Bruker support (#702)

* Added Bruker data handling files to the most updated version of master.

* Renamed Bruker classes to BrukerFileReader

* Added tests for loading Bruker data

* Added .dll required to run Bruker sourced methods

* Added test data references.

* Added all test data files from the requisite .d directories.

* Added documentation.

* Added more documentation.

* Added dependencies of baf2sql_c.dll

* Added more unit tests

* Anonymized lockinfo files.

* Changed namespace in from IO.* to Readers for the Bruker file readers.

mzLib/Development/Development.csproj

@@ -16,11 +16,9 @@
   <ItemGroup>
     <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj" />
     <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj" />
-    <ProjectReference Include="..\MzML\MzML.csproj" />
     <ProjectReference Include="..\Proteomics\Proteomics.csproj" />
     <ProjectReference Include="..\Readers\Readers.csproj" />
     <ProjectReference Include="..\SpectralAveraging\SpectralAveraging.csproj" />
-    <ProjectReference Include="..\ThermoRawFileReader\ThermoRawFileReader.csproj" />
   </ItemGroup>
 
   <ItemGroup>

mzLib/Readers/Bruker/AcqKeyRow.cs

@@ -0,0 +1,30 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace Readers
+{
+	// class used as a one-to-one map of sqlite object in bruker analysis.baf file for conversion to MsDataScan. 
+	internal class AcqKeyRow
+	{
+		public int Id { get; set; }
+		// 0 = positive, 1 = negative 
+		public int Polarity { get; set; }
+		// 0 = MS
+		// 2 = MS/MS
+		// 4 = in-source CID
+		// 5 = broadband CID
+		// 255 = unknown
+		public int ScanMode { get; set; }
+		// 1 = (axial or orthogonal) TOF, linear detection mode
+		// 2 = (axial or orthogonal) TOF, reflector detection mode
+		// 33 = FTMS
+		// 255 = unknown
+		public int AcquisitionMode { get; set; }
+		// 0 = MS (no fragmentation),
+		// 1 = MS/MS
+		public int MsLevel { get; set; }
+	}
+}