public static void Quantify(this QuantDataCollection quantData, RawDataCollection rawData, IRawDataPlus rawFile, string labelingReagent) { MassAnalyzerType quantAnalyzer = rawData.methodData.QuantAnalyzer; if (quantAnalyzer == MassAnalyzerType.MassAnalyzerFTMS) { rawData.ExtractCentroidStreams(rawFile, rawData.methodData.AnalysisOrder); } else { rawData.ExtractSegmentScans(rawFile, rawData.methodData.AnalysisOrder); } int[] scans; ScanIndex scanIndex = rawData.scanIndex; Dictionary <int, CentroidStreamData> centroidScans = rawData.centroidStreams; Dictionary <int, SegmentedScanData> segmentScans = rawData.segmentedScans; scans = scanIndex.ScanEnumerators[scanIndex.AnalysisOrder]; ProgressIndicator progress = new ProgressIndicator(scans.Length, "Quantifying reporter ions"); quantData.LabelingReagents = labelingReagent; foreach (int scan in scans) { if (quantAnalyzer == MassAnalyzerType.MassAnalyzerFTMS) { quantData.Add(scan, new QuantifyReporters(centroidScans[scan], labelingReagent).quantData); } else { quantData.Add(scan, new QuantifyReporters(segmentScans[scan], labelingReagent).quantData); } progress.Update(); } progress.Done(); rawData.Performed.Add(Operations.Quantification); }
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); } } }