public ChromPeak CalcChromPeak(CrawdadPeak peakMax, ChromPeak.FlagValues flags, out CrawdadPeak peak)
{
// Reintegrate all peaks to the max peak, even the max peak itself, since its boundaries may
// have been extended from the Crawdad originals.
if (peakMax == null)
{
peak = null;
return(ChromPeak.EMPTY);
}
peak = CalcPeak(peakMax.StartIndex, peakMax.EndIndex);
return(new ChromPeak(Finder, peak, flags, Times, Intensities, MassErrors10X));
}
public ChromPeak CalcChromPeak(IFoundPeak peakMax, ChromPeak.FlagValues flags, out IFoundPeak peak)
{
// Reintegrate all peaks to the max peak, even the max peak itself, since its boundaries may
// have been extended from the Crawdad originals.
if (peakMax == null)
{
peak = null;
return(ChromPeak.EMPTY);
}
peak = CalcPeak(peakMax.StartIndex, peakMax.EndIndex);
// If a forced peak is found to be sufficiently coeluting with the max peak, then clear the forced flag
if ((flags & ChromPeak.FlagValues.forced_integration) != 0 && AreCoeluting(peakMax, peak))
{
flags &= ~ChromPeak.FlagValues.forced_integration;
}
return(new ChromPeak(Finder, peak, flags, TimeIntensities, RawTimes));
}
/// <summary>
/// Returns a ChromPeak and IFoundPeak that match the start and end times a particular other IFoundPeak
/// that was found by Crawdad.
/// </summary>
public Tuple <ChromPeak, IFoundPeak> IntegrateFoundPeak(IFoundPeak peakMax, ChromPeak.FlagValues flags)
{
Assume.IsNotNull(PeakFinder);
var interpolatedPeak = PeakFinder.GetPeak(peakMax.StartIndex, peakMax.EndIndex);
if ((flags & ChromPeak.FlagValues.forced_integration) != 0 && ChromData.AreCoeluting(peakMax, interpolatedPeak))
{
flags &= ~ChromPeak.FlagValues.forced_integration;
}
var chromPeak = new ChromPeak(PeakFinder, interpolatedPeak, flags, InterpolatedTimeIntensities, RawTimeIntensities?.Times);
if (TimeIntervals != null)
{
chromPeak = IntegratePeakWithoutBackground(InterpolatedTimeIntensities.Times[peakMax.StartIndex], InterpolatedTimeIntensities.Times[peakMax.EndIndex], flags);
}
return(Tuple.Create(chromPeak, interpolatedPeak));
}
public ChromPeak CalcChromPeak(IFoundPeak peakMax, ChromPeak.FlagValues flags, TimeIntervals timeIntervals, out IFoundPeak peak)
{
// Reintegrate all peaks to the max peak, even the max peak itself, since its boundaries may
// have been extended from the Crawdad originals.
if (peakMax == null)
{
peak = null;
return(ChromPeak.EMPTY);
}
var peakIntegrator = new PeakIntegrator(TimeIntensities, Finder)
{
RawTimeIntensities = RawTimeIntensities,
TimeIntervals = timeIntervals
};
var tuple = peakIntegrator.IntegrateFoundPeak(peakMax, flags);
peak = tuple.Item2;
return(tuple.Item1);
}
/// <summary>
/// Return the ChromPeak with the specified start and end times chosen by a user.
/// </summary>
public ChromPeak IntegratePeak(float startTime, float endTime, ChromPeak.FlagValues flags)
{
if (TimeIntervals != null)
{
// For a triggered acquisition, we just use the start and end time supplied by the
// user and Crawdad is not involved with the peak integration.
return(IntegratePeakWithoutBackground(startTime, endTime, flags));
}
if (PeakFinder == null)
{
PeakFinder = CreatePeakFinder(InterpolatedTimeIntensities);
}
int startIndex = InterpolatedTimeIntensities.IndexOfNearestTime(startTime);
int endIndex = InterpolatedTimeIntensities.IndexOfNearestTime(endTime);
if (startIndex == endIndex)
{
return(ChromPeak.EMPTY);
}
var foundPeak = PeakFinder.GetPeak(startIndex, endIndex);
return(new ChromPeak(PeakFinder, foundPeak, flags, InterpolatedTimeIntensities, RawTimeIntensities?.Times));
}
public ChromPeak CalcChromPeak(CrawdadPeak peakMax, ChromPeak.FlagValues flags)
{
_chromPeak = Data.CalcChromPeak(peakMax, flags, out _crawPeak);
return(_chromPeak);
}
/// <summary>
/// Returns a ChromPeak with the specified start and end times and no background subtraction.
/// </summary>
private ChromPeak IntegratePeakWithoutBackground(float startTime, float endTime, ChromPeak.FlagValues flags)
{
if (TimeIntervals != null)
{
var intervalIndex = TimeIntervals.IndexOfIntervalEndingAfter(startTime);
if (intervalIndex >= 0 && intervalIndex < TimeIntervals.Count)
{
startTime = Math.Max(startTime, TimeIntervals.Starts[intervalIndex]);
endTime = Math.Min(endTime, TimeIntervals.Ends[intervalIndex]);
}
}
return(new ChromPeak(RawTimeIntensities ?? InterpolatedTimeIntensities, startTime, endTime, flags));
}
public ChromPeak CalcChromPeak(IFoundPeak peakMax, ChromPeak.FlagValues flags, TimeIntervals timeIntervals)
{
_chromPeak = Data.CalcChromPeak(peakMax, flags, timeIntervals, out _crawPeak);
return(_chromPeak);
}
