public Dictionary <string, dynamic> GenerateMetrics(Run <Scan> run, int division, bool irt)
{
Run = run;
if (run.LastScanTime != 0 && run.StartTime != 1000000)
{
//Acquire RTDuration: last minus first
RTDuration = run.LastScanTime - run.StartTime;
}
else
{
Logger.Error("StartTime {0} or lastScanTime {0} for the run is null. RTDuration is therefore zero", run.StartTime, run.LastScanTime);
RTDuration = 0;
}
//Interpolate, Smooth, create chromatogram and generate chromatogram metrics
ChromatogramMetricGenerator chromatogramMetrics = new ChromatogramMetricGenerator();
chromatogramMetrics.GenerateChromatogram(run);
if (irt)
{
chromatogramMetrics.GenerateiRTChromatogram(run);
}
//Calculating the largestswath
if (run.Ms2Scans.Max(x => x.IsolationWindowUpperOffset) == 100000 || run.Ms2Scans.Max(x => x.IsolationWindowLowerOffset) == 100000)
{
Logger.Error(("IsolationWindowUpperOffset {0} or IsolationWindowLowerOffset {0} for the one of the scans has not been changed from default value. swathSizeDifference is therefore zero", run.Ms2Scans.Max(x => x.IsolationWindowUpperOffset), run.Ms2Scans.Max(x => x.IsolationWindowLowerOffset)));
swathSizeDifference = 0;
}
else
{
swathSizeDifference = run.Ms2Scans.Max(x => x.IsolationWindowUpperOffset + x.IsolationWindowLowerOffset) - run.Ms2Scans.Min(x => x.IsolationWindowUpperOffset + x.IsolationWindowLowerOffset);
}
// This method will group the scans into swaths of the same number, return the number of swaths in a full cycle (maxswath) and call a FileMaker method to write out the metrics.
SwathGrouper swathGrouper = new SwathGrouper {
};
SwathMetrics = swathGrouper.GroupBySwath(run);
//Retrieving Density metrics
Density = run.Ms2Scans.OrderBy(g => g.Density).Select(g => g.Density).ToList();
RTGrouper rtGrouper = new RTGrouper {
};
RtMetrics = rtGrouper.DivideByRT(run, division, RTDuration);
return(AssembleMetrics());
}
public Dictionary <string, dynamic> GenerateMetrics(Run run, int division, string inputFilePath, bool irt, bool combine, bool lastFile, string date)
{
Run = run;
if (run.LastScanTime != 0 && run.StartTime != 1000000)
{
//Acquire RTDuration: last minus first
RTDuration = run.LastScanTime - run.StartTime;
}
else
{
Logger.Error("StartTime {0} or lastScanTime {0} for the run is null. RTDuration is therefore zero", run.StartTime, run.LastScanTime);
RTDuration = 0;
}
//Interpolate, Smooth, create chromatogram and generate chromatogram metrics
ChromatogramMetricGenerator chromatogramMetrics = new ChromatogramMetricGenerator();
chromatogramMetrics.GenerateChromatogram(run);
if (irt)
{
chromatogramMetrics.GenerateiRTChromatogram(run);
}
//Calculating the largestswath
if (run.Ms2Scans.Max(x => x.IsolationWindowUpperOffset) == 100000 || run.Ms2Scans.Max(x => x.IsolationWindowLowerOffset) == 100000)
{
Logger.Error(("IsolationWindowUpperOffset {0} or IsolationWindowLowerOffset {0} for the one of the scans has not been changed from default value. swathSizeDifference is therefore zero", run.Ms2Scans.Max(x => x.IsolationWindowUpperOffset), run.Ms2Scans.Max(x => x.IsolationWindowLowerOffset)));
swathSizeDifference = 0;
}
else
{
swathSizeDifference = run.Ms2Scans.Max(x => x.IsolationWindowUpperOffset + x.IsolationWindowLowerOffset) - run.Ms2Scans.Min(x => x.IsolationWindowUpperOffset + x.IsolationWindowLowerOffset);
}
// This method will group the scans into swaths of the same number, return the number of swaths in a full cycle (maxswath) and call a FileMaker method to write out the metrics.
SwathGrouper swathGrouper = new SwathGrouper {
};
SwathMetrics = swathGrouper.GroupBySwath(run);
//Retrieving Density metrics
Density = run.Ms2Scans.OrderBy(g => g.Density).Select(g => g.Density).ToList();
RTGrouper rtGrouper = new RTGrouper {
};
RtMetrics = rtGrouper.DivideByRT(run, division, RTDuration);
FileMaker fileMaker = new FileMaker(division, inputFilePath, run, SwathMetrics, RtMetrics, RTDuration, swathSizeDifference, run.Ms2Scans.Count(), Density.Sum(), Density.ElementAt(Density.Count() / 2), InterQuartileRangeCalculator.CalcIQR(Density), run.Ms1Scans.Count(), date);
fileMaker.MakeComprehensiveMetricsFile();
if (run.IRTPeaks != null && run.IRTPeaks.Count() > 0)
{
fileMaker.MakeiRTmetricsFile(run);
}
fileMaker.MakeMetricsPerRTsegmentFile(RtMetrics);
fileMaker.MakeMetricsPerSwathFile(SwathMetrics);
if (combine && lastFile)
{
if (run.IRTPeaks != null && run.IRTPeaks.Count() > 0)
{
string[] iRTFilename = { "AllIRTMetrics_", date, ".tsv" };
fileMaker.CombineMultipleFilesIntoSingleFile(date + "_iRTMetrics_*", string.Join("", iRTFilename));
}
string[] swathFilename = { "AllMetricsBySwath_", date, ".tsv" };
string[] rtFilename = { "AllRTDividedMetrics_", date, ".tsv" };
string[] ComprehensiveFilename = { "AllComprehensiveMetrics_", date, ".tsv" };
fileMaker.CheckOutputDirectory(inputFilePath);
fileMaker.CombineMultipleFilesIntoSingleFile(date + "_MetricsBySwath_*", string.Join("", swathFilename));
fileMaker.CombineMultipleFilesIntoSingleFile(date + "_RTDividedMetrics_*", string.Join("", rtFilename));
fileMaker.CombineMultipleFilesIntoSingleFile(date + "_ComprehensiveMetrics_*", string.Join("", ComprehensiveFilename));
}
return(AssembleMetrics());
}
