public void PickChromatogramPeaks()
{
// Make sure times are evenly spaced before doing any peak detection.
EvenlySpaceTimes();
// Pick peak groups at the precursor level
foreach (var chromDataSet in _dataSets)
{
chromDataSet.PickChromatogramPeaks(_retentionTimes, _isAlignedTimes);
}
// Merge where possible and pick peak groups at the peptide level
_listListPeakSets.Clear();
foreach (var dataSets in ComparableDataSets)
{
_listListPeakSets.Add(PickPeptidePeaks(dataSets.ToArray()));
}
// Adjust peak dimensions based on peak picking
foreach (var chromDataSet in _dataSets)
{
chromDataSet.GeneratePeakData();
}
var detailedCalcs = DetailedPeakFeatureCalculators.Select(calc => (IPeakFeatureCalculator)calc).ToList();
foreach (var listPeakSets in _listListPeakSets)
{
var maxPossibleShift = GetMaxPossibleShift(listPeakSets);
// Score the peaks under the legacy model score
foreach (var peakSet in listPeakSets.Where(peakSet => peakSet != null))
{
var context = new PeakScoringContext(_document);
context.AddInfo(_predictedRetentionTime);
context.AddInfo(maxPossibleShift);
peakSet.ScorePeptideSets(context, detailedCalcs);
}
SortAndLimitPeaks(listPeakSets);
}
// Propagate sorting down to precursor level
UpdatePrecursorsFromPeptidePeaks();
// Sort transition group level peaks by retention time and record the best peak
foreach (var chromDataSet in _dataSets)
{
chromDataSet.StorePeaks();
}
}
public void ScorePeptideSets(PeakScoringContext context, IList <IPeakFeatureCalculator> detailFeatureCalculators)
{
var modelCalcs = ScoringModel.PeakFeatureCalculators;
var detailFeatures = new float [detailFeatureCalculators.Count];
var modelFeatures = new float [modelCalcs.Count];
// Here we score both the detailFeatureCalculators (for storage)
// and the peak calculators of the legacy model (for import-stage peak scoring)
// This will cause some scores to be calculated multiple times, but score
// caching should make this fast.
var allFeatureCalculators = detailFeatureCalculators.Union(modelCalcs);
// Calculate summary data once for all scores
var summaryData = new PeptidePeakDataConverter <IDetailedPeakData>(this);
foreach (var calc in allFeatureCalculators)
{
float feature;
var summaryCalc = calc as SummaryPeakFeatureCalculator;
if (summaryCalc != null)
{
feature = summaryCalc.Calculate(context, summaryData);
}
else
{
feature = calc.Calculate(context, this);
}
int detailIndex = detailFeatureCalculators.IndexOf(calc);
if (detailIndex != -1)
{
detailFeatures[detailIndex] = feature;
}
int modelIndex = modelCalcs.IndexOf(calc);
if (modelIndex != -1)
{
modelFeatures[modelIndex] = double.IsNaN(feature) ? 0 : feature;
}
}
CombinedScore = ScoringModel.Score(modelFeatures);
foreach (var peak in this.Where(peak => peak.PeakGroup != null))
{
peak.PeakGroup.DetailScores = detailFeatures;
}
}
