public static void WriteSpectrumAsRcode0(this IRawDataPlus rawFile, string filename)
{
int idx_CHARGE = rawFile.GetChargeIdx();
int firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
int lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
int charge = -1;
double pc = -1;
using (System.IO.StreamWriter file =
new System.IO.StreamWriter(filename))
{
for (int scanNumber = firstScanNumber; scanNumber < lastScanNumber; scanNumber++)
{
var scanTrailer = rawFile.GetTrailerExtraInformation(scanNumber);
var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber);
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
try{
var reaction0 = scanEvent.GetReaction(0);
pc = reaction0.PrecursorMass;
}
catch {
pc = -1;
}
try{
charge = int.Parse(scanTrailer.Values.ToArray()[idx_CHARGE]);
}
catch {
charge = -1;
}
file.WriteLine("e$Spectrum[[{0}]] <- list(", scanNumber);
file.WriteLine("\tscan = {0};", scanNumber);
file.WriteLine("\tscanType = \"{0}\";", scanStatistics.ScanType.ToString());
file.WriteLine("\trtinseconds = {0};", Math.Round(scanStatistics.StartTime * 60 * 1000) / 1000);
file.WriteLine("\tprecursorMass = {0};", pc);
file.WriteLine("\tMSOrder = '{0}';", scanFilter.MSOrder.ToString());
file.WriteLine("\tcharge = {0}", charge);
file.WriteLine(")");
}
}
}
public static void GetIndex(this IRawDataPlus rawFile)
{
int firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
int lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
int idx_CHARGE = rawFile.GetChargeIdx();
double charge, precursorMass;
Console.WriteLine("scan;scanType;rtinseconds;precursorMass;MSOrder;charge");
for (int scanNumber = firstScanNumber; scanNumber < lastScanNumber; scanNumber++)
{
var scanTrailer = rawFile.GetTrailerExtraInformation(scanNumber);
var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber);
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
try{
var reaction0 = scanEvent.GetReaction(0);
precursorMass = reaction0.PrecursorMass;
} catch {
precursorMass = -1;
}
try{
charge = int.Parse(scanTrailer.Values.ToArray()[idx_CHARGE]);
} catch {
charge = -1;
}
Console.WriteLine("{0};{1};{2};{3};{4};{5}", scanNumber,
scanStatistics.ScanType.ToString(),
Math.Round(scanStatistics.StartTime * 60 * 1000) / 1000,
precursorMass,
scanFilter.MSOrder.ToString(),
charge);
}
}
