public static CalculatedPeaks Calculate(PeptideFileAnalysis peptideFileAnalysis, IEnumerable <CalculatedPeaks> otherPeaks)
{
var tracerFormulae = peptideFileAnalysis.TurnoverCalculator.ListTracerFormulas();
var result = new CalculatedPeaks(peptideFileAnalysis);
if (!peptideFileAnalysis.AutoFindPeak)
{
var previous = peptideFileAnalysis.PeakData;
if (previous.Peaks.Count == tracerFormulae.Count)
{
for (int i = 0; i < previous.Peaks.Count; i++)
{
var peak = previous.Peaks[i];
if (result._peaks.Count == 0)
{
result.MakeBasePeak(tracerFormulae[i], peak.StartTime, peak.EndTime);
}
else
{
result.MakeSecondaryPeak(tracerFormulae[i], peak.StartTime, peak.EndTime);
}
}
var maxArea = result._peaks.Values.Max(peak => peak.Area);
result = result.ChangeBasePeak(result._peaks.First(kvp => kvp.Value.Area.Equals(maxArea)).Key);
result.IntegrationNote = IntegrationNote.Manual;
}
}
if (result._peaks.Count == 0)
{
result.LookForBestPeak(otherPeaks);
}
result.FinishCalculation();
return(result);
}
private TracerChromatograms GetTracerChromatograms()
{
if (_tracerChromatograms == null)
{
_tracerChromatograms = PeptideFileAnalysis.GetTracerChromatograms(_smoothChromatograms);
}
return(_tracerChromatograms);
}
public CalculatedPeaks GetCalculatePeaks(PeptideFileAnalysis peptideFileAnalysis)
{
if (null == _calculatedPeaks)
{
return(null);
}
CalculatedPeaks calculatedPeaks;
_calculatedPeaks.TryGetValue(peptideFileAnalysis.Id, out calculatedPeaks);
return(calculatedPeaks);
}
public List <PeptideFileAnalysis> GetFileAnalyses()
{
var result = new List <PeptideFileAnalysis>();
using (var session = Workspace.OpenSession())
{
var criteria = session.CreateCriteria(typeof(DbPeptideFileAnalysis))
.Add(Restrictions.Eq("MsDataFile", session.Load <DbMsDataFile>(Id)));
foreach (DbPeptideFileAnalysis peptideFileAnalysis in criteria.List())
{
int index = Workspace.PeptideAnalyses.IndexOfKey(peptideFileAnalysis.PeptideAnalysis.GetId());
if (index >= 0)
{
result.Add(PeptideFileAnalysis.GetPeptideFileAnalysis(
Workspace.PeptideAnalyses[index],
peptideFileAnalysis));
}
}
}
return(result);
}
public PeptideDistributions(PeptideFileAnalysis peptideFileAnalysis) : base(peptideFileAnalysis.Workspace)
{
Parent = peptideFileAnalysis;
SetId(peptideFileAnalysis.Id);
IsDirty = true;
}
public PeptideDistributions(PeptideFileAnalysis peptideFileAnalysis, DbPeptideFileAnalysis dbPeptideFileAnalysis)
: base(peptideFileAnalysis.Workspace, dbPeptideFileAnalysis)
{
Parent = peptideFileAnalysis;
}
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;
}
private CalculatedPeaks(PeptideFileAnalysis peptideFileAnalysis)
{
PeptideFileAnalysis = peptideFileAnalysis;
AutoFindPeak = peptideFileAnalysis.AutoFindPeak;
}
