Exemple #1
0
        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());
        }
Exemple #2
0
        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());
        }