public static double GetMedianMSFillTime(Dictionary <int, double> FillTimes, ScanIndex Index, MSOrderType MsOrder)
{
return((from x in Index.ScanEnumerators[MsOrder] select FillTimes[x]).ToArray().Percentile(50));
}
public static double GetMedianSummedMSIntensity(Dictionary <int, double> SummedIntensities, ScanIndex Index, MSOrderType MsOrder)
{
return((from x in Index.ScanEnumerators[MsOrder] select SummedIntensities[x]).ToArray().Percentile(50));
}
public static double[] GetFaimsVoltages(Dictionary <int, double> FaimsVoltages, ScanIndex Index, MSOrderType MsOrder)
{
//return (double[])(from x in Index.ScanEnumerators[MsOrder] select FaimsVoltages[x]).ToArray().Distinct();
List <double> faimsVoltageSet = new List <double>();
faimsVoltageSet = (from x in Index.ScanEnumerators[MsOrder] select FaimsVoltages[x]).ToList();
var DistinctFaimsVoltages = faimsVoltageSet.Distinct().ToArray();
return(DistinctFaimsVoltages);
}
public static void ExtractSegmentScans(this RawDataCollection rawData, IRawDataPlus rawFile, MSOrderType MSOrder)
{
if (MSOrder == MSOrderType.Ms)
{
if (rawData.Performed.Contains(Operations.Ms1SegmentedScans))
{
return;
}
}
else
{
if (MSOrder == MSOrderType.Ms2)
{
if (rawData.Performed.Contains(Operations.Ms2SegmentedScans))
{
return;
}
}
else
{
if (rawData.Performed.Contains(Operations.Ms3SegmentedScans))
{
return;
}
}
}
Log.Information("Extracting {MSOrder} segment scans", MSOrder);
IEnumerable <int> scans = rawData.scanIndex.ScanEnumerators[MSOrder];
ProgressIndicator progress = new ProgressIndicator(scans.Count(), string.Format("Extracting {0} segment scans", MSOrder));
try
{
rawData.Extract(rawFile, scans, progress);
}
catch (Exception e)
{
Log.Error(e, "Failed while extracting {MSOrder} segment scans", MSOrder);
throw e;
}
progress.Done();
if (MSOrder == MSOrderType.Ms)
{
rawData.Performed.Add(Operations.Ms1SegmentedScans);
}
else
{
if (MSOrder == MSOrderType.Ms2)
{
rawData.Performed.Add(Operations.Ms2SegmentedScans);
}
else
{
rawData.Performed.Add(Operations.Ms3SegmentedScans);
}
}
}
public override MassSpectrumItem GetInitalSelectedSpectrum(MSOrderType msOrder)
{
return(SelectSpectralTreeNode(m_unknownFeatureIonInstanceItems.First().RetentionTime, msOrder));
}
public static void WriteChromatogram(this RawDataCollection rawData, IRawDataPlus rawFile, MSOrderType order, bool TIC, bool BP, string outputDirectory)
{
List <Operations> operations = new List <Operations>()
{
Operations.RetentionTimes
};
//MSOrderType order = (MSOrderType)msOrder;
MassAnalyzerType analyzer = rawData.methodData.MassAnalyzers[order];
if (analyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
if (order == MSOrderType.Ms)
{
operations.Add(Operations.Ms1CentroidStreams);
}
if (order == MSOrderType.Ms2)
{
operations.Add(Operations.Ms2CentroidStreams);
}
if (order == MSOrderType.Ms3)
{
operations.Add(Operations.Ms3CentroidStreams);
}
}
else
{
if (order == MSOrderType.Ms)
{
operations.Add(Operations.Ms1SegmentedScans);
}
if (order == MSOrderType.Ms2)
{
operations.Add(Operations.Ms2SegmentedScans);
}
if (order == MSOrderType.Ms3)
{
operations.Add(Operations.Ms3SegmentedScans);
}
}
CheckIfDone.Check(rawData, rawFile, operations);
int[] scans = rawData.scanIndex.ScanEnumerators[order];
if (TIC)
{
ProgressIndicator progress = new ProgressIndicator(scans.Length, String.Format("Writing {0} TIC chromatogram", order));
progress.Start();
string fileName = ReadWrite.GetPathToFile(outputDirectory, rawData.rawFileName, "_" + order + "_TIC_chromatogram.txt");
using (StreamWriter f = new StreamWriter(fileName))
{
f.WriteLine("RetentionTime\tIntensity");
if (analyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
foreach (int scan in scans)
{
if (rawData.centroidStreams[scan].Intensities.Length > 0)
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], rawData.centroidStreams[scan].Intensities.Sum());
}
else
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], 0);
}
progress.Update();
}
}
else
{
foreach (int scan in scans)
{
if (rawData.segmentedScans[scan].Intensities.Length > 0)
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], rawData.segmentedScans[scan].Intensities.Sum());
}
else
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], 0);
}
progress.Update();
}
}
}
progress.Done();
}
if (BP)
{
ProgressIndicator progress = new ProgressIndicator(scans.Length, String.Format("Writing {0} base peak chromatogram", order));
progress.Start();
string fileName = ReadWrite.GetPathToFile(outputDirectory, rawData.rawFileName, "_" + order + "_BP_chromatogram.txt");
using (StreamWriter f = new StreamWriter(fileName))
{
f.WriteLine("RetentionTime\tIntensity");
if (analyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
foreach (int scan in scans)
{
if (rawData.centroidStreams[scan].Intensities.Length > 0)
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], rawData.centroidStreams[scan].Intensities.Max());
}
else
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], 0);
}
progress.Update();
}
}
else
{
foreach (int scan in scans)
{
if (rawData.segmentedScans[scan].Intensities.Length > 0)
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], rawData.segmentedScans[scan].Intensities.Max());
}
else
{
f.WriteLine("{0}\t{1}", rawData.retentionTimes[scan], 0);
}
progress.Update();
}
}
}
progress.Done();
}
}
public override MassSpectrumItem GetInitalSelectedSpectrum(MSOrderType msOrder)
{
return SelectSpectralTreeNode(m_unknownFeatureIonInstanceItems.First().RetentionTime, msOrder);
}
