public static void QcDIA(IRawDataPlus rawFile, WorkflowParameters parameters)
{
rawFile.SelectInstrument(Device.MS, 1);
rawFile.CheckIfBoxcar();
ScanIndex Index = Extract.ScanIndices(rawFile);
MethodDataContainer methodData = Extract.MethodData(rawFile, Index);
CentroidStreamCollection centroidStreams = new CentroidStreamCollection();
SegmentScanCollection segmentScans = new SegmentScanCollection();
(centroidStreams, segmentScans) = Extract.MsData(rawFile: rawFile, index: Index);
TrailerExtraCollection trailerExtras = Extract.TrailerExtras(rawFile, Index);
RetentionTimeCollection retentionTimes = Extract.RetentionTimes(rawFile, Index);
ScanMetaDataCollectionDIA metaData = MetaDataProcessingDIA.AggregateMetaDataDIA(centroidStreams, segmentScans, methodData,
trailerExtras, retentionTimes, Index);
RawMetricsDataDIA metrics = MetaDataProcessingDIA.GetMetricsDataDIA(metaData, methodData, rawFile.FileName, retentionTimes, Index);
QcDataContainer qcData = new QcDataContainer();
qcData.DIA = metrics;
QcDataCollection qcDataCollection = QC.QcWorkflow.LoadOrCreateQcCollection(parameters);
QC.QcWorkflow.UpdateQcCollection(qcDataCollection, qcData, methodData, rawFile.FileName);
}
public static Dictionary <int, double> Top80Frac(CentroidStreamCollection centroidStreams,
SegmentScanCollection segmentScans, ScanIndex index)
{
ConcurrentDictionary <int, double> top80 = new ConcurrentDictionary <int, double>();
int chunkSize = Constants.MultiThreading.ChunkSize(index.allScans.Keys.Count());
var batches = index.allScans.Keys.Chunk(chunkSize);
Parallel.ForEach(batches, Constants.MultiThreading.Options(), batch =>
{
foreach (int scan in batch)
{
if (index.allScans[scan].MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
top80.AddOrUpdate(scan, centroidStreams[scan].Intensities.FractionOfScansConsumingTotalIntensity(percent: 80), (a, b) => b);
}
else
{
top80.AddOrUpdate(scan, segmentScans[scan].Intensities.FractionOfScansConsumingTotalIntensity(percent: 80), (a, b) => b);
}
}
});
var topOut = new Dictionary <int, double>();
foreach (var item in top80)
{
topOut.Add(item.Key, item.Value);
}
return(topOut);
}
public static Dictionary <int, double> SummedIntensities(CentroidStreamCollection centroidStreams,
SegmentScanCollection segmentScans, ScanIndex index)
{
ConcurrentDictionary <int, double> summedInt = new ConcurrentDictionary <int, double>();
int chunkSize = Constants.MultiThreading.ChunkSize(index.allScans.Keys.Count());
var batches = index.allScans.Keys.Chunk(chunkSize);
Parallel.ForEach(batches, Constants.MultiThreading.Options(), batch =>
{
foreach (int scan in batch)
{
if (index.allScans[scan].MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
summedInt.AddOrUpdate(scan, centroidStreams[scan].Intensities.Sum(), (a, b) => b);
}
else
{
summedInt.AddOrUpdate(scan, segmentScans[scan].Intensities.Sum(), (a, b) => b);
}
}
});
var sumsOut = new Dictionary <int, double>();
foreach (var item in summedInt)
{
sumsOut.Add(item.Key, item.Value);
}
return(sumsOut);
}
public static Dictionary <int, Distribution> IntensityDistributions(CentroidStreamCollection centroidStreams,
SegmentScanCollection segmentScans, ScanIndex index)
{
ConcurrentDictionary <int, Distribution> intDist = new ConcurrentDictionary <int, Distribution>();
int chunkSize = Constants.MultiThreading.ChunkSize(index.allScans.Keys.Count());
var batches = index.allScans.Keys.Chunk(chunkSize);
Parallel.ForEach(batches, Constants.MultiThreading.Options(), batch =>
{
foreach (int scan in batch)
{
if (index.allScans[scan].MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
intDist.AddOrUpdate(scan, new Distribution(centroidStreams[scan].Intensities), (a, b) => b);
}
else
{
intDist.AddOrUpdate(scan, new Distribution(segmentScans[scan].Intensities), (a, b) => b);
}
}
});
Dictionary <int, Distribution> distOut = new Dictionary <int, Distribution>();
foreach (var item in intDist)
{
distOut.Add(item.Key, item.Value);
}
return(distOut);
}
public static (CentroidStreamCollection centroids, SegmentScanCollection segments) MsData(IRawDataPlus rawFile, ScanIndex index)
