public static void ExtractAll(this RawDataCollection rawData, IRawDataPlus rawFile)
{
Log.Information("Beginning extraction of all possible data");
rawFile.SelectInstrument(Device.MS, 1);
rawData.ExtractPrecursorScans(rawFile);
ProgressIndicator P = new ProgressIndicator(rawData.scanIndex.allScans.Count(), "Extracting raw data");
TrailerExtraIndices indices = new TrailerExtraIndices(rawFile);
for (int i = 1; i <= rawData.scanIndex.allScans.Count(); i++)
{
try
{
// first get out the mass spectrum
if (rawData.scanIndex.allScans[i].MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
rawData.centroidStreams.Add(i, new CentroidStreamData(rawFile.GetCentroidStream(i, false)));
}
else
{
rawData.segmentedScans.Add(i, new SegmentedScanData(rawFile.GetSegmentedScanFromScanNumber(i, null)));
}
// add the trailer extra data
rawData.trailerExtras.Add(i, TrailerExtras.ExtractTrailerExtra(rawData, rawFile, i, indices));
rawData.Performed.Add(Operations.TrailerExtras);
// add the retention time
rawData.retentionTimes.Add(i, rawFile.RetentionTimeFromScanNumber(i));
rawData.Performed.Add(Operations.RetentionTimes);
// add the precursor mass
PrecursorMasses.ExtractPrecursorMasses(rawData, rawFile, i);
rawData.Performed.Add(Operations.PrecursorMasses);
P.Update();
}
catch (Exception e)
{
Log.Error("Extraction failed on scan {Scan}", i);
throw e;
}
}
if (rawData.methodData.AnalysisOrder == MSOrderType.Ms2 | rawData.methodData.AnalysisOrder == MSOrderType.Ms3)
{
rawData.Performed.Add(Operations.Ms1CentroidStreams);
if (rawData.methodData.MassAnalyzers[MSOrderType.Ms2] == MassAnalyzerType.MassAnalyzerFTMS)
{
rawData.Performed.Add(Operations.Ms2CentroidStreams);
}
else
{
rawData.Performed.Add(Operations.Ms2SegmentedScans);
}
}
if (rawData.methodData.AnalysisOrder == MSOrderType.Ms3)
{
if (rawData.methodData.MassAnalyzers[MSOrderType.Ms3] == MassAnalyzerType.MassAnalyzerFTMS)
{
rawData.Performed.Add(Operations.Ms3CentroidStreams);
}
else
{
rawData.Performed.Add(Operations.Ms3SegmentedScans);
}
}
P.Done();
}
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);
}
}
}
public static void ExtractScanIndex(this RawDataCollection rawData, IRawDataPlus rawFile)
{
Log.Information("Extracting scan indices");
Dictionary <int, (MSOrderType MSOrder, MassAnalyzerType MassAnalyzer)> allScans;
allScans = new Dictionary <int, (MSOrderType MSOrder, MassAnalyzerType MassAnalyzer)>();
MSOrderType AnalysisOrder;
List <int> ms1 = new List <int>();
List <int> ms2 = new List <int>();
List <int> ms3 = new List <int>();
List <int> msAny = new List <int>();
// populate the scan indices
IEnumerable <int> scans = rawFile.GetFilteredScanEnumerator(rawFile.GetFilterFromString("")); // get all scans
foreach (int scan in scans)
{
IScanEvent scanEvent = rawFile.GetScanEventForScanNumber(scan);
allScans.Add(scan, (scanEvent.MSOrder, scanEvent.MassAnalyzer));
msAny.Add(scan);
if (allScans[scan].MSOrder == MSOrderType.Ms)
{
ms1.Add(scan);
}
if (allScans[scan].MSOrder == MSOrderType.Ms2)
{
ms2.Add(scan);
}
if (allScans[scan].MSOrder == MSOrderType.Ms3)
{
ms3.Add(scan);
}
}
// determine the msorder of the experiment
if ((ms1.Count > 0) & (ms2.Count == 0) & (ms3.Count == 0))
{
AnalysisOrder = MSOrderType.Ms;
}
else
{
if ((ms1.Count > 0) & (ms2.Count > 0) & (ms3.Count == 0))
{
AnalysisOrder = MSOrderType.Ms2;
}
else
{
AnalysisOrder = MSOrderType.Ms3;
}
}
rawData.scanIndex = new ScanIndex();
rawData.scanIndex.allScans = allScans;
rawData.scanIndex.AnalysisOrder = AnalysisOrder;
rawData.scanIndex.ScanEnumerators.Add(MSOrderType.Any, msAny.ToArray());
rawData.scanIndex.ScanEnumerators.Add(MSOrderType.Ms, ms1.ToArray());
rawData.scanIndex.ScanEnumerators.Add(MSOrderType.Ms2, ms2.ToArray());
rawData.scanIndex.ScanEnumerators.Add(MSOrderType.Ms3, ms3.ToArray());
// we need to check if it is a boxcar file because those have some scan index issues
bool isBoxCar = rawFile.GetScanEventForScanNumber(1).MassRangeCount > 1;
rawData.Performed.Add(Operations.ScanIndex);
if (isBoxCar)
{
Log.Information("Raw file looks like a boxcar run. Scan indices being adjusted to account for missing scan dependents.");
rawData.ExtractPrecursorScans(rawFile);
rawData.scanIndex.ScanEnumerators[rawData.scanIndex.AnalysisOrder] = rawData.precursorScans.Keys.ToArray();
}
}
