private static void Main(string[] args)
{
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, EnableExtendedFlags);
if (args.Length % 2 != 0)
{
PrintUsageInfo("The number of arguments must be even.");
return;
}
// initialize parameters
var paramDic = new Dictionary <string, string>
{
{ "-s", null },
{ "-d", null },
{ "-o", null },
{ "-e", "1" },
{ "-ntt", "2" },
{ "-mod", null },
{ "-t", "10" },
{ "-f", "10" },
{ "-tda", "0" },
{ "-minLength", "6" },
{ "-maxLength", "40" },
{ "-minCharge", "1" },
{ "-maxCharge", "4" },
{ "-minFragCharge", "1" },
{ "-maxFragCharge", "3" }
};
for (var i = 0; i < args.Length / 2; i++)
{
var key = args[2 * i];
var value = args[2 * i + 1];
if (!paramDic.ContainsKey(key))
{
PrintUsageInfo("Invalid parameter: " + key);
return;
}
paramDic[key] = value;
}
var parameters = new BottomUpInputParameters();
var message = parameters.Parse(paramDic);
if (message != null)
{
PrintUsageInfo(message);
return;
}
Console.WriteLine(Name + " " + Version);
parameters.Display();
parameters.Write();
foreach (string specFilePath in parameters.SpecFilePaths)
{
var bottomUpLauncher = new IcBottomUpLauncher(
specFilePath,
parameters.DatabaseFilePath,
parameters.OutputDir,
parameters.AminoAcidSet,
parameters.Enzyme,
parameters.MinSequenceLength,
parameters.MaxSequenceLength,
parameters.MinPrecursorIonCharge,
parameters.MaxPrecursorIonCharge,
parameters.MinProductIonCharge,
parameters.MaxProductIonCharge,
parameters.PrecursorIonTolerancePpm,
parameters.ProductIonTolerancePpm,
parameters.Tda,
parameters.NumTolerableTermini
);
bottomUpLauncher.RunSearch(CorrThreshold);
}
}
private static void Main(string[] args)
{
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, EnableExtendedFlags);
if (args.Length % 2 != 0)
{
PrintUsageInfo("The number of arguments must be even.");
return;
}
// initialize parameters
var paramDic = new Dictionary<string, string>
{
{"-s", null},
{"-d", null},
{"-o", null},
{"-e", "1"},
{"-ntt", "2"},
{"-mod", null},
{"-t", "10"},
{"-f", "10"},
{"-tda", "0"},
{"-minLength", "6"},
{"-maxLength", "40"},
{"-minCharge", "1"},
{"-maxCharge", "4"},
{"-minFragCharge", "1"},
{"-maxFragCharge", "3"}
};
for (var i = 0; i < args.Length / 2; i++)
{
var key = args[2 * i];
var value = args[2 * i + 1];
if (!paramDic.ContainsKey(key))
{
PrintUsageInfo("Invalid parameter: " + key);
return;
}
paramDic[key] = value;
}
var parameters = new BottomUpInputParameters();
var message = parameters.Parse(paramDic);
if (message != null)
{
PrintUsageInfo(message);
return;
}
Console.WriteLine(Name + " " + Version);
parameters.Display();
parameters.Write();
foreach (string specFilePath in parameters.SpecFilePaths)
{
var bottomUpLauncher = new IcBottomUpLauncher(
specFilePath,
parameters.DatabaseFilePath,
parameters.OutputDir,
parameters.AminoAcidSet,
parameters.Enzyme)
{
MinSequenceLength = parameters.MinSequenceLength,
MaxSequenceLength = parameters.MaxSequenceLength,
MinPrecursorIonCharge = parameters.MinPrecursorIonCharge,
MaxPrecursorIonCharge = parameters.MaxPrecursorIonCharge,
MinProductIonCharge = parameters.MinProductIonCharge,
MaxProductIonCharge = parameters.MaxProductIonCharge,
PrecursorIonTolerancePpm = parameters.PrecursorIonTolerancePpm,
ProductIonTolerancePpm = parameters.ProductIonTolerancePpm,
//RunTargetDecoyAnalysisBool = parameters.TdaBool,
RunTargetDecoyAnalysis = parameters.Tda,
NumTolerableTermini = parameters.NumTolerableTermini,
};
bottomUpLauncher.RunSearch(CorrThreshold);
}
}