public string ToXML(FAIMStoMzXMLProcessor processor)
{
// place scan byte depth into our tracking list
var index = new Index(processor.ByteTracking.CurrentScan, processor.ByteTracking.ByteDepth + 3);
processor.ByteTracking.ScanOffsets.Add(index);
FilterLine = FixFilterLine();
var sb = new StringBuilder();
sb.AppendFormat(" <scan num=\"{0}\"", processor.ByteTracking.CurrentScan).AppendLine();
sb.AppendFormat(" msLevel=\"{0}\"", MsLevel).AppendLine();
sb.AppendFormat(" peaksCount=\"{0}\"", PeaksCount).AppendLine();
sb.AppendFormat(" polarity=\"{0}\"", Polarity).AppendLine();
sb.AppendFormat(" scanType=\"{0}\"", ScanType).AppendLine();
sb.AppendFormat(" filterLine=\"{0}\"", FilterLine).AppendLine();
sb.AppendFormat(" retentionTime=\"{0}\"", RetentionTime).AppendLine();
sb.AppendFormat(" lowMz=\"" + Math.Round(LowMz, 3) + "\"").AppendLine();
sb.AppendFormat(" highMz=\"" + Math.Round(HighMz, 3) + "\"").AppendLine();
sb.AppendFormat(" basePeakMz=\"" + Math.Round(BasePeakMz, 3) + "\"").AppendLine();
sb.AppendFormat(" basePeakIntensity=\"" + FormatSpecialNumber(BasePeakIntensity) + "\"").AppendLine();
sb.AppendFormat(" totIonCurrent=\"" + FormatSpecialNumber(TotIonCurrent) + "\"").AppendLine();
sb.AppendFormat(" collisionEnergy=\"" + CollisionEnergy + "\">").AppendLine();
sb.AppendLine(PrecursorMz.ToXML());
sb.AppendLine(PeakData.ToXML(4));
sb.Append(" </scan>");
processor.ByteTracking.CurrentScan++;
return(sb.ToString());
}
// for outputting valid MzXML strings to file
public string ToXML(FAIMStoMzXMLProcessor processor)
{
// place scan byte depth into our tracking list
var index = new Index(processor.ByteTracking.CurrentScan, processor.ByteTracking.ByteDepth + 2);
processor.ByteTracking.ScanOffsets.Add(index);
FilterLine = FixFilterLine();
var sb = new StringBuilder();
sb.AppendFormat(" <scan num=\"{0}\"", processor.ByteTracking.CurrentScan).AppendLine();
sb.AppendFormat(" msLevel=\"{0}\"", MsLevel).AppendLine();
sb.AppendFormat(" peaksCount=\"{0}\"", PeaksCount).AppendLine();
sb.AppendFormat(" polarity=\"{0}\"", Polarity).AppendLine();
sb.AppendFormat(" scanType=\"{0}\"", ScanType).AppendLine();
sb.AppendFormat(" filterLine=\"{0}\"", FilterLine).AppendLine();
sb.AppendFormat(" retentionTime=\"{0}\"", RetentionTime).AppendLine();
sb.AppendFormat(" lowMz=\"" + Math.Round(LowMz, 3) + "\"").AppendLine();
sb.AppendFormat(" highMz=\"" + Math.Round(HighMz, 3) + "\"").AppendLine();
sb.AppendFormat(" basePeakMz=\"" + Math.Round(BasePeakMz, 3) + "\"").AppendLine();
sb.AppendFormat(" basePeakIntensity=\"" + FormatSpecialNumber(BasePeakIntensity) + "\"").AppendLine();
sb.AppendFormat(" totIonCurrent=\"" + FormatSpecialNumber(TotIonCurrent) + "\">").AppendLine();
sb.AppendLine(PeakData.ToXML(3));
// advance the byteTracker for Ms2 Indices
processor.ByteTracker(sb.ToString(), true);
processor.ByteTracking.CurrentScan++;
foreach (var ms2 in Ms2s)
{
var ms2String = ms2.ToXML(processor);
sb.AppendLine(ms2String);
// advance byteTracker for the Ms2 Entry
processor.ByteTracker(ms2String);
}
sb.Append(" </scan>");
processor.ByteTracker(" </scan>");
return(sb.ToString());
}
private static void Main(string[] args)
{
try
{
if (args.Length == 0)
{
var exePath = ProcessFilesOrDirectoriesBase.GetAppPath();
Console.WriteLine("WriteFaimsXMLFromRawFile version " + GetAppVersion());
Console.WriteLine();
Console.WriteLine(ConsoleMsgUtils.WrapParagraph(
"This program converts a Thermo .raw file with FAIMS scans into a series of .mzXML files, " +
"creating one .mzXML file for each FAIMS compensation voltage (CV) value in the .raw file."));
Console.WriteLine();
Console.WriteLine("Syntax:");
Console.WriteLine("{0} InstrumentFile.raw [Output_Directory_Path]", Path.GetFileName(exePath));
Console.WriteLine();
Console.WriteLine("Wild cards are supported, e.g. *.raw");
Console.WriteLine();
// ReSharper disable StringLiteralTypo
Console.WriteLine("Program written by Dain Brademan for the Joshua Coon Research Group (University of Wisconsin) in 2018");
Console.WriteLine("Converted to use ThermoFisher.CommonCore DLLs by Matthew Monroe for PNNL (Richland, WA) in 2020");
Console.WriteLine("E-mail: [email protected] or [email protected] or [email protected]");
Console.WriteLine("Website: https://github.com/PNNL-Comp-Mass-Spec/FAIMS-MzXML-Generator/releases or");
Console.WriteLine(" https://github.com/coongroup/FAIMS-MzXML-Generator");
// ReSharper restore StringLiteralTypo
return;
}
var inputFilePathSpec = args[0];
string outputDirectoryPath;
if (args.Length > 1)
{
outputDirectoryPath = args[1];
}
else
{
outputDirectoryPath = string.Empty;
}
var processor = new FAIMStoMzXMLProcessor();
RegisterEvents(processor);
processor.QuickCVLookup = false;
var success = processor.ProcessFiles(inputFilePathSpec, outputDirectoryPath);
if (success)
{
Console.WriteLine("Processing completed");
}
System.Threading.Thread.Sleep(750);
}
catch (Exception ex)
{
ConsoleMsgUtils.ShowError("Error in Program.Main", ex);
}
}
