json pretty print and other small fixes

Author: nielshulstaert

MainClass.cs

@@ -107,7 +107,7 @@ private static void XicParametersParsing(string[] args)
 
                 if (parameters.help)
                 {
-                    ShowHelp("usage is (use -option=value for the optional arguments):", null,
+                    ShowHelp("usage is:", null,
                         optionSet);
                     return;
                 }
@@ -184,19 +184,19 @@ private static void XicParametersParsing(string[] args)
             }
             catch (OptionException optionException)
             {
-                ShowHelp("Error - usage is (use -option=value for the optional arguments):", optionException,
+                ShowHelp("Error - usage is:", optionException,
                     optionSet);
             }
             catch (ArgumentNullException)
             {
                 if (parameters.help)
                 {
-                    ShowHelp("usage is (use -option=value for the optional arguments):", null,
+                    ShowHelp("usage is:", null,
                         optionSet);
                 }
                 else
                 {
-                    ShowHelp("Error - usage is (use -option=value for the optional arguments):", null,
+                    ShowHelp("Error - usage is:", null,
                         optionSet);
                 }
             }
@@ -274,7 +274,7 @@ private static void SpectrumQueryParametersParsing(string[] args)
 
                 if (parameters.help)
                 {
-                    ShowHelp("usage is (use -option=value for the optional arguments):", null,
+                    ShowHelp("usage is:", null,
                         optionSet);
                     return;
                 }
@@ -302,19 +302,19 @@ private static void SpectrumQueryParametersParsing(string[] args)
             }
             catch (OptionException optionException)
             {
-                ShowHelp("Error - usage is (use -option=value for the optional arguments):", optionException,
+                ShowHelp("Error - usage is:", optionException,
                     optionSet);
             }
             catch (ArgumentNullException)
             {
                 if (parameters.help)
                 {
-                    ShowHelp("usage is (use -option=value for the optional arguments):", null,
+                    ShowHelp("usage is:", null,
                         optionSet);
                 }
                 else
                 {
-                    ShowHelp("Error - usage is (use -option=value for the optional arguments):", null,
+                    ShowHelp("Error - usage is:", null,
                         optionSet);
                 }
             }
@@ -451,10 +451,9 @@ private static void RegularParametersParsing(string[] args)
 
                 if (help)
                 {
-                    string helpmessage = String.Format("usage is {0} [subcommand] [options]\nsubcommand is xic|query\n",
-                        Assembly.GetExecutingAssembly().GetName().Name);
-                    ShowHelp(helpmessage +
-                             "(use -option=value for the optional arguments):", null,
+                    var helpMessage =
+                        $"usage is {Assembly.GetExecutingAssembly().GetName().Name}.exe [subcommand] [options]\noptional subcommands are xic|query (use [subcommand] -h for more info]):";
+                    ShowHelp(helpMessage, null,
                         optionSet);
                     return;
                 }
@@ -660,19 +659,19 @@ private static void RegularParametersParsing(string[] args)
             }
             catch (OptionException optionException)
             {
-                ShowHelp("Error - usage is (use -option=value for the optional arguments):", optionException,
+                ShowHelp("Error - usage is:", optionException,
                     optionSet);
             }
             catch (ArgumentNullException)
             {
                 if (help)
                 {
-                    ShowHelp("usage is (use -option=value for the optional arguments):", null,
+                    ShowHelp("usage is:", null,
                         optionSet);
                 }
                 else
                 {
-                    ShowHelp("Error - usage is (use -option=value for the optional arguments):", null,
+                    ShowHelp("Error - usage is:", null,
                         optionSet);
                 }
             }

Query/PROXISpectrum.cs Query/ProxiSpectrum.csQuery/PROXISpectrum.cs renamed to Query/ProxiSpectrum.cs

@@ -7,22 +7,22 @@
 
 namespace ThermoRawFileParser.Query
 {
-    public class PROXISpectrum
+    public class ProxiSpectrum
     {
         public List<double> mzs { get; set; }
         public List<double> intensities { get; set; }
-        public List<PROXICVTerm> attributes { get; set; }
+        public List<ProxiCvTerm> attributes { get; set; }
 
-        public PROXISpectrum()
+        public ProxiSpectrum()
         {
             mzs = new List<double>();
             intensities = new List<double>();
-            attributes = new List<PROXICVTerm>();
+            attributes = new List<ProxiCvTerm>();
         }
 
         public void AddAttribute(string accession=null, string cvGroup=null, string name=null, string value=null, string valueAccession=null)
         {
-            attributes.Add(new PROXICVTerm(accession, cvGroup, name, value, valueAccession));
+            attributes.Add(new ProxiCvTerm(accession, cvGroup, name, value, valueAccession));
         }
 
         public void AddMz(IList<double> mzList)