public bool IsValidFilter(string filter)
{
if (rawFile.GetFilterFromString(filter) == null)
{
return(false);
}
return(true);
}
private static bool IsValidFilter(IRawDataPlus rawFile, string filter)
{
if (rawFile.GetFilterFromString(filter) == null)
{
return(false);
}
return(true);
}
public static ScanIndex ScanIndices(IRawDataPlus rawFile)
{
rawFile.SelectInstrument(Device.MS, 1);
Log.Information("Extracting scan indices");
Dictionary <int, ScanData> allScans;
allScans = new Dictionary <int, ScanData>();
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
ProgressIndicator P = new ProgressIndicator(scans.Count(), "Extracting scan indices");
foreach (int scan in scans)
{
IScanEvent scanEvent = rawFile.GetScanEventForScanNumber(scan);
ScanData scanData = new ScanData();
scanData.MassAnalyzer = scanEvent.MassAnalyzer;
scanData.MSOrder = scanEvent.MSOrder;
allScans.Add(scan, scanData);
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);
}
P.Update();
}
P.Done();
// 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;
}
}
ScanIndex scanIndex = new ScanIndex();
scanIndex.allScans = allScans;
scanIndex.AnalysisOrder = AnalysisOrder;
scanIndex.ScanEnumerators.Add(MSOrderType.Any, msAny.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms, ms1.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms2, ms2.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms3, ms3.ToArray());
return(scanIndex);
}
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();
}
}
