DependentsAndPrecursorScansByScanDependents(IRawDataPlus rawFile, ScanIndex index)
{
rawFile.SelectInstrument(Device.MS, 1);
Log.Information("Extracting scan dependents/precursor scans");
PrecursorScanCollection precursorScans = new PrecursorScanCollection();
ScanDependentsCollections dependents = new ScanDependentsCollections();
int ms2Scan = -1;
int ms3Scan = -1;
IEnumerable <int> scans = index.ScanEnumerators[MSOrderType.Ms];
ProgressIndicator progress = new ProgressIndicator(scans.Count(), "Indexing linked scan events");
foreach (int scan in scans)
{
var scanDependents = rawFile.GetScanDependents(scan, 4);
dependents[scan] = scanDependents;
// check if the ms1 scan has dependent scans
if (scanDependents == null)
{
continue;
}
for (int i = 0; i < scanDependents.ScanDependentDetailArray.Length; i++)
{
if (index.AnalysisOrder == MSOrderType.Ms2) // it is ms2
{
ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
precursorScans[ms2Scan] = new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan);
}
else // it is ms3
{
ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
var ms2Dependents = rawFile.GetScanDependents(ms2Scan, 4).ScanDependentDetailArray;
if (ms2Dependents.Length != 0) // make sure there is ms3 data
{
ms3Scan = ms2Dependents[0].ScanIndex;
precursorScans[ms2Scan] = new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan);
precursorScans[ms3Scan] = new PrecursorScanData(ms3scan: ms3Scan, ms2Scan: ms2Scan, masterScan: scan);
}
else
{
// there is no ms3 scan, so we only add the ms2 scan
precursorScans[ms2Scan] = new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan);
}
}
}
progress.Update();
}
progress.Done();
return(precursorScans, dependents);
}
public static ScanDependentsCollections ScanDependents(IRawDataPlus rawFile, ScanIndex index)
{
rawFile.SelectInstrument(Device.MS, 1);
ScanDependentsCollections scanDependents = new ScanDependentsCollections();
foreach (int scan in index.ScanEnumerators[MSOrderType.Ms])
{
scanDependents[scan] = rawFile.GetScanDependents(scan, 4);
}
return(scanDependents);
}
public static Dictionary <int, int> MS2ScansPerCycle(ScanDependentsCollections scanDependents, ScanIndex index)
{
Dictionary <int, int> mS2ScansPerCycle = new Dictionary <int, int>();
foreach (int scan in index.ScanEnumerators[MSOrderType.Ms])
{
// if the ms1 scan has no scan dependents then topN = 0
if (scanDependents[scan] == null)
{
mS2ScansPerCycle.Add(scan, 0);
}
else
{
mS2ScansPerCycle.Add(scan, scanDependents[scan].ScanDependentDetailArray.Length);
}
}
return(mS2ScansPerCycle);
}
DependentsAndPrecursorScansByScanDependentsParallel(IRawFileThreadManager rawFileManager, ScanIndex index)
{
//rawFile.SelectInstrument(Device.MS, 1);
Log.Information("Extracting scan dependents/precursor scans");
ConcurrentDictionary <int, PrecursorScanData> precursorScans = new ConcurrentDictionary <int, PrecursorScanData>();
ConcurrentDictionary <int, IScanDependents> dependents = new ConcurrentDictionary <int, IScanDependents>();
//Dictionary<int, PrecursorScanData> precursorScans = new Dictionary<int, PrecursorScanData>();
//Dictionary<int, IScanDependents> dependents = new Dictionary<int, IScanDependents>();
//ConcurrentBag<(int scan, PrecursorScanData data)> precursorBag = new ConcurrentBag<(int scan, PrecursorScanData data)>();
//ConcurrentBag<(int scan, IScanDependents data)> dependentsBag = new ConcurrentBag<(int scan, IScanDependents data)>();
var updateProgressLock = new object();
var addLockTarget = new object();
IEnumerable <int> scans = index.ScanEnumerators[MSOrderType.Ms];
ProgressIndicator progress = new ProgressIndicator(scans.Count(), "Indexing linked scan events");
var batches = scans.Chunk(Constants.MultiThreading.ChunkSize(scans.Count()));
Parallel.ForEach(batches, Constants.MultiThreading.Options(), batch =>
{
int ms2Scan = -1;
int ms3Scan = -1;
IScanDependents scanDependents;
var rawFile = rawFileManager.CreateThreadAccessor();
rawFile.SelectInstrument(Device.MS, 1);
foreach (int scan in batch)
{
scanDependents = rawFile.GetScanDependents(scan, 2);
dependents.AddOrUpdate(scan, scanDependents, (a, b) => b);
// check if the ms1 scan has dependent scans
if (scanDependents == null)
{
return;
}
for (int i = 0; i < scanDependents.ScanDependentDetailArray.Length; i++)
{
if (index.AnalysisOrder == MSOrderType.Ms2) // it is ms2
{
ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
//precursorScans.AddOrUpdate(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan), (a, b) => b);
precursorScans.TryAdd(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
}
else // it is ms3
{
ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
var ms2Dependents = rawFile.GetScanDependents(ms2Scan, 2).ScanDependentDetailArray;
if (ms2Dependents.Length != 0) // make sure there is ms3 data
{
ms3Scan = ms2Dependents[0].ScanIndex;
precursorScans.AddOrUpdate(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan), (a, b) => b);
precursorScans.AddOrUpdate(ms3Scan, new PrecursorScanData(ms3scan: ms3Scan, ms2Scan: ms2Scan, masterScan: scan), (a, b) => b);
}
else
{
// there is no ms3 scan, so we only add the ms2 scan
precursorScans.AddOrUpdate(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan), (a, b) => b);
}
}
}
lock (updateProgressLock)
{
progress.Update();
}
}
});
progress.Done();
var outScans = new PrecursorScanCollection();
var outDependents = new ScanDependentsCollections();
foreach (var item in precursorScans)
{
outScans.Add(item.Key, item.Value);
}
foreach (var item in dependents)
{
outDependents.Add(item.Key, item.Value);
}
// check for missing precursor information
/*
* foreach (int scan in index.ScanEnumerators[MSOrderType.Ms2])
* {
* if (outScans.Keys.Contains(scan))
* {
* outScans.HasPrecursorData.Add(scan, true);
* }
* else
* {
* outScans.HasPrecursorData.Add(scan, false);
* }
* }*/
return(outScans, outDependents);
}
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);
}
