private void FinishCalculation()
{
double totalArea = _peaks.Values.Sum(p => p.Area);
double tracerPercent = 0;
double totalScore = 0;
var tracerChromatograms = GetTracerChromatograms();
foreach (var entry in _peaks.ToArray())
{
var peak = entry.Value;
peak.RelativeAmount = totalArea == 0 ? 0 : peak.Area / totalArea;
tracerPercent += peak.RelativeAmount * peak.TracerPercent;
totalScore += peak.Area *
tracerChromatograms.GetScore(
tracerChromatograms.ChromatogramSet.IndexFromTime(peak.StartTime),
tracerChromatograms.ChromatogramSet.IndexFromTime(peak.EndTime));
_peaks[entry.Key] = peak;
}
TracerPercent = tracerPercent;
DeconvolutionScore = totalArea == 0 ? 0 : totalScore / totalArea;
IDictionary <TracerFormula, double> bestMatch;
var peaksDict = ToDictionary();
double turnover;
double turnoverScore;
PrecursorEnrichmentFormula = PeptideAnalysis.GetTurnoverCalculator().ComputePrecursorEnrichmentAndTurnover(peaksDict, out turnover, out turnoverScore, out bestMatch);
if (PrecursorEnrichmentFormula != null)
{
PrecursorEnrichment = PrecursorEnrichmentFormula.Values.Sum() / 100.0;
Turnover = turnover;
TurnoverScore = turnoverScore;
}
}
public void Dispose()
{
if (_peptideAnalysis != null)
{
_peptideAnalysis.DecChromatogramRefCount();
_peptideAnalysis = null;
}
}
public static PeptideFileAnalysis GetPeptideFileAnalysis(
PeptideAnalysis peptideAnalysis, DbPeptideFileAnalysis dbPeptideFileAnalysis)
{
PeptideFileAnalysis peptideFileAnalysis;
peptideAnalysis.FileAnalyses.TryGetValue(dbPeptideFileAnalysis.GetId(), out peptideFileAnalysis);
return(peptideFileAnalysis);
}
public override WorkspaceData SetData(WorkspaceData workspaceData, PeptideFileAnalysisData value)
{
var peptideAnalysisData = PeptideAnalysis.GetData(workspaceData);
peptideAnalysisData =
peptideAnalysisData.SetFileAnalyses(peptideAnalysisData.FileAnalyses.Replace(Id, value));
return(PeptideAnalysis.SetData(workspaceData, peptideAnalysisData));
}
public void SetCalculatedPeaks(CalculatedPeaks calculatedPeaks)
{
if (calculatedPeaks.AutoFindPeak)
{
throw new InvalidOperationException();
}
Data = Data.SetPeaks(false, calculatedPeaks.ToPeakSetData());
PeptideAnalysis.InvalidatePeaks();
}
public override PeptideFileAnalysisData GetData(WorkspaceData workspaceData)
{
var peptideAnalysisData = PeptideAnalysis.GetData(workspaceData);
PeptideFileAnalysisData peptideFileAnalysisData = null;
if (null != peptideAnalysisData)
{
peptideAnalysisData.FileAnalyses.TryGetValue(Id, out peptideFileAnalysisData);
}
return(peptideFileAnalysisData);
}
public bool IsMzKeySetComplete(ICollection <MzKey> mzKeys)
{
for (int charge = PeptideAnalysis.MinCharge; charge <= PeptideAnalysis.MaxCharge; charge++)
{
for (int massIndex = 0; massIndex < PeptideAnalysis.GetMassCount(); massIndex++)
{
if (!mzKeys.Contains(new MzKey(charge, massIndex)))
{
return(false);
}
}
}
return(true);
}
public static PeptideFileAnalysis EnsurePeptideFileAnalysis(PeptideAnalysis peptideAnalysis, MsDataFile msDataFile)
{
var workspace = peptideAnalysis.Workspace;
using (var session = workspace.OpenSession())
{
var criteria = session.CreateCriteria(typeof(DbPeptideFileAnalysis))
.Add(Restrictions.Eq("PeptideAnalysis", session.Load <DbPeptideAnalysis>(peptideAnalysis.Id)))
.Add(Restrictions.Eq("MsDataFile", session.Load <DbMsDataFile>(msDataFile.Id)));
var dbPeptideAnalysis = (DbPeptideFileAnalysis)criteria.UniqueResult();
if (dbPeptideAnalysis != null)
{
return(GetPeptideFileAnalysis(peptideAnalysis, dbPeptideAnalysis));
}
}
if (!msDataFile.HasTimes())
{
return(null);
}
using (var session = workspace.OpenWriteSession())
{
var dbPeptideAnalysis = session.Load <DbPeptideAnalysis>(peptideAnalysis.Id);
var psmTimesByDataFileId = dbPeptideAnalysis.Peptide.PsmTimesByDataFileId(session);
var dbPeptideFileAnalysis = CreatePeptideFileAnalysis(session, msDataFile, dbPeptideAnalysis, psmTimesByDataFileId);
if (dbPeptideFileAnalysis == null)
{
return(null);
}
session.BeginTransaction();
session.Save(dbPeptideFileAnalysis);
dbPeptideAnalysis.FileAnalysisCount++;
session.Update(dbPeptideAnalysis);
session.Save(new DbChangeLog(peptideAnalysis));
session.Transaction.Commit();
workspace.ChromatogramGenerator.SetRequeryPending();
workspace.DatabasePoller.LoadAndMergeChanges(null);
return(workspace.PeptideAnalyses.FindByKey(dbPeptideAnalysis.GetId())
.FileAnalyses.FindByKey(dbPeptideFileAnalysis.GetId()));
}
}
public PeptideFileAnalyses(PeptideAnalysis peptideAnalysis) : base(peptideAnalysis.Workspace)
{
PeptideAnalysis = peptideAnalysis;
}
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;
}
public PeptideAnalysis(Workspace workspace, PeptideAnalysis peptideAnalysis) : base(workspace, peptideAnalysis.Id)
{
_chromatogramRefCount = 0;
}
public RefCountHolder(PeptideAnalysis peptideAnalysis)
{
_peptideAnalysis = peptideAnalysis;
}
public PeptideFileAnalysis(PeptideAnalysis peptideAnalysis, long id, PeptideFileAnalysisData peptideFileAnalysisData)
: base(peptideAnalysis.Workspace, id, peptideFileAnalysisData)
{
PeptideAnalysis = peptideAnalysis;
}
public String GetLabel()
{
return(PeptideAnalysis.GetLabel() + " " + MsDataFile.Label);
}