{
rawFile.SelectInstrument(Device.MS, 1);
CentroidStreamCollection centroids = new CentroidStreamCollection();
SegmentScanCollection segments = new SegmentScanCollection();
CentroidStream centroid;
SegmentedScan segment;
var scans = index.allScans;
//var lockTarget = new object(); // this is so we can keep track of progress in the parallel loop
ProgressIndicator P = new ProgressIndicator(scans.Count(), "Extracting scan data");
P.Start();
foreach (int scan in scans.Keys)
{
// first get out the mass spectrum
if (index.allScans[scan].MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
centroid = rawFile.GetCentroidStream(scan, false);
centroids[scan] = new CentroidStreamData(centroid);
}
else
{
segment = rawFile.GetSegmentedScanFromScanNumber(scan, null);
segments[scan] = new SegmentedScanData(segment);
}
//lock (lockTarget)
//{
// P.Update();
//}
P.Update();
}
P.Done();
return(centroids, segments);
}
public static void WriteSearchMGF(WorkflowParameters parameters, CentroidStreamCollection centroids, SegmentScanCollection segments, RetentionTimeCollection retentionTimes,
PrecursorMassCollection precursorMasses, PrecursorScanCollection precursorScans, TrailerExtraCollection trailerExtras, MethodDataContainer methodData,
ScanIndex index, string rawFileName, bool fixedScans = false)
{
var pars = parameters.QcParams.SearchParameters;
int[] scans = AdditionalMath.SelectRandomScans(scans: index.ScanEnumerators[MSOrderType.Ms2],
num: parameters.QcParams.NumberSpectra, fixedScans: parameters.QcParams.FixedScans);
string mgfFile = ReadWrite.GetPathToFile(parameters.QcParams.QcSearchDataDirectory, rawFileName, ".mgf");
MgfWriter.WriteMGF(rawFileName, centroids, segments, parameters, retentionTimes, precursorMasses, precursorScans,
trailerExtras, methodData, index, outputFile: mgfFile, scans: scans);
}
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 ScanMetaDataCollectionDIA AggregateMetaDataDIA(CentroidStreamCollection centroidStreams, SegmentScanCollection segmentScans, MethodDataContainer methodData,
TrailerExtraCollection trailerExtras, RetentionTimeCollection retentionTimes, ScanIndex index, int maxProcesses)
{
//ProgressIndicator progress = new ProgressIndicator(index.ScanEnumerators[MSOrderType.Any].Count(),
// "Formatting scan meta data");
ScanMetaDataCollectionDIA metaData = new ScanMetaDataCollectionDIA();
int[] scans = index.ScanEnumerators[MSOrderType.Any];
double isoWindow = MetaDataCalculations.Ms1IsoWindow(methodData);
Console.WriteLine("Aggregating meta data");
metaData.FillTime = MetaDataCalculations.FillTimes(trailerExtras, index);
metaData.DutyCycle = MetaDataCalculations.DutyCycle(retentionTimes, index);
metaData.IntensityDistribution = MetaDataCalculations.IntensityDistributions(centroidStreams, segmentScans, index, maxProcesses);
metaData.SummedIntensity = MetaDataCalculations.SummedIntensities(centroidStreams, segmentScans, index, maxProcesses);
metaData.FractionConsumingTop80PercentTotalIntensity = MetaDataCalculations.Top80Frac(centroidStreams, segmentScans, index, maxProcesses);
//Task.WaitAll();
return(metaData);
}
public static QuantDataCollection Quantify(CentroidStreamCollection centroidScans, SegmentScanCollection segmentScans, WorkflowParameters parameters, MethodDataContainer methodData, ScanIndex index)
{
int[] scans = index.ScanEnumerators[index.AnalysisOrder];
QuantDataCollection quantData = new QuantDataCollection();
ProgressIndicator progress = new ProgressIndicator(scans.Length, "Quantifying reporter ions");
string labelingReagents = parameters.ParseParams.LabelingReagents;
quantData.LabelingReagents = labelingReagents;
foreach (int scan in scans)
{
if (methodData.QuantAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
quantData.Add(scan, QuantifyReporters.QuantifyOneScan(centroidScans[scan], labelingReagents));
}
else
{
quantData.Add(scan, QuantifyReporters.QuantifyOneScan(segmentScans[scan], labelingReagents));
}
progress.Update();
}
progress.Done();
return(quantData);
}
