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);
}
