private static bool DisplayTypeMatches(LibraryChromGroup.ChromData chromData, DisplayTypeChrom displayType)
{
switch (displayType)
{
case DisplayTypeChrom.products:
return(chromData.IonType != IonType.precursor);
case DisplayTypeChrom.precursors:
return(chromData.IonType == IonType.precursor);
default:
return(true);
}
}
private static bool IonMatches(Transition transition, LibraryChromGroup.ChromData chromData)
{
if (transition.IonType.Equals(chromData.IonType) && transition.Charge == chromData.Charge)
{
if (transition.IsPrecursor())
{
return(transition.MassIndex == chromData.MassIndex);
}
else
{
return(transition.Ordinal == chromData.Ordinal);
}
}
return(false);
}
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 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 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);
}
public static void MakeChromatogramInfo(double precursorMz, LibraryChromGroup chromGroup, LibraryChromGroup.ChromData chromData, out ChromatogramInfo chromatogramInfo, out TransitionChromInfo transitionChromInfo)
{
var crawPeakFinder = new CrawdadPeakFinder();
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 ChromGroupHeaderInfo5(new ChromGroupHeaderInfo(
(float)precursorMz, 0, 1, 0, peaks.Length, 0, 0,
chromGroup.Times.Length, 0, 0));
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);
}
