public static void MakeChromatogramInfo(SignedMz precursorMz, LibraryChromGroup chromGroup, LibraryChromGroup.ChromData chromData, out ChromatogramInfo chromatogramInfo, out TransitionChromInfo transitionChromInfo)
{
var crawPeakFinder = Crawdads.NewCrawdadPeakFinder();
crawPeakFinder.SetChromatogram(chromGroup.Times, chromData.Intensities);
var crawdadPeak =
crawPeakFinder.GetPeak(
FindNearestIndex(chromGroup.Times, (float)chromGroup.StartTime),
FindNearestIndex(chromGroup.Times, (float)chromGroup.EndTime));
var chromPeak = new ChromPeak(crawPeakFinder, crawdadPeak, 0, chromGroup.Times, chromData.Intensities, null);
transitionChromInfo = new TransitionChromInfo(null, 0, chromPeak, new float?[0], Annotations.EMPTY,
UserSet.FALSE);
var peaks = new[] { chromPeak };
var header = new ChromGroupHeaderInfo(precursorMz,
0, // file index
1, // numTransitions
0, // startTransitionIndex
peaks.Length, // numPeaks
0, // startPeakIndex
0, // startscoreindex
0, // maxPeakIndex
chromGroup.Times.Length, // numPoints
0, // compressedSize
0, // uncompressedsize
0, //location
0, -1, -1, null, null);
chromatogramInfo = new ChromatogramInfo(header,
new Dictionary <Type, int>(), 0,
new ChromCachedFile[0],
new[] { new ChromTransition(chromData.Mz, 0, 0, 0, ChromSource.unknown), },
peaks, null,
chromGroup.Times, new[] { chromData.Intensities }, null, null);
}
private IEnumerable <IFoundPeak> FindIntervalPeaks(float intervalStart, float intervalEnd, IList <int> identifiedIndices)
{
int startIndex = Times.BinarySearch(intervalStart);
if (startIndex < 0)
{
startIndex = Math.Max(0, ~startIndex - 1);
}
int endIndex = Times.BinarySearch(intervalEnd);
if (endIndex < 0)
{
endIndex = Math.Min(Times.Count - 1, ~endIndex);
}
if (endIndex <= startIndex)
{
yield break;
}
var times = Times.Skip(startIndex).Take(endIndex - startIndex + 1).ToArray();
var intensities = Intensities.Skip(startIndex).Take(endIndex - startIndex + 1).ToArray();
var subIdentifiedIndices = identifiedIndices.Select(index => index - startIndex).ToArray();
var subFinder = Crawdads.NewCrawdadPeakFinder();
subFinder.SetChromatogram(times, intensities);
foreach (var peak in subFinder.CalcPeaks(MAX_PEAKS, subIdentifiedIndices))
{
yield return(Finder.GetPeak(peak.StartIndex + startIndex, peak.EndIndex + startIndex));
}
}
public void FindPeaks(double[] retentionTimes, TimeIntervals timeIntervals, ExplicitRetentionTimeInfo explicitRT)
{
Finder = Crawdads.NewCrawdadPeakFinder();
Finder.SetChromatogram(Times, Intensities);
if (timeIntervals == null)
{
RawPeaks = Finder.CalcPeaks(MAX_PEAKS, TimesToIndices(retentionTimes));
}
else
{
var identifiedIndices = TimesToIndices(retentionTimes);
var allPeaks = timeIntervals.Intervals.SelectMany(interval =>
FindIntervalPeaks(interval.Key, interval.Value, identifiedIndices));
RawPeaks = allPeaks.OrderByDescending(peak => Tuple.Create(peak.Identified, peak.Area))
.Take(MAX_PEAKS).ToArray();
}
// Calculate smoothing for later use in extending the Crawdad peaks
IntensitiesSmooth = ChromatogramInfo.SavitzkyGolaySmooth(Intensities.ToArray());
// Accept only peaks within the user-provided RT window, if any
if (explicitRT != null)
{
var winLow = (float)(explicitRT.RetentionTime - 0.5 * (explicitRT.RetentionTimeWindow ?? 0));
var winHigh = winLow + (float)(explicitRT.RetentionTimeWindow ?? 0);
RawPeaks = RawPeaks.Where(rp =>
{
var t = Times[rp.TimeIndex];
return(winLow <= t && t <= winHigh);
});
}
}
