Tims tof reader

.github/workflows/dotnet.yml

@@ -18,6 +18,10 @@ jobs:
         dotnet-version: 8.0.x
     - name: Restore dependencies
       run: cd mzLib && dotnet restore
+    - name: Install Visual c++ build tools
+      uses: crazy-max/ghaction-chocolatey@v3
+      with:
+        args: install visualcpp-build-tools
     - name: Build
       run: cd mzLib && dotnet build --no-restore
     - name: Build (Test)

mzLib/MassSpectrometry/MsDataScan.cs

@@ -27,9 +27,29 @@ namespace MassSpectrometry
 {
     public class MsDataScan
     {
-        public MsDataScan(MzSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder, bool isCentroid, Polarity polarity, double retentionTime, MzRange scanWindowRange, string scanFilter, MZAnalyzerType mzAnalyzer,
-            double totalIonCurrent, double? injectionTime, double[,] noiseData, string nativeId, double? selectedIonMz = null, int? selectedIonChargeStateGuess = null, double? selectedIonIntensity = null, double? isolationMZ = null,
-            double? isolationWidth = null, DissociationType? dissociationType = null, int? oneBasedPrecursorScanNumber = null, double? selectedIonMonoisotopicGuessMz = null, string hcdEnergy = null, string scanDescription = null)
+        public MsDataScan(MzSpectrum massSpectrum, 
+            int oneBasedScanNumber, 
+            int msnOrder, 
+            bool isCentroid, 
+            Polarity polarity, 
+            double retentionTime, 
+            MzRange scanWindowRange, 
+            string scanFilter, 
+            MZAnalyzerType mzAnalyzer,
+            double totalIonCurrent, 
+            double? injectionTime, 
+            double[,] noiseData, 
+            string nativeId, 
+            double? selectedIonMz = null, 
+            int? selectedIonChargeStateGuess = null, 
+            double? selectedIonIntensity = null, 
+            double? isolationMZ = null,
+            double? isolationWidth = null, 
+            DissociationType? dissociationType = null, 
+            int? oneBasedPrecursorScanNumber = null, 
+            double? selectedIonMonoisotopicGuessMz = null, 
+            string hcdEnergy = null,
+            string scanDescription = null)
         {
             OneBasedScanNumber = oneBasedScanNumber;
             MsnOrder = msnOrder;
@@ -61,7 +81,7 @@ public MsDataScan(MzSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder,
         /// </summary>
         public MzSpectrum MassSpectrum { get; protected set; }
 
-        public int OneBasedScanNumber { get; private set; }
+        public int OneBasedScanNumber { get; protected set; }
         public int MsnOrder { get; }
         public double RetentionTime { get; }
         public Polarity Polarity { get; }
@@ -70,7 +90,7 @@ public MsDataScan(MzSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder,
         public string ScanFilter { get; }
         public string NativeId { get; private set; }
         public bool IsCentroid { get; }
-        public double TotalIonCurrent { get; }
+        public double TotalIonCurrent { get; protected set; }
         public double? InjectionTime { get; }
         public double[,] NoiseData { get; }
 
@@ -82,7 +102,7 @@ public MsDataScan(MzSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder,
         public double? SelectedIonMZ { get; private set; } // May be adjusted by calibration
         public DissociationType? DissociationType { get; }
         public double? IsolationWidth { get; }
-        public int? OneBasedPrecursorScanNumber { get; private set; }
+        public int? OneBasedPrecursorScanNumber { get; protected set; }
         public double? SelectedIonMonoisotopicGuessIntensity { get; private set; } // May be refined
         public double? SelectedIonMonoisotopicGuessMz { get; private set; } // May be refined
         public string HcdEnergy { get; private set; }

mzLib/MassSpectrometry/MzSpectra/MzPeak.cs

@@ -1,4 +1,6 @@
-namespace MassSpectrometry
+using System;
+
+namespace MassSpectrometry
 {
     public class MzPeak
     {

mzLib/MzLibUtil/ClassExtensions.cs

@@ -57,6 +57,18 @@ public static T[] SubArray<T>(this T[] data, int index, int length)
             return result;
         }
 
+        public static bool ToEnum<T>(this int modeInt, out T result) where T : Enum
+        {
+            Type enumType = typeof(T);
+            if (!Enum.IsDefined(enumType, modeInt))
+            {
+                result = default(T);
+                return false;
+            }
+            result = (T)Enum.ToObject(enumType, modeInt);
+            return true;
+        }
+
         /// <summary>
         /// Checks if two collections are equivalent, regardless of the order of their contents
         /// </summary>

mzLib/Readers/Bruker/BrukerFileReader.cs

@@ -378,7 +378,7 @@ private List<StepsRow> GetFullStepsTable()
 		/// <param name="reader">SQLiteReader object, initialized after the execution of a command.</param>
 		/// <returns>Return null exception if there is an error in the data format of the baf file.</returns>
 		/// <exception cref="ArgumentNullException"></exception>
-		private T SqlColumnReader<T>(SQLiteDataReader reader) where T: new()
+		public static T SqlColumnReader<T>(SQLiteDataReader reader) where T: new()
 		{
 			// get all the property names, then iterate over that. 
 			// The objects should be exact 1:1 column corresponding so as 
@@ -516,7 +516,7 @@ private static void ThrowLastBaf2SqlError()
 		}
 
 		/* ----------------------------------------------------------------------------------------------- */
-		private static byte[] ConvertStringToUTF8ByteArray(String input)
+		public static byte[] ConvertStringToUTF8ByteArray(String input)
 		{
 			byte[] utf8 = Encoding.UTF8.GetBytes(input);
 			var result = new byte[utf8.Length + 1];