/// <summary>
/// Builds an in memory retention time index of mass spectra ids.
/// </summary>
public static IMzLiteArray <RtIndexEntry> BuildRtIndex(
this IMzLiteDataReader dataReader,
string runID,
int msLevel = 1)
{
if (dataReader == null)
{
throw new ArgumentNullException("dataReader");
}
if (string.IsNullOrWhiteSpace(runID))
{
throw new ArgumentNullException("runID");
}
IEnumerable <MassSpectrum> massSpectra = dataReader.ReadMassSpectra(runID);
List <RtIndexEntry> entries = new List <RtIndexEntry>();
RtIndexEntry entry;
foreach (var ms in massSpectra)
{
if (TryCreateEntry(ms, msLevel, out entry))
{
entries.Add(entry);
}
}
entries.Sort(new RtIndexEntrySorting());
return(MzLiteArray.ToMzLiteArray(entries));
}
/// <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 static MassSpectrum ReadMassSpectrum(
this IMzLiteDataReader dataReader,
RtIndexEntry entry)
{
if (dataReader == null)
{
throw new ArgumentNullException("dataReader");
}
return(dataReader.ReadMassSpectrum(entry.SpectrumID));
}
public static Peak1DArray ReadSpectrumPeaks(
this IMzLiteDataReader dataReader,
RtIndexEntry entry)
{
if (dataReader == null)
{
throw new ArgumentNullException("dataReader");
}
return(dataReader.ReadSpectrumPeaks(entry.SpectrumID));
}
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 static SWATHIndexer Build(IMzLiteDataReader reader, string runID, Func <MassSpectrum, SWATHIndexerItem> createItem)
{
IList <SWATHIndexerItem> list = new List <SWATHIndexerItem>(65000);
foreach (MassSpectrum ms in reader.ReadMassSpectra(runID))
{
SWATHIndexerItem item = createItem.Invoke(ms);
if (item != null)
{
list.Add(item);
}
}
SWATHIndexer indexer = new SWATHIndexer();
indexer.items = new SWATHIndexerItem[list.Count];
list.CopyTo(indexer.items, 0);
Array.Sort(indexer.items, new ItemSorting());
return(indexer);
}
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));
}
public static SWATHIndexer Build(IMzLiteDataReader reader, string runID)
{
return(Build(reader, runID, CreateItem));
}
