Tims tof reader

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/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/MzLibUtil/MzLibUtil.csproj

@@ -11,7 +11,6 @@
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="CsvHelper" Version="32.0.3" />
     <PackageReference Include="Easy.Common" Version="6.7.0" />
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
     <PackageReference Include="Microsoft.Extensions.ObjectPool" Version="9.0.0" />

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];

mzLib/Readers/MsDataFileReader.cs

@@ -20,6 +20,7 @@ public static MsDataFile GetDataFile(string filePath)
                 SupportedFileType.MzML => new Mzml(filePath),
                 SupportedFileType.Mgf => new Mgf(filePath),
                 SupportedFileType.BrukerD => new BrukerFileReader(filePath), 
+                SupportedFileType.BrukerTimsTof => new TimsTofFileReader(filePath),
                 _ => throw new MzLibException("File type not supported"),
             };
         }

mzLib/Readers/Readers.csproj

@@ -1,17 +1,19 @@
-<Project Sdk="Microsoft.NET.Sdk">
+<Project Sdk="Microsoft.NET.Sdk">
 
 	<PropertyGroup>
 		<TargetFramework>net8.0</TargetFramework>
 		<Platforms>x64</Platforms>
 		<ImplicitUsings>enable</ImplicitUsings>
 		<Nullable>enable</Nullable>
+		<AllowUnsafeBlocks>true</AllowUnsafeBlocks>
 	</PropertyGroup>
 
 	<ItemGroup>
 		<PackageReference Include="CsvHelper" Version="32.0.3" />
 		<PackageReference Include="OpenMcdf" Version="2.3.1" />
 		<PackageReference Include="OpenMcdf.Extensions" Version="2.3.1" />
 		<PackageReference Include="System.Data.SQLite" Version="1.0.118" />
+		<PackageReference Include="System.Runtime.InteropServices" Version="4.3.0" />
 	</ItemGroup>
 
 	<ItemGroup>
@@ -21,7 +23,6 @@
 	</ItemGroup>
 
 	<ItemGroup>
-
 		<Reference Include="ThermoFisher.CommonCore.BackgroundSubtraction">
 			<HintPath>Thermo\ThermoFisher.CommonCore.BackgroundSubtraction.dll</HintPath>
 		</Reference>
@@ -70,6 +71,18 @@
 		<None Update="Thermo\ThermoFisher.CommonCore.RawFileReader.dll">
 			<CopyToOutputDirectory>Always</CopyToOutputDirectory>
 		</None>
+		<None Update="timsdata.dll">
+		  <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
+		</None>
+		<None Update="timsdata.lib">
+		  <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
+		</None>
+		<None Update="timsTOF\baf2sql_c.dll">
+		  <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+		</None>
+		<None Update="timsTOF\baf2sql_c.lib">
+		  <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+		</None>
 	</ItemGroup>
 
 </Project>

mzLib/Readers/Thermo/ThermoRawFileReader.cs

@@ -526,8 +526,6 @@ private static DissociationType GetDissociationType(ActivationType activationTyp
             }
         }
 
-
-
         /// <summary>
         /// Gets all the MS orders of all scans in a dynamic connection. This is useful if you want to open all MS1 scans
         /// without loading all of the other MSn scans.

mzLib/Readers/Util/SupportedFileTypes.cs

@@ -12,7 +12,6 @@
         ThermoRaw,
         MzML,
         Mgf,
-        BrukerD,
         psmtsv,
         //osmtsv
         ToppicPrsm,
@@ -27,7 +26,9 @@
         MsPathFinderTDecoys,
         MsPathFinderTAllResults,
         CruxResult,
-        ExperimentAnnotation
+        ExperimentAnnotation,
+        BrukerD,
+        BrukerTimsTof
     }
 
     public static class SupportedFileTypeExtensions
@@ -51,6 +52,7 @@
                 SupportedFileType.MzML => ".mzML",
                 SupportedFileType.Mgf => ".mgf",
                 SupportedFileType.BrukerD => ".d",
+                SupportedFileType.BrukerTimsTof => ".d",
                 SupportedFileType.psmtsv => ".psmtsv",
                 //SupportedFileType.osmtsv => ".osmtsv",
                 SupportedFileType.ToppicPrsm => "_prsm.tsv",
@@ -76,7 +78,14 @@
                 case ".raw": return SupportedFileType.ThermoRaw;
                 case ".mzml": return SupportedFileType.MzML;
                 case ".mgf": return SupportedFileType.Mgf;
-                case ".d": return SupportedFileType.BrukerD;
+                case ".d":
+                    if(!Directory.Exists(filePath)) throw new FileNotFoundException();
+                    var fileList = Directory.GetFiles(filePath).Select(p => Path.GetFileName(p));
+                    if (fileList.Any(file => file == "analysis.baf"))
+                        return SupportedFileType.BrukerD;
+                    if (fileList.Any(file => file == "analysis.tdf"))
+                        return SupportedFileType.BrukerTimsTof;
+                    throw new MzLibException("Bruker file type not recognized");
                 case ".psmtsv": return SupportedFileType.psmtsv;
                 //case ".osmtsv": return SupportedFileType.osmtsv;
                 case ".feature":