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);
}
public void SetCalculatedPeaks(CalculatedPeaks calculatedPeaks)
{
if (calculatedPeaks.AutoFindPeak)
{
throw new InvalidOperationException();
}
Data = Data.SetPeaks(false, calculatedPeaks.ToPeakSetData());
PeptideAnalysis.InvalidatePeaks();
}
public void Save(ISession session)
{
var dbPeptideFileAnalysis = session.Get <DbPeptideFileAnalysis>(Id);
dbPeptideFileAnalysis.AutoFindPeak = AutoFindPeak;
dbPeptideFileAnalysis.Note = Data.Note;
dbPeptideFileAnalysis.ValidationStatus = Data.ValidationStatus;
session.Update(dbPeptideFileAnalysis);
if (null != CalculatedPeaks)
{
CalculatedPeaks.Save(session);
}
}
public CalculatedPeaks AutoSizePeak(TracerFormula tracerFormula, AdjustPeaksMode adjustPeaksMode)
{
if (tracerFormula.Equals(BasePeakKey))
{
return(this);
}
var result = new CalculatedPeaks(PeptideFileAnalysis)
{
AutoFindPeak = false,
};
var oldBasePeak = _peaks[BasePeakKey];
result.MakeBasePeak(BasePeakKey, oldBasePeak.StartTime, oldBasePeak.EndTime);
foreach (var entry in _peaks)
{
if (entry.Key.Equals(BasePeakKey))
{
continue;
}
Peak?newPeak = null;
if (entry.Key.Equals(tracerFormula))
{
double width = oldBasePeak.EndTime - oldBasePeak.StartTime;
if (adjustPeaksMode == AdjustPeaksMode.Full)
{
newPeak = result.FindMatchingPeak(tracerFormula);
}
else if (adjustPeaksMode == AdjustPeaksMode.Overlapping)
{
newPeak = result.FindMatchingPeak(tracerFormula, entry.Value.StartTime - width, entry.Value.EndTime + width);
}
else if (adjustPeaksMode == AdjustPeaksMode.Narrow)
{
newPeak = result.FindMatchingPeak(tracerFormula,
Math.Min(entry.Value.StartTime, entry.Value.EndTime - width),
Math.Max(entry.Value.EndTime, entry.Value.StartTime + width));
}
}
if (newPeak == null)
{
result.MakeSecondaryPeak(entry.Key, entry.Value.StartTime, entry.Value.EndTime);
}
}
result.FinishCalculation();
return(result);
}
public CalculatedPeaks ChangeBasePeak(TracerFormula baseTracerFormula)
{
CalculatedPeaks result = new CalculatedPeaks(PeptideFileAnalysis)
{
AutoFindPeak = false,
};
var basePeak = _peaks[baseTracerFormula];
result.MakeBasePeak(baseTracerFormula, basePeak.StartTime, basePeak.EndTime);
foreach (var entry in _peaks)
{
if (entry.Key.Equals(baseTracerFormula))
{
continue;
}
result.MakeSecondaryPeak(entry.Key, entry.Value.StartTime, entry.Value.EndTime);
}
result.FinishCalculation();
return(result);
}
public CalculatedPeaks ChangeTime(TracerFormula tracerFormula, double newStartTime, double newEndTime)
{
CalculatedPeaks result = new CalculatedPeaks(PeptideFileAnalysis)
{
AutoFindPeak = false,
};
Peak oldBasePeak = _peaks[BasePeakKey];
bool isBasePeak;
if (tracerFormula.Equals(BasePeakKey))
{
result.MakeBasePeak(BasePeakKey, newStartTime, newEndTime);
isBasePeak = true;
}
else
{
result.MakeBasePeak(BasePeakKey, oldBasePeak.StartTime,
oldBasePeak.EndTime);
isBasePeak = false;
}
foreach (var entry in _peaks)
{
if (entry.Key.Equals(tracerFormula))
{
if (isBasePeak)
{
continue;
}
result.MakeSecondaryPeak(tracerFormula, newStartTime, newEndTime);
}
else
{
result.MakeSecondaryPeak(entry.Key, entry.Value.StartTime, entry.Value.EndTime);
}
}
result.FinishCalculation();
return(result);
}
public void EnsurePeaksCalculated()
{
if (0 == GetChromatogramRefCount())
{
throw new InvalidOperationException("No chromatograms");
