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); } }