogramSetData value)
{
return(new PeptideFileAnalysisData(this)
{
ChromatogramSet = value
});
}
public PeptideFileAnalysisData SetChromatogramSet(ChromatogramSetData value)
{
return new PeptideFileAnalysisData(this){ChromatogramSet = value};
}
public TracerChromatograms(PeptideFileAnalysis peptideFileAnalysis, ChromatogramSetData chromatogramSet, bool smoothed)
{
Smoothed = smoothed;
ChromatogramSet = chromatogramSet;
PeptideFileAnalysis = peptideFileAnalysis;
var pointDict = new Dictionary<TracerFormula, IList<double>>();
var chromatogramsDict = new Dictionary<MzKey, IList<double>>();
var turnoverCalculator = PeptideAnalysis.GetTurnoverCalculator();
double massAccuracy = PeptideAnalysis.GetMassAccuracy();
foreach (var chromatogramEntry in ChromatogramSet.Chromatograms)
{
if (PeptideAnalysis.ExcludedMasses.Contains(chromatogramEntry.Key.MassIndex))
{
continue;
}
var chromatogram = chromatogramEntry.Value;
var mzRange = turnoverCalculator.GetMzs(chromatogramEntry.Key.Charge)[chromatogramEntry.Key.MassIndex];
var intensities = chromatogram.ChromatogramPoints.Select(point=>point.GetIntensity(mzRange, massAccuracy)).ToArray();
if (smoothed)
{
intensities = SavitzkyGolaySmooth(intensities);
}
chromatogramsDict.Add(chromatogramEntry.Key, intensities);
}
int massCount = PeptideFileAnalysis.PeptideAnalysis.GetMassCount();
var times = chromatogramSet.Times.ToArray();
var scores = new List<double>();
var tracerFormulas = turnoverCalculator.ListTracerFormulas();
var theoreticalIntensities = turnoverCalculator.GetTheoreticalIntensities(tracerFormulas);
for (int i = 0; i < times.Length; i++)
{
var intensities = new List<double>();
for (int iMass = 0; iMass < massCount; iMass++)
{
double intensity = 0;
for (int charge = PeptideAnalysis.MinCharge; charge <= PeptideAnalysis.MaxCharge; charge++)
{
IList<double> chromatogram;
if (chromatogramsDict.TryGetValue(new MzKey(charge, iMass), out chromatogram))
{
intensity += chromatogram[i];
}
else
{
intensity = double.NaN;
}
}
intensities.Add(intensity);
}
double score;
IDictionary<TracerFormula, IList<double>> predictedIntensities;
PeptideAnalysis.GetTurnoverCalculator().GetTracerAmounts(intensities, out score, out predictedIntensities, tracerFormulas, theoreticalIntensities);
foreach (var entry in predictedIntensities)
{
IList<double> list;
if (!pointDict.TryGetValue(entry.Key, out list))
{
list = new List<double>();
pointDict.Add(entry.Key, list);
}
list.Add(entry.Value.Sum());
}
scores.Add(score);
}
var points = new SortedDictionary<TracerFormula, IList<double>>();
var peaks = new Dictionary<TracerFormula, IList<CrawdadPeak>>();
foreach (var entry in pointDict)
{
points.Add(entry.Key, entry.Value);
CrawPeakFinderWrapper peakFinder = new CrawPeakFinderWrapper();
peakFinder.SetChromatogram(times, entry.Value);
peaks.Add(entry.Key, peakFinder.CalcPeaks(MaxPeaks));
}
Points = points;
Scores = scores;
Times = chromatogramSet.Times;
RawPeaks = peaks;
}
