/*
+ "\t" + scanStatistics.TIC.ToString()
+ "\t" + scanStatistics.ScanType.ToString()
+ "\t" + scanStatistics.CycleNumber.ToString()
+ "\t" + scanStatistics.Frequency.ToString()
+ "\t" + scanStatistics.HighMass.ToString()
+ "\t" + scanFilter.IonizationMode.ToString()
+ "\t" + scanFilter.MSOrder.ToString()
+ "\t" + scanFilter.MassAnalyzer.ToString()
+ "\t" + scanFilter.Detector.ToString()
+ "\t" + scanFilter.Lock.ToString() + "\t");
+
+ try
+ {
+ var reaction0 = scanEvent.GetReaction(0);
+ file.Write(reaction0.PrecursorMass
+ "\t" + reaction0.LastPrecursorMass
+ "\t" + reaction0.CollisionEnergy
+ "\t" + reaction0.IsolationWidth
+ );
+ }
+ catch
+ {
+ file.Write("NA\tNA\tNA\tNA");
+ }
+
+
*/
/// <summary>
/// write file header (metainfo) into R code
/// </summary>
public static void PrintHeaderAsRcode(this IRawDataPlus rawFile, string filename)
{
using (System.IO.StreamWriter file =
new System.IO.StreamWriter(filename))
{
file.WriteLine("#R\n\n");
file.WriteLine("e$info <- list()\n");
file.WriteLine("e$info$`RAW file` <- '" + Path.GetFileName(rawFile.FileName) + "'");
file.WriteLine("e$info$`RAW file version` <- '" + rawFile.FileHeader.Revision + "'");
file.WriteLine("e$info$`Creation date` <- '" + rawFile.FileHeader.CreationDate + "'");
file.WriteLine("e$info$Operator <- '" + rawFile.FileHeader.WhoCreatedId + "'");
file.WriteLine("e$info$`Number of instruments` <- {0}", rawFile.InstrumentCount);
file.WriteLine("e$info$Description <- '" + rawFile.FileHeader.FileDescription + "'");
file.WriteLine("e$info$`Instrument model` <- '{0}'", rawFile.GetInstrumentData().Model);
file.WriteLine("e$info$`Instrument name` <- '{0}'", rawFile.GetInstrumentData().Name);
file.WriteLine("e$info$`Instrument method` <- '" + rawFile.SampleInformation.InstrumentMethodFile.Replace("\\", "/") + "'");
//file.WriteLine("e$info$`Instrument method` <- '{0}'", rawFile.GetAllInstrumentFriendlyNamesFromInstrumentMethod().Length);
file.WriteLine("e$info$`Serial number` <- '{0}'", rawFile.GetInstrumentData().SerialNumber);
file.WriteLine("e$info$`Software version` <- '{0}'", rawFile.GetInstrumentData().SoftwareVersion);
file.WriteLine("e$info$`Firmware version` <- '{0}'", rawFile.GetInstrumentData().HardwareVersion);
file.WriteLine("e$info$Units <- '{0}'", rawFile.GetInstrumentData().Units);
file.WriteLine("e$info$`Mass resolution` <- '{0:F3}'", rawFile.RunHeaderEx.MassResolution);
file.WriteLine("e$info$`Number of scans` <- {0}", rawFile.RunHeaderEx.SpectraCount);
int firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
int lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
file.WriteLine("e$info$`Number of ms2 scans` <- {0}", Enumerable.Range(1, lastScanNumber - firstScanNumber).Count(x => rawFile.GetFilterForScanNumber(x).ToString().Contains("Full ms2")));
file.WriteLine("e$info$`Scan range` <- c({0}, {1})", firstScanNumber, lastScanNumber);
double startTime = rawFile.RunHeaderEx.StartTime;
double endTime = rawFile.RunHeaderEx.EndTime;
file.WriteLine("e$info$`Time range` <- c({0:F2}, {1:F2})", startTime, endTime);
file.WriteLine("e$info$`Mass range` <- c({0:F4}, {1:F4})", rawFile.RunHeaderEx.LowMass, rawFile.RunHeaderEx.HighMass);
var firstFilter = rawFile.GetFilterForScanNumber(firstScanNumber);
var lastFilter = rawFile.GetFilterForScanNumber(lastScanNumber);
int numberFilters = rawFile.GetFilters().Count;
file.WriteLine("e$info$`Scan filter (first scan)` <- '{0}'", firstFilter.ToString());
file.WriteLine("e$info$`Scan filter (last scan)` <- '{0}'", lastFilter.ToString());
file.WriteLine("e$info$`Total number of filters` <- '{0}'", numberFilters);
file.WriteLine("e$info$`Sample name` <- '{0}' ", rawFile.SampleInformation.SampleName);
file.WriteLine("e$info$`Sample id` <- '{0}' ", rawFile.SampleInformation.SampleId);
file.WriteLine("e$info$`Sample type` <- '{0}' ", rawFile.SampleInformation.SampleType);
file.WriteLine("e$info$`Sample comment` <- '{0}' ", rawFile.SampleInformation.Comment);
file.WriteLine("e$info$`Sample vial` <- '{0}' ", rawFile.SampleInformation.Vial);
file.WriteLine("e$info$`Sample volume` <- '{0}' ", rawFile.SampleInformation.SampleVolume);
file.WriteLine("e$info$`Sample injection volume` <- '{0}' ", rawFile.SampleInformation.InjectionVolume);
file.WriteLine("e$info$`Sample row number` <- '{0}' ", rawFile.SampleInformation.RowNumber);
file.WriteLine("e$info$`Sample dilution factor` <- '{0}' ", rawFile.SampleInformation.DilutionFactor);
file.WriteLine("e$info$`Sample barcode` <- '{0}' ", rawFile.SampleInformation.Barcode);
file.WriteLine("e$info$`User text 0` <- '{0}' ", rawFile.SampleInformation.UserText[0]);
file.WriteLine("e$info$`User text 1` <- '{0}' ", rawFile.SampleInformation.UserText[1]);
file.WriteLine("e$info$`User text 2` <- '{0}' ", rawFile.SampleInformation.UserText[2]);
file.WriteLine("e$info$`User text 3` <- '{0}' ", rawFile.SampleInformation.UserText[3]);
file.WriteLine("e$info$`User text 4` <- '{0}' ", rawFile.SampleInformation.UserText[4]);
}
}