public static ScanEventReactionCollection ScanEvents(IRawDataPlus rawFile, ScanIndex index)
{
if (index.AnalysisOrder == MSOrderType.Ms)
{
Console.WriteLine("This is not an Orbitrap file. Skipping reaction event extraction.");
return(null);
}
else
{
rawFile.SelectMsData();
ScanEventReactionCollection events = new ScanEventReactionCollection();
Log.Information("Extracting scan events");
ProgressIndicator P = new ProgressIndicator(index.ScanEnumerators[MSOrderType.Any].Length, "Extracting reaction events");
P.Start();
foreach (int scan in index.ScanEnumerators[index.AnalysisOrder])
{
events.Add(scan, rawFile.GetScanEventForScanNumber(scan).GetReaction(0));
P.Update();
}
P.Done();
return(events);
}
}
public static ScanEventReactionCollection ScanEvents(IRawDataPlus rawFile, ScanIndex index)
{
rawFile.SelectMsData();
ScanEventReactionCollection events = new ScanEventReactionCollection();
Log.Information("Extracting scan events");
ProgressIndicator P = new ProgressIndicator(index.ScanEnumerators[MSOrderType.Any].Length, "Extracting reaction events");
P.Start();
foreach (int scan in index.ScanEnumerators[index.AnalysisOrder])
{
events.Add(scan, rawFile.GetScanEventForScanNumber(scan).GetReaction(0));
P.Update();
}
P.Done();
return(events);
}
public static ScanMetaDataCollectionDDA AggregateMetaDataDDA(CentroidStreamCollection centroidStreams, SegmentScanCollection segmentScans, MethodDataContainer methodData,
PrecursorScanCollection precursorScans, TrailerExtraCollection trailerExtras, PrecursorMassCollection precursorMasses,
RetentionTimeCollection retentionTimes, ScanDependentsCollections scanDependents, ScanEventReactionCollection reactions, ScanIndex index)
{
//ProgressIndicator progress = new ProgressIndicator(index.ScanEnumerators[MSOrderType.Any].Count(),
// "Formatting scan meta data");
ScanMetaDataCollectionDDA metaData = new ScanMetaDataCollectionDDA();
int[] scans = index.ScanEnumerators[MSOrderType.Any];
double isoWindow = MetaDataCalculations.Ms1IsoWindow(methodData);
Console.WriteLine("Calculating meta data");
Console.WriteLine(" MS1 isolation interference");
metaData.Ms1IsolationInterference = MetaDataCalculations.Ms1Interference(centroidStreams, precursorMasses, trailerExtras,
precursorScans, reactions, index);
Console.WriteLine(" MS2 scan cycle density");
metaData.MS2ScansPerCycle = MetaDataCalculations.MS2ScansPerCycle(scanDependents, index);
Console.WriteLine(" Ion injection time");
metaData.FillTime = MetaDataCalculations.FillTimes(trailerExtras, index);
Console.WriteLine(" Duty cycle");
metaData.DutyCycle = MetaDataCalculations.DutyCycle(retentionTimes, index);
Console.WriteLine(" Intensity distribution");
metaData.IntensityDistribution = MetaDataCalculations.IntensityDistributions(centroidStreams, segmentScans, index);
Console.WriteLine(" Summed intensities");
metaData.SummedIntensity = MetaDataCalculations.SummedIntensities(centroidStreams, segmentScans, index);
metaData.FractionConsumingTop80PercentTotalIntensity = MetaDataCalculations.Top80Frac(centroidStreams, segmentScans, index);
//Task.WaitAll();
return(metaData);
}
public static Dictionary <int, double> Ms1Interference(CentroidStreamCollection centroidStreams, PrecursorMassCollection precursorMasses,
TrailerExtraCollection trailerExtras, PrecursorScanCollection precursorScans, ScanEventReactionCollection reactions, ScanIndex index)
{
ConcurrentDictionary <int, double> interference = new ConcurrentDictionary <int, double>();
int chunkSize = Constants.MultiThreading.ChunkSize(index.ScanEnumerators[index.AnalysisOrder].Count());
var batches = index.ScanEnumerators[index.AnalysisOrder].Chunk(chunkSize);
Parallel.ForEach(batches, Constants.MultiThreading.Options(), batch =>
{
foreach (int scan in batch)
{
int preScan = precursorScans[scan].MasterScan;
interference.AddOrUpdate(scan, Algorithms.Ms1Interference.CalculateForOneScan(centroidStreams[preScan], reactions[scan],
precursorMasses[scan].MonoisotopicMZ, trailerExtras[scan].ChargeState), (a, b) => b);
}
});
var interferenceOut = new Dictionary <int, double>();
foreach (var item in interference)
{
interferenceOut.Add(item.Key, item.Value);
}
return(interferenceOut);
}
