public static void ExtractRetentionTimes(this RawDataCollection rawData, IRawDataPlus rawFile)
{
if (rawData.Performed.Contains(Operations.RetentionTimes))
{
return;
}
if (!rawData.Performed.Contains(Operations.ScanIndex))
{
rawData.ExtractScanIndex(rawFile);
}
Log.Information("Extracting retention times");
rawData.retentionTimes = new Dictionary <int, double>();
IEnumerable <int> scans = rawData.scanIndex.ScanEnumerators[MSOrderType.Any];
ProgressIndicator progress = new ProgressIndicator(scans.Count(), "Extracting retention times");
foreach (int scan in scans)
{
try
{
rawData.retentionTimes.Add(scan, rawFile.RetentionTimeFromScanNumber(scan));
}
catch (Exception e)
{
Log.Error(e, "Failed during extraction of retention time for scan {Scan}", scan);
throw e;
}
progress.Update();
}
progress.Done();
rawData.Performed.Add(Operations.RetentionTimes);
}
public static void ExtractPrecursorScans(this RawDataCollection rawData, IRawDataPlus rawFile)
{
if (rawData.Performed.Contains(Operations.PrecursorScans))
{
return;
}
if (!rawData.Performed.Contains(Operations.ScanIndex))
{
rawData.ExtractScanIndex(rawFile);
}
Log.Information("Extracting scan dependents/precursor scans");
int ms2Scan = -1;
int ms3Scan = -1;
IEnumerable <int> scans = rawData.scanIndex.ScanEnumerators[MSOrderType.Ms];
ProgressIndicator progress = new ProgressIndicator(scans.Count(), "Indexing linked scan events");
foreach (int scan in scans)
{
var scanDependents = rawFile.GetScanDependents(scan, 4);
// check if the ms1 scan has dependent scans
if (scanDependents == null)
{
continue;
}
for (int i = 0; i < scanDependents.ScanDependentDetailArray.Length; i++)
{
if (rawData.scanIndex.AnalysisOrder == MSOrderType.Ms2) // it is ms2
{
ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
rawData.precursorScans.Add(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
}
else // it is ms3
{
ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
if (rawFile.GetScanDependents(ms2Scan, 4).ScanDependentDetailArray.Length != 0) // make sure there is ms3 data
{
ms3Scan = rawFile.GetScanDependents(ms2Scan, 4).ScanDependentDetailArray[0].ScanIndex;
rawData.precursorScans.Add(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
rawData.precursorScans.Add(ms3Scan, new PrecursorScanData(ms3scan: ms3Scan, ms2Scan: ms2Scan, masterScan: scan));
}
else
{
// there is no ms3 scan, so we only add the ms2 scan
rawData.precursorScans.Add(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
}
}
}
progress.Update();
}
progress.Done();
rawData.Performed.Add(Operations.PrecursorScans);
}
public static void ExtractMethodData(this RawDataCollection rawData, IRawDataPlus rawFile)
{
if (rawData.Performed.Contains(Operations.MethodData))
{
return;
}
if (!rawData.Performed.Contains(Operations.ScanIndex))
{
rawData.ExtractScanIndex(rawFile);
}
Log.Information("Extracting method/instrument information");
rawData.methodData = new Containers.MethodData();
rawData.methodData.AnalysisOrder = rawData.scanIndex.AnalysisOrder;
int firstQuantScan = rawData.scanIndex.ScanEnumerators[rawData.scanIndex.AnalysisOrder][0];
rawData.methodData.QuantAnalyzer = rawData.scanIndex.allScans[firstQuantScan].MassAnalyzer;
int firstMs1Scan = rawData.scanIndex.ScanEnumerators[MSOrderType.Ms][0];
rawData.methodData.MassAnalyzers.Add(MSOrderType.Ms, rawData.scanIndex.allScans[firstMs1Scan].MassAnalyzer);
int firstMs2Scan = rawData.scanIndex.ScanEnumerators[MSOrderType.Ms2][0];
rawData.methodData.MassAnalyzers.Add(MSOrderType.Ms2, rawData.scanIndex.allScans[firstMs2Scan].MassAnalyzer);
rawData.methodData.MSOrderEnumerator.Add(MSOrderType.Ms);
rawData.methodData.MSOrderEnumerator.Add(MSOrderType.Ms2);
int n = rawData.scanIndex.ScanEnumerators[MSOrderType.Ms2].Count();
