static int Main(string[] args)
{
var options = new ConverterOptions();
var asmName = typeof(Program).GetTypeInfo().Assembly.GetName();
var programVersion = typeof(Program).GetTypeInfo().Assembly.GetName().Version;
var version = string.Format("version {0}.{1}.{2}", programVersion.Major, programVersion.Minor, programVersion.Build);
if (!CommandLineParser <ConverterOptions> .ParseArgs(args, options, asmName.Name, version) || !options.ValidateArgs())
{
System.Threading.Thread.Sleep(1500);
return(-1);
}
options.OutputSetOptions();
#if !DEBUG
try
{
#endif
var converter = new MzidToTsvConverter();
converter.ConvertToTsv(options);
Console.WriteLine("Conversion finished!");
System.Threading.Thread.Sleep(700);
return(0);
#if !DEBUG
}
catch (Exception e)
{
Console.WriteLine("Conversion failed: " + e.Message);
Console.WriteLine(e.StackTrace);
System.Threading.Thread.Sleep(1500);
var errorCode = e.Message.GetHashCode();
if (errorCode == 0)
{
return(-1);
}
return(errorCode);
}
#endif
}
// Ignore Spelling: Bryson, Conf
private static int Main(string[] args)
{
var asmName = typeof(Program).GetTypeInfo().Assembly.GetName();
var exeName = Path.GetFileName(Assembly.GetExecutingAssembly().Location); // Alternatively: System.AppDomain.CurrentDomain.FriendlyName
var programVersion = typeof(Program).GetTypeInfo().Assembly.GetName().Version;
var version = $"version {programVersion.Major}.{programVersion.Minor}.{programVersion.Build}";
var parser = new CommandLineParser <ConverterOptions>(asmName.Name, version)
{
ProgramInfo = "This program converts a .mzid file created by MS-GF+ into a tab-delimited text file.",
ContactInfo = "Program written by Bryson Gibbons for the Department of Energy " + Environment.NewLine +
"(PNNL, Richland, WA)" + Environment.NewLine + Environment.NewLine +
string.Format(
"Version: {0}.{1}.{2} ({3})",
programVersion.Major, programVersion.Minor, programVersion.Build, ConverterOptions.PROGRAM_DATE) +
Environment.NewLine + Environment.NewLine +
"E-mail: [email protected] or [email protected]" + Environment.NewLine +
"Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://panomics.pnnl.gov/ or https://www.pnnl.gov/integrative-omics",
UsageExamples =
{
exeName + " Results.mzid",
exeName + " Results.mzid -unroll",
exeName + " Results.mzid -unroll -showDecoy",
}
};
parser.AddParamFileKey("Conf");
var parseResults = parser.ParseArgs(args);
var options = parseResults.ParsedResults;
if (!parseResults.Success)
{
Thread.Sleep(1500);
return(-1);
}
if (!options.ValidateArgs(out var errorMessage))
{
parser.PrintHelp();
Console.WriteLine();
ConsoleMsgUtils.ShowWarning("Validation error:");
ConsoleMsgUtils.ShowWarning(errorMessage);
Thread.Sleep(1500);
return(-1);
}
options.OutputSetOptions();
try
{
var converter = new MzidToTsvConverter();
converter.ConvertToTsv(options);
Console.WriteLine();
Console.WriteLine("Conversion finished!");
Thread.Sleep(700);
return(0);
}
catch (Exception ex)
{
ConsoleMsgUtils.ShowError("Conversion failed", ex);
Thread.Sleep(1500);
var errorCode = ex.Message.GetHashCode();
if (errorCode == 0)
{
return(-1);
}
return(errorCode);
}
}
