public BoxCar_Planner(string parameterfilename, string logfilename) { parameter_file = parameterfilename; Parameters = Parameter_Parser.read_parameters(parameter_file); isolation_width = Convert.ToDouble(Parameters["Isolation_Width_Da"]); scan_limit_per_cycle = Convert.ToInt32(Parameters["MS2_Per_Cycle"]); exclusion_time_interval = TimeSpan.FromSeconds(Convert.ToInt32(Parameters["Exclusion_Time"])); mz_tolerance = Convert.ToDouble(Parameters["Exclusion_Width_Da"]); logfile = new System.IO.StreamWriter(logfilename); }
public DD_Planner_AGC_Threshold(string parameterfilename, string logfilename) { parameter_file = parameterfilename; Parameters = Parameter_Parser.read_parameters(parameter_file); isolation_width = Convert.ToDouble(Parameters["Isolation_Width_Da"]); scan_limit_per_cycle = Convert.ToInt32(Parameters["MS2_Per_Cycle"]); exclusion_time_interval = TimeSpan.FromSeconds(Convert.ToInt32(Parameters["Exclusion_Time"])); mz_tolerance = Convert.ToDouble(Parameters["Exclusion_Width_Da"]); PrecursorIntensityThreshold = Convert.ToDouble(Parameters["Precursor_Threshold"]); logfile = new System.IO.StreamWriter(logfilename); scaninfo_file = new System.IO.StreamWriter(logfilename + "_SCANINFO.txt"); }
public DD_Planner(string parameterfilename, string logfilename) { parameter_file = parameterfilename; Parameters = Parameter_Parser.read_parameters(parameter_file); isolation_width = Convert.ToDouble(Parameters["Isolation_Width_Da"]); scan_limit_per_cycle = Convert.ToInt32(Parameters["MS2_Per_Cycle"]); TimeSpan exclusion_time_interval = TimeSpan.FromSeconds(Convert.ToInt32(Parameters["Exclusion_Time"])); mz_tolerance = Convert.ToDouble(Parameters["Exclusion_Width_Da"]); PrecursorIntensityThreshold = Convert.ToDouble(Parameters["Precursor_Threshold"]); PrecursorAGCThreshold = Convert.ToDouble(Parameters["AGC_Threshold"]); if (Parameters["Exclusion_List_Type"] == "MZ") { exclusion_list = new Basic_ExclusionList(exclusion_time_interval, mz_tolerance); } else if (Parameters["Exclusion_List_Type"] == "MZ_Charge") { exclusion_list = new Charge_ExclusionList(exclusion_time_interval, mz_tolerance); } else if (Parameters["Exclusion_List_Type"] == "MZ_IntMultiple") { double override_int = Convert.ToDouble(Parameters["Intensity_Override_Multiple"]); exclusion_list = new Intensity_ExclusionList(exclusion_time_interval, mz_tolerance, override_int); } else { throw new System.ArgumentException("Misisng or invalid Exclusion_List_Type parameter."); } logfile = new System.IO.StreamWriter(logfilename); scaninfo_file = new System.IO.StreamWriter(logfilename + "_SCANINFO.txt"); }
static void Main(string[] args) { Console.WriteLine("QE SuperMethodApp Version: April 5th."); string filename; string parameterfile; bool automatic_mode; if (args.Length > 0) { filename = args[1]; parameterfile = args[0]; automatic_mode = true; } else { filename = "C:/Xcalibur/data/test_raw_file.raw"; parameterfile = "//rc-data1.dfci.harvard.edu/blaise/ms_data_share/Max/QE_API/ParameterFiles/QE_DD.txt"; automatic_mode = false; } Debug.Assert(File.Exists(parameterfile)); IDictionary <string, string> parameters = Parameter_Parser.read_parameters(parameterfile); string logfilename = String.Concat(filename, "_log.txt"); if (!parameters.ContainsKey("MethodType")) { throw new System.ArgumentException("Parameter file must contain a 'MethodType' line."); } Planner run_planner = null; switch (parameters["MethodType"]) { case "DataDependent": run_planner = new DD_Planner(parameterfile, logfilename); Console.WriteLine("Data-Dependent Mode."); break; //case "DataDependent_AGC": // run_planner = new DD_Planner_AGC(parameterfile, logfilename); // Console.WriteLine("Data-Dependent AGC-Enabled Mode."); // break; //case "DataDependent_AGC_Threshold": // run_planner = new DD_Planner_AGC_Threshold(parameterfile, logfilename); // Console.WriteLine("Data-Dependent AGC-Threshold-Enabled Mode."); // break; case "BoxCar": run_planner = new BoxCar_Planner(parameterfile, logfilename); Console.WriteLine("BoxCar Mode."); break; default: throw new System.ArgumentException("Invalid MethodType in parameter file: {0}", parameters["MethodType"]); } Debug.Assert(run_planner != null); Machinist machine_obj = new Machinist(); machine_obj.RunMachine(run_planner, filename, automatic_mode); }