Correct counting of spectra

Author: caetera

MainClass.cs

@@ -19,7 +19,7 @@ public static class MainClass
         private static readonly ILog Log =
             LogManager.GetLogger(System.Reflection.MethodBase.GetCurrentMethod().DeclaringType);
 
-        public const string Version = "1.3.1-pre";
+        public const string Version = "1.3.1";
 
         public static void Main(string[] args)
         {

Properties/AssemblyInfo.cs

@@ -9,7 +9,7 @@
 [assembly: AssemblyConfiguration("")]
 [assembly: AssemblyCompany("")]
 [assembly: AssemblyProduct("ThermoRawFileParser")]
-[assembly: AssemblyCopyright("Copyright ©  2017")]
+[assembly: AssemblyCopyright("Copyright ©  2017 - 2020")]
 [assembly: AssemblyTrademark("")]
 [assembly: AssemblyCulture("")]
 
@@ -31,7 +31,7 @@
 // You can specify all the values or you can default the Build and Revision Numbers 
 // by using the '*' as shown below:
 // [assembly: AssemblyVersion("1.0.*")]
-[assembly: AssemblyVersion("1.2.3.0")]
-[assembly: AssemblyFileVersion("1.2.3.0")]
+[assembly: AssemblyVersion("1.3.1.0")]
+[assembly: AssemblyFileVersion("1.3.1.0")]
 
 [assembly: log4net.Config.XmlConfigurator(ConfigFile = "log4net.config")]

Writer/MzMlSpectrumWriter.cs

@@ -593,7 +593,17 @@ private string GetTotalScanNumber()
 
             _rawFile.SelectInstrument(Device.MS, 1);
 
-            numScans += 1 + _rawFile.RunHeader.LastSpectrum - _rawFile.RunHeader.FirstSpectrum;
+            var levelFilter = _rawFile.GetFilterFromString("");
+
+            foreach (var level in ParseInput.MsLevel)
+            {
+                levelFilter.MSOrder = (MSOrderType)level;
+
+                var filteredScans = _rawFile.GetFilteredScansListByScanRange(levelFilter, _rawFile.RunHeader.FirstSpectrum, _rawFile.RunHeader.LastSpectrum);
+
+                numScans += filteredScans.Count;
+            }
+            
 
             if (ParseInput.AllDetectors)
             {