public void FindPeaks(double[] retentionTimes)
{
Finder = Crawdads.NewCrawdadPeakFinder();
Finder.SetChromatogram(Times, Intensities);
RawPeaks = Finder.CalcPeaks(MAX_PEAKS, TimesToIndices(retentionTimes));
// Calculate smoothing for later use in extending the Crawdad peaks
IntensitiesSmooth = ChromatogramInfo.SavitzkyGolaySmooth(Intensities.ToArray());
}
public void SetExplicitPeakBounds(ExplicitPeakBounds peakBounds)
{
Finder = Crawdads.NewCrawdadPeakFinder();
Finder.SetChromatogram(Times, Intensities);
if (peakBounds.IsEmpty)
{
RawPeaks = new IFoundPeak[0];
}
else
{
RawPeaks = new[] { Finder.GetPeak(TimeToIndex(peakBounds.StartTime), TimeToIndex(peakBounds.EndTime)) };
}
}
public void FindPeaks(double[] retentionTimes, bool requireDocNode)
{
Finder = Crawdads.NewCrawdadPeakFinder();
Finder.SetChromatogram(Times, Intensities);
if (requireDocNode && DocNode == null)
{
RawPeaks = new IFoundPeak[0];
}
else
{
RawPeaks = Finder.CalcPeaks(MAX_PEAKS, TimesToIndices(retentionTimes));
// Calculate smoothing for later use in extending the Crawdad peaks
IntensitiesSmooth = ChromatogramInfo.SavitzkyGolaySmooth(Intensities.ToArray());
}
}
public static void MakeChromatogramInfo(SignedMz precursorMz, LibraryChromGroup chromGroup, LibraryChromGroup.ChromData chromData, out ChromatogramInfo chromatogramInfo, out TransitionChromInfo transitionChromInfo)
{
var timeIntensities = new TimeIntensities(chromGroup.Times, chromData.Intensities, null, null);
var crawPeakFinder = Crawdads.NewCrawdadPeakFinder();
crawPeakFinder.SetChromatogram(chromGroup.Times, chromData.Intensities);
var crawdadPeak =
crawPeakFinder.GetPeak(
FindNearestIndex(chromGroup.Times, (float)chromGroup.StartTime),
FindNearestIndex(chromGroup.Times, (float)chromGroup.EndTime));
var chromPeak = new ChromPeak(crawPeakFinder, crawdadPeak, 0, timeIntensities, null);
transitionChromInfo = new TransitionChromInfo(null, 0, chromPeak,
IonMobilityFilter.EMPTY, // CONSIDER(bspratt) IMS in chromatogram libraries?
new float?[0], Annotations.EMPTY,
UserSet.FALSE);
var peaks = new[] { chromPeak };
var header = new ChromGroupHeaderInfo(precursorMz,
0, // file index
1, // numTransitions
0, // startTransitionIndex
peaks.Length, // numPeaks
0, // startPeakIndex
0, // startscoreindex
0, // maxPeakIndex
chromGroup.Times.Length, // numPoints
0, // compressedSize
0, // uncompressedsize
0, //location
0, -1, -1, null, null, null, eIonMobilityUnits.none); // CONSIDER(bspratt) IMS in chromatogram libraries?
var driftTimeFilter = IonMobilityFilter.EMPTY; // CONSIDER(bspratt) IMS in chromatogram libraries?
var groupInfo = new ChromatogramGroupInfo(header,
new Dictionary <Type, int>(),
new byte[0],
new ChromCachedFile[0],
new[] { new ChromTransition(chromData.Mz, 0, (float)(driftTimeFilter.IonMobility.Mobility ?? 0), (float)(driftTimeFilter.IonMobilityExtractionWindowWidth ?? 0), ChromSource.unknown), },
peaks,
null)
{
TimeIntensitiesGroup = TimeIntensitiesGroup.Singleton(timeIntensities)
};
chromatogramInfo = new ChromatogramInfo(groupInfo, 0);
}
public void SetExplicitPeakBounds(PeakBounds peakBounds)
{
Finder = Crawdads.NewCrawdadPeakFinder();
Finder.SetChromatogram(Times, Intensities);
RawPeaks = new [] { Finder.GetPeak(TimeToIndex(peakBounds.StartTime), TimeToIndex(peakBounds.EndTime)) };
}
public void SkipFindingPeaks(double[] retentionTimes)
{
Finder = Crawdads.NewCrawdadPeakFinder();
Finder.SetChromatogram(Times, Intensities);
RawPeaks = new IFoundPeak[0];
}