double ms2window = rawFile.GetScanEventForScanNumber(rawData.scanIndex.ScanEnumerators[MSOrderType.Ms2][n / 2]).GetIsolationWidth(0);
if (rawData.methodData.AnalysisOrder == MSOrderType.Ms3)
{
int firstMs3Scan = rawData.scanIndex.ScanEnumerators[MSOrderType.Ms3][0];
rawData.methodData.MassAnalyzers.Add(MSOrderType.Ms3, rawData.scanIndex.allScans[firstMs3Scan].MassAnalyzer);
rawData.methodData.MSOrderEnumerator.Add(MSOrderType.Ms3);
double ms3ms1window = rawFile.GetScanEventForScanNumber(firstMs3Scan).GetIsolationWidth(0);
double ms3ms2window = rawFile.GetScanEventForScanNumber(firstMs3Scan).GetIsolationWidth(1);
rawData.methodData.IsolationWindow = (MS2 : ms2window, (MS1Window : ms3ms1window, MS2Window : ms3ms2window));
}
else
{
rawData.methodData.IsolationWindow = (MS2 : ms2window, (MS1Window : -1, MS2Window : -1));
}
rawData.Performed.Add(Operations.MethodData);
}
public static void Check(this RawDataCollection rawData, IRawDataPlus rawFile, List <Operations> operations)
{
if (operations.Contains(Operations.MethodData))
{
if (!rawData.Performed.Contains(Operations.MethodData))
{
rawData.ExtractMethodData(rawFile);
}
}
if (operations.Contains(Operations.PrecursorMasses))
{
if (!rawData.Performed.Contains(Operations.PrecursorMasses))
{
rawData.ExtractPrecursorMasses(rawFile);
}
}
if (operations.Contains(Operations.PrecursorScans))
{
if (!rawData.Performed.Contains(Operations.PrecursorScans))
{
rawData.ExtractPrecursorScans(rawFile);
}
}
if (operations.Contains(Operations.RetentionTimes))
{
if (!rawData.Performed.Contains(Operations.RetentionTimes))
{
rawData.ExtractRetentionTimes(rawFile);
}
}
if (operations.Contains(Operations.ScanIndex))
{
if (!rawData.Performed.Contains(Operations.ScanIndex))
{
rawData.ExtractScanIndex(rawFile);
}
}
if (operations.Contains(Operations.TrailerExtras))
{
if (!rawData.Performed.Contains(Operations.TrailerExtras))
{
rawData.ExtractTrailerExtra(rawFile);
}
}
if (operations.Contains(Operations.Ms1CentroidStreams))
{
if (!rawData.Performed.Contains(Operations.Ms1CentroidStreams))
{
rawData.ExtractCentroidStreams(rawFile, MSOrder: MSOrderType.Ms);
}
}
if (operations.Contains(Operations.Ms2CentroidStreams))
{
if (!rawData.Performed.Contains(Operations.Ms2CentroidStreams))
{
rawData.ExtractCentroidStreams(rawFile, MSOrder: MSOrderType.Ms2);
}
}
if (operations.Contains(Operations.Ms3CentroidStreams))
{
if (!rawData.Performed.Contains(Operations.Ms3CentroidStreams))
{
rawData.ExtractCentroidStreams(rawFile, MSOrder: MSOrderType.Ms3);
}
}
if (operations.Contains(Operations.Ms1SegmentedScans))
{
if (!rawData.Performed.Contains(Operations.Ms1SegmentedScans))
{
rawData.ExtractSegmentScans(rawFile, MSOrder: MSOrderType.Ms);
}
}
if (operations.Contains(Operations.Ms2SegmentedScans))
{
if (!rawData.Performed.Contains(Operations.Ms2SegmentedScans))
{
rawData.ExtractSegmentScans(rawFile, MSOrder: MSOrderType.Ms2);
}
}
if (operations.Contains(Operations.Ms3SegmentedScans))
{
if (!rawData.Performed.Contains(Operations.Ms3SegmentedScans))
{
rawData.ExtractSegmentScans(rawFile, MSOrder: MSOrderType.Ms3);
}
}
if (operations.Contains(Operations.MetaData))
{
if (!rawData.Performed.Contains(Operations.MetaData))
{
rawData.metaData.AggregateMetaData(rawData, rawFile);
}
}
if (operations.Contains(Operations.PeakRetAndInt))
{
if (!rawData.Performed.Contains(Operations.PeakRetAndInt))
{
AnalyzePeaks.CalcPeakRetTimesAndInts(rawData, rawFile);
}
}
if (operations.Contains(Operations.PeakShape))
{
if (!rawData.Performed.Contains(Operations.PeakShape))
{
AnalyzePeaks.CalculatePeakShapes(rawData, rawFile);
}
}
if (operations.Contains(Operations.PeakArea))
{
if (!rawData.Performed.Contains(Operations.PeakArea))
{
AnalyzePeaks.QuantifyPrecursorPeaks(rawData, rawFile);
}
}
}
