private static int RtRangeCompare(SwathSpectrumEntry item, SwathQuery query)
{
if (item.Rt < query.RtRange.LowValue)
{
return(-1);
}
if (item.Rt > query.RtRange.HighValue)
{
return(1);
}
return(0);
}
public Peak2D[] GetMS2(
IMzLiteDataReader dataReader,
SwathQuery query,
Func <IEnumerable <Peak1D>, RangeQuery, Peak1D> mzRangeSelector = null)
{
if (dataReader == null)
{
throw new ArgumentNullException("dataReader");
}
if (query == null)
{
throw new ArgumentNullException("query");
}
if (mzRangeSelector == null)
{
mzRangeSelector = GetClosestMz;
}
MSSwath swath = swathList.SearchClosestTargetMz(query);
if (swath == null)
{
return(new Peak2D[0]);
}
SwathSpectrumEntry swathSpec = swath.SearchClosestRt(query);
if (swathSpec == null)
{
return(new Peak2D[0]);
}
Peak1DArray spectrumPeaks = dataReader.ReadSpectrumPeaks(swathSpec.SpectrumID);
Peak2D[] ms2Peaks = new Peak2D[query.CountMS2Masses];
for (int i = 0; i < query.CountMS2Masses; i++)
{
RangeQuery mzRange = query[i];
IEnumerable <Peak1D> mzPeaks = BinarySearch.Search(spectrumPeaks.Peaks, mzRange, MzRangeCompare);
Peak1D p = mzRangeSelector(mzPeaks, mzRange);
ms2Peaks[i] = new Peak2D(p.Intensity, p.Mz, swathSpec.Rt);
}
return(ms2Peaks);
}
private static bool TryCreateSwathSpectrum(MassSpectrum ms, out SwathSpectrumEntry sws)
{
sws = null;
int msLevel;
if (!ms.TryGetMsLevel(out msLevel) || msLevel != 2)
{
return(false);
}
if (ms.Precursors.Count < 1 ||
ms.Precursors[0].SelectedIons.Count < 1 ||
ms.Scans.Count < 1)
{
return(false);
}
double rt, mz, mzLow, mzHeigh;
var isoWin = ms.Precursors[0].IsolationWindow;
var scan = ms.Scans[0];
if (scan.TryGetScanStartTime(out rt) &&
isoWin.TryGetIsolationWindowTargetMz(out mz) &&
isoWin.TryGetIsolationWindowLowerOffset(out mzLow) &&
isoWin.TryGetIsolationWindowUpperOffset(out mzHeigh))
{
sws = new SwathSpectrumEntry(
ms.ID,
mz,
mz - mzLow,
mz + mzHeigh,
rt);
return(true);
}
else
{
return(false);
}
}
public static SwathIndexer Create(IMzLiteDataReader dataReader, string runID)
{
if (dataReader == null)
{
throw new ArgumentNullException("dataReader");
}
if (string.IsNullOrWhiteSpace(runID))
{
throw new ArgumentNullException("runID");
}
var spectra = SwathSpectrumEntry.Scan(dataReader.ReadMassSpectra(runID));
var groups = spectra.GroupBy(x => x.SwathWindow, new SwathWindowGroupingComparer()).ToArray();
var swathes = new MSSwath[groups.Length];
for (int i = 0; i < groups.Length; i++)
{
swathes[i] = new MSSwath(groups[i].Key, groups[i].ToArray());
}
SwathList swathList = new SwathList(swathes);
return(new SwathIndexer(swathList));
}
private static double CalcLockRtDiffAbs(SwathSpectrumEntry swathSpectrum, SwathQuery query)
{
return(Math.Abs(swathSpectrum.Rt - query.RtRange.LockValue));
}