Added class framework

InstrumentControl/CommandLineOptions/CommandLineParser.cs

@@ -0,0 +1,13 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace InstrumentControl.CommandLineOptions
+{
+    public static class CommandLineParser
+    {
+
+    }
+}

InstrumentControl/CommandLineOptions/CommonOptions.cs

@@ -0,0 +1,34 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using CommandLine; 
+
+namespace InstrumentControl.CommandLineOptions
+{
+    public class CommonOptions
+    {
+
+    }
+    public class SpectrumAveragerOptions : CommonOptions
+    {
+        [Option(Default = (string)"NoRejection")]
+        public string? RejectionType { get; set; }
+        [Option(Default = (string)"NoWeight")]
+        public string? WeightingType { get; set; }
+        [Option(Default = (string)"SpectrumBinning")]
+        public string? SpectrumMergeType { get; set; }
+        [Option(Default = (double)0.9)]
+        public double Percentile { get; set; }
+        [Option(Default = (double)1.3)]
+        public double MinSigmaValue { get; set; }
+        [Option(Default = (double)1.3)]
+        public double MaxSigmaValue { get; set; }   
+        [Option(Default = (double)0.02)]
+        public double BinSize { get; set; }
+
+    }
+
+
+}

InstrumentControl/InstrumentControl.csproj

@@ -17,6 +17,7 @@
 	</ItemGroup>
 
   <ItemGroup>
+    <PackageReference Include="CommandLineParser" Version="2.9.1" />
     <PackageReference Include="mzLib" Version="1.0.529" />
     <PackageReference Include="System.Resources.Extensions" Version="6.0.0" />
   </ItemGroup>

InstrumentControl/Tasks/InstrumentControlTask.cs

@@ -4,7 +4,7 @@
 using System.Linq;
 using System.Text;
 using System.Threading.Tasks;
-
+using CommandLine; 
 namespace InstrumentControl
 {
     public abstract class InstrumentControlTask
@@ -26,7 +26,6 @@ public void Run()
             Console.WriteLine("Executed {0} Task in {1} ms", TaskType, watch.ElapsedMilliseconds);
         }
 
-        public abstract void RunSpecific();
-
+        public virtual void RunSpecific() { }
     }
 }

InstrumentControl/Tasks/SpectrumAveragingTask.cs

@@ -7,6 +7,7 @@
 using System.Linq;
 using System.Text;
 using System.Threading.Tasks;
+using InstrumentControl.CommandLineOptions; 
 
 namespace InstrumentControl
 {