public clsHornTransform()
{
TransformParameters = new clsHornTransformParameters
{
IsotopeFitType = enmIsotopeFitType.AREA,
MaxCharge = 10,
MaxMW = 10000,
MaxFit = 0.15,
MinS2N = 5,
DeleteIntensityThreshold = 1,
MinIntensityForScore = 1,
O16O18Media = false,
//Charge carrier mass = [atomic mass of hydrogen (1.007825) - atomic mass of an electron (0.00054858)]
CCMass = 1.00727638,
NumPeaksForShoulder = 1,
CheckAllPatternsAgainstCharge1 = false,
IsActualMonoMZUsed = false,
LeftFitStringencyFactor = 1,
RightFitStringencyFactor = 1,
};
//_reportO18Plus2Da = false;
DebugFlag = false;
}
public int RunDeconMSn(string[] args)
{
try
{
var strAppFolder = Path.GetDirectoryName(System.Reflection.Assembly.GetExecutingAssembly().Location);
var strSVMParamFilePath = Path.Combine(strAppFolder, "svm_params.xml");
if (args.Length == 0)
{
PrintUsage();
return(0);
}
var procRunner = new clsProcRunner();
var transformParameters = new clsHornTransformParameters();
var dtaGenParameters = new clsDTAGenerationParameters();
var peakParameters = new clsPeakProcessorParameters();
var error = false;
dtaGenParameters.SVMParamFile = strSVMParamFilePath;
dtaGenParameters.CentroidMSn = false;
var sw = new Stopwatch();
sw.Start();
// First check for a parameter file defined using -P
if (args.Length > 0)
{
foreach (var currentArg in args)
{
if (!currentArg.StartsWith("-P") || currentArg.ToLower().StartsWith("-progress"))
{
continue;
}
var stringParamFile = currentArg.Substring(2);
Console.WriteLine("Reading Parameter File " + stringParamFile);
var rdr = new XmlTextReader(stringParamFile);
//Read each node in the tree.
while (rdr.Read())
{
switch (rdr.NodeType)
{
case XmlNodeType.Element:
if (string.Equals(rdr.Name, "PeakParameters", StringComparison.OrdinalIgnoreCase))
{
peakParameters.LoadV1PeakParameters(rdr);
}
else if (string.Equals(rdr.Name, "HornTransformParameters", StringComparison.OrdinalIgnoreCase))
{
#pragma warning disable 618
transformParameters.LoadV1HornTransformParameters(rdr);
#pragma warning restore 618
}
else if (string.Equals(rdr.Name, "DTAGenerationParameters", StringComparison.OrdinalIgnoreCase))
{
dtaGenParameters.LoadV1DTAGenerationParameters(rdr);
}
break;
default:
break;
}
}
rdr.Close();
}
}
var filenameDefined = false;
var stringSpectraFormat = "ALL";
if (args.Length == 0)
{
PrintUsage();
return(0);
}
// Read the remaining parameters
foreach (var arg in args)
{
var currentArg = GetCommandLineArg(arg);
if (currentArg == "-?" || currentArg == "/?" || currentArg == "-help" || currentArg == "/help")
{
PrintUsage();
return(0);
}
if (currentArg.ToLower().StartsWith("-progress"))
{
dtaGenParameters.WriteProgressFile = true;
continue;
}
if (currentArg.ToLower().StartsWith("-centroid"))
{
dtaGenParameters.CentroidMSn = true;
continue;
}
if (!currentArg.StartsWith("-"))
{
// Treat the first non-switch parameter as the dataset to process
if (!filenameDefined)
{
procRunner.FileName = currentArg;
filenameDefined = true;
}
else
{
Console.WriteLine("Ignoring extra argument " + currentArg);
}
continue;
}
if (currentArg.Length <= 1)
{
Console.WriteLine("Ignoring invalid argument " + currentArg);
continue;
}
switch (currentArg[1])
{
case 'I':
if (GetParamInt(currentArg, "Minimum ion count", out var minIonCount))
{
dtaGenParameters.MinIonCount = minIonCount;
}
else
{
error = true;
}
break;
case 'F':
if (GetParamInt(currentArg, "First scan", out var scanFirst))
{
dtaGenParameters.MinScan = scanFirst;
}
else
{
error = true;
}
break;
case 'L':
if (GetParamInt(currentArg, "Last scan", out var scanLast))
{
dtaGenParameters.MaxScan = scanLast;
}
else
{
error = true;
}
break;
case 'B':
if (GetParamDbl(currentArg, "Min mass", out var minMass))
{
dtaGenParameters.MinMass = minMass;
}
else
{
error = true;
}
break;
case 'T':
if (GetParamDbl(currentArg, "Max mass", out var maxMass))
{
dtaGenParameters.MaxMass = maxMass;
