/// <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);
}
/// <summary>
/// Get all peaks by rt range.
/// </summary>
public static IEnumerable <TPeak> RtSearch <TPeak>(
this IMzLiteArray <TPeak> peaks,
RangeQuery rtRange) where TPeak : Peak2D
{
if (peaks == null)
{
throw new ArgumentNullException("peaks");
}
return(BinarySearch.Search(peaks, rtRange, RtSearchCompare));
}
/// <summary>
/// Get all rt index entries by rt range.
/// </summary>
public static IEnumerable <RtIndexEntry> Search(
this IMzLiteArray <RtIndexEntry> rti,
RangeQuery rtRange)
{
if (rti == null)
{
throw new ArgumentNullException("rti");
}
return(BinarySearch.Search(rti, rtRange, RtSearchCompare));
}
public SwathQuery(double targetMz, RangeQuery rtRange, params RangeQuery[] ms2Masses)
{
if (ms2Masses == null)
{
throw new ArgumentNullException("ms2Masses");
}
this.targetMz = targetMz;
this.rtRange = rtRange;
this.ms2Masses = ms2Masses;
}
private static int MzRangeCompare(Peak1D p, RangeQuery mzRange)
{
if (p.Mz < mzRange.LowValue)
{
return(-1);
}
if (p.Mz > mzRange.HighValue)
{
return(1);
}
return(0);
}
private static int RtSearchCompare <TPeak>(
TPeak p,
RangeQuery rtRange)
where TPeak : Peak2D
{
if (p.Rt < rtRange.LowValue)
{
return(-1);
}
if (p.Rt > rtRange.HighValue)
{
return(1);
}
return(0);
}
private static int MzSearchCompare <TPeak>(
TPeak p,
RangeQuery mzRange)
where TPeak : Peak1D
{
if (p.Mz < mzRange.LowValue)
{
return(-1);
}
if (p.Mz > mzRange.HighValue)
{
return(1);
}
return(0);
}
private static int RtSearchCompare(
RtIndexEntry entry,
RangeQuery rtRange)
{
if (entry.Rt < rtRange.LowValue)
{
return(-1);
}
if (entry.Rt > 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);
}
//public Peak2D[,] GetRTProfiles(
// IMzLiteDataReader dataReader,
// SwathQuery query,
// bool getLockMz,
// Func<Peak1DArray, RangeQuery, Peak1D> mzRangeSelector)
//{
// var swathSpectra = swathList.SearchAllTargetMz(query)
// .SelectMany(x => x.SearchAllRt(query))
// .ToArray();
// if (swathSpectra.Length > 0)
// {
// Peak2D[,] profile = new Peak2D[query.CountMS2Masses, swathSpectra.Length];
// for (int specIdx = 0; specIdx < swathSpectra.Length; specIdx++)
// {
// var swathSpec = swathSpectra[specIdx];
// var pa = dataReader.ReadSpectrumPeaks(swathSpec.SpectrumID);
// for (int ms2MassIndex = 0; ms2MassIndex < query.CountMS2Masses; ms2MassIndex++)
// {
// RangeQuery mzRange = query[ms2MassIndex];
// Peak1D p = mzRangeSelector(pa, mzRange);
// if (getLockMz)
// {
// profile[ms2MassIndex, specIdx] = new Peak2D(p.Intensity, mzRange.LockValue, swathSpec.Rt);
// }
// else
// {
// profile[ms2MassIndex, specIdx] = new Peak2D(p.Intensity, p.Mz, swathSpec.Rt);
// }
// }
// }
// return profile;
// }
// else
// {
// return empty2D;
// }
//}
/// <summary>
/// The default mz range peak selector function.
/// </summary>
private static Peak1D GetClosestMz(IEnumerable <Peak1D> peaks, RangeQuery mzRange)
{
return(peaks
.DefaultIfEmpty(new Peak1D(0, mzRange.LockValue))
.ItemAtMin(x => Math.Abs(x.Mz - mzRange.LockValue)));
}
