/// <summary>
/// Extract a rt profile for specified target mass and rt range.
/// Mz range peak aggregation is closest lock mz.
/// </summary>
/// <returns>
/// Profile array with index corresponding to continous mass spectra over rt range and mz range given.
/// </returns>
public static Peak2D[] RtProfile(
this IMzLiteDataReader dataReader,
IMzLiteArray <RtIndexEntry> rtIndex,
RangeQuery rtRange,
RangeQuery mzRange)
{
if (dataReader == null)
{
throw new ArgumentNullException("dataReader");
}
if (rtIndex == null)
{
throw new ArgumentNullException("rtIndex");
}
var entries = rtIndex.Search(rtRange).ToArray();
var profile = new Peak2D[entries.Length];
for (int rtIdx = 0; rtIdx < entries.Length; rtIdx++)
{
var entry = entries[rtIdx];
var peaks = dataReader.ReadSpectrumPeaks(entry).Peaks;
var p = peaks.MzSearch(mzRange)
.DefaultIfEmpty(new Peak1D(0, mzRange.LockValue))
.ClosestMz(mzRange.LockValue)
.AsPeak2D(entry.Rt);
profile[rtIdx] = p;
}
return(profile);
}
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);
}