}
else
{
error = true;
}
break;
case 'C':
if (GetParamInt(currentArg, "Consider charge", out var considerCharge))
{
dtaGenParameters.ConsiderChargeValue = considerCharge;
}
else
{
error = true;
}
dtaGenParameters.ConsiderChargeValue = considerCharge;
break;
case 'S':
stringSpectraFormat = currentArg.Substring(2);
if (string.Equals(stringSpectraFormat, "ETD", StringComparison.OrdinalIgnoreCase))
{
dtaGenParameters.SpectraType = SPECTRA_TYPE.ETD;
}
else if (string.Equals(stringSpectraFormat, "CID", StringComparison.OrdinalIgnoreCase))
{
dtaGenParameters.SpectraType = SPECTRA_TYPE.CID;
}
else if (string.Equals(stringSpectraFormat, "HCD", StringComparison.OrdinalIgnoreCase))
{
dtaGenParameters.SpectraType = SPECTRA_TYPE.HCD;
}
else
{
stringSpectraFormat = "ALL";
dtaGenParameters.SpectraType = SPECTRA_TYPE.ALL;
}
break;
case 'X':
var outputFileFormat = currentArg.Substring(2);
if (string.Equals(outputFileFormat, "MGF", StringComparison.OrdinalIgnoreCase))
{
dtaGenParameters.OutputType = OUTPUT_TYPE.MGF;
}
else if (string.Equals(outputFileFormat, "LOG", StringComparison.OrdinalIgnoreCase))
{
dtaGenParameters.OutputType = OUTPUT_TYPE.LOG;
}
else if (string.Equals(outputFileFormat, "CDTA", StringComparison.OrdinalIgnoreCase))
{
dtaGenParameters.OutputType = OUTPUT_TYPE.CDTA;
}
else if (string.Equals(outputFileFormat, "MZXML", StringComparison.OrdinalIgnoreCase))
{
dtaGenParameters.OutputType = OUTPUT_TYPE.MZXML;
}
else if (string.Equals(outputFileFormat, "DTA", StringComparison.OrdinalIgnoreCase))
{
dtaGenParameters.OutputType = OUTPUT_TYPE.DTA;
}
else
{
PrintUsage();
error = true;
}
break;
case 'D':
var outputFolderPath = currentArg.Substring(2);
procRunner.OutputPathForDTACreation = outputFolderPath;
break;
case 'G': // Used by Extract_msn; ignored by DeconMSn
break;
case 'M': // Used by Extract_msn; ignored by DeconMSn
break;
case 'P': // Already handled above
break;
default:
Console.WriteLine("Unrecognized argument: " + currentArg);
error = true;
break;
} // Switch
if (!error)
{
continue;
}
Console.WriteLine();
Console.WriteLine("For program syntax, run " + GetExeName() + " without any parameters");
System.Threading.Thread.Sleep(1500);
return(-1);
}
if (!filenameDefined)
{
PrintUsage();
return(-1);
}
var filenameToProcess = procRunner.FileName;
Console.WriteLine("Processing File {0}", filenameToProcess);
Console.WriteLine();
// Display the settings
Console.WriteLine("Minimum Number of ions for valid MSn scan: {0}", dtaGenParameters.MinIonCount);
Console.WriteLine("Scan Start: {0}", dtaGenParameters.MinScan);
Console.WriteLine("Scan End: {0}", dtaGenParameters.MaxScan);
Console.WriteLine("m/z Start: {0}", dtaGenParameters.MinMass);
Console.WriteLine("m/z End: {0}", dtaGenParameters.MaxMass);
if (dtaGenParameters.ConsiderChargeValue > 0)
{
Console.WriteLine("-C enabled with {0}", dtaGenParameters.ConsiderChargeValue);
}
Console.WriteLine("Spectra to process: {0}", stringSpectraFormat);
var outputTypeName = dtaGenParameters.OutputTypeName;
Console.WriteLine("Output format: {0}", outputTypeName);
Console.WriteLine("Create progress file: {0}", dtaGenParameters.WriteProgressFile);
Console.WriteLine("Centroid profile mode MSn spectra: {0}", dtaGenParameters.CentroidMSn.ToString());
Console.WriteLine();
procRunner.HornTransformParameters = transformParameters;
procRunner.PeakProcessorParameters = peakParameters;
procRunner.DTAGenerationParameters = dtaGenParameters;
procRunner.CreateDTAFile();
sw.Stop();
Console.WriteLine();
Console.WriteLine("Done. Finished processing in {0:F1} seconds.", sw.Elapsed.TotalSeconds);
System.Threading.Thread.Sleep(1500);
return(0);
}
catch (Exception ex)
{
Console.WriteLine();
Console.WriteLine("Error processing: " + ex.Message);
Console.WriteLine(PRISM.clsStackTraceFormatter.GetExceptionStackTraceMultiLine(ex));
System.Threading.Thread.Sleep(2000);
return(-1);
}
}