}
if (null != _calculatedPeaks)
{
return;
}
var peaksList = new List <CalculatedPeaks>();
var peptideFileAnalyses = FileAnalyses.ToArray();
Array.Sort(peptideFileAnalyses,
(f1, f2) => (null == f1.PsmTimes).CompareTo(null == f2.PsmTimes)
);
bool changed = false;
foreach (var peptideFileAnalysis in peptideFileAnalyses)
{
if (peptideFileAnalysis.ChromatogramSet == null ||
!peptideFileAnalysis.IsMzKeySetComplete(peptideFileAnalysis.ChromatogramSet.Chromatograms.Keys))
{
continue;
}
var peaks = peptideFileAnalysis.CalculatedPeaks;
if (peaks == null || changed)
{
peaks = CalculatedPeaks.Calculate(peptideFileAnalysis, peaksList);
changed = changed || peaks != null;
}
peaksList.Add(peaks);
}
SetCalculatedPeaks(peaksList);
}
public CalculatedPeaks ChangeTime(TracerFormula tracerFormula, double newStartTime, double newEndTime)
{
CalculatedPeaks result = new CalculatedPeaks(PeptideFileAnalysis)
{
AutoFindPeak = false,
};
Peak oldBasePeak = _peaks[BasePeakKey];
bool isBasePeak;
if (tracerFormula.Equals(BasePeakKey))
{
result.MakeBasePeak(BasePeakKey, newStartTime, newEndTime);
isBasePeak = true;
}
else
{
result.MakeBasePeak(BasePeakKey, oldBasePeak.StartTime,
oldBasePeak.EndTime);
isBasePeak = false;
}
foreach (var entry in _peaks)
{
if (entry.Key.Equals(tracerFormula))
{
if (isBasePeak)
{
continue;
}
result.MakeSecondaryPeak(tracerFormula, newStartTime, newEndTime);
}
else
{
result.MakeSecondaryPeak(entry.Key, entry.Value.StartTime, entry.Value.EndTime);
}
}
result.FinishCalculation();
return result;
}
public CalculatedPeaks ChangeBasePeak(TracerFormula baseTracerFormula)
{
CalculatedPeaks result = new CalculatedPeaks(PeptideFileAnalysis)
{
AutoFindPeak = false,
};
var basePeak = _peaks[baseTracerFormula];
result.MakeBasePeak(baseTracerFormula, basePeak.StartTime, basePeak.EndTime);
foreach (var entry in _peaks)
{
if (entry.Key.Equals(baseTracerFormula))
{
continue;
}
result.MakeSecondaryPeak(entry.Key, entry.Value.StartTime, entry.Value.EndTime);
}
result.FinishCalculation();
return result;
}
public CalculatedPeaks AutoSizePeak(TracerFormula tracerFormula, AdjustPeaksMode adjustPeaksMode)
{
if (tracerFormula.Equals(BasePeakKey))
{
return this;
}
var result = new CalculatedPeaks(PeptideFileAnalysis)
{
AutoFindPeak = false,
};
var oldBasePeak = _peaks[BasePeakKey];
result.MakeBasePeak(BasePeakKey, oldBasePeak.StartTime, oldBasePeak.EndTime);
foreach (var entry in _peaks)
{
if (entry.Key.Equals(BasePeakKey))
{
continue;
}
Peak? newPeak = null;
if (entry.Key.Equals(tracerFormula))
{
double width = oldBasePeak.EndTime - oldBasePeak.StartTime;
if (adjustPeaksMode == AdjustPeaksMode.Full)
{
newPeak = result.FindMatchingPeak(tracerFormula);
}
else if (adjustPeaksMode == AdjustPeaksMode.Overlapping)
{
newPeak = result.FindMatchingPeak(tracerFormula, entry.Value.StartTime - width, entry.Value.EndTime + width);
}
else if (adjustPeaksMode == AdjustPeaksMode.Narrow)
{
newPeak = result.FindMatchingPeak(tracerFormula,
Math.Min(entry.Value.StartTime, entry.Value.EndTime - width),
Math.Max(entry.Value.EndTime, entry.Value.StartTime + width));
}
}
if (newPeak == null)
{
result.MakeSecondaryPeak(entry.Key, entry.Value.StartTime, entry.Value.EndTime);
}
}
result.FinishCalculation();
return result;
}
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;
}